Molecular cloning studies have revealed the existence of two additional genes that encode phosphoribosyl pyrophosphate synthetase-like proteins, one widely expressed (phosphoribosyl pyrophosphate synthetase 2) and one whose expression appears to be confined to the testis (phosphoribosyl pyrophosphate synthetase 1-like 1) (Taira et al. 1989; 1991). Neither of these proteins has been purified and characterized enzymatically, nor have variations in the abundance or sequence of either protein been associated with alterations in human nucleotide metabolism (Roessler et al. 1993; Becker et al. 1996), so their dimerization and ability to catalyze the synthesis of PRPP from D-ribose 5-phosphate are inferred here on the basis of their predicted amino acid sequence similarity to phosphoribosyl pyrophosphate synthetase 1.
R-HSA-1971475 A tetrasaccharide linker sequence is required for GAG synthesis The biosynthesis of dermatan sulfate/chondroitin sulfate and heparin/heparan sulfate glycosaminoglycans (GAGs) starts with the formation of a tetrasaccharide linker sequence to the core protein. The first step is the addition of xylose to the hydroxy group of specific serine residues on the core protein. Subsequent additions of two galactoses and a glucuronide moiety completes the linker sequence. From here, the next hexosamine addition is critical as it determines which GAG is formed (Lamberg & Stoolmiller 1974, Pavao et al. 2006).
R-HSA-5619084 ABC transporter disorders The ATP-binding cassette (ABC) transporters form a large family of transmembrane proteins that utilise the energy from the hydrolysis of ATP to facilitate the movement of a wide variety of substrates against a concentration gradient across membrane bilayers. Substrates include amino acids, lipids, inorganic ions, peptides, saccharides, peptides for antigen presentation, metals, drugs, and proteins. Of the 48 known ABC transporters in humans, 15 are associated with a defined human disease (Tarling et al. 2013, Woodward et al. 2011, Dean 2005, Kemp et al. 2011, Ueda 2011, Chen & Tiwari 2011).
R-HSA-1369062 ABC transporters in lipid homeostasis A defined subset of the ABC transporter superfamily, the ABCA transporters, are highly expressed in monocytes and macrophages and are regulated by cholesterol flux which may indicate their role in in chronic inflammatory diseases (Schmitz and Kaminski 2001, Schmitz et al. 2000). Some D and G members of the ABC transporter family are also important in lipid transport (Voloshyna & Reiss 2011, Morita & Imanaka 2012, Morita et al. 2011).
R-HSA-382556 ABC-family proteins mediated transport The ATP-binding cassette (ABC) superfamily of active transporters involves a large number of functionally diverse transmembrane proteins. They transport a variety of compounds through membranes against steep concentration gradients at the cost of ATP hydrolysis. These substrates include amino acids, lipids, inorganic ions, peptides, saccharides, peptides for antigen presentation, metals, drugs, and proteins. The ABC transporters not only move a variety of substrates into and out of the cell, but are also involved in intracellular compartmental transport. Energy derived from the hydrolysis of ATP is used to transport the substrate across the membrane against a concentration gradient. Human genome contains 48 ABC genes; 16 of these have a known function and 14 are associated with a defined human disease (Dean et al. 2001, Borst and Elferink 2002, Rees et al. 2009).
R-HSA-9033807 ABO blood group biosynthesis Perhaps the most important and widely studied blood group is the ABO blood group. It consists of antigens found on the outer surface of red cells and corresponding antibodies in plasma. The majority of the world's population (~80%) are 'secretors' which means that the antigens present in their blood will also be found in other body fluids such as saliva. An individual can be a Secretor (Se) or a non-secretor (se) and this is completely independent of whether the individual is of blood type A, B, AB, or O. From a very early age, the immune system develops antibodies against whichever ABO blood group antigens are not found on the individual's RBCs. Thus, a blood group A individual will have anti-B antibodies and a blood group B individual will have anti-A antibodies. Individuals with the most common blood group, O, will have both anti-A and anti-B in their plasma. Blood group AB is the least common, and these individuals will have neither anti-A nor anti-B in their plasma.
The primary structure of these antigens is an oligosaccharide precursor sequence on to which one or more sugars are attached at specific locations. The blood group oligosaccharide antigens A, B and H are produced by enzymes expressed by these genes and form the basis of the ABO 'blood type' phenotypes. A and B antigens were originally identified on red blood cells (RBCs) but later identified on other cell types and in bodily secretions. The ABO blood group system is important in blood transfusion, cell/tissue/organ transplantation and forensic evidence at crime scenes.
The H antigen is formed with the addition of a fucose sugar onto one of two precursor oligosaccharide sequences (Type 1 chains are Gal β1,3 GlcNAc β1,3 Gal R and Type 2 chains are Gal β1,4 GlcNAc β1,3 Gal R; where R is a glycoprotein (Type 1) or glycosphingolipid (Type 2). Type 2 chains are only found on RBCs, epithelial cells and endothelial cells. The H gene expressed in hematopoietic cells produces α-1,2-fucosyltransferase 1 (FUT1) which adds a fucose to Type 2 chains to form the H antigen in non-secretors. Type 1 chains are found in secretors. The Se gene expressed in secretory glands produces α-1,2-fucosyltransferase 2 (FUT2) which adds a fucose to Type 1 chains to form the H antigen in secretors.
The H antigen is abundant in individuals with blood group O and is the essential precursor for the production of A and B antigens. A and B antigens are formed by the action of glycosyltransferases encoded by functional alleles at the ABO genetic locus. The co dominant A allele encodes A transferase, which transfers an N acetylgalactosamine (GalNAc) sugar to the H antigen forming the A antigen. Similarly, the co dominant B allele encodes B transferase, which transfers a galactose (Gal) sugar to the H antigen forming the B antigen. Individuals who have both A and B alleles form the AB antigen. Individuals who are homozygous for the recessive O allele express the H antigen but do not form A or B antigens as they lack both the glycosyltransferase enzymes for their formation. Mutant alleles of the corresponding FUT1 or FUT2 genes result in either a H– phenotype (Bombay phenotype, Oh) or a weak H phenotype (para Bombay) where the affected individual cannot form H, A or B antigens (Kaneko et al. 1997, Koda et al. 1997). The biosyntheses of the A, B and H antigens are described in this section (Ewald & Sumner 2016, Scharberg et al. 2016).
R-HSA-9660821 ADORA2B mediated anti-inflammatory cytokines production The natural ligand for adenosine receptor A2B (ADORA2B) is extracellular adenosine (Ad-Rib), formed from the reduction of ATP by ENTDPases. ATP enters the extracellular space in response to parasite infection, tissue injury, apoptosis amongst other stress factors and has chemotactic and excitatory effects (Cekic et al.2016).
The reduction of ATP to Ade Rib is thought to be a regulatory mechanism by which the synthesis of anti inflammatory cytokines is induced. In addition, killing mechanisms are switched off (Figueiredo et al. 2016). Accordingly, increased expression of ADORA2B in monocytes correlates with higher Leishmania donovani parasites loads alongside increment of IL10 production (Vijayamahantesh et al. 2016). Exacerbation of lesion development in L. amazonensis infected mice also correlated with high amounts of Ade Rib (Figueiredo et al. 2016).
R-HSA-418592 ADP signalling through P2Y purinoceptor 1 Co-activation of P2Y1 and P2Y12 is necessary for complete platelet activation. P2Y1 is coupled to Gq and helps trigger the release of calcium from internal stores, leading to weak and reversible platelet aggregation. P2Y12 is Gi coupled, inhibiting adenylate cyclase, leading to decreased cAMP, a consequent decrease in cAMP-dependent protein kinase activity which increases cytoplasmic [Ca2+], necessary for activation (Woulfe et al. 2001).
In activated platelets, P2Y12 signaling is required for the amplification of aggregation induced by all platelet agonists including collagen, thrombin, thromboxane, adrenaline and serotonin. P2Y12 activation causes potentiation of thromboxane generation, secretion leading to irreversible platelet aggregation and thrombus stabilization.
R-HSA-392170 ADP signalling through P2Y purinoceptor 12 Co-activation of P2Y1 and P2Y12 is necessary for complete platelet activation. P2Y1 is coupled to Gq and helps trigger the release of calcium from internal stores, leading to weak and reversible platelet aggregation. P2Y12 is Gi coupled, inhibiting adenylate cyclase, leading to decreased cAMP, a consequent decrease in cAMP-dependent protein kinase activity which increases cytoplasmic [Ca2+], necessary for activation (Woulfe et al. 2001).
In activated platelets, P2Y12 signaling is required for the amplification of aggregation induced by all platelet agonists including collagen, thrombin, thromboxane, adrenaline and serotonin. P2Y12 activation causes potentiation of thromboxane generation, secretion leading to irreversible platelet aggregation and thrombus stabilization.
R-HSA-198323 AKT phosphorylates targets in the cytosol Following activation, AKT can phosphorylate an array of target proteins in the cytoplasm, many of which are involved in cell survival control. Phosphorylation of TSC2 feeds positively to the TOR kinase, which, in turn, contributes to AKT activation (positive feedback loop).
R-HSA-198693 AKT phosphorylates targets in the nucleus After translocation into the nucleus, AKT can phosphorylate a number of targets there such as CREB, forkhead transcription factors, SRK and NUR77.
R-HSA-211163 AKT-mediated inactivation of FOXO1A The unphosphorylated form of FOXO1A shuttles between the nucleus and cytoplasm, maintaining a substantial concentration of this protein in the nucleoplasm, where it functions as a transcription factor. Phosphorylation of the protein, catalyzed by activated AKT, causes its exclusion from the nucleus (Zhang et al. 2002).
R-HSA-9700645 ALK mutants bind TKIs Aberrant signaling by activated forms of ALK can be inhibited by tyrosine kinase inhibitors (TKIs). ALK, like other tyrosine kinase receptors, is activated through a series of phosphorylation and conformational changes that move the receptor from the inactive form to the fully activated form. Type II TKIs bind to the inactive form of the receptor at a site adjacent to the ATP-binding cleft, while type I TKIs bind to the active form (reviewed in Roskoski, 2013). Type I inhibitors crizotinib, brigatinib, alectinib, ceritinib and lorlatinib are all approved for treatment of ALK-dependent cancer. Development of resistance to TKIs is not uncommon, however, either through acquisition of secondary mutations or through activation of bypass pathways that remove the dependence on ALK signaling (reviewed in Lovly and Pao, 2012; Lin et al, 2017; Della Corte et al, 2018).
R-HSA-112122 ALKBH2 mediated reversal of alkylation damage AlkB is an E.coli alpha-ketoglutarate- and Fe(II)-dependent dioxygenase that oxidizes the relevant methyl groups and releases them as formaldehyde. Two human homologs of AlkB, ALKBH2 and ALKBH3, both remove 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) from methylated polynucleotides in an alpha-ketoglutarate-dependent reaction. They act by direct damage reversal with the regeneration of the unsubstituted bases. E.coli AlkB and human ALKBH2 and ALKBH3 can also repair 1-ethyladenine (1-etA) residues in DNA with the release of acetaldehyde (Duncan et al., 2002, Lee et al. 2005).
R-HSA-112126 ALKBH3 mediated reversal of alkylation damage ALKBH3, like ALKBH2, is a homolog of E.coli alpha-ketoglutarate- and Fe(II)-dependent dioxygenase AlkB that oxidizes methyl groups on alkylated DNA bases and releases them as formaldehyde. Like ALKBH2, ALKBH3 removes 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) from methylated polynucleotides in an alpha-ketoglutarate-dependent reaction and regenerates unsubstituted bases. Like ALKBH2, ALKBH3 can also repair 1-ethyladenine (1-etA) residues in DNA with the release of acetaldehyde (Duncan et al., 2002, Lee et al. 2005). While ALKBH2 has a preference for double strand DNA (dsDNA), ALKBH3 has a preference for single strand DNA (ssDNA). ALKBH3 efficiently repairs dsDNA in the presence of ASCC3 DNA helicase, which unwinds dsDNA, thus providing the single strand substrate for ALKBH3 (Dango et al. 2011).
R-HSA-163680 AMPK inhibits chREBP transcriptional activation activity AMP-activated protein kinase (AMPK) is a sensor of cellular energy levels. A high cellular ratio of AMP:ATP triggers the phosphorylation and activation of AMPK. Activated AMPK in turn phosphorylates a wide array of target proteins, as shown in the figure below (reproduced from (Hardie et al. 2003), with the permission of D.G. Hardie). These targets include ChREBP (Carbohydrate Response Element Binding Protein), whose inactivation by phosphorylation reduces transcription of key enzymes of the glycolytic and lipogenic pathways.
R-HSA-5467333 APC truncation mutants are not K63 polyubiquitinated APC has been shown to be reversibly modified with K63-linked polyubiquitin chains. This modification is required for the assembly of the destruction complex and subsequent degradation of beta-catenin in the absence of WNT ligand. K63-polyubiquitination of APC is lacking in a number of colorectal cancer cell lines expressing truncated forms of APC, and these lines have aberrantly high beta-catenin levels and WNT pathway activation (Tran and Polakis, 2012).
R-HSA-5467337 APC truncation mutants have impaired AXIN binding Mutations in the APC tumor suppressor gene are common in colorectal and other cancers and cluster in the central mutation cluster region (MCR) of the gene (Miyoshi et al, 1992; Nagase and Nakamura, 1993; Dihlmann et al, 1999; reviewed in Bienz and Clevers, 2000). These mutations generally result in truncated proteins that destabilize the destruction complex and result in elevated WNT pathway activation (reviewed in Polakis, 2000).
R-HSA-179409 APC-Cdc20 mediated degradation of Nek2A Like Cyclin A, NIMA-related kinase 2A (Nek2A) is degraded during pro-metaphase in a checkpoint-independent manner.
R-HSA-174143 APC/C-mediated degradation of cell cycle proteins The Anaphase Promoting Complex or Cyclosome (APC/C) functions during mitosis to promote sister chromatid separation and mitotic exit through the degradation of mitotic cyclins and securin. This complex is also active in interphase insuring the appropriate length of the G1 phase (reviewed in Peters, 2002). The APC/C contains at least 12 subunits and functions as an ubiquitin-protein ligase (E3) promoting the multiubiquitination of its target proteins (see Gieffers et al., 2001).
In the ubiquitination reaction, ubiquitin is activated by the formation of a thioester bond with the (E1) ubiquitin activating enzyme then transferred to a cysteine residue within the ubiquitin conjugating enzyme (E2) and ultimately to a lysine residue within the target protein, with the aid of ubiquitin-protein ligase activity of the APC/C. The ubiquitin chains generated are believed to target proteins for destruction by the 26S proteasome (Reviewed in Peters, 1994 )
The activity of the APC/C is highly periodic during the cell cycle and is controlled by a combination of regulatory events. The APC/C is activated by phosphorylation and the regulated recruitment of activating subunits and is negatively regulated by sequestration by kinetochore-associated checkpoint proteins. The Emi1 protein associates with Cdh1 and Cdc20, inhibiting the APC/C between G1/S and prophase. RSSA1 may play a similar role in ihibiting the APC during early mitosis.
Following phosphorylation of the APC/C core subunits by mitotic kinases, the activating subunit, Cdc20 is recruited to the APC/C and is responsible for mitotic activities, including the initiation of sister chromatid separation and the timing of exit from mitosis (See Zachariae and Nasmyth, 1999). Substrates of the Cdc20:APC/C complex, which are recognized by a motif known as the destruction box (D box) include Cyclin A, Nek2, Securin and Cyclin B. Degradation of Securin and Cyclin B does not occur until the mitotic spindle checkpoint has been satisfied (see Castro et al. 2005).
Cdc20 is degraded late in mitosis (Reviewed in Owens and Hoyt, 2005). At this time the activating subunit, Cdh1, previously maintained in an inactive phosphorylated state by mitotic kinases, is dephosphorylated and associates with and activates the APC/C. The APC/C:Cdh1 complex recognizes substrates containing a D box, a KEN box (Pfleger and Kirschner, 2000) or a D box activated (DAD) domain (Castro et al., 2002) sequence and promotes the ordered degration of mitotic cyclins and other mitotic proteins culminating with its own ubiquitin-conjugating enzyme (E2) subunit UbcH10 (Rape et al., 2006). This ordered degradation promotes the stability of Cyclin A at the end of G1. This stabilization, in turn, promotes the phosphorylation of Cdh1 and its abrupt dissociation from the APC/C, allowing accumulation of cyclins for the next G1/S transition (Sorensen et al., 2001).
R-HSA-174048 APC/C:Cdc20 mediated degradation of Cyclin B The degradation of cyclin B1, which appears to occur at the mitotic spindle, is delayed until the metaphase /anaphase transition by the spindle assembly checkpoint and is required in order for sister chromatids to separate (Geley et al. 2001;Hagting et al, 2002).
R-HSA-174154 APC/C:Cdc20 mediated degradation of Securin The separation of sister chromatids in anaphase requires the destruction of the anaphase inhibitor, securin. Securin associates with and inactivates the protease, separase. Separase cleaves the cohesin subunit, Scc1 that is responsible for the cohesion of sister chromatids (reviewed in Nasmyth et al., 2000). Securin destruction begins at metaphase after the mitotic spindle checkpoint has been satisfied (Hagting et al., 2002).
R-HSA-176409 APC/C:Cdc20 mediated degradation of mitotic proteins Following phosphorylation of the APC/C core subunits by mitotic kinases, the activating protein, Cdc20 is recruited to the APC and promotes the multiubiquitination and subsequent degradation of the mitotic cyclins (Cyclin A and Cyclin B) as well as the protein securin which functions in sister chromatid cohesion. Timely degradation of these proteins is essential for sister chromatid separation and the proper timing of exit from mitosis (See Zachariae and Nasmyth, 1999). Cdc20 is degraded late in mitosis (Reviewed in Owens and Hoyt, 2005)
R-HSA-174178 APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 From late mitosis through G1 phase APC/C:Cdh1 insures the continued degradation of the mitotic proteins and during mitotic exit and G1 its substrates include Cdc20, Plk1, Aurora A, Cdc6 and Geminin (see Castro et al., 2005). Rape et al. have recently demonstrated that the order in which APC/C targeted proteins are degraded is determined by the processivity of multiubiquitination of these substrates. Processive substrates acquire a polyubiquitin chain upon binding to the APC/C once and are degraded. Distributive substrates bind, dissociate and reassociate with the APC/C multiple times before acquiring an ubiquitin chain of sufficient length to insure degradation. In addition, distributive substrates that dissociate from the APC/C with short ubiquitin chains are targeted for deubiquitination (Rape et al., 2006).
R-HSA-179419 APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint APC:CDC20 mediates the degradation of a number of cell cycle proteins including Cyclin A and Nek2A.
R-HSA-5649702 APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway NEIL1 and NEIL2 have a dual DNA glycosylase and beta/delta lyase activity. The AP (apurinic/apyrimidinic) site-directed lyase activity of NEIL1 and NEIL2 is their major physiological role, as they can act on AP sites generated spontaneously or by other DNA glycosylases. NEIL1 or NEIL2 cleave the damaged DNA strand 5' to the AP site, producing a 3' phosphate terminus (3'Pi) and a 5' deoxyribose phosphate terminus (5'dRP). DNA polymerase beta (POLB) excises 5'dRP residue but is unable to add the replacement nucleotide to DNA with the 3'Pi end. PNKP, a DNA 3' phosphatase, removes 3'Pi and enables POLB to incorporate the replacement nucleotide, which is followed by ligation of repaired DNA strand by XRCC1:LIG3 complex (Whitehouse et al. 2001, Wiederhold et al. 2004, Das et al. 2006).
R-HSA-180689 APOBEC3G mediated resistance to HIV-1 infection Representatives of the apolipoprotein B mRNA editing enzyme catalytic polypeptide 3 (APOBEC3) family provide innate resistance to exogeneous and endogenous retroviruses (see Cullen 2006 for a recent review). Humans and other primates encode a cluster of seven different cytidine deaminases with APOBEC3G, APOBEC3F and APOBEC3B having some anti HIV-1 activity. Our understanding is most complete for APOBEC3G which has been described first and the reactions described herein will focus on this representative enzyme.
APOBEC3G is a cytoplasmic protein which strongly restricts replication of Vif deficient HIV-1 (Sheehy 2002). It is expressed in cell populations that are susceptible to HIV infection (e.g., T-lymphocytes and macrophages). In the producer cell, APOBEC3G is incorporated into budding HIV-1 particles through an interaction with HIV-1 gag nucleocapsid (NC) protein in a RNA-dependent fashion.
Within the newly infected cell (= target cell), virus-associated APOBEC3G regulates the infectivity of HIV-1 by deaminating cytidine to uracil in the minus-strand viral DNA intermediate during reverse transcription. Deamination results in the induction of G-to-A hypermutations in the plus-strand viral DNA which subsequently can either be integrated as a non-functional provirus or degraded before integration.
R-HSA-5624958 ARL13B-mediated ciliary trafficking of INPP5E ARL13B is a ciliary-localized small GTPase with an atypical C-terminus containing a coiled coil domain and a proline rich domain (PRD) (Hori et al, 2008). Mutations in ARL13B are associated with the development of the ciliopathy Joubert's Syndrome (Cantagrel et al, 2008; Parisi et al, 2009). Studies in C. elegans and vertebrates suggest that ARL13B may play a role in stabilizing the interaction between the IFT A and B complexes and the kinesin-2 motors during anterograde traffic in the cilium (Cevik et al, 2010; Li et al, 2010; Cevik et al, 2013; reviewed in Li et al, 2012; Zhang et al, 2013). Recent work has shown an additional role for ARL13B in trafficking the inositol polyphosphate-5-phosphatase E (INPP5E) to the cilium through a network that also involves the phosphodiesterase PDE6D and the centriolar protein CEP164 (Humbert et al, 2012; Thomas et al, 2014; reviewed in Zhang et al, 2013). Mutations in INPP5E are also associated with the development of Joubert syndrome and other ciliopathies (Bielas et al, 2009; Jacoby et al, 2009; reviewed in Conduit et al, 2012).
R-HSA-170984 ARMS-mediated activation ARMS (Ankyrin-Rich Membrane Spanning/Kidins 220) is a 220kD tetraspanning adaptor protein which becomes rapidly tyrosine phosphorylated by active Trk receptors. ARMS is another adaptor protein which is involved in the activation of Rap1 and the subsequent prolonged activation of the MAPK cascade.
R-HSA-9717264 ASP-3026-resistant ALK mutants ASP3026 is a second generation tyrosine kinase inhibitor with activity against ALK fusions in non-small cell lung cancers (NSCLC) and anaplastic large cell lymphomas (ALCLs). This pathway describes ALK mutants that are resistant to inhibition by ASP3026 (Amin et al, 2016; Katayama et al, 2014; George et al, 2008; Mori et al, 2014; reviewed Roskoski, 2013; Lovly and Pao, 2012)
R-HSA-380994 ATF4 activates genes in response to endoplasmic reticulum stress ATF4 is a transcription factor and activates expression of IL-8, MCP1, IGFBP-1, CHOP, HERP1 and ATF3.
R-HSA-381183 ATF6 (ATF6-alpha) activates chaperone genes The N-terminal fragment of ATF6-alpha contains a bZIP domain and binds the sequence CCACG in ER Stress Response Elements (ERSEs). ATF6-alpha binds ERSEs together with the heterotrimeric transcription factor NF-Y, which binds the sequence CCAAT in the ERSEs, and together the two factors activate transcription of ER stress-responsive genes. Evidence from overexpression and knockdowns indicates that ATF6-alpha is a potent activator but its homolog ATF6-beta is not and ATF6-beta may actually reduce expression of ER stress proteins.
R-HSA-381033 ATF6 (ATF6-alpha) activates chaperones ATF6-alpha is a transmembrane protein that normally resides in the Endoplasmic Reticulum (ER) membrane. Here its luminal C-terminal domain is associated with BiP, shielding 2 Golgi-targeting regions and thus keeping ATF6-alpha in the ER. Upon interaction of BiP with unfolded proteins in the ER, ATF6-alpha dissociates and transits to the Golgi where it is cleaved by the S1P and S2P proteases that reside in the Golgi, releasing the N-terminal domain of ATF6-alpha into the cytosol. After transiting to the nucleus, the N-terminal domain acts as a transcription factor to activate genes encoding chaperones.
R-HSA-8874177 ATF6B (ATF6-beta) activates chaperones Like its homolog ATF6 (reviewed in Fox and Andrew 2015), ATF6B is activated by cleavage in response to endoplasmic reticulum (ER) stress (Haze et al. 2001). In unstressed cells, ATF6B spans the ER membrane where its lumenal domain probably forms a complex with HSPA5 (BiP, GRP78). During ER stress, HSPA5 dissociates from ATF6B exposing Golgi localization signals in the lumenal domain of ATF6B and causing ATF6B to traffic to the Golgi membrane. The Golgi-resident proteases MBTPS1 (S1P) and MBTPS2 (S2P) cleave ATF6B and release the cytoplasmic domain, which contains a transcription activation domain, a bZIP dimerization domain, and a nuclear localization signal (Haze et al. 2001). N-glycosylation in the lumenal domain of ATF6B is required for cleavage (Guan et al. 2009). The cytoplasmic fragment traffics to the nucleus where it acts as a weak transcription activator (Haze et al. 2001). By forming heterodimers with the strong activator ATF6, ATF6B acts as an inhibitory modulator of ATF6 (Thuerauf et al. 2004, Thuerauf et al. 2007).
R-HSA-1296025 ATP sensitive Potassium channels ATP sensitive K+ channels couple intracellular metabolism with membrane excitability. These channels are inhibited by ATP so are open in low metabolic states and close in high metabolic states, resulting in membrane depolarization triggering responses such as insulin secretion, modulation of vascular smooth muscle and cardioprotection. The channel comprises four Kir6.x subunits and four regulatory sulphonylurea receptors (SUR) (Akrouh et al, 2009).
R-HSA-450408 AUF1 (hnRNP D0) binds and destabilizes mRNA AUF1 (hnRNP D0) dimers bind U-rich regions of AU-rich elements (AREs) in the 3' untranslated regions of mRNAs. The binding causes AUF1 dimers to assemble into higher order tetrameric complexes. Diphosphorylated AUF1 bound to RNA recruits additional proteins, including eIF4G, polyA-binding protein, Hsp, Hsc70, Hsp27, NSEP-1, NSAP-1, and IMP-2 which target the mRNA and AUF1 for degradation. Unphosphorylated AUF1 is thought to be less able to recruit additional proteins. AUF1 also interacts directly or indirectly with HuR and the RNA-induced silencing complex (RISC).
AUF1 complexed with RNA and other proteins is ubiquitinated and targeted for destruction by the proteasome while the bound mRNA is degraded. Inhibition of ubiquitin addition to AUF1 blocks mRNA degradation. The mechanism by which ubiquitin-dependent proteolysis is coupled to mRNA degradation is unknown.
At least 4 isoforms of AUF1 exist: p45 (45 kDa) contains all exons, p42 lacks exon 2, p40 lacks exon 7, and p37 lacks exons 2 and 7. The presence of exon 7 in p42 and p45 seems to block ubiquitination while the absence of exon 7 (p37 and p40) targets AUF1 for ubiquitination and destabilizes bound RNAs. Lack of exon 2 (p37 and p42) is associated with higher affinity for RNA and 14-3-3sigma (SFN).
AUF1 binds and destabilizes mRNAs encoding Interleukin-1 beta (IL1B), Tumor Necrosis Factor alpha (TNFA), Cyclin-dependent kinase inhibitor 1 (CDNK1A, p21), Cyclin-D1 (CCND1), Granulocyte-macrophage colony stimulating factor (GM-CSF, CSF2), inducible Nitric oxide synthase (iNOS, NOS2), Proto-oncogene cFos (FOS), Myc proto-oncogene (MYC), Apoptosis regulator Bcl-2 (BCL2).
R-HSA-8854518 AURKA Activation by TPX2 TPX2 binds to aurora kinase A (AURKA) at centrosomes and promotes its activation by facilitating AURKA active conformation and autophosphorylation of the AURKA threonine residue T288 (Bayliss et al. 2003, Xu et al. 2011, Giubettini et al. 2011, Dodson and Bayliss 2012).
R-HSA-5467340 AXIN missense mutants destabilize the destruction complex Alterations in AXIN1 have been detected in a number of different cancers including liver and colorectal cancer and medullablastoma, among others (reviewed in Salahshor and Woodgett, 2005). Missense and nonsense mutations that disrupt or remove protein-protein interaction domains are common, and AXIN variants in cancers tend to disrupt the formation of a functional destruction complex (Satoh et al, 2000; Taniguchi et al, 2002; Webster et al, 2000; Shimizu et al, 2002).
R-HSA-2161522 Abacavir ADME Abacavir is a nucleoside analogue reverse transcriptase inhibitor with antiretroviral activity, widely used in combination with other drugs to treat HIV-1 infection (Yuen et al. 2008). Its uptake across the plasma membrane is mediated by organic cation transporters SLC22A1, 2, and 3; the transport proteins ABCB1 and ABCG2 mediate its efflux. Abacavir itself is a prodrug. Activation requires phosphorylation by a cytosolic adenosine phosphotransferase and deamination by ADAL deaminase to yield carbovir monophosphate. Cytosolic nucleotide kinases convert carbovir monophosphate to carbovir triphosphate, the active HIV reverse transcriptase inhibitor. Abacavir can be glucuronidated or oxidized to a 5'-carboxylate; these are the major forms in which it is excreted from the body.
R-HSA-2161541 Abacavir metabolism Abacavir activation proceeds steps of phosphorylation, deamination to yield carbovir monophosphate, and phosphorylation of the latter compound to yield the triphosphate. In addition, abacavir can be conjugated with glucuronide or oxidized to its 5'-carboxylate derivative, the two major forms in which it is excreted from the body (Yuen et al. 2008).
R-HSA-2161517 Abacavir transmembrane transport Cytosolic levels of abacavir are determined by the balance of its facilitated diffusion into the cell mediated by organic cation transporters SLC22A1, 2, and 3, and its ATP-dependent efflux from cells mediated by ABCG2 and ABCB1 (Klaasen and Aleksunes 2010; Pan et al. 2007; Shaik et al. 2007).
R-HSA-73930 Abasic sugar-phosphate removal via the single-nucleotide replacement pathway Abasic sugar phosphate removal via the single nucleotide replacement pathway requires displacement of DNA glycosylase by APEX1, APEX1-mediated endonucleolytic cleavage at the 5' side of the base free deoxyribose residue, recruitment of POLB to the AP site and excision of the abasic sugar phosphate (5'dRP) residue at the strand break (Lindahl and Wood, 1999).
R-HSA-9659787 Aberrant regulation of mitotic G1/S transition in cancer due to RB1 defects RB1 protein, also known as pRB or retinoblastoma protein, is a nuclear protein that plays a major role in the regulation of the G1/S transition during mitotic cell cycle in multicellular eukaryotes. RB1 performs this function by binding to activating E2Fs (E2F1, E2F2 and E2F3), and preventing transcriptional activation of E2F1/2/3 target genes, which include a number of genes involved in DNA synthesis. RB1 binds E2F1/2/3 through the so-called pocket region, which is formed by two parts, pocket domain A (amino acid residues 373-579) and pocket domain B (amino acid residues 640-771). Besides intact pocket domains, RB1 requires an intact nuclear localization signal (NLS) at its C-terminus (amino acid residues 860-876) to be fully functional (reviewed by Classon and Harlow 2002, Dick 2007). Functionally characterized RB1 mutations mostly affect pocket domains A and B and the NLS. RB1 mutations reported in cancer are, however, scattered over the entire RB1 coding sequence and the molecular consequences of the vast majority of these mutations have not been studied (reviewed by Dick 2007).
Many viral oncoproteins inactivate RB1 by competing with E2F1/2/3 for binding to the pocket region of RB1. RB1 protein is targeted by the large T antigen of the Simian virus 40 (SV40), the adenoviral E1A protein, and the E7 protein of oncogenic human papilloma viruses (HPVs) (reviewed by Classon and Harlow 2002).
R-HSA-9687139 Aberrant regulation of mitotic cell cycle due to RB1 defects RB1 was the first tumor suppressor gene discovered. Bi-allelic loss of function of the RB1 gene, located at the chromosomal band 13q14, is the underlying cause of both familial and sporadic retinoblastoma, a pediatric eye cancer (reviewed by Lohmann and Gallie 2000, Knudson 2001, Corson and Gallie 2007). Besides retinoblastoma, carriers of germline RB1 mutations are predisposed to an array of other cancers, called second primary tumors, such as pinealoblastoma, osteosarcoma, leiomyosarcoma, rhabdomyosarcoma and melanoma (reviewed by Lohmann and Gallie 2000).
Inactivating somatic mutations in the RB1 gene are frequent in bladder cancer (Cancer Genome Atlas Research Network 2014), osteosarcoma (Ren and Gu 2017), ovarian cancer (Liu et al. 1994, Kuo et al. 2009, Cancer Genome Atlas Research Network 2011), small-cell lung carcinoma (reviewed by Gazdar et al. 2017), liver cancer (Ahn et al. 2014, Bayard et al. 2018) and esophageal cancer (Gao et al. 2014, Kishino et al. 2016, Salem et al. 2018).
The vast majority of RB1 mutations in cancer represent complete genomic deletions or nonsense and frameshift mutations that are predicted to result in null alleles. Missense mutations are rare and usually result in partially active RB1 mutants. Functionally characterized RB1 missense mutations and inframe deletions mostly affect pocket domains A and B and the nuclear localization signal (NLS). RB1 missense mutations reported in cancer are, however, scattered over the entire RB1 coding sequence and the molecular consequences of the vast majority of these mutations have not been studied (reviewed by Dick 2007).
The RB1 protein product, also known as pRB or retinoblastoma protein, is a nuclear protein that plays a major role in the regulation of the G1/S transition during mitotic cell cycle in multicellular eukaryotes. RB1 performs this function by binding to activating E2Fs (E2F1, E2F2 and E2F3), and preventing transcriptional activation of E2F1/2/3 target genes, which include a number of genes involved in DNA synthesis (reviewed by Classon and Harlow 2002, Dick 2007). RB1 also regulates mitotic exit by acting on SKP2, a component of the SCF E3 ubiquitin ligase complex. RB1 facilitates degradation of SKP2 by the anaphase promoting complex/cyclosome (APC/C), thus preventing SKP2-mediated degradation of the cyclin-dependent kinase inhibitor CDKN1B (p27Kip1). RB1-dependent accumulation of p27Kip1 plays an important role in mitotic exit and RB1-mediated tumor suppression (reviewed by Dyson 2016).
In addition to its role in regulation of the G1/S transition and mitotic exit, RB1 also performs other, non-canonical, functions, such as its role in the maintenance of genomic stability, which is linked to its role in chromosome condensation during mitotic prophase. The impact of RB1 mutations on these E2F-independent functions, which are still important for RB1-mediated tumor suppression, has been poorly studied (reviewed by Chau and Wang 2003, Burkhart and Sage 2008, Manning and Dyson 2012, Dyson 2016, Dick et al. 2018).
R-HSA-9687136 Aberrant regulation of mitotic exit in cancer due to RB1 defects RB1 regulates mitotic exit by acting on SKP2, a component of the SCF E3 ubiquitin ligase complex. RB1 facilitates degradation of SKP2 by the anaphase promoting complex/cyclosome (APC/C), thus preventing SKP2-mediated degradation of the cyclin-dependent kinase inhibitor CDKN1B (p27Kip1). RB1-dependent accumulation of p27Kip1 plays an important role in mitotic exit and RB1-mediated tumor suppression (reviewed by Dyson 2016).
R-HSA-2978092 Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate Somatic mutations affecting arginine residue 132 of IDH1 (isocitrate dehydrogenase 1, a cytosolic enzyme that normally catalyzes the NADP+-dependent conversion of isocitrate to 2-oxoglutarate), are very commonly found in human glioblastomas (Parsons et al. 2008). These mutant proteins efficiently catalyze the NADPH-dependent reduction of 2-oxoglutarate to form 2-hydroxyglutarate. Cells expressing the mutant protein accumulate elevated levels of 2-hydroxyglutarate, probably in the cytosol as IDH1 is a cytosolic enzyme. The fate of the 2-hydroxyglutarate is unclear, but the high frequency with which the mutation is found in surveys of primary tumors is consistent with the possibility that it is advantageous to the tumor cells (Dang et al 2009).
R-HSA-167242 Abortive elongation of HIV-1 transcript in the absence of Tat This event was inferred from the corresponding Reactome human Poll II transcription elongation event. The details specific to HIV-1 transcription elongation are described below. In the absence of the HIV-1 Tat protein, the RNA Pol II complexes associated with the HIV-1 template are non-processive. RNA Pol II is arrested after promoter clearance by the negative transcriptional elongation factors DSIF and NELF as occurs during early elongation of endogenous templates (Wada et al, 1998; Yamaguchi et al. 1999). This arrest cannot be overcome by P-TEFb mediated phosphorylation in the absence of Tat however, and elongation aborts resulting in the accumulation of short transcripts (Kao et al., 1987).
R-HSA-156582 Acetylation N-acetyltransferases (NATs; EC 2.3.1.5) utilize acetyl Co-A in acetylation conjugation reactions. This is the preferred route of conjugating aromatic amines (R-NH2, converted to aromatic amides R-NH-COCH3) and hydrazines (R-NH-NH2, converted to R-NH-NH-COCH3). Aliphatic amines are not substrates for NAT. The basic reaction is
Acetyl-CoA + an arylamine = CoA + an N- acetylarylamine
CDK5-mediated phosphorylation of NTRK2 was suggested to influence the level of AKT activity, downstream mTOR signaling and DLG4 (PSD-95) expression, but further elucidation is needed (Lai et al. 2012).
Signaling by TRKB and CDK5 plays a role in inflammation induced hypersensitivity to heat-triggered pain in rats (Zhang et al. 2014). R-HSA-9028731 Activated NTRK2 signals through FRS2 and FRS3 Adapter proteins FRS2 and FRS3 can both bind to the cytoplasmic tail of activated NTRK2 (TRKB) receptor, which is followed by NTRK2-mediated phosphorylation of FRS2 and FRS3. NTRK2 signaling through FRS3 has been poorly characterized (Easton et al. 1999, Yuen and Mobley 1999, Dixon et al. 2006, Zeng et al. 2014). Phosphorylated FRS2 is known to recruit GRB2 (presumably in complex with SOS1) and PTPN11 (SHP2) to activated NTRK2, leading to augmentation of RAS signaling (Easton et al. 1999, Easton 2006). R-HSA-9032500 Activated NTRK2 signals through FYN In mouse brain, Fyn activation downstream of Bdnf-induced Ntrk2 (TrkB) signaling results in increased protein levels of AMPA receptor subunits Gria2 (GluR2), Gria3 (GluR3) and Gria1 (GluR1) without change in mRNA levels (Narisawa-Saito et al. 1999).
BDNF-mediated activation of NTRK2 increases phosphorylation of voltage gated sodium channels by FYN, resulting in decrease of sodium currents (Ahn et al. 2007).
FYN activation downstream of NTRK2 is implicated in olygodendrocyte myelination and contributes to BDNF-induced activation of ERK1/2 (MAPK3/1) through an unknown mechanism (Peckham et al. 2015).
Besides acting downstream of NTRK2, FYN and other SRC kinases, activated by other receptors such as GPCRs, may phosphorylate NTRK2 and enhance its catalytic activity (Rajagopal and Chao 2006, Huang and McNamara 2010).
R-HSA-9028335 Activated NTRK2 signals through PI3K Neurotrophin receptor NTRK2 (TRKB), activated by BDNF or NTF4, activates PI3K, resulting in formation of the PIP3 secondary messenger. PIP3 activates AKT signaling, and AKT signaling activates mTOR signaling (Yuen and Mobley 1999, Cao et al. 2013).
R-HSA-9026527 Activated NTRK2 signals through PLCG1 Activation of the neurotrophin receptor NTRK2 (TRKB) by BDNF or NTF4 triggers downstream PLCgamma (PLCG1) signaling, resulting in formation of secondary messengers DAG and IP3 (Eide et al. 1996, Minichiello et al. 1998, McCarthy and Feinstein 1999, Yuen and Mobley 1999, Minichiello et al. 2002, Yamada et al. 2002).
R-HSA-9026519 Activated NTRK2 signals through RAS Activation of the neurotrophin receptor NTRK2 (TRKB) by BDNF or NTF4 triggers downstream RAS signaling. The best studied mechanism for activation of RAS signaling downstream of NTRK2 is through SHC1-mediated recruitment of the GRB2:SOS1 complex, triggering SOS1-mediated guanine nucleotide exchange on RAS and formation of active RAS:GTP complexes (Minichiello et al. 1998, McCarthy and Feinstein 1999, Yuen and Mobley 1999).
R-HSA-9603381 Activated NTRK3 signals through PI3K The PI3K complex, composed of PIK3R1 and PIK3CA, co-immunoprecipitates with NTRK3 (TRKC), activated by NTF3 (NT-3) treatment (Yuen and Mobley 1999). Activation of NTRK3 correlates with activating phosphorylation of AKT, the main mediator of PI3K signaling (Tognon et al. 2001, Jin et al. 2008), and is dependent on PI3K activity (Tognon et al. 2001). NTRK3-mediated activation of PI3K signaling depends on SRC activation and the adaptor protein IRS1, but the exact mechanism is not known (Morrison et al. 2002, Lannon et al. 2004, Jin et al. 2008).
R-HSA-9034793 Activated NTRK3 signals through PLCG1 The receptor tyrosine kinase NTRK3 (TRKC), when activated by its ligand NTF3 (NT-3), induces PLCG1 phosphorylation, triggering PLCG1 signaling (Marsh and Palfrey 1996, Yuen and Mobley 1999).
R-HSA-9034864 Activated NTRK3 signals through RAS Upon activation by NTF3 (NT-3), the receptor tyrosine kinase NTRK3 (TRKC) triggers RAS signaling through adaptor proteins SHC1 and GRB2 (Marsh and Palfrey 1996, Gunn-Moore et al. 1997, Yuen and Mobley 1999). ERK activation downstream of NTRK3 may increase cell motility through WAVE. The mechanism is not known (Gromnitza et al. 2018).
R-HSA-5625886 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 PKN1, activated by phosphorylation at threonine T774, binds activated AR (androgen receptor) and promotes transcription from AR-regulated promoters. On one hand, phosphorylated PKN1 promotes the formation of a functional complex of AR with the transcriptional coactivator NCOA2 (TIF2) (Metzger et al. 2003). On the other hand, binding of phosphorylated PKN1, in complex with the activated AR, to androgen-reponsive promoters of KLK2 and KLK3 (PSA) genes, leads to PKN1-mediated histone phosphorylation. PKN1-phosphorylated histones recruit histone demethylases KDM4C (JMJD2C) and KDM1A (LSD1), and the ensuing demethylation of histones associated with the promoter regions of KLK2 and KLK3 genes increases their transcription (Metzger et al. 2005, Metzger et al. 2008).
R-HSA-2033519 Activated point mutants of FGFR2 Autosomal dominant mutations in FGFR2 are associated with the development of a range of skeletal disorders including Beare-Stevensen cutis gyrata syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome, Crouzon syndrome and Apert Syndrome (reveiwed in Burke, 1998; Webster and Donoghue 1997; Cunningham, 2007). Mutations that give rise to Crouzon, Jackson-Weiss and Pfeiffer syndromes tend to cluster in the third Ig-like domain of the receptor, either in exon IIIa (shared by the IIIb and the IIIc isoforms) or in the FGFR2c-specific exon IIIc. These mutations frequently involve creation or removal of a cysteine residue, leading to the formation of an unpaired cysteine residue that is thought to promote intramolecular dimerization and thus constitutive, ligand-independent activation (reviewed in Burke, 1998; Webster and Donoghue, 1997; Cunningham, 2007). Mutations in FGFR2 that give rise to Apert Syndrome cluster to the highly conserved Pro-Ser dipeptide in the IgII-Ig III linker; mutations in the paralogous residues of FGFR1 and 3 give rise to Pfeiffer and Muenke syndromes, respectively (Muenke, 1994; Wilkie, 1995; Bellus, 1996). Development of Beare-Stevensen cutis gyrata is associated with mutations in the transmembrane-proximal region of the receptor (Przylepa, 1996), and similar mutations in FGFR3 are linked to the development of thanatophoric dysplasia I (Tavormina, 1995a). These mutations all affect FGFR2 signaling without altering the intrinsic kinase activity of the receptor.
Activating point mutations have also been identified in FGFR2 in ~15% of endometrial cancers, as well as to a lesser extent in ovarian and gastric cancers (Dutt, 2008; Pollock, 2007; Byron, 2010; Jang, 2001). These mutations are found largely in the extracellular region and in the kinase domain of the receptor, and parallel activating mutations seen in autosomal dominant disorders described above.
Activating mutations in FGFR2 are thought to contribute to receptor activation through diverse mechanisms, including constitutive ligand-independent dimerization (Robertson, 1998), expanded range and affinity for ligand (Ibrahimi, 2004b; Yu, 2000) and enhanced kinase activity (Byron, 2008; Chen, 2007).
R-HSA-111452 Activation and oligomerization of BAK protein tBID binds to its mitochondrial partner BAK to release cytochrome c. Activated tBID results in an allosteric activation of BAK. This may induce its intramembranous oligomerization into a pore for cytochrome c efflux.
R-HSA-165158 Activation of AKT2 RAC serine/threonine-protein kinases (AKT, PKB) are serine/threonine kinases belonging to the cAMP-dependent protein kinase A/ protein kinase G/ protein kinase C (AGC) superfamily of protein kinases. They share structural homology within their catalytic domains and have similar mechanisms of activation. Mammals have three AKT genes, named RAC-alpha serine/threonine-protein kinase (AKT1, PKB, PKB-alpha), RAC-beta serine/threonine-protein kinase (AKT2, PKB-beta and RAC-gamma serine/threonine-protein kinase (AKT3, PKB-gamma, STK2). All share a conserved domain structure: an amino terminal pleckstrin homology (PH) domain, a central kinase domain and a carboxyl-terminal regulatory domain that contains a hydrophobic motif that is characteristic of AGC kinases. The PH domain interacts with membrane lipid products such as phosphatidylinositol (3,4,5) trisphosphate (PIP3) produced by phosphatidylinositol 3-kinase (PI3-kinase). Biochemical analysis. The PH domain of AKT binds to PIP3 and PIP2 with similar affinity (James et al. 1996, Frech et al. 1997). The kinase catalytic domain of Akt/PKB is highly similar to other AGC kinases (Peterson & Schreiber 1999). Phosphorylation of a conserved threonine residue in this region (T308 in AKT1) results in partial activation (Alessi et al. 1996). The carboxyl terminal extension has the hydrophobic motif FPQFSY. Phosphorylation of serine or threonine residue in this motif is necessary for full kinase activation. Deletion of this motif completely abolishes activity (Andjelković et al. 1997).
R-HSA-399710 Activation of AMPA receptors AMPA receptors are functionally either Ca permeable or Ca impermeable based on the subunit composition. Ca permeability is determined by GluR2 subunit which undergoes post-transcriptional RNA editing that changes glutamine (Q) at the pore to arginine (R). Incorporation of even a single subunit in the AMPA receptor confers Ca-limiting properties. Ca permeable AMPA receptors permit Ca and Na whereas Ca impermeable AMPA receptors permit only Na. In general, glutamatergic neurons contain Ca impermeable AMPA receptors and GABAergic interneurons contain Ca permeable AMPA receptors. However, some synapses do contain a mixture of Ca permeable and Ca impermeable AMPA receptors. GluR1-4 are encoded by four genes however, alternative splicing generates several functional subunits namely long and short forms of GluR1 and GluR2. GluR4 has long tail only and GluR3 has short tail only. Besides the differences in the tail length, flip/flop isoforms are generated by an interchangeable exon that codes the fourth membranous domain towards the C terminus. The fip/flop isoforms determine rate of desensitization/resensitization and the rate of channel closing. Receptors homomers or heteromers assembled from the combination of GluR1-4 subunits that vary in C tail length and flip/flop versions generates a whole battery of functionally distinct AMPA receptors.
R-HSA-9619483 Activation of AMPK downstream of NMDARs Activation of NMDA receptors (NMDARs) leads to activation of AMP-activated kinase (AMPK) in a CAMKK2-dependent manner. Overactivation of CAMKK2 or AMPK in neurons can lead to dendritic spine loss and is implicated in synaptotoxicity of beta-amyloids in Alzheimer's disease (Mairet-Coello et al. 2013).
R-HSA-176814 Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins APC/C:Cdc20 is first activated at the prometaphase/metaphase transition through phosphorylation of core subunits of the APC/C by mitotic kinases as well as recruitment of the APC/C activator protein Cdc20. APC/C:Cdc20 promotes the multiubiquitination and ordered degradation of Cyclin A and Nek2 degradation in prometaphase followed by Cyclin B and securin in metaphase (Reviewed in Castro et al., 2005).
R-HSA-176187 Activation of ATR in response to replication stress Genotoxic stress caused by DNA damage or stalled replication forks can lead to genomic instability. To guard against such instability, genotoxically-stressed cells activate checkpoint factors that halt or slow cell cycle progression. Among the pathways affected are DNA replication by reduction of replication origin firing, and mitosis by inhibiting activation of cyclin-dependent kinases (Cdks). A key factor involved in the response to stalled replication forks is the ATM- and rad3-related (ATR) kinase, a member of the phosphoinositide-3-kinase-related kinase (PIKK) family. Rather than responding to particular lesions in DNA, ATR and its binding partner ATRIP (ATR-interacting protein) sense replication fork stalling indirectly by associating with persistent ssDNA bound by RPA. These structures would be formed, for example, by dissociation of the replicative helicase from the leading or lagging strand DNA polymerase when the polymerase encounters a DNA lesion that blocks DNA synthesis. Along with phosphorylating the downstream transducer kinase Chk1 and the tumor suppressor p53, activated ATR modifies numerous factors that regulate cell cycle progression or the repair of DNA damage. The persistent ssDNA also stimulates recruitment of the RFC-like Rad17-Rfc2-5 alternative clamp-loading complex, which subsequently loads the Rad9-Hus1-Rad1 complex onto the DNA. The latter '9-1-1' complex serves to facilitate Chk1 binding to the stalled replication fork, where Chk1 is phosphorylated by ATR and thereby activated. Upon activation, Chk1 can phosphorylate additional substrates including the Cdc25 family of phosphatases (Cdc25A, Cdc25B, and Cdc25C). These enzymes catalyze the removal of inhibitory phosphate residues from cyclin-dependent kinases (Cdks), allowing their activation. In particular, Cdc25A primarily functions at the G1/S transition to dephosphorylate Cdk2 at Thr 14 and Tyr 15, thus positively regulating the Cdk2-cyclin E complex for S-phase entry. Cdc25A also has mitotic functions. Phosphorylation of Cdc25A at Ser125 by Chk1 leads to Cdc25A ubiquitination and degradation, thus inhibiting DNA replication origin firing. In contrast, Cdc25B and Cdc25C regulate the onset of mitosis through dephosphorylation and activation of Cdk1-cyclin B complexes. In response to replication stress, Chk1 phosphorylates Cdc25B and Cdc25C leading to Cdc25B/C complex formation with 14-3-3 proteins. As these complexes are sequestered in the cytoplasm, they are unable to activate the nuclear Cdk1-cyclin B complex for mitotic entry.
These events are outlined in the figure. Persistent single-stranded DNA associated with RPA binds claspin (A) and ATR:ATRIP (B), leading to claspin phosphorylation (C). In parallel, the same single-stranded DNA:RPA complex binds RAD17:RFC (D), enabling the loading of RAD9:HUS1:RAD1 (9-1-1) complex onto the DNA (E). The resulting complex of proteins can then repeatedly bind (F) and phosphorylate (G) CHK1, activating multiple copies of CHK1. R-HSA-111447 Activation of BAD and translocation to mitochondria The switching on/off of its phosphorylation by growth/survival factors regulates BAD activity. BAD remains sequestered by 14-3-3 scaffold proteins after phosphorylation by Akt1. Calcineurin activates BAD by dephosphorylation. R-HSA-114452 Activation of BH3-only proteins The BH3-only members act as sentinels that selectively trigger apoptosis in response to developmental cues or stress-signals like DNA damages. Widely expressed mammalian BH3-only proteins are thought to act by binding to and neutralizing their pro-survival counterparts. Activation of BH3-only proteins directly or indirectly results in the activation of proapoptotic BAX and BAK to trigger cell death. Anti-apoptotic BCL-2 or BCL-XL may bind and sequester BH3-only molecules to prevent BAX, BAK activation. The individual BH3-only members are held in check by various mechanisms with in the cells. They are recruited for death duties in response to death cues by diverse activation processes.The mechanisms involved in activation and release of BH3-only proteins for apoptosis will be discussed in this section.
The following figure has been reproduced here with the kind permission from the authors.
R-HSA-111446 Activation of BIM and translocation to mitochondria BIM acts as a sentinel to check the integrity of the cytoskeleton. It exists as two variant proteins: BIM-EL and BIM-L. In healthy cells, these two isoforms are sequestered to the dynein motor complex on microtubules via the dynein light chain DLC1. JNK or MAPK8 releases BIM in response to UV irradiation by phosphorylation.
R-HSA-139910 Activation of BMF and translocation to mitochondria In healthy cells, BMF is bound to the myosin V motor complex through its interaction with DLC2. UV irradiation or anoikis induces MAPK8 (JNK) to phosphorylate Dynein Light Chain 2 (DLC2) to release BMF.
R-HSA-174577 Activation of C3 and C5 The 3 pathways of complement activation converge on the cleavage of C3 by C3 convertases. C3 convertase cleaves C3 into C3a and C3b - a central step of complement activation. C3a remains in the fluid phase and acts as an anaphylatoxin, whereas C3b can form additional C3 convertases hastening the production of C3b. Besides, C3b binds to C3 convertases to form C5 convertase, which can act as an opsonin, or is degraded into fragments which cannot form an active convertase.
R-HSA-451308 Activation of Ca-permeable Kainate Receptor Kainate receptors that are assembled with subunits GRIK1-5, are Ca2+ permeable if GRIK1 and GRIK2 are not edited at the Q/R or other sites.
These channels permit Ca2+ upon activation by glutamate or other agonists.
R-HSA-1296041 Activation of G protein gated Potassium channels Activation of Kir 3 channels occurs after binding of G beta gamma subunits of GPCR. Activation of Kir3/GIRK leads to K+ efflux. The dissociation of GPCR into G alpha and G beta gamma subunits is activated by the activation of GABA B receptor by GABA binding.
R-HSA-991365 Activation of GABAB receptors GABA B receptors are metabotropic receptors that are functionally linked to C type G protein coupled receptors.? GABA B receptors are activated upon ligand binding. The GABA B1 subunit binds ligand and GABA B2 subunit modulates the activity of adenylate cyclase via the intracellular loop.? GABA B receptors show inhibitory activity via Galpha/G0 subunits via the inhibition of adenylate cyclase or via the activity of Gbeta/gamma subunits that mediate the inhibition of voltage gated Ca2+ channels.
R-HSA-5619507 Activation of HOX genes during differentiation Hox genes encode proteins that contain the DNA-binding homeobox motif and control early patterning of segments in the embryo as well as later events in development (reviewed in Rezsohazy et al. 2015). Mammals have 39 Hox genes arrayed in 4 linear clusters, with each cluster containing 9 to 11 genes. Based on homologies, the genes have been assigned to 13 paralogous groups. The nomenclature of Hox genes uses a letter to indicate the cluster and a number to indicate the paralog group. For example, HOXA4 is the gene in cluster A that is most similar with genes of paralog group 4 from other clusters.
One of the most striking aspects of mammalian Hox gene function is the mechanism of their activation during embryogenesis: the order of genes in a cluster correlates with the timing and location of their activation such that genes at the 3' end of a cluster are activated first and genes at the 5' end of a cluster are activated last. (5' and 3' refer to the transcriptional orientation of the genes in the cluster.) Because development of segments of the embryo proceeds from anterior to posterior this means that the anterior boundaries of expression of 3' genes are more anterior (rostral) and the anterior boundaries of expression of 5' genes are more posterior (caudal). Expression of HOX genes initiates in the posterior primitive streak at the beginning of gastrulation at approximately E7.5 in mouse. As gastrulation proceeds, further 5' genes are sequentially activated and they too undergo the same chromatin changes and migration. After formation of the axis of the embryo, similar waves of activation of HOXA and HOXD clusters occur in developing limbs beginning at about E9. Retinoids, especially all trans retinoic acid (atRA), participate in initiating the process via retinoid receptors. Other factors such as FGFs and Wnt, also regulate Hox expression. After activation, Hox genes participate in maintaining their own expression (autoregulation), activating later, 5' Hox genes, and repressing prior, 3' Hox genes (crossregulation). Differentiation of embryonal carcinoma cells and embryonic stem cells in response to retinoic acid is used to model the process in vitro (reviewed in Gudas et al. 2013).
Activation of Hox genes is accompanied by a change from bivalent chromatin to euchromatin (reviewed in Soshnikova and Duboule 2009). Bivalent chromatin has extensive methylation of lysine-9 on histone H3 (H3K9me3), a repressive mark, with interspersed punctate regions of methylation of lysine-4 on histone H3 (H3K4me2, H3K4me3), an activating mark. Euchromatization initiates at the 3' ends of clusters and proceeds towards the 5' ends, with the euchromatin migrating to an active region of the nucleus (reviewed in Montavon and Duboule 2013). This change in chromatin reflects a loss of H3K27me3 and a gain of H3K4me2,3. Polycomb repressive complexes bind H3K27me3 and are responsible for maintenance of repression, KDM6A and KDM6B histone demethylases remove H3K27me3, and members of the trithorax family of histone methylases (KMT2A, KMT2C, KMT2D) methylate H3K4.
R-HSA-936964 Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) Cell stimulation with viral double-stranded (ds) RNA and bacterial lipopolysaccharide (LPS) activate Toll-like receptors 3 (TLR3) and TLR4, respectively, triggering the activation the activation of two IKK-related serine/threonine kinases, TANK-binding kinase 1 (TBK1) and IκB kinase ε (IKKε, IKBKE) which directly phosphorylate interferon regulatory factor 3 (IRF3) and IRF7 promoting their dimerization and translocation into the nucleus. Although both kinases show structural and functional similarities, it seems that TBK1 and IKBKE differ in their regulation of downstream signaling events of TLR3/TLR4.
IRF3 activation and interferon β (IFNβ) production by poly(I:C), a synthetic analog of dsRNA, are decreased in TBK1-deficient mouse fibroblasts, whereas normal activation was observed in the IKBKE-deficient fibroblasts. However, in double-deficient mouse fibroblasts, the activation of IRF3 is completely abolished, suggesting a partially redundant functions of TBK1 and IKKε (IKBKE) (Hemmi H et al., 2004).
The poly(I:C)-induced phosphorylation of TBK1 and IRF3 was abolished in TRIF (TICAM1)-knockout human keratinocyte HACAT cells (Bakshi S et al., 2017). TICAM1 is utilized as an adaptor protein by TLR3 and TLR4 (Yamamoto M et al., 2003).
TLR3 recruits and activates PI3 kinase (PI3K), which activates the downstream kinase, Akt, leading to full phosphorylation and activation of IRF3 (Sarkar SN et al., 2004). When PI3K is not recruited to TLR3 or its activity is blocked, IRF3 is only partially phosphorylated and fails to bind the promoter of the target gene (Sarkar SN et al., 2004).
R-HSA-1592389 Activation of Matrix Metalloproteinases The matrix metalloproteinases (MMPs), previously known as matrixins, are classically known to be involved in the turnover of extracellular matrix (ECM) components. However, recent high throughput proteomics analyses have revealed that ~80% of MMP substrates are non-ECM proteins including cytokines, growth factor binding protiens, and receptors. It is now clear that MMPs regulate ECM turnover not only by cleaving ECM components, but also by the regulation of cell signalling, and that some MMPs are beneficial and may be drug anti-targets. Thus, MMPs have important roles in many processes including embryo development, morphogenesis, tissue homeostasis and remodeling. They are implicated in several diseases such as arthritis, periodontitis, glomerulonephritis, atherosclerosis, tissue ulceration, and cancer cell invasion and metastasis. All MMPs are synthesized as preproenzymes. Alternate splice forms are known, leading to nuclear localization of select MMPs. Most are secreted from the cell, or in the case of membrane type (MT) MMPs become plasma membrane associated, as inactive proenzymes. Their subsequent activation is a key regulatory step, with requirements specific to MMP subtype.
R-HSA-1169091 Activation of NF-kappaB in B cells DAG and calcium activate protein kinase C beta (PKC-beta, Kochs et al. 1991) which phosphorylates CARMA1 and other proteins (Sommer et al. 2005). Phosphorylated CARMA1 recruits BCL10 and MALT1 to form the CBM complex (Sommer et al. 2005, Tanner et al. 2007) which, in turn, recruits the kinase TAK1 and the IKK complex (Sommer et al. 2005, Shinohara et al. 2005 using chicken cells). TAK1 phosphorylates the IKK-beta subunit, activating it (Wang et al. 2001). The IKK complex then phosphorylates IkB complexed with NF-kappaB dimers in the cytosol (Zandi et al. 1998, Burke et al. 1999, Heilker et al. 1999), resulting in the degradation of IkB (Miyamoto et al. 1994, Traenckner et al. 1994, Alkalay et al. 1995, DiDonato et al. 1995, Li et al. 1995, Lin et al. 1995, Scherer et al. 1995, Chen et al. 1995). NF-kappaB dimers are thereby released and are translocated to the nucleus where they activate transcription (Baeuerle and Baltimore 1988, Blank et al. 1991, Ghosh et al. 2008, Fagerlund et al. 2008).
R-HSA-2980767 Activation of NIMA Kinases NEK9, NEK6, NEK7 NEK6 and NEK7 are activated during mitosis by another NIMA family kinase, NEK9 (Belham et al. 2003, Richards et al. 2009), which is activated by CDK1- and PLK1-mediated phosphorylation (Roig et al. 2002, Bertran et al. 2011).
R-HSA-442755 Activation of NMDA receptors and postsynaptic events NMDA receptors are a subtype of ionotropic glutamate receptors that are specifically activated by a glutamate agonist N-methyl-D-aspartate (NMDA). Activation of NMDA receptors involves opening of the ion channel that allows the influx of Ca2+. NMDA receptors are central to activity dependent changes in synaptic strength and are predominantly involved in the synaptic plasticity that pertains to learning and memory. A unique feature of NMDA receptors, unlike other glutamate receptors, is the requirement for dual activation, both voltage-dependent and ligand-dependent activation. The ligand-dependent activation of NMDA receptors requires co-activation by two ligands, glutamate and glycine. However, at resting membrane potential, the pore of ligand-bound NMDA receptors is blocked by Mg2+. The voltage dependent Mg2+ block is relieved upon depolarization of the post-synaptic membrane. NMDA receptors are coincidence detectors, and are activated only if there is a simultaneous activation of both pre- and post-synaptic cell. Upon activation, NMDA receptors allow the influx of Ca2+ that initiates various molecular signaling cascades involved in the processes of learning and memory. For review, please refer to Cohen and Greenberg 2008, Hardingham and Bading 2010, Traynelis et al. 2010, and Paoletti et al. 2013.
R-HSA-111448 Activation of NOXA and translocation to mitochondria NOXA is transactivated in a p53-dependent manner and by E2F1. Activated NOXA is translocated to mitochondria.
R-HSA-451307 Activation of Na-permeable kainate receptors Kainate receptors that are formed by subunits GRIK1 and or GRIK2 that are edited at the Q/R and other editing sites in GRIK2 are Ca2+ impermeable. They permit the passage of Na+ ions. Glutamine in GRIK1 at position 636 is replaced by arginine by an editing step which occurs posttranscriptioanlly. GRIK2 is glutamine 621 is edited to arginine. GRIK2 is also edited at 571 (Y/C) where a tyrosine residue is changed to cysteine and 567 (I/V) where an isoleucine is changed to valine. All three sites are edited postranscriptionally. A fully edited GRIK2 at all three sites is impermeable to calcium ions.
R-HSA-2151209 Activation of PPARGC1A (PGC-1alpha) by phosphorylation The transcriptional coactivator PPARGC1A (PGC-1alpha), one of the master regulators of mitochondrial biogenesis, is activated by phosphorylation. Energy depletion causes a reduction in ATP and an increase in AMP which activates AMPK. AMPK in turn phosphorylates PPARGC1A. Likewise, p38 MAPK is activated by muscle contraction (possibly via calcium and CaMKII) and phosphorylates PPARGC1A. PPARGC1A does not bind DNA directly, but rather interacts with other transcription factors. Deacetylation of PPARGC1A by SIRT1 appears to follow phosphorylation however the role of deacetylation is unresolved (Canto et al. 2009, Gurd et al. 2011, Philp et al. 2011)
R-HSA-139915 Activation of PUMA and translocation to mitochondria Puma is transactivated in a p53-dependent manner and by E2F1. Activated Puma is translocated to mitochondria.
R-HSA-428540 Activation of RAC1 A low level of RAC1 activity is essential to maintain axon outgrowth. ROBO activation recruits SOS, a dual specificity GEF, to the plasma membrane via Dock homolog NCK (NCK1 or NCK2) to activate RAC1 during midline repulsion.
R-HSA-9619229 Activation of RAC1 downstream of NMDARs Activation of calcium/calmodulin-dependent kinase kinases, CaMKKs (CAMKK1 and CAMKK2), upon calcium influx through activated NMDA receptors, leads to activation of the cytosolic calcium/calmodulin kinase CaMKI (CAMK1). One of the CAMK1 targets is the RAC1 guanine nucleotide exchange factor ARHGEF7 (beta-Pix). Activation of RAC1 is involved in NMDA-receptor triggered synaptogenesis (Saneyoshi et al. 2008).
R-HSA-1169092 Activation of RAS in B cells RasGRP1 and RasGRP3 bind diacylglycerol at the plasma membrane (Lorenzo et al. 2001) and are phosphorylated by protein kinase C (Teixeira et al. 2003, Zheng et al. 2005). Phosphorylated RasGRP1 (Roose et al. 2007) and RasGRP3 (Ohba et al. 2000, Yamashita et al. 2000, Rebhun et al. 2000, Lorenzo et al. 2001) then catalyze the exchange of GDP for GTP bound by RAS, thereby activating RAS.
R-HSA-5635838 Activation of SMO Activation of the transmembrane protein SMO in response to Hh stimulation is a major control point in the Hh signaling pathway (reviewed in Ayers and Therond, 2010; Jiang and Hui, 2008). In the absence of ligand, SMO is inhibited in an unknown manner by the Hh receptor PTCH. PTCH regulates SMO in a non-stoichiometric manner and there is little evidence that endogenous PTCH and SMO interact directly (Taipale et al, 2002; reviewed in Huangfu and Anderson, 2006). PTCH may regulate SMO activity by controlling the flux of sterol-related SMO agonists and/or antagonists, although this has not been fully substantiated (Khaliullina et al, 2009; reviewed in Rohatgi and Scott, 2007; Briscoe and Therond, 2013).
PTCH-mediated inhibition of SMO is relieved upon ligand stimulation of PTCH, but the mechanisms for this relief are again unknown. SMO and PTCH appear to have opposing localizations in both the 'off' and 'on' state, with PTCH exiting and SMO entering the cilium upon Hh pathway activation (Denef et al, 2000; Rohatgi et al, 2007; reviewed in Goetz and Anderson, 2010; Hui and Angers, 2011). Activation of SMO involves a conserved phosphorylation-mediated conformational change in the C-terminal tails that destabilizes an intramolecular interaction and promotes the interaction between adjacent tails in the SMO dimer. In Drosophila, this phosphorylation is mediated by PKA and CK1, while in vertebrates it appears to involve ADRBK1/GRK2 and CSNK1A1. Sequential phosphorylations along multiple serine and threonine motifs in the SMO C-terminal tail appear to allow a graded response to Hh ligand concentration in both flies and vertebrates (Zhao et al, 2007; Chen et al, 2010; Chen et al, 2011). In flies, Smo C-terminal tail phosphorylation promotes an association with the Hedgehog signaling complex (HSC) through interaction with the scaffolding kinesin-2 like protein Cos2, activating the Fu kinase and ultimately releasing uncleaved Ci from the complex (Zhang et al, 2005; Ogden et al, 2003; Lum et al, 2003; reviewed in Mukhopadhyay and Rohatgi, 2014). In vertebrates, SMO C-terminal tail phosphorylation and conformational change is linked to its KIF7-dependent ciliary accumulation (Chen et al, 2011; Zhao et al, 2007; Chen et al, 2010). In the cilium, SMO is restricted to a transition-zone proximal region known as the EvC zone (Yang et al, 2012; Blair et al, 2011; Pusapati et al, 2014; reviewed in Eggenschwiler 2012). Both SMO phosphorylation and its ciliary localization are required to promote the Hh-dependent dissociation of the GLI:SUFU complex, ultimately allowing full-length GLI transcription factors to translocate to the nucleus to activate Hh-responsive genes (reviewed in Briscoe and Therond, 2013).
R-HSA-187015 Activation of TRKA receptors Trk receptors can either be activated by neurotrophins or by two G-protein-coupled receptors (GPCRs) although the biological relevance of GPCRs remains to be shown.
R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis In mammals, anterior Hox genes may be defined as paralog groups 1 to 4 (Natale et al. 2011), which are involved in development of the hindbrain through sequential expression in the rhombomeres, transient segments of the neural tube that form during development of the hindbrain (reviewed in Alexander et al. 2009, Soshnikova and Duboule 2009, Tumpel et al. 2009, Mallo et al. 2010, Andrey and Duboule 2014). Hox gene activation during mammalian development has been most thoroughly studied in mouse embryos and the results have been extended to human development by in vitro experiments with human embryonal carcinoma cells and human embryonic stem cells.
Expression of a typical anterior Hox gene has an anterior boundary located at the junction between two rhombomeres and continues caudally to regulate segmentation and segmental fate in ectoderm, mesoderm, and endoderm. Anterior boundaries of expression of successive Hox paralog groups are generally separated from each other by 2 rhombomeres. For example, HOXB2 is expressed in rhombomere 3 (r3) and caudally while HOXB3 is expressed in r5 and caudally. Exceptions exist, however, as HOXA1, HOXA2, and HOXB1 do not follow the rule and HOXD1 and HOXC4 are not expressed in rhombomeres. Hox genes within a Hox cluster are expressed colinearly: the gene at the 3' end of the cluster is expressed earliest, and hence most anteriorly, then genes 5' are activated sequentially in the same order as they occur in the cluster.
Activation of expression occurs epigenetically by loss of polycomb repressive complexes and change of bivalent chromatin to active chromatin through, in part, the actions of trithorax family proteins (reviewed in Soshnikova and Duboule 2009). Hox gene expression initiates in the posterior primitive streak that will contribute to extraembryonic mesoderm. Expression then extends anteriorly into the cells that will become the embryo, where expression is first observed in presumptive lateral plate mesoderm and is transmitted to both paraxial mesoderm and neurectoderm formed by gastrulation along the primitive streak (reviewed in Deschamps et al. 1999, Casaca et al. 2014).
Prior to establishment of the rhombomeres, expression of HOXA1 and HOXB1 is initiated near the future site of r3 and caudally by a gradient of retinoic acid (RA). (Mechanisms of retinoic acid signaling are reviewed in Cunningham and Duester 2015.) The RA is generated by the ALDH1A2 (RALDH2) enzyme located in somites flanking the caudal hindbrain and degraded by CYP26 enzymes expressed initially in anterior neural ectoderm of the early gastrula and then throughout most of the hindbrain (reviewed in White and Schilling 2008). HOXA1 with PBX1,2 and MEIS2 directly activate transcription of ALDH1A2 to maintain retinoic acid synthesis in the somitic mesoderm (Vitobello et al. 2011). Differentiation of embryonal carcinoma cells and embryonic stem cells in response to retinoic acid is used to model the process of differentiation in vitro (reviewed in Soprano et al. 2007, Gudas et al. 2013).
HOXA1 appears to set the anterior limit of HOXB1 expression (Barrow et al. 2000). HOXB1 initiates expression of EGR2 (KROX20) in presumptive r3. EGR2 then activates HOXA2 expression in r3 and r5 while HOXB1, together with PBX1 and MEIS:PKNOX1 (MEIS:PREP), activates expression of HOXA2 in r4 and caudal rhombomeres. AP-2 transcription factors maintain expression of HOXA2 in neural crest cells (Maconochie et al. 1999). HOXB1 also activates expression of HOXB2 in r3 and caudal rhombomeres. EGR2 negatively regulates HOXB1 so that by the time rhombomeres appear, HOXB1 is restricted to r4 and HOXA1 is no longer detectable (Barrow et al. 2000). EGR2 and MAFB (Kreisler) then activate HOXA3 and HOXB3 in r5 and caudal rhombomeres. Retinoic acid activates HOXA4, HOXB4, and HOXD4 in r7, the final rhombomere. HOX proteins, in turn, activate expression of genes in combination with other factors, notably members of the TALE family of transcription factors (PBX, PREP, and MEIS, reviewed in Schulte and Frank 2014, Rezsohazy et al. 2015). HOX proteins also participate in non-transcriptional interactions (reviewed in Rezsohazy 2014). In zebrafish, Xenopus, and chicken factors such as Meis3, Fgf3, Fgf8, and vHNF regulate anterior hox genes (reviewed in Schulte and Frank 2014), however less is known about the roles of homologous factors in mammals.
Mutations in HOXA1 in humans have been observed to cause developmental abnormalities located mostly in the head and neck region (Tischfield et al. 2005, Bosley et al. 2008). A missense mutation in HOXA2 causes microtia, hearing impairment, and partially cleft palate (Alasti et al. 2008). A missense mutation in HOXB1 causes a similar phenotype to the Hoxb1 null mutation in mice: bilateral facial palsy, hearing loss, and strabismus (improper alignment of the eyes) (Webb et al. 2012).
R-HSA-111459 Activation of caspases through apoptosome-mediated cleavage Procaspase-3 and 7 are cleaved by the apoptosome.
R-HSA-2426168 Activation of gene expression by SREBF (SREBP) After transiting to the nucleus SREBPs (SREBP1A/1C/2, SREBFs) bind short sequences, sterol regulatory elements (SREs), in the promoters of target genes (reviewed in Eberle et al. 2004, Weber et al. 2004). SREBPs alone are relatively weak activators of transcription, with SREBP1C being significantly weaker than SREBP1A or SREBP2. In combination with other transcription factors such as SP1 and NF-Y the SREBPs are much stronger activators. SREBP1C seems to more specifically target genes involved in fatty acid synthesis while SREBP2 seems to target genes involved in cholesterol synthesis (Pai et al. 1998).
R-HSA-451326 Activation of kainate receptors upon glutamate binding Kainate receptors are found both in the presynaptc terminals and the postsynaptic neurons.
Kainate receptor activation could lead to either ionotropic activity (influx of Ca2+ or Na+ and K+) in the postsynaptic neuron or coupling of the receptor with G proteins in the presynaptic and the postsynaptic neurons.
Kainate receptors are tetramers made from subunits GRIK1-5 or GluR5-7 and KA1-2. Activation of kainate receptors made from GRIK1 or KA2 release Ca2+ from the intracellular stores in a G protein-dependent manner. The G protein involved in this process is sensitive to pertussis toxin.
R-HSA-450341 Activation of the AP-1 family of transcription factors Activator protein-1 (AP-1) is a collective term referring to a group of transcription factors that bind to promoters of target genes in a sequence-specific manner. AP-1 family consists of hetero- and homodimers of bZIP (basic region leucine zipper) proteins, mainly of Jun-Jun, Jun-Fos or Jun-ATF.
AP-1 members are involved in the regulation of a number of cellular processes including cell growth, proliferation, survival, apoptosis, differentiation, cell migration. The ability of a single transcription factor to determine a cell fate critically depends on the relative abundance of AP-1 subunits, the composition of AP-1 dimers, the quality of stimulus, the cell type, the co-factor assembly.
AP-1 activity is regulated on multiple levels; transcriptional, translational and post-translational control mechanisms contribute to the balanced production of AP-1 proteins and their functions. Briefly, regulation occurs through:
In addition to its role in energy generation, the citric acid cycle is a source of carbon skeletons for amino acid metabolism and other biosynthetic processes. One such process included here is the interconversion of 2-hydroxyglutarate, probably derived from porphyrin and amino acid metabolism, and 2-oxoglutarate (alpha-ketoglutarate), a citric acid cycle intermediate.
R-HSA-5423646 Aflatoxin activation and detoxification Aflatoxins are among the principal mycotoxins produced as secondary metabolites by the molds Aspergillus flavus and Aspergillus parasiticus that contaminate economically important food and feed crops (Wild & Turner 2002). Aflatoxin B1 (AFB1) is the most potent naturally occurring carcinogen known and is also an immunosuppressant. It is a potent hepatocarcinogenic agent in many species, and has been implicated in the etiology of human hepatocellular carcinoma. Poultry, especially turkeys, are extremely sensitive to the toxic and carcinogenic action of AFB1 present in animal feed, resulting in multi-million dollar losses to the industry. Discerning the biochemical and molecular mechanisms of this extreme sensitivity of poultry to AFB1 will help with the development of new strategies to increase aflatoxin resistance (Rawal et al. 2010, Diaz & Murcia 2011).
AFB1 has one major genotoxic metabolic fate, conversion to AFXBO, and several others that are less mutagenic but that can still be quite toxic. AFB1 can be oxidised to the toxic AFB1 exo 8,9 epoxide (AFXBO) product by several cytochrome P450 enzymes, especially P450 3A4 in the liver. This 8,9 epoxide can react with the N7 atom of a guanyl base of DNA to produce adducts by intercalating between DNA base pairs. The exo epoxide is unstable in solution, however, and can react spontaneously to form a diol that is no longer reactive with DNA. The diol product in turn undergoes base-catalysed rearrangement to a dialdehyde that can react with protein lysine residues. AFB1 can also be metabolised to products (AFQ1, AFM1, AFM1E) which have far less genotoxic consequences than AFB1. The main route of detoxification of AFB1 is conjugation of its reactive 8,9-epoxide form with glutathione (GSH). This reaction is carried out by trimeric glutathione transferases (GSTs), providing a chemoprotective mechanism against toxicity. Glutathione conjugates are usually excreted as mercapturic acids in urine (Guengerich et al. 1998, Hamid et al. 2013). The main metabolic routes of aflatoxin in humans are described here.
R-HSA-9646399 Aggrephagy When the capacity of the proteosome to degrade misfolded proteins is limited, the alternate route to eliminate denatured proteins is via forming aggresomes - a process known as aggrephagy. Aggresome formation starts with ubiquitination of misfolded proteins following transport to the microtubule-organizing center (MTOC) with the help of dynein motor proteins. At the MTOC the cargo is encapsulated with intermediate filament proteins to result in the aggresome. Subsequently, this aggresome recruits chaperones that result in its autophagic elimination (Garcia Mata R et al. 2002).
R-HSA-351143 Agmatine biosynthesis Agmatine is an amine that is formed by decarboxylation of L-arginine by the enzyme arginine decarboxylase (ADC) and hydrolyzed by the enzyme agmatinase to putrescine. Agmatine binds to several target receptors in the brain and has been proposed as a novel neuromodulator (Reghunathan 2006). Agmatine has the potential to serve in the coordination of the early and repair phase pathways of arginine in inflammation (Satriano, 2003).
R-HSA-8964540 Alanine metabolism The interconversion of alanine and pyruvate, annotated here, is a key connection among the processes of protein turnover and energy metabolism in the human body (Felig 1975; Owen et al. 1979).
R-HSA-9730737 Alkylating DNA damage induced by chemotherapeutic drugs This pathway describes how chemotherapeutic drugs commonly used in cancer treatment produce alkylating DNA damage that is repaired through the base excision repair (BER) pathway. For review, please refer to Fu et al. 2012.
R-HSA-1462054 Alpha-defensins Humans have 7 alpha defensin genes plus 5 pseudogenes (see HGNC at http://www.genenames.org/genefamilies/DEFA). Alpha-defensins have six cysteines linked 1-6, 2-4, 3-5. The canonical sequence of alpha-defensins in humans is x1-2CXCRx2-3Cx3Ex3GxCx3Gx5CCx1-4, where x represents any amino acid residue.
Human alpha-defensins 1-4 are often called human neutrophil peptides (HNP1-4) as they were initially identified in neutrophil primary (azurophilic) granules. Alpha-defensins 5 and 6 (HD5, HD6) are products of Paneth cells. HNP-1 and -3 peptides are 30 residues long, differing only in the first amino acid. They are encoded by the genes DEFA1 and DEFA3 respectively. These exhibit copy number polymorphism, with some individuals having 4-14 copies per diploid genome, while 10-37% of individuals have no copies of DEFA3 (Aldred et al. 2005, Linzmier & Ganz 2005, Ballana et al. 2007). HNP-4, encoded by DEFA4, is 33 amino acids long of which 22 differ from the other HNPs (Wilde et al. 1989). It is a minor component of neutrophil granules compared to HNP1-3. In contrast to DEFA1 and DEFA3, the genes for HNP-4, HD-5 and HD-6 are only found as two copies per diploid genome (Linzmeier & Ganz 2005). HNP-2 is 29 amino acids in length and is the proteolytic product of cleavage of the N-terminal amino acid from either HNP-1 and/or HNP-3 (Selsted et al. 1985).
R-HSA-389599 Alpha-oxidation of phytanate Phytanic acid arises through ruminant metabolism of chlorophyll and enters the human diet as a constituent of dairy products (Baxter 1968). It can act as an agonist for PPAR and other nuclear hormone receptors, but its normal role in human physiology, if any, is unclear. It is catabolized via a five-step alpha-oxidation reaction sequence that yields pristanoyl-CoA, which is turn is a substrate for beta-oxidation. These reactions take place in the peroxisomal matrix and their failure is associated with Refsum disease (Wanders et al. 2003).
R-HSA-9645460 Alpha-protein kinase 1 signaling pathway Immune recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRR) often activates proinflammatory nuclear factor kappa B (NF-κB) signalling. Lipopolysaccharide (LPS) is a well-known PAMP produced by gram-negative bacteria. LPS is recognized by toll like receptor 4 (TLR4) and is a strong activator of NF-κB inflammatory responses (Akashi S et al. 2003). LPS is also recognized in the cytosol by mouse caspase-11 and related human caspase-4 and caspase-5, which stimulate pyroptosis, a proinflammatory form of cell death (Kayagaki N et al. 2011; Shi J et al. 2015). Key metabolic intermediates in LPS biosynthesis, d-glycero-β-d-manno-heptose 1,7-bisphosphate (HBP) and ADP L-glycero-β-d-manno-heptose (ADP-heptose) were reported to activate the NF-κB pathway and trigger the innate immune responses (Milivojevic M et al. 2017; Zimmermann S et al. 2017; Zhou P et al. 2018; García-Weber D; 2018). ADP-heptose but not HBP can enter host cells autonomously (Zhou P et al. 2018). During infection, ADP-heptose or HBP translocate into the host cytosol where their presence is sensed by alpha-protein kinase 1 (ALPK1) (Zimmermann S et al. 2017; Zhou P et al. 2018). ADP-heptose directly binds and activates ALPK1 (Garcia-Weber D et al. 2018; Zhou P et al. 2018); instead, HBP is converted by host-derived adenylyltransferases, such as nicotinamide nucleotide adenylyltransferases, to ADP-heptose 7-P, a substrate which can then activate ALPK1 (Zhou P et al. 2018). The ADP-heptose binding to ALPK1 is thought to trigger conformational changes and stimulate the kinase domain of ALPK1 (Zhou P et al. 2018). ALPK1 kinase activity in turn leads to the phosphorylation-dependent oligomerization of the tumor necrosis factor (TNF-α) receptor–associated factor (TRAF)–interacting protein with the forkhead-associated domain (TIFA) (Zimmermann S et al. 2017; Zhou P et al. 2018). This process activates TRAF6 oligomerization and ubiquitination, and the recruitment of transforming growth factor β-activated kinase 1 (TAK1)-binding protein 2 (TAB2), a component of the TAK1 (MAP3K7) complex (Ea CK et al. 2004; Gaudet RG et al. 2017). This TIFA oligomer signaling platform was given the term: TIFAsome. TIFAsome-activated TAK1 induces NF-κB nuclear translocation and proinflammatory gene expression. The ALPK1-TIFA signaling pathway has been identified in human embryonic kidney cells, intestinal epithelial cells, gastric cells and cervical cancer cells (Gaudet RG et al. 2015, 2017; Stein SC et al. 2017; Gall A et al. 2017; Zimmermann S et al. 2017; Milivojevic M et al. 2017; Zhou P et al. 2018). In vivo studies demonstrate that ADP-heptose and Burkholderia cenocepacia trigger massive inflammatory responses with increased production of several NF-κB-dependent cytokines and chemokines in wild type (WT), but not in Alpk1-/- mice (Zhou P et al. 2018).
This Reactome module describes ALPK1 as a cytosolic innate immune receptor for bacterial ADP-heptose. R-HSA-9006821 Alternative Lengthening of Telomeres (ALT) Alternative lengthening of telomeres (ALT) is a homologous recombination repair-directed telomere synthesis that takes place in 5-15% of tumors. ALT positive tumors often harbor loss-of-function mutations in ATRX (Alpha thalassemia mental retardation X-linked) or, more rarely, DAXX (Death domain-associated protein 6) chromatin remodeling factors, which may act to inhibit DNA recombination at telomere ends (reviewed by Gocha et al. 2013). The nuclear receptor complex NuRD-ZNF827 contributes to the recruitment of homologous recombination (HR) machinery to telomeres (Conomos et al. 2014). ALT is most prevalent in subsets of sarcomas, including osteosarcomas and some soft tissue sarcomas, brain cancers and neuroblastomas (Heaphy et al. 2011, Arora and Azzalin 2015). For review, please refer to Nabetani and Ishikawa 2011, Pickett and Reddel 2015, Verma and Greenberg 2016, Amorim et al. 2016, Sommer and Royle 2020, Zhang and Zou 2020. R-HSA-173736 Alternative complement activation The proteins participating in alternative pathway activation are C3 (and C3b), the factors B, D, and properdin. In the first place, alternative pathway activation is a positive feedback mechanism to increase C3b. When C3b binds covalently to sugars on a cell surface, it can become protected. Then Factor B binds to C3b. In the presence of Factor D, bound Factor B is cleaved to Ba and Bb. Bb contains the active site for a C3 convertase. Properdin then binds to C3bBb to stabilize the C3bBb convertase on cell surface leading to cleavage of C3. Finally, a C3bBb3b complex forms and this is a C5 convertase. R-HSA-140179 Amine Oxidase reactions Human amine oxidases (AO) catalyze the oxidative deamination of biogenic amines (neurotransmitters such as serotonin, noradrenaline, the hormone adrenaline and polyamines such as the spermines) and xenobiotic amines (exogenous dietary tyramine and phenylethylamine). The basic reaction is the oxidative cleavage of the alpha-H to form an imine product with the concomitant reduction of a FAD cofactor. The imine product then hydrolyses to an aldehyde and ammonia (or amine for secondary and tertiary amine substrates). Reduced FAD is reoxidized to form hydrogen peroxide to complete the catalytic cycle.
The reaction can be summarized as
RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2
The resultant hydrogen peroxide is the source of the most toxic free radical, the hydroxyl radical (.OH). This free radical is produced in the Fenton reaction with the use of ferrous (Fe2+) iron.
R-HSA-375280 Amine ligand-binding receptors The class A (rhodopsin-like) GPCRs that bind to classical biogenic amine ligands are annotated here. The amines involved (acetylcholine, adrenaline, noradrenaline, dopamine, serotonin and histamine) can all act as neurotransmitters in humans. The so-called 'trace amines', used when referring to p-tyramine, beta-phenylethylamine, tryptamine and octopamine, can also bind to recently-discovered GPCRs. R-HSA-156587 Amino Acid conjugation Xenobiotics that contain either a carboxylic group or an aromatic hydroxylamine group are possible substrates for amino acid conjugation. Xenobiotics with a carboxylic group conjugate with an amino group of amino acids such as glycine, taurine and glutamine. The hydroxylamine group conjugates with the carboxylic group of amino acids such as proline and serine. The amino acid is first activated by an aminoacyl-tRNA-synthetase which then reacts with the hydroxylamine group to form a reactive N-ester. N-esters can degrade to form electrophilic nitrenium (R-N+-R') and carbonium (R-C+H2) ions. The pyrolysis product of tryptophan, an N-hydroxy intermediate, can potentially form these reactive electrophilic ions. R-HSA-352230 Amino acid transport across the plasma membrane Amino acid transport across plasma membranes is critical to the uptake of these molecules from the gut, to their reabsortion in the kidney proximal tubulues, and to their distribution to cells in which they are required for the synthesis of proteins and of amino acid derived small molecules such as neurotransmitters. Physiological studies have defined 18 "systems" that mediate amino acid transport, each characterized by its amino acid substrates, as well as its pH sensitivity and its association (or not) with ion transport. More recently, molecular cloning studies have allowed the identification of the plasma membrane transport proteins that mediate these reactions. Amino acid uptake mediated by 17 of these transporters is annotated here (Broer 2008). R-HSA-9639288 Amino acids regulate mTORC1 The mTORC1 complex acts as an integrator that regulates translation, lipid synthesis, autophagy, and cell growth in response to multiple inputs, notably glucose, oxygen, amino acids, and growth factors such as insulin (reviewed in Sabatini 2017, Meng et al. 2018, Kim and Guan 2019).AMPs have also been referred to as cationic host defense peptides, anionic antimicrobial peptides/proteins, cationic amphipathic peptides, cationic AMPs, host defense peptides and alpha-helical antimicrobial peptides (Brown KL & Hancock RE 2006; Harris F et al. 2009; Groenink J et al. 1999; Bradshaw J 2003; Riedl S et al. 2011; Huang Y et al. 2010).
The Reactome module describes the interaction events of various types of human AMPs, such as cathelicidin, histatins and neutrophil serine proteases, with conserved patterns of microbial membranes at the host-pathogen interface. The module includes also proteolytic processing events for dermcidin (DCD) and cathelicidin (CAMP) that become functional upon cleavage. In addition, the module highlights an AMP-associated ability of the host to control metal quota at inflammation sites to influence host-pathogen interactions.
R-HSA-1169410 Antiviral mechanism by IFN-stimulated genes Interferons activate JAK–STAT signaling, which leads to the transcriptional induction of hundreds of IFN-stimulated genes (ISGs). The ISG-encoded proteins include direct effectors which inhibit viral infection through diverse mechanisms as well as factors that promote adaptive immune responses. The ISG proteins generated by IFN pathways plays key roles in the induction of innate and adaptive immune responses.
R-HSA-109581 Apoptosis Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of "cell-death", and the mechanisms of various apoptotic pathways are still being revealed today.
The two principal pathways of apoptosis are (1) the Bcl-2 inhibitable or intrinsic pathway induced by various forms of stress like intracellular damage, developmental cues, and external stimuli and (2) the caspase 8/10 dependent or extrinsic pathway initiated by the engagement of death receptors
The caspase 8/10 dependent or extrinsic pathway is a death receptor mediated mechanism that results in the activation of caspase-8 and caspase-10. Activation of death receptors like Fas/CD95, TNFR1, and the TRAIL receptor is promoted by the TNF family of ligands including FASL (APO1L OR CD95L), TNF, LT-alpha, LT-beta, CD40L, LIGHT, RANKL, BLYS/BAFF, and APO2L/TRAIL. These ligands are released in response to microbial infection, or as part of the cellular, humoral immunity responses during the formation of lymphoid organs, activation of dendritic cells, stimulation or survival of T, B, and natural killer (NK) cells, cytotoxic response to viral infection or oncogenic transformation.
The Bcl-2 inhibitable or intrinsic pathway of apoptosis is a stress-inducible process, and acts through the activation of caspase-9 via Apaf-1 and cytochrome c. The rupture of the mitochondrial membrane, a rapid process involving some of the Bcl-2 family proteins, releases these molecules into the cytoplasm. Examples of cellular processes that may induce the intrinsic pathway in response to various damage signals include: auto reactivity in lymphocytes, cytokine deprivation, calcium flux or cellular damage by cytotoxic drugs like taxol, deprivation of nutrients like glucose and growth factors like EGF, anoikis, transactivation of target genes by tumor suppressors including p53.
In many non-immune cells, death signals initiated by the extrinsic pathway are amplified by connections to the intrinsic pathway. The connecting link appears to be the truncated BID (tBID) protein a proteolytic cleavage product mediated by caspase-8 or other enzymes.
R-HSA-140342 Apoptosis induced DNA fragmentation DNA fragmentation in response to apoptotic signals is achieved, in part, through the activity of apoptotic nucleases, termed DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) (reviewed in Widlak and Garrard, 2005). In non-apoptotic cells, DFF is a nuclear heterodimer consisting of a 45 kD chaperone and inhibitor subunit (DFF45)/inhibitor of CAD (ICAD-L)] and a 40 kD nuclease subunit (DFF40/CAD)( Liu et al. 1997, 1998; Enari et al. 1998). During apoptosis, activated caspase-3 or -7 cleave DFF45/ICAD releasing active DFF40/CAD nuclease. The activity of DFF is tightly controlled at multiple stages. During translation, DFF45/ICAD, Hsp70, and Hsp40 proteins play a role in insuring the appropriate folding of DFF40 during translation(Sakahira and Nagata, 2002). The nuclease activity of DFF40 is enhanced by the chromosomal proteins histone H1, Topoisomerase II and HMGB1/2(Widlak et al., 2000). In addition, the inhibitors (DFF45/35; ICAD-S/L) are produced in stoichiometric excess (Widlak et al., 2003).
R-HSA-351906 Apoptotic cleavage of cell adhesion proteins Apoptotic cells show dramatic rearrangements of tight junctions, adherens junctions, and desmosomes (Abreu et al., 2000). Desmosome-specific members of the cadherin superfamily of cell adhesion molecules including desmoglein-3, plakophilin-1 and desmoplakin are cleaved by caspases after onset of apoptosis (Weiske et al., 2001). Cleavage results in the disruption of the desmosome structure and thus contributes to cell rounding and disintegration of the intermediate filament system (Weiske et al., 2001).
R-HSA-111465 Apoptotic cleavage of cellular proteins Apoptotic cell death is achieved by the caspase-mediated cleavage of various vital proteins. Among caspase targets are proteins such as E-cadherin, Beta-catenin, alpha fodrin, GAS2, FADK, alpha adducin, HIP-55, and desmoglein involved in cell adhesion and maintenance of the cytoskeletal architecture. Cleavage of proteins such as APC and CIAP1 can further stimulate apoptosis by produce proapoptotic proteins (reviewed in Fischer et al., 2003. See also Wee et al., 2006 and the CASVM Caspase Substrates Database: http://www.casbase.org/casvm/squery/index.html ).
R-HSA-75153 Apoptotic execution phase In the execution phase of apoptosis, effector caspases cleave vital cellular proteins leading to the morphological changes that characterize apoptosis. These changes include destruction of the nucleus and other organelles, DNA fragmentation, chromatin condensation, cell shrinkage and cell detachment and membrane blebbing (reviewed in Fischer et al., 2003).
R-HSA-111471 Apoptotic factor-mediated response In response to apoptotic signals, mitochondrial proteins are released into the cytosol and activate both caspase-dependent and -independent cell death pathways. Cytochrome c induces apoptosome formation, AIF and endonuclease G function in caspase independent apoptotic nuclear DNA damage. Smac/DIABLO and HtrA2/OMI promote both caspase activation and caspase-independent cytotoxicity (Saelens et al., 2004).
R-HSA-445717 Aquaporin-mediated transport Aquaporins (AQP's) are six-pass transmembrane proteins that form channels in membranes. Each monomer contains a central channel formed in part by two asparagine-proline-alanine motifs (NPA boxes) that confer selectivity for water and/or solutes. The monomers assemble into tetramers. During passive transport by Aquaporins most aquaporins (i.e. AQP0/MIP, AQP1, AQP2, AQP3, AQP4, AQP5, AQP7, AQP8, AQP9, AQP10) transport water into and out of cells according to the osmotic gradient across the membrane. Four aquaporins (the aquaglyceroporins AQP3, AQP7, AQP9, AQP10) conduct glycerol, three aquaporins (AQP7, AQP9, AQP10) conduct urea, and one aquaporin (AQP6) conducts anions, especially nitrate. AQP8 also conducts ammonia in addition to water.
AQP11 and AQP12, classified as group III aquaporins, were identified as a result of the genome sequencing project and are characterized by having variations in the first NPA box when compared to more traditional aquaporins. Additionally, a conserved cysteine residue is present about 9 amino acids downstream from the second NPA box and this cysteine is considered indicative of group III aquaporins. Purified AQP11 incorporated into liposomes showed water transport. Knockout mice lacking AQP11 had fatal cyst formation in the proximal tubule of the kidney. Exogenously expressed AQP12 showed intracellular localization. AQP12 is expressed exclusively in pancreatic acinar cells.
Aquaporins are important in fluid and solute transport in various tissues. During Transport of glycerol from adipocytes to the liver by Aquaporins, glycerol generated by triglyceride hydrolysis is exported from adipocytes by AQP7 and is imported into liver cells via AQP9. AQP1 plays a role in forming cerebrospinal fluid and AQP1, AQP4, and AQP9 appear to be important in maintaining fluid balance in the brain. AQP0, AQP1, AQP3, AQP4, AQP8, AQP9, and AQP11 play roles in the physiology of the hepatobiliary tract.
In the kidney, water and solutes are passed out of the bloodstream and into the proximal tubule via the slit-like structure formed by nephrin in the glomerulus. Water is reabsorbed from the filtrate during its transit through the proximal tubule, the descending loop of Henle, the distal convoluted tubule, and the collecting duct. Aquaporin-1 (AQP1) in the proximal tubule and the descending thin limb of Henle is responsible for about 90% of reabsorption (as estimated from mouse knockouts of AQP1). AQP1 is located on both the apical and basolateral surface of epithelial cells and thus transports water through the epithelium and back into the bloodstream. In the collecting duct epithelial cells have AQP2 on their apical surfaces and AQP3 and AQP4 on their basolateral surfaces to transport water across the epithelium. Vasopressin regulates renal water homeostasis via Aquaporins by regulating the permeability of the epithelium through activation of a signaling cascade leading to the phosphorylation of AQP2 and its translocation from intracellular vesicles to the apical membrane of collecting duct cells.
Here, three views of aquaporin-mediated transport have been annotated: a generic view of transport mediated by the various families of aquaporins independent of tissue type (Passive transport by Aquaporins), a view of the role of specific aquaporins in maintenance of renal water balance (Vasopressin regulates renal water homeostasis via Aquaporins), and a view of the role of specific aquaporins in glycerol transport from adipocytes to the liver (Transport of glycerol from adipocytes to the liver by Aquaporins).
R-HSA-2142753 Arachidonate metabolism Eicosanoids, oxygenated, 20-carbon fatty acids, are autocrine and paracrine signaling molecules that modulate physiological processes including pain, fever, inflammation, blood clot formation, smooth muscle contraction and relaxation, and the release of gastric acid. Eicosanoids are synthesized in humans primarily from arachidonate (all-cis 5,8,11,14-eicosatetraenoate) that is released from membrane phospholipids. Once released, arachidonate is acted on by prostaglandin G/H synthases (PTGS, also known as cyclooxygenases (COX)) to form prostaglandins and thromboxanes, by arachidonate lipoxygenases (ALOX) to form leukotrienes, epoxygenases (cytochrome P450s and epoxide hydrolase) to form epoxides such as 15-eicosatetraenoic acids, and omega-hydrolases (cytochrome P450s) to form hydroxyeicosatetraenoates (Buczynski et al. 2009, Vance & Vance 2008).
Levels of free arachidonate in the cell are normally very low so the rate of synthesis of eicosanoids is determined primarily by the activity of phospholipase A2, which mediates phospholipid cleavage to generate free arachidonate. The enzymes involved in arachidonate metabolism are typically constitutively expressed so the subset of these enzymes expressed by a cell determines the range of eicosanoids it can synthesize.
Eicosanoids are unstable, undergoing conversion to inactive forms with half-times under physiological conditions of seconds or minutes. Many of these reactions appear to be spontaneous.
R-HSA-426048 Arachidonate production from DAG Diacylglycerol (DAG) is an important source of arachidonic acid, a signalling molecule and the precursor of the prostaglandins. In human platelet almost all the DAG produced from phosphatidylinositol degradation contains arachidonate (Takamura et al. 1987). DAG is hydrolysed by DAG lipase to 2-arachidonylglycerol (2-AG) which is further hydrolysed by monoacylglycerol lipase. 2-AG is an agonist of cannabinoid receptor 1.
R-HSA-211957 Aromatic amines can be N-hydroxylated or N-dealkylated by CYP1A2 CYP1A2 oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. It is most active in catalyzing N-hydroxylation or N-dealkylation reactions.
R-HSA-8937144 Aryl hydrocarbon receptor signalling The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that belongs to the basic helix-loop-helix/PER-ARNT-SIM family of DNA binding proteins and controls the expression of a diverse set of genes. Two major types of environmental compounds can activate AHR signaling: halogenated aromatic hydrocarbons such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and polycyclic aromatic hydrocarbons (PAH) such as benzo(a)pyrene. Unliganded AHR forms a complex in the cytosol with two copies of 90kD heat shock protein (HSP90AB1), one X-associated protein (AIP), and one p23 molecular chaperone protein (PTGES3). After ligand binding and activation, the AHR complex translocates to the nucleus, disassociates from the chaperone subunits, dimerises with the aryl hydrocarbon receptor nuclear translocator (ARNT) and transactivates target genes via binding to xenobiotic response elements (XREs) in their promoter regions. AHR targets genes of Phase I and Phase II metabolism, such as cytochrome P450 1A1 (CYP1A1), cytochorme P450 1B1 (CYP1B1), NAD(P)H:quinone oxidoreductase I (NQO1) and aldehyde dehydrogenase 3 (ALHD3A1). This is thought to be an organism's response to foreign chemical exposure and normally, foreign chemicals are made less reactive by the induction and therefore increased activity of these enzymes (Beischlag et al. 2008).
AHR itself is regulated by the aryl hydrocarbon receptor repressor (AHRR, aka BHLHE77, KIAA1234), an evolutionarily conserved bHLH-PAS protein that inhibits both xenobiotic-induced and constitutively active AHR transcriptional activity in many species. AHRR resides predominantly in the nuclear compartment where it competes with AHR for binding to ARNT. As a result, there is competition between AHR:ARNT and AHRR:ARNT complexes for binding to XREs in target genes and AHRR can repress the transcription activity of AHR (Hahn et al. 2009, Haarmann-Stemmann & Abel 2006).
R-HSA-446203 Asparagine N-linked glycosylation N-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley et al. 2009). An early study in 1999 revealed that about 50% of the proteins in the Swiss-Prot database at the time were N-glycosylated (Apweiler et al. 1999). It is now established that the majority of the proteins in the secretory pathway require glycosylation in order to achieve proper folding.
The addition of an N-glycan to a protein can have several roles (Shental-Bechor & Levy 2009). First, glycans enhance the solubility and stability of the proteins in the ER, the golgi and on the outside of the cell membrane, where the composition of the medium is strongly hydrophilic and where proteins, that are mostly hydrophobic, have difficulty folding properly. Second, N-glycans are used as signal molecules during the folding and transport process of the protein: they have the role of labels to determine when a protein must interact with a chaperon, be transported to the golgi, or targeted for degradation in case of major folding defects. Third, and most importantly, N-glycans on completely folded proteins are involved in a wide range of processes: they help determine the specificity of membrane receptors in innate immunity or in cell-to-cell interactions, they can change the properties of hormones and secreted proteins, or of the proteins in the vesicular system inside the cell.
All N-linked glycans are derived from a common 14-sugar oligosaccharide synthesized in the ER, which is attached co-translationally to a protein while this is being translated inside the reticulum. The process of the synthesis of this glycan, known as Synthesis of the N-glycan precursor or LLO, constitutes one of the most conserved pathways in eukaryotes, and has been also observed in some eubacteria. The attachment usually happens on an asparagine residue within the consensus sequence asparagine-X-threonine by an complex called oligosaccharyl transferase (OST).
After being attached to an unfolded protein, the glycan is used as a label molecule in the folding process (also known as Calnexin/Calreticulin cycle) (Lederkremer 2009). The majority of the glycoproteins in the ER require at least one glycosylated residue in order to achieve proper folding, even if it has been shown that a smaller portion of the proteins in the ER can be folded without this modification.
Once the glycoprotein has achieved proper folding, it is transported via the cis-Golgi through all the Golgi compartments, where the glycan is further modified according to the properties of the glycoprotein. This process involves relatively few enzymes but due to its combinatorial nature, can lead to several millions of different possible modifications. The exact topography of this network of reactions has not been established yet, representing one of the major challenges after the sequencing of the human genome (Hossler et al. 2006).
Since N-glycosylation is involved in an great number of different processes, from cell-cell interaction to folding control, mutations in one of the genes involved in glycan assembly and/or modification can lead to severe development problems (often affecting the central nervous system). All the diseases in genes involved in glycosylation are collectively known as Congenital Disorders of Glycosylation (CDG) (Sparks et al. 2003), and classified as CDG type I for the genes in the LLO synthesis pathway, and CDG type II for the others.
R-HSA-8963693 Aspartate and asparagine metabolism These reactions mediate the synthesis of aspartate and asparagine from glutamate, TCA cycle intermediates, and ammonia and and allow the utilization of carbon atoms from these amino acids for glucose synthesis under fasting conditions (Felig 1975; Owen et al. 1979).
R-HSA-9749641 Aspirin ADME In water aspirin (acetylsalicylic acid, ASA) dissolves, dissociating into the acetylsalicylate ion (ASA-). ASA- is an anti-clotting agent and nonsteroidal anti-inflammatory drug (NSAID); the therapeutic effects are mediated through its interaction with PTGS enzymes. On a molar basis ASA- (a) is more potent as an analgesic/anti-inflammatory agent, (b) has greater gastric ulcerogenic activity, and (c) is much more effective as an inhibitor of prostaglandin biosynthesis and platelet aggregation than salicylate (ST) (Flower 1974; Mills et al, 1974; Rainsford 1975; Rainsford 1977).
Acetylsalicylic acid is only slightly soluble in conditions being found in the stomach mucosa, mostly because of unavailability of sufficient amount of solvent. The absorption, as well as the absorbing area, increases in the small intestine. Further increased absorption is achieved by dissolving tablets before ingestion or usage of ASA salts (Dressman et al, 2012). Practically 100% of therapeutic aspirin doses are taken up, mostly by intestinal mucosal cells (Artursson & Karlsson, 1991; Yee 1997).
Only a few percent of ASA- remain unchanged, the rest is hydrolyzed to salicylate (ST). The major route of ST catabolism is conjugation with glycine to form salicyluric acid. This accounts for 20–65% of the products. Conjugation to glucuronides (ester and ether) removes up to 42% of ST. Finally, a minor part also gets hydroxylated by cytochromes (Hutt et al, 1986).
R-HSA-175474 Assembly Of The HIV Virion Virion assembly packages all the components required for infectivity. These steps include two copies of the positive sense genomic viral RNA, cellular tRNALys, the viral envelope (Env) protein, the Gag polyprotein, and the three viral enzymes: protease (PR), reverse transcriptase (RT), and integrase (IN). The viral enzymes are packaged as domains within the Gag-Pro-Pol polyprotein.
R-HSA-9609736 Assembly and cell surface presentation of NMDA receptors N-methyl-D-aspartate receptors (NMDARs) are tetramers that consist of two GluN1 (GRIN1) subunits and two subunits that belong to either the GluN2 (GRIN2) subfamily (GluN2A, GluN2B, GluN2C and GluN2D) or the GluN3 (GRIN3) subfamily (GluN3A and GluN3B). The GluN2/GluN3 subunits in the NMDA tetramer can either be identical, constituting an NMDA di-heteromer (di-heterotetramer), which consists of two subunit types, GluN1 and one of GluN2s/GluN3s, or they can be two different GluN2/GluN3 proteins, constituting an NMDA tri-heteromer (tri-heterotetramer), which consists of three subunit types, GluN1 and two of GluN2s/GluN3s (Monyer et al. 1992, Wafford et al. 1993, Sheng et al. 1994, Dunah et al. 1998, Perez-Otano et al. 2001, Chatterton et al. 2002, Matsuda et al. 2002, Yamakura et al. 2005, Nilsson et al. 2007, Hansen et al. 2014, Kaiser et al. 2018, Bhattacharya et al. 2018, Bhattacharya and Traynelis 2018).
NMDA tetramers assemble in the endoplasmic reticulum and traffic to the plasma membrane as part of transport vesicles (McIlhinney et al. 1998, Perez-Otano et al. 2001). NMDA receptor subunits undergo N-glycosylation, which impacts their trafficking from the endoplasmic reticulum to the plasma membrane. Trafficking efficiency may vary among different subunits of NMDARs (Lichnereva et al. 2015). Mechanistic details, such as glycosyl transferases involved and the type of sugar side chains added, are not known.
As there are eight splicing isoforms of GluN1, four different GluN2 and two different GluN3 proteins, many different combinations of NMDAR subunits are possible, but only a handful of distinct NMDAR receptors have been experimentally confirmed and functionally studied. The composition of NMDARs affects trafficking, spatial (including synaptic) localization, ligand preference, channel conductivity and downstream signal transmission. Prevalent NMDARs differ at different stages of neuronal development, in different regions of the central nervous system, and at different levels of neuronal activity. For review, please refer to Lau and Zukin 2007, Traynelis et al. 2010, Paoletti et al. 2013, Pérez-Otaño et al. 2016, Iacobucci and Popescu 2017.
R-HSA-9820962 Assembly and release of respiratory syncytial virus (RSV) virions A mature virion of the respiratory syncytial virus (RSV) consists of the ribonucleoprotein complex (RNP) surrounded by the protein matrix and a lipid bilayer envelope. The RNP is composed of the genomic negative sense single-stranded (-ssRNA) that is tightly associated with the N protein (nucleoprotein) and the RNA-dependent RNA polymerase complex (RdRP). The RdRP consists of the L protein subunit (large polymerase subunit), the P protein subunit (phosphoprotein polymerase cofactor), and the M2-1 protein, which acts as a transcription processivity factor. The matrix consists of the M (matrix) protein. The M2-1 protein serves as the bridge between the RNP and the M protein. The matrix supports the viral envelope. The viral envelope contains three embedded viral proteins: fusion protein (F), attachment protein (G), and a small hydrophobic protein (SH). The M protein associates with the cytoplasmic domain of the F protein. The SH protein forms a pentameric ion channel in the viral envelope and is thought to delay apoptosis of infected cells. The assembly and budding of RSV virions primarily occurs at the apical surface of ciliated airway epithelial cells where viral filaments containing RNPs form. The budding of RSV virions requires interactions between viral proteins, host cytoskeletal proteins, and membrane. For review, please refer to Shaikh and Crowe 2013, and Battles and McLellan 2019.
Based on the findings that P, M, and F proteins are sufficient for formation of viral‑like particles (VLPs), P protein, particularly its highly phosphorylated serine/threonine‑rich region between amino acids 39 and 57 that likely interacts with M and/or F proteins, may play an important role in the assembly (Meshram and Oomens 2019).
R-HSA-168316 Assembly of Viral Components at the Budding Site Following synthesis on membrane-bound ribosomes, the three viral integral membrane proteins, HA (hemagglutinin), NA (neuraminidase) and M2 (ion channel) enter the host endoplasmic reticulum (ER) where all three are folded and HA and NA are glycosylated. Subsequently HA is assembled into a trimer. HA, NA and M2 are transported to the Golgi apparatus where cysteine residues on HA and M2 are palmitoylated. Furin cleaves HA into HA1 and HA2 subunits and all three proteins are directed to the virus assembly site on the apical plasma membrane via apical sorting signals. The signals for HA and NA reside on the transmembrane domains (TMD) while the sorting signal for M2 is not yet characterized. The TMDs of HA and NA also contain the signals for lipid raft association. Lipid rafts are non-ionic detergent-resistant lipid microdomains within the plasma membrane that are rich in sphingolipids and cholesterol. Examination of purified virus particles indicates that influenza virus buds preferentially from these microdomains.
R-HSA-8963889 Assembly of active LPL and LIPC lipase complexes Lipoprotein lipase (LPL) and hepatic triacylglycerol lipase (LIPC) enzymes on the lumenal surfaces of capillary endothelia mediate the hydrolysis of triglyceride molecules in circulating lipoprotein particles.
LPL is widely expressed in the body and is especially abundant in adipocytes and skeletal and cardiac myocytes. Activation of the protein requires glycosylation, dimerization, and glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1 (GPIHBP1), which delivers it to heparan sulfate proteoglycan (HSPG) associated with the plasma membrane. It is inactivated by proteolytic cleavage (Berryman & Bensadoun 1995; Sukonina et al. 2006; Young et al. 2011).
Expression of the LPL gene is transcriptionally regulated by Cyclic AMP-responsive element-binding protein 3-like protein 3 (CREB3L3), which also regulates the expression of APOA4, APOA5, APOC2, CIDEC and FGF21 (Lee et al. 2011).
Maturation of LIPC enzyme requires association with LMF1 protein (or possibly, inferred from sequence similarity, LMF2). Heparin binding stabilizes LIPC in its active dimeric form (Babilonia-Rosa & Neher 2014).
R-HSA-2022090 Assembly of collagen fibrils and other multimeric structures Collagen trimers in triple-helical form, referred to as procollagen or collagen molecules, are exported from the ER and trafficked through the Golgi network before secretion into the extracellular space. For fibrillar collagens namely types I, II, III, V, XI, XXIV and XXVII (Gordon & Hahn 2010, Ricard-Blum 2011) secretion is concomitant with processing of the N and C terminal collagen propeptides. These processed molecules are known as tropocollagens, considered to be the units of higher order collagen structures. They form within the extracellular space via a process that can proceed spontaneously, but in the cellular environment is regulated by many collagen binding proteins such as the FACIT (Fibril Associated Collagens with Interrupted Triple helices) family collagens and Small Leucine-Rich Proteoglycans (SLRPs). The architecture formed ultimately depends on the collagen subtype and the cellular conditions. Structures include the well-known fibrils and fibres formed by the major structural collagens type I and II plus several different types of supramolecular assembly (Bruckner 2010). The mechanical and physical properties of tissues depend on the spatial arrangement and composition of these collagen-containing structures (Kadler et al. 1996, Shoulders & Raines 2009, Birk & Bruckner 2011).
Fibrillar collagen structures are frequently heterotypic, composed of a major collagen type in association with smaller amounts of other types, e.g. type I collagen fibrils are associated with types III and V, while type II fibrils frequently contain types IX and XI (Wess 2005). Fibres composed exclusively of a single collagen type probably do not exist, as type I and II fibrils require collagens V and XI respectively as nucleators (Kadler et al. 2008, Wenstrup et al. 2011). Much of the structural understanding of collagen fibrils has been obtained with fibril-forming collagens, particularly type I, but some central features are believed to apply to at least the other fibrillar collagen subtypes (Wess 2005). Fibril diameter and length varies considerably, depending on the tissue and collagen types (Fang et al. 2012). The reasons for this are poorly understood (Wess 2005).
Some tissues such as skin have fibres that are approximately the same diameter while others such as tendon or cartilage have a bimodal distribution of thick and thin fibrils. Mature type I collagen fibrils in tendon are up to 1 cm in length, with a diameter of approx. 500 nm. An individual fibrillar collagen triple helix is less than 1.5 nm in diameter and around 300 nm long; collagen molecules must assemble to give rise to the higher-order fibril structure, a process known as fibrillogenesis, prevented by the presence of C-terminal propeptides (Kadler et al. 1987). In electron micrographs, fibrils have a banded appearance, due to regular gaps where fewer collagen molecules overlap, which occur because the fibrils are aligned in a quarter-stagger arrangement (Hodge & Petruska 1963). Collagen microfibrils are believed to have a quasi-hexagonal unit cell, with tropocollagen arranged to form supertwisted, right-handed microfibrils that interdigitate with neighbouring microfibrils, leading to a spiral-like structure for the mature collagen fibril (Orgel et al. 2006, Holmes & Kadler 2006).
Neighbouring tropocollagen monomers interact with each other and are cross-linked covalently by lysyl oxidase (Orgel et al. 2000, Maki 2006). Mature collagen fibrils are stabilized by lysyl oxidase-mediated cross-links. Hydroxylysyl pyridinoline and lysyl pyridinoline cross-links form between (hydroxy) lysine and hydroxylysine residues in bone and cartilage (Eyre et al. 1984). Arginoline cross-links can form in cartilage (Eyre et al. 2010); mature bovine articular cartilage contains roughly equimolar amounts of arginoline and hydroxylysyl pyridinoline based on peptide yields. Mature collagen fibrils in skin are stabilized by the lysyl oxidase-mediated cross-link histidinohydroxylysinonorleucine (Yamauch et al. 1987). Due to the quarter-staggered arrangement of collagen molecules in a fibril, telopeptides most often interact with the triple helix of a neighbouring collagen molecule in the fibril, except for collagen molecules in register staggered by 4D from another collagen molecule. Fibril aggregation in vitro can be unipolar or bipolar, influenced by temperature and levels of C-proteinase, suggesting a role for the N- and C- propeptides in regulation of the aggregation process (Kadler et al. 1996). In vivo, collagen molecules at the fibril surface may retain their N-propeptides, suggesting that this may limit further accretion, or alternatively represents a transient stage in a model whereby fibrils grow in diameter through a cycle of deposition, cleavage and further deposition (Chapman 1989).
In vivo, fibrils are often composed from more than one type of collagen. Type III collagen is found associated with type I collagen in dermal fibrils, with the collagen III on the periphery, suggesting a regulatory role (Fleischmajer et al. 1990). Type V collagen associates with type I collagen fibrils, where it may limit fibril diameter (Birk et al. 1990, White et al. 1997). Type IX associates with the surface of narrow diameter collagen II fibrils in cartilage and the cornea (Wu et al. 1992, Eyre et al. 2004). Highly specific patterns of crosslinking sites suggest that collagen IX functions in interfibrillar networking (Wess 2005). Type XII and XIV collagens are localized near the surface of banded collagen I fibrils (Nishiyama et al. 1994). Certain fibril-associated collagens with interrupted triple helices (FACITs) associate with the surface of collagen fibrils, where they may serve to limit fibril fusion and thereby regulate fibril diameter (Gordon & Hahn 2010). Collagen XV, a member of the multiplexin family, is almost exclusively associated with the fibrillar collagen network, in very close proximity to the basement membrane. In human tissues collagen XV is seen linking banded collagen fibers subjacent to the basement membrane (Amenta et al. 2005). Type XIV collagen, SLRPs and discoidin domain receptors also regulate fibrillogenesis (Ansorge et al. 2009, Kalamajski et al. 2010, Flynn et al. 2010).
Collagen IX is cross-linked to the surface of collagen type II fibrils (Eyre et al. 1987). Type XII and XIV collagens are found in association with type I (Walchli et al. 1994) and type II (Watt et al. 1992, Eyre 2002) fibrils in cartilage. They are thought to associate non-covalently via their COL1/NC1 domains (Watt et al. 1992, Eyre 2002).
Some non-fibrillar collagens form supramolecular assemblies that are distinct from typical fibrils. Collagen VII forms anchoring fibrils, composed of antiparallel dimers that connect the dermis to the epidermis (Bruckner-Tuderman 2009). During fibrillogenesis, the nascent type VII procollagen molecules dimerize in an antiparallel manner. The C-propeptides are then removed by Bone morphogenetic protein 1 (Rattenholl et al. 2002) and the processed antiparallel dimers aggregate laterally. Collagens VIII and X form hexagonal networks and collagen VI forms beaded filament (Gordon & Hahn 2010, Ricard-Blum et al. 2011).
R-HSA-68616 Assembly of the ORC complex at the origin of replication Human ORC1 can associate with DNA origin of replication sites independently of other origin of replication complex (ORC) subunits (Hoshina et al. 2013; Eladl et al. 2021). ORC1 localizes to condensed chromosomes during early mitosis (M phase) and serves as a nucleating center for the assembly of the ORC and, subsequently, the pre-replication complex. ORC1 remains associated with late replication origins throughout late G1. Upon S phase entry, ORC1 undergoes ubiquitin-mediated degradation, leading to dissociation of the ORC from chromatin (Kara et al. 2015).
Most human replication origins contain guanine (G)-rich sequences which may form G-quadruplex (G4) structures (Besnard et al. 2012) and these G4 structures may mediate the recognition of replication origins by ORC1 (Hoshina et al. 2013; Eladl et al. 2021). Besides binding to nucleosome-free replication origin DNA, ORC1 interacts with neighboring nucleosomes (Hizume et al. 2013), in particular with nucleosomes containing histone H4 dimethylated at lysine 21 (H4K20me2 mark), which is enriched at replication origins. Binding of ORC1 to H4K20me2 facilitates ORC1 binding to replication origins and ORC chromatin loading (Kuo et al. 2012, Zhang et al. 2015).
ORC1 binding sites are universally associated with transcription start sites (TSSs) of coding and non-coding RNAs. Replication origins associated with moderate to high transcription level TSSs (belonging to coding RNAs) fire in early S phase, while those associated with low transcription level TSSs (belonging to non-coding RNAs) fire throughout the S phase (Dellino et al. 2013).
ORC2 forms a heterodimer with ORC3, which is a prerequisite for the association of ORC5 and, subsequently, ORC4 (Ranjan and Gossen 2006; Siddiqui and Stillman 2007). ORC1 binds to the ORC(2-5) complex in the nucleus to form a stable ORC(1-5) complex (Radichev et al. 2006; Ghosh et al. 2011). ORC1 is necessary for the association of the ORC(2-5) complex to chromatin (Radichev et al. 2006). The ORC(2-5) complex exhibits a tightly autoinhibited conformation, with the winged-helix domain (WHD) of ORC2 completely blocking the central DNA-binding channel. Binding of ORC1 remodels the WHD of ORC2, moving it away from the central channel and partially relieving the autoinhibition (Cheng et al. 2020, Jaremko et al. 2020). ORC6 associates with the ORC(1-5) complex to form the ORC(1-6) complex (Ghosh et al. 2011). The association of ORC6 with the ORC(1-5) complex is weak and it frequently does not co-immunoprecipitate with the other ORC(1-5) subunits. ORC4 is the only ORC(1-5) subunit that was shown to directly bind to ORC6 (Radichev et al. 2006). Some ORC6 mutations reported in Meier-Gorlin syndrome were shown to interfere with ORC6 incorporation into the ORC (Balasov et al. 2015).
R-HSA-9683439 Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) In a sequence of ten reactions, mature non-structural proteins (nsp) generated by cleavage of the SARS-CoV-1 pp1a / pp1ab polyproteins are assembled to form a replication – transcription complex (Fung & Liu 2019; Kirchdoerfer & Ward 2019).
R-HSA-9694271 Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) This COVID-19 pathway has been created by a combination of computational inference from SARS-CoV-1 data (https://reactome.org/documentation/inferred-events) and manual curation, as described in the summation for the overall SARS-CoV-2 infection pathway.
In a sequence of ten reactions, mature non-structural proteins (nsp) generated by cleavage of the SARS-CoV-1 pp1a / pp1ab polyproteins are assembled to form the RTC (Fung & Liu 2019; Kirchdoerfer & Ward 2019). Six of these ten steps have been directly studied in SARS-CoV-2: binding of nsp7 to nsp8 (Gao et al. 2020, Li et al. 2020, Konkolova et al. 2020), recruitment of nsp12 (Gao et al. 2020, Hillen et al. 2020, Li et al. 2020, Yin et al. 2020), binding of nsp14 and nsp10 (Li et al. 2020), binding of nsp13 to nsp12 (Chen et al. 2020) formation of the nsp15 hexamer (Kim et al. 2020), and binding of nsp16 to nsp12 (Li et al. 2020, Rosas-Lemus et al. 2020, Viswanathan et al. 2020).
R-HSA-68867 Assembly of the pre-replicative complex DNA replication pre-initiation in eukaryotic cells begins with the formation of the pre-replicative complex (pre-RC) during the late M phase and continues in the G1 phase of the mitotic cell cycle, a process also called DNA replication origin licensing. The association of initiation proteins (ORC, Cdc6, Cdt1, Mcm2-7) with the origin of replication in both S. cerevisiae and humans has been demonstrated by chromatin immunoprecipitation experiments. In S. cerevisiae, pre-replicative complexes are assembled from late M to G1. In mammalian cells as well, pre-replicative complexes are assembled from late M to G1, as shown by biochemical fractionation and immunostaining. There are significant sequence similarities among some of the proteins in the pre-replicative complex. The ORC subunits Orc1, Orc4 and Orc5 are homologous to one another and to Cdc6. The six subunits of the Mcm2-7 complex are homologous to one another. In addition, Orc1, Orc4, Orc5, Cdc6, and the Mcm2-7 subunits, are members of the AAA+ superfamily of ATPases. Since the initial identification of these pre-RC components other factors that participate in this complex have been found, including Cdt1 in human, Xenopus, S. pombe, and S. cerevisiae cells.
R-HSA-390471 Association of TriC/CCT with target proteins during biosynthesis TRiC has broad recognition specificities, but in the cell it interacts with only a defined set of substrates (Yam et al. 2008). Many of its substrates that are targeted during biosynthesis are conserved between mammals and yeast (Yam et al. 2008).
R-HSA-210455 Astrocytic Glutamate-Glutamine Uptake And Metabolism In astrocytic glutamate-glutamine cycle, the excess glutamate released by the pre-synaptic neuron in the synaptic cleft is transported into the astrocyte by a family glutamate transporters called the excitatory amino acid transporters 1 and 2, EAAT1 and EAAT2. Astrocytes carrying these transporters exist in close apposition to the synapse to clear excess glutamate to prevent excessive activation of neurons and hence neuronal death. Glutamate in astrocytes is converted to glutamine by glutamine synthetase. Glutamine is then transported into the extracellular space by system N transporters. The glutamate in the extracellular space is available for neuronal uptake.
R-HSA-4608870 Asymmetric localization of PCP proteins One of the hallmarks of the Planar Cell Polarity pathway is the asymmetric distribution of proteins on opposite membranes of a single cell. In Drosophila, Stbm and Pk (homologues to the human VANGL1/2 and PRICKLE1/2/3) colocalize opposite Fz, Dsh and Dgo (FZD, DVL, and ANKRD6, respectively). The two complexes antagonize each other, with Fz:Dsh:Dgo acting to promote signaling downstream of Dsh, while the Stbm:Pk complex restricts this signaling (reviewed in Seifert and Mlodzik, 2007). Asymmetric localization of some PCP proteins is also seen in vertebrates (Montcouquiol et al, 2003, 2006; Wang et al, 2006, Narimatsu et al, 2009) although the patterns of localization differ from that of flies. The details of how localization is established and how the asymmetrical distribution of proteins is translated into gross morphological processes remain to be fully elucidated.
R-HSA-9754706 Atorvastatin ADME Atorvastatin (ATV, brand name Lipitor), is a lipid-lowering drug of the statin class of medications. It inhibits the endogenous production of cholesterol in the liver, thereby lowering abnormally high cholesterol and lipid levels, and ultimately reducing the risk of cardiovascular disease. Statins inhibit the enzyme hydroxymethylglutaryl-coenzyme A reductase (HMGCR) , which catalyzes the critical step in cholesterol biosynthesis of HMG-CoA conversion to mevalonic acid. Statins are the most commonly prescribed medication for treating abnormal lipid levels (Malhotra & Goa 2001). ATV and its hydroxy-metabolites collectively inhibit HMGCR to reduce circulating low-density lipoprotein cholesterol.
ATV is transported in the blood almost exclusively bound to plasma proteins (>98%) (Lennernas 2003), and is subject to pre‑systemic clearance at the gastrointestinal tract and to first‑pass hepatic clearance, which explains its low systemic bioavailability (~12%) (Garcia et al. 2003). Organic anion transporters OATP1B1, OATP1B3 and OATP2B1, encoded by SLCO1B1, SLCO1B3, and SLCO2B1, respectively are expressed on the sinusoidal membrane of hepatocytes and can facilitate the liver uptake of drugs such as ATV (Kalliokoski & Niemi 2009).
In hepatocytes (and to a lesser extent, the GI tract), ATV can be hydroxylated by cytochrome P450 3A4 (CYP3A4) to hydroxy-metabolites, or undergo lactonization via an unstable acyl glucuronide intermediate to ATV lactone (ATVL) mediated by UGT1A3 and 1A1. ATVL may also be hydroxylated by CYP3A4 to hydroxylactone-metabolites. The lactone metabolites are inactive against HMGCR, but can be hydrolyzed via paraoxonases (PONs) to their corresponding hydroxy acids, which are active against HMGCR. Elimination of ATV and its metabolites is principally biliary with apparently no significant enterohepatic recirculation. Half-life (t1/2) is approximately 14 h for atorvastatin and 20–30 h for its metabolites (Schachter 2005).
R-HSA-9678110 Attachment and Entry Coronavirus replication is initiated by the binding of S protein to the cell surface receptor(s). The S protein is composed of two functional domains, S1 (bulb) which mediates receptor binding and S2 (stalk) which mediates membrane fusion. Specific interaction between S1 and the cognate receptor triggers a drastic conformational change in S2, leading to fusion between the virus envelope and the cellular membrane and release of the viral nucleocapsid into the host cell cytosol. Receptor binding is the major determinant of the host range and tissue tropism for a coronavirus. Some human coronaviruses (HCoVs ) have adopted cell surface enzymes as receptors, angiotensin converting enzyme 2 (ACE2) for SARS-CoV-1 and HCoV NL63. The receptor-bound S protein is activated by cleavage into S1 and S2, mediated by one of two of two host proteases, the endosomal cysteine protease cathepsin L and another trypsin like serine protease. Type II transmembrane serine proteases TMPRSS2 and TMPRSS11D have also been implicated in the activation of S protein of SARS-CoV-1. Host factors may play additional roles in viral entry (not annotated here). Valosin containing protein (VCP) contributes by a poorly understood mechanism to the release of coronavirus from early endosomes. Host factors may also restrict the attachment and entry of HCoV. Some interferon inducible transmembrane proteins (IFITMs) exhibited broad spectrum antiviral functions against various RNA viruses including SARS-CoV-1 while others may facilitate HCoV entry into host cells (Fung & Liu 2019).
R-HSA-9694614 Attachment and Entry This COVID-19 event has been created by a combination of computational inference (see https://reactome.org/documentation/inferred-events) from SARS-CoV-1 data and manual curation, as described in the summation for the overall SARS-CoV-2 infection pathway.
Coronavirus replication is initiated by the binding of S protein to the cell surface receptor(s). The S protein is composed of two functional domains, S1 (bulb) which mediates receptor binding and S2 (stalk) which mediates membrane fusion. Specific interaction between S1 and the cognate receptor triggers a drastic conformational change in S2, leading to fusion between the virus envelope and the cellular membrane and release of the viral nucleocapsid into the host cell cytosol. Receptor binding is the major determinant of the host range and tissue tropism for a coronavirus. Some human coronaviruses (HCoVs) have adopted cell surface enzymes as receptors, angiotensin converting enzyme 2 (ACE2) for SARS-CoV-2 (reviewed by Jackson et al, 2022), SARS-CoV-1, and HCoV NL63. The receptor-bound S protein is activated by cleavage into S1 and S2, mediated by one of two host proteases, the endosomal cysteine protease cathepsin L and another trypsin like serine protease. Type II transmembrane serine proteases TMPRSS2 and TMPRSS11D have also been implicated in the activation of S protein of SARS-CoV-2. Host factors may play additional roles in viral entry (not annotated here). Valosin containing protein (VCP) contributes by a poorly understood mechanism to the release of coronavirus from early endosomes. Host factors may also restrict the attachment and entry of HCoV.
R-HSA-162791 Attachment of GPI anchor to uPAR The mature form of urokinase plasminogen activator receptor (uPAR) is attached to the plasma membrane by a glycosylphosphatidylinositol (GPI) anchor (Ploug et al. 1991). As nascent uPAR polypeptide moves into the lumen of the endoplasmic reticulum, it is attacked by a transamidase complex that cleaves the uPAR polypeptide after residue 305, releasing the carboxyterminal peptide of uPAR and replacing it with an acylated GPI moiety. In a second step, the GPI moiety is deacylated, yielding a uPAR-GPI conjugate that can be efficiently transported to the Golgi apparatus.
R-HSA-3371568 Attenuation phase Attenuation of the heat shock transcriptional response occurs during continuous exposure to intermediate heat shock conditions or upon recovery from stress (Abravaya et al. 1991). The attenuation phase of HSF1 cycle involves the transcriptional silencing of HSF1 bound to HSE, the release of HSF1 trimers from HSE and dissociation of HSF1 trimers to monomers. HSF1-driven heat stress associated transcription was shown to depend on inducible and reversible acetylation of HSF1 at Lys80, which negatively regulates DNA binding activity of HSF1 (Westerheide SD et al. 2009). In addition, the attenuation of HSF1 activation takes place when enough HSP70/HSP40 is produced to saturate exposed hydrophobic regions of proteins damaged as a result of heat exposure. The excess HSP70/HSP40 binds to HSF1 trimer, which leads to its dissociation from the promoter and conversion to the inactive monomeric form (Abravaya et al. 1991; Shi Y et al. 1998). Interaction of HSP70 with the transcriptional corepressor repressor element 1-silencing transcription factor corepressor (CoREST) assists in terminating heat-shock response (Gomez AV et al. 2008). HSF1 DNA-binding and transactivation activity were also inhibited upon interaction of HSF1-binding protein (HSBP1) with active trimeric HSF1(Satyal SH et al. 1998).
R-HSA-174084 Autodegradation of Cdh1 by Cdh1:APC/C Cdh1 is degraded by the APC/C during in G1 and G0. This auto-regulation may contribute to reducing the levels of Cdh1 levels during G1 and G0 (Listovsky et al., 2004).
R-HSA-349425 Autodegradation of the E3 ubiquitin ligase COP1 COP1 is one of several E3 ubiquitin ligases responsible for the tight regulation of p53 abundance. Following DNA damage, COP1 dissociates from p53 and is inactivated by autodegradation via a pathway involving ATM phosphorylation of COP1 on Ser(387), autoubiquitination and proteasome mediated degradation. Destruction of COP1 results in abrogation of the ubiquitination and degradation of p53 (Dornan et al., 2006).
R-HSA-177539 Autointegration results in viral DNA circles In this pathway, the viral integration machinery uses a site within the viral DNA as an integration target. This results in a covalent rearrangment of the viral DNA. The resulting DNA forms are not substrates for integration.
It has been suggested that the cellular BAF protein binds to viral DNA and diminishes autointegration by coating and condensing the viral DNA, thereby making it a less efficient integration target.
R-HSA-9612973 Autophagy Autophagy is an intracellular degradation process that is triggered by cellular stresses. There are three primary types of autophagy - macroautophagy, chaperone-mediated autophagy (CMA) and late endosomal microautophagy. Despite being morphologically distinct, all three processes culminate in the delivery of cargo to the lysosome for degradation and recycling (Parzych KR et al, 2014). In macroautophagy a double membrane compartment sequesters the cargo and delivers it to the lysosome. Chaperones are used to deliver specific cargo proteins to the lysosome in CMA. In microautophagy invaginations of the endosomal membrane are used to capture cargo from the cytosol. Autophagy can target a wide range of entities ranging from bulk proteins and lipids to cell organelles and pathogens giving rise to several subclasses such as mitophagy, lipophagy, xenophagy, etc. (Shibutani ST 2014 et al).
R-HSA-422475 Axon guidance Axon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, which senses the guidance cues in the environment through guidance cue receptors and responds by undergoing cytoskeletal changes that determine the direction of axon growth.
Guidance cues present in the surrounding environment provide the necessary directional information for the trip. These extrinsic cues have been divided into attractive or repulsive signals that tell the growth cone where and where not to grow.
Genetic and biochemical studies have led to the identification of highly conserved families of guidance molecules and their receptors that guide axons. These include netrins, Slits, semaphorins, and ephrins, and their cognate receptors, DCC and or uncoordinated-5 (UNC5), roundabouts (Robo), neuropilin and Eph. In addition, many other classes of adhesion molecules are also used by growth cones to navigate properly which include NCAM and L1CAM.
For review of axon guidance, please refer to Russel and Bashaw 2018, Chedotal 2019, Suter and Jaworski 2019).
Axon guidance cues and their receptors are implicated in cancer progression (Biankin et al. 2012), where they likely contribute to cell migration and angiogenesis (reviewed by Mehlen et al. 2011).
R-HSA-193634 Axonal growth inhibition (RHOA activation) p75NTR can also form a receptor complex with the Nogo receptor (NgR). Such complexes mediates axonal outgrowth inhibitory signals of MDGIs (myelin-derived growth-inhibitors), such as Nogo66, myelin-associated glycoprotein (MAG), and oligodendrocyte myelin glycoprotein (OMGP).
R-HSA-209563 Axonal growth stimulation Complex formation between p75NTR and RHOA can leads to inhibition of RHOA activity and axonal growth.
R-HSA-9748787 Azathioprine ADME Thiopurines were originally developed for cancer treatment in the early 1950s, with 6-mercaptopurine (6MP) being the first thiopurine approved by the FDA for the treatment of leukaemia, just two years after its discovery. Azathioprine (AZA), a prodrug of 6MP, was developed by the addition of a nitroimidazol group a few years later to bypass the high first-pass metabolism of 6MP due to oxidation in intestinal cells by xanthine oxidase (XDH). AZA is a thiopurine prodrug, and its pharmacological action is based on the release of the active metabolite 6-mercaptopurine (6MP) which is further metabolised to pharmacoligically active 6-thioguanine nucleotides (6-TGNs). These 6-TGNs achieve their cytotoxic effects in one of four ways
1. Incorporation of 6-thioguanosine triphosphate (6TGTP) into RNA
2. Incorporation of 6-thiodeoxyguanosine triphosphate (6TdGTP) into DNA
3. Inhibition of de novo purine synthesis by methylmercaptopurine nucleotides such as methylthioinosine monophosphate (meTIMP)
4. Inhibition of RAC1 by 6TGTP which induces apoptosis in activated T-cells.
While AZA has been supplanted as an antitumour drug, it remains useful as an immunosuppressant antimetabolite drug indicated to treat rheumatoid arthritis, Crohn's disease, ulcerative colitis, cancer and to prevent rejection in kidney transplant patients (Axelrad et al. 2016, Tominaga et al. 2021).
The molecular steps of AZA metabolism are described in this pathway (Cuffari et al. 1996, Dubinsky 2004). Briefly, oral AZA is rapidly converted to 6MP. Initial 6MP metabolism occurs along competing catabolic (XDH, TPMT) and anabolic (HPRT) enzymatic pathways. Once formed, 6-thiosine 5′-monophosphate (6TIMP) is further metabolized by inosine monophosphate dehydrogenase (IMPDH) and guanosine monophosphate synthetase (GMPS) to 6-thioguanosine 5′monophosphate (6TGMP). 6TGMP is then converted to the pharmacologically-active di- and tri- derivatives by their respective kinases.
R-HSA-5250924 B-WICH complex positively regulates rRNA expression The B-WICH complex is a large 3 Mdalton complex containing SMARCA5 (SNF2H), BAZ1B (WSTF), ERCC6 (CSB), MYO1C (Nuclear myosin 1c), SF3B1, DEK, MYBBP1A, and DDX21 (Cavellan et al. 2006, Percipalle et al. 2006, Vintermist et al. 2001, Sarshad et al. 2013, Shen et al. 2013, reviewed in Percipalle and Farrants 2006). B-WICH is found at active rRNA genes as well as at 5S rRNA and 7SL RNA genes. B-WICH appears to remodel chromatin and recruit histone acetyltransferases that modify histones to transcriptionally active states.
R-HSA-5620922 BBSome-mediated cargo-targeting to cilium The BBSome is a stable complex consisting of 7 Bardet-Biedl proteins (BBS1, 2, 4, 5, 7, 8 and 9) and BBIP10 that has roles in promoting IFT and trafficking proteins to the cilum (Blacque et al, 2004; Nachury et al, 2007; Loktev et al, 2008; Jin et al, 2010; reviewed in Sung and Leroux 2013). The BBSome is the primary effector of ARL6/BBS3, a small GTPase that binds the BBSome in complex with associated membrane proteins that are destined for the ciliary membrane (Jin et al, 2010; Nachury et al, 2007; Zhang et al, 2011; Seo et al, 2011). Components of the BBSome are enriched in TPR and beta-propeller motifs and are thought to form a linear coat on membranes that functions with ARL6 to target proteins to the cilium (Jin et al, 2010; reviewed in Nachury et al, 2010).
R-HSA-9859138 BCKDH synthesizes BCAA-CoA from KIC, KMVA, KIV The mitochondrial branched-chain alpha-ketoacid dehydrogenase (BCKDH) complex catalyzes the reactions of alpha-ketoisocaproate, alpha-keto beta-methylvalerate, or alpha-ketoisovalerate with CoA and NAD+ to form isovaleryl-CoA, alpha-methylbutyryl-CoA, or isobutyryl-CoA, respectively, and CO2 and NADH (Chuang and Shih, 2001). While bovine and microbial BCKD complexes have been characterized most extensively (Reed and Hackert 1990), structural studies of individual components and subcomplexes of human BCKD have confirmed their structures and roles in the overall oxidative decarboxylation process and have related these features to the disruptive effects of mutations on branched-chain amino acid metabolism in vivo: E1a and E1b components (AEvarsson et al., 2000), E2 (Chang et al., 2002), and E3 (DLD)(Brautigam et al., 2005). In addition, structural studies have confirmed the lipoylation of lysine residue 105 in E2 protein (Chang et al., 2002) and the loss of an aminoterminal mitochondrial transport sequence from mature E3 protein (Brautigam et al., 2005). Loss of mitochondrial transport sequences from proteins E1a, E1b, and E2 has been demonstrated by sequence analysis (Wynn et al., 1999). Defects in E1a, E1b, and E2 may cause so-called maple syrup urine disease, with accumulation of the abovementioned amino acids and their corresponding keto acids, leading to encephalopathy and progressive neurodegeneration (MSUD, MIM:248600; reviewed in Xu et al., 2020). Defects in the E3 (DLD) subunit, shared with other ketoacid dehydrogenase complexes, typically present as neonatal lactic acidosis due to lack of pyruvate dehydrogenase activity although symptoms of BCKDH deficiency may also be present.
R-HSA-9024909 BDNF activates NTRK2 (TRKB) signaling Signaling by the neurotrophin receptor tyrosine kinase NTRK2 (TRKB) can be activated by binding to brain-derived neurotrophic factor (BDNF), which functions as a ligand for NTRK2 (Soppet et al. 1991, Klein et al. 1991). Binding to BDNF triggers NTRK2 dimerization (Ohira et al. 2001) and trans-autophosphorylation of NTRK2 dimers on conserved tyrosine residues in the cytoplasmic tail of the receptor (Guiton et al. 1994, Minichiello et al. 1998, McCarty and Feinstein 1999). Phosphorylated tyrosine residues subsequently serve as docking sites for recruitment of effector proteins that trigger downstream signaling cascades.
R-HSA-111453 BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members Bcl-2 interacts with tBid (Yi et al. 2003), BIM (Puthalakath et al. 1999), PUMA (Nakano and Vousden 2001), NOXA (Oda et al. 2000), BAD (Yang et al. 2005), BMF (Puthalakath et al. 2001), resulting in inactivation of BCL2. Binding of BCL2 to tBID inhibits BID-induced cytochrome C release and apoptosis (Yi et al. 2003). BH3 only proteins associate with and inactivate anti-apoptotic BCL-XL.
R-HSA-1368108 BMAL1:CLOCK,NPAS2 activates circadian gene expression As inferred from mouse, BMAL1:CLOCK (ARNTL:CLOCK) and BMAL1:NPAS2 (ARNTL:NPAS2) heterodimers bind to sequence elements (E boxes) in the promoters of target genes and enhance transcription (Gekakis et al. 1998, reviewed in Munoz and Baler 2003).
R-HSA-9824439 Bacterial Infection Pathways Bacterial infection pathways aim to capture molecular mechanisms of human bacterial diseases related to bacterial adhesion to and invasion of human host cells and tissues, toxigenicity (interaction of bacterially-produced toxins with the human host), and evasion of the host's immune defense.
Bacterial infection pathways currently include some metabolic processes mediated by intracellular Mycobacterium tuberculosis, the actions of clostridial, anthrax, and diphtheria toxins, and the entry of Listeria monocytogenes into human cells.
Clostridial toxins are produced by anaerobic spore-forming gram-positive bacilli of the genus Clostridium. Clostridium tetani causes tetanus, Clostridium botulinum causes botulism, Clostridium perfringens causes gas gangrene, and Clostridium difficile causes pseudomembranous colitis. The anthrax toxin is produced by the aerobic spore-forming gram-positive bacilli of the species Bacillus anthracis. The diphtheria toxin is produced by aerobic nonspore-forming gram-positive bacilli of the species Corynebacterium diphtheriae infected with the bacterial virus corynephage beta. Enterobacterial toxins are produced by pathogenic strains of Enterobacteriaceae, aerobic gram-negative bacilli that are part of normal intestinal flora, such as Escherichia coli.
Mycobacterium tuberculosis bacteria are acid-fast, aerobic, nonspore-forming bacilli that cause tuberculosis, a wide-spread disease that usually affects the lungs.
Listeria monocytogenes bacteria are aerobic nonspore-forming gram-positive bacilli that cause listeriosis.
R-HSA-73884 Base Excision Repair Of the three major pathways involved in the repair of nucleotide damage in DNA, base excision repair (BER) involves the greatest number of individual enzymatic activities. This is the consequence of the numerous individual glycosylases, each of which recognizes and removes a specific modified base(s) from DNA. BER is responsible for the repair of the most prevalent types of DNA lesions, oxidatively damaged DNA bases, which arise as a consequence of reactive oxygen species generated by normal mitochondrial metabolism or by oxidative free radicals resulting from ionizing radiation, lipid peroxidation or activated phagocytic cells. BER is a two-step process initiated by one of the DNA glycosylases that recognizes a specific modified base(s) and removes that base through the catalytic cleavage of the glycosydic bond, leaving an abasic site without disruption of the phosphate-sugar DNA backbone. Subsequently, abasic sites are resolved by a series of enzymes that cleave the backbone, insert the replacement residue(s), and ligate the DNA strand. BER may occur by either a single-nucleotide replacement pathway or a multiple-nucleotide patch replacement pathway, depending on the structure of the terminal sugar phosphate residue. The glycosylases found in human cells recognize "foreign adducts" and not standard functional modifications such as DNA methylation (Lindahl and Wood 1999, Sokhansanj et al. 2002).
R-HSA-73929 Base-Excision Repair, AP Site Formation Base excision repair is initiated by DNA glycosylases that hydrolytically cleave the base-deoxyribose glycosyl bond of a damaged nucleotide residue, releasing the damaged base (Lindahl and Wood 1999, Sokhansanj et al. 2002).
R-HSA-210991 Basigin interactions Basigin is a widely expressed transmembrane glycoprotein that belongs to the Ig superfamily and is highly enriched on the surface of epithelial cells. Basigin is involved in intercellular interactions involved in various immunologic phenomena, differentiation, and development, but a major function of basigin is stimulation of synthesis of several matrix metalloproteinases. Basigin also induces angiogenesis via stimulation of VEGF production.
Basigin has an extracellular region with two Ig-like domains of which the N-term Ig-like domain is involved in interactions. It undergoes interactions between basigin molecules on opposing cells or on neighbouring cells. It also interacts with a variety of other proteins like caveolin-1, cyclophilins, integrins and annexin II that play important roles in cell proliferation, energy metabolism, migration, adhesion and motion, especially in cancer metastasis.
R-HSA-1461957 Beta defensins Humans have 38 beta-defensin genes plus 9-10 pseudogenes (details available on the HGNC website at http://www.genenames.org/genefamilies/DEFB). Many beta-defensins are encoded by recently duplicated genes giving rise to identical transcripts. Nomenclature is confusing and currently in transition. Uniprot recommended names are used throughout this pathway.
Many beta-defensins show expression that correlates with infection (Sahl et al. 2005, Pazgier et al. 2006). All so far characterized beta-defensins, i.e. beta-defensin 1 (hBD1), 4A (hBD2), 103 (hBD3), 104 (hBD4), 106 (hBD6), 118 (hBD18) and 128 (hBD28) have antimicrobial properties (Pazgier et al. 2006). For beta-defensins 4A, 103 and 118 (hBD2, 3, and 18) this has been shown to correlate with membrane permeabilization effects (Antcheva et al. 2004, Sahl et al. 2005, Yenugu et al. 2004). Electrostatic interaction and disruption of microbial membranes is widely believed to the primary mechanism of action for beta-defensins. Two models explain how membrane disruption takes place, the 'pore model' which postulates that beta-defensins form transmembrane pores in a similar manner to alpha-defensins, and the 'carpet model', which suggests that beta-defensins act as detergents. Beta-defensins contain 6 conserved cysteine residues that in beta-defensins 1, 4A and 103 (hBD1-3) are experimentally confirmed to be cross-linked 1-5, 2-4, 3-6. The canonical sequence for beta-defensins is x2-10Cx5-6(G/A)xCX3-4Cx9-13Cx4-7CCxn. Structurally they are similar to alpha-defensins but with much shorter pre-regions. Though dimerization of some beta-defensins has been reported this is not the case for all and it is unclear whether it is required for function. The majority of functional studies have focused on beta-defensin 103 (hBD3), which has the most significant antimicrobial activity at physiological salt concentrations (Harder et al. 2001). Beta-defensin 103 is highly cationic with a net charge of +11 e0. It exhibits broad-spectrum antimicrobial activity against gram-positive bacteria and some gram-negative bacteria (Harder et al. 2001), though some species are highly resistant (Sahly et al. 2003). Sensitivity correlates with lipid composition of the membrane, with more negatively-charged lipids correlating with larger beta-defensin 103-induced changes in membrane capacitance (Bohling et al. 2006). Though membrane disruption is widely believed to be the primary mechanism of action of beta-defensins they have other antimicrobial properties, such as inhibition of cell wall biosynthesis (Sass et al. 2010), and chemoattractant effects (Yang et al. 1999, Niyonsaba et al. 2002, 2004). The chemotactic activity of beta-defensins 1, 4A and 103 (hBD1-3) for memory T cells and immature DCs is mediated through binding to the chemokine receptor CCR6 and probably another unidentified Gi-coupled receptor (Yang et al. 1999, 2000).
Like defensins, the human cathelicidin LL37 peptide is rich in positively-charged residues (Lehrer & Ganz 2002).
Expression of certain beta-defensins can be induced in response to various signals, such as bacteria, pathogen-associated molecular patterns (PAMPs), or proinflammatory cytokines (Ganz 2003, Yang et al. 2004). Like the alpha-defensins, copy number variation has been reported for DEFB4, DEFB103 and DEFB104 with individuals having 2-12 copies per diploid genome. In contrast DEFB1 does not show such variation but exhibits a number of SNPs (Hollox et al. 2003, Linzmier & Ganz 2005).
R-HSA-77352 Beta oxidation of butanoyl-CoA to acetyl-CoA The seventh and final pass through the beta-oxidation spiral picks up where the last left off with the saturated fatty acid butanoyl-CoA and at the third step produces acetoacetyl-CoA, which can be used to generate 2 acetyl-CoA molecules or can be turned toward the synthesis of ketone bodies pathway. Four enzymatic steps are required starting with SCAD CoA dehydrogenase (Short Chain) activity, followed by the enoyl-CoA hydratase activity of crotonase, the 3-hydroxyacyl-CoA dehydrogenase activity of the short chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD). The final enzymatic step, creating two acetyl-CoA molecules requires a specific ketoacyl-CoA thiolase, Acetoacetyl-CoA thiolase.
R-HSA-77346 Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA The fourth pass through the beta-oxidation spiral picks up where the last left off with the saturated fatty acid decanoyl-CoA and produces octanoyl-CoA. Four enzymatic steps are required starting with MCAD CoA dehydrogenase (Medium Chain) activity, followed by the enoyl-CoA hydratase activity of crotonase, the 3-hydroxyacyl-CoA dehydrogenase activity of the short chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD), and completed by the ketoacyl-CoA thiolase activity, present in the mitochondrial membrane associated trifunctional protein. Note that the 3-hydroxyacyl-CoA dehydrogenase activity of SCHAD is not actually limited to short chain fatty acids, in fact SCHAD has a broad substrate specificity.
R-HSA-77350 Beta oxidation of hexanoyl-CoA to butanoyl-CoA The sixth pass through the beta-oxidation spiral picks up where the last left off with the saturated fatty acid hexanoyl-CoA and produces butanoyl-CoA. Four enzymatic steps are required starting with SCAD CoA dehydrogenase (Short Chain) activity, followed by the enoyl-CoA hydratase activity of crotonase, the 3-hydroxyacyl-CoA dehydrogenase activity of the short chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD), and completed by the ketoacyl-CoA thiolase activity, present in the mitochondrial membrane associated trifunctional protein.
R-HSA-77310 Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA The third pass through the beta-oxidation spiral picks up where the last left off with the saturated fatty acid lauroyl-CoA and produces decanoyl-CoA. Four enzymatic steps are required starting with LCAD CoA dehydrogenase (Long Chain) activity, followed by the enoyl-CoA hydratase activity of crotonase, the 3-hydroxyacyl-CoA dehydrogenase activity of the short chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD), and completed by the ketoacyl-CoA thiolase activity, present in the mitochondrial membrane associated trifunctional protein. Note that the 3-hydroxyacyl-CoA dehydrogenase activity of SCHAD is not actually limited to short chain fatty acids, in fact SCHAD has a broad substrate specificity.
R-HSA-77285 Beta oxidation of myristoyl-CoA to lauroyl-CoA The second pass through the beta-oxidation spiral starts with the saturated fatty acid myristoyl-CoA (from the first swing through the beta oxidation spiral) and produces lauroyl-CoA. Four enzymatic steps are required starting with LCAD CoA dehydrogenase (Long Chain) activity, followed by three enzymatic steps, enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase, and ketoacyl-CoA thiolase activities, all present in the mitochondrial membrane associated trifunctional protein.
R-HSA-77348 Beta oxidation of octanoyl-CoA to hexanoyl-CoA The fifth pass through the beta-oxidation spiral picks up where the last left off with the saturated fatty acid octanoyl-CoA and produces hexanoyl-CoA. Four enzymatic steps are required starting with MCAD CoA dehydrogenase (Medium Chain) activity, followed by the enoyl-CoA hydratase activity of crotonase, the 3-hydroxyacyl-CoA dehydrogenase activity of the short chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD), and completed by the ketoacyl-CoA thiolase activity, present in the mitochondrial membrane associated trifunctional protein.
R-HSA-77305 Beta oxidation of palmitoyl-CoA to myristoyl-CoA This first pass through the beta-oxidation spiral starts with the saturated fatty acid palmitoyl-CoA and produces myristoyl-CoA. Four enzymatic steps are required, starting with VLCAD CoA dehydrogenase (Very Long Chain) activity, followed by three enzymatic steps, enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase, and ketoacyl-CoA thiolase activities, all present in the mitochondrial membrane associated trifunctional protein.
R-HSA-3858494 Beta-catenin independent WNT signaling Humans and mice have 19 identified WNT proteins that were originally classified as either 'canonical' or 'non-canonical' depending upon whether they were able to transform the mouse mammary epithelial cell line C57MG and to induce secondary axis formation in Xenopus (Wong et al, 1994; Du et al, 1995). So-called canonical WNTs, including Wnt1, 3, 3a and 7, initiate signaling pathways that destabilize the destruction complex and allow beta-catenin to accumulate and translocate to the nucleus where it promotes transcription (reviewed in Saito-Diaz et al, 2013). Non-canonical WNTs, including Wnt 2, 4, 5a, 5b, 6, 7b, and Wnt11 activate beta-catenin-independent responses that regulate many aspects of morphogenesis and development, often by impinging on the cytoskeleton (reviewed in van Amerongen, 2012). Two of the main beta-catenin-independent pathways are the Planar Cell Polarity (PCP) pathway, which controls the establishment of polarity in the plane of a field of cells, and the WNT/Ca2+ pathway, which promotes the release of intracellular calcium and regulates numerous downstream effectors (reviewed in Gao, 2012; De, 2011).
R-HSA-196299 Beta-catenin phosphorylation cascade Degradation of beta-catenin is initiated following amino-terminal serine/threonine phosphorylation. Phosphorylation of B-catenin at S45 by CK1 alpha primes the subsequent sequential GSK-3-mediated phosphorylation at Thr41, Ser37 and Ser33 (Amit et al., 2002 ; Lui et al., 2002).
R-HSA-9915355 Beta-ketothiolase deficiency ACAT1 is a mitochondrial enzyme that plays a role in metabolism of ketone bodies and isoleucine catabolism (Fukao et al, 1991; Haapalainen et al, 2007; reviewed in Fukao et al, 2019). As part of isoleucine catabolism in the mitochondria, ACAT1 catalyzes the thiolytic degradation of alpha-methylacetoacetyl-CoA to propionyl-CoA and acetyl-CoA (Fukao et al, 1991; Happalainen et al, 2007). Mutations in ACAT1 that affect protein stability and enzymatic activity are associated with beta-ketothiolase deficiency, also known as alpha-methylacetoacetic aciduria, an inborn error of metabolism that is identified by the presence of isoleucine intermediate metabolites in bodily fluids (Daum et al, 1973; Schutgens et al, 1982; Fukao et al, 1991; Fukao et al, 1992; Wakazono et al, 1995; Fukao et al, 1998; Sakurai et al, 2007; reviewed in Korman, 2006; Fukao et al, 2019). Neonatal onset is rare and most affected individuals present between 6 and 18 months with metabolic acidosis, lethargy, vomiting and sometimes coma (reviewed in Korman, 2006). As with other disorders of branched-chain metabolism, there is not a direct correlation between genotype and severity of phenotypic presentation (reviewed in Korman, 2006).
R-HSA-389887 Beta-oxidation of pristanoyl-CoA Pristanoyl-CoA, generated in the peroxisome by alpha-oxidation of dietary phytanic acid, is further catabolized by three cycles of peroxisomal beta-oxidation to yield 4,8-dimethylnonanoyl-CoA, acetyl-CoA and two molecules of propionyl-CoA. These molecules in turn are converted to carnitine conjugates, which can be transported to mitochondria (Wanders and Waterham 2006, Verhoeven et al. 1998, Ferdinandusse et al. 1999).
R-HSA-390247 Beta-oxidation of very long chain fatty acids Linear fatty acids containing more than 18 carbons are broken down by beta-oxidation in peroxisomes to yield acetyl-CoA and medium chain-length fatty acyl CoA's such as octanoyl-CoA (Wanders and Waterham 2006).
R-HSA-425381 Bicarbonate transporters Respiratory oxidation in the mitochondria produces carbon dioxide (CO2) as a waste product. CO2 is in equilibrium with bicarbonate (HCO3-) and is the body's central pH buffering system. HCO3- is charged so cannot move across membranes unaided. The bicarbonate transport proteins move bicarbonate across the membrane. There are 14 genes which encode these transport proteins in mammals. Applying the Human Genome Organization's sytematic nomenclature to human genes, the bicarbonate transporters belong to the SLC4A and SLC26A families. Within SLC4A, there are two distinct subfamilies, functionally corresponding to the electroneutral Cl-/HCO3- exchangers and Na+-coupled HCO3- co-transporters (Romero MF et al, 2004; Cordat E and Casey JR, 2009).
R-HSA-194068 Bile acid and bile salt metabolism In a healthy adult human, about 500 mg of cholesterol is converted to bile salts daily. Newly synthesized bile salts are secreted into the bile and released into the small intestine where they emulsify dietary fats (Russell 2003). About 95% of the bile salts in the intestine are recovered and returned to the liver (Kullak-Ublick et al. 2004; Trauner and Boyer 2002). The major pathway for bile salt synthesis in the liver begins with the conversion of cholesterol to 7alpha-hydroxycholesterol. Bile salt synthesis can also begin with the synthesis of an oxysterol - 24-hydroxycholesterol or 27-hydroxycholesterol. In the body, the initial steps of these two pathways occur in extrahepatic tissues, generating intermediates that are transported to the liver and converted to bile salts via the 7alpha-hydroxycholesterol pathway. These extrahepatic pathways contribute little to the total synthesis of bile salts, but are thought to play important roles in extrahepatic cholesterol homeostasis (Javitt 2002).
R-HSA-2173782 Binding and Uptake of Ligands by Scavenger Receptors Scavenger receptors bind free extracellular ligands as the initial step in clearance of the ligands from the body (reviewed in Ascenzi et al. 2005, Areschoug and Gordon 2009, Nielsen et al. 2010). Some scavenger receptors, such as the CD163-haptoglobin system, are specific for only one ligand. Others, such as the SCARA receptors (SR-A receptors) are less specific, binding several ligands which share a common property, such as polyanionic charges.
Brown and Goldstein originated the idea of receptors dedicated to scavenging aberrant molecules such as modified low density lipoprotein particles (Goldstein et al. 1979) and such receptors have been shown to participate in pathological processes such as atherosclerosis. Based on homology, scavenger receptors have been categorized into classes A-H (reviewed in Murphy et al. 2005).
R-HSA-173107 Binding and entry of HIV virion HIV enters cells by fusion at the cell surface, that results in a productive infection. The envelope (Env) protein of HIV mediates entry. Env is composed of a surface subunit, gp120, and a transmembrane subunit, gp41, which assemble as heterotrimers on the virion surface.The trimeric, surface gp120 protein (SU) on the virion engages CD4 on the host cell, inducing conformational changes that promote binding to select chemokine receptors CCR5 and CXCR4.
The sequential interplay between SU, CD4 and chemokine coreceptors prompts a conformational change in the transmembrane gp41. This coiled coil protein, assembled as a trimer on the virion membrane, springs open to project three peptide fusion domains that 'harpoon' the lipid bilayer of the target cell. A hairpin structure (also referred to as a "coiled coil bundle") is subsequently formed when the extracellular portion of gp41 collapses, and this hairpin formation promotes the fusion of virion and target cell membranes by bringing them into close proximity. Virion and target cell membrane fusion leads to the release of HIV viral cores into the cell interior.
R-HSA-4411364 Binding of TCF/LEF:CTNNB1 to target gene promoters The genes regulated by beta-catenin and TCF/LEF are involved in a diverse range of functions in cellular proliferation, differentiation, embryogenesis and tissue homeostasis, and include transcription factors, cell cycle regulators, growth factors, proteinases and inflammatory cytokines, among others (reviewed in Vlad et al, 2008). A number of WNT signaling components are themselves positively or negatively regulated targets of TCF/LEF-dependent transcription, establishing feedback loops to enhance or restrict signaling (see for instance, Khan et al 2007; Chamorro et al, 2005; Roose et al, 1999; Lustig et al, 2002). Other than a few of these general feedback targets (e.g. Axin2), most target genes are cell- and/or tissue-specific. A list of WNT/beta-catenin-dependent target genes is maintained at http://www.standford.edu/group/nusselab/cgi-bin/wnt/target_genes.
R-HSA-141333 Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB Human monoamine oxidases (MAOs) are flavin-containing enzymes that are present on the outer mitochondrial membrane and act on primary, secondary and tertiary amines. In contrast to the P450s which have a large number of isozymes, MAOs number only two isozymes, MAO-A and MAO-B. These gene products share over 70% sequence identity, are approximately 59KDa in size and have overlapping substrates (for example dopamine, tryamine and tryptamine) but each form also has distinct substrate specificities. MAO-A (primary type in fibroblasts) preferentially oxidises serotonin (5-Hydroxytryptamine) whereas MAO-B (primary type in platelets) prefers phenylethylamine. MAOs are of particular clinical interest because of the use of MAO inhibitors (MAOI) as antidepressants or in the treatment of neurodegenerative diseases Benedetti 2001, Beedham 1997).
R-HSA-211859 Biological oxidations All organisms are constantly exposed to foreign chemicals every day. These can be man-made (drugs, industrial chemicals) or natural (alkaloids, toxins from plants and animals). Uptake is usually via ingestion but inhalation and transdermal routes are also common.
The very nature of many chemicals that make them suitable for uptake by these routes, in other words their lipophilicty (favours fat solubility) is also the main reason organisms have developed mechanisms that convert them to hydrophilic (favours water solubility) compounds which are readily excreted via bile and urine. Otherwise, lipophilic chemicals would accumulate in the body and overwhelm defense mechanisms. This process is called biotransformation and is catalyzed by enzymes mainly in the liver of higher organisms but a number of other organs have considerable ability to process xenobiotica such as kidneys, gut and lungs. As well as xenobiotics, many endogenous compounds are commonly eliminated by this process.
This mechanism is of ancient origin and a major factor for its development in animals is plants. Most animals are plant eaters and thus are subject to a huge variety of chemical compounds which plants produce to stop themselves being eaten. This complex set of enzymes have several features which make them ideal for biotransformation;
(1) metabolites of the parent chemical are usually made more water soluble so it favours rapid excretion via bile and urine
(2) the enzymes possess broad and overlapping specificity to be able to deal with newly exposed chemicals
(3) metabolites of the parent generally don't have adverse biological effects.
In the real world however, all these criteria have exceptions. Many chemicals are transformed into reactive metabolites. In pharmacology, the metabolites of some parent drugs exert the desired pharmacological effect but in the case of polycyclic aromatic hydrocarbons (PAHs), which can undergo epoxidation, it results in the formation of an electrophile which can attack proteins and DNA.
Metabolism of xenobiotica occurs in several steps called Phase 1 (functionalization) and Phase 2 (conjugation). To improve water solubility, a functional group is added to or exposed on the chemical in one or more steps (Phase 1) to which hydrophilic conjugating species can be added (Phase 2). Functional groups can either be electrophilic (epoxides, carbonyl groups) or nucleophilic (hydroxyls, amino and sulfhydryl groups, carboxylic groups) (see picture).
Once chemicals undergo functionalization, the electrophilic or nucleophilic species can be detrimental to biological systems. Electrophiles can react with electron-rich macromolecules such as proteins, DNA and RNA by covalent interaction whilst nucleophiles have the potential to interact with biological receptors. That's why conjugation is so important as it mops up these potentially reactive species.
Many chemicals, when exposed to certain metabolizing enzymes can induce those enzymes, a process called enzyme induction. The effect of this is that these chemicals accelerate their own biotransformation and excretion. The reverse is also true where some chemicals cause enzyme inhibition. Some other factors that alter enzyme levels are sex, age and genetic predisposition. Between species, there can be considerable differences in biotransformation ability which is a problem faced by drug researchers interpreting toxicological results to humans.
R-HSA-2466712 Biosynthesis of A2E, implicated in retinal degradation Lipofuscin is a yellow-brown pigment grain composed mainly of lipids but also sugars and certain metals. Accumulation of lipofuscin is associated with degenerative diseases such as Alzheimer's disease, Parkinson's disease, chronic obstructive pulmonary disease and retinal macular degeneration.
A prominent component of lipofuscin in retinal pigment epithelial (RPE) cells is the bisretinoid A2E (di-retinoid-pyridinium-ethanolamine), the end-product of the condensation of 2 molecules of all-trans-retinal (atRAL) and phosphatidylethanolamine (PE) in photoreceptor outer disc membranes. Once formed, A2E is phagocytosed, together with outer segments (Kevany & Palczewski 2010), to RPE where it accumulates. There is no evidence as yet to indicate that A2E can be catabolised (Sparrow et al. 2012, Sparrow et al. 2010). A simplified biosynthetic pathway for A2E is described here.
R-HSA-9018676 Biosynthesis of D-series resolvins The D-series resolvins (RvD1-6) are biosynthesised from the precursor ω-3 fatty acid docosahexaenoic acid (DHA), either via aspirin-triggered cylcooxygenase catalysis (17(R) AT-RvDs) or via the lipoxygenase pathway (described here) forming the epimeric 17(S)-RvD1-6 resolvins (Serhan et al. 2014, Bannenberg & Serhan 2010).
R-HSA-9018677 Biosynthesis of DHA-derived SPMs Docosahexaenoic acid (DHA), a major ω-3 polyunsaturated fatty acid (PUFA) found in fish oil is the source of D-series resolvins (RvDs), one of the specialized proresolving mediators (SPMs) that show potent anti-inflammatory and pro-resolving actions (Molfino et al. 2017). The biosynthesis of RvDs occurs mainly during the process of inflammation when endothelial cells interact with leukocytes. Dietary DHA circulates in plasma or is present in cellular membranes as it can easily integrate into membranes. On injury or infection, DHA moves with edema into the tissue sites of acute inflammation where it is converted to exudate RvDs to interact with local immune cells (Kasuga et al. 2008). The initial transformation of DHA by aspirin-acetylated cyclooxygenase-2 or cyclooxygenase-mediated catalysis can produce stereospecific D-resolvins (18(R)- or 18(S)-RvDs respectively). Combinations of oxidation, reduction and hydrolysis reactions determine the type of D-resolvin formed (RvD1-6) (Serhan et al. 2002, Serhan & Petasis 2011, Serhan et al. 2014).
R-HSA-9026395 Biosynthesis of DHA-derived sulfido conjugates The polyunsaturated fatty acid (PUFA) ω-3 docosahexaenoic acid (DHA) is a precursor for the production of novel sulfido-peptide conjugated mediators with structural similarity to the cysteinyl-leukotrienes and with novel biological properties. They are produced from specialised proresolving mediators (SPMs) in human macrophages and are termed protectin conjugates in tissue regeneration (PCTR), resolvin conjugates in tissue regeneration (RCTR), and maresin conjugates in tissue regeneration (MCTR) because they regulate mechanisms in inflammation resolution as well as tissue regeneration (Dalli et al. 2014, 2015, 2016, Serhan et al. 2017). Their biosynthesis is descibed in this section.
R-HSA-9018683 Biosynthesis of DPA-derived SPMs Docosapentaenoic acid (DPA), a C22:5 long-chain ω3 or ω6 polyunsaturated fatty acid (PUFA), is found in algal and fish oils, created via linoleic acid metabolism and is a metabolite in DHA metabolism. It can be acted upon by lipoxygenases to produce mono-, di- and tri-hydroxy derivatives in neutrophils and macrophages. These DPA derivatives are another branch of the specialised proresolving mediators (SPMs) produced from long-chain fatty acids which have anti-inflammatory properties, even though mechanisms of their anti-inflammatory action have not been fully elucidated (Bannenberg & Serhan 2010, Dangi et al. 2010, Vik et al. 2017, Hansen et al. 2017).
The biosynthesis of SPMs derived from the two isomers of DPA, DPAn-6 (cis-4,7,10,13,16-docosapentaenoic acid) and DPAn-3 (cis-7,10,13,16,19-docosapentaenoic acid), is described here. The only difference between the two isomers is the position of the first double bond; ω-3 for DPAn-3 and ω-6 for DPAn-6. The products of these isomers were characterised by analogy in structure and action to docosahexaenoic acid (DHA)-derived and eicosapentaenoic acid (EPA)-derived resolvins, protectins and maresins (Serhan et al. 2002, Bannenberg & Serhan 2010, Serhan et al. 2015).
R-HSA-9025094 Biosynthesis of DPAn-3 SPMs The polyunsaturated fatty acid (PUFA) ω-3 cis-7,10,13,16,19-docosapentaenoic acid (DPAn-3) is an intermediate in the biosynthesis of docosahexaenoic acid (DHA) from eicosapentaenoic acid (EPA) and is also a precursor for the production of novel bioactive mediators. The proposed biosynthesis of specialised proresolving mediators (SPMs) derived from DPAn-3 is described here (Dalli et al. 2013, Hansen et al. 2017, Vik et al. 2017). The products of the ω-3 isomer were characterised based on DHA (docosahexaenoic acid) derived resolvins, protectins and maresins (Serhan et al. 2002, Bannenberg & Serhan 2010). The same biosynthetic route as DHA-derived SPMs is probably how DPAn-3 products are also formed (Dalli et al. 2013).
R-HSA-9026403 Biosynthesis of DPAn-3-derived 13-series resolvins Neutrophils adherence to the vascular endothelium is a critical and early event in the innate immune response to injury or invading pathogens (Sadik et al. 2011). Studies of the lipid fraction from neutrophil-endothelial cell cultures resulted in the discovery of four novel specialised proresolving mediators (SPMs) (Dalli et al. 2015). Results from LC/MS-MS metabololipidomics using a chemically-synthesised precursor (13(R)-hydroxy-DPAn-3) identified four mediators generated from this precursor.
The polyunsaturated fatty acid (PUFA) ω-3 cis-7,10,13,16,19-docosapentaenoic acid (DPAn-3) is an intermediate in the biosynthesis of docosahexaenoic acid (DHA) from eicosapentaenoic acid (EPA) and is also a precursor for the production of novel bioactive mediators. DPAn-3 can form this precursor when acted upon by cyclooxygenase 2 (COX2). Thus these novel 13-series resolvins (RvT1-4) originate from DPAn-3 (Primdahl et al. 2016). In E. coli-infected mice, RvTs accelerated resolution of inflammation and increased survival. RvTs also regulated human and mouse phagocyte responses, stimulating bacterial phagocytosis and regulating inflammasome components (Dalli et al. 2015). The biosynthetic routes of these RvTs are described here. RvT formation requires neutrophil-endothelial cell interaction and is thought to proceed via a two-step process; COX2 hydroxylates DPAn-3 to 13(R)-DPAn-3 which trafficks to adjacent neutrophils where it is lipoxygenated by 5-lipoxygenase to RvT1-4 (Vik et al. 2017).
R-HSA-9026290 Biosynthesis of DPAn-3-derived maresins The polyunsaturated fatty acid (PUFA) ω-3 cis-7,10,13,16,19-docosapentaenoic acid (DPAn-3) is an intermediate in the biosynthesis of docosahexaenoic acid (DHA) from eicosapentaenoic acid (EPA) and is also a precursor for the production of novel bioactive mediators.The proposed biosynthesis of maresins derived from DPAn-3 is described here (Dalli et al. 2013, Hansen et al. 2017, Vik et al. 2017). 12-lipoxygenase oxygenates DPAn-3 to its 14(S) hydroperoxy epimer from which maresins are formed via a combination of oxygenation, reduction and hydrolysis reactions (Dalli et al. 2013). The products of the ω-3 isomer were characterised based on docosahexaenoic acid (DHA)-derived maresins (Serhan et al. 2015) and were demonstrated to have similar potent systemic anti-inflammatory and tissue protective actions as DHA-derived specialised proresolving mediators (SPMs) (Dalli et al. 2013). The same biosynthetic route as DHA-derived SPMs is probably how DPAn-3 products are also formed (Dalli et al. 2013).
R-HSA-9026286 Biosynthesis of DPAn-3-derived protectins and resolvins The polyunsaturated fatty acid (PUFA) ω-3 cis-7,10,13,16,19-docosapentaenoic acid (DPAn-3) is an intermediate in the biosynthesis of docosahexaenoic acid (DHA) from eicosapentaenoic acid (EPA) and is also a precursor for the production of novel bioactive mediators. The proposed biosynthesis of resolvins and protectins derived from DPAn-3 is described here (Dalli et al. 2013, Hansen et al. 2017, Vik et al. 2017). 15-lipoxygenase oxygenates DPAn-3 to its 17(S) hydroperoxy epimer from which resolvins and protectins are formed via a combination of oxygenation, reduction and hydrolysis reactions (Dalli et al. 2013). The products of the ω-3 isomer were characterised based on docosahexaenoic acid (DHA)-derived resolvins and protectins (Serhan et al. 2002) and were demonstrated to have similar potent systemic anti-inflammatory and tissue protective actions as DHA-derived specialised proresolving mediators (SPMs) (Dalli et al. 2013). The same biosynthetic route as DHA-derived SPMs is probably how DPAn-3 products are also formed (Dalli et al. 2013).
R-HSA-9025106 Biosynthesis of DPAn-6 SPMs The biosynthesis of specialised proresolving mediators (SPMs) derived from the ω-6 isomer of DPA, DPAn-6 (cis-4,7,10,13,16-docosapentaenoic acid) is described here (Dangi et al. 2010). The products of the ω-6 isomer were characterised by analogy in structure and action to docosahexaenoic acid (DHA)-derived and eicosapentaenoic acid (EPA)-derived resolvins (Serhan et al. 2002, Bannenberg & Serhan 2010).
R-HSA-9023661 Biosynthesis of E-series 18(R)-resolvins Eicosapentaenoic acid (EPA), a major ω-3 polyunsaturated fatty acid (PUFA) found in fish oil is the source of E-series resolvins, one of the specialized proresolving mediators (SPMs) that show potent anti-inflammatory and pro-resolving actions (Molfino et al. 2017, Calder 2017). The initial transformation of EPA can be mediated by either cytochrome P450s or aspirin-acetylated cyclooxygenase-2, resulting in 18(R)- and 18(S)-stereospecific E-resolvins. Combinations of oxidation, reduction and hydrolysis reactions determine the type of E-resolvin formed (RvE1, RvE2 or RvE3) (Serhan & Petasis 2011). Aspirin acetylation of cyclooxygenase isoforms results in changed activities. Acetylation of cyclooxygenase-1 results in its inhibition and thereby halting production of inflammatory mediators. However, acetylation of cyclooxygenase-2 transforms its enzyme activity from a cyclooxygenase to a lipoxygenase, thereby blocking prostaglandin biosynthesis and, additionally, initiating the production of SPMs (Arita et al. 2005, Kyriakopoulos et al. 2017). The biosynthesis of 18(R) E-resolvins is described here.
R-HSA-9018896 Biosynthesis of E-series 18(S)-resolvins Eicosapentaenoic acid (EPA), a major ω-3 polyunsaturated fatty acid (PUFA) found in fish oil is the source of E-series resolvins, one of the specialized proresolving mediators (SPMs) that show potent anti-inflammatory and pro-resolving actions (Molfino et al. 2017, Calder 2017). The initial transformation of EPA can be mediated by either cytochrome P450s and/or aspirin-acetylated cyclooxygenase-2, resulting in stereospecific formation of 18(R)- and 18(S) E-resolvins. Combinations of oxidation, reduction and hydrolysis reactions determine the type of E-resolvin formed (RvE1, RvE2 or RvE3) (Serhan & Petasis 2011). Aspirin acetylation of cyclooxygenase isoforms results in changed activities. Acetylation of cyclooxygenase-1 results in its inhibition and thereby halting production of inflammatory mediators. However, acetylation of cyclooxygenase-2 transforms its enzyme activity from a cyclooxygenase to a lipoxygenase, thereby blocking prostaglandin biosynthesis and, additionally, initiating the production of SPMs (Arita et al. 2005, Kyriakopoulos et al. 2017). The biosynthesis of 18(S) E-resolvins is described here.
R-HSA-9018679 Biosynthesis of EPA-derived SPMs Eicosapentaenoic acid (EPA), a major ω-3 polyunsaturated fatty acid (PUFA) found in fish oil is the source of E-series resolvins (RvEs), one of the specialized proresolving mediators (SPMs) that show potent anti-inflammatory and pro-resolving actions (Molfino et al. 2017). The biosynthesis of RvEs occurs mainly during the process of inflammation when endothelial cells interact with leukocytes. EPA, circulating in plasma or released/mobilised from damaged cellular membranes on injury or infection, moves with edema into the tissue sites of acute inflammation where it is converted to exudate RvEs to interact with local immune cells (Kasuga et al. 2008). The initial transformation of EPA by aspirin-acetylated cyclooxygenase 2- and/or cytochrome P450-mediated catalysis can produce stereospecific resolvins (18(R)- or 18(S)-RvEs). Combinations of oxidation, reduction and hydrolysis reactions determine the type of resolvin formed (RvE1, RvE2 or RvE3) (Serhan et al. 2000, 2002, Serhan & Petasis 2011, Maehre et al. 2015).
R-HSA-2142700 Biosynthesis of Lipoxins (LX) Lipoxins A4 (LXA4) and B4 (LXB4), structurally characterized from human neutrophils incubated with 15-hydroperoxy-eicosatetraenoic acid (15-HpETE), each contain three hydroxyl moieties and a conjugated tetraene. The third hydroxyl of LXA4 is positioned at C-6, and of LXB4 at C-14. The action of arachidonate 5-lipoxygenase (ALOX5), in concert with an arachidonate 12-lipoxygenase (ALOX12) or arachidonate 15-lipoxygenase (ALOX15) activity, has been shown to produce lipoxins by three distinct pathways. Neutrophil ALOX5 can produce and secrete leukotriene A4 (LTA4) that is taken up by platelets, where it is acted upon by ALOX12 to form lipoxins. Likewise, ALOX15s can generate either 15-hydroperoxy-eicosatetraenoic acid (15-HpETE) or 15-hydro-eicosatetraenoic acid (15-HETE) that can be taken up by monocytes and neutrophils, where highly expressed ALOX5 uses it to generate lipoxins. Finally, aspirin acetylated prostaglandin G/H synthase 2 (PTGS2), rendered unable to synthesize prostaglandins, can act as a 15-lipoxygenase. This leads to the formation of 15R-HETE and culminates in creation of epi-lipoxins, which have altered stereochemistry at the C-15 hydroxyl but similar biological potency (Chiang et al. 2006, Buczynski et al. 2009, Vance & Vance 2008, Stsiapanava et al. 2017).
R-HSA-9020265 Biosynthesis of aspirin-triggered D-series resolvins The D-series resolvins (RvD1-6) are biosynthesised from the precursor ω-3 fatty acid docosahexaenoic acid (DHA), either via the lipoxygenase pathway (17(S)-RvDs) or via aspirin-triggered cylcooxygenase catalysis (described here) forming the epimeric 17(R)-RvD1-6 resolvins (Serhan et al. 2014, Bannenberg & Serhan 2010).
R-HSA-9027604 Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives Electrophilic oxo-derivatives of ω-3 polyunsaturated fatty acids (ω-3 PUFAs) are generated in macrophages and neutrophils in response to inflammation and oxidative stress to promote the resolution of inflammation. Being electrophilic, these derivatives reversibly bind to nucleophilic residues on target proteins (thiolates of cysteines and amino groups of histidine and lysine), triggering the activation of cytoprotective pathways. These include the Nrf2 antioxidant response, the heat shock response and the peroxisome proliferator activated receptor γ (PPARγ) and suppressing the NF-κB proinflammatory pathway (Cipollina 2015). Thus, these electrophilic derivatives transduce anti-inflammatory actions rather than suppress the production of pro-inflammatory arachidonic acid metabolites. An oxo-derivative of EPA has been shown to ablate leukemia stem cells in mice, which may represent a novel chemoprotective action for some oxo-derivatives (Hedge et al. 2011, Finch et al. 2015). In humans, dietary supplementation with ω-3 PUFAs has been reported to increase the formation of oxo-derivatives (Yates et al. 2014). The enzymes cyclooxygenases (COX), lipoxygenases (LOs) and cytochromes P450s, acting alone or in concerted transcellular biosynthesis, initially form epoxy or hydroxy intermediates of ω-3 PUFAs docosahexaenoic acid (DHA), docosapentaenoic acid (DPAn-3) and eicosapentaenoic acid (EPA) before these are further oxidised to electrophilic α,β-unsaturated keto-derivatives by cellular dehydrogenases.
R-HSA-9026762 Biosynthesis of maresin conjugates in tissue regeneration (MCTR) Resolution of inflammation is carried out by endogenous mediators termed specialised proresolving mediators (SPMs). Macrophages are central to the acute inflammatory response, governing both initiation and resolution phases, depending on the macrophage subtype activated. Human macrophages involved in resolution produce a family of bioactive peptide-conjugated mediators called maresin conjugates in tissue regeneration (MCTR). These mediators stimulate human phagocytotic functions, promote the resolution of bacterial infections, counterregulate the production of proinflammatory mediators and promote tissue repair and regeneration (Dalli et al. 2016). The proposed biosynthetic pathway is as follows. The maresin epoxide intermediate 13(S),14(S)-epoxy-MaR (13(S),14(S)-epoxy-docosahexaenoic acid) can be converted to MCTR1 (13(R)-glutathionyl, 14(S)-hydroxy-docosahexaenoic acid) by LTC4S and GSTM4. MCTR1 can be converted to MCTR2 (13(R)-cysteinylglycinyl, 14(S)-hydroxy-docosahexaenoic acid) by γ-glutamyl transferase (GGT). Finally, a dipeptidase can cleave the cysteinyl-glycinyl bond of MCTR2 to give MCTR3 (13(R)-cysteinyl, 14(S)-hydroxy-docosahexaenoic acid) (Dalli et al. 2016, Serhan et al. 2017).
R-HSA-9027307 Biosynthesis of maresin-like SPMs Maresin-like mediators MaR-L1, Mar-L2 and 14,21-dihydroxy docosahexaenoic acids are normally synthesized by leukocytes, platelets and macrophages, via the pathways described here. Impaired production of these specialised proresolving mediators (SPMs) in diabetic skin wounds is associated with impaired macrophage function and delayed or absent wound healing (Brem & Tomic-Canic 2007, Boniakowski et al 2017). Macrophages play critical roles in wound healing by mechanisms as yet unknown. They are active in both the initiation (M1 macrophage phenotype) and the resolution (M2 macrophage phenotype) of inflammatory processes. In a pathological state, the switch from the M1 phenotype macrophage to the M2 phenotype macrophage may be delayed or fail to occur, which can result in chronic low-grade inflammation. This macrophage phenotype skewing toward an inflammatory phenotype has been implicated in the pathogenesis of type 2 diabetes (T2D) and the non-healing of diabetic wounds (Boniakowski et al 2017, Pradhan et al. 2009).
Administration of maresin-like SPMs to diabetic mice with induced wounds have been shown to act as autocrine/paracrine factors in restoring reparative functions of macrophages (Hong et al. 2014, Tian et al. 2011a, 2011b, Lu et al. 2010, Hellman et al. 2012).
R-HSA-9018682 Biosynthesis of maresins Maresins 1 and 2 (MaR1 and MaR2) are derived through the action of lipoxygenase 12 on the ω-3 fatty acid docosahexaenoic acid (DHA). MaRs are mainly produced by macrophages hence the derivation of the name from MAcrophage mediator RESolving INflammation. MaR1 exhibits potent anti-inflammatory, pro-resolving, analgesic and wound healing activities. Major cellular targets for the actions of MaR1 are vascular smooth muscle (VSM) cells and vascular endothelial cells. In these cells MaR1 attenuates the adhesion of monocytes to the endothelium induced by TNF-alpha. Maresin 1 also inhibits the production of reactive oxygen species by both VSM and endothelial cells. The major mechanism through which MaR1 exerts these effects is through down-regulation of the transcription factor, nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB). MaR2 has been shown to reduce neutrophil infiltration and to enhance macrophage-mediated phagocytosis of dead and dying cells, a process termed efferocytosis. Two related structures, the maresin-like mediators (MaR-L1 and MaR-L2), are generated when the maresins produced by macrophages are released and acted upon by leukocytes and platelets (Hong et al. 2014). These, together with 14,21-dihydroxy-DHAs, rescue the reparative function of diabetes-impaired macrophages in diabetic wound healing (Hong et al. 2014, Tian et al. 2011, Boniakowski et al. 2017).
R-HSA-9026766 Biosynthesis of protectin and resolvin conjugates in tissue regeneration (PCTR and RCTR) Activated human macrophages and PMNs are able to produce 17-series sulfido-conjugated specialised proresolving mediators (SPMs) that are able to resolve acute inflammation and promote tissue regeneration. The ω-3 polyunsaturated fatty acid docosahexaenoic acid (DHA) is the source of these novel SPMs termed resolvin conjugates in tissue regeneration (RCTR) and protectin conjugates in tissue regeneration (PCTR). protectin conjugate in tissue regeneration PCTR and RCTR are thus named because they share proposed biosynthetic pathways, structural features, and biological actions with the DHA-derived protectins and resolvins (respectively) as well as displaying potent tissue-regenerative actions (Serhan et al. 2014).
The proposed biosynthetic pathways for PCTRs and RCTRs are described here (Dalli et al. 2015, Serhan et al. 2017). Mammalian lipoxygenases insert molecular oxygen predominantly in the S-stereochemistry, so the hydroxy groups at the 7- and 17-positions are presumed to be in the S-configuration. The R-containing diastereomers of these products may also possess biological activity in the resolution of inflammation and tissue regeneration but they are not described here.
R-HSA-9018681 Biosynthesis of protectins Docosahexaenoic acid (DHA), a major ω-3 polyunsaturated fatty acid (PUFA) found in fish oil is the source of protectins (PDs), one of the specialized proresolving mediators (SPMs) that show potent anti-inflammatory and pro-resolving actions (Molfino et al. 2017, Balas & Durand 2016). The switch from synthesis of pro-inflammatory eicosanoids, such as the prostaglandins and the thromboxanes, to the pro-resolving lipoxins, resolvins and protectins, occurs via induction of the 15-lipoxygenase enzyme.
Protectin, identified as (N)PD1 (N signifies neuroprotectin when produced in neural tissues) is derived from DHA through the actions of 15-lipoxygenase then enzymatic hydrolysis. Aspirin can also trigger the formation of epimeric protectin (AT-PD1) (Serhan et al. 2015). An additional protectin (DX) is formed through the sequential actions of two lipoxygenase reactions. The biosynthesis of these protectins is described here (Balas & Durand 2016, Balas et al. 2014, Serhan et al. 2014, Serhan et al. 2015).
R-HSA-9018678 Biosynthesis of specialized proresolving mediators (SPMs) A host’s normal protective response to tissue injury or pathogenic infection is acute inflammation. The condition of acute inflammation is created by the release of pro-inflammatory lipid mediators such as leukotrienes (LTs) and prostaglandins (PGs) that launch a series of signaling cascades to destroy invading pathogens and to repair damaged tissue (Libby 2007). The potent chemotactic agent leukotriene B4 (LTB4) promotes the recruitment of neutrophils (PMNs) to inflamed tissues, while the prostaglandins E2 and D2 (PGE2 and PGD2) further accelerate the inflammatory process. If left unchecked, the inflammatory response can initiate chronic systemic inflammatory disorders associated with cardiovascular disease, rheumatoid arthritis, periodontal disease, asthma, diabetes, inflammatory bowel disease (IBD), Alzheimer’s disease and age-related macular degeneration (AMD). The specific role by which inflammation contributes to their pathogenesis is not fully understood.
To prevent the onset of chronic inflammation, a lipid mediator class switch is thought to occur from the initial actions of pro-inflammatory lipid mediators to the anti-inflammatory and pro-resolving actions of lipoxins, resolvins, protectins and maresins (collectively called specialized proresolving mediators (SPMs)). Nanopicogram quantities of different lipid mediators are generated at different times during the evolution of the inflammatory response and these mediators coincide with distinct cellular events. The class switch activates leukocyte translational regulation of the enzymes required to produce pro-resolving lipid mediators (Levy et al. 2001). Each family of these PSMs exert specialized actions, including blocking neutrophil recruitment, promoting the recruitment and activation of monocytes, as well as mediating the nonphlogistic phagocytosis and lymphatic clearance of apoptotic neutrophils by activated macrophages (ie without inducing inflammation) and mediating tissue regeneration. Eventually, through the combined actions of these mediators, the resolution of inflammation is completed and homeostasis is reached (Serhan 2010, Bannenberg & Serhan 2010, Freire & Van Dyke 2013, Serhan et al. 2014).
SPMs are derived from polyunsaturated fatty acids (PUFAs) (Molfino et al. 2017). PUFAs of the ω-3 series are essential nutrients since they cannot be produced by humans (Duvall & Levy 2016) and are primarily found in dietary fish oils (Calder 2013) and in plants (Baker et al. 2016). The ω-3 PUFAs eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) and docosapentaenoic acid (DPAn-3) circulate in the bloodstream after dietary intake and are easily incorporated into cellular membranes in a time- and dose-dependent manner (Calder 2009), as well as being present in inflammatory exudates (Kasuga et al. 2008). They can be mobilised by phospholipase A2 from cellular membranes on injury or infection when they are converted to exudate SPMs (Serhan et al. 2002) to interact with local immune cells (Kasuga et al. 2008). EPA is the source for E-series resolvins while DHA is the source for D-series resolvins, protectins, maresins and sulfido conjugates in tissue regeneration mediators (Serhan et al. 2017). The ω-6 fatty acid arachidonic acid (AA) is the source for lipoxins. ω-3 or ω-6 PUFA docosapentaenoic acids (DPAn-3 and DPAn-6) are the sources of DPA-derived resolvins, protectins and maresins (Vik et al. 2017). Aspirin can also trigger the production of epimeric SPMs via acetylated PTGS2 (prostaglandin G/H synthase, COX2) (Serhan & Chiang 2002). Combinations of oxidation, reduction and hydrolysis can generate numerous SPMs. Electrophilic oxo-derivatives of ω-3 PUFAs are a class of oxidised derivatives that are generated in macrophages and neutrophils by the actions of 5-lipoxygenase, cyclooxygenase-2 and acetylated cyclooxygenase-2, followed by dehydrogenation. Being electrophilic, oxo-derivative SPMs reversibly bind to nucleophilic residues on target proteins, triggering the activation of cytoprotective pathways (Cipollina 2015). The pathways in this section describe the biosynthesis of these SPMs.
R-HSA-446193 Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein N-linked glycosylation commences with the 14-step synthesis of a dolichol lipid-linked oligosaccharide (LLO) consisting of 14 sugars (2 core GlcNAcs, 9 mannoses and 3 terminal GlcNAcs). This pathway is highly conserved in eukaryotes, and a closely related pathway is found in many eubacteria and Archaea. Mutations in the genes associated with N-glycan precursor synthesis lead to a diverse group of disorders collectively known as Congenital Disorders of Glycosylation (type I and II) (Sparks et al. 1993). The phenotypes of these disorders reflect the important role that N-glycosylation has during development, controlling the folding and the properties of proteins in the secretory pathway, and proteins that mediate cell-to-cell interactions or timing of development.
R-HSA-196780 Biotin transport and metabolism Biotin (Btn) is an essential cofactor in a variety of carboxylation reactions (Zempleni et al. 2009). Humans cannot synthesize Btn but it is abundant in the human diet and can be taken up from the intestinal lumen by the SLC5A6 transporter. Its uptake, intracellular translocation, covalent conjugation to apoenzymes, and salvage are described here.
R-HSA-9636467 Blockage of phagosome acidification Acidification of the phagosome occurs by insertion of ATPases into the phagosomal membrane in preparation for fusion with lysosomes. The pH of phagosomes containing Mtb never drops below 6.5 due to Mtb interfering with several acidification mechanisms (Queval et al. 2017).
R-HSA-9033658 Blood group systems biosynthesis The association between blood type and disease has been studied since the beginning of the 20th Century (Anstee 2010, Ewald & Sumner 2016). Landsteiner's discovery of blood groups in 1900 was based on agglutination patterns of red blood cells when blood types from different donors were mixed (Landsteiner 1931, Owen 2000, Tan & Graham 2013). His work is the basis of routine compatibility testing and transfusion practices today. The immune system of patients receiving blood transfusions will attack any donor red blood cells that contain antigens that differ from their self-antigens. Therefore, matching blood types is essential for safe blood transfusions. Landsteiner's classification of the ABO blood groups confirmed that antigens were inherited characteristics. In the 1940s, it was established that the specificity of blood group antigens was determined by their unique oligosaccharide structures. Since then, exponential advances in technology have resulted in the identification of over 300 blood group antigens, classified into more than 35 blood group systems by the International Society of Blood Transfusion (ISBT) (Storry et al. 2016).
Blood group antigens comprise either a protein portion or oligosaccharide sequence attached on a glycolipid or glycoprotein. The addition of one or more specific sugar molecules to this oligosaccharide sequence at specific positions by a variety of glycosyltransferases results in the formation of mature blood group antigens. The genes that code for glycosytransferases can contain genetic changes that produce antigenic differences, resulting in new antigens or loss of expression. Blood group antigens are found on red blood cells (RBCs), platelets, leukocytes, and plasma proteins and also exist in soluble form in bodily secretions such as breast milk, seminal fluid, saliva, sweat, gastric secretions and urine. Blood groups are implicated in many diseases such as those related to malignancy (Rummel & Ellsworth 2016), the cardiovascular system (Liumbruno & Franchini 2013), metabolism (Meo et al. 2016, Ewald & Sumner 2016) and infection (Rios & Bianco 2000, McCullough 2014). The most important and best-studied blood groups are the ABO, Lewis and Rhesus systems. The biosynthesis of the antigens in these systems is described in this section.
R-HSA-70895 Branched-chain amino acid catabolism The branched-chain amino acids, leucine, isoleucine, and valine, are all essential amino acids (i.e., ones required in the diet). They are major constituents of muscle protein. The breakdown of these amino acids starts with two common steps catalyzed by enzymes that act on all three amino acids: reversible transamination by branched-chain amino acid aminotransferase, and irreversible oxidative decarboxylation by the branched-chain ketoacid dehydrogenase complex. Isovaleryl-CoA is produced from leucine by these two reactions, alpha-methylbutyryl-CoA from isoleucine, and isobutyryl-CoA from valine. These acyl-CoA's undergo dehydrogenation, catalyzed by three different but related enzymes, and the breakdown pathways then diverge. Leucine is ultimately converted to acetyl-CoA and acetoacetate; isoleucine to acetyl-CoA and succinyl-CoA; and valine to succinyl-CoA. Under fasting conditions, substantial amounts of all three amino acids are generated by protein breakdown. In muscle, the final products of leucine, isoleucine, and valine catabolism can be fully oxidized via the citric acid cycle; in liver they can be directed toward the synthesis of ketone bodies (acetoacetate and acetyl-CoA) and glucose (succinyl-CoA) (Neinast et al. 2019).
R-HSA-9912481 Branched-chain ketoacid dehydrogenase kinase deficiency Branched-chain ketoacid dehydrogenase kinase deficiency (BCKDKD) is a neurological disorder that arises due to mutations in branched-chain ketoacid dehydrogenase kinase (BCKDK) (Joshi et al 2006; Novarino et al, 2012; Garcia-Cazorla et al, 2014; Tangeraas et al, 2023). BCKDK is a negative regulator of the branched-chain ketoacid dehydrogenase complex (BCKDH), the enzyme responsible for oxidative decarboxylation of branched-chain amino acid derivatives. BCKDK-dependent phosphorylation of serine residues in the E1 alpha subunit of the enzyme BCKDHA inactivates the BCKDH (Popov et al, 1992; Li et al, 2004; Wynn et al, 2004).
Inactivating mutations of BCKDK are associated with impaired intellectual development, microencephaly and autism (Joshi et al 2006; Novarino et al, 2012; Garcia-Cazorla et al, 2014; Tangeraas et al, 2023). Consistent with the role of BCKDK in inhibiting BCKDH activity, inactivating mutations in BCKDK result in higher levels of BCKDH activity and reduced BCAAs in plasma, tissues and urine in mouse models, patients and cell lines (Joshi et al, 2006; Novarino et al, 2012). Symptoms of BCKDK deficiency are alleviated in mouse models by dietary supplementation with a BCAA-enriched diet (Joshi et al, 2006; Novarino et al, 2012).
R-HSA-352238 Breakdown of the nuclear lamina Activated caspases cleave nuclear lamins causing the irreversible breakdown of the nuclear lamina.
R-HSA-168302 Budding The process by which influenza virus particles bud from an infected cell is not very well understood. Accumulation of M1 at the inner leaflet of the plasma membrane is thought to be the trigger for the initiation of bud formation. This bud formation continues until the inner core of the virus is completely enveloped. Completion of the budding process requires the membrane at the base of the bud to fuse. Although M1 is thought to be the driving force for bud formation, other viral and cellular proteins have been demonstrated to affect size and shape of the virus particle. Generally, influenza virus particles are either spherical or filamentous and this characteristic morphology is genetically linked to the M segment (Bourmakina, 2003; Roberts, 1998). Host factors such as polarization and the actin cytoskeleton play a critical role in determining the shape of filamentous particles (Roberts, 1998; Simpson-Holley, 2002).
R-HSA-162588 Budding and maturation of HIV virion With the virus components precariously assembled on the inner leaflet of the plasma membrane, the host cell machinery is required for viral budding. The virus takes advantage of the host ESCRT pathway to terminate Gag polymerization and catalyze release. The ESCRT pathway is normally responsible for membrane fission that creates cytoplasm filled vesicular bodies. In this case HIV (and other viruses) take advantage of the ESCRT cellular machinery to facilitate virion budding from the host.
R-HSA-450385 Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA Butyrate Response Factor 1 (BRF1, ZFP36L1, not to be confused with transcription factor IIIB) binds AU-rich elements in the 3' region of mRNAs. After binding, BRF1 recruits exonucleases (XRN1 and the exosome) and decapping enzymes (DCP1a and DCP2) to hydrolyze the RNA. The ability of BRF1 to direct RNA degradation is controlled by phosphorylation of BRF1. Protein kinase B/AKT1 phosphorylates BRF1 at serines 92 and 203. Phosphorylated BRF1 can still bind RNA but is sequestered by binding 14-3-3 protein, preventing BRF1 from destabilizing RNA. BRF1 is also phosphorylated by MK2 at serines 54, 92, 203, and at an unknown site in the C-terminus. It is unknown if this particular phosphorylated form of BRF1 binds 14-3-3.
R-HSA-8851680 Butyrophilin (BTN) family interactions Butyrophilins (BTNs) and butyrophilin like (BTNL) molecules are regulators of immune responses that belong to the immunoglobulin (Ig) superfamily of transmembrane proteins. They are structurally related to the B7 family of co-stimulatory molecules and have similar immunomodulatory functions (Afrache et al. 2012, Arnett & Viney 2014). BTNs are implicated in T cell development, activation and inhibition, as well as in the modulation of the interactions of T cells with antigen presenting cells and epithelial cells. Certain BTNsare genetically associated with autoimmune and inflammatory diseases (Abeler Domer et al. 2014).
The human butyrophilin family includes seven members that are subdivided into three subfamilies: BTN1, BTN2 and BTN3. The BTN1 subfamily contains only the prototypic single copy BTN1A1 gene, whereas the BTN2 and BTN3 subfamilies each contain three genes BTN2A1, BTN2A2 and BTN2A3, and BTN3A1, BTN3A2 and BTN3A3, respectively (note that BTN2A3 is a pseudogene). BTN1A1 has a crucial function in the secretion of lipids into milk (Ogg et al. 2004) and collectively, BTN2 and BTN3 proteins are cell surface transmembrane glycoproteins, that act as regulators of immune responses. BTNL proteins share considerable homology to the BTN family members. The human genome contains four BTNL genes: BTNL2, 3, 8 and 9 (Abeler Domer et al. 2014).
R-HSA-5621481 C-type lectin receptors (CLRs) Pathogen recognition is central to the induction of T cell differentiation. Groups of pathogens share similar structures known as pathogen-associated molecular patterns (PAMPs), which are recognised by pattern recognition receptors (PRRs) expressed on dendritic cells (DCs) to induce cytokine expression. PRRs include archetypical Toll-like receptors (TLRs) and non-TLRs such as retinoic acid-inducible gene I (RIG-I)-like receptors, C-type lectin receptors (CLRs) and intracellular nucleotide-binding domain and leucine-rich-repeat-containing family (NLRs). PRR recognition of PAMPs can lead to the activation of intracellular signalling pathways that elicit innate responses against pathogens and direct the development of adaptive immunity.
CLRs comprises a large family of receptors which bind carbohydrates, through one or more carbohydrate recognition domains (CRDs), or which possess structurally similar C-type lectin-like domains (CTLDs) which do not necessarily recognise carbohydrate ligands. Some CLRs can induce signalling pathways that directly activate nuclear factor-kB (NF-kB), whereas other CLRs affect signalling by Toll-like receptors. These signalling pathways trigger cellular responses, including phagocytosis, DC maturation, chemotaxis, the respiratory burst, inflammasome activation, and cytokine production.
R-HSA-75102 C6 deamination of adenosine Hydrolytic deamination of adenosine leads to inosine. Ammonia is presumed to be released during this reaction.
R-HSA-5218900 CASP8 activity is inhibited Cell death triggered by extrinsic stimuli via death receptors or toll-like receptors (e.g., TLR3, TLR4) may result in either apoptosis or regulated necrosis (necroptosis) (Holler N et al. 2000; Kalai M et al. 2002; Kaiser WJ and Offermann MK 2005; Yang P et al. 2007). Caspase-8 (CASP8) is a cysteine protease, which functions as a key mediator for determining which form of cell death will occur (Kalai M et al. 2002). The proteolytic activity of a fully processed, heterotetrameric form of CASP8 in human and rodent cells is required for proapoptotic signaling and also for a cleavage of kinases RIPK1 and RIPK3, while at the same time preventing RIPK1/RIPK3-dependent regulated necrosis (Juo P et al. 1998; Lin Y et al. 1999; Holler N et al. 2000; Hopkins-Donaldson S et al. 2000). A blockage of CASP8 activity in the presence of caspase inhibitors such as Z-VAD-FMK (pan-caspase inhibitor), endogenous FLIP(S) or viral FLIP-like protein was found to switch signaling to necrotic cell death (Thome M et al. 1997; Kalai M et al. 2002; Feoktistova M et al. 2011; Sawai H 2013).
R-HSA-9662834 CD163 mediating an anti-inflammatory response High expression of the membrane protein CD163 in macrophages is a characteristic of tissues responding to inflammation elicited either by an intracellular pathogen infection (such as Mycobacterium leprae or Leishmania spp.) or due to an acute or chronic inflammatory disorder. The soluble form of this molecule, sCD163, is considered to be a potential inflammation biomarker and a therapeutic target; sCD163 is formed from the increased shedding of CD163 mediated by the tumor necrosis factor-α (TNF-α) cleaving enzyme, ADAM17 (Etzerodt & Moestrup 2013, Silva et al. 2017). The biological function of sCD163 is not yet clear, although several possible functions have been proposed: opsonization of Staphylococcus aureus, inhibition of T-cell proliferation and inhibition of tumor necrosis factor-like weak inducer of apoptosis (TWEAK) (Tran et al. 2005).
R-HSA-5621575 CD209 (DC-SIGN) signaling CD209 (also called as DC-SIGN (DC-specific intracellular adhesion molecule-3-grabbing non-integrin)) is a type II transmembrane C-type lectin receptor preferentially expressed on dendritic cells (DCs). CD209 functions as a pattern recognition receptor (PRR) that recognises several microorganisms and pathogens, contributing to generation of pathogen-tailored immune responses (Gringhuis & Geijtenbeek 2010, den Dunnen et al. 2009, Svajger et al. 2010). CD209 interacts with different mannose-expressing pathogens such as Mycobacterium tuberculosis and HIV-1 (Gringhuis et al. 2007, Geijtenbeek et al. 2000a). It also acts as an adhesion receptor that interacts with ICAM2 (intracellular adhesion molecule-2) on endothelial cells and ICAM3 on T cells (Geijtenbeek et al. 2000b,c). CD209 functions not only as an independent PRR, but is also implicated in the modulation of Toll-like receptor (TLR) signaling at the level of the transcription factor NF-kB (Gringhuis et al. 2009). CLEC7A (Dectin-1) and CD209 (DC-SIGN) signalling modulates Toll-like receptor (TLR) signalling through the kinase RAF1 that is independent of the SYK pathway but integrated with it at the level of NF-kB activation. The activation of RAF1 by CLEC7A or CD209 does not lead to activation of extracellular signal-regulated kinase 1 (ERK1)/2 or Mitogen-activated protein kinase kinase 1 (MEK1)/2 but leads to the phosphorylation and subsequent acetylation of RELA (p65). RELA phosphorylated on S276 not only positively regulates the activity of p65 through acetylation of p65, but also represses RELB activity by sequestering active RELB into inactive p65-RELB dimers that do not bind DNA (Gringhuis et al. 2007, Svajger et al. 2010, Jacque et al. 2005). RAF1-dependent signaling pathway is crucial in dectin-1 mediated immunity as it modulates both the canonical (promoting p65 phosphorylation and acetylation) and non-canonical (forming inactive p65-RELB dimers) NK-kB activation.
R-HSA-5690714 CD22 mediated BCR regulation BCR activation is highly regulated and coreceptors like CD22 (SIGLEC2) set a signalling threshold to prevent aberrant immune response and autoimmune disease (Cyster et al. 1997, Han et al. 2005). CD22 is a glycoprotein found on the surface of B cells during restricted stages of development. CD22 is a member of the receptors of the sialic acid-binding Ig-like lectin (Siglec) family which binds specifically to the terminal sequence N-acetylneuraminic acid alpha(2-6) galactose (NeuAc-alpha(2-6)-Gal) present on many B-cell glycoproteins (Powell et al. 1993, Sgroi et al. 1993). CD22 has seven immunoglobulin (Ig)-like extracellular domains and a cytoplasmic tail containing six tyrosines, three of which belong to the inhibitory immunoreceptor tyrosine-based inhibition motifs (ITIMs) sequences. Upon BCR cross-linking CD22 is rapidly tyrosine phosphorylated by the tyrosine kinase Lyn, thereby recruiting and activating tyrosine phosphatase, SHP-1 and inhibiting calcium signalling.
R-HSA-389356 CD28 co-stimulation In naive T cells, CD28 costimulation enhances cell cycle entry, potently stimulates expression of both the mitogenic lymphokine interleukin-2 (IL-2) and its receptor, and stimulates the activation of an antiapoptotic program. CD28 engages with one or both members of the B7 receptor family, B7.1 and B7.2. Upon ligand binding the tyrosines and proline-rich motifs present in the cytoplasmic tail of CD28 are phosphorylated by Lck or Fyn. Upon phosphorylation CD28 recruits and induces phosphorylation and activation of a more restricted set of intracellular signaling components that, together with those mobilized by the TCR, contribute to convert membrane-based biochemical and biophysical changes into gene activation events. Proteins like PI3K, Vav-1, Tec and Itk kinases, AKT, and the Dok-1 adaptor have been identified as elements of the CD28 signaling pathway by biochemical or genetic approaches or both.
R-HSA-389357 CD28 dependent PI3K/Akt signaling PI3Ks can be activated by a number of different receptors, including the TcR (T cell receptor), co-stimulatory receptors (CD28), cytokine receptors and chemokine receptors. However, the specific roles of PI3Ks downstream of these receptors vary. CD28 contains the YMNM consensus PI3K-binding motif, and PI3K recruitment by CD28 contributes to or complements TCR-dependent PI3K signaling. Activation of PI3K promotes PIP3 production at the plasma membrane and several potential target molecules for this phospholipid have been implicated in PI3K pathways downstream of the TcR and CD28. Of these targets, at least Vav and Akt have been implicated in CD28 costimulation of T cell activation. AKT/PKB connects PI3K to signaling pathways that promote cytokine transcription, survival, cell-cycle entry and growth.
R-HSA-389359 CD28 dependent Vav1 pathway CD28 binds to several intracellular proteins including PI3 kinase, Grb-2, Gads and ITK. Grb-2 specifically co-operates with Vav-1 in the up-regulation of NFAT/AP-1 transcription. CD28 costimulation resulted in a prolonged and sustained phosphorylation and membrane localization of Vav1 in comparison to T-cell receptor activation alone. Tyrosine-phosphorylated Vav1 is an early point of integration between the signaling routes triggered by the T-cell receptor and CD28.
Vav1 transduces TCR and co-stimulatory signals to multiple biochemical pathways and several cytoskeleton-dependent processes. The products of Vav1 activation, Rac1 and Cdc42, in turn activate the mitogen-activated protein kinases JNK and p38. Vav1 is also required for TCR-induced calcium flux, activation of the ERK MAP kinase pathway, activation of the NF-kB transcription factor, inside-out activation of the integrin LFA-1, TCR clustering, and polarisation of the T cell.
R-HSA-9013148 CDC42 GTPase cycle This pathway catalogues CDC42 guanine nucleotide exchange factors (GEFs), GTPase activator proteins (GAPs), GDP dissociation inhibitors (GDIs) and CDC42 effectors. CDC42 is one of the three best characterized RHO GTPases, the other two being RHOA and RAC1. By regulating the cytoskeleton, CDC42 regulates cell polarity across different species, from yeast to humans (Pichaud et al. 2019, Woods and Lew 2019). CDC42 is an essential regulator of polarized morphogenesis in epithelial cells, where it coordinates formation of the apical membrane and lumen formation, as well as junction maturation (Pichaud et al. 2019). CDC42 plays a role in cell-to-cell adhesion and cell cycle regulation (Xiao et al. 2018). CDC42 takes part in the regulation of membrane trafficking. Dysfunction of several CDC42-specific GEFs has been shown to impair intracellular trafficking (Egorov and Polishchuk 2017). CDC42 participates in insulin synthesis and secretion and contributes to the pathogenesis of insulin resistance and diabetic nephropathy (Huang et al. 2019). CDC42 is often dysregulated in cancer because a number of GEFs and GEF activators that act upstream of RAC1 and CDC42 are known oncogenes (Aguilar et al. 2017; Maldonado et al. 2018; Zhang et al. 2019; Maldonado et al. 2020). CDC4 promotes cancer cell proliferation, survival, invasion, migration and metastasis (Xiao et al. 2018), especially under hyperglycemia (Huang et al. 2019).
R-HSA-68689 CDC6 association with the ORC:origin complex Cdc6 is a regulator of DNA replication initiation in both yeasts and human cells (Mendez and Stillman 2000), but its mechanism of action differs between the two systems. Genetic studies in budding yeast (S. cerevisiae) and fission yeast (S. pombe) indicate that the normal function of Cdc6 protein is required to restrict DNA replication to once per cell cycle. Specifically, Cdc6 may function as an ATPase switch linked to Mcm2-7:Cdt1 association with the Cdc6:ORC:origin complex (Lee and Bell 2000). In S. cerevisiae, Cdc6 protein is expressed late in the M phase of the cell cycle and, in cells with a prolonged G1 phase, late in G1. This protein has a short half-life, and is destroyed by ubiquitin-mediated proteolysis, mediated by the SCF complex (Piatti et al. 1995, Drury et al. 1997, Drury et al. 2000, Perkins et al. 2001). Human Cdc6 protein levels are reduced early in G1 but otherwise are constant throughout the cell cycle (Petersen et al. 2000). Some reports have suggested that after cells enter S phase, Cdc6 is phosphorylated, excluded from the nucleus and subject to ubiquitination and degradation (Saha et al. 1998, Jiang et al. 1999, Petersen et al. 1999). Replenishing Cdc6 protein levels during G1 appears to be regulated by E2F transcription factors (Yan et al. 1998).
R-HSA-9833576 CDH11 homotypic and heterotypic interactions Based on surface plasmon resonance experiments, CDH11 forms a specificity subgroup with CDH8 and, probably, CDH24. CDH11 forms homotypic trans dimers (Patel et al. 2006, Brasch et al. 2018), and heterotypic trans dimers with CDH8 (Brasch et al. 2018) and, based on sequence similarity, probably with CDH24 (Brasch et al. 2018).
R-HSA-69017 CDK-mediated phosphorylation and removal of Cdc6 As cells enter S phase, HsCdc6p is phosphorylated by CDK promoting its export from the nucleus (see Bell and Dutta 2002).
R-HSA-447041 CHL1 interactions Close homolog of L1 (CHL1) is a member of the L1 family of cell adhesion molecules expressed by subpopulations of neurons and glia in the central and peripheral nervous system. CHL1 like L1 promotes neuron survival and neurite outgrowth. CHL1 shares the basic structural arrangement of L1 family members yet in contrast to all the members it is not capable of forming homophilic adhesion. The second Ig-like domain of CHL1 contains the integrin interaction motif RGD rather than with in the sixth Ig-like domain as in L1, however the sixth Ig-like domain of CHL1 has another potential integrin binding motif DGEA. CHL1 binds NP-1 via the Ig1 sequence FASNRL to mdediate repulsive axon guidance to Sema3A. CHL1 is the only L1 family member with an altered sequence (FIGAY) in the ankyrin-binding domain, and it lacks the sorting/endocytosis RSLE motif, which is characteristic of other L1 family members.
R-HSA-5607763 CLEC7A (Dectin-1) induces NFAT activation CLEC7A (Dectin-1) signals through the classic calcineurin/NFAT pathway through Syk activation phospholipase C-gamma 2 (PLCG2) leading to increased soluble IP3 (inositol trisphosphate). IP3 is able to bind endoplasmic Ca2+ channels, resulting in an influx of Ca2+ into the cytoplasm. This increase in calcium concentration induces calcineurin activation and consequently, dephosphorylation of NFAT and its translocation into the nucleus, triggering gene transcription and extracellular release of Interleukin-2 (Plato et al. 2013, Goodridge et al. 2007, Mourao-Sa et al. 2011).
R-HSA-5607764 CLEC7A (Dectin-1) signaling CLEC7A (also known as Dectin-1) is a pattern-recognition receptor (PRR) expressed by myeloid cells (macrophages, dendritic cells and neutrophils) that detects pathogens by binding to beta-1,3-glucans in fungal cell walls and triggers direct innate immune responses to fungal and bacterial infections. CLEC7A belongs to thetype-II C-type lectin receptor (CLR) family that can mediate its own intracellular signaling. Upon binding particulate beta-1,3-glucans, CLEC7A mediates intracellular signalling through its cytoplasmic immunoreceptor tyrosine-based activation motif (ITAM)-like motif (Brown 2006). CLEC7A signaling can induce the production of various cytokines and chemokines, including tumour-necrosis factor (TNF), CXC-chemokine ligand 2 (CXCL2, also known as MIP2), interleukin-1beta (IL-1b), IL-2, IL-10 and IL-12 (Brown et al. 2003), it also triggers phagocytosis and stimulates the production of reactive oxygen species (ROS), thus contributing to microbial killing (Gantner et al. 2003, Herre et al. 2004, Underhill et al. 2005, Goodridge at al. 2011, Reid et al. 2009). These cellular responses mediated by CLEC7A rely on both Syk-dependent and Syk-independent signaling cascades. The pathways leading to the Syk-dependent activation of NF-kB can be categorised into both canonical and non-canonical routes (Gringhuis et al. 2009). Activation of the canonical NF-kB pathway is essential for innate immunity, whereas activation of the non-canonical pathway is involved in lymphoid organ development and adaptive immunity (Plato et al. 2013).
R-HSA-5660668 CLEC7A/inflammasome pathway Antifungal immunity through the induction of T-helper 17 cells (TH17) responses requires the production of mature, active interleukin-1beta (IL1B). CLEC7A (dectin-1) through the SYK route induces activation of NF-kB and transcription of the gene encoding pro-IL1B via the CARD9-BCL10-MALT1 complex as well as the formation and activation of a MALT1-caspase-8-ASC complex that mediated the processing of pro-IL1B. The inactive precursor pro-IL1B has to be processed into mature bioactive form of IL1B and is usually mediated by inflammatory cysteine protease caspase-1. Gringhuis et al. showed that CLEC7A mediated processing of IL1B occurs through two distinct mechanisms: CLEC7A triggering induced a primary noncanonical caspase-8 inflammasome for pro-IL1B processing that was independent of caspase-1 activity, whereas some fungi triggered a second additional mechanism that required activation of the NLRP3/caspase 1 inflammasome. Unlike the canonical caspase-1 inflammasome, CLEC7A mediated noncanonical caspase-8-dependent inflammasome is independent of pathogen internalization. CLEC7A/inflammasome pathway enables the host immune system to mount a protective TH17 response against fungi and bacterial infection (Gringhuis et al. 2012, Cheng et al. 2011).
R-HSA-6811434 COPI-dependent Golgi-to-ER retrograde traffic Retrograde traffic from the cis-Golgi to the ERGIC or the ER is mediated in part by microtubule-directed COPI-coated vesicles (Letourneur et al, 1994; Shima et al, 1999; Spang et al, 1998; reviewed in Lord et al, 2013; Spang et al, 2013). These assemble at the cis side of the Golgi in a GBF-dependent fashion and are tethered at the ER by the ER-specific SNAREs and by the conserved NRZ multisubunit tethering complex, known as DSL in yeast (reviewed in Tagaya et al, 2014; Hong and Lev, 2014). Typical cargo of these retrograde vesicles includes 'escaped' ER chaperone proteins, which are recycled back to the ER for reuse by virtue of their interaction with the Golgi localized KDEL receptors (reviewed in Capitani and Sallese, 2009; Cancino et al, 2013).
R-HSA-6811436 COPI-independent Golgi-to-ER retrograde traffic In addition to the better characterized COPI-dependent retrograde Golgi-to-ER pathway, a second COPI-independent pathway has also been identified. This pathway is RAB6 dependent and transports cargo such as glycosylation enzymes and Shiga and Shiga-like toxin through tubular carriers rather than vesicles (White et al, 1999; Girod et al, 1999; reviewed in Heffernan and Simpson, 2014). In the absence of a COPI coat, the membrane curvature necessary to initiate tubulation may be provided through the action of phospholipase A, which hydrolyzes phospholipids at the sn2 position to yield lysophospholipids. This activity is countered by lysophospholipid acyltransferases, and the balance of these may influence whether transport tubules or transport vesicles form (de Figuiredo et al, 1998; reviewed in Bechler et al, 2012). RAB6-dependent tubules also depend on the dynein-dynactin motor complex and the hoomodimeric Bicaudal proteins (Matanis et al, 2002; Yamada et al, 2013; reviewed in Heffernan and Simpson, 2014).
R-HSA-6807878 COPI-mediated anterograde transport The ERGIC (ER-to-Golgi intermediate compartment, also known as vesicular-tubular clusters, VTCs) is a stable, biochemically distinct compartment located adjacent to ER exit sites (Ben-Tekaya et al, 2005; reviewed in Szul and Sztul, 2011). The ERGIC concentrates COPII-derived cargo from the ER for further anterograde transport to the cis-Golgi and also recycles resident ER proteins back to the ER through retrograde traffic. Both of these pathways appear to make use of microtubule-directed COPI-coated vesicles (Pepperkok et al, 1993; Presley et al, 1997; Scales et al, 1997; Stephens and Pepperkok, 2002; Stephens et al, 2000; reviewed in Lord et al, 2001; Spang et al, 2013).
R-HSA-204005 COPII-mediated vesicle transport COPII components (known as Sec13p, Sec23p, Sec24p, Sec31p, and Sar1p in yeast) traffic cargo from the endoplasmic reticulum to the ER-Golgi intermediate compartment (ERGIC). COPII-coated vesicles were originally discovered in the yeast Saccharomyces cerevisiae using genetic approaches coupled with a cell-free assay. The mammalian counterpart of this pathway is represented here. Newly synthesized proteins destined for secretion are sorted into COPII-coated vesicles at specialized regions of the ER. These vesicles leave the ER, become uncoated and subsequently fuse with the ERGIC membrane.
R-HSA-140180 COX reactions Arachidonic acid (AA) is a 20 carbon unsaturated fatty acid which is present in the lipid bilayer of all mammalian cells. AA is released from the membrane by phospholipases, thus making it available for conversion to bioactive lipids. The cyclooxygenase pathway is one of three pathways (the others being lipoxygenase and P450 monooxygenase pathways) that perform this conversion.\n\nThe enzyme that acts in the cyclooxygenase pathway is called cyclooxygenase (COX) or prostaglandin H synthase (PGHS). PGHS exhibits a dual catalytic activity, a cyclooxygenase and a peroxidase. The cyclooxygenase catalyzes the initial conversion of AA to an intermediate, prostaglandin G2 (PGG2) whilst the peroxidase converts PGG2 to prostaglandin H2 (PGH2) via a two-electron reduction. PGH2 is the intermediate for products that play critical roles in immune function regulation, kidney development and mucosal integrity of the GI tract.\n\nPGHS exists in two isoforms, 1 and 2 and both forms can perform the above reactions. Form 1 is constitutively expressed in most tissues and is involved in performing normal physiological functions. Form 2, in contrast, is inducible and is involved in critical steps of rheumatic disease, inflammation and tumorigenesis.
R-HSA-199920 CREB phosphorylation Nerve growth factor (NGF) activates multiple signalling pathways that mediate the phosphorylation of CREB at the critical regulatory site, serine 133. CREB phosphorylation at serine 133 is a crucial event in neurotrophin signalling, being mediated by ERK/RSK, ERK/MSK1 and p38/MAPKAPK2 pathways. Several kinases, such as MSK1, RSK1/2/3 (MAPKAPK1A/B/C), and MAPKAPK2, are able to directly phosphorylate CREB at S133. MSK1 is also able to activate ATF (Cyclic-AMP-dependent transcription factor). However, the NGF-induced CREB phosphorylation appears to correlate better with activation of MSK1 rather than RSK1/2/3, or MAPKAPK2. In retrograde signalling, activation of CREB occurs within 20 minutes after neurotrophin stimulation of distal axons.
R-HSA-442742 CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling Ca2+ influx through the NMDA receptor activates RAS guanyl nucleotide exchange factor RasGRF, which promotes formation of active RAS:GTP complexes (Anborgh et al. 1999, Krapivinsky et al. 2003). CaMKII, also activated by NMDA receptor-mediated Ca2+ influx, can contribute to activation of RAS/RAF/MAPK signaling by phosphorylation of RAF1 (Salzano et al. 2012). ERKs (MAPK1 and MAPK3), activated downstream of RAS signaling, phosphorylate ribosomal protein S6 kinases (RSKs), initiating activation of RSKs (reviewed by Anjum and Blenis 2012). Activated RSKs phosphorylate the transcription factor CREB1 at serine residue S133, thus stimulating CREB1-mediated transcription (De Cesare et al. 1998, Harum et al. 2001, Schinelli et al. 2001, Song et al. 2003).
R-HSA-442720 CREB1 phosphorylation through the activation of Adenylate Cyclase Ca2+ influx through activated NMDA receptors in the post synaptic neurons activates adenylate cyclase-mediated signal transduction, leading to the activation of PKA and phosphorylation and activation of CREB1 induced transcription (Masada et al. 2012, Chetkovich et al. 1991, Chetkovich and Sweatt 1993
R-HSA-442729 CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde In addition to inducing long-term potentiation (LTP), NMDA receptor-mediated activation of CaMKII leads to transcriptional changes that are implicated in LTP maintenance (reviewed by Miyamoto 2006). CaMKII-gamma (CAMK2G) isoform is involved in nuclear shuttling of the calcium/calmodulin complex (CALM1:4xCa2+), which enables CaMKK-mediated activation of the nuclear calcium/calmodulin dependent kinase CaMKIV (CAMK4). Activated CaMKIV phosphorylates the transcription factor CREB1 and activates CREB1-mediated transcription (Ma et al. 2014, Cohen et al. 2018).
R-HSA-8874211 CREB3 factors activate genes Members of the CREB3 family (also known as the OASIS family) are tissue-specific proteins that each contain a transcription activation domain, a basic leucine zipper (bZIP) domain that promotes dimerization and DNA binding, and a transmembrane domain that anchors the protein to the membrane of the endoplasmic reticulum (ER) (reviewed in Asada et al. 2011, Chan et al. 2011, Kondo et al. 2011, Fox and Andrew 2015). The family includes CREB3 (LUMAN), CREB3L1 (OASIS), CREB3L2 (BBF2H7, Tisp40), CREB3L3 (CREB-H), and CREB3L4 (CREB4). Activation of the proteins occurs when they transit from the ER to the Golgi and are cleaved sequentially by the Golgi resident proteases MBTPS1 (S1P) and MBTPS2 (S2P), a process known as regulated intramembrane proteolysis that releases the cytoplasmic region of the protein containing the transcription activation domain and the bZIP domain. This protein fragment then transits from the cytosol to the nucleus where it activates transcription of target genes. CREB3L1, CREB3L2, and CREB3L3 are activated by ER stress, although the mechanisms that cause the transit of the CREB3 proteins are not fully characterized. Unlike the ATF6 factors, CREB3 proteins do not appear to interact with HSPA5 (BiP) and therefore do not appear to sense unfolded proteins by dissociation of HSPA5 when HSPA5 binds the unfolded proteins.
R-HSA-399956 CRMPs in Sema3A signaling CRMPs are a small family of plexinA-interacting cytosolic phosphoproteins identified as mediators of Sema3A signaling and neuronal differentiation. After Sema3A activation Plexin-A bound CRMP's undergo phosphorylation by Cdk5, GSK3beta and Fes kinases. Phosphorylation of CRMPs by these kinases blocks the ability of CRMP to bind to tubulin dimers, subsequently induces depolymerization of F-actin, and ultimately leads to growth cone collapse.
R-HSA-2024101 CS/DS degradation Lysosomal degradation of glycoproteins is part of the cellular homeostasis of glycosylation (Winchester 2005). The steps outlined below describe the degradation of chondroitin sulfate and dermatan sulfate. Complete degradation of glycoproteins is required to avoid build up of glycosaminoglycan fragments which can cause lysosomal storage diseases. Complete degradation steps are not shown as they are repetitions of the main ones described here. The proteolysis of the core protein of the glycoprotein is not shown here.
R-HSA-389513 CTLA4 inhibitory signaling CTLA4 is one of the best studied inhibitory receptors of the CD28 superfamily. CTLA4 inhibits T cell activation by reducing IL2 production and IL2 expression, and by arresting T cells at the G1 phase of the cell cycle. CTLA-4 expressed by a T cell subpopulation exerts a dominant control on the proliferation of other T cells, which limits autoreactivity. CTLA4 also blocks CD28 signals by competing for the ligands B71 and B72 in the limited space between T cells and antigenpresenting cells. Though the mechanism is obscure, CTLA4 may also propagate inhibitory signals that actively counter those produced by CD28. CTLA4 can also function in a ligand-independent manner.
CTLA-4 regulates the activation of pathogenic T cells by directly modulating T cell receptor signaling (i.e. TCR-zeta chain phosphorylation) as well as downstream biochemical signals (i.e. ERK activation). The cytoplasmic region of CTLA4 contains a tyrosine motif YVKM and a proline rich region. After TCR stimulation, it undergoes tyrosine phosphorylation by src kinases, inducing surface retention.
R-HSA-5358747 CTNNB1 S33 mutants aren't phosphorylated S33 mutations of beta-catenin interfere with GSK3 phosphorylation and result in stabilization and nuclear localization of the protein and enhanced WNT signaling (Groen et al, 2008; Nhieu et al, 1999; Clements et al, 2002; reviewed in Polakis, 2000). S33 mutations have been identified in cancers of the central nervous system, liver, endometrium and stomach, among others (reviewed in Polakis, 2000).
R-HSA-5358749 CTNNB1 S37 mutants aren't phosphorylated S37 mutations of beta-catenin interfere with GSK3 phosphorylation and stabilize the protein, resulting in enhanced WNT pathway signaling (Nhieu et al, 1999; Clements et al, 2002; reviewed in Polakis, 2000). S37 mutations have been identified in cancers of the brain, liver, ovary and large intestine, among others (reviewed in Polakis, 2000).
R-HSA-5358751 CTNNB1 S45 mutants aren't phosphorylated S45 mutants of beta-catenin have been identified in colorectal and hepatocellular carcinomas, soft tissue cancer and Wilms Tumors, among others (reviewed in Polakis, 2000). These mutations abolish the CK1alpha phosphorylation site of beta-catenin which acts as a critical priming site for GSK3 phosphorylation of T41( and subsequently S37 and S33) thus preventing its ubiquitin-mediated degradation (Morin et al, 1997; Amit et al, 2002).
R-HSA-5358752 CTNNB1 T41 mutants aren't phosphorylated T41 mutations of beta-catenin interfere with GSK3 phosphorylation and result in stabilization and nuclear accumulation of the protein (Moreno-Bueno et al, 2002; Taniguchi et al, 2002; reviewed in Polakis, 2012). T41 mutations have been identified in cancers of the liver and brain, as well as in the pituitary, endometrium, large intestine and skin, among others (reviewed in Polakis, 2000; Saito-Diaz et al, 2013).
R-HSA-211999 CYP2E1 reactions CYP2E1 can metabolize and activate a large number of solvents and industrial monomers as well as drugs. This quality of CYP2E1 may make it an important determinant of human susceptibility to the toxic effects of industrial and environmental chemicals. Typical CYP2E1 substrates include acetaminophen, benzene, CCl4, halothane, ethanol and vinyl chloride. CYP2E1 contributes to oxidative stress by producing oxidising species called reactive oxygen species (ROS) which can lead to damage to mitochondria, DNA and initiate lipid peroxidation or even cell death.
R-HSA-111996 Ca-dependent events Calcium, as the ion Ca2+, is essential in many biological processes. The majority of Ca2+ in many organisms is bound to phosphates which form skeletal structures and also buffer Ca2+ levels in extracellular fluids (typically 1 millimolar). Intracellular free Ca2+, by contrast, is 10,000 times lower than the outside of the cell (typically 10 micromolar). This concentration gradient is used to import Ca2+ into cells where it acts as a second messenger.
R-HSA-1296052 Ca2+ activated K+ channels Ca2+ activated potassium channels are expressed in neuronal and non-neuronal tissue such as smooth muscle, epithelial cell and sensory cells. Ca2+ activated potassium channels are activated when the Ca2+ ion concentration increased, The efflux of K+ via these channels leads to repolarization/hyperpolarization of the membrane potential which limits the Ca2+ influx though voltage activated Ca2+ channels (VGCC) thereby regulating the influx of Ca2+ flow via VGCC.
R-HSA-4086398 Ca2+ pathway A number of so called non-canonical WNT ligands have been shown to promote intracellular calcium release upon FZD binding. This beta-catenin-independent WNT pathway acts through heterotrimeric G proteins and promotes calcium release through phophoinositol signaling and activation of phosphodiesterase (PDE). Downstream effectors include the calcium/calmodulin-dependent kinase II (CaMK2) and PKC (reviewed in De, 2011). The WNT Ca2+ pathway is important in dorsoventral polarity, convergent extension and organ formation in vertebrates and also has roles in negatively regulating 'canonical' beta-catenin-dependent transcription. Non-canonical WNT Ca2+ signaling is also implicated in inflammatory response and cancer (reviewed in Kohn and Moon, 2005; Sugimura and Li, 2010).
R-HSA-111997 CaM pathway Calmodulin (CaM) is a small acidic protein that contains four EF-hand motifs, each of which can bind a calcium ion, therefore it can bind up to four calcium ions. The protein has two approximately symmetrical domains, separated by a flexible hinge region. Calmodulin is the prototypical example of the EF-hand family of Ca2+-sensing proteins. Changes in intracellular Ca2+ concentration regulate calmodulin in three distinct ways. First, by directing its subcellular distribution. Second, by promoting association with different target proteins. Third, by directing a variety of conformational states in calmodulin that result in target-specific activation. Calmodulin binds and activates several effector protein (e.g. the CaM-dependent adenylyl cyclases, phosphodiesterases, protein kinases and the protein phosphatase calcineurin).
R-HSA-111932 CaMK IV-mediated phosphorylation of CREB The Ca2+-calmodulin-dependent protein kinase (CaM kinase) cascade includes three kinases: CaM-kinase kinase (CaMKK); and the CaM kinases CaMKI and CaMKIV, which are phosphorylated and activated by CaMKK. Members of this cascade respond to elevation of intracellular Ca2+ levels. CaMKK and CaMKIV localize both to the nucleus and to the cytoplasm, whereas CaMKI is only cytosolic. Nuclear CaMKIV regulates transcription through phosphorylation of several transcription factors, including CREB. In the cytoplasm, there is extensive cross-talk between CaMKK, CaMKIV and other signaling cascades, including those that involve the cAMP-dependent kinase (PKA), MAP kinases and protein kinase B (PKB/Akt).
R-HSA-2025928 Calcineurin activates NFAT Signaling by the B cell receptor and the T cell receptor stimulate transcription by NFAT factors via calcium (reviewed in Gwack et al. 2007). Cytosolic calcium from intracellular stores and extracellular sources binds calmodulin and activates the protein phosphatase calcineurin. Activated calcineurin dephosphorylates NFATs in the cytosol, exposing nuclear localization sequences on the NFATs and causing the NFATs to be imported into the nucleus where they regulate transcription of target genes in complexes with other transcription factors such as AP-1 and JUN. Calcineurin in the target of the immunosuppressive drugs cyclosporin A and FK-506 (reviewed in Lee and Park 2006).
R-HSA-419812 Calcitonin-like ligand receptors The calcitonin peptide family comprises calcitonin, amylin, calcitonin gene-related peptide (CGRP), adrenomedullin (AM) and intermedin (AM2). Calcitonin is a 32 amino acid peptide, involved in bone homeostasis (Sexton PM et al, 1999). Amylin is a product of the islet beta-cell (Cooper GJ et al, 1987), along with insulin and probably has a hormonal role in the regulation of nutrient intake (Young A and Denaro M, 1998). Adrenomedullin (AM) is a ubiquitously expressed peptide initially isolated from phaechromocytoma (a tumour of the adrenal medulla) (Kitamura K et al, 1993). Both AM and AM2 (Takei Y et al, 2004) belong to a family of calcitonin-related peptide hormones important for regulating diverse physiologic functions and the chemical composition of fluids and tissues.
The receptor family for these peptides consists of two class B GPCRs, the calcitonin receptor (CT) and calcitonin receptor-like receptor (CL) (Poyner DR er al, 2002). Whilst the receptor for calcitonin is a conventional class B GPCR, the receptors for CGRP, AM and amylin require additional proteins, called the receptor activity modifying proteins (RAMPs). There are three RAMPs in mammals; they interact with the CT receptor to convert it to receptors for amylin. For CGRP and AM, the related CL interacts with RAMP1 to give a CGRP receptor and RAMP2 or 3 to give AM receptors. CL by itself will bind no known endogenous ligand.
R-HSA-111933 Calmodulin induced events One important physiological role for Calmodulin is the regulation of adenylylcyclases. Four of the nine known adenylylcyclases are calcium sensitive, in particular type 8 (AC8).
R-HSA-901042 Calnexin/calreticulin cycle The unfolded protein is recognized by a chaperon protein (calnexin or calreticulin) and the folding process starts. The binding of these protein requires a mono-glucosylated glycan (Caramelo JJ and Parodi AJ, 2008) and lectin-based interaction with client proteins is the predominant contributor to chaperone activity of calreticulin (inferred from the mouse homolog in Lum et al. 2016).
R-HSA-111957 Cam-PDE 1 activation Human Ca2+/calmodulin-dependent phosphodiesterase PDE1 is activated by the binding of calmodulin in the presence of Ca(2+). PDE1 has three subtypes PDE1A, PDE1B and PDE1C and their role is to hydrolyze both cGMP and cAMP. Their role is to antagonize the increased concentration of the intracellular second messengers determined by the synthetic activity of the adenylate cyclase enzymes thus governing intracellular cAMP dynamics in response to changes in the cytosolic Ca2+ concentration. PDE1 are mainly cytosolic but different isoforms are expressed in different tissues.
R-HSA-72737 Cap-dependent Translation Initiation Translation initiation is a complex process in which the Met-tRNAi initiator, 40S, and 60S ribosomal subunits are assembled by eukaryotic initiation factors (eIFs) into an 80S ribosome at the start codon of an mRNA. The basic mechanism for this process can be described as a series of five steps: 1) formation of a pool of free 40S subunits, 2) formation of the ternary complex (Met-tRNAi/eIF2/GTP), and subsequently, the 43S complex (comprising the 40S subunit, Met-tRNAi/eIF2/GTP, eIF3 and eIF1A), 3) activation of the mRNA upon binding of the cap-binding complex eIF4F, and factors eIF4A, eIF4B and eIF4H, with subsequent binding to the 43S complex, 4) ribosomal scanning and start codon recognition, and 5) GTP hydrolysis and joining of the 60S ribosomal subunit.
R-HSA-8955332 Carboxyterminal post-translational modifications of tubulin Tubulins fold into compact globular domains with less structured carboxyterminal tails. These tails vary in sequence between tubulin isoforms and are exposed on the surfaces of microtubules. They can undergo a variety of posttranslational modifications, including the attachment and removal of polyglutamate chains and in the case of alpha-tunulins the loss and reattachment of a terminal tyrosine (Tyr) residue. These modifications are associated with changes in the rigidity and stability of microtubules (Song & Brady 2015; Yu et al. 2015).
Mutations affecting these modification processes can have severe effects on phenotype (e.g., Ikegami et al. 2007). Nevertheless, the precise molecular mechanisms by which these changes in tubulin structure modulate its functions remain unclear, so these modification processes are simply annotated here as a series of chemical transformations of tubulins.
R-HSA-5576891 Cardiac conduction The normal sequence of contraction of atria and ventricles of the heart require activation of groups of cardiac cells. The mechanism must elicit rapid changes in heart rate and respond to changes in autonomic tone. The cardiac action potential controls these functions. Action potentials are generated by the movement of ions through transmembrane ion channels in cardiac cells. Like skeletal myocytes (and axons), in the resting state, a given cardiac myocyte has a negative membrane potential. In both muscle types, after a delay (the absolute refractory period), K+ channels reopen and the resulting flow of K+ out of the cell causes repolarisation. The voltage-gated Ca2+ channels on the cardiac sarcolemma membrane are generally triggered by an influx of Na+ during phase 0 of the action potential. Cardiac muscle cells are so tightly bound that when one of these cells is excited the action potential spreads to all of them. The standard model used to understand the cardiac action potential is the action potential of the ventricular myocyte (Park & Fishman 2011, Grant 2009).
The action potential has 5 phases (numbered 0-4). Phase 4 describes the membrane potential when a cell is not being stimulated. The normal resting potential in the ventricular myocardium is between -85 to -95 mV. The K+ gradient across the cell membrane is the key determinant in the normal resting potential. Phase 0 is the rapid depolarisation phase in which electrical stimulation of a cell opens the closed, fast Na+ channels, causing a large influx of Na+ creating a Na+ current (INa+). This causes depolarisation of the cell. The slope of phase 0 represents the maximum rate of potential change and differs in contractile and pacemaker cells. Phase 1 is the inactivation of the fast Na+ channels. The transient net outward current causing the small downward deflection (the "notch" of the action potetial) is due to the movement of K+ and Cl- ions. In pacemaker cells, this phase is due to rapid K+ efflux and closure of L-type Ca2+ channels. Phase 2 is the plateau phase which is sustained by a balance of Ca2+ influx and K+ efflux. This phase sustains muscle contraction. Phase 3 of the action potential is where a concerted action of two outward delayed currents brings about repolarisation back down to the resting potential (Bartos et al. 2015).
R-HSA-9733709 Cardiogenesis Gradients of Bone Morphogenetic Protein (BMP), Wingless-related integration site (WNT), and NODAL promote the formation of cardiac progenitors anteriolateral to the primitive streak during gastrulation (reviewed in Munoz-Chapuli and Perez-Pomares 2010, Cui et al. 2018, Prummel et al. 2020, Witman et al. 2019, Miyamoto e al. 2021). Eomesodermin (EOMES) and TBXT (T, Brachyury) expressed in the cardiac mesoderm activate expression of MESP1, a master regulator of cardiogenesis and the first observed marker of cardiac progenitors. MESP1-expressing cells migrate anteriorly towards the midline to form the cardiac crescent posterior to the head folds at about 2 weeks of gestation in humans (E7.5 in mice).
Within the cardiac crescent, two populations of cells can be identified based on gene expression and timing of contribution to the developing heart: the first heart field (FHF) forms the initial heart tube and contributes to the systemic ventricle (the left ventricle in crocodilians, birds, and mammals), the septum, and, to a lesser extent, the atria; the second heart field (SHF) extends the poles of the heart and contributes to the atria, the outflow tract, the septum, and the right ventricle, which is responsible for pulmonary circulation and distinguishes crocodilians, birds, and mammals (reviewed in Meilhac and Buckingham 2018).
At about 3 weeks gestation in humans (E8 in mice), FHF cells migrate axially to the midline and fuse to form the heart tube. Elongation of the heart tube leads to rightward looping and eventual formation of atria and ventricles (reviewed in Desgrange et al. 2018). FHF cells do not proliferate as much as SHF cells and mostly differentiate into cardiomyocytes due to the actions of myocardial differentiation factors such as NKX2-5, GATA4, TBX5, and HAND1. SHF cells are initially located in the posterior region of the cardiac crescent then, during formation of the heart tube, become located at the arterial and venous poles of the heart tube. SHF cells proliferate more than FHF cells and can differentiate to form cardiomyocytes, endothelial cells, smooth muscle cells, and fibroblasts. A reservoir of SHF progenitors located at the core of the pharyngeal mesoderm continuously contributes to the developing heart. Proliferating SHF cells express FGF8 and FGF10 driven by ISL1 and TBX1.
Cardiac progenitors are regulated by a distinct set of transcription factors and mutations in these factors and other factors involved in gene expression are responsible for congenital heart defects (reviewed in Diab et al. 2021, Houyel and Meilhac 2021, Kodo et al. 2021, Miyamoto et al. 2021, Lescroart and Zaffran 2022, Wang et al. 2022). Additionally, combinations of these transcription factors are now being used to reprogram fibroblasts and other cell types into cardiomyocytes for repairing damaged hearts (reviewed in Adams et al. 2021, Garry et al. 2021, Kim et al. 2022, Thomas et al. 2022, Zhu et al. 2022). TBXT (T, Brachyury) is expressed early in developing mesoderm and is activated by WNT signaling, which maintains proliferation and is subsequently downregulated during differentiation. Activation of MESP1 expression by TBXT and EOMES occurs early in gastrulation. MESP1 is expressed in both the FHF and the SHF. MESP1, in turn, directly activates two key regulators of cardiac development: GATA4 and NKX2-5 (NKX2.5, the ortholog of Tinman in Drosophila). Bone Morphogenetic Protein (BMP) signaling originating from BMPs secreted by underlying endoderm also enhances expression of GATA4 and NKX2-5, apparently through binding of SMAD proteins to the promoters of GATA4 and NKX2-5. GATA4 and NKX2-5 proteins, in turn, regulate each other's expression and directly interact to regulate downstream target genes. NKX2-5 directly activates GATA6 throughout the cardiac mesoderm.
The FHF is characterized by expression of TBX5 and HCN4; the SHF is characterized by transient expression of TBX1, ISL1, FGF8, FGF10, and SIX2. In the FHF, NKX2-5 binds the promoter of the TBX5 gene and activates transcription. TBX5, in turn, directly activates expression of SRF. TBX5 protein interacts directly with NKX2-5 and GATA4 proteins to activate further downstream targets. Sonic hedgehog (SHH) from the pharyngeal endoderm and WNT signaling maintain proliferation of SHF cells, In the SHF, TBX1, GATA4 and LEF1:CTNN1 (LEF1:Beta-catenin from Wnt signaling) directly activate ISL1, characteristic of SHF cells, and ISL1 then activates expression of HAND2 (dHAND), also characteristic of SHF cells.
R-HSA-5694530 Cargo concentration in the ER Computational analysis suggests that ~25% of the proteome may be exported from the ER in human cells (Kanapin et al, 2003). These cargo need to be recognized and concentrated into COPII vesicles, which range in size from 60-90 nm, and which move cargo from the ER to the ERGIC in mammalian cells (reviewed in Lord et al, 2013; Szul and Sztul, 2011). Recognition of transmembrane cargo is mediated by interaction with one of the 4 isoforms of SEC24, a component of the inner COPII coat (Miller et al, 2002; Miller et al, 2003; Mossessova et al, 2003; Mancias and Goldberg, 2008). Soluble cargo in the ER lumen is concentrated into COPII vesicles through interaction with a receptor of the ERGIC-53 family, the p24 family or the ERV family. Each of these families of transmembrane receptors interact with cargo through their lumenal domains and with components of the COPII coat with their cytoplasmic domains and are packaged into the COPII vesicle along with the cargo. The receptors are subsequently recycled to the ER in COPI vesicles through retrograde traffic (reviewed in Dancourt and Barlowe, 2010). Packaging of large cargo such as fibrillar collagen depends on the transmembrane accessory factors MIA3 (also known as TANGO1) and CTAGE5. Like the ERGIC, p24 and ERV cargo receptors, MIA3 and MIA2 (also known as CTAGE5) interact both with the collagen cargo and with components of the COPII coat. Unlike the other cargo receptors, however, MIA3 and MIA2 are not loaded into the vesicle but remain in the ER membrane (reviewed in Malhotra and Erlmann, 2011; Malhotra et al, 2015).
R-HSA-8856825 Cargo recognition for clathrin-mediated endocytosis Recruitment of plasma membrane-localized cargo into clathrin-coated endocytic vesicles is mediated by interaction with a variety of clathrin-interacting proteins collectively called CLASPs (clathrin-associated sorting proteins). CLASP proteins, which may be monomeric or tetrameric, are recruited to the plasma membrane through interaction with phosphoinsitides and recognize linear or conformational sequences or post-translational modifications in the cytoplasmic tails of the cargo protein. Through bivalent interactions with clathrin and/or other CLASP proteins, they bridge the recruitment of the cargo to the emerging clathrin coated pit (reviewed in Traub and Bonifacino, 2013). The tetrameric AP-2 complex, first identified in early studies of clathrin-mediated endocytosis, was at one time thought to be the primary CLASP protein involved in cargo recognition at the plasma membrane, and indeed plays a key role in the endocytosis of cargo carrying dileucine- or tyrosine-based motifs.
A number of studies have been performed to test whether AP-2 is essential for all forms of clathrin-mediated endocytosis (Keyel et al, 2006; Motely et al, 2003; Huang et al, 2004; Boucrot et al, 2010; Henne et al, 2010; Johannessen et al, 2006; Gu et al, 2013; reviewed in Traub, 2009; McMahon and Boucrot, 2011). Although depletion of AP-2 differentially affects the endocytosis of different cargo, extensive depletion of AP-2 through RNAi reduces clathrin-coated pit formation by 80-90%, and the CCPs that do form still contain AP-2, highlighting the critcical role of this complex in CME (Johannessen et al, 2006; Boucrot et al, 2010; Henne et al, 2010).
In addition to AP-2, a wide range of other CLASPs including proteins of the beta-arrestin, stonin and epsin families, engage sorting motifs in other cargo and interact either with clathrin, AP-2 or each other to facilitate assembly of a clathin-coated pit (reviewed in Traub and Bonifacino, 2013).
R-HSA-5620920 Cargo trafficking to the periciliary membrane Proteomic studies suggest that the cilium is home to approximately a thousand proteins, and has a unique protein and lipid make up relative to the bulk cytoplasm and plasma membrane (Pazour et al, 2005; Ishikawa et al, 2012; Ostrowoski et al, 2002; reviewed in Emmer et al, 2010; Rohatgi and Snell, 2010). In addition, the cilium is a dynamic structure, and the axoneme is continually being remodeled by addition and removal of tubulin at the distal tip (Marshall and Rosenbaum, 2001; Stephens, 1997; Song et al, 2001). As a result, the function and structure of this organelle relies on the directed trafficking of protein and vesicles to the cilium. Small GTPases of the RAS, RAB, ARF and ARL families are involved in cytoskeletal organization and membrane traffic and are required to regulate the traffic from the Golgi and the trans-Golgi network to the cilium (reviewed in Deretic, 2013; Li et al, 2012). ARF4 is a Golgi-resident GTPase that acts in conjunction with a ciliary-targeting complex consisting of the ARF-GAP ASAP1, RAB11A, the RAB11 effector FIP3 and the RAB8A guanine nucleotide exchange factor RAB3IP/RABIN8 to target cargo bearing a putative C-terminal VxPx targeting motif to the cilium. A well-studied example of this system involves the trafficking of rhodopsin to the retinal rod photoreceptors, a specialized form of the cilium (reviewed in Deretic, 2013). ARL3, ARL13B and ARL6 are all small ARF-like GTPases with assorted roles in ciliary trafficking and maintenance. Studies in C. elegans suggest that ARL3 and ARL13B have opposing roles in maintaining the stability of the anterograde IFT trains in the cilium (Li et al, 2010). In addition, both ARL3 and ARL13B have roles in facilitating the traffic of subsets of ciliary cargo to the cilium. Myristoylated cargo such as peripheral membrane protein Nephrocystin-3 (NPHP3) is targeted to the cilium in a UNC119- and ARL3-dependent manner, while ARL13B is required for the PDE6-dependent ciliary localization of INPP5E (Wright et al, 2011; Humbert et al, 2012; reviewed in Li et al, 2012). ARL6 was also identified as BBS3, a gene that when mutated gives rise to the ciliopathy Bardet-Biedl syndrome (BBS). ARL6 acts upstream of a complex of 8 other BBS-associated proteins known as the BBSome. ARL6 and the BBSome are required for the ciliary targeting of proteins including the melanin concentrating hormone receptor (MCHR) and the somatostatin receptor (SSTR3), among others (Nachury et al, 2007; Loktev et al, 2008; Jin et al, 2010; Zhang et al, 2011). Both the BBSome and ARL6 may continue to be associated with cargo inside the cilium, as they are observed to undergo typical IFT movements along the axoneme (Fan et al, 2004; Lechtreck et al, 2009; reviewed in Li et al, 2012).
R-HSA-200425 Carnitine shuttle The mitochondrial carnitine system catalyzes the transport of long-chain fatty acids into the mitochondrial matrix where they undergo beta oxidation. This transport system consists of the malonyl-CoA sensitive carnitine palmitoyltransferase I (CPT-I) localized in the mitochondrial outer membrane, the carnitine:acylcarnitine translocase, an integral inner membrane protein, and carnitine palmitoyltransferase II localized on the matrix side of the inner membrane. (Kerner & Hoppel, 2000; Ramsay et al. 2001). Additional reactions annotated here enable the uptake of carnitine and the regulation of fatty acid biosynthesis at the level of ACACA and ACACB to minimize simultaeous mitochondrial catabolism and cytosolic biosynthesis of long-chain fatty acids.
R-HSA-71262 Carnitine synthesis Carnitine is required for the shuttling of fatty acids into the mitochondrial matrix and its deficiency is associated with metabolic diseases. It is abundant in a typical Western diet but can also be synthesized in four steps from trimethyllysine (generated in turn by the S-adenosyl-methionine-mediated methylation of lysine residues in proteins, followed by protein hydrolysis). The enzymes that catalyze the first three steps of carnitine synthesis, converting trimethyllysine to gamma-butyrobetaine, are widely distributed in human tissues. The enzyme that catalyzes the last reaction, converting gamma-butyrobetaine to carnitine, is found only in liver and kidney cells, and at very low levels in brain tissues. Other tissues that require carnitine, such as muscle, are dependent on transport systems that mediate its export from the liver and uptake by other tissues (Bremer 1983; Kerner & Hoppel 1998; Rebouche & Engel 1980; Vaz & Wanders 2002).
R-HSA-140534 Caspase activation via Death Receptors in the presence of ligand Caspase-8 is synthesized as zymogen (procaspase-8) and is formed from procaspase-8 as a cleavage product. However, the cleavage itself appears not to be sufficient for the formation of an active caspase-8. Only the coordinated dimerization and cleavage of the zymogen produce efficient activation in vitro and apoptosis in cellular systems [Boatright KM and Salvesen GS 2003; Keller N et al 2010; Oberst A et al 2010].
The caspase-8 zymogens are present in the cells as inactive monomers, which are recruited to the death-inducing signaling complex (DISC) by homophilic interactions with the DED domain of FADD. The monomeric zymogens undergo dimerization and the subsequent conformational changes at the receptor complex, which results in the formation of catalytically active form of procaspase-8.[Boatright KM et al 2003; Donepudi M et al 2003; Keller N et al 2010; Oberst A et al 2010]. R-HSA-418889 Caspase activation via Dependence Receptors in the absence of ligand In the presence of Netrin1, DCC and UNC5 generate attractive and repulsive signals to growing axons. In the absence of Netrin-1, DCC induces cell death signaling initiated via caspase cleavage of DCC and the interaction of caspase-9. Recent reports have shown that UNC5 receptors similarly induce apoptosis in the absence of Netrin-1. These reactions proceed without a requirement for cytochrome c release from mitochondria or interaction with apoptotic protease activating factor 1 (APAF1). DCC thus regulates an apoptosome-independent pathway for caspase activation. DCC and UNC-5 are hence defined as dependence receptors. Dependence receptors exhibit dual functions depending on the availability of ligand. They create cellular states of dependence on their respective ligands by either inducing apoptosis when unoccupied by the ligand, or inhibiting apoptosis in the presence of the ligand. R-HSA-5357769 Caspase activation via extrinsic apoptotic signalling pathway Caspases, a family of cysteine proteases, execute apoptotic cell death. Caspases exist as inactive zymogens in cells and undergo a cascade of catalytic activation at the onset of apoptosis. Initiation of apoptosis occurs through either a cell-intrinsic or cell-extrinsic pathway. Extrinsic pathway cell death signals originate at the plasma membrane where:
A family of protein serine/threonine kinases known as the cyclin-dependent kinases (CDKs) controls progression through the cell cycle. As the name suggests, the activity of the catalytic subunit is dependent on binding to a cyclin partner. The human genome encodes several cyclins and several CDKs, with their names largely derived from the order in which they were identified. The oscillation of cyclin abundance is one important mechanism by which these enzymes phosphorylate key substrates to promote events at the relevant time and place. Additional post-translational modifications and interactions with regulatory proteins ensure that CDK activity is precisely regulated, frequently confined to a narrow window of activity.
In addition, genome integrity in the cell cycle is maintained by the action of a number of signal transduction pathways, known as cell cycle checkpoints, which monitor the accuracy and completeness of DNA replication during S phase and the orderly chromosomal condensation, pairing and partition into daughter cells during mitosis.
Replication of telomeric DNA at the ends of human chromosomes and packaging of their centromeres into chromatin are two aspects of chromosome maintenance that are integral parts of the cell cycle.
Meiosis is the specialized form of cell division that generates haploid gametes from diploid germ cells, associated with recombination (exchange of genetic material between chromosomal homologs). R-HSA-69620 Cell Cycle Checkpoints A hallmark of the human cell cycle in normal somatic cells is its precision. This remarkable fidelity is achieved by a number of signal transduction pathways, known as checkpoints, which monitor cell cycle progression ensuring an interdependency of S-phase and mitosis, the integrity of the genome and the fidelity of chromosome segregation.
Checkpoints are layers of control that act to delay CDK activation when defects in the division program occur. As the CDKs functioning at different points in the cell cycle are regulated by different means, the various checkpoints differ in the biochemical mechanisms by which they elicit their effect. However, all checkpoints share a common hierarchy of a sensor, signal transducers, and effectors that interact with the CDKs.
The stability of the genome in somatic cells contrasts to the almost universal genomic instability of tumor cells. There are a number of documented genetic lesions in checkpoint genes, or in cell cycle genes themselves, which result either directly in cancer or in a predisposition to certain cancer types. Indeed, restraint over cell cycle progression and failure to monitor genome integrity are likely prerequisites for the molecular evolution required for the development of a tumor. Perhaps most notable amongst these is the p53 tumor suppressor gene, which is mutated in >50% of human tumors. Thus, the importance of the checkpoint pathways to human biology is clear. R-HSA-69278 Cell Cycle, Mitotic The events of replication of the genome and the subsequent segregation of chromosomes into daughter cells make up the cell cycle. DNA replication is carried out during a discrete temporal period known as the S (synthesis)-phase, and chromosome segregation occurs during a massive reorganization of cellular architecture at mitosis. Two gap-phases separate these cell cycle events: G1 between mitosis and S-phase, and G2 between S-phase and mitosis. Cells can exit the cell cycle for a period and enter a quiescent state known as G0, or terminally differentiate into cells that will not divide again, but undergo morphological development to carry out the wide variety of specialized functions of individual tissues.
A family of protein serine/threonine kinases known as the cyclin-dependent kinases (CDKs) controls progression through the cell cycle. As the name suggests, the kinase activity of the catalytic subunits is dependent on binding to cyclin partners, and control of cyclin abundance is one of several mechanisms by which CDK activity is regulated throughout the cell cycle.
A complex network of regulatory processes determines whether a quiescent cell (in G0 or early G1) will leave this state and initiate the processes to replicate its chromosomal DNA and divide. This regulation, during the Mitotic G1-G1/S phases of the cell cycle, centers on transcriptional regulation by the DREAM complex, with major roles for D and E type cyclin proteins.
Chromosomal DNA synthesis occurs in the S phase, or the synthesis phase, of the cell cycle. The cell duplicates its hereditary material, and two copies of each chromosome are formed. A key aspect of the regulation of DNA replication is the assembly and modification of a pre-replication complex assembled on ORC proteins.
Mitotic G2-G2/M phases encompass the interval between the completion of DNA synthesis and the beginning of mitosis. During G2, the cytoplasmic content of the cell increases. At G2/M transition, duplicated centrosomes mature and separate and CDK1:cyclin B complexes become active, setting the stage for spindle assembly and chromosome condensation at the start of mitotic M phase. Mitosis, or M phase, results in the generation of two daughter cells each with a complete diploid set of chromosomes. Events of the M/G1 transition, progression out of mitosis and division of the cell into two daughters (cytokinesis) are regulated by the Anaphase Promoting Complex.
The Anaphase Promoting Complex or Cyclosome (APC/C) plays additional roles in regulation of the mitotic cell cycle, insuring the appropriate length of the G1 phase. The APC/C itself is regulated by phosphorylation and interactions with checkpoint proteins. R-HSA-204998 Cell death signalling via NRAGE, NRIF and NADE p75NTR is a key regulator of neuronal apoptosis, both during development and after injury. Apoptosis is triggered by binding of either mature neurotrophin or proneurotrophin (proNGF, proBDNF). ProNGF is at least 10 times more potent than mature NGF in inducing apoptosis. TRKA signalling protects neurons from apoptosis. The molecular mechanisms involved in p75NTR-apoptosis are not well understood. The death signalling requires activation of c-JUN N-terminal Kinase (JNK), as well as transcriptional events. JNK activation appears to involve the receptor interacting proteins TRAF6, NRAGE, and Rac. The transcription events are thought to be regulated by another p75-interacting protein, NRIF. Two other p75-interacting proteins, NADE and Necdin, have been implicated in apoptosis, but their role is less clear. R-HSA-446728 Cell junction organization Cell junction organization in Reactome currently covers aspects of cell-cell junction organization, cell-extracellular matrix interactions, and Type I hemidesmosome assembly. R-HSA-9664424 Cell recruitment (pro-inflammatory response) Migration of immune cells is orchestrated by a fine balance of cytokine and chemokine responses. During Leishmania macrophage interaction, either pro inflammatory or anti-inflammatory cytokines are produced, having an impact in the establishment of infection and further clinical outcome (Navas et al. 2014). Toll like receptors, GPCRs such as the purinergic receptors P2YRs, complement receptor 3A and interleukin receptor 15 amongst others, have been associated with the production of pro inflammatory cytokines (Lai and Gallo 2012 & Cekic et al. 2016). A strong pro inflammatory response in the acute phase of the infection helps to control the parasite load when the recruited cells enhance microbiocidal mechanisms. However, alterations in the chemokine network may contribute to uncontrolled immune responses that can modulate parasite survival and promote or mitigate the associated immunopathology, thereby influencing the outcome of infection (Navas et al. 2014). R-HSA-1222541 Cell redox homeostasis The most important response of Mtb to oxidative stress is provided by catalase and peroxiredoxins, both of which get their reducing equivalents through a network of disulfide proteins and, finally, from NAD(P)H. Multiple redundancies make choosing a good drug target difficult (Koul et al. 2011). Optimum efficacy can only be expected from inhibitors of the most upstream components of the redox cascades, i.e. the NAD(P)H-dependent reductases TrxB and Lpd (Jaeger & Flohe 2006). R-HSA-202733 Cell surface interactions at the vascular wall Leukocyte extravasation is a rigorously controlled process that guides white cell movement from the vascular lumen to sites of tissue inflammation. The powerful adhesive interactions that are required for leukocytes to withstand local flow at the vessel wall is a multistep process mediated by different adhesion molecules. Platelets adhered to injured vessel walls form strong adhesive substrates for leukocytes. For instance, the initial tethering and rolling of leukocytes over the site of injury are mediated by reversible binding of selectins to their cognate cell-surface glycoconjugates.
Endothelial cells are tightly connected through various proteins, which regulate the organization of the junctional complex and bind to cytoskeletal proteins or cytoplasmic interaction partners that allow the transfer of intracellular signals. An important role for these junctional proteins in governing the transendothelial migration of leukocytes under normal or inflammatory conditions has been established.
This pathway describes some of the key interactions that assist in the process of platelet and leukocyte interaction with the endothelium, in response to injury. R-HSA-1500931 Cell-Cell communication Cell-to-Cell communication is crucial for multicellular organisms because it allows organisms to coordinate the activity of their cells. Some cell-to-cell communication requires direct cell-cell contacts mediated by receptors on their cell surfaces. Members of the immunoglobulin superfamily (IgSF) proteins are some of the cell surface receptors involved in cell-cell recognition, communication and many aspects of the axon guidance and synapse formation-the crucial processes during embryonal development (Rougon & Hobert 2003).
Processes annotated here as aspects of cell junction organization mediate the formation and maintenance of adherens junctions, tight junctions, and gap junctions, as well as aspects of cellular interactions with extracellular matrix and hemidesmosome assembly. Nephrin protein family interactions are central to the formation of the slit diaphragm, a modified adherens junction. Interactions among members of the signal regulatory protein family are important for the regulation of migration and phagocytosis by myeloid cells.
R-HSA-421270 Cell-cell junction organization Epithelial cell-cell contacts consist of three major adhesion systems: adherens junctions (AJs), tight junctions (TJs), and desmosomes. These adhesion systems differ in their function and composition. AJs play a critical role in initiating cell-cell contacts and promoting the maturation and maintenance of the contacts (reviewed in Ebnet, 2008; Hartsock and Nelson, 2008). TJs form physical barriers in various tissues and regulate paracellular transport of water, ions, and small water soluble molecules (reviewed in Rudini and Dejana, 2008; Ebnet, 2008; Aijaz et al., 2006; Furuse and Tsukit, 2006). Desmosomes mediate strong cell adhesion linking the intermediate filament cytoskeletons between cells and playing roles in wound repair, tissue morphogenesis, and cell signaling (reviewed in Holthofer et al., 2007).
R-HSA-446353 Cell-extracellular matrix interactions Cell-extracellular matrix (ECM) interactions play a critical role in regulating a variety of cellular processes in multicellular organisms including motility, shape change, survival, proliferation and differentiation. Cell-ECM contact is mediated by transmembrane cell adhesion receptors, such as integrins, that interact with extracellular matrix proteins as well as a number of cytoplasmic adaptor proteins. Many of these adaptor proteins physically interact with the actin cytoskeleton or function in signal transduction.
Several protein complexes interact with the cytoplasmic tail of integrins and function in transducing bi-directional signals between the ECM and intracellular signaling pathways (reviewed in Sepulveda et al., 2005).
Early events that are triggered by interactions with ECM, such as formation/turnover of Focal Adhesions, regulation of actin dynamics and protrusion of lamellipodia to promote cellular spreading and motility are modulated by PINCH- ILK- parvin complexes (see Sepulveda et al., 2005). A number of partners of the PINCH-ILK-parvin complex components have been identified that regulate and/or mediate the functions of these complexes (reviewed in Wu, 2004). Interactions with some of these partners modulate cytoskeletal remodeling and cell spreading.
R-HSA-2559583 Cellular Senescence Cellular senescence involves irreversible growth arrest accompanied by phenotypic changes such as enlarged morphology, reorganization of chromatin through formation of senescence-associated heterochromatic foci (SAHF), and changes in gene expression that result in secretion of a number of proteins that alter local tissue environment, known as senescence-associated secretory phenotype (SASP).
Senescence is considered to be a cancer protective mechanism and is also involved in aging. Senescent cells accumulate in aged tissues (reviewed by Campisi 1997 and Lopez-Otin 2013), which may be due to an increased senescence rate and/or decrease in the rate of clearance of senescent cells. In a mouse model of accelerated aging, clearance of senescent cells delays the onset of age-related phenotypes (Baker et al. 2011).
Cellular senescence can be triggered by the aberrant activation of oncogenes or loss-of-function of tumor suppressor genes, and this type of senescence is known as the oncogene-induced senescence, with RAS signaling-induced senescence being the best studied. Oxidative stress, which may or may not be caused by oncogenic RAS signaling, can also trigger senescence. Finally, the cellular senescence program can be initiated by DNA damage, which may be caused by reactive oxygen species (ROS) during oxidative stress, and by telomere shortening caused by replicative exhaustion which may be due to oncogenic signaling. The senescent phenotype was first reported by Hayflick and Moorhead in 1961, when they proposed replicative senescence as a mechanism responsible for the cessation of mitotic activity and morphological changes that occur in human somatic diploid cell strains as a consequence of serial passaging, preventing the continuous culture of untransformed cells-the Hayflick limit (Hayflick and Moorhead 1961).
Secreted proteins that constitute the senescence-associated secretory phenotype (SASP), also known as the senescence messaging secretome (SMS), include inflammatory and immune-modulatory cytokines, growth factors, shed cell surface molecules and survival factors. The SASP profile is not significantly affected by the type of senescence trigger or the cell type (Coppe et al. 2008), but the persistent DNA damage may be a deciding SASP initiator (Rodier et al. 2009). SASP components function in an autocrine manner, reinforcing the senescent phenotype (Kuilman et al. 2008, Acosta et al. 2008), and in the paracrine manner, where they may promote epithelial-to-mesenchymal transition (EMT) and malignancy in the nearby premalignant or malignant cells (Coppe et al. 2008).
Senescent cells may remain viable for years, such as senescent melanocytes of moles and nevi, or they can be removed by phagocytic cells. The standard marker for immunohistochemical detection of senescent cells is senescence-associated beta-galactosidase (SA-beta-Gal), a lysosomal enzyme that is not required for senescence.
For reviews of this topic, please refer to Collado et al. 2007, Adams 2009, Kuilman et al. 2010. For a review of differential gene expression between senescent and immortalized cells, please refer to Fridman and Tainsky 2008. R-HSA-189200 Cellular hexose transport Two gene families are responsible for glucose transport in humans. SLC2 (encoding GLUTs) and SLC5 (encoding SGLTs) families mediate glucose absorption in the small intestine, glucose reabsorption in the kidney, glucose uptake by the brain across the blood-brain barrier and glucose release by all cells in the body. Glucose is taken up from interstitial fluid by a passive, facilitative transport driven by the diffusion gradient of glucose (and other sugars) across the plasma membrane. This process is mediated by a family of Na+-independent, facilitative glucose transporters (GLUTs) encoded by the SLC2A gene family (Zhao & Keating 2007; Wood & Trayhurn 2003). There are 14 members belonging to this family (GLUT1-12, 14 and HMIT (H+/myo-inositol symporter)). The GLUT family can be subdivided into three subclasses (I-III) based on sequence similarity and characteristic sequence motifs (Joost & Thorens 2001).
Hexoses, notably fructose, glucose, and galactose, generated in the lumen of the small intestine by breakdown of dietary carbohydrate are taken up by enterocytes lining the microvilli of the small intestine and released from them into the blood. Uptake into enterocytes is mediated by two transporters localized on the lumenal surfaces of the cells, SGLT1 (glucose and galactose, together with sodium ions) and GLUT5 (fructose). GLUT2, localized on the basolateral surfaces of enterocytes, mediates the release of these hexoses into the blood (Wright et al. 2004). GLUT2 may also play a role in hexose uptake from the gut lumen into enterocytes when the lumenal content of monosaccharides is very high (Kellet & Brot-Laroche 2005) and GLUT5 mediates fructose uptake from the blood into cells of the body, notably hepatocytes.
Cells take up glucose by facilitated diffusion, via glucose transporters (GLUTs) associated with the plasma membrane, a reversible reaction. Four tissue-specific GLUT isoforms are known. Glucose in the cytosol is phosphorylated by tissue-specific kinases to yield glucose 6-phosphate, which cannot cross the plasma membrane because of its negative charge. In the liver, this reaction is catalyzed by glucokinase which has a low affinity for glucose (Km about 10 mM) but is not inhibited by glucose 6-phosphate. In other tissues, this reaction is catalyzed by isoforms of hexokinase. Hexokinases are feedback-inhibited by glucose 6-phosphate and have a high affinity for glucose (Km about 0.1 mM). Liver cells can thus accumulate large amounts of glucose 6-phosphate but only when blood glucose concentrations are high, while most other tissues can take up glucose even when blood glucose concentrations are low but cannot accumulate much intracellular glucose 6-phosphate. These differences are consistent with the view that that the liver functions to buffer blood glucose concentrations, while most other tissues take up glucose to meet immediate metabolic needs.
Glucose 6-phosphatase, expressed in liver and kidney, allows glucose 6-phosphate generated by gluconeogenesis (both tissues) and glycogen breakdown (liver) to leave the cell. The absence of glucose 6-phosphatase from other tissues makes glucose uptake by these tissues essentially irreversible, consistent with the view that cells in these tissues take up glucose for local metabolic use.
Class II facilitative transporters consist of GLUT5, 7, 9 and 11 (Zhao & Keating 2007, Wood & Trayhurn 2003).
R-HSA-9711123 Cellular response to chemical stress Cells are equipped with versatile physiological stress responses to prevent hazardous consequences resulting from exposure to chemical insults of endogenous and exogenous origin. Even at equitoxic doses, different stressors induce distinctive and complex signaling cascades. The responses typically follow cell perturbations at the subcellular organelle level.
Expression of heme oxygenase 1 (HMOX1) is regulated by various indicators of cell stress. Cytoprotection by HMOX1 is exerted directly by HMOX1 and by the antioxidant metabolites it produces through the degradation of heme (Origassa et al, 2013; Ryter et al, 2006).
Reactive oxygen and nitrogen species (RONS) are important mediators of chemical stress, as they are produced endogenously in mitochondria, and also result from redox activities of many toxins and heavy metal cations. The points of RONS action in the cell are plasma and ER membrane lipids, as well as DNA, both acting as sensors for the cellular response. On the other hand, chemotherapeutic agents exert their action via generation of RONS and induction of cancer cell apoptosis, while drug resistance associates with RONS-induced cancer cell survival (Sampadi et al, 2020; Moldogazieva et al, 2018).
R-HSA-3371556 Cellular response to heat stress In response to exposure to elevated temperature and certain other proteotoxic stimuli (e.g., hypoxia, free radicals) cells activate a number of cytoprotective mechanisms known collectively as "heat shock response". Major aspects of the heat shock response (HSR) are evolutionarily conserved events that allow cells to recover from protein damage induced by stress (Liu XD et al. 1997; Voellmy R & Boellmann F 2007; Shamovsky I & Nudler E 2008; Anckar J & Sistonen L 2011). The main hallmark of HSR is the dramatic alteration of the gene expression pattern. A diverse group of protein genes is induced by the exposure to temperatures 3-5 degrees higher than physiological. Functionally, most of these genes are molecular chaperones that ensure proper protein folding and quality control to maintain cell proteostasis.
At the same time, heat shock-induced phosphorylation of translation initiation factor eIF2alpha leads to the shutdown of the nascent polypeptide synthesis reducing the burden on the chaperone system that has to deal with the increased amount of misfolded and thermally denatured proteins (Duncan RF & Hershey JWB 1989; Sarkar A et al. 2002; Spriggs KA et al. 2010).
The induction of HS gene expression primarily occurs at the level of transcription and is mediated by heat shock transcription factor HSF1(Sarge KD et al. 1993; Baler R et al. 1993). Human cells express five members of HSF protein family: HSF1, HSF2, HSF4, HSFX and HSFY. HSF1 is the master regulator of the heat inducible gene expression (Zuo J et al. 1995; Akerfelt M et al. 2010). HSF2 is activated in response to certain developmental stimuli in addition to being co-activated with HSF1 to provide promoter-specific fine-tuning of the HS response by forming heterotrimers with HSF1 (Ostling P et al. 2007; Sandqvist A et al. 2009). HSF4 lacks the transcription activation domain and acts as a repressor of certain genes during HS (Nakai A et al. 1997; Tanabe M et al. 1999; Kim SA et al. 2012). Two additional family members HSFX and HSFY, which are located on the X and Y chromosomes respectively, remain to be characterized (Bhowmick BK et al. 2006; Shinka T et al. 2004; Kichine E et al. 2012).
Under normal conditions HSF1 is present in both cytoplasm and nucleus in the form of an inactive monomer. The monomeric state of HSF1 is maintained by an intricate network of protein-protein interactions that include the association with HSP90 multichaperone complex, HSP70/HSP40 chaperone machinery, as well as intramolecular interaction of two conserved hydrophobic repeat regions. Monomeric HSF1 is constitutively phosphorylated on Ser303 and Ser 307 by (Zou J et al. 1998; Knauf U et al. 1996; Kline MP & Moromoto RI 1997; Guettouche T et al. 2005). This phosphorylation plays an essential role in ensuring cytoplasmic localization of at least a subpopulation of HSF1 molecules under normal conditions (Wang X et al. 2004).
Exposure to heat and other proteotoxic stimuli results in the release of HSF1 from the inhibitory complex with chaperones and its subsequent trimerization, which is promoted by its interaction with translation elongation factor eEF1A1 (Baler R et al. 1993; Shamovsky I et al. 2006; Herbomel G et al 2013). The trimerization is believed to involve intermolecular interaction between hydrophobic repeats 1-3 leading to the formation of a triple coil structure. Additional stabilization of the HSF1 trimer is provided by the formation of intermolecular S-S bonds between Cys residues in the DNA binding domain (Lu M et al.2008). Trimeric HSF1 is predominantly localized in the nucleus where it binds the specific sequence in the promoter of hsp genes (Sarge KD et al. 1993; Wang Y and Morgan WD 1994). The binding sequence for HSF1 (HSE, heat shock element) contains series of inverted repeats nGAAn in head-to-tail orientation, with at least three elements being required for the high affinity binding. Binding of the HSF1 trimer to the promoter is not sufficient to induce transcription of the gene (Cotto J et al. 1996). In order to do so, HSF1 needs to undergo inducible phosphorylation on specific Ser residues such as Ser230, Ser326. This phosphorylated form of HSF1 trimer is capable of increasing the promoter initiation rate. HSF1 bound to DNA promotes recruiting components of the transcription mediator complex and relieving promoter-proximal pause of RNA polymerase II through its interaction with TFIIH transcription factor (Yuan CX & Gurley WB 2000).
HSF1 activation is regulated in a precise and tight manner at multiple levels (Zuo J et al. 1995; Cotto J et al. 1996). This allows fast and robust activation of HS response to minimize proteotoxic effects of the stress. The exact set of HSF1 inducible genes is probably cell type specific. Moreover, cells in different pathophysiological states will display different but overlapping profile of HS inducible genes. R-HSA-1234174 Cellular response to hypoxia Oxygen plays a central role in the functioning of human cells: it is both essential for normal metabolism and toxic. Here we have annotated one aspect of cellular responses to oxygen, the role of hypoxia-inducible factor in regulating cellular transcriptional responses to changes in oxygen availability.
In the presence of oxygen members of the transcription factor family HIF-alpha, comprising HIF1A, HIF2A (EPAS1), and HIF3A, are hydroxylated on proline residues by PHD1 (EGLN2), PHD2 (EGLN1), and PHD3 (EGLN3) and on asparagine residues by HIF1AN (FIH) (reviewed in Pouyssegur et al. 2006, Semenza 2007, Kaelin and Ratcliffe 2008, Nizet and Johnson 2009, Brahimi-Horn and Pouyssegur 2009, Majmundar et al. 2010, Loenarz and Schofield 2011). Both types of reaction require molecular oxygen as a substrate and it is probable that at least some HIF-alpha molecules carry both hydroxylated asparagine and hydroxylated proline (Tian et al. 2011).
Hydroxylated asparagine interferes with the ability of HIF-alpha to interact with p300 and CBP while hydroxylated proline facilitates the interaction of HIF-alpha with the E3 ubiquitin ligase VHL, causing ubiquitination and proteolysis of HIF-alpha. Hypoxia inhibits both types of hydroxylation, resulting in the stabilization of HIF-alpha, which then enters the nucleus, binds HIF-beta, and recruits p300 and CBP to activate target genes such as EPO and VEGF.
R-HSA-9840373 Cellular response to mitochondrial stress Mitochondrial stress caused by depolarization of the mitochondrial inner membrane, inhibition of proton flux across the mitochondrial inner membrane, or insufficient protein import capacity caused by inhibition of ATP synthase or iron deficiency is communicated to the cytosol and nucleus, resulting in decreased protein production and increased transcription of chaperones and metabolic genes among others. This pathway is known as the mitochondrial stress response and is a part of mitochondrial signaling and the integrated stress response (Reviewed in Eckl et al. 2021, Picard and Shirihai 2022, Lu et al. 2022, Liu and Birsoy 2023). The mitochondrial stress response participates in adapting cells to harsher environments and, hence, plays a role in tumor progression and metastasis (reviewed in Lee et al. 2022).
In unstressed mitochondria, DELE1 is constitutively imported into the mitochondrial matrix and degraded by the LONP1 ATP-dependent protease (Fessler et al. 2022, Sekine et al. 2023). Mitochondrial stress inhibits the complete transit of DELE1 into the matrix and activates the inner membrane protease OMA1 by self-cleavage (Fessler et al. 2022, Sekine et al. 2023, inferred from the mouse Oma1 homolog in Baker et al. 2014, Zhang et al. 2014). Activated OMA1 cleaves the N-terminal region of DELE1 on the outer face of the inner membrane as DELE1 is unable to fully cross the inner membrane (Fessler et al. 2020, Guo et al. 2020, Fessler et al. 2022). The resulting C-terminal fragment of DELE1 egresses from the intermembrane space to the cytosol where it oligomerizes to form an octamer (Yang et al. 2023) which binds and activates EIF2AK1, a constituent kinase of the integrated stress response that phosphorylates EIF2S1, the alpha subunit of the eukaryotic translation initiation factor 2 (eIF2) (Fessler et al. 2020, Guo et al. 2020, Cheng et al. 2022). Phosphorylation of EIF2S1 inhibits general translation but increases translation of specific mRNAs that possess upstream open reading frames (reviewed in Wek 2018). Among these mRNAs are the transcription factors DDIT3 (CHOP), ATF4, and ATF5, which activate expression of chaperone genes among others.
R-HSA-9711097 Cellular response to starvation Deprivation of nutrients triggers diverse short- and long terms adaptations in cells. Here we have annotated two aspects of cellular responses to amino acid deprivation, ones mediated by EIF2AK4 and ones mediated by mTORC.
EIF2AK4 (GCN2) senses amino acid deficiency by binding uncharged tRNAs near the ribosome, and phosphorylating EIF2S1 (reviewed in Chaveroux et al. 2010, Castilho et al. 2014, Gallinetti et al. 2013, Bröer and Bröer 2017, Wek 2018). This reduces translation of most mRNAs but increases translation of mRNAs, notably ATF4, that mediate stress responses (reviewed in Kilberg et al. 2012, Wortel et al. 2017; Dever and Hinnebusch 2005).
The mTORC1 complex acts as an integrator that regulates translation, lipid synthesis, autophagy, and cell growth in response to multiple inputs, notably glucose, oxygen, amino acids, and growth factors such as insulin (reviewed in Sabatini 2017, Meng et al. 2018, Kim and Guan 2019).
MTOR, the kinase subunit of mTORC1, is activated by interaction with RHEB:GTP at the cytosolic face of lysosomal membrane (Long et al. 2005, Tee et al. 2005, Long et al. 2007, Yang et al. 2017). This process is regulated by various individual amino acids (reviewed in Zhuang et al. 2019, Wolfson and Sabatini 2017, Yao et al. 2017) and is reversed in response to the removal of amino acids, through the action of TSC1 (Demetriades et al. 2014).
R-HSA-9855142 Cellular responses to mechanical stimuli Molecular mechanosensors are biomolecules that convert a physical force into an intracellular chemical signal (reviewed in Martino et al. 2018, Li et al. 2022). One of the most common types of mechanosensor is the mechanically gated ion channel such as PIEZO1 (reviewed in Fang et al. 2021). Other mechanosensors include integrins (reviewed in Hirata et al. 2015), receptor tyrosine kinases, and G protein-coupled receptors (reviewed in Xiao et al. 2023). After activation by force, mechanosensors then activate mechanotransducers such as kinases and channels to amplify and transfer the signal to chemical processes that produce downstream effects such as changes in gene expression and cell growth (reviewed in Martino et al. 2018).
Mechanosensors and mechanotransducers enable endothelial cells to respond to laminar and turbulent blood flow (reviewed in Davis et al. 2023, Rahaman et al. 2023, Lim and Harraz 2024), osteocytes to respond to mechanical load (reviewed in Qin et al. 2021, Moharrer and Boerckel 2022, Wang et al. 2023), and specialized cellular structures such as Merkel cells and Pacinian corpuscles to respond to touch (reviewed in Handler and Ginty 2021, Logan et al. 2024).
R-HSA-8953897 Cellular responses to stimuli Individual cells detect and respond to diverse external molecular and physical signals. Appropriate responses to these signals are essential for normal development, maintenance of homeostasis in mature tissues, and effective defensive responses to potentially noxious agents (Kultz 2005). It is convenient, if somewhat arbitrary, to distinguish responses to signals involved in development and homeostasis from ones involved in stress responses, and that classification is followed here, with macroautophagy and responses to metal ions classified as responses to normal external stimuli, while responses to hypoxia, reactive oxygen species, and heat, and the process of cellular senescence are classified as stress responses. Signaling cascades are integral components of all of these response mechanisms but because of their number and diversity, they are grouped in a separate signal transduction superpathway in Reactome.
R-HSA-2262752 Cellular responses to stress Cells are subject to external molecular and physical stresses such as foreign molecules that perturb metabolic or signaling processes, and changes in temperature or pH. Cells are also subject to internal molecular stresses such as production of reactive metabolic byproducts. The ability of cells and tissues to modulate molecular processes in response to such stresses is essential to the maintenance of tissue homeostasis (Kultz 2005). Specific stress-related processes annotated here are cellular response to hypoxia, cellular response to heat stress, cellular senescence, HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand, response of EIF2AK1 (HRI) to heme deficiency, heme signaling, cellular response to chemical stress, cellular response to starvation, and unfolded protein response.
R-HSA-380287 Centrosome maturation The centrosome is the primary microtubule organizing center (MTOC) in vertebrate cells and plays an important role in orchestrating the formation of the mitotic spindle. Centrosome maturation is an early event in this process and involves a major reorganization of centrosomal material at the G2/M transition. During maturation, centrosomes undergo a dramatic increase in size and microtubule nucleating capacity. As part of this process, a number of proteins and complexes, including some that are required for microtubule nucleation and anchoring, are recruited to the centrosome while others that are required for organization of interphase microtubules and centrosome cohesion are lost (reviewed in Schatten, 2008; Raynaud-Messina and Merdes 2007).
R-HSA-193681 Ceramide signalling In certain cell types, ligand binding to p75NTR leads to ceramide production, which can mediate either cell survival (e.g. in noecotical subplate neurons) or apoptosis (e.g. in oligodendrocytes). Low levels of ceramide are also able to stimulate axonal outgrowth in hippocampal neurons.
R-HSA-163765 ChREBP activates metabolic gene expression ChREBP (Carbohydrate Response Element Binding Protein) is a large multidomain protein containing a nuclear localization signal near its amino terminus, polyproline domains, a basic helix-loop-helix-leucine zipper domain, and a leucine-zipper-like domain (Uyeda et al., 2002). Its dephosphorylation in response to molecular signals associated with the well-fed state allows it to enter the nucleus, interact with MLX protein, and bind to ChRE DNA sequence motifs near Acetyl-CoA carboxylase, Fatty acid synthase, and Pyruvate kinase (L isoform) genes (Ishi et al.2004). This sequence of events is outlined schematically in the picture below (adapted from Kawaguchi et al. (2001) - copyright (2001) National Academy of Sciences, U.S.A.).
R-HSA-9613829 Chaperone Mediated Autophagy In contrary to the vesicle-mediated macroautophagy, the chaperone mediated mechanism of autophagy selectively targets individual proteins to the lysosome for degradation. Chaperones bind intracellular proteins based on recognition motifs and transports them from the cytosol to the lysosomal membrane. Subsequently, the protein is translocated into the lumen for digestion (Cuervo A M et al. 2014, Kaushik S et al. 2018).
R-HSA-390466 Chaperonin-mediated protein folding The eukaryotic chaperonin TCP-1 ring complex (TRiC/ CCT) plays an essential role in the folding of a subset of proteins prominent among which are the actins and tubulins (reviewed in Altschuler and Willison, 2008). CCT/TRiC is an example of a type II chaperonin, defined (in contrast to type I) as functioning in the absence of a cochaperonin. TriC/CCT is a multisubunit toroidal complex that forms a cylinder containing two back-to-back stacked rings enclosing a cavity where substrate folding occurs in an ATP dependent process (reviewed in Altschuler and Willison, 2008 ). CCT/TriC contains eight paralogous subunits that are conserved throughout eukaryotic organisms (Leroux and Hartl 2000; Archibald et al. 2001; Valpuesta et al. 2002). CCT-mediated folding of non-native substrate protein involves capture through hydrophobic contacts with multiple chaperonin subunits followed by transfer of the protein into the central ring cavity where it folds. Although folding is initiated within this central cavity, only 5%-20% of proteins that are released have partitioned to the native state. The remaining portion is then recaptured by other chaperonin molecules (Cowan and Lewis 2001). This cycling process may be repeated multiple times before a target protein partitions to the native state. In the cell, binding to CCT occurs via presentation of target protein bound to upstream chaperones. During translation, the emerging polypeptide chain may be transferred from the ribosome to CCT via the chaperone Prefoldin (Vainberg et al., 1998) or the Hsp70 chaperone machinery (Melville et al., 2003). While the majority of CCT substrates ultimately partition to the native state as soluble, monomeric proteins, alpha and beta tubulin are unusual in that they require additional cofactors that are required to assemble the tubulin heterodimer (Cowan and Lewis 2001).
R-HSA-380108 Chemokine receptors bind chemokines Chemokine receptors are cytokine receptors found on the surface of certain cells, which interact with a type of cytokine called a chemokine. Following interaction, these receptors trigger a flux of intracellular calcium which leads to chemotaxis. Chemokine receptors are divided into different families, CXC chemokine receptors, CC chemokine receptors, CX3C chemokine receptors and XC chemokine receptors that correspond to the 4 distinct subfamilies of chemokines they bind.
R-HSA-75035 Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex DNA damage induced activation of the checkpoint kinases Chk1/Chk2(Cds1) results in the conversion and/or maintenance of CyclinB:Cdc2 complex in its Tyrosine 15 phosphorylated (inactive) state. Cdc2 activity is regulated by a balance between the phosphorylation and dephosphorylation by the Wee1/Myt1 kinase and Cdc25 phosphatase. Inactivation of the Cyclin B:Cdc2 complex likely involves both inactivation of Cdc25 and/or stimulation of Wee1/Myt1 kinase activity.
R-HSA-191273 Cholesterol biosynthesis Cholesterol is synthesized de novo from acetyl CoA. The overall synthetic process is outlined in the attached illustration. Enzymes whose regulation plays a major role in determining the rate of cholesterol synthesis in the body are highlighted in red, and connections to other metabolic processes are indicated. The transformation of zymosterol into cholesterol can follow either of routes, one in which reduction of the double bond in the isooctyl side chain is the final step (cholesterol synthesis via desmosterol, also known as the Bloch pathway) and one in which this reduction is the first step (cholesterol biosynthesis via lathosterol, also known as the Kandutsch-Russell pathway). The former pathway is prominent in the liver and many other tissues while the latter is prominent in skin, where it may serve as the source of the 7-dehydrocholesterol that is the starting point for the synthesis of D vitamins. Defects in several of the enzymes involved in this process are associated with human disease and have provided useful insights into the regulatory roles of cholesterol and its synthetic intermediates in human development (Gaylor 2002; Herman 2003; Kandutsch & Russell 1960; Mitsche et al. 2015; Song et al. 2005).
R-HSA-6807047 Cholesterol biosynthesis via desmosterol The transformation of zymosterol into cholesterol can follow either of routes, one in which reduction of the double bond in the isooctyl side chain is the final step (cholesterol synthesis via desmosterol, also known as the Bloch pathway) and one in which this reduction is the first step (cholesterol biosynthesis via lathosterol, also known as the Kandutsch-Russell pathway). The former pathway is prominent in the liver and many other tissues while the latter is prominent in skin, where it may serve as the source of the 7-dehydrocholesterol that is the starting point for the synthesis of D vitamins (Mitsche et al. 2015).
R-HSA-6807062 Cholesterol biosynthesis via lathosterol The transformation of zymosterol into cholesterol can follow either of routes, one in which reduction of the double bond in the isooctyl side chain is the final step (cholesterol synthesis via desmosterol, also known as the Bloch pathway) and one in which this reduction is the first step (cholesterol biosynthesis via lathosterol, also known as the Kandutsch-Russell pathway). The former pathway is prominent in the liver and many other tissues while the latter is prominent in skin, where it may serve as the source of the 7-dehydrocholesterol that is the starting point for the synthesis of D vitamins (Kandutsch & Russell 1960; Mitsche et al. 2015).
R-HSA-6798163 Choline catabolism Choline is an essential water-soluble nutrient in humans, serving as a precursor of phospholipids and the neurotransmitter acetylcholine. It is often associated with B vitamins based on its chemical structure but it isn't an official B vitamin. Its oxidation to betaine provides a link to folate-dependent, one-carbon metabolism where betaine is a methyl donor in the methionine cycle. Betaine is further metabolised to dimethylglycine which is cleared by the kidney (Ueland 2011, Hollenbeck 2012).
R-HSA-2022870 Chondroitin sulfate biosynthesis Chondroitin sulfate (CS) glycosaminoglycan consists of N-acetylgalactosamine (GalNAc) residues alternating in glycosidic linkages with glucuronic acid (GlcA). GalNAc residues are sulfated to varying degrees on 4- and/or 6- positions. The steps below describe the biosynthesis of a simple CS molecule (Pavao et al. 2006, Silbert & Sugumaran 2002).
R-HSA-1793185 Chondroitin sulfate/dermatan sulfate metabolism Chondroitin sulfate (CS) is a sulfated glycosaminoglycan (GAG). CS chains are unbranched polysaccharides of varying length containing two alternating monosaccharides: D-glucuronic acid (GlcA) and N-acetyl-D-galactosamine (GalNAc). The chains are usually attached to proteins forming a proteoglycan. CS is an important structural component of cartilage due to it's ability to withstand compression. It is also a widely used dietary supplement for osteoarthritis. When some of the GlcA residues are epimerized into L-iduronic acid (IdoA) the resulting disaccharide is then referred to as dermatan sulfate (DS) (Silbert & Sugumaran 2002). DS is the most predominant GAG in skin but is also found in blood vessels, heart valves, tendons, and the lungs. It may play roles in cardiovascular disease, tumorigenesis, infection, wound repair and fibrosis (Trowbridge & Gallo 2002).
R-HSA-9821002 Chromatin modifications during the maternal to zygotic transition (MZT) Chromatin in the zygotic pronuclei transitions to a more open and accessible conformation by DNA demethylation and changes to histone modifications. As development proceeds through the cleavage stages to the blastocyst, chromatin continues to become more accessible until DNA methylation and a more restrictive chromatin conformation are re-established after implantation of the embryo in the uterus.
In the oocyte, H3K9me2 produced by EHMT2 (G9a, KMT1C) and H3K9me3 produced by SETDB1 (KMT1E) are transmitted to the female pronucleus of the zygote and protect maternal DNA from active demethylation (inferred from mouse zygotes in Zeng et al. 2019, reviewed in de Macedo et al. 2021). DPPA3 binds H3K9me2, preventing the 5-methylcytosine oxidase TET3 from being recruited to chromatin (inferred from mouse homologs in Nakamura et al. 2007, Wossidlo et al. 2011, Nakamura et al. 2012). DPPA3 also displaces UHRF1 from chromatin, preventing the maintenance DNA methylase DNMT1 from being recruited to chromatin and thus allowing passive DNA demethylation to occur in the female genome (inferred from mouse homologs in Funaki et al. 2014, Li et al. 2018, Du et al. 2019, Mulholland et al. 2020).
In the male pronucleus of the zygote, AICDA (AID) deaminates cytosine residues and long patch repair replaces the mismatches and adjacent 5-methylcytidine residues with cytidine (Santos et al. 2013, Franchini et al. 2014). After this initial demethylation, TET3 is recruited to chromatin by METTL23 and STGP4 (GSE) (inferred from mouse homologs in Hatanaka et al. 2017) where it oxidizes remaining 5-methylcytidine to 5-hydroxymethylcytidine, which is removed by base excision repair and replaced with cytidine (inferred from mouse homologs in Gu et al. 2011, Iqbal et al. 2011, Wossidlo et al. 2011, Santos et al. 2013, Amouroux et al. 2016, Hatanaka et al. 2017).
The repressive mark H3K27me3 decreases in 2-cell embryos near developmentally related genes (Xia et al. 2019). The H3K27me3 demethylases KDM6B (inferred from bovine embryos in Chung et al. 2017, Canovas et al. 2012) and KDM6A (inferred from mouse embryos in Bai et al. 2019) appear to play a role in the decrease of H3K27me3, as downregulation of them impairs H3K27me3 loss, zygotic genome activation, and embryonic development. Embryonic development also requires H3K36me3, a permissive mark located in transcribed gene bodies that is produced in the oocyte by SETD2 (inferred from mouse embryos in Xu et al. 2019).
In mouse oocytes, H3K4me3 occurs in unusually broad regions that span genes Dahl et al. 2016, Zhang et al. 2016). These broad regions persist in the zygote and into the 2-cell stage. In the late 2-cell stage the more usual patterns of H3K4me3 are established as sharp peaks of H3K4me3 near the transcription start sites and stop sites of genes. The histone methyltransferase KMT2B is at least partly responsible for establishing the broad regions of H3K4me3 in the oocyte and the histone demethylases KDM5B and KDM5A remove the broad H3K4me3 in the late 2-cell stage embryo (inferred from mouse homologs in Dahl et al. 2016, reviewed in Eckerseley-Maslin et al. 2018).
In human oocytes and zygotes, however, broad regions of H3K4me3 are not observed across genes but are located across distal, CpG-rich domains which have partial DNA methylation (Xia et al. 2019). At the 8-cell stage, expression of KDM5B increases and the H3K4me3 at the distal domains is lost as zygotic genome activation occurs, suggesting a role for KDM5B in loss of H3K4me3 (Xia et al. 2019).
R-HSA-3247509 Chromatin modifying enzymes Eukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect it from damage. Access to DNA is achieved by highly regulated local chromatin decondensation.
The 'building block' of chromatin is the nucleosome. This contains ~150 bp of DNA wrapped around a histone octamer which consists of two each of the core histones H2A, H2B, H3 and H4 in a 1.65 left-handed superhelical turn (Luger et al. 1997, Andrews & Luger 2011).
Most organisms have multiple genes encoding the major histone proteins. The replication-dependent genes for the five histone proteins are clustered together in the genome in all metazoans. Human replication-dependent histones occur in a large cluster on chromosome 6 termed HIST1, a smaller cluster HIST2 on chromosome 1q21, and a third small cluster HIST3 on chromosome 1q42 (Marzluff et al. 2002). Histone genes are named systematically according to their cluster and location within the cluster.
The 'major' histone genes are expressed primarily during the S phase of the cell cycle and code for the bulk of cellular histones. Histone variants are usually present as single-copy genes that are not restricted in their expression to S phase, contain introns and are often polyadenylated (Old & Woodland 1984). Some variants have significant differences in primary sequence and distinct biophysical characteristics that are thought to alter the properties of nucleosomes. Others localize to specific regions of the genome. Some variants can exchange with pre-existing major histones during development and differentiation, referred to as replacement histones (Kamakaka & Biggins 2005). These variants can become the predominant species in differentiated cells (Pina & Suau 1987, Wunsch et al. 1991). Histone variants may have specialized functions in regulating chromatin dynamics.
The H2A histone family has the highest sequence divergence and largest number of variants. H2A.Z and H2A.XH2A are considered 'universal variants', found in almost all organisms (Talbert & Henikoff 2010). Variants differ mostly in the C-terminus, including the docking domain, implicated in interactions with the (H3-H4)x2 tetramer within the nucleosome, and in the L1 loop, which is the interaction interface of H2A-H2B dimers (Bonisch & Hake 2012). Canonical H2A proteins are expressed almost exclusively during S-phase. There are several nearly identical variants (Marzluff et al. 2002). No functional specialization of these canonical H2A isoforms has been demonstrated (Bonisch & Hake 2012). Reversible histone modifications such as acetylation and methylation regulate transcription from genomic DNA, defining the 'readability' of genes in specific tissues (Kouzarides 2007, Marmorstein & Trievel 2009, Butler et al. 2012).
N.B. The coordinates of post-translational modifications represented here follow Reactome standardized naming, which includes the UniProt standard practice whereby coordinates refer to the translated protein before any further processing. Histone literature typically refers to coordinates of the protein after the initiating methionine has been removed; therefore the coordinates of post-translated histone residues described here are frequently +1 when compared with the literature. For more information on Reactome's standards for naming pathway events, the molecules that participate in them and representation of post-translational modifications, please refer to Naming Conventions on the Reactome Wiki or Jupe et al. 2014.
R-HSA-4839726 Chromatin organization Chromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance of the physical structure of eukaryotic chromatin. These processes include histone modification, DNA modification, and transcription. The modifications are bound by specific proteins that alter the conformation of chromatin.
R-HSA-73886 Chromosome Maintenance Maintenance of chromosomal organization is critical for stable chromosome function. Two aspects of maintenance annotated in Reactome are centromeric chromatin assembly outside the context of DNA replication, involving nucleosome assembly with the histone H3 variant CenH3 (also called CENP-A), and the maintenance of telomeres, protein-DNA complexes at the ends of linear chromosomes that are important for genome stability.
R-HSA-8963888 Chylomicron assembly Chylomicrons transport triacylglycerol, phospholipid, and cholesterol derived from dietary lipid from the small intestine to other tissues of the body. Each chylomicron assembles around a single molecule of apolipoprotein B-48 (Phillips et al. 1997) which at the time the particle leaves the intestine and enters the lymphatic circulation is complexed with >200,000 molecules of triacylglycerol (TG), ~35,000 of phospholipid, ~11,000 of cholesterol ester, ~8,000 of free cholesterol, ~60 copies of apolipoprotein A-I, ~15 copies of apolipoprotein A-IV, and copies of apolipoprotein A-II (Bhattacharya and Redgrave 1981).
R-HSA-8964026 Chylomicron clearance Circulating chylomicrons acquire molecules of apolipoproteins C and E and through interaction with endothelial lipases lose a large fraction of their triacylglycerol. These changes convert them to chylomicron remnants which bind to LDL receptors, primarily on the surfaces of liver cells, clearing them from the circulation.
This binding and clearance process involves several steps and requires the presence of heparan sulfate proteoglycan (HSPG)-associated hepatic lipase (HL). The molecular details of LDLR binding, and of the following steps of remnant endocytosis, are inferred from those of the coorresponding step of LDLR-mediated low-density lipoprotein (LDL) endocytosis (Redgrave 2004).
R-HSA-8963901 Chylomicron remodeling As chylomicrons circulate in the body, they acquire molecules of apolipoproteins C and E, and through interaction with endothelial lipases can lose a large fraction of their triacylglycerol. These changes convert them to chylomicron remnants which bind to LDL receptors, primarily on the surfaces of liver cells, clearing them from the circulation. This whole sequence of events is rapid: the normal lifespan of a chylomicron is 30 - 60 minutes (Redgrave 2004).
R-HSA-5617833 Cilium Assembly Cilia are membrane covered organelles that extend from the surface of eukaryotic cells. Cilia may be motile, such as respiratory cilia) or non-motile (such as the primary cilium) and are distinguished by the structure of their microtubule-based axonemes. The axoneme consists of nine peripheral doublet microtubules, and in the case of many motile cilia, may also contain a pair of central single microtubules. These are referred to as 9+0 or 9+2 axonemes, respectively. Relative to their non-motile counterparts, motile cilia also contain additional structures that contribute to motion, including inner and outer dynein arms, radial spokes and nexin links. Four main types of cilia have been identified in humans: 9+2 motile (such as respiratory cilia), 9+0 motile (nodal cilia), 9+2 non-motile (kinocilium of hair cells) and 9+0 non-motile (primary cilium and photoreceptor cells) (reviewed in Fliegauf et al, 2007). This pathway describes cilia formation, with an emphasis on the primary cilium. The primary cilium is a sensory organelle that is required for the transduction of numerous external signals such as growth factors, hormones and morphogens, and an intact primary cilium is needed for signaling pathways mediated by Hh, WNT, calcium, G-protein coupled receptors and receptor tyrosine kinases, among others (reviewed in Goetz and Anderson, 2010; Berbari et al, 2009; Nachury, 2014). Unlike the motile cilia, which are generally present in large numbers on epithelial cells and are responsible for sensory function as well as wave-like beating motions, the primary cilium is a non-motile sensory organelle that is present in a single copy at the apical surface of most quiescent cells (reviewed in Hsiao et al, 2012). Cilium biogenesis involves the anchoring of the basal body, a centriole-derived organelle, near the plasma membrane and the subsequent polymerization of the microtubule-based axoneme and extension of the plasma membrane (reviewed in Ishikawa and Marshall, 2011; Reiter et al, 2012). Although the ciliary membrane is continuous with the plasma membrane, the protein and lipid content of the cilium and the ciliary membrane are distinct from those of the bulk cytoplasm and plasma membrane (reviewed in Emmer et al, 2010; Rohatgi and Snell, 2010). This specialized compartment is established and maintained during cilium biogenesis by the formation of a ciliary transition zone, a proteinaceous structure that, with the transition fibres, anchors the basal body to the plasma membrane and acts as a ciliary pore to limit free diffusion from the cytosol to the cilium (reviewed in Nachury et al, 2010; Reiter et al, 2012). Ciliary components are targeted from the secretory system to the ciliary base and subsequently transported to the ciliary tip, where extension of the axoneme occurs, by a motor-driven process called intraflagellar transport (IFT). Anterograde transport of cargo from the ciliary base to the tip of the cilium requires kinesin-2 type motors, while the dynein-2 motor is required for retrograde transport back to the ciliary base. In addition, both anterograde and retrograde transport depend on the IFT complex, a multiprotein assembly consisting of two subcomplexes, IFT A and IFT B. The primary cilium is a dynamic structure that undergoes continuous steady-state turnover of tubulin at the tip; as a consequence, the IFT machinery is required for cilium maintenance as well as biogenesis (reviewed in Bhogaraju et al, 2013; Hsiao et al, 2012; Li et al, 2012; Taschner et al, 2012; Sung and Leroux, 2013). The importance of the cilium in signaling and cell biology is highlighted by the wide range of defects and disorders, collectively known as ciliopathies, that arise as the result of mutations in genes encoding components of the ciliary machinery (reviewed in Goetz and Anderson, 2010; Madhivanan and Aguilar, 2014).
R-HSA-9793528 Ciprofloxacin ADME Ciprofloxacin (Cipro) is a widely used broad spectrum bacterial antibiotic. Due to its association with disabling and potentially persistent adverse reactions and current high levels of resistance its use is now recommended in patients who have no alternative treatment option for respiratory and urinary tract infections, skin and soft tissue infections, bone and joint infections, infectious diarrhea, typhoid fever and gonorrhea with susceptible strains. Adverse reactions include tendinitis, tendon rupture, peripheral neuropathy, and CNS effects. The usual dosages are 250 mg and 500 mg (FDA, 2016; Bayer Inc, 2020).
Cipro is highly soluble in aqeuous media below pH 5 and above pH 10. About 60 to 80 percent are taken up by the body. The main absorption site of ciprofloxacin is the upper GI tract, up to the jejunum (Harder et al, 1990; summarized in Olivera et al, 2011). In the context of the Biopharmaceutics Classification System (BCS) Cipro is "not highly soluble", and "not highly permeable". It is classified as BCS class 2, 3, and 4, and uptake and efflux transporters have a big effect on its absorption and excretion. BCS class 4 drugs are primarily excreted unchanged via the biliary or renal routes (Wu and Benet, 2005).
Very high concentrations of Cipro with respect to plasma concentrations are seen in kidney and gall bladder; high concentrations are also found in liver, prostatic tissue, and lung. The main excretion routes for unchanged Cipro are renal (about 65% of plasma amount) and intestinal (about 10%) (Rohwedder et al, 1990; Viell et al, 1992; reviewed by Sörgel, 1989). The intestinal figure includes excretion through epithelial GI cells, and through hepatic cells and the bile duct. The rest of plasma Cipro (10 to 20%) is metabolised, with the major species recovered from urine being oxociprofloxacin and, in faeces, sulfociprofloxacin. Both account for about five per cent each of total excretion (reviewed by Campoli-Richards et al, 1988).
R-HSA-400253 Circadian Clock At the center of the mammalian circadian clock is a negative transcription/translation-based feedback loop: The BMAL1:CLOCK/NPAS2 (ARNTL:CLOCK/NPAS2) heterodimer transactivates CRY and PER genes by binding E-box elements in their promoters; the CRY and PER proteins then inhibit transactivation by BMAL1:CLOCK/NPAS2. BMAL1:CLOCK/NPAS2 activates transcription of CRY, PER, and several other genes in the morning. Levels of PER and CRY proteins rise during the day and inhibit expression of CRY, PER, and other BMAL1:CLOCK/NPAS2-activated genes in the afternoon and evening. During the night CRY and PER proteins are targeted for degradation by phosphorylation and polyubiquitination, allowing the cycle to commence again in the morning.
Transcription of the BMAL1 (ARNTL) gene is controlled by ROR-alpha and REV-ERBA (NR1D1), both of which are targets of BMAL1:CLOCK/NPAS2 in mice and both of which compete for the same element (RORE) in the BMAL1 promoter. ROR-alpha (RORA) activates transcription of BMAL1; REV-ERBA represses transcription of BMAL1. This mutual control forms a secondary, reinforcing loop of the circadian clock. REV-ERBA shows strong circadian rhythmicity and confers circadian expression on BMAL1.
BMAL1 can form heterodimers with either CLOCK or NPAS2, which act redundantly but show different tissue specificity. The BMAL1:CLOCK and BMAL1:NPAS2 heterodimers activate a set of genes that possess E-box elements (consensus CACGTG) in their promoters. This confers circadian expression on the genes. The PER genes (PER1, PER2, PER3) and CRY genes (CRY1, CRY2) are among those activated by BMAL1:CLOCK and BMAL1:NPAS2. PER and CRY mRNA accumulates during the morning and the proteins accumulate during the afternoon. PER and CRY proteins form complexes in the cytosol and these are bound by either CSNK1D or CSNK1E kinases which phosphorylate PER and CRY. The phosphorylated PER:CRY:kinase complex is translocated into the nucleus due to the nuclear localization signal of PER and CRY. Within the nucleus the PER:CRY complexes bind BMAL1:CLOCK and BMAL1:NPAS2, inhibiting their transactivation activity and their phosphorylation. This reduces expression of the target genes of BMAL1:CLOCK and BMAL1:NPAS2 during the afternoon and evening.
PER:CRY complexes also traffic out of the nucleus into the cytosol due to the nuclear export signal of PER. During the night PER:CRY complexes are polyubiquitinated and degraded, allowing the cycle to begin again. Phosphorylated PER is bound by Beta-TrCP1, a cytosolic F-box type component of some SCF E3 ubiquitin ligases. CRY is bound by FBXL3, a nucleoplasmic F-box type component of some SCF E3 ubiquitin ligases. Phosphorylation of CRY1 by Adenosine monophosphate-activated kinase (AMPK) enhances degradation of CRY1. PER and CRY are subsequently polyubiquitinated and proteolyzed by the 26S proteasome.
The circadian clock is cell-autonomous and some, but not all cells of the body exhibit circadian rhythms in metabolism, cell division, and gene transcription. The suprachiasmatic nucleus (SCN) in the hypothalamus is the major clock in the body and receives its major input from light (via retinal neurons) and a minor input from nutrient intake. The SCN and other brain tissues determine waking and feeding cycles and influence the clocks in other tissues by hormone secretion and nervous stimulation. Independently of the SCN, other tissues such as liver receive inputs from signals from the brain and from nutrients.
R-HSA-71403 Citric acid cycle (TCA cycle) In the citric acid or tricarboxylic acid (TCA) cycle, the acetyl group of acetyl CoA (derived primarily from oxidative decarboxylation of pyruvate, beta-oxidation of long-chain fatty acids, and catabolism of ketone bodies and several amino acids) can be completely oxidized to CO2 in reactions that also yield one high-energy phosphate bond (as GTP or ATP) and four reducing equivalents (three NADH + H+, and one FADH2). Then, the electron transport chain oxidizes NADH and FADH2 to yield nine more high-energy phosphate bonds (as ATP). All reactions of the citric acid cycle take place in the mitochondrion.
Eight canonical reactions mediate the synthesis of citrate from acetyl-CoA and oxaloacetate and the metabolism of citrate to re-form oxaloacetate. Three reactions are reversible: the interconversions of citrate and isocitrate, of fumarate and malate, and of malate and oxaloacetate. The reverse reactions are irrelevant under normal physiological conditions but appear to have a role in glucose- and glutamine-stimulated insulin secretion (Zhang et al., 2020) and cancer metabolism (e.g., Jiang et al., 2016). Succinate synthesis from succinyl-CoA can be coupled to the phosphorylation of either GDP (the canonical reaction) or ADP; we annotate both reactions. Two mitochondrial isocitrate dehydrogenase isozymes catalyze the oxidative decarboxylation of isocitrate to form alpha-ketoglutarate (2-oxoglutarate): IDH3 catalyzes the canonical reaction coupled to the reduction of NAD+, while IDH2 catalyzes the same reaction coupled to the reduction of NADP+, a reaction whose normal physiological function is unclear. Both reactions are annotated.
The cyclical nature of the reactions responsible for the oxidation of acetate was first suggested by Hans Krebs from biochemical studies of pigeon breast muscle (Krebs et al., 1938; Krebs and Eggleston, 1940). Ochoa and colleagues studied many molecular details of individual reactions, mainly by studying enzymes purified from pig hearts (Ochoa, 1980). While the human homologs of these enzymes have all been identified, their biochemical characterization has, in general, been limited, and many molecular details of the human reactions are inferred from those worked out in studies of the model systems. Studies examining the impact of elevated citric acid cycle intermediates such as succinate and fumarate led to the recognition of the role of metabolites in driving cancer progression ('oncometabolites') (Pollard et al., 2005; reviewed in Hayashi et al., 2018). The role of TCA enzymes in disease was reviewed by Kang et al., 2021.
R-HSA-373076 Class A/1 (Rhodopsin-like receptors) Rhodopsin-like receptors (class A/1) are the largest group of GPCRs and are the best studied group from a functional and structural point of view. They show great diversity at the sequence level and thus, can be subdivided into 19 subfamilies (Subfamily A1-19) based on a phylogenetic analysis (Joost P and Methner A, 2002). They represent members which include hormone, light and neurotransmitter receptors and encompass a wide range of functions including many autocrine, paracrine and endocrine processes.
R-HSA-373080 Class B/2 (Secretin family receptors) This family is known as Family B (secretin-receptor family, family 2) G-protein-coupled receptors. Family B GPCRs include secretin, calcitonin, parathyroid hormone/parathyroid hormone-related peptides and vasoactive intestinal peptide receptors; all of which activate adenylyl cyclase and the phosphatidyl-inositol-calcium pathway (Harmar AJ, 2001).
R-HSA-420499 Class C/3 (Metabotropic glutamate/pheromone receptors) The class C G-protein-coupled receptors are a class of G-protein coupled receptors that include the metabotropic glutamate receptors and several additional receptors (Brauner-Osborne H et al, 2007). Family C GPCRs have a large extracellular N-terminus which binds the orthosteric (endogenous) ligand. The shape of this domain is often likened to a clam. Several allosteric ligands to these receptors have been identified and these bind within the seven transmembrane region.
R-HSA-983169 Class I MHC mediated antigen processing & presentation Major histocompatibility complex (MHC) class I molecules play an important role in cell mediated immunity by reporting on intracellular events such as viral infection, the presence of intracellular bacteria or tumor-associated antigens. They bind peptide fragments of these proteins and presenting them to CD8+ T cells at the cell surface. This enables cytotoxic T cells to identify and eliminate cells that are synthesizing abnormal or foreign proteins. MHC class I is a trimeric complex composed of a polymorphic heavy chain (HC or alpha chain) and an invariable light chain, known as beta2-microglobulin (B2M) plus an 8-10 residue peptide ligand. Represented here are the events in the biosynthesis of MHC class I molecules, including generation of antigenic peptides by the ubiquitin/26S-proteasome system, delivery of these peptides to the endoplasmic reticulum (ER), loading of peptides to MHC class I molecules and display of MHC class I complexes on the cell surface.
R-HSA-9603798 Class I peroxisomal membrane protein import Most peroxisomal membrane proteins (PMPs) are inserted into the peroxisomal membrane by the receptor-chaperone PEX19 and the docking receptor PEX3 (Soukupova et al. 1999, Muntau et al. 2003, Fang et al. 2004, Fujiki et al. 2006, Matsuzono and Fujiki 2006, Matsuzono et al. 2006, Pinto et al. 2006, Sato et al. 2008, Sato et al. 2010, Schmidt et al. 2010, Hattula et al. 2014, reviewed in Fujiki et al. 2014, Mayerhofer 2016). PEX19 binds the PMP as it is translated in the cytosol. Recognition of the PMP by PEX 19 appears to depend on positively charged residues in the transmembrane domain of the PMP (Costello et al. 2017). The PEX19:PMP complex then interacts with PEX3 located in the peroxisomal membrane. Through a mechanism that is not yet clear, the PMP is inserted into the peroxisomal membrane and PEX19 dissociates from PEX3. A current model involves transfer of the PMP from PEX19 to a hydrophobic region of PEX3 followed by insertion of the PMP into the membrane (Chen et al. 2014, reviewed by Giannopoulou et al. 2016). The process does not appear to require hydrolysis of ATP or GTP (Pinto et al. 2006).
Unlike other PMPs, PEX3 is inserted into the peroxisomal membrane by binding PEX19 and then docking with PEX16 (Matsuzaki and Fujiki 2008). Both PEX3 and PEX16 can also be co-translationally inserted into the endoplasmic reticulum membrane (Kim et al. 2006, Yonekawa et al. 2011, Aranovich et al. 2014, Hua et al. 2015, Mayerhofer et al. 2016). This region of the ER membrane then buds to contribute to new peroxisomes. PEX3 is also observed to insert into the mitochondrial outer membrane (Sugiura et al. 2017). Regions of the ER membrane and mitochondrial outer membrane are then released to form pre-peroxisomal vesicles which fuse to form new peroxisomes (Sugiura et al. 2017). Peroxisomes therefore appear to arise from fission of existing peroxisomes and production of new peroxisomes from precursors derived from mitochondria and the ER (Sugiura et al. 2017, reviewed in Fujiki et al. 2014, Hua and Kim 2016).
R-HSA-1296053 Classical Kir channels Classical Kir channels are inwardly rectifying K+ channels with strong inwardly rectifying currents that contribute to highly negative resting membrane potential, prolonged action potential plateau and rapid repolarization in the final stage of action potential. Classical Kir channels are found in various cells such as cardiac myocytes, purkinje fibers, atrial and ventricular tissues. Rectification is caused by intracellular Mg2+ ions and polyamines.
R-HSA-173623 Classical antibody-mediated complement activation C1, the first component of complement is a complex containing three protein species, C1q, C1r, and C1s. C1q is assembled from six identical subunits each of which consists of three homologous chains (A, B, and C). These chains form a globular domain at the C-terminus, followed by the "neck" and a coil in the "stalk." The six subunits are held together by the collagenous stalk parts (giving rise to the comparison of C1q with a "bunch of six tulips"). The stalks also interact with the [C1s:C1r:C1r:C1s] tetramer assembled in a linear chain. Binding of an antigen to an antibody of the IgM or IgG class induces a conformational change in the Fc domain of the antibody that allows it to bind to the C1q component of C1. C1 activation requires interaction with two separate Fc domains, so pentavalent IgM antibody is far more efficient at complement activation than IgG antibody. Antibody binding results in a conformational change in the C1r component of the C1 complex and a proteolytic cleavage of C1r, activating it. Active C1r then cleaves and activates the C1s component of the C1 complex (Muller-Eberhard 1988).
R-HSA-8856828 Clathrin-mediated endocytosis Clathrin-mediated endocytosis (CME) is one of a number of process that control the uptake of material from the plasma membrane, and leads to the formation of clathrin-coated vesicles (Pearse et al, 1975; reviewed in Robinson, 2015; McMahon and Boucrot, 2011; Kirchhausen et al, 2014). CME contributes to signal transduction by regulating the cell surface expression and signaling of receptor tyrosine kinases (RTKs) and G-protein coupled receptors (GPCRs). Most RTKs exhibit a robust increase in internalization rate after binding specific ligands; however, some RTKs may also exhibit significant ligand-independent internalization (reviewed in Goh and Sorkin, 2013). CME controls RTK and GPCR signaling by organizing signaling both within the plasma membrane and on endosomes (reviewed in Eichel et al, 2016; Garay et al, 2015; Vieira et al, 1996; Sorkin and von Zastrow, 2014; Di Fiori and von Zastrow, 2014; Barbieri et al, 2016). CME also contributes to the uptake of material such as metabolites, hormones and other proteins from the extracellular space, and regulates membrane composition by recycling membrane components and/or targeting them for degradation.
Clathrin-mediated endocytosis involves initiation of clathrin-coated pit (CCP) formation, cargo selection, coat assembly and stabilization, membrane scission and vesicle uncoating. Although for simplicity in this pathway, the steps leading to a mature CCP are represented in a linear and temporally distinct fashion, the formation of a clathrin-coated vesicle is a highly heterogeneous process and clear temporal boundaries between these processes may not exist (see for instance Taylor et al, 2011; Antonescu et al, 2011; reviewed in Kirchhausen et al, 2014). Cargo selection in particular is a critical aspect of the formation of a mature and stable CCP, and many of the proteins involved in the initiation and maturation of a CCP contribute to cargo selection and are themselves stabilized upon incorporation of cargo into the nascent vesicle (reviewed in Kirchhausen et al, 2014; McMahon and Boucrot, 2011).
Although the clathrin triskelion was identified early as a major component of the coated vesicles, clathrin does not bind directly to membranes or to the endocytosed cargo. Vesicle formation instead relies on many proteins and adaptors that can bind the plasma membrane and interact with cargo molecules. Cargo selection depends on the recognition of endocytic signals in cytoplasmic tails of the cargo proteins by adaptors that interact with components of the vesicle's inner coat. The classic adaptor for clathrin-coated vesicles is the tetrameric AP-2 complex, which along with clathrin was identified early as a major component of the coat. Some cargo indeed bind directly to AP-2, but subsequent work has revealed a large family of proteins collectively known as CLASPs (clathrin- associated sorting proteins) that mediate the recruitment of diverse cargo into the emerging clathrin-coated vesicles (reviewed in Traub and Bonifacino, 2013). Many of these CLASP proteins themselves interact with AP-2 and clathrin, coordinating cargo recruitment with coat formation (Schmid et al, 2006; Edeling et al, 2006; reviewed in Traub and Bonifacino, 2013; Kirchhausen et al, 2014).
Initiation of CCP formation is also influenced by lipid composition, regulated by clathrin-associated phosphatases and kinases (reviewed in Picas et al, 2016). The plasma membrane is enriched in PI(4,5)P2. Many of the proteins involved in initiating clathrin-coated pit formation bind to PI(4,5)P2 and induce membrane curvature through their BAR domains (reviewed in McMahon and Boucrot, 2011; Daumke et al, 2014). Epsin also contributes to early membrane curvature through its Epsin N-terminal homology (ENTH) domain, which promotes membrane curvature by inserting into the lipid bilayer (Ford et al, 2002).
Following initiation, some CCPs progress to formation of vesicles, while others undergo disassembly at the cell surface without producing vesicles (Ehrlich et al, 2004; Loerke et al, 2009; Loerke et al, 2011; Aguet et al, 2013; Taylor et al, 2011). The assembly and stabilization of nascent CCPs is regulated by several proteins and lipids (Mettlen et al, 2009; Antonescu et al, 2011).
Maturation of the emerging clathrin-coated vesicle is accompanied by further changes in the lipid composition of the membrane and increased membrane curvature, promoted by the recruitment of N-BAR domain containing proteins (reviewed in Daumke et al, 2014; Ferguson and De Camilli, 2012; Picas et al, 2016). Some N-BAR domain containing proteins also contribute to the recruitment of the large GTPase dynamin, which is responsible for scission of the mature vesicle from the plasma membrane (Koh et al, 2007; Lundmark and Carlsson, 2003; Soulet et al, 2005; David et al, 1996; Owen et al, 1998; Shupliakov et al, 1997; Taylor et al, 2011; Ferguson et al, 2009; Aguet et al, 2013; Posor et al, 2013; Chappie et al, 2010; Shnyrova et al, 2013; reviewed in Mettlen et al, 2009; Daumke et al, 2014). After vesicle scission, the clathrin coat is dissociated from the new vesicle by the ATPase HSPA8 (also known as HSC70) and its DNAJ cofactor auxilin, priming the vesicle for fusion with a subsequent endocytic compartment and releasing clathrin for reuse (reviewed in McMahon and Boucrot, 2011; Sousa and Laufer, 2015).
R-HSA-110331 Cleavage of the damaged purine Damaged purines are cleaved from the sugar-phosphate backbone by purine-specific glycosylases (Saparbaev and Laval 1994, Lindahl and Wood 1999).
R-HSA-110329 Cleavage of the damaged pyrimidine Damaged pyrimidines are cleaved by pyrimide-specific glycosylases (Lindahl and Wood 1999).
R-HSA-9759218 Cobalamin (Cbl) metabolism The reactions by which adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl) cofactors are synthesized and regenerated are annotated here (Banerjee et al. 2021).
R-HSA-196741 Cobalamin (Cbl, vitamin B12) transport and metabolism Vitamin B12 (cobalamin) is a water soluble vitamin, consisting of a planar corrin ring coordinating with a cobalt atom through four nitrogen atoms. A 5,6 dimethylbenzamidizole base coordinates with the cobalt atom in the lower axial position. Groups that can coordinate with the cobalt atom in the upper axial position include methyl (methylcobalamin, MetCbl), adenosyl (adenosylcobalamin, AdoCbl) and cyano (cyanocobalamin (CNCbl)). Only bacteria and archaea synthesise cobalamin so humans need a dietary intake to prevent deficiency. Food derived from animals provides cobalamins (RCbl) including MeCbl and AdoCbl. CNCbl, a semi synthetic form of the vitamin produced from bacterial hydroxocobalamin is provided by many pharmaceuticals, supplements, and food additives.
Cbl derivatives function as cofactors in two reactions, AdoCbl in the conversion of homocysteine to methionine and MetCbl in the conversion of L-methylmalonyl CoA to succinyl CoA. Both reactions are essential for normal human function, however, and defects in the steps by which Cbl or CNCbl is taken up from the diet, transported to metabolically active cells, and transformed to AdoCbl and MeCbl are associated with severe defects in blood formation and neural function (Banerjee et al. 2021, Froese & Gravel 2010, Green 2010, Nielsen et al. 2012, Quadros 2010; Seetharam 1999).
The overall process of Cbl utilization is presented here in three parts: its uptake from the diet into gut enterocytes, its release into the blood, circulation within the body (including renal re-uptake), and delivery to the cells where it is used, and its metabolism in those cells to generate AdoCbl and MeCbl.
R-HSA-196783 Coenzyme A biosynthesis Coenzyme A (CoA) is a ubiquitous cofactor that functions as an acyl group carrier in diverse processes including fatty acid metabolism and the TCA cycle (Lipmann 1953). It is synthesized from the vitamin pantothenate in a sequence of five reactions (Daugherty et al. 2002; Leonardi et al. 2005; Robishaw and Neely 1985). These reactions all occur in the cytosol or the mitochondrial intermembrane space (Leonardi et al. 2005). A recently described transport protein appears to mediate the uptake of Coenzyme A into the mitochondrial matrix (Prohl et al. 2001).
R-HSA-2470946 Cohesin Loading onto Chromatin In mitotic telophase, as chromosomes decondense, cohesin complex associated with PDS5 (PDS5A and PDS5B) and WAPAL (WAPL) proteins is loaded onto chromatin (Shintomi and Hirano, 2009, Kueng et al. 2006, Gandhi et al. 2006, Chan et al. 2012). Cohesin loading is facilitated by the complex of NIPBL (SCC2) and MAU2 (SCC4) proteins, which constitute an evolutionarily conserved cohesin loading complex. MAU2 depletion in HeLa cells results in 2-3-fold reduction in the amount of cohesin in the chromatin fraction (Watrin et al. 2006). NIPBL mutations are the cause of the Cornelia de Lange syndrome, a dominantly inherited disorder characterized by facial malformations, limb defects, and growth and cognitive retardation (Tonkin et al. 2004). Cornelia de Lange syndrome can also be caused by mutations in cohesin subunits SMC1A (Musio et al. 2006, Borck et al. 2007, Deardorff et al. 2007, Pie et al. 2010) and SMC3 (Deardorff et al. 2007).
R-HSA-1650814 Collagen biosynthesis and modifying enzymes The biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proline and lysine residues may be hydroxylated by prolyl 3-, prolyl 4- and lysyl hydroxylases. 4-hydroxyproline is essential for intramolecular hydrogen bonding and stability of the triple helical collagenous domain. In fibril forming collagens approximately 50% of prolines are 4-hydroxylated; the extent of this and of 3-hydroxyproline and lysine hydroxylation varies between tissues and collagen types (Kivirikko et al. 1972, 1992). Hydroxylysine molecules can form cross-links between collagen molecules in fibrils, and are sites for glycosyl- and galactosylation. Collagen peptides all have non-collagenous domains; collagens within the subclasses have common chain structures. These non-collagenous domains have regulatory functions; some are biologically active when cleaved from the main peptide chain. Fibrillar collagens all have a large triple helical domain (COL1) bordered by N and C terminal extensions, called the N and C propeptides, which are cleaved prior to formation of the collagen fibril. The C propeptide, also called the NC1 domain, is highly conserved. It directs chain association during intracellular assembly of the procollagen molecule from three collagen propeptide alpha chains (Hulmes 2002). The N-propeptide has a short linker (NC2) connecting the main triple helix to a short minor one (COL2) and a globular N-terminal region NC3. NC3 domains are variable both in size and the domains they contain.
Collagen propeptides typically undergo a number of post-translational modifications. Proline and lysine residues are hydroxylated by prolyl 3-, prolyl 4- and lysyl hydroxylases. 4-hydroxyproline is essential for intramolecular hydrogen bonding and stability of the triple helical collagenous domain. Prolyl 4-hydroxylase may also have a role in alpha chain association as no association of the C-propeptides of type XII collagen was seen in the presence of prolyl 4-hydroxylase inhibitors (Mazzorana et al. 1993, 1996). In fibril forming collagens approximately 50% of prolines are 4-hydroxylated; the extent of this is species dependent, lower hydroxylation correlating with lower ambient temperature and thermal stability (Cohen-Solal et al. 1986, Notbohm et al. 1992). Similarly the extent of 3-hydroxyproline and lysine hydroxylation varies between tissues and collagen types (Kivirikko et al. 1992). Hydroxylysine molecules can form cross-links between collagen molecules in fibrils, and are sites for glycosyl- and galactosylation.
Collagen molecules fold and assemble through a series of distinct intermediates (Bulleid 1996). Individual collagen polypeptide chains are translocated co-translationally across the membrane of the endoplasmic reticulum (ER). Intra-chain disulfide bonds are formed within the N-propeptide, and hydroxylation of proline and lysine residues occurs within the triple helical domain (Kivirikko et al. 1992). When the peptide chain is fully translocated into the ER lumen the C-propeptide folds, the conformation being stabilized by intra-chain disulfide bonds (Doege and Fessler 1986). Pro alpha-chains associate via the C-propeptides (Byers et al. 1975, Bachinger et al. 1978), or NC2 domains for FACIT family collagens (Boudko et al. 2008) to form an initial trimer which can be stabilized by the formation of inter-chain disulfide bonds (Schofield et al. 1974, Olsen et al. 1976), though these are not a prerequisite for further folding (Bulleid et al. 1996). The triple helix then nucleates and folds in a C- to N- direction. The association of the individual chains and subsequent triple helix formation are distinct steps (Bachinger et al. 1980). The N-propeptides associate and in some cases form inter-chain disulfide bonds (Bruckner et al., 1978). Procollagen is released via carriers into the exracellular space (Canty & Kadler 2005). Fibrillar procollagens undergo removal of the C- and N-propeptides by procollagen C and N proteinases respectively, both Zn2+ dependent metalloproteinases. Propeptide processing is a required step for normal collagen I and III fibril formation, but collagens can retain some or all of their non-collagenous propeptides. Retained collagen type V and XI N-propeptides contribute to the control of fibril growth by sterically limiting lateral molecule addition (Fichard et al. 1995). Processed fibrillar procollagen is termed tropocollagen, which is considered to be the unit of higher order fibrils and fibres. Tropocollagens of the fibril forming collagens I, II, III, V and XI sponteneously aggregate in vitro in a manner that has been compared with crystallization, commencing with a nucleation event followed by subsequent organized aggregation (Silver et al. 1992, Prockop & Fertala 1998). Fibril formation is stabilized by lysyl oxidase catalyzed crosslinks between adjacent molecules (Siegel & Fu 1976).
R-HSA-8948216 Collagen chain trimerization The C-propeptides of collagen propeptide chains are essential for the association of three peptide chains into a trimeric but non-helical procollagen. This initial binding event determines the composition of the trimer, brings the individual chains into the correct register and initiates formation of the triple helix at the C-terminus, which then proceeds towards the N-terminus in a zipper-like fashion (Engel & Prockop 1991). Most early refolding studies were performed with collagen type III, which contains a disulfide linkage at the C-terminus of its triple helix (Bächinger et al. 1978, Bruckner et al. 1978) that acts as a permanent linker even after removal of the non-collagenous domains.
Mutations within the C-propeptides further suggest that they are crucial for the correct interaction of the three polypeptide chains and for subsequent correct folding (refs. in Boudko et al. 2011).
R-HSA-1442490 Collagen degradation Collagen fibril diameter and spatial organisation are dependent on the species, tissue type and stage of development (Parry 1988). The lengths of collagen fibrils in mature tissues are largely unknown but in tendon can be measured in millimetres (Craig et al. 1989). Collagen fibrils isolated from adult bovine corneal stroma had ~350 collagen molecules in transverse section, tapering down to three molecules at the growing tip (Holmes & Kadler 2005).
The classical view of collagenases is that they actively unwind the triple helical chain, a process termed molecular tectonics (Overall 2002, Bode & Maskos 2003), before preferentially cleaving the alpha2 chain followed by the remaining chains (Chung et al. 2004). More recently it has been suggested that collagen fibrils exist in an equilibrium between protected and vulnerable states (Stultz 2002, Nerenberg & Stultz 2008). The prototypical triple-helical structure of collagen does not fit into the active site of collagenase MMPs. In addition the scissile bonds are not solvent-exposed and are therefore inaccessible to the collagenase active site (Chung et al. 2004, Stultz 2002). It was realized that collagen must locally unfold into non-triple helical regions to allow collagenolysis. Observations using circular dichroism and differential scanning calorimetry confirm that there is considerable heterogeneity along collagen fibres (Makareeva et al. 2008) allowing access for MMPs at physiological temperatures (Salsas-Escat et al. 2010).
Collagen fibrils with cut chains are unstable and accessible to proteinases that cannot cleave intact collagen strands (Woessner & Nagase 2000, Somerville et al. 2003). Continued degradation leads to the formation of gelatin (Lovejoy et al. 1999). Degradation of collagen types other than I-III is less well characterized but believed to occur in a similar manner.
Metalloproteinases (MMPs) play a major part in the degradation of several extracellular macromolecules including collagens. MMP1 (Welgus et al. 1981), MMP8 (Hasty et al. 1987), and MMP13 (Knauper et al. 1996), sometimes referred to as collagenases I, II and III respectively, are able to initiate the intrahelical cleavage of the major fibril forming collagens I, II and III at neutral pH, and thus thought to define the rate-limiting step in normal tissue remodeling events. All can cleave additional substrates including other collagen subtypes. Collagenases cut collagen alpha chains at a single conserved Gly-Ile/Leu site approximately 3/4 of the molecule's length from the N-terminus (Fields 1991, Chung et al. 2004). The cleavage site is characterised by the motif G(I/L)(A/L); the G-I/L bond is cleaved. In collagen type I this corresponds to G953-I954 in the Uniprot canonical alpha chain sequences (often given as G775-I776 in literature). It is not clear why only this bond is cleaved, as the motif occurs at several other places in the chain. MMP14, a membrane-associated MMP also known as Membrane-type matrix metalloproteinase 1 (MT-MMP1), is able to cleave collagen types I, II and III (Ohuchi et al. 1997).
R-HSA-1474290 Collagen formation Collagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in mammals making up about 25% to 35% of whole-body protein content. A defining feature of collagens is the formation of trimeric left-handed polyproline II-type helical collagenous regions. The packing within these regions is made possible by the presence of the smallest amino acid, glycine, at every third residue, resulting in a repeating motif Gly-X-Y where X is often proline (Pro) and Y often 4-hydroxyproline (4Hyp). Gly-Pro-Hyp is the most common triplet in collagen (Ramshaw et al. 1998). Collagen peptide chains also have non-collagenous domains, with collagen subclasses having common chain structures. Collagen fibrils are mostly found in fibrous tissues such as tendon, ligament and skin. Other forms of collagen are abundant in cornea, cartilage, bone, blood vessels, the gut, and intervertebral disc. In muscle tissue, collagen is a major component of the endomysium, constituting up to 6% of muscle mass. Gelatin, used in food and industry, is collagen that has been irreversibly hydrolyzed. On the basis of their fibre architecture in tissues, the genetically distinct collagens have been divided into subgroups. Group 1 collagens have uninterrupted triple-helical domains of about 300 nm, forming large extracellular fibrils. They are referred to as the fibril-forming collagens, consisting of collagens types I, II, III, V, XI, XXIV and XXVII. Group 2 collagens are types IV and VII, which have extended triple helices (>350 nm) with imperfections in the Gly-X-Y repeat sequences. Group 3 are the short-chain collagens. These have two subgroups. Group 3A have continuous triple-helical domains (type VI, VIII and X). Group 3B have interrupted triple-helical domains, referred to as the fibril-associated collagens with interrupted triple helices (FACIT collagens, Shaw & Olsen 1991). FACITs include collagen IX, XII, XIV, XVI, XIX, XX, XXI, XXII and XXVI plus the transmembrane collagens (XIII, XVII, XXIII and XXV) and the multiple triple helix domains and interruptions (Multiplexin) collagens XV and XVIII (Myllyharju & Kivirikko 2004). The non-collagenous domains of collagens have regulatory functions; several are biologically active when cleaved from the main peptide chain. Fibrillar collagen peptides all have a large triple helical domain (COL1) bordered by N and C terminal extensions, called the N- and C-propeptides, which are cleaved prior to formation of the collagen fibril. The intact form is referred to as a collagen propeptide, not procollagen, which is used to refer to the trimeric triple-helical precursor of collagen before the propeptides are removed. The C-propeptide, also called the NC1 domain, directs chain association during assembly of the procollagen molecule from its three constituent alpha chains (Hulmes 2002).
Fibril forming collagens are the most familiar and best studied subgroup. Collagen fibres are aggregates or bundles of collagen fibrils, which are themselves polymers of tropocollagen complexes, each consisting of three polypeptide chains known as alpha chains. Tropocollagens are considered the subunit of larger collagen structures. They are approximately 300 nm long and 1.5 nm in diameter, with a left-handed triple-helical structure, which becomes twisted into a right-handed coiled-coil 'super helix' in the collagen fibril. Tropocollagens in the extracellular space polymerize spontaneously with regularly staggered ends (Hulmes 2002). In fibrillar collagens the molecules are staggered by about 67 nm, a unit known as D that changes depending upon the hydration state. Each D-period contains slightly more than four collagen molecules so that every D-period repeat of the microfibril has a region containing five molecules in cross-section, called the 'overlap', and a region containing only four molecules, called the 'gap'. The triple-helices are arranged in a hexagonal or quasi-hexagonal array in cross-section, in both the gap and overlap regions (Orgel et al. 2006). Collagen molecules cross-link covalently to each other via lysine and hydroxylysine side chains. These cross-links are unusual, occuring only in collagen and elastin, a related protein.
The macromolecular structures of collagen are diverse. Several group 3 collagens associate with larger collagen fibers, serving as molecular bridges which stabilize the organization of the extracellular matrix. Type IV collagen is arranged in an interlacing network within the dermal-epidermal junction and vascular basement membranes. Type VI collagen forms distinct microfibrils called beaded filaments. Type VII collagen forms anchoring fibrils. Type VIII and X collagens form hexagonal networks. Type XVII collagen is a component of hemidesmosomes where it is complexed wtih alpha6Beta4 integrin, plectin, and laminin-332 (de Pereda et al. 2009). Type XXIX collagen has been recently reported to be a putative epidermal collagen with highest expression in suprabasal layers (Soderhall et al. 2007). Collagen fibrils/aggregates arranged in varying combinations and concentrations in different tissues provide specific tissue properties. In bone, collagen triple helices lie in a parallel, staggered array with 40 nm gaps between the ends of the tropocollagen subunits, which probably serve as nucleation sites for the deposition of crystals of the mineral component, hydroxyapatite (Ca10(PO4)6(OH)2) with some phosphate. Collagen structure affects cell-cell and cell-matrix communication, tissue construction in growth and repair, and is changed in development and disease (Sweeney et al. 2006, Twardowski et al. 2007). A single collagen fibril can be heterogeneous along its axis, with significantly different mechanical properties in the gap and overlap regions, correlating with the different molecular organizations in these regions (Minary-Jolandan & Yu 2009).
R-HSA-140875 Common Pathway of Fibrin Clot Formation The common pathway consists of the cascade of activation events leading from the formation of activated factor X to the formation of active thrombin, the cleavage of fibrinogen by thrombin, and the formation of cleaved fibrin into a stable multimeric, cross-linked complex. Thrombin also efficiently catalyzes the activation of several factors required earlier in the clotting cascade, thus acting in effect as a positive regulator of clotting. At the same time, thrombin activates protein C, which in turn catalyzes the inactivation of several of these upstream factors, thereby limiting the clotting process. Thrombin can be trapped in stable, inactive complexes with: antithrombin-III (SERPINC1), a circulating blood protein; heparin cofactor II (SERPIND1) which inhibits thrombin in a dermatan sulfate–dependent manner in the arterial vasculature; protein C inhibitor (SERPINA5) that inhibits thrombin in complex with thrombomodulin; and Protease nexin-1 (SERPINE2) that inhibits thrombin at the vessel wall and platelet surface. The quantitative interplay among these positive and negative modulators is critical to the normal regulation of clotting, facilitating the rapid formation of a protective clot at the site of injury, while limiting and physically confining the process.
These events are outlined in the drawing: black arrows connect the substrates (inputs) and products (outputs) of individual reactions, and blue lines connect output activated enzymes to the other reactions that they catalyze.
R-HSA-8948700 Competing endogenous RNAs (ceRNAs) regulate PTEN translation Coding and non-coding RNAs can prevent microRNAs from binding to PTEN mRNA. These RNAs are termed competing endogenous RNAs or ceRNAs. Transcripts of the pseudogene PTENP1 and mRNAs transcribed from SERINC1, VAPA and CNOT6L genes exhibit this activity (Poliseno et al. 2010, Tay et al. 2011, Tay et al. 2014). SERINC1 mRNA will be annotated in this context when additional experimental details become available.
R-HSA-166658 Complement cascade In the complement cascade, a panel of soluble molecules rapidly and effectively senses a danger or damage and triggers reactions to provide a response that discriminates among foreign intruders, cellular debris, healthy and altered host cells (Ricklin D et al. 2010). Complement proteins circulate in the blood stream in functionally inactive states. When triggered the complement cascade generates enzymatically active molecules (such as C3/C5 convertases) and biological effectors: opsonins (C3b, C3d and C4b), anaphylatoxins (C3a and C5a), and C5b, which initiates assembly of the lytic membrane attack complex (MAC). Three branches lead to complement activation: the classical, lectin and alternative pathways (Kang YH et al. 2009; Ricklin D et al. 2010). The classical pathway is initiated by C1 complex binding to immune complexes, pentraxins or other targets such as apoptotic cells leading to cleavage of C4 and C2 components and formation of the classical C3 convertase, C4bC2a. The lectin pathway is activated by binding of mannan-binding lectin (MBL) to repetitive carbohydrate residues, or by binding of ficolins to carbohydrate or acetylated groups on target surfaces. MBL and ficolins interact with MBL-associated serine proteases (MASP) leading to cleavage of C4 and C2 and formation of the classical C3 convertase, C4bC2a. The alternative pathway is spontaneously activated by the hydrolysis of the internal thioester group of C3 to give C3(H2O). Alternative pathway activation involves interaction of C3(H2O) and/or previously generated C3b with factor B, which is cleaved by factor D to generate the alternative C3 convertases C3(H2O)Bb and/or C3bBb. All three pathways merge at the proteolytic cleavage of component C3 by C3 convertases to form opsonin C3b and anaphylatoxin C3a. C3b covalently binds to glycoproteins scattered across the target cell surface. This is followed by an amplification reaction that generates additional C3 convertases and deposits more C3b at the local site. C3b can also bind to C3 convertases switching them to C5 convertases, which mediate C5 cleavage leading to MAC formation. Thus, the activation of the complement system leads to several important outcomes: opsonization of target cells to enhance phagocytosis, lysis of target cells via membrane attack complex (MAC) assembly on the cell surface, production of anaphylatoxins C3a/C5a involved in the host inflammatory response, C5a-mediated leukocyte chemotaxis, and clearance of antibody-antigen complexes. The complement system is able to distinguish between pathological and physiological challenges, i.e. the outcomes of complement activation are predetermined by the trigger and are tightly tuned by a combination of initiation events with several regulatory mechanisms. These regulatory mechanisms use soluble (e.g., C4BP, CFI and CFH) and membrane-bound regulators (e.g., CR1, CD46(MCP), CD55(DAF) and CD59) and are coordinated by complement receptors such as CR1, CR2, etc. In response to microbial infection complement activation results in flagging microorganisms with opsonins for facilitated phagocytosis, formation of MAC on cells such as Gram-negative bacteria leading to cell lysis, and release of C3a and C5a to stimulate downstream immune responses and to attract leukocytes. Most pathogens can be eliminated by these complement-mediated host responses, though some pathogenic microorganisms have developed ways of avoiding complement recognition or blocking host complement attack resulting in greater virulence (Lambris JD et al. 2008; Serruto D et al. 2010). All three complement pathways (classical, lectin and alternative) have been implicated in clearance of dying cells (Mevorach D et al. 1998; Ogden CA et al. 2001; Gullstrand B et al.2009; Kemper C et al. 2008). Altered surfaces of apoptotic cells are recognized by complement proteins leading to opsonization and subsequent phagocytosis. In contrast to pathogens, apoptotic cells are believed to induce only a limited complement activation by allowing opsonization of altered surfaces but restricting the terminal pathway of MAC formation (Gershov D et al. 2000; Braunschweig A and Jozsi M 2011). Thus, opsonization facilitates clearance of dying cells and cell debris without triggering danger signals and further inflammatory responses (Fraser DA et al. 2007, 2009; Benoit ME et al. 2012). C1q-mediated complement activation by apoptotic cells has been shown in a variety of human cells: keratinocytes, human umbilical vein endothelial cells (HUVEC), Jurkat T lymphoblastoid cells, lung adenocarcinoma cells (Korb LC and Ahearn JM 1997; Mold C and Morris CA 2001; Navratil JS et al. 2001; Nauta AJ et al. 2004). In addition to C1q the opsonization of apoptotic Jurkat T cells with MBL also facilitated clearance of these cells by both dendritic cells (DC) and macrophages (Nauta AJ et al. 2004). Also C3b, iC3b and C4b deposition on apoptotic cells as a consequence of activation of the complement cascade may promote complement-mediated phagocytosis. C1q, MBL and cleavage fragments of C3/C4 can bind to several receptors expressed on macrophages (e.g. cC1qR (calreticulin), CR1, CR3, CR4) suggesting a potential clearance mechanism through this interaction (Mevorach D et al. 1998; Ogden CA et al. 2001). Apoptosis is also associated with an altered expression of complement regulators on the surface of apoptotic cells. CD46 (MCP) bound to the plasma membrane of a healthy cell protects it from complement-mediated attack by preventing deposition of C3b and C4b, and reduced expression of CD46 on dying cells may lead to enhanced opsonization (Elward K et al. 2005). Upregulation of CD55 (DAF) and CD59 on apoptotic cell surfaces may protect damaged cells against complement mediated lysis (Pedersen ED et al. 2007; Iborra A et al. 2003; Hensel F et al. 2001). In addition, fluid-phase complement regulators such as C4BP, CFH may also inhibit lysis of apoptotic cells by limiting complement activation (Trouw LA et al 2007; Braunschweig A and Jozsi M. 2011). Complement facilitates the clearance of immune complexes (IC) from the circulation (Chevalier J and Kazatchkine MD 1989; Nielsen CH et al. 1997). Erythrocytes bear clusters of complement receptor 1 (CR1 or CD35), which serves as an immune adherence receptor for C3 and/or C4 fragments deposited on IC that are shuttled to liver and spleen, where IC are transferred and processed by tissue macrophages through an Fc receptor-mediated process. Complement proteins are always present in the blood and a small percentage spontaneously activate. Inappropriate activation leads to host cell damage, so on healthy human cells any complement activation or amplification is strictly regulated by surface-bound regulators that accelerate decay of the convertases (CR1, CD55), act as a cofactor for the factor I (CFI)-mediated degradation of C3b and C4b (CR1, CD46), or prevent the formation of MAC (CD59). Soluble regulators such as C4BP, CFH and FHL1 recognize self surface pattern-like glycosaminoglycans and further impair activation. Complement components interact with other biological systems. Upon microbial infection complement acts in cooperation with Toll-like receptors (TLRs) to amplify innate host defense. Anaphylatoxin C5a binds C5a receptor (C5aR) resulting in a synergistic enhancement of the TLR and C5aR-mediated proinflammatory cytokine response to infection. This interplay is negatively modulated by co-ligation of TLR and the second C5a receptor, C5L2, suggesting the existence of complex immunomodulatory interactions (Kohl J 2006; Hajishengallis G and Lambris JD 2010). In addition to C5aR and C5L2, complement receptor 3 (CR3) facilitates TLR2 or TLR4 signaling pathways by promoting a recruitment of their sorting adaptor TIRAP (MAL) to the receptor complex (van Bruggen R et al. 2007; Kagan JC and Medzhitov R 2006). Complement may activate platelets or facilitate biochemical and morphological changes in the endothelium potentiating coagulation and contributing to homeostasis in response to injury (Oikonomopoulou K et al. 2012). The interplay of complement and coagulation also involves cleavage of C3 and C5 convertases by coagulation proteases, generating biologically active anaphylatoxins (Amara U et al. 2010). Complement is believed to link the innate response to both humoral and cell-mediated immunity (Toapanta FR and Ross TM 2006; Mongini PK et al. 1997). The majority of published data is based on experiments using mouse as a model organism. Further characterization of the influence of complement on B or T cell activation is required for the human system, since differences between murine models and the human system are not yet fully determined. Complement is also involved in regulation of mobilization and homing of hematopoietic stem/progenitor cells (HSPCs) from bone marrow to the circulation and peripheral tissue in order to accommodate blood cell replenishment (Reca R et al. 2006). Thus, the complement system orchestrates the host defense by sensing a danger signal and transmitting it into specific cellular responses while extensively communicating with associated biological pathways ranging from immunity and inflammation to homeostasis and development. Originally the larger fragment of Complement Factor 2 (C2) was designated C2a. However, complement scientists decided that the smaller of all C fragments should be designated with an 'a', the larger with a 'b', changing the nomenclature for C2. Recent literature may use the updated nomenclature and refer to the larger C2 fragment as C2b, and refer to the classical C3 convertase as C4bC2b. Throughout this pathway Reactome adheres to the original convention to agree with the current (Sep 2013) Uniprot names for C2 fragments. The complement cascade pathway is organised into the following sections: initial triggering, activation of C3 and C5, terminal pathway and regulation.
R-HSA-6799198 Complex I biogenesis Complex I (NADH:ubiquinone oxidoreductase or NADH dehydrogenase) utilises NADH formed from glycolysis and the TCA cycle to pump protons out of the mitochondrial matrix. It is the largest enzyme complex in the electron transport chain, containing 11 core and 34 accessory subunits. Seven subunits (ND1-6, ND4L) are encoded by mitochondrial DNA, the remainder are encoded in the nucleus. The enzyme has a FMN prosthetic group and 8 Iron-Sulfur (Fe-S) clusters. The subunits are assembled together in a coordinated manner via preassembled subcomplexes to form the mature holoenzyme. At least 24 so-called "assembly factor" proteins, acting intrinsically or transiently, are required for constructing complex I although their exact roles in the biogenesis are not fully understood (Fernandez-Vizarra et al. 2009, Mckenzie & Ryan 2010, Mimaki et al. 2012, Andrews et al. 2013; reviewed by Laube et al., 2024).
R-HSA-9865881 Complex III assembly Assembly of the cytochrome c (cytochrome bc1) reductase (Complex III) was mainly investigated in yeast. The process in humans is considered to recapitulate the process in the yeast system based on the high similarity in structure and composition of the yeast and human complexes. Human Complex III probably consists of two identical sub-complexes, each containing at least 11 subunits: the catalytic core containing cytochrome b (MT-CYTB), cytochrome c1 (CYC1), and the Rieske protein (UQCRFS1), as well as the additional subunits UQCRC1, UQCRC2, UQCRC10, UQCRC11, UQCRCB, UQCRCH, UQCRCQ (Guo et al., 2017; Dennerlein et al., 2021; reviewed in Ndi et al., 2018; Signes & Fernandez-Vizarra, 2018). While complex I, III, and IV form a supercomplex, there is no evidence of any physiological advantage of this configuration (reviewed in Kohler et al., 2023; Brischigliaro et al., 2023). Mutations in nuclear genes coding for subunits of Complex III, as well as assembly factors, can cause complex III deficiency (MC3D; reviewed in Fernández-Vizarra & Zeviani, 2015).
R-HSA-9864848 Complex IV assembly At least 30 proteins are required to form the functional human complex IV, 14 of which are complex subunits. The complex contains the cofactors heme a, heme a3, and one mononuclear copper (CuB) center in the COX1 subunit, and a binuclear copper (CuA) in COX2, as well as several lipid molecules (phosphatidylethanolamine, PE, cardiolipin, CL) in different subunits (PDB 5Z62; Zong et al., 2018). The insertion of these cofactors is an intricate process requiring many assembly factors (Nývltová et al, 2022; reviewed in Mick et al., 2011; Timón-Gómez et al., 2018; Watson & McStay, 2020; Dennerlein et al., 2023).
Mutations in any complex IV subunits or assembly factors lead to different types of complex IV deficiency, usually manifesting as Leigh syndrome (MIM:220110; reviewed in Pecina et al., 2004; Čunátová et al., 2020)
R-HSA-2514853 Condensation of Prometaphase Chromosomes The condensin I complex is evolutionarily conserved and consists of five subunits: two SMC (structural maintenance of chromosomes) family subunits, SMC2 and SMC4, and three non-SMC subunits, NCAPD2, NCAPH and NCAPG. The stoichiometry of the complex is 1:1:1:1:1 (Hirano and Mitchinson 1994, Hirano et al. 1997, Kimura et al. 2001). SMC2 and SMC4 subunits, shared between condensin I and condensin II, are DNA-dependent ATPases, and condensins are able to introduce positive supercoils into DNA in an ATP-dependent manner (Kimura and Hirano 1997).
Protein levels of condensin subunits are constant during the cell cycle, however condensins are enriched on mitotic chromosomes. Four of the five subunits, SMC4, NCAPD2, NCAPG and NCAPH, are phosphorylated in both mitotic and interphase HeLa cells, but on different sites (Takemoto et al. 2004). CDK1 (CDC2) in complex with CCNB (cyclin B) phosphorylates NCAPD2, NCAPG and NCAPH in mitosis (Kimura et al. 1998, Kimura et al. 2001, Takemoto et al. 2006, Murphy et al. 2008), but other mitotic kinases, such as PLK1 (St-Pierre et al. 2009), and other post-translational modifications, such as acetylation, may also be involved (reviewed by Bazile et al. 2010). Global proteomic analysis of human cell lines has identified N6-acetylation of lysine residues in condensin subunits SMC2, SMC4 and NCAPH (Choudhary et al. 2009). Another high throughput proteomic study showed that condensin I subunits NCAPD2 and NCAPH are phosphorylated upon DNA damage, probably by ATM or ATR kinase (Matsuoka et al. 2007).
As condensin I is cytosolic, it gains access to chromosomes only after the nuclear envelope breakdown at the start of prometaphase (Ono et al. 2004). Condensin I, activated by CDK1-mediated phosphorylation, promotes hypercondensation of chromosomes that were condensed in prophase through the action of condensin II (Hirota et al. 2004). AURKB may also regulate association of condensin I complex with chromatin (Lipp et al. 2007). Protein phosphatase PP2A acts independently of its catalytic activity to target condensin II complex to chromatin, but does not interact with condensin I (Takemoto et al. 2009). Full activation of condensin I requires dephosphorylation of sites modified by CK2 during interphase (Takemoto et al. 2006). Besides being essential for chromosome condensation in mitosis, condensin I may also contribute to cohesin removal from chromosome arms in prometaphase, but the exact mechanism is not known (Hirota et al. 2004).
R-HSA-2299718 Condensation of Prophase Chromosomes In mitotic prophase, the action of the condensin II complex enables initial chromosome condensation.
The condensin II complex subunit NCAPD3 binds monomethylated histone H4 (H4K20me1), thereby associating with chromatin (Liu et al. 2010). Binding of the condensin II complex to chromatin is partially controlled by the presence of RB1 (Longworth et al. 2008).
Two mechanisms contribute to the accumulation of H4K20me1 at mitotic entry. First, the activity of SETD8 histone methyltransferase peaks at G2/M transition (Nishioka et al. 2002, Rice et al. 2002, Wu et al. 2010). Second, the complex of CDK1 and cyclin B1 (CDK1:CCNB1) phosphorylates PHF8 histone demethylase at the start of mitosis, removing it from chromatin (Liu et al. 2010).
Condensin II complex needs to be phosphorylated by the CDK1:CCNB1 complex, and then phosphorylated by PLK1, in order to efficiently condense prophase chromosomes (Abe et al. 2011).
R-HSA-177135 Conjugation of benzoate with glycine Benzoic acid, widely used as a food preservative, is converted to hippuric acid by activation and conjugation with glycine. This was one of the first detoxification pathways discovered, and was formerly exploited clinically as an alternative means of nitrogen excretion in patients with urea cycle defects (Brusilow and Horwich 2001).
R-HSA-159424 Conjugation of carboxylic acids Xenobiotics and endogenous compounds containing carboxylate groups can be activated with coenzyme A to produce acyl-CoA thioesters and then conjugated with the amino groups of glycine or glutamine to form amide-linked conjugates. Clinically important substrates include benzoic acid, phenylacetic acid, and salicylic acid.
R-HSA-177162 Conjugation of phenylacetate with glutamine Phenylacetate metabolism is of clinical importance because its conjugation with glutamine to form phenylacetylglutamine, which can be excreted in the urine, provides an alternative pathway for nitrogen excretion in patients with urea cycle defects (James et al. 1972; Batshaw et al. 2001; Brusilow and Horwich 2001). This conjugation proceeds in two steps. First, phenylacetate and ATP react with coenzyme A to form phenylacetyl CoA, AMP, and pyrophosphate (Vessey et al. 1999). Two human CoA ligases have been characterized that catalyze this reaction efficiently in vitro: acyl-CoA synthetase medium-chain family member 1 (BUCS1) (Fujino et al. 2001) and xenobiotic/medium-chain fatty acid:CoA ligase (Vessey et al. 2003). Their relative contributions to phenylacetate metabolism in vivo are unknown. Second, phenylacetyl CoA and glutamine react to form phenyacetyl glutamine and Coenzyme A. The enzyme that catalyzes this reaction has been purified from human liver mitochondria and shown to be a distinct polypeptide species from glycine-N-acyltransferase (Webster et al. 1976). This human glutamine-N-acyltransferase activity has not been characterized by sequence analysis at the protein or DNA level, however, and thus cannot be associated with a known human protein in the annotation of phenylacetate conjugation.
R-HSA-177128 Conjugation of salicylate with glycine In the body, aspirin (acetylsalicylic acid) is hydrolyzed to salicylate (ST). ST can then be hydroxylated to yield gentisic acid, conjugated with glucuronate, or conjugated with glycine to yield molecules that are excreted by the kidneys. The third of these conjugation processes is annotated here. It is the major route of ST catabolism and accounts for 20–65% of the products (Hutt et al, 1986). The conjugation proceeds in two steps. First, ST and ATP react with coenzyme A to form salicylate-CoA (ST-CoA), AMP, and pyrophosphate in a reaction catalyzed by xenobiotic/medium-chain fatty acid:CoA ligase (Vessey et al. 2003). Second, ST-CoA and glycine react to form salicyluric acid and Coenzyme A (Mawal and Qureshi 1994).
R-HSA-5674400 Constitutive Signaling by AKT1 E17K in Cancer While AKT1 gene copy number, expression level and phosphorylation are often increased in cancer, only one low frequency point mutation has been repeatedly reported in cancer and functionally studied. This mutation represents a substitution of a glutamic acid residue with lysine at position 17 of AKT1, and acts by enabling AKT1 to bind PIP2. PIP2-bound AKT1 is phosphorylated by TORC2 complex and by PDPK1 that is always present at the plasma membrane, due to low affinity for PIP2. Therefore, E17K substitution abrogates the need for PI3K in AKT1 activation (Carpten et al. 2007, Landgraf et al. 2008).
R-HSA-2219530 Constitutive Signaling by Aberrant PI3K in Cancer Signaling by PI3K/AKT is frequently constitutively activated in cancer via gain-of-function mutations in one of the two PI3K subunits - PI3KCA (encoding the catalytic subunit p110alpha) or PIK3R1 (encoding the regulatory subunit p85alpha). Gain-of-function mutations activate PI3K signaling by diverse mechanisms. Mutations affecting the helical domain of PIK3CA and mutations affecting nSH2 and iSH2 domains of PIK3R1 impair inhibitory interactions between these two subunits while preserving their association. Mutations in the catalytic domain of PIK3CA enable the kinase to achieve an active conformation. PI3K complexes with gain-of-function mutations therefore produce PIP3 and activate downstream AKT in the absence of growth factors (Huang et al. 2007, Zhao et al. 2005, Miled et al. 2007, Horn et al. 2008, Sun et al. 2010, Jaiswal et al. 2009, Zhao and Vogt 2010, Urick et al. 2011).
R-HSA-5637810 Constitutive Signaling by EGFRvIII In glioblastoma, the most prevalent EGFR mutation, present in ~25% of tumors, is the deletion of the ligand binding domain of EGFR, accompanied with amplification of the mutated allele, which results in over-expression of the mutant protein known as EGFRvIII. EGFRvIII mutant is not able to bind a ligand, but dimerizes and autophosphorylates spontaneously and is therefore constitutively active (Fernandes et al. 2001). Point mutations in the extracellular domain of EGFR are also frequently found in glioblastoma, but ligand binding ability and responsiveness are preserved (Lee et al. 2006).
Similar to EGFR kinase domain mutants, EGFRvIII mutant needs to maintain association with the chaperone heat shock protein 90 (HSP90) for proper functioning (Shimamura et al. 2005, Lavictoire et al. 2003). CDC37 is a co-chaperone of HSP90 that acts as a scaffold and regulator of interaction between HSP90 and its protein kinase clients. CDC37 is frequently over-expressed in cancers involving mutant kinases and acts as an oncogene (Roe et al. 2004, reviewed by Gray Jr. et al. 2008).
Expression of EGFRvIII mutant results in aberrant activation of downstream signaling cascades, namely RAS/RAF/MAP kinase signaling and PI3K/AKT signaling, and possibly signaling by PLCG1, which leads to increased cell proliferation and survival, providing selective advantage to cancer cells that harbor EGFRvIII (Huang et al. 2007).
EGFRvIII mutant does not autophosorylate on the tyrosine residue Y1069 (i.e. Y1045 in the mature protein), a docking site for CBL, and is therefore unable to recruit CBL ubiquitin ligase, which enables it to escape degradation (Han et al. 2006)
R-HSA-1236382 Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants Signaling by EGFR is frequently activated in cancer through activating mutations in the coding sequence of the EGFR gene, resulting in expression of a constitutively active mutant protein.
Epidermal growth factor receptor kinase domain mutants are present in ~16% of non-small-cell lung cancers (NSCLCs), but are also found in other cancer types, such as breast cancer, colorectal cancer, ovarian cancer and thyroid cancer. EGFR kinase domain mutants harbor activating mutations in exons 18-21 which code for the kinase domain (amino acids 712-979) . Small deletions, insertions or substitutions of amino acids within the kinase domain lock EGFR in its active conformation in which the enzyme can dimerize and undergo autophosphorylation spontaneously, without ligand binding (although ligand binding ability is preserved), and activate downstream signaling pathways that promote cell survival (Greulich et al. 2005, Zhang et al. 2006, Yun et al. 2007, Red Brewer et al. 2009).
Point mutations in the extracellular domain of EGFR are frequently found in glioblastoma. Similar to kinase domain mutations, point mutations in the extracellular domain result in constitutively active EGFR proteins that signal in the absence of ligands, but ligand binding ability and responsiveness are preserved (Lee et al. 2006).
EGFR kinase domain mutants need to maintain association with the chaperone heat shock protein 90 (HSP90) for proper functioning (Shimamura et al. 2005, Lavictoire et al. 2003). CDC37 is a co-chaperone of HSP90 that acts as a scaffold and regulator of interaction between HSP90 and its protein kinase clients. CDC37 is frequently over-expressed in cancers involving mutant kinases and acts as an oncogene (Roe et al. 2004, reviewed by Gray Jr. et al. 2008).
Over-expression of the wild-type EGFR or EGFR cancer mutants results in aberrant activation of downstream signaling cascades, namely RAS/RAF/MAP kinase signaling and PI3K/AKT signaling, and possibly signaling by PLCG1, which leads to increased cell proliferation and survival, providing selective advantage to cancer cells that harbor activating mutations in the EGFR gene (Sordella et al. 2004, Huang et al. 2007).
While growth factor activated wild-type EGFR is promptly down-regulated by internalization and degradation, cancer mutants of EGFR demonstrate prolonged activation (Lynch et al. 2004). Association of HSP90 with EGFR kinase domain mutants negatively affects CBL-mediated ubiquitination, possibly through decreasing the affinity of EGFR kinase domain mutants for phosphorylated CBL, so that CBL dissociates from the complex upon phosphorylation and cannot perform ubiquitination (Yang et al. 2006, Padron et al. 2007).
Various molecular therapeutics are being developed to target aberrantly activated EGFR in cancer. Non-covalent (reversible) small tyrosine kinase inhibitors (TKIs), such as gefitinib and erlotinib, selectively bind kinase domain of EGFR, competitively inhibiting ATP binding and subsequent autophosphorylation of EGFR dimers. EGFR kinase domain mutants sensitive to non-covalent TKIs exhibit greater affinity for TKIs than ATP compared with the wild-type EGFR protein, and are therefore preferential targets of non-covalent TKI therapeutics (Yun et al. 2007). EGFR proteins that harbor point mutations in the extracellular domain also show sensitivity to non-covalent tyrosine kinase inhibitors (Lee et al. 2006). EGFR kinase domain mutants harboring small insertions in exon 20 or a secondary T790M mutation are resistant to reversible TKIs (Balak et al. 2006) due to increased affinity for ATP (Yun et al. 2008), and are targets of covalent (irreversible) TKIs that form a covalent bond with EGFR cysteine residue C397. However, effective concentrations of covalent TKIs also inhibit wild-type EGFR, causing severe side effects (Zhou et al. 2009). Hence, covalent TKIs have not shown much promise in clinical trials (Reviewed by Pao and Chmielecki in 2010).
R-HSA-2691232 Constitutive Signaling by NOTCH1 HD Domain Mutants The heterodimerization (HD) domain of NOTCH1, responsible for association of NOTCH1 extracellular and transmembrane regions after furin-mediated cleavage of NOTCH1 precursor, is one of the hotspots for gain-of-function NOTCH1 mutations in T-cell acute lymphoblastic leukemia (T-ALL) (Weng et al. 2004). NOTCH1 HD domain mutants are responsive to ligand binding, but the activation (through cleavage of S2 and S3 sites and release of the intracellular domain NICD1) also happens spontaneously, in the absence of DLL and JAG ligands (Malecki et al. 2006). The following NOTCH1 HD domain mutants were directly functionally studied by Malecki et al.: NOTCH1 V1576E, NOTCH1 F1592S, NOTCH1 L1593P, NOTCH1 L1596H, NOTCH1 R1598P, NOTCH1 I1616N, NOTCH1 I1616T, NOTCH1 V1676D, NOTCH1 L1678P, NOTCH1 I1680N, NOTCH1 A1701P and NOTCH1 I1718T; other frequent NOTCH1 HD domain mutants (NOTCH1 L1574P, NOTCH1 L1574Q and NOTCH1 L1600P) are assumed to behave in a similar way.
R-HSA-2894862 Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants When found in cis, HD and PEST domain mutations act synergistically, increasing NOTCH1 transcriptional activity up to ~40-fold, compared with up to ~10-fold and up to ~2-fold increase with HD mutations alone and PEST domain mutations alone, respectively (Weng et al. 2004). HD domain mutations enable spontaneous, ligand-independent, proteolytic release of the NICD1 fragment, although mutants remain responsive to ligand binding (Malecki et al. 2006), while PEST domain mutations prolong NICD1 half-life and transcriptional activity through interference with FBXW7 (FBW7)-mediated ubiquitination and degradation (Thompson et al. 2007, O'Neil et al. 2007). NOTCH1 HD+PEST domain mutants annotated here are NOTCH1 L1600P;P2514Rfs*4, NOTCH1 L1600P;Q2440*, NOTCH1 L1600P;Q2395* and NOTCH1 L1574P;P2474Afs*4.
R-HSA-2644606 Constitutive Signaling by NOTCH1 PEST Domain Mutants As NOTCH1 PEST domain is intracellular, NOTCH1 PEST domain mutants are expected to behave as the wild-type NOTCH1 with respect to ligand binding and proteolytic cleavage mediated activation of signaling. However, once the NICD1 fragment of NOTCH1 is released, PEST domain mutations prolong its half-life and transcriptional activity through interference with FBXW7 (FBW7)-mediated ubiquitination and degradation of NICD1 (Weng et al. 2004, Thompson et al. 2007, O'Neil et al. 2007). All NOTCH1 PEST domain mutants annotated here (NOTCH1 Q2395*, NOTCH1 Q2440*, NOTCH1 P2474Afs*4 and NOTCH1 P2514Rfs*4) either have a truncated PEST domain or lack the PEST domain completely.
R-HSA-2660826 Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant NOTCH1 t(7;9)(NOTCH1:M1580_K2555) mutant is expressed in a small subset of T-cell acute lymphoblastic leukemia (T-ALL) patients. This mutant protein results from a translocation that joins a portion of intron 24 of the NOTCH1 gene to the promoter sequence of T-cell receptor beta (TCRB), leading to overexpression of a truncated NOTCH1 protein in T-cells and their precursors. The truncated NOTCH1 contains amino acids 1580 to 2555 of the wild-type NOTCH1, lacking almost the entire extracellular domain, including EGF and LIN12 repeats (Ellisen et al. 1991). As EGF repeats are needed for NOTCH1 interaction with its ligands (DLL1, DLL4, JAG1, JAG2), the mutant NOTCH1 t(7;9)(NOTCH1:M1580_K2555) does not bind a ligand. The constitutive activity of NOTCH1 t(7;9)(NOTCH1:M1580_K2555) is based on its constitutive proteolytic processing into NOTCH1 intracellular domain (NICD1) by ADAM10/17 protease and gamma-secretase complex, as proteolytic cleavage sites are exposed in the absence of ligand binding in the mutant protein. Constitutively produced NICD1 accumulates in the nucleus, leading to aberrant activation of NOTCH1 target genes which play important roles in the development of T lymphocytes (Washburn et al. 1997. Radtke et al. 1999, Maillard et al. 2004, Sambandam et al. 2005, Tan et al. 2005). Infection of bone marrow cells with recombinant retroviruses that code for truncated NOTCH1 that resembles t(7;9)(NOTCH1:M1580_K2555) resulted in T-ALL-like illness in a portion of mice that received the infected bone-marrow transplant, with all tumors overexpressing truncated forms of NOTCH1 (Pear et al. 1996).
R-HSA-9634285 Constitutive Signaling by Overexpressed ERBB2 Overexpression of ERBB2 (HER2), usually as a consequence of ERBB2 gene amplification, results in formation of ERBB2 homodimers. Under normal conditions, only ERBB2 heterodimers form, as ERBB2 is expressed at low levels.
ERBB2 homodimerization leads to activation of ERBB2 signaling in the absence of growth factors. Signaling by ERBB2 homodimers mainly activates the RAS/RAF/MAPK signaling cascade, while PI3K/AKT signaling is not significantly affected (Pickl and Ries 2009).
Trastuzumab (Herceptin), a recombinant antibody clinically approved as an anti-cancer therapeutic for ERBB2-overexpressing cancers, preferentially binds to ERBB2 homodimers (Pickl and Ries 2009).
Accurate functional analysis of ERBB2 signaling may require 3D instead of 2D cell culture (Pickl and Ries 2009).
R-HSA-176407 Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase The activity of the APC/C must be appropriately regulated during the cell cycle to ensure the timely degradation of its substrates. Of particular importance is the conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase. Phosphorylation of both the APC/C complex and Cdh1 regulate this conversion. During mitosis, several APC/C subunits are phosphorylated increasing the activity of APC/C:Cdc20. However, phosphorylation of Cdh1 by mitotic Cyclin:Cdk complexes prevents it from activating the APC/C. Dephosphorylation of Cdh1 in late anaphase by Cdc14a results in the activation of APC/C:Cdh1 (reviewed in Castro et al, 2005).
R-HSA-6814122 Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding The chaperonin complex TRiC/CCT is needed for the proper folding of all five G-protein beta subunits (Wells et al. 2006). TRiC/CCT cooperates with the phosducin-like protein PDCL (commonly known as PhLP or PhLP1), which interacts with both TRiC/CCT and G-protein beta subunits 1-5 (GNB1, GNB2, GNB3, GNB4, GNB5) (Dupre et al. 2007, Howlett et al. 2009). PDCL enables completion of G-protein beta folding by TRiC/CCT, promotes release of folded G-protein beta subunits 1-4 (GNB1, GNB2, GNB3, GNB4) from the chaperonin complex, and facilitates the formation of the heterodimeric G-protein beta:gamma complex between G-protein beta subunits 1-4 and G-protein gamma subunits 1-12 (Lukov et al. 2005, Lukov et al. 2006, Howlett et al. 2009, Lai et al. 2013, Plimpton et al. 2015, Xie et al. 2015). In the case of G-protein beta 5 (GNB5), PDCL stabilizes the interaction of GNB5 with the TRiC/CCT and promotes GNB5 folding, thus positively affecting formation of GNB5 dimers with RGS family proteins (Howlett et al. 2009, Lai et al. 2013, Tracy et al. 2015). However, over-expression of PDCL interferes with formation of GNB5:RGS dimers as PDCL and RGS proteins bind to the same regions of the GNB5 protein (Howlett et al. 2009).
R-HSA-389958 Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding In the case of actin and tubulin folding, and perhaps other substrates, the emerging polypeptide chain is transferred from the ribosome to TRiC via Prefoldin (Vainberg et al., 1998).
R-HSA-388841 Costimulation by the CD28 family Optimal activation of T-lymphocytes requires at least two signals. A primary one is delivered by the T-cell receptor (TCR) complex after antigen recognition and additional costimulatory signals are delivered by the engagement of costimulatory receptors such as CD28. The best-characterized costimulatory pathways are mediated by a set of cosignaling molecules belonging to the CD28 superfamily, including CD28, CTLA4, ICOS, PD1 and BTLA receptors. These proteins deliver both positive and negative second signals to T-cells by interacting with B7 family ligands expressed on antigen presenting cells. Different subsets of T-cells have very different requirements for costimulation. CD28 family mediated costimulation is not required for all T-cell responses in vivo, and alternative costimulatory pathways also exist. Different receptors of the CD28 family and their ligands have different regulation of expression. CD28 is constitutively expressed on naive T cells whereas CTLA4 expression is dependent on CD28/B7 engagement and the other receptor members ICOS, PD1 and BTLA are induced after initial T-cell stimulation.
The positive signals induced by CD28 and ICOS molecules are counterbalanced by other members of the CD28 family, including cytotoxic T-lymphocyte associated antigen (CTLA)4, programmed cell death (PD)1, and B and T lymphocyte attenuator (BTLA), which dampen immune responses. The balance of stimulatory and inhibitory signals is crucial to maximize protective immune responses while maintaining immunological tolerance and preventing autoimmunity.
The costimulatory receptors CD28, CTLA4, ICOS and PD1 are composed of single extracellular IgV-like domains, whereas BTLA has one IgC-like domain. Receptors CTLA4, CD28 and ICOS are covalent homodimers, due to an interchain disulphide linkage. The costimulatory ligands B71, B72, B7H2, B7H1 and B7DC, have a membrane proximal IgC-like domain and a membrane distal IgV-like domain that is responsible for receptor binding and dimerization. CD28 and CTLA4 have no known intrinsic enzymatic activity. Instead, engagement by their physiologic ligands B71 and B72 leads to the physical recruitment and activation of downstream T-cell effector molecules.
R-HSA-71288 Creatine metabolism In humans, creatine is synthesized primarily in the liver and kidney, from glycine, arginine, and S-adenosylmethionine, in a sequence of two reactions. From the liver, creatine is exported to tissues such as skeletal muscle and brain, where it undergoes phosphorylation and serves as a short-term energy store. The mechanism by which creatine leaves producer tissues is unclear, but its uptake by consumer tissues is mediated by the SLC6A8 transporter.
Once formed, phosphocreatine undergoes a slow spontaneous reaction to form creatinine, which is excreted from the body.
R-HSA-166786 Creation of C4 and C2 activators Two pathways lead to a complex capable of activating C4 and C2.
The classical pathway is triggered by activation of the C1-complex, which consists of hexameric molecule C1q and a tetramer comprising two C1r and two C1s serine proteinases. This occurs when C1q binds to IgM or IgG complexed with antigens, a single IgM can initiate the pathway while multiple IgGs are needed, or when C1q binds directly to the surface of the pathogen. Binding leads to conformational changes in C1q, activating the serine protease activity of C1r, which then cleaves C1s, another serine protease. The C1r:C1s component is now capable of splitting C4 and C2 to produce the classical C3-convertase C4b2a. C1r and C1s are additionally controlled by C1-inhibitor.(Kerr MA 1980)
The lectin pathway is similar in operation but has different components.
Mannose-binding lectin (MBL) or ficolins (L-ficolin, M-ficolin and H-ficolin) initiate the lectin pathway cascade by binding to specific carbohydrate patterns on pathogenic cell surfaces. MBL and ficolins circulate in plasma in complexes with homodimers of MBL-associated serine proteases (MASP) (Fujita et al. 2004; Hajela et al. 2002). Upon binding of human lectin (MBL or ficolins) to the target surface the complex of lectin:MASP undergoes conformational changes, which results in the activation of MASPs by cleavage (Matsushita M et al. 2000; Fujita et al. 2004). Activated MASPs become capable of C4 and C2 cleavage, giving rise to the same C3 convertase C4b:C2a as the classical pathway.
R-HSA-8949613 Cristae formation Cristae are invaginations of the inner mitochondrial membrane that extend into the matrix and are lined with cytochrome complexes and F1Fo ATP synthase complexes. Cristae increase the surface area of the inner membranes allowing greater numbers of respiratory complexes. Cristae are also believed to serve as "proton pockets" to generate localized regions of higher membrane potential. The steps in the biogenesis of cristae are not yet completely elucidated (reviewed in Zick et al. 2009) but the formation of the Mitochondrial Contact Site and Cristae Organizing System (MICOS, formerly also known as MINOS, reviewed in Rampelt et al. 2016, Kozjak-Pavlovic 2016, van der Laan et al. 2016) and localized concentrations of cardiolipin are known to define the inward curvature of the inner membrane at the bases of cristae. MICOS also links these regions of the inner membrane with complexes (the SAM complex and, in fungi, the TOM complex) embedded in the outer membrane. CHCHD3 (MIC19) and IMMT (MIC60) subunits of MICOS also interact with OPA1 at the inner membrane (Darshi et al. 2011, Glytsou et al. 2016).
Formation of dimers or oligomers of the F1Fo ATP synthase complex causes extreme curvature of the inner membrane at the apices of cristae (reviewed in Seelert and Dencher 2011, Habersetzer et al. 2013). Defects in either MICOS or F1Fo ATP synthase oligomerization produce abnormal mitochondrial morphologies.
R-HSA-1236973 Cross-presentation of particulate exogenous antigens (phagosomes) Dendritic cells (DCs) take up and process exogenous particulate or cell-associated antigens such as microbes or tumor cells for MHC-I cross-presentation. Particulate antigens have been reported to be more efficiently cross-presented than soluble antigens by DCs (Khor et al. 2008). Particulate antigens are internalized by phagosomes. There are two established models that explain the mechanism by which exogenous particulate antigens are presented through MHC I; the cytosolic pathway where internalized antigens are somehow translocated from phagosomes into cytosol for proteasomal degradation and the vacuolar pathway (Lin et al. 2008, Amigorena et al. 2010).
R-HSA-1236978 Cross-presentation of soluble exogenous antigens (endosomes) Exogenous soluble antigens are cross-presented by dendritic cells, albeit with lower efficiency than for particulate substrates. Soluble antigens destined for cross-presentation are taken up by distinct endocytosis mechanisms which route them into stable early endosomes and then to the cytoplasm for proteasomal degradation and peptide loading.
R-HSA-2243919 Crosslinking of collagen fibrils After removal of the N- and C-procollagen propeptides, fibrillar collagen molecules aggregate into microfibrillar arrays, stabilized by covalent intermolecular cross-links. These depend on the oxidative deamination of specific lysine or hydroxylysine residues in the telopeptide region by lysyl oxidase (LOX) with the subsequent spontaneous formation of covalent intermolecular cross-links (Pinnell & Martin 1968, Siegel et al. 1970, 1974, Maki 2009, Nishioka et al. 2012). Hydroxylysine is formed intracellularly by lysine hydroxylases (LH). There are different forms of LH responsible for hydroxylation of helical and telopeptide lysines (Royce & Barnes 1985, Knott et al.1997, Takaluoma et al. 2007, Myllyla 2007). The chemistry of the cross-links formed depends on whether lysines or hydroxylysines are present in the telopeptides (Barnes et al. 1974), which depends on the proportion of collagen lysines post-translationally converted to hydroxylysine by LH. The lysine pathway predominates in adult skin, cornea and sclera while the hydroxylysine pathway occurs primarily in bone, cartilage, ligament, tendons, embryonic skin and most connective tissues (Eyre 1987, Eyre & Wu 2005, Eyre et al. 2008). Oxidative deamination of lysine or hydroxylysine residues by LOX generates the allysine and hydroxyallysine aldehydes respectively. These can spontaneously react with either another aldehyde to form an aldol condensation product (intramolecular cross-link), or with an unmodified lysine or hydroxylysine residue to form intermolecular cross-links.
The pathway of cross-linking is regulated primarily by the hydroxylation pattern of telopeptide and triple-helix domain lysine residues. When lysine residues are the source of aldehydes formed by lysyl oxidase the allysine cross-linking pathway leads to the formation of aldimine cross-links (Eyre & Wu 2005). These are stable at physiological conditions but readily cleaved at acid pH or elevated temperature. When hydroxylysine residues are the source of aldehydes formed by lysyl oxidase the hydroxyallysine cross-linking pathway leads to the formation of more stable ketoimine cross-links.
Telopeptide lysine residues can be converted by LOX to allysine, which can react with a helical hydroxylysine residue forming the lysine aldehyde aldimine cross-link dehydro hydroxylysino norleucine (deHHLNL) (Bailey & Peach 1968, Eyre et al. 2008). If the telopeptide residue is hydroxylysine, the hydroxyallysine formed by LOX can react with a helical hydroxylysine forming the Schiff base, which spontaneously undergoes an Amadori rearrangement resulting in the ketoimine cross link hydroxylysino 5 ketonorleucine (HLKNL). This stable cross-link is formed in tissues where telopeptide residues are predominanly hydroxylated, such as foetal bone and cartilage, accounting for the relative insolubility of collagen from these tissues (Bailey et al. 1998). In bone, telopeptide hydroxyallysines can react with the epsilon-amino group of a helical lysine (Robins & Bailey 1975). The resulting Schiff base undergoes Amadori rearrangement to form lysino-hydroxynorleucine (LHNL). An alternative mechanism of maturation of ketoimine cross-links has been reported in cartilage leading to the formation of arginoline (Eyre et al. 2010).
These divalent crosslinks greatly diminish as connective tissues mature, due to further spontaneous reactions (Bailey & Shimokomaki 1971, Robins & Bailey 1973) with neighbouring peptides that result in tri- and tetrafunctional cross-links. In mature tissues collagen cross-links are predominantly trivalent. The most common are pyridinoline or 3-hydroxypyridinium cross-links, namely hydroxylysyl-pyridinoline (HL-Pyr) and lysyl-pyridinoline (L-Pyr) cross-links (Eyre 1987, Ogawa et al. 1982, Fujimoto et al. 1978). HL-Pyr is formed from three hydroxylysine residues, HLKNL plus a further hydroxyallysine. It predominates in highly hydroxylated collagens such as type II collagen in cartilage. L-Pyr is formed from two hydroxylysines and a lysine, LKNL plus a further hydroxyallysine, found mostly in calcified tissues (Bailey et al. 1998). Trivalent collagen cross-links can also form as pyrroles, either Lysyl-Pyrrole (L-Pyrrole) or hydroxylysyl-pyrrole (HL-Pyrrole), respectively formed when LKNL or HLKNL react with allysine (Scott et al. 1981, Kuypers et al. 1992). A further three-way crosslink can form when DeH-HLNL reacts with histidine to form histidino-hydroxylysinonorleucine (HHL), found in skin and cornea (Yamauchi et al. 1987, 1996). This can react with an additional lysine to form the tetrafunctional cross-link histidinohydroxymerodesmosine (Reiser et al. 1992, Yamauchi et al. 1996).
Another mechanism which could be involved in the cross-linking of collagen IV networks is the sulfilimine bond (Vanacore et al. 2009), catalyzed by peroxidasin, an enzyme found in basement membrane (Bhave 2012).
To improve clarity inter-chain cross-linking is represented here for Collagen type I only. Although the formation of each type of cross-link is represented here as an independent event, the partial and random nature of lysine hydroxylation and subsequent lysyl oxidation means that any combination of these cross-linking events could occur within the same collagen fibril .
R-HSA-69273 Cyclin A/B1/B2 associated events during G2/M transition Cell cycle progression is regulated by cyclin-dependent protein kinases at both the G1/S and the G2/M transitions. The G2/M transition is regulated through the phosphorylation of nuclear lamins and histones (reviewed in Sefton, 2001).
The two B-type cyclins localize to different regions within the cell and are thought to have specific roles as CDK1-activating subunits (see Bellanger et al., 2007). Cyclin B1 is primarily cytoplasmic during interphase and translocates into the nucleus at the onset of mitosis (Jackman et al., 1995; Hagting et al., 1999). Cyclin B2 colocalizes with the Golgi apparatus and contributes to its fragmentation during mitosis (Jackman et al., 1995; Draviam et al., 2001).
R-HSA-69656 Cyclin A:Cdk2-associated events at S phase entry Cyclin A:Cdk2 plays a key role in S phase entry by phosphorylation of proteins including Cdh1, Rb, p21 and p27. During G1 phase of the cell cycle, cyclin A is synthesized and associates with Cdk2. After forming in the cytoplasm, the Cyclin A:Cdk2 complexes are translocated to the nucleus (Jackman et al.,2002). Prior to S phase entry, the activity of Cyclin A:Cdk2 complexes is negatively regulated through Tyr 15 phosphorylation of Cdk2 (Gu et al., 1995) and also by the association of the cyclin kinase inhibitors (CKIs), p27 and p21. Phosphorylation of cyclin-dependent kinases (CDKs) by the CDK-activating kinase (CAK) is required for the activation of the CDK2 kinase activity (Aprelikova et al., 1995). The entry into S phase is promoted by the removal of inhibitory Tyr 15 phosphates from the Cdk2 subunit of Cyclin A:Cdk2 complex by the Cdc25 phosphatases (Blomberg and Hoffmann, 1999) and by SCF(Skp2)-mediated degradation of p27/p21 (see Ganoth et al., 2001). While Cdk2 is thought to play a primary role in regulating entry into S phase, recent evidence indicates that Cdk1 is equally capable of promoting entry into S phase and the initiation of DNA replication (see Bashir and Pagano, 2005). Thus, Cdk1 complexes may also play a significant role at this point in the cell cycle.
R-HSA-69231 Cyclin D associated events in G1 Three D-type cyclins are essential for progression from G1 to S-phase. These D cyclins bind to and activate both CDK4 and CDK6. The formation of all possible complexes between the D-type cyclins and CDK4/6 is promoted by the proteins, p21(CIP1/WAF1) and p27(KIP1). The cyclin-dependent kinases are then activated due to phosphorylation by CAK. The cyclin dependent kinases phosphorylate the RB1 protein and RB1-related proteins p107 (RBL1) and p130 (RBL2). Phosphorylation of RB1 leads to release of activating E2F transcription factors (E2F1, E2F2 and E2F3). After repressor E2Fs (E2F4 and E2F5) dissociate from phosphorylated RBL1 and RBL2, activating E2Fs bind to E2F promoter sites, stimulating transcription of cell cycle genes, which then results in proper G1/S transition. The binding and sequestration of p27Kip may also contribute to the activation of CDK2 cyclin E/CDK2 cyclin A complexes at the G1/S transition (Yew et al., 2001).
R-HSA-69202 Cyclin E associated events during G1/S transition The transition from the G1 to S phase is controlled by the Cyclin E:Cdk2 complexes. As the Cyclin E:Cdk2 complexes are formed, the Cdk2 is phosphorylated by the Wee1 and Myt1 kinases. This phosphorylation keeps the Cdk2 inactive. In yeast this control is called the cell size checkpoint control. The dephosphorylation of the Cdk2 by Cdc25A activates the Cdk2, and is coordinated with the cells reaching the proper size, and with the DNA synthesis machinery being ready. The Cdk2 then phosphorylates G1/S specific proteins, including proteins required for DNA replication initiation. The beginning of S-phase is marked by the first nucleotide being laid down on the primer during DNA replication at the early-firing origins.Failure to appropriately regulate cyclin E accumulation can lead to accelerated S phase entry, genetic instability, and tumorigenesis. The amount of cyclin E protein in the cell is controlled by ubiquitin-mediated proteolysis (see Woo, 2003).This pathway has not yet been annotated in Reactome.
R-HSA-1614603 Cysteine formation from homocysteine Transsulfuration is the interconversion of homocysteine and cysteine, and it fully takes place in bacteria and some plants and fungi. Animals however have only one direction of this bidirectional path, the synthesis of cysteine from homocysteine via cystathionine. Because excess cysteine is degraded to hydrogen sulfide, which is now known as a neuromodulator and smooth muscle relaxant, this pathway is also the main source of its production, which takes place in the cytosol, as well as in extracellular space (Dominy & Stipanuk 2004, Bearden et al. 2010).
R-HSA-211897 Cytochrome P450 - arranged by substrate type
The P450 isozyme system is the major phase 1 biotransforming system in man, accounting for more than 90% of drug biotransformations. This system has huge catalytic versatility and a broad substrate specificity, acting upon xenobiotica and endogenous compounds. It is also called the mixed-function oxidase system, the P450 monooxygenases and the heme-thiolate protein system. All P450 enzymes are a group of heme-containing isozymes which are located on the membrane of the smooth endoplasmic reticulum. They can be found in all tissues of the human body but are most concentrated in the liver. The name "cytochrome P450" (CYP) is derived from the spectral absorbance maximum at 450nm when carbon monoxide binds to CYP in its reduced (ferrous, Fe2+) state. The basic reaction catalyzed by CYP is mono-oxygenation, that is the transfer of one oxygen atom from molecular oxygen to a substrate. The other oxygen atom is reduced to water during the reaction with the equivalents coming from the cofactor NADPH. The basic reaction is;
RH (substrate) + O2 + NADPH + H+ = ROH (product) + H2O + NADP+
The end results of this reaction can be (N-)hydroxylation, epoxidation, heteroatom (N-, S-) oxygenation, heteroatom (N-, S-, O-) dealkylation, ester cleavage, isomerization, dehydrogenation, replacement by oxygen or even reduction under anaerobic conditions.
The metabolites produced from these reactions can either be mere intermediates which have relatively little reactivity towards cellular sysytems and are readily conjugated, or, they can be disruptive to cellular systems. Indeed, inert compounds need to be prepared for conjugation and thus the formation of potentially reactive metabolites is in most cases unavoidable.
There are 57 human CYPs (in 18 families and 42 subfamilies), mostly concentrated in the endoplasmic reticulum of liver cells although many tissues have them to some extent (Nelson DR et al, 2004). CYPs are grouped into 14 families according to their sequence similarity. Generally, enzymes in the same family share 40% sequence similarity and 55% within a subfamily. Nomenclature of P450s is as follows. CYP (to represent cytochrome P450 superfamily), followed by an arabic number for the family, a capital letter for the subfamily and finally a second arabic number to denote the isoenzyme. An example is CYP1A1 which is the first enzyme in subfamily A of cytochrome P450 family 1.
The majority of the enzymes are present in the CYP1-4 families. CYP1-3 are primarily concerned with xenobiotic biotransformation whereas the other CYPs deal primarily with endogenous compounds. The CYP section is structured by the typical substrate they act upon. Of the 57 human CYPs, 7 encode mitochondrial enzymes, all involved in sterol biosynthesis. Of the remaining 50 microsomal enzymes, 20 act upon endogenous compounds, 15 on xenobiotics and 15 are the so-called "orphan enzymes" with no substrate identified.
The P450 catalytic cycle (picture) shows the steps involved when a substrate binds to the enzyme.
(1) The normal state of a P450 with the iron in its ferric [Fe3+] state.
(2) The substrate binds to the enzyme.
(3) The enzyme is reduced to the ferrous [Fe2+] state by the addition of an electron from NADPH cytochrome P450 reductase. The bound substrate facilitates this process.
(4,5) Molecular oxygen binds and forms an Fe2+OOH complex with the addition of a proton and a second donation of an electron from either NADPH cytochrome P450 reductase or cytochrome b5. A second proton cleaves the Fe2+OOH complex to form water.
(6) An unstable [FeO]3+ complex donates its oxygen to the substrate (7). The oxidised substrate is released and the enzyme returns to its initial state (1).
R-HSA-111461 Cytochrome c-mediated apoptotic response Upon its release from the mitochondrial intermembrane space, cytochrome c (CYSC) binds to and causes an ATP-mediated conformational change in the cytoplasmic adaptor protein apoptotic protease‑activating factor 1 (APAF1). This conformational change triggers the formation of procaspase-9-activating oligomeric protein complex named apoptosome. The active caspase‑9 holoenzyme activates downstream effector caspases‑3 and ‑7. The activated effector caspases then cleave various cellular proteins. R-HSA-1280215 Cytokine Signaling in Immune system Cytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concentrations. Cytokines bind to specific membrane receptors, which then signal the cell via second messengers, to regulate cellular activity. R-HSA-9707564 Cytoprotection by HMOX1 Expression of heme oxygenase 1 (HMOX1) is regulated by various indicators of cell stress, while HMOX2 is expressed constitutively. Both catalyze the breakdown of heme into biliverdin (BV), carbon monoxide (CO), and ferrous iron. Biliverdin is immediately reduced to bilirubin (BIL). Both bilirubin and carbon monoxide can localize to different compartments and outside the cell. Cytoprotection by HMOX1 is exerted directly by HMOX1 and by the antioxidant metabolites produced through the degradation of heme. Additionally, due to the reactive nature of labile heme, its degradation is intrinsically protective.Detection of cytosolic DNA requires multiple and possibly redundant sensors leading to activation of the transcription factor NF-kappaB and TBK1-mediated phosphorylation of the transcription factor IRF3. Cytosolic DNA also activates caspase-1-dependent maturation of the pro-inflammatory cytokines interleukin IL-1beta and IL-18. This pathway is mediated by AIM2. R-HSA-156584 Cytosolic sulfonation of small molecules Two groups of sulfotransferease (SULT) enzymes catalyze the transfer of a sulfate group from 3-phosphoadenosine 5-phosphosulfate (PAPS) to a hydroxyl group on an acceptor molecule, yielding a sulfonated acceptor and 3-phosphoadenosine 5-phosphate (PAP). One is localized to the Golgi apparatus and mediates the sulfonation of proteoglycans. The second, annotated here, is cytosolic and mediates the sulfonation of a diverse array of small molecules, increasing their solubilities in water and modifying their physiological functions. There are probably thirteen or more human cytosolic SULT enzymes; eleven of these have been purified and characterized enzymatically, and are annotated here (Blanchard et al. 2004; Gamage et al. 2005). These enzymes appear to be active as dimers. Their substrate specificities are typically broad, and not related in an obvious way to their structures; indeed, apparently orthologous human and rodent SULT enzymes can have different substrate specificities (Glatt 2000), and none has been exhaustively characterized. The substrates listed in the table and annotated here are a sample of the known ones, chosen to indicate the range of activity of these enzymes and to capture some of their known physiologically important targets. Absence of a small molecule - enzyme pair from the table, however, may only mean that it has not yet been studied. R-HSA-379716 Cytosolic tRNA aminoacylation Cytosolic tRNA synthetases catalyze the reactions of tRNAs encoded in the nuclear genome, their cognate amino acids, and ATP to form aminoacyl-tRNAs, AMP, and pyrophosphate. Eight of the tRNA synthetases, those specific for arginine, aspartate, glutamate and proline, glutamine, isoleucine, leucine, lysine, and methionine, associate to form a complex with three accessory proteins. Each of the component synthetases is active in vitro as a purified protein; complex formation is thought to channel aminoacylated tRNAs more efficiently to the site of protein synthesis in mRNA:ribosome complexes (Quevillon et al. 1999; Wolfe et al. 2003, 2005). R-HSA-1489509 DAG and IP3 signaling This pathway describes the generation of DAG and IP3 by the PLCgamma-mediated hydrolysis of PIP2 and the subsequent downstream signaling events. R-HSA-2172127 DAP12 interactions DNAX activation protein of 12kDa (DAP12) is an immunoreceptor tyrosine-based activation motif (ITAM)-bearing adapter molecule that transduces activating signals in natural killer (NK) and myeloid cells. It mediates signalling for multiple cell-surface receptors expressed by these cells, associating with receptor chains through complementary charged transmembrane amino acids that form a salt-bridge in the context of the hydrophobic lipid bilayer (Lanier et al. 1998). DAP12 homodimers associate with a variety of receptors expressed by macrophages, monocytes and myeloid cells including TREM2, Siglec H and SIRP-beta, as well as activating KIR, LY49 and the NKG2C proteins expressed by NK cells. DAP12 is expressed at the cell surface, with most of the protein lying on the cytoplasmic side of the membrane (Turnbull & Colonna 2007, Tessarz & Cerwenka 2008). R-HSA-2424491 DAP12 signaling In response to receptor ligation, the tyrosine residues in DAP12's immunoreceptor tyrosine-based activation motif (ITAM) are phosphorylated by Src family kinases. These phosphotyrosines form the docking site for the protein tyrosine kinase SYK in myeloid cells and SYK and ZAP70 in NK cells. DAP12-bound SYK autophosphorylates and phosphorylates the scaffolding molecule LAT, recruiting the proximal signaling molecules phosphatidylinositol-3-OH kinase (PI3K), phospholipase-C gamma (PLC-gamma), GADS (GRB2-related adapter downstream of SHC), SLP76 (SH2 domain-containing leukocyte protein of 76 kDa), GRB2:SOS (Growth factor receptor-bound protein 2:Son of sevenless homolog 1) and VAV. All of these intermediate signalling molecules result in the recruitment and activation of kinases AKT, CBL (Casitas B-lineage lymphoma) and ERK (extracellular signal-regulated kinase), and rearrangement of the actin cytoskeleton (actin polymerization) finally leading to cellular activation. PLC-gamma generates the secondary messengers diacylglycerol (DAG) and inositol-1,4,5-trisphosphate (InsP3), leading to activation of protein kinase C (PKC) and calcium mobilization, respectively (Turnbull & Colonna 2007, Klesney-Tait et al. 2006). R-HSA-180024 DARPP-32 events Dopamine- and cAMP-regulated phosphoprotein, Mr 32 kDa (DARPP-32), was identified as a major target for dopamine and protein kinase A (PKA) in striatum. Recent advances now indicate that regulation DARPP-32 phosphorylation provides a mechanism for integrating information arriving at dopaminoceptive neurons, in multiple brain regions, via a variety of neurotransmitters, neuromodulators, neuropeptides, and steroid hormones. Activation of PKA or PKG stimulates DARPP-32 phosphorylation at Thr34, converting DARPP-32 into a potent inhibitor of protein phosphatase-1 (PP-1). DARPP-32 is also phosphorylated at Thr75 by Cdk5, converting DARPP-32 into an inhibitor of PKA. Thus, DARPP-32 has the unique property of being a dual-function protein, acting either as an inhibitor of PP-1 or of PKA. R-HSA-418885 DCC mediated attractive signaling The DCC family includes DCC and neogenin in vertebrates. DCC is required for netrin-induced axon attraction. DCC is a transmembrane protein lacking any identifiable catalytic activity. Protein tyrosine kinase 2/FAK and src family kinases bind constitutively to the cytoplasmic domain of DCC and their activation couples to downstream intracellular signaling complex that directs the organization of actin. R-HSA-168928 DDX58/IFIH1-mediated induction of interferon-alpha/beta RIG-I-like helicases (RLHs) the retinoic acid inducible gene-I (RIG-I) and melanoma differentiation associated gene 5 (MDA5) are RNA helicases that recognize viral double-stranded RNA (dsRNA) present within the cytoplasm (Yoneyama M & Fujita T 2007, 2008). Upon viral infection dsRNA is generated by positive-strand RNA virus families such as Flaviviridae and Coronaviridae, negative-strand RNA virus families including Orthomyxoviridae and Paramyxoviridae, and DNA virus families such as Herpesviridae and Adenoviridae (Weber F et al. 2006; Son KN et al. 2015). Functionally RIG-I and MDA5 positively regulate the IFN genes in a similar fashion, however they differ in their response to different viral species. RIG-I is essential for detecting influenza virus, Sendai virus, VSV and Japanese encephalitis virus (JEV), whereas MDA5 is essential in sensing encephalomyocarditis virus (EMCV), Mengo virus and Theiler's virus, all of which belong to the picornavirus family. RIG-I and MDA5 signalling results in the activation of IKK epsilon and (TKK binding kinase 1) TBK1, two serine/threonine kinases that phosphorylate interferon regulatory factor 3 and 7 (IRF3 and IRF7). Upon phosphorylation, IRF3 and IRF7 translocate to the nucleus and subsequently induce interferon alpha (IFNA) and interferon beta (IFNB) gene transcription (Yoneyama M et al. 2004; Yoneyama M & Fujita T 2007, 2008). R-HSA-3134963 DEx/H-box helicases activate type I IFN and inflammatory cytokines production DHX36 and DHX9 are aspartate-glutamate-any amino acid aspartate/histidine (DExD/H) box helicase (DHX) proteins that localize in the cytosol. The DHX RNA helicases family includes a large number of proteins that are implicated in RNA metabolism. Members of this family, RIG-1 and MDA5, have been shown to sense a non-self RNA leading to type I IFN production. RNA helicases DHX36 and DHX9 were found to trigger host responses to non-self DNA in MyD88-dependent manner. DHX36 sensed CpG class A, while DHX9 sensed CpG class B. Both DHX36 and DHX9 were critical for antiviral immune responses in viral DNA-stimulated human plasmacytoid dendritic cells (pDC) (Kim T et al. 2010). R-HSA-73893 DNA Damage Bypass In addition to various processes for removing lesions from the DNA, cells have developed specific mechanisms for tolerating unrepaired damage during the replication of the genome. These mechanisms are collectively called DNA damage bypass pathways. The Y family of DNA polymerases plays a key role in DNA damage bypass.
Y family DNA polymerases, REV1, POLH (DNA polymerase eta), POLK (DNA polymerase kappa) and POLI (DNA polymerase iota), as well as the DNA polymerase zeta (POLZ) complex composed of REV3L and MAD2L2, are able to carry out translesion DNA synthesis (TLS) or replicative bypass of damaged bases opposite to template lesions that arrest high fidelity, highly processive replicative DNA polymerase complexes delta (POLD) and epsilon (POLE). REV1, POLH, POLK, POLI and POLZ lack 3'->5' exonuclease activity and exhibit low fidelity and weak processivity. The best established TLS mechanisms are annotated here. TLS details that require substantial experimental clarification have been omitted. For recent and past reviews of this topic, please refer to Lehmann 2000, Friedberg et al. 2001, Zhu and Zhang 2003, Takata and Wood 2009, Ulrich 2011, Saugar et al. 2014. R-HSA-5696394 DNA Damage Recognition in GG-NER In global genome nucleotide excision repair (GG-NER), the DNA damage is recognized by two protein complexes. The first complex consists of XPC, RAD23A or RAD23B, and CETN2. This complex probes the DNA helix and recognizes damage that disrupts normal Watson-Crick base pairing, which results in binding of the XPC:RAD23:CETN2 complex to the undamaged DNA strand. The second complex is a ubiquitin ligase UV-DDB that consists of DDB2, DDB1, CUL4A or CUL4B and RBX1. The UV-DDB complex is necessary for the recognition of UV-induced DNA damage and may contribute to the retention of the XPC:RAD23:CETN2 complex at the DNA damage site. The UV-DDB complex binds the damaged DNA strand (Fitch et al. 2003, Wang et al. 2004, Moser et al. 2005, Camenisch et al. 2009, Oh et al. 2011). R-HSA-73942 DNA Damage Reversal DNA damage can be directly reversed by dealkylation (Mitra and Kaina 1993). Three enzymes play a major role in reparative DNA dealkylation: MGMT, ALKBH2 and ALKBH3. MGMT dealkylates O-6-methylguanine in a suicidal reaction that inactivates the enzyme (Daniels et al. 2000, Rasimas et al. 2004, Duguid et al. 2005, Tubbs et al. 2007), while ALKBH2 and ALKBH3 dealkylate 1-methyladenine, 3-methyladenine, 3-methylcytosine and 1-ethyladenine (Duncan et al. 2002, Dango et al. 2011). R-HSA-2559586 DNA Damage/Telomere Stress Induced Senescence Reactive oxygen species (ROS), whose concentration increases in senescent cells due to oncogenic RAS-induced mitochondrial dysfunction (Moiseeva et al. 2009) or due to environmental stress, cause DNA damage in the form of double strand breaks (DSBs) (Yu and Anderson 1997). In addition, persistent cell division fueled by oncogenic signaling leads to replicative exhaustion, manifested in critically short telomeres (Harley et al. 1990, Hastie et al. 1990). Shortened telomeres are no longer able to bind the protective shelterin complex (Smogorzewska et al. 2000, de Lange 2005) and are recognized as damaged DNA.
The evolutionarily conserved MRN complex, consisting of MRE11A (MRE11), RAD50 and NBN (NBS1) subunits, binds DSBs (Lee and Paull 2005) and shortened telomeres that are no longer protected by shelterin (Wu et al. 2007). Once bound to the DNA, the MRN complex recruits and activates ATM kinase (Lee and Paull 2005, Wu et al. 2007), leading to phosphorylation of ATM targets, including TP53 (p53) (Banin et al. 1998, Canman et al. 1998, Khanna et al. 1998). TP53, phosphorylated on serine S15 by ATM, binds the CDKN1A (also known as p21, CIP1 or WAF1) promoter and induces CDKN1A transcription (El-Deiry et al. 1993, Karlseder et al. 1999). CDKN1A inhibits the activity of CDK2, leading to G1/S cell cycle arrest (Harper et al. 1993, El-Deiry et al. 1993).
SMURF2 is upregulated in response to telomere attrition in human fibroblasts and induces senecscent phenotype through RB1 and TP53, independently of its role in TGF-beta-1 signaling (Zhang and Cohen 2004). The exact mechanism of SMURF2 involvement is senescence has not been elucidated. R-HSA-5693606 DNA Double Strand Break Response DNA double-strand break (DSB) response involves sensing of DNA DSBs by the MRN complex which triggers ATM activation. ATM phosphorylates a number of proteins involved in DNA damage checkpoint signaling, as well as proteins directly involved in the repair of DNA DSBs. For a recent review, please refer to Ciccia and Elledge, 2010. R-HSA-5693532 DNA Double-Strand Break Repair Double-strand breaks (DSBs), one of the most deleterious types of DNA damage along with interstrand crosslinks, are caused by ionizing radiation or certain chemicals such as bleomycin. DSBs also occur physiologically, during the processes of DNA replication, meiotic exchange, and V(D)J recombination.
DSBs are sensed (detected) by the MRN complex. Binding of the MRN complex to the DSBs usually triggers ATM kinase activation, thus initiating the DNA double strand break response. ATM phosphorylates a number of proteins involved in DNA damage checkpoint signaling, as well as proteins directly involved in the repair of DNA DSBs. DSBs are repaired via homology directed repair (HDR) or via nonhomologous end-joining (NHEJ).
HDR requires resection of DNA DSB ends. Resection creates 3'-ssDNA overhangs which then anneal with a homologous DNA sequence. This homologous sequence can then be used as a template for DNA repair synthesis that bridges the DSB. HDR preferably occurs through the error-free homologous recombination repair (HRR), but can also occur through the error-prone single strand annealing (SSA), or the least accurate microhomology-mediated end joining (MMEJ). MMEJ takes place when DSB response cannot be initiated.
While HRR is limited to actively dividing cells with replicated DNA, error-prone NHEJ pathway functions at all stages of the cell cycle, playing the predominant role in both the G1 phase and in S-phase regions of DNA that have not yet replicated. During NHEJ, the Ku70:Ku80 heterodimer (also known as the Ku complex or XRCC5:XRCC6) binds DNA DSB ends, competing away the MRN complex and preventing MRN-mediated resection of DNA DSB ends. The catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs, PRKDC) is then recruited to DNA-bound Ku to form the DNA-PK holoenzyme. Two DNA-PK complexes, one at each side of the break, bring DNA DSB ends together, joining them in a synaptic complex. DNA-PK complex recruits DCLRE1C (ARTEMIS) to DNA DSB ends, leading to trimming of 3'- and 5'-overhangs at the break site, followed by ligation.
For review of this topic, please refer to Ciccia and Elledge 2010. R-HSA-73894 DNA Repair DNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, environmental chemicals and radiation that damage their DNA, thus corrupting genetic information. In addition, normal cellular pH and temperature create conditions that are hostile to the integrity of DNA and its nucleotide components. DNA damage can also arise as a consequence of spontaneous errors during DNA replication. The DNA repair machinery continuously scans the genome and maintains genome integrity by removing or mending any detected damage.
Depending on the type of DNA damage and the cell cycle status, the DNA repair machinery utilizes several different pathways to restore the genome to its original state. When the damage and circumstances are such that the DNA cannot be repaired with absolute fidelity, the DNA repair machinery attempts to minimize the harm and patch the insulted genome well enough to ensure cell viability.
Accumulation of DNA alterations that are the result of cumulative DNA damage and utilization of "last resort" low fidelity DNA repair mechanisms is associated with cellular senescence, aging, and cancer. In addition, germline mutations in DNA repair genes are the underlying cause of many familial cancer syndromes, such as Fanconi anemia, xeroderma pigmentosum, Nijmegen breakage syndrome and Lynch syndrome, to name a few.
When the level of DNA damage exceeds the capacity of the DNA repair machinery, apoptotic cell death ensues. Actively dividing cells have a very limited time available for DNA repair and are therefore particularly sensitive to DNA damaging agents. This is the main rationale for using DNA damaging chemotherapeutic drugs to kill rapidly replicating cancer cells.
There are seven main pathways employed in human DNA repair: DNA damage bypass, DNA damage reversal, base excision repair, nucleotide excision repair, mismatch repair, repair of double strand breaks and repair of interstrand crosslinks (Fanconi anemia pathway). DNA repair pathways are intimately associated with other cellular processes such as DNA replication, DNA recombination, cell cycle checkpoint arrest and apoptosis.
The DNA damage bypass pathway does not remove the damage, but instead allows translesion DNA synthesis (TLS) using a damaged template strand. Translesion synthesis allows cells to complete DNA replication, postponing the repair until cell division is finished. DNA polymerases that participate in translesion synthesis are error-prone, frequently introducing base substitutions and/or small insertions and deletions.
The DNA damage reversal pathway acts on a very narrow spectrum of damaging base modifications to remove modifying groups and restore DNA bases to their original state.
The base excision repair (BER) pathway involves a number of DNA glycosylases that cleave a vast array of damaged bases from the DNA sugar-phosphate backbone. DNA glycosylases produce a DNA strand with an abasic site. The abasic site is processed by DNA endonucleases, DNA polymerases and DNA ligases, the choice of which depends on the cell cycle stage, the identity of the participating DNA glycosylase and the presence of any additional damage. Base excision repair yields error-free DNA molecules.
Mismatch repair (MMR) proteins recognize mismatched base pairs or small insertion or deletion loops during DNA replication and correct erroneous base pairing by excising mismatched nucleotides exclusively from the nascent DNA strand, leaving the template strand intact.
Nucleotide excision repair pathway is involved in removal of bulky lesions that cause distortion of the DNA double helix. NER proteins excise the oligonucleotide that contains the lesion from the affected DNA strand, which is followed by gap-filling DNA synthesis and ligation of the repaired DNA molecule.
Double strand breaks (DSBs) in the DNA can be repaired via a highly accurate homologous recombination repair (HRR) pathway, or through error-prone nonhomologous end joining (NHEJ), single strand annealing (SSA) and microhomology-mediated end joining (MMEJ) pathways. DSBs can be directly generated by some DNA damaging agents, such as X-rays and reactive oxygen species (ROS). DSBs can also be intermediates of the Fanconi anemia pathway.
Interstrand crosslinking (ICL) agents damage the DNA by introducing covalent bonds between two DNA strands, which disables progression of the replication fork. The Fanconi anemia proteins repair the ICLs by unhooking them from one DNA strand. TLS enables the replication fork to bypass the unhooked ICL, resulting in two replicated DNA molecules, one of which contains a DSB and triggers double strand break repair, while the sister DNA molecule contains a bulky unhooked ICL, which is removed through NER.
Single strand breaks (SSBs) in the DNA, generated either by DNA damaging agents or as intermediates of DNA repair pathways such as BER, are converted into DSBs if the repair is not complete prior to DNA replication. Simultaneous inhibition of DSB repair and BER through cancer mutations and anti-cancer drugs, respectively, is synthetic lethal in at least some cancer settings, and is a promising new therapeutic strategy.
For reviews of DNA repair pathways, please refer to Lindahl and Wood 1999 and Curtin 2012.
R-HSA-69306 DNA Replication Studies in the past decade have suggested that the basic mechanism of DNA replication initiation is conserved in all kingdoms of life. Initiation in unicellular eukaryotes, in particular Saccharomyces cerevisiae (budding yeast), is well understood, and has served as a model for studies of DNA replication initiation in multicellular eukaryotes, including humans. In general terms, the first step of initiation is the binding of the replication initiator to the origin of replication. The replicative helicase is then assembled onto the origin, usually by a helicase assembly factor. Either shortly before or shortly after helicase assembly, some local unwinding of the origin of replication occurs in a region rich in adenine and thymine bases (often termed a DNA unwinding element, DUE). The unwound region provides the substrate for primer synthesis and initiation of DNA replication. The best-defined eukaryotic origins are those of S. cerevisiae, which have well-conserved sequence elements for initiator binding, DNA unwinding and binding of accessory proteins. In multicellular eukaryotes, unlike S. cerevisiae, these loci appear not to be defined by the presence of a DNA sequence motif. Indeed, choice of replication origins in a multicellular eukaryote may vary with developmental stage and tissue type. In cell-free models of metazoan DNA replication, such as the one provided by Xenopus egg extracts, there are only limited DNA sequence specificity requirements for replication initiation (Kelly & Brown 2000; Bell & Dutta 2002; Marahrens & Stillman 1992; Cimbora & Groudine 2001; Mahbubani et al 1992, Hyrien & Mechali 1993).
R-HSA-69002 DNA Replication Pre-Initiation Although, DNA replication occurs in the S phase of the cell cycle, the formation of the DNA replication pre-initiation complex begins during G1 phase.
R-HSA-5334118 DNA methylation Methylation of cytosine is catalyzed by a family of DNA methyltransferases (DNMTs): DNMT1, DNMT3A, and DNMT3B transfer methyl groups from S-adenosylmethionine to cytosine, producing 5-methylcytosine and homocysteine (reviewed in Klose and Bird 2006, Ooi et al. 2009, Jurkowska et al. 2011, Moore et al. 2013). (DNMT2 appears to methylate RNA rather than DNA.) DNMT1, the first enzyme discovered, preferentially methylates hemimethylated CG motifs that are produced by replication (template strand methylated, synthesized strand unmethylated). Thus it maintains existing methylation through cell division. DNMT3A and DNMT3B catalyze de novo methylation at unmethylated sites that include both CG dinucleotides and non-CG motifs.
DNA from adult humans contains about 0.76 to 1.00 mole percent 5-methylcytosine (Ehrlich et al. 1982, reviewed in Klose and Bird 2006, Ooi et al. 2009, Moore et al. 2013). Methylation of DNA occurs at cytosines that are mainly located in CG dinucleotides. CG dinucleotides are unevenly distributed in the genome. Promoter regions tend to have a high CG-content, forming so-called CG-islands (CGIs), while the CG-content in the remaining part of the genome is much lower. CGIs tend to be unmethylated, while the majority of CGs outside CGIs are methylated. Methylation in promoters and first exons tends to repress transcription while methylation in gene bodies (regions of genes downstream of the promoter and first exon) correlates with transcription (reviewed in Ehrlich and Lacey 2013, Kulis et al. 2013). Proteins such as MeCP2 and MBDs specifically bind 5-methylcytosine and may recruit other factors.
Mammalian development has two major episodes of genome-wide demethylation and remethylation (reviewed in Zhou 2012, Guibert and Weber 2013, Hackett and Surani 2013, Dean 2014). In mice about 1 day after fertilization the paternal genome is actively demethylated by TET proteins together with thymine DNA glycosylase and the maternal genome is demethylated by passive dilution during replication, however methylation at imprinted sites is maintained. The genome has its lowest methylation level about 3.5 days post-fertilization. Remethylation occurs by 6.5 days post-fertilization. The second demethylation-remethylation event occurs in primordial germ cells of the developing embryo about 12.5 days post-fertilization. DNMT3A and DNMT3B, together with the non-catalytic DNMT3L, play major roles in the remethylation events (reviewed in Chen and Chan 2014). How the methyltransferases are directed to particular regions of the genome remains an area of active research. The mechanisms at each locus may differ in detail but a connection between histone modifications and DNA methylation has been observed (reviewed in Rose and Klose 2014).
R-HSA-68952 DNA replication initiation DNA polymerases are not capable of de novo DNA synthesis and require synthesis of a primer, usually by a DNA-dependent RNA polymerase (primase) to begin DNA synthesis. In eukaryotic cells, the primer is synthesized by DNA polymerase alpha:primase. First, the DNA primase portion of this complex synthesizes approximately 6-10 nucleotides of RNA primer and then the DNA polymerase portion synthesizes an additional 20 nucleotides of DNA (Frick & Richardson 2002; Wang et al 1984).
R-HSA-69190 DNA strand elongation Accurate and efficient genome duplication requires coordinated processes to replicate two template strands at eucaryotic replication forks. Knowledge of the fundamental reactions involved in replication fork progression is derived largely from biochemical studies of the replication of simian virus and from yeast genetic studies. Since duplex DNA forms an anti-parallel structure, and DNA polymerases are unidirectional, one of the new strands is synthesized continuously in the direction of fork movement. This strand is designated as the leading strand. The other strand grows in the direction away from fork movement, and is called the lagging strand. Several specific interactions among the various proteins involved in DNA replication underlie the mechanism of DNA synthesis, on both the leading and lagging strands, at a DNA replication fork. These interactions allow the replication enzymes to cooperate in the replication process (Hurwitz et al 1990; Brush et al 1996; Ayyagari et al 1995; Budd & Campbell 1997; Bambara et al 1997).
R-HSA-376172 DSCAM interactions DSCAM (Down syndrome cell adhesion molecule) is one of the members of the Ig superfamily CAMs with a domain architecture comprising 10 Ig domains, 6 fibronectin type III (FN) repeats, a single transmembrane and a C terminal cytoplasmic domain. DSCAM is implicated in Down syndrome (DS) due to the chromosomal location of the DSCAM gene, but no evidence supports a direct involvement of DSCAM with DS. It likely functions as a cell surface receptor mediating axon pathfinding. Besides these important implications, little is known about the physiological function or the molecular mechanism of DSCAM signal transduction in mammalian systems. A closely related DSCAM paralogue Down syndrome cell adhesion moleculelike protein 1 (DSCAML1) is present in humans. Both these proteins are involved in homophilic intercellular interactions.
R-HSA-9669914 Dasatinib-resistant KIT mutants Dasatinib is a type II tyrosine kinase inhibitor that is active against KIT receptors with mutations in the juxtamembrane and activation loop domains, but shows only partial activity against KIT receptors with mutations at residue V654 (Schittenhelm et al, 2006; Serrano et al, 2019).
R-HSA-3769402 Deactivation of the beta-catenin transactivating complex The mechanisms involved in downregulation of TCF-dependent transcription are not yet very well understood. beta-catenin is known to recruit a number of transcriptional repressors, including Reptin, SMRT and NCoR, to the TCF/LEF complex, allowing the transition from activation to repression (Bauer et al, 2000; Weiske et al, 2007; Song and Gelmann, 2008). CTNNBIP1 (also known as ICAT) and Chibby are inhibitors of TCF-dependent signaling that function by binding directly to beta-catenin and preventing interactions with critical components of the transactivation machinery (Takemaru et al, 2003; Li et al, 2008; Tago et al, 2000; Graham et al, 2002; Daniels and Weiss, 2002). Chibby additionally promotes the nuclear export of beta-catenin in conjunction with 14-3-3/YWHAZ proteins (Takemura et al, 2003; Li et al, 2008). A couple of recent studies have also suggested a role for nuclear APC in the disassembly of the beta-catenin activation complex (Hamada and Bienz, 2004; Sierra et al, 2006). It is worth noting that while some of the players involved in the disassembly of the beta-catenin transactivating complex are beginning to be worked out in vitro, the significance of their role in vivo is not yet fully understood, and some can be knocked out with little effect on endogenous WNT signaling (see for instance Voronina et al, 2009).
R-HSA-429947 Deadenylation of mRNA Deadenylation of mRNA proceeds in two steps. According to current models, in the first step the poly(A) tail is shortened from about 200 adenosine residues to about 80 residues by the PAN2-PAN3 complex. In the second step the poly(A) tail is further shortened to 10-15 residues by either the CCR4-NOT complex or by the PARN exoribonuclease. How a particular mRNA is targeted to CCR4-NOT or PARN is unknown.
A number of other deadenylase enzymes can be identified in genomic searches. One particularly interesting one is nocturin, a protein that is related to the CCR-1 deadenylase and plays a role in circadian rhythms.
There is also evidence for networking between deadenylation and other aspects of gene expression. CCR4-NOT, for example, is known to be a transcription factor. PARN is part of a complex that regulates poly(A) tail length and hence translation in developing oocytes.
R-HSA-429914 Deadenylation-dependent mRNA decay After undergoing rounds of translation, mRNA is normally destroyed by the deadenylation-dependent pathway. Though the trigger is unclear, deadenylation likely proceeds in two steps: one catalyzed by the PAN2-PAN3 complex that shortens the poly(A) tail from about 200 adenosine residues to about 80 residues and one catalyzed by the CCR4-NOT complex or by the PARN enzyme that shortens the tail to about 10-15 residues.
After deadenylation the mRNA is then hydrolyzed by either the 5' to 3' pathway or the 3' to 5' pathway. It is unknown what determinants target a mRNA to one pathway or the other.
The 5' to 3' pathway is initiated by binding of the Lsm1-7 complex to the 3' oligoadenylate tail followed by decapping by the DCP1-DCP2 complex. The 5' to 3' exoribonuclease XRN1 then hydrolyzes the remaining RNA.
The 3' to 5' pathway is initiated by the exosome complex at the 3' end of the mRNA. The exosome processively hydrolyzes the mRNA from 3' to 5', leaving only a capped oligoribonucleotide. The cap is then removed by the scavenging decapping enzyme DCPS.
R-HSA-73887 Death Receptor Signaling The death receptors (DR), all cell-surface receptors, that belong to the TNF receptor superfamily (TNFRSF). The term death receptor refers to those members of the TNFRSF that contain a "death domain" (DD) within their cytoplasmic tail which provides the capacity for protein–protein interactions with other DD-containing proteins suach as FADD. The main signals transmitted from TNF death receptors such as TNFR1, TRAIL-R, and CD95/FAS in response to their cognate ligand binding result in an apoptotic signaling pathway characterized by direct activation of intracellular cysteine proteases (caspases), without directly involving the mitochondrial death pathway. However, these death receptors have also been shown to initiate survival signals via the activation of transcription factors NFκappaB and AP1. This project describes an assembly of the death-inducing signaling complex (DISC) downstream of TNFR1, TRAIL-R, and CD95/FAS and shows protein composition and stoichiometry within the DISC. However, the DISC signaling complex may vary in its components stoichiometry. DR signaling may trigger formation of higher order receptor structures or signaling through rearrangement of receptor chains, which is not reflected here. The project also describes neuron-type-specific signaling by the p75NTR death receptor (also known as NGFR) that can regulate a number of different biological activities in response to ligand binding, including cell death and/or survival, axonal growth and synaptic plasticity.
R-HSA-5607761 Dectin-1 mediated noncanonical NF-kB signaling In addition to the activation of canonical NF-kB subunits, activation of SYK pathway by Dectin-1 leads to the induction of the non-canonical NF-kB pathway, which mediates the nuclear translocation of RELB-p52 dimers through the successive activation of NF-kB-inducing kinase (NIK) and IkB kinase-alpha (IKKa) (Geijtenbeek & Gringhuis 2009, Gringhuis et al. 2009). Noncanonical activity tends to build more slowly and remain sustained several hours longer than does the activation of canonical NF-kB. The noncanonical NF-kB pathway is characterized by the post-translational processing of NFKB2 (Nuclear factor NF-kappa-B) p100 subunit to the mature p52 subunit. This subsequently leads to nuclear translocation of p52:RELB (Transcription factor RelB) complexes to induce cytokine expression of some genes (C-C motif chemokine 17 (CCL17) and CCL22) and transcriptional repression of others (IL12B) (Gringhuis et al. 2009, Geijtenbeek & Gringhuis 2009, Plato et al. 2013).
R-HSA-5621480 Dectin-2 family Dendritic cell-associated C-type lectin-2 (Dectin-2) family of C-type lectin receptors (CLRs) includes Dectin-2 (CLEC6A), blood dendritic antigen 2 (BDCA2/CLEC4C), macrophage C-type lectin (MCL/CLEC4D), Dendritic cell immunoreceptor (DCIR/CLEC4A) and macrophage inducible C-type lectin (Mincle/CLEC4E). These receptors possesses a single extracellular conserved C-type lectin domain (CTLD) with a short cytoplasmic tail that induces intracellular signalling indirectly by binding with the FCERG (High affinity immunoglobulin epsilon receptor subunit gamma) except for DCIR that has a longer cytoplasmic tail with an integral inhibitory signalling motif (Graham & Brown. 2009, Kerschera et al. 2013). CLEC6A (Dectin-2) binds to high mannose containing pathogen-associated molecular patterns (PAMPs) expressed by fungal hyphae, and CLEC4E (mincle) binds to alpha-mannaosyl PAMPs on fungal, mycobacterial and necrotic cell ligands. Both signaling pathways lead to Toll-like receptor (TLR)-independent production of cytokines such as tumor necrosis factor (TNF) and interleukin 6 (IL6). Similarities with Dectin-1 (CLC7A) signaling pathway suggests that both these CLRs couple SYK activation to NF-kB activation using a complex involving CARD9, BCL10 and MALT1 (Geijtenbeek & Gringhuis 2009).
R-HSA-5682113 Defective ABCA1 causes TGD In an ATP-dependent reaction, ATP-binding cassette sub-family A member 1 (ABCA1) mediates the movement of intracellular cholesterol to the extracellular face of the plasma membrane. Cholesterol associated with cytosolic vesicles is a substrate for this reaction. Under physiologocal conditions, the active form of ABCA1 is post-translationally modified (palmitoylated and phosphorylated), predominantly a tetramer and is associated with apolipoprotein A-I (APOA1). Defects in ABCA1 can cause Tangier disease (TGD; MIM:205400 aka high density lipoprotein deficiency type 1), an autosomal recessive disorder characterised by significantly reduced levels of plasma high density lipoproteins (HDL) resulting in tissue accumulation of cholesterol esters (Brooks-Wilson et al. 1999). Low HDL levels are among the most common biochemical abnormalities observed in coronary heart disease (CHD) patients (Kolovou et al. 2006, Iatan et al. 2008, Iatan et al. 2012).
R-HSA-5682294 Defective ABCA12 causes ARCI4B ATP-binding cassette sub-family A member 12 (ABCA12) is thought to function as an epidermal keratinocyte lipid transporter. These lipids form extracellular lipid layers in the stratum corneum of the epidermis, essential for skin barrier function. Defects in ABCA12 results in the loss of the skin lipid barrier, leading to autosomal recessive congenital ichthyosis 4B (ARCI4B; MIM:242500, aka harlequin ichthyosis, HI). ARCI4B shows the most severe phenotype of the congenital ichthyoses, with newborns having a thick covering of armour-like scales. The skin dries out to form hard diamond-shaped plaques separated by fissures. Affected babies are often born prematurely and rarely survive the perinatal period (Akiyama et al. 2005, Akiyama 2010, 2014).
R-HSA-5688399 Defective ABCA3 causes SMDP3 ATP-binding cassette sub-family A member 3 (ABCA3) plays an important role in the formation of pulmonary surfactant, probably by transporting phospholipids such as phosphatidylcholine (PC) and phosphatidylglycerol (PG) from the ER membrane to lamellar bodies (LBs). PC and PG are the major phospholipid constituents of pulmonary surfactant. LBs are the surfactant storage organelles of type II epithelial cells from where phospholipids can be secreted together with surfactant proteins (SFTPs) into the alveolar airspace. Defects in ABCA3 can cause pulmonary surfactant metabolism dysfunction type 3 (SMDP3; MIM:610921), resulting in respiratory distress in newborns and interstitial lung disease (ILD) in children (Whitsett et al. 2015).
R-HSA-5683678 Defective ABCA3 causes SMDP3 ATP-binding cassette sub-family A member 3 (ABCA3) is thought to play a role in the formation of pulmonary surfactant by transporting lipids such as cholesterol into lamellar bodies (LBs) in alveolar type II cells. In LBs, surfactant proteins and lipids are assembled into bilayer membranes that are secreted into the alveolar airspace, where they form a surface film at the air–liquid interface. Defects in ABCA3 can cause pulmonary surfactant metabolism dysfunction 3 (SMDP3), a usually fatal pulmonary disease in newborns, characterised by the absence of normal LBs and the presence of electron-dense inclusions within small vesicular structures. Loss of secretion of lipid pulmonary surfactants causes excessive lipoprotein accumulation in the alveoli resulting in severe respiratory distress (Shulenin et al. 2004, Quazi & Molday 2011, Tarling et al. 2014, Whitsett et al. 2015).
R-HSA-5678520 Defective ABCB11 causes PFIC2 and BRIC2 The bile salt export pump ABCB11 mediates the release of bile salts from liver cells into bile. Defects in ABCB11 can cause two clinically distinct forms of cholestasis; progressive familial intrahepatic cholestasis 2 (PFIC2; MIM:601847) and benign recurrent intrahepatic cholestasis 2 (BRIC2; MIM:605479). Cholestasis is characterized by the retention of bile acids or salts. Bile acids can damage hepatocytes and bile duct cells leading to inflammation, fibrosis, cirrhosis and eventually carcinogenesis. PFIC2 patients suffer from chronic cholestasis and develop liver fibrosis, cirrhosis and end-stage liver disease before adulthood. BRIC2 patients experience intermittent episodes of cholestasis that resolve spontaneously after weeks or months (Strubbe et al. 2012, Cuperus et al. 2014).
R-HSA-5678771 Defective ABCB4 causes PFIC3, ICP3 and GBD1 Multidrug resistance protein 3 (ATP-binding cassette sub-family B member 4, ABCB4 aka MDR3) mediates the ATP-dependent export of organic anions, phospholipids and drugs from hepatocytes into the canalicular lumen in the presence of bile salts, especially the export of phospholipids such as phosphatidylcholine (PC). Biliary phospholipids associate with bile salts and cholesterol in mixed micelles, thereby reducing the detergent activity and cytotoxicity of bile salts and preventing cholesterol crystallisation. Thus, ABCB4 plays a crucial role in bile formation and lipid homeostasis. Defects in ABCB4 result in a wide spectrum of cholestasis phenotypes, from progressive familial intrahepatic cholestasis 3 (PFIC3; MIM:602347) and intrahepatic cholestasis of pregnancy 3 (ICP3; MIM:614972) to gallbladder disease 1 (GBD1; MIM:600803) (Jacquemin et al. 2001, Davit-Spraul et al. 2010, Jacquemin 2012). In PFIC3, the biliary phospholipid level is substantially decreased despite the presence of bile acids. Cholestasis may be caused by the toxicity of detergent bile salts that are not associated with phospholipids, leading to bile canaliculus and biliary epithelium damage. ICP3 is a reversible form of cholestasis in the third trimester of pregnancy and quickly disappears after childbearing. GBD1 is one of the major digestive diseases. Gallstones composed of cholesterol (cholelithiasis) are the common manifestations of GBD1 in western countries. Most people with gallstones remain asymptomatic throughout their lifetimes but approximately 10-50% of individuals eventually develop symptoms.
R-HSA-5683371 Defective ABCB6 causes MCOPCB7 ATP-binding cassette sub-family B member 6 (ABCB6), uniquely located on the outer mitochondrial membrane in homodimeric form, plays a crucial role in haem synthesis by mediating porphyrin uptake into the mitochondria. Defects in ABCB6 can cause isolated colobomatous microphthalmia 7 (MCOPCB7; MIM:614497), a developmental defect of the eye resulting from abnormal or incomplete fusion of the optic fissure with associated microphthalmia (eyeballs are abnormally small). Coloboma is thought to play an important role in the early development of the CNS, including that of the eye (Wang et al. 2012).
R-HSA-5679001 Defective ABCC2 causes DJS Canalicular multispecific organic anion transporter 1 (ABCC2 aka multidrug resistance-associated protein 2, MRP2), in addition to transporting many organic anions, mediates the ATP-dependent transport of glutathione and glucuronate conjugates from hepatocytes into bile. ABCC2 transports with high affinity and efficiency mono- and di-glucuronated bilirubin into bile. Bilirubin, the end product of heme breakdown, is an important constituent of bile and is responsible for its characteristic colour. Defects in ABCC2 can cause Dubin-Johnson syndrome (DJS; MIM:237500), an autosomal recessive disorder characterised by conjugated hyperbilirubinemia (Dubin & Johnson 1954, Keppler 2014, Erlinger et al. 2014).
R-HSA-5690338 Defective ABCC6 causes PXE The multidrug resistance associated protein (MRPs) subfamily of the ABC transporter family can transport a wide and diverse range of organic anions that can be endogenous compounds and xenobiotics and their metabolites. The multidrug resistance-associated protein 6 (ABCC6 aka MOAT-E) can actively transport organic anions. Defects in ABCC6 can cause pseudoxanthoma elasticum (PXE; MIM:264800), a rare multisystem disorder characterized by accumulation of mineralized and fragmented elastic fibers in the skin, vasculature and the Burch membrane of the eye (Finger et al. 2009).
R-HSA-5683177 Defective ABCC8 can cause hypo- and hyper-glycemias ATP-binding cassette sub-family C member 8 (ABCC8) is a subunit of the beta-cell ATP-sensitive potassium channel (KATP). KATP channels play an important role in the control of insulin release. Elevation of the ATP:ADP ratio closes KATP channels leading to cellular depolarisation, calcium influx and exocytosis of insulin from its storage granules. Defects in ABCC8 can cause dysregulation of insulin secretion resulting in hyperglycemias or hypoglycemias. Specific phenotypes observed are noninsulin-dependent diabetes mellitus (NIDDM; MIM:125853), permanent neonatal diabetes mellitus (PNDM; MIM:606176), transient neonatal diabetes mellitus 2 (TNDM2; MIM:610374), familial hyperinsulinemic hypoglycemia 1 (HHF1; MIM:256450) and leucine-induced hypoglycemia (LIH; MIM:240800) (Edghill et al. 2010, Flanagan et al. 2009, Yorifuji 2014, Yang et al. 2010, Chandran et al. 2014).
R-HSA-5678420 Defective ABCC9 causes CMD10, ATFB12 and Cantu syndrome ATP-binding cassette sub-family C member 9 (ABCC9) forms cardiac and smooth muscle-type KATP channels with ATP-sensitive inward rectifier potassium channel 11 (KCNJ11). KCNJ11 forms the channel pore while ABCC9 is required for activation and regulation (Babenko et al. 1998, Tammaro & Ashcroft 2007). Inward rectifier potassium channels favor the flow of potassium into the cell rather than out of it. KATP channels open and close in response to intracellular changes in the ADP/ATP ratio, thereby linking the metabolic state of the cell to its membrane potential. Inhibition of KATP channel activity causes membrane depolarization and thereby activation of voltage-dependent Ca2+ channels, leading to Ca2+ influx and a rise in intracellular Ca2+ concentration. Correct maintenance of calcium balance is essential for the normal functioning of the heart.
Defects in ABCC9 can cause dilated cardiomyopathy 10 (CMD10: MIM:608569), a disorder characterised by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia (Bienengraeber et al. 2004). Defects in ABCC9 can also cause familial atrial fibrillation 12 (ATFB12; MIM:614050), characterised by disorganized atrial electrical activity and ineffective atrial contraction resulting in blood stasis in the atria and reduces ventricular filling. It can result in palpitations, syncope, thromboembolic stroke, and congestive heart failure (Olson et al. 2007). Defects in ABCC9 can also cause hypertrichotic osteochondrodysplasia (Cantu syndrome; MIM:239850), a rare disorder characterised by congenital hypertrichosis, neonatal macrosomia, a distinct osteochondrodysplasia and cardiomegaly (van Bon et al. 2012, Harakalova et al. 2012).
R-HSA-5684045 Defective ABCD1 causes ALD The 70-kDa peroxisomal membrane protein (PMP70) and the adrenoleukodystrophy protein (ALDP aka ABCD1) are half ATP binding cassette (ABC) transporters in the peroxisome membrane. They are involved in metabolic transport of long and very long chain fatty acids into peroxisomes. Mutations in the ALD gene result in the X-linked neurodegenerative disorder adrenoleukodystrophy (ALD; MIM:300100). ABCD1 deficiency impairs the peroxisomal beta-oxidation of very long-chain fatty acids (VLCFA) and facilitates their further chain elongation by ELOVL1 resulting in accumulation of VLCFA in plasma and tissues. While all patients with ALD have mutations in the ABCD1 gene, there is no general genotype-phenotype correlation. In addition to ABCD1, other genes and environmental factors determine clinical features of ALD (Kemp et al. 2012, Berger et al. 2014).
R-HSA-5683329 Defective ABCD4 causes MAHCJ ATP-binding cassette sub-family D member 4 (ABCD4) is thought to mediate the lysosomal export of cobalamin (Cbl aka vitamin B12) into the cytosol, making it available for the production of Cbl cofactors. Cbl is an important cofactor for correct haematological and neurological functions. Defects in ABCD4 can cause methylmalonic aciduria and homocystinuria, cblJ type (MAHCJ; MIM:614857), a genetically heterogeneous metabolic disorder of Cbl metabolism characterised by decreased levels of the coenzymes adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl). Clinically, symptoms include feeding difficulties, poor growth, hypotonia, lethargy, anaemia and delayed development (Coelho et al. 2012).
R-HSA-5679096 Defective ABCG5 causes sitosterolemia ATP-binding cassette sub-family G member 5 (ABCG5 aka sterolin-1), is a "half transporter", that forms a complex with another half transporter ABCG8 (aka sterolin-2) in the endoplasmic reticulum. This complex translocates to the plasma membrane to mediate the ATP-dependent intestinal absorption and facilitation of biliary secretion of cholesterol and phytosterols (e.g. sitosterol). Defects in either of these half transporters result in loss of enterocyte discrimination between cholesterol and sitosterol causing sterol accumulation and predisposition for atherosclerosis. Defects in ABCG5 are the cause of sitosterolemia (MIM:210250), characterised by unrestricted intestinal absorption of both cholesterol and plant-derived sterols causing hypercholesterolemia and premature coronary atherosclerosis. Patients with sitosterolemia absorb between 15 and 60% of ingested sitosterol and excrete only a fraction of this into the bile (Berge et al. 2000, Othman et al. 2013, Yu et al. 2014).
R-HSA-5679090 Defective ABCG8 causes GBD4 and sitosterolemia ATP-binding cassette sub-family G member 8 (ABCG8 aka sterolin-2), is a "half transporter", that forms a complex with another half transporter ABCG5 in the endoplasmic reticulum. This complex translocates to the plasma membrane to mediate the ATP-dependent intestinal absorption and facilitation of biliary secretion of cholesterol and phytosterols (eg sitosterol). Defects in either of these half transporters result in loss of enterocyte discrimination between cholesterol and sitosterol causing sterol accumulation and predisposition for atherosclerosis. Defects in ABCG8 are the cause of gallbladder disease 4 (GBD4; MIM:611465), one of the major digestive diseases. Gallstones are composed of cholesterol (cholelithiasis) and are the common manifestations of GBD in western countries (Buch et al. 2007, Rudkowska & Jones 2008, Jakulj et al. 2010). Defects in ABCG8 also cause sitosterolemia (MIM:210250), characterised by unrestricted intestinal absorption of both cholesterol and plant-derived sterols causing hypercholesterolemia and premature coronary atherosclerosis. Patients with sitosterolemia absorb between 15 and 60% of ingested sitosterol, and they excrete only a fraction into the bile (Berge et al. 2000, Othman et al. 2013, Yu et al. 2014).
R-HSA-5579031 Defective ACTH causes obesity and POMCD The precursor peptide pro-opiomelanocortin (POMC) gives rise to many peptide hormones through cleavage. The cleavage products corticotropin (ACTH) and beta-lipotropin give rise to smaller peptides that have distinct biologic activities: alpha-melanotropin and corticotropin-like intermediate lobe peptide (CLIP) are formed from ACTH; gamma-LPH and beta-endorphin are formed from beta-LPH. ACTH (POMC(138-176) stimulates the adrenal glands to release cortisol, a glucocorticoid released in response to stress whose primary functions are to stimulate gluconeogenesis, suppress the immune system and aid metabolism of fats, proteins and carbohydrates.
Defects in ACTH can cause obesity (MIM:601665) resulting in excessive accumulation of body fat (Challis et al. 2002, Millington 2013). Defects in ACTH can also cause pro-opiomelanocortinin deficiency (POMCD; MIM:609734) where affected individuals present early-onset obesity, adrenal insufficiency and red hair (Krude et al. 1998, Krude et al. 2003).
R-HSA-5579007 Defective ACY1 causes encephalopathy Aminoacylase 1 (ACY1) is a cytosolic, homodimeric zinc-binding metalloenzyme with a wide range of tissue expression. It hydrolyses acylated L-amino acids (except L-aspartate) into L-amino acids and an acyl group. It can also hydrolyse N-acetylcysteine-S-conjugates. Defects in ACY1 can cause aminoacylase-1 deficiency (ACY1D; MIM:609924) resulting in encephalopathy, delay in psychomotor development, seizures and increased urinary excretion of several N-acetylated amino acids (Sass et al. 2006, Sass et al. 2007).
R-HSA-9734735 Defective ADA disrupts (deoxy)adenosine deamination Normally in humans, adenosine and deoxyadenosine can be deaminated to inosine and deoxyinosine, catalyzed by ADA (adenosine deaminase). In the absence of ADA activity, however, accumulated nucleosides disrupt lymphoid cell function, leading to severe combined immunodeficiency (Hirschhorn et al. 1989, 1990).
R-HSA-5578997 Defective AHCY causes HMAHCHD Adenosylhomocysteinase (AHCY) is a tetrameric, NAD+-bound, cytosolic protein that regulates all adenosylmethionine (AdoMet) dependent transmethylations by hydrolysing the feedback inhibitor adenosylhomocysteine (AdoHcy) to homocysteine (HCYS) and adenosine (Ade-Rib). Defects in AHCY cause Hypermethioninemia with S-adenosylhomocysteine hydrolase deficiency (HMAHCHD; MIM:613752), a metabolic disorder characterised by hypermethioninemia associated with failure to thrive, psychomotor retardation, facial dysmorphism with abnormal hair and teeth and myocardiopathy (Baric et al. 2004).
R-HSA-4549380 Defective ALG1 causes CDG-1k Chitobiosyldiphosphodolichol beta-mannosyltransferase (ALG1) normally tranfers a mannose moiety to the lipid-linked oligosaccharide (LLO aka N-glycan precursor) which is required for subsequent N-glycosylation of proteins. Defects in ALG1 can cause congenital disorder of glycosylation 1k (ALG1-CDG, previously known as CDG1k; MIM:608540), a multisystem disorder characterised by under-glycosylated serum glycoproteins. CDG type 1 diseases result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. Compared to other CDGs, ALG1-CDG has a very severe phenotype, which can result in an early death (Schwarz et al. 2004, Kranz et al. 2004, Dupre et al. 2010).
R-HSA-4551295 Defective ALG11 causes CDG-1p GDP-Man:Man(3)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase (ALG11) transfers the fourth and fifth mannoses (Man) to the N-glycan precursor in an alpha-1,2 orientation. These additions are the last two on the cytosolic side of the ER membrane before the N-glycan is flipped to the luminal side of the membrane. Recently discovered defects in ALG11 have been linked to congential disorder of glycosylation, type 1p (ALG11-CDG, CGD1p) (Rind et al. 2010, Thiel et al. 2012). The disease is a multi-system disorder characterised by under-glycosylated serum glycoproteins. Early-onset developmental retardation, dysmorphic features, hypotonia, coagulation disorders and immunodeficiency are reported features of this disorder (Rind et al. 2010, Thiel et al. 2012).
R-HSA-4720489 Defective ALG12 causes CDG-1g Dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase (ALG12) (Chantret et al. 2002) normally tranfers the 8th mannose moiety to the lipid-linked oligosaccharide (LLO aka N-glycan precursor) which is required for subsequent N-glycosylation of proteins. Defects in ALG12 are associated with congenital disorder of glycosylation 1g (ALG12-CDG, CDG1g; MIM:607143), a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins (Chantret et al. 2002, Grubenmann et al. 2002). CDG type 1 diseases result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency.
R-HSA-5633231 Defective ALG14 causes ALG14-CMS UDP-N-acetylglucosamine transferase subunit ALG14 homolog (ALG14) forms a complex with ALG13 protein and is required for the addition of the second N-acetylglucosamine (GlcNAc) to the lipid linked oligosaccharide (LLO) intermediate (GlcNAcDOLDP) (Gao et al. 2005). Defects in ALG14 can cause congenital myasthenic syndrome (ALG14-CMS), which is due to a defect in neuromuscular signal transmission (Cossins et al. 2013). The most commonly affected muscles include proximal limb muscles. Mutations causing ALG14-CMS include p.P65L and p.R104* (Cossins et al. 2013).
R-HSA-4549349 Defective ALG2 causes CDG-1i Alpha 1,3/1,6 mannosyltransferase ALG2 (ALG2) is a bifunctional mannosyltransferase normally tranfers a mannose moiety to the lipid linked oligosaccharide (LLO aka N glycan precursor) which is required for subsequent N glycosylation of proteins. Defects in ALG2 can cause congenital disorder of glycosylation 1i (ALG2-CDG, previously known as CDG1i; MIM:607906), a multisystem disorder characterised by under glycosylated serum glycoproteins. CDG type 1 diseases result in a wide phenotypic spectrum, from poor neurological development, psychomotor retardation and dysmorphic features to hypotonia, coagulation abnormalities and immunodeficiency (Thiel et al. 2003). Defect in ALG2 can also cause congenital myasthenic syndrome (ALG2-CMS), which is due to a defect in neuromuscular signal transmission (Cossins et al. 2013). The most commonly affected muscles include proximal limb muscles. Mutations causing ALG2-CMS include p.V68G and p.72_75delinsSPR (Cossins et al. 2013).
R-HSA-4720475 Defective ALG3 causes CDG-1d Dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase (ALG3) adds the sixth mannose (although the first to be derived from dolichyl-phosphate-mannose, DOLPman) to the lipid-linked oligosaccharide (LLO) intermediate GlcNAc(2) Man(5) (PPDol)1 (Korner et al. 1999). Defects in ALG3 are associated with congenital disorder of glycosylation 1d (ALG3-CDG, CDG1d; MIM:601110), a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins. CDG type 1 diseases result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency (Sun et al. 2005).
R-HSA-4724289 Defective ALG6 causes CDG-1c Dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase (ALG6) normally adds the first glucose moiety to the lipid-linked oligosaccharide precursor (LLO aka N-glycan precursor) which is required for subsequent N-glycosylation of proteins (Imbach et al. 1999). Defects in ALG6 can cause congenital disorder of glycosylation 1c (ALG6-CDG, CDG-1c; MIM:603147), a multisystem disorder characterised by under-glycosylated serum glycoproteins (Imbach et al. 1999, Imbach et al. 2000, Westphal et al. 2000, Sun et al. 2005). ALG6 deficiency is accompanied by an accumulation of the N-glycan precursor (GlcNAc)2 (Man)9 (PP-Dol)1 and is the second most common CDG disease subtype after PMM2-CDG (CDG-1a) (Imbach et al. 1999). CDG type 1 diseases result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency.
R-HSA-4724325 Defective ALG8 causes CDG-1h The probable dolichyl pyrophosphate Glc1Man9GlcNAc2 alpha-1,3-glucosyltransferase (ALG8) (Stanchi et al. 2001, Chantret et al. 2003) normally adds the second glucose moiety to the lipid-linked oligosaccharide precursor (LLO aka N-glycan precursor) which is required for subsequent N-glycosylation of proteins. Defects in ALG8 can cause congenital disorder of glycosylation 1h (ALG8-CDG, CDG-1h; MIM:608104), a multisystem disorder characterised by under-glycosylated serum glycoproteins (Chantret et al. 2003, Schollen et al. 2004). ALG8 deficiency is accompanied by an accumulation of the N-glycan precursor (Glc)1 (GlcNAc)2 (Man)9 (PP-Dol)1. CDG type 1 diseases result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency.
R-HSA-4720454 Defective ALG9 causes CDG-1l Alpha-1,2-mannosyltransferase ALG9 (ALG9) normally catalyses the transfer of mannose to the lipid-linked oligosaccharide (LLO) precursor. It adds the 7th and 9th mannose moieties to LLO. Defects in ALG9 are associated with congenital disorder of glycosylation 1l (ALG9-CDG, CDG1l; MIM:608776), a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins. CDG type 1 diseases result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency (Frank et al. 2004, Weinstein et al. 2005). The LLO profile showed accumulation of (GlcNAc)2 (Man)6 (PP-Dol)1 and (GlcNAc)2 (Man)8 (PP-Dol)1 fragments, suggesting a defect in ALG9 and correlating with the normal function of ALG9 in adding the 7th and 9th mannose moieties (Frank et al. 2004).
R-HSA-3359462 Defective AMN causes MGA1 Defects in AMN cause recessive hereditary megaloblastic anemia 1 (RH-MGA1 aka MGA1 Norwegian type or Imerslund-Grasbeck syndrome, I-GS; MIM:261100). The Norwegian cases described by Imerslund were due to defects in AMN (Imerslund 1960). The resultant malabsorption of Cbl (vitamin B12) leads to impaired B12-dependent folate metabolism and ultimately impaired thymine synthesis and DNA replication.
R-HSA-9734195 Defective APRT disrupts adenine salvage Normally in humans, adenine formed in processes such as polyamine biosynthesis can be salvaged by conversion to AMP, catalyzed by APRT (adenine phosphoribosyltransferase). In the absence of APRT activity, however, accumulated adenine is instead converted to 2,8-dioxo-adenine. Accumulation of insoluble crystals of 2,8-dioxo-adenine in the kidneys causes the kidney damage that is a major symptom of APRT deficiency in humans (Van Acker et al. 1977; Bollée et al. 2012).
R-HSA-5619099 Defective AVP does not bind AVPR1A,B and causes neurohypophyseal diabetes insipidus (NDI) Arginine vasopressin (AVP(20-28)) is a 9 amino-acid long signal peptide produced by cleavage of the precursor protein AVP in the hypothalamus. It mediates the reabsorption of water in the kidney and its synthesis and release are physiologically regulated by plasma osmolarity, blood pressure and/or blood volume. AVP(20-28) binds to vasopressin receptors AVPR1 and 2, located on the basolateral surface of the kidney collecting duct. This binding results in interaction of AVPRs with the G protein alpha-s. Following a cascade of downstream events, ultimately the water channel aquaporin 2 (AQP2) translocates from intracellular stores to the apical surface where it functions as the entry site for water reabsorption. When water balance is achieved, plasma levels of AVP(20-28) drop and AQP2 levels in the apical plasma membrane are decreased.
Mutations in AVP make it unavailable to its AVPRs in the kidney, resulting in dysregulation of water reabsorption. This can cause familial neurohypophyseal diabetes insipidus (FNDI), an autosomal dominant disorder characterised by persistent excessive thirst resulting in constant drinking (polydipsia) and passage of large volumes of urine (polyuria). In FNDI, the production and release of AVP from the posterior pituitary gland is impaired (Moeller et al. 2013).
R-HSA-9036092 Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) Arginine vasopressin (AVP(20-28)) is a 9 amino-acid long signal peptide produced by cleavage of the precursor protein AVP in the hypothalamus. It mediates the reabsorption of water in the kidney and its synthesis and release are physiologically regulated by plasma osmolarity, blood pressure and/or blood volume. AVP(20-28) binds to vasopressin receptors AVPR1 and 2, located on the basolateral surface of the kidney collecting duct. This binding results in interaction of AVPRs with the G protein alpha-s. Following a cascade of downstream events, ultimately the water channel aquaporin 2 (AQP2) translocates from intracellular stores to the apical surface where it functions as the entry site for water reabsorption. When water balance is achieved, plasma levels of AVP(20-28) drop and AQP2 levels in the apical plasma membrane are decreased.
Mutations in AVP make it unavailable to its AVPRs in the kidney, resulting in dysregulation of water reabsorption. This can cause familial neurohypophyseal diabetes insipidus (FNDI), an autosomal dominant disorder characterised by persistent excessive thirst resulting in constant drinking (polydipsia) and passage of large volumes of urine (polyuria). In FNDI, the production and release of AVP from the posterior pituitary gland is impaired (Moeller et al. 2013).
R-HSA-4420332 Defective B3GALT6 causes EDSP2 and SEMDJL1 The biosynthesis of dermatan sulfate/chondroitin sulfate and heparin/heparan sulfate glycosaminoglycans (GAGs) starts with the formation of a tetrasaccharide linker sequence attached to the core protein. Beta-1,3-galactosyltransferase 6 (B3GALT6) is one of the critical enzymes involved in the formation of this linker sequence. Defects in B3GALT6 causes Ehlers-Danlos syndrome progeroid type 2 (EDSP2; MIM:615349), a severe disorder resulting in a broad spectrum of skeletal, connective tissue and wound healing problems. Defects in B3GALT6 can also cause spondyloepimetaphyseal dysplasia with joint laxity type 1 (SEMDJL1; MIM:271640), characterised by spinal deformaty and lax joints, especially of the hands and respiratory compromise resulting in early death (Nakajima et al. 2013, Malfait et al. 2013).
R-HSA-5083635 Defective B3GALTL causes PpS Human beta-1,3-glucosyltransferase like protein (B3GALTL, HGNC Approved Gene Symbol: B3GLCT; MIM:610308; CAZy family GT31), localised on the ER membrane, glucosylates O-fucosylated proteins. The resultant glc-beta-1,3-fuc disaccharide modification on thrombospondin type 1 repeat (TSR1) domain-containing proteins is thought to assist in the secretion of many of these proteins from the ER lumen, and mediate an ER quality-control mechanism of folded TSRs (Vasudevan et al. 2015). Defects in B3GALTL can cause Peters plus syndrome (PpS; MIM:261540), an autosomal recessive disorder characterised by anterior eye chamber defects, short stature, delay in growth and mental developmental and cleft lip and/or palate (Heinonen & Maki 2009).
R-HSA-3560801 Defective B3GAT3 causes JDSSDHD Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferases1, 2 and 3 (B3GAT1-3) are involved in forming the linker tetrasaccharide present in heparan sulfate and chondroitin sulfate. Defects in B3GAT3 cause multiple joint dislocations, short stature, craniofacial dysmorphism, and congenital heart defects (JDSSDHD; MIM:245600). This is an autosomal recessive disease characterized by dysmorphic facies, elbow, hip and knee dislocations, clubfeet, short stature and cardiovascular defects (Steel & Kohl 1972, Bonaventure et al. 1992, Baasanjav et al. 2011). JDSSDHD has phenotypic similarities to Larsen syndrome (Larsen et al. 1950).
R-HSA-3656244 Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) Congenital disorders of glycosylation (CDG, previously called carbohydrate-deficient glycoprotein syndromes, CDGSs), are a group of hereditary multisystem disorders. They are characterized biochemically by hypoglycosylation of glycoproteins, diagnosed by isoelectric focusing (IEF) of serum transferrin. There are two types of CDG, types I and II. Type I CDG has defects in the assembly of lipid-linked oligosaccharides or their transfer onto nascent glycoproteins, whereas type II CDG comprises defects of trimming, elongation, and processing of protein-bound glycans. Clinical symptoms are dominated by severe psychomotor and mental retardation, as well as blood coagulation abnormalities (Jaeken 2013). B4GALT1-CDG (CDG type IId) is a multisystem disease, characterized by dysmorphic features, hydrocephalus, hypotonia and blood clotting abnormalities (Hansske et al. 2002).
R-HSA-4793953 Defective B4GALT1 causes CDG-2d Congenital disorders of glycosylation (CDG, previously called carbohydrate-deficient glycoprotein syndromes, CDGSs), are a group of hereditary multisystem disorders. They are characterized biochemically by hypoglycosylation of glycoproteins, diagnosed by isoelectric focusing (IEF) of serum transferrin. There are two types of CDG, types I and II. Type I CDG has defects in the assembly of lipid-linked oligosaccharides or their transfer onto nascent glycoproteins, whereas type II CDG comprises defects of trimming, elongation, and processing of protein-bound glycans. Clinical symptoms are dominated by severe psychomotor and mental retardation, as well as blood coagulation abnormalities (Jaeken 2013). B4GALT1-CDG (CDG type IId) is a multisystem disease, characterized by dysmorphic features, hydrocephalus, hypotonia and blood clotting abnormalities (Hansske et al. 2002).
R-HSA-3560783 Defective B4GALT7 causes EDS, progeroid type Ehlers–Danlos syndrome (EDS) is a group of inherited connective tissue disorders, caused by a defect in the synthesis of collagen types I or III. Abnormal collagen renders connective tissues more elastic. The severity of the mutation can vary from mild to life-threatening. There is no cure and treatment is supportive, including close monitoring of the digestive, excretory and particularly the cardiovascular systems. Defective B4GALT7, a galactosyltransferase important in proteoglycan synthesis, causes the progeroid variant of EDS (MIM:130070). Features include an aged appearance, developmental delay, short stature, generalized osteopenia, defective wound healing, hypermobile joints, hypotonic muscles, and loose but elastic skin (Okajima et al. 1999).
R-HSA-3371598 Defective BTD causes biotidinase deficiency BTD deficiency is an autosomal recessive disorder in which the body is unable to recycle and reuse biotin (Btn). This results in a secondary Btn deficiency that leads to juvenile-onset multiple carboxylase deficiency (MIM:253260) (Wolf 2012, Wolf et al. 1983). Patients present with neurological and cutaneous symptoms, including seizures, hypotonia, skin rash, and alopecia, usually between the second and fifth months of life (Wolf 2010). Children with profound BTD deficiency are treated with pharmacological doses of biotin (5-20 mg daily). Neonatal screening for BTD deficiency is performed in most states of the United States and many other countries.
R-HSA-9605310 Defective Base Excision Repair Associated with MUTYH MUTYH gene is located on chromosome 1 and encodes a DNA glycosylase involved in base excision repair (BER). MUTYH (MYH) functions as an adenine DNA glycosylase and removes adenines and 2-hydroxyadenines on the newly synthesized DNA strand mispaired with guanines or 8-oxoguanines. 8-oxogunanines are produced by oxidation of guanines in DNA or by incorporation of 8-oxodGTP from the nucleotide pool into the newly synthesized DNA strand. Germline mutations in MUTYH cause the MUTYH-associated polyposis (MAP), a syndrome that resembles the familial adenomatous polyposis (FAP) syndrome, caused by mutations in the APC tumor suppressor gene. MAP is also known as the familial adenomatous polyposis 2 (FAP2) (OMIM:608456). MAP-affected individuals are predisposed to development of multiple colorectal adenomas and colorectal cancer. MAP is largely inherited in an autosomally recessive manner, with both MUTYH alleles affected. The predisposition of heterozygous MUTYH mutation carriers to MAP has not been completely ruled out (Fleischmann et al. 2004).
MUTYH is most frequently affected by missense mutations in MAP patients, with two major mutations, Y165C and G382D, reported in about 80% of MAP patients of European origin. In Japanese patients, the most frequently reported mutation was Q324H (Yanaru-Fujisawa et al. 2008). Residues Y165C and G382D in the abundant MUTYH isoform MUTYH alpha-3 (MUTYH-3), used in the majority of functional studies, correspond to Y176C and G393D, respectively, in the canonical UniProt isoform (MUTYH alpha-1) and to Y179C and G396, respectively, in the longest NCBI isoform, which is used as a reference isoform in the database InSiGHT (International Society for Gastrointestinal Hereditary Tumours Database). However, both the canonical UniProt and NCBI MUTYH isoforms are expressed at very low levels or not at all (Plotz et al. 2012). In addition to the isoform MUTYH alpha-3, the other two abundant MUTYH isoforms are MUTYH beta-3 and MUTYH gamma-3 (Plotz et al. 2012), which differ from MUTYH alpha-3 in the first exon used. Exons 1-alpha and 1-beta contain sequences that resemble a mitochondrial targeting signal (MTS). It was reported that MUTYH alpha-3 and MUTYH beta-3 predominantly localize to mitochondria, while MUTYH gamma-3 predominantly localizes to the nucleus (Takao et al. 1999). However, a nuclear localization signal is located at the C-terminus of all MUTYH isoforms and other studies suggested that all isoforms can localize to the nucleus and only a small fraction of MUTYH is targeted to the mitochondria (Ohtsubo et al. 2000, Ichinoe et al. 2004). A small number of functional studies of MUTYH mutants uses the MUTYH isoform gama-3 (Goto et al. 2010, Shinmura et al. 2012). Nuclear localization of MUTYH may be affected by a splicing site variant (Tao et al. 2004).
MAP, compared with APC-associated FAP, is characterized by a later age of onset and a smaller number and size of polyps. Germline MUTYH mutations are associated with an increased incidence of duodenal polyps, gastric cancer, melanoma, breast cancer, dental and dermoid cysts, and osteomas. MUTYH mutations are rarely reported in the sporadic colorectal cancer. Tumors that develop in MAP patients are characterized with an excess of G:C -> T:A transversions in tumor suppressor genes, such as APC, and oncogenes, such as KRAS, which is a consequence of MUTYH functional impairment.
A single nucleotide polymorphism (SNP) at the splice donor site was reported to affect translation efficiency of MUTYH transcript, but its relevance for cancer predisposition has not been clarified (Yamaguchi et al. 2002). Catalytic activity of MUTYH and its mutants may be affected by posttranslational modifications (Parker et al. 2003, Kundu et al. 2010). Some MUTYH mutations reported in colorectal cancer do not affect MUTYH catalytic activity but disrupt the interaction of MUTYH with other proteins involved in DNA repair (Tominaga et al. 2004, Turco et al. 2013).
For review, please refer to Chow et al. 2004, Nielsen et al. 2011, Venesio et al. 2012, Mazzei et al. 2013.
R-HSA-9616334 Defective Base Excision Repair Associated with NEIL1 NEIL1 is an enzyme with dual DNA glycosylase and beta/delta lyase activity involved in base excision repair pathway (BER), the primary repair pathway for oxidative DNA damage. NEIL1 can detect and remove DNA damage resulting from oxidation of adenine, guanine and thymine, in the form of 4,6-diamino-5-formamidopyrimidine (FapyA), 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG), and thymine glycol (Tg), respectively. NEIL1 can also detect and remove dihydrouracil (DHU), which results from deamination of cytosine. Several low frequency NEIL1 polymorphisms, present in about 1% of general population in the United States have been reported. Different polymorphisms have different effects on NEIL1 function, and it was suggested that NEIL1 polymorphisms and NEIL1 deficiency or haploinsuficiency may be involved in predisposition to cancer and in metabolic syndrome (Roy et al. 2007, Vartanian et al. 2006, Sampath et al. 2011, Prakash et al. 2014). One polymorphism, NEIL1 G83D, is associated with primary sclerosing cholangitis and cholangiocarcinoma (Forsbring et al. 2009). NEIL1 G83D variant exhibits impaired DNA glycosylase activity towards different damaged DNA bases (Roy et al. 2007, Prakash et al. 2014) and induces genomic instability (Galick et al. 2017).
NEIL1 E28del, an in frame deletion variant of NEIL1 reported in gastric (stomach) cancer, where glutamate at position 28 is deleted, does not cleave Tg from damaged DNA (Shinmura et al. 2004).
NEIL1 Q282TER, a NEIL1 variant which lacks the putative nuclear localization signal (NLS), localizes to the cytosol and is therefore not able to access damaged DNA substrates, but its involvement in cancer is uncertain (Shinmura et al. 2015).
Reduced expression of NEIL1 and NEIL2 genes, accompanied with increased NEIL3 gene expression was detected in various cancers. NEIL1 gene silencing by promoter hypermethylation may be one of the underlying mechanisms for reduced NEIL1 expression in cancer (Shinmura et al. 2016).
Infection with the Hepatitis C virus (HCV) leads to decreased NEIL1 expression in liver cells, through an unknown mechanism (Pal et al. 2010).
Mice that are double knockout for Neil1 and Nthl1 genes accumulate DNA damage in the form of FapyA and FapyG and are more prone to development of lung adenocarcinoma than single Neil1 or Nthl1 gene knockouts (Chan et al. 2009). Another study reported that Neil1 knockout mice did not show a predisposition to tumour formation, and neither did double knockouts of Neil1 and Neil2, nor triple knockouts of Neil1, Neil2 and Neil3. Neil1 knockout mice are obese, consistent with the metabolic syndrome, but double knockouts of Neil1 and Neil2 do not display obesity (Rolseth et al. 2017).
R-HSA-9629232 Defective Base Excision Repair Associated with NEIL3 NEIL3 is a DNA N-glycosylase involved in base excision repair (BER), the primary repair pathway for oxidative DNA damage. NEIL3 can detect and remove oxidized guanine, in the form of 5-guanidinohydatoin and spiroiminodihydantoin, and oxidized thymine, in the form of thymine glycol. NEIL3 has a preference for single strand DNA (ssDNA) and is implicated in repair of oxidative DNA damage at telomeres (Zhou et al. 2013). A NEIL3 disease variant NEIL3 D132 is unable to cleave 5 guanidinohydantoin (Gh) from oxidatively damaged DNA. Individuals harboring a NEIL3 D132V homozygous mutation are predisposed to development of autoimmune diseases (Massaad et al. 2016) and NEIL3 depletion is also associated with an increase in telomere damage and loss (Zhou et al. 2017). NEIL3 unhooks DNA interstrand cross-links (ICLs) during DNA replication. NEIL3 resolves psoralen- and abasic site-induced ICLs in a Fanconi anemia (FA) pathway-independent manner (Semlow et al. 2016, Martin et al. 2017).
A polymorphism in one of the NEIL3 gene splice sites may increase the risk of myocardial infarction (Skarpengland et al. 2015). NEIL3 expression in the heart increases after heart failure in humans and after myocardial infarction in mouse disease models. Neil3 knockout mice show increased mortality after myocardial infarction, but there is no increase in the amount of DNA damage in Neil3 knockout hearts. In the heart, NEIL3 may function in the epigenetic regulation of gene expression and facilitate transcriptional response to myocardial infarction (Olsen et al. 2017). NEIL3 mRNA expression is increased in human carotid plaques and Neil3 deficiency accelerates plaque formation in Apoe knockout mice, but it appears that this is not correlated with oxidative DNA damage (Skarpengland et al. 2016).
The function of NEIL3 in removal of hydantoins from single strand DNA may be important for removal of replication blocks in proliferating cells. Mouse embryonic fibroblasts and neuronal stem cell derived from Neil3 knockout mouse embryos show decreased proliferation capacity and increased sensitivity to DNA damaging agents (Rolseth et al. 2013). NEIL3 may be required for maintenance of adult neurogenesis, as Neil3 knockout mice exhibit learning and memory deficits and synaptic irregularities in the hippocampus (Regnell et al. 2012). In addition, NEIL3 deficient neuronal stem cells exhibits signs of premature senescence (Reis and Hermanson 2012) and Neil3 knockout mice show reduced ability to augment neurogenesis to repair damage induced hypoxia ischemia (Sejersted et al. 2011).
Mice that are triple knockout for Neil1, Neil2 and Neil3 do not show a predisposition to tumour formation or changes in telomere length (Rolseth et al. 2017).
R-HSA-9616333 Defective Base Excision Repair Associated with NTHL1 NTHL1 is a DNA N-glycosylase that catalyzes the first step in base excision repair (BER), the primary repair pathway for oxidative DNA damage. NTHL1 can recognize and remove oxidized cytosine, adenine and thymine, in the form of cytosine glycol (Cg), 4,6-diamino-5-formamidopyrimidine (FapyA), and thymine glycol (Tg), respectively. NTHL1 can also recognize and remove dihydrouracil (DHU), produced by cytosine deamination. Germline mutations that impair function of NTHL1 predispose affected patients to a cancer syndrome (NTHL1 syndrome) that involves adenomatous polyposis and colorectal cancer, similar to MUTYH-associated polyposis (MAP), but also causes development of tumors in other organs, such as breast, bladder, skin, uterus and brain. Only patients with mutations in both alleles of NTHL1 are affected, indicative of an autosomally recessive inheritance (Weren et al. 2015, Rivera et al. 2015, Broderick et al. 2017, Grolleman et al. 2019). Some common NTHL1 polymorphisms may results in reduced NTHL1 function, but predisposition of affected individuals to cancer has not been studied in full (Galick et al. 2013). Mice that are double knockout for Neil1 and Nthl1 genes accumulate DNA damage in the form of FapyA and FapyG and are more prone to development of lung adenocarcinoma than single Neil1 or Nthl1 gene knockouts (Chan et al. 2009). Biallelic loss-of-function mutations in NTHL1 result in a mutational signature characterized by C>T transitions at non-CpG sites (Grolleman et al. 2019). For review, please refer to Weren et al. 2018.
Besides loss-of-function mutations, NTHL1 is amplified and overexpressed in some cancers. NTHL1 overexpression leads to genomic instability in non-transformed human bronchial epithelial cells and may lead to malignant transformation (Limpose et al. 2018).
R-HSA-9656249 Defective Base Excision Repair Associated with OGG1 OGG1 is the main DNA glycosylase responsible for removal of 8-oxoguanine (8oxoG), the most frequent type of oxidative DNA damage, from DNA and initiation of the base excision repair (Klungland et al. 1999, Minowa et al. 2000). A frequent OGG1 polymorphism increases the risk of breast and lung cancer in affected individuals, and inactivating mutations in OGG1 have been reported in various cancer types and in Alzheimer's disease. Ogg1 knockout mice are predisposed to cancer. For review, please refer to Boiteux et al. 2017.
R-HSA-5083632 Defective C1GALT1C1 causes TNPS Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1 (C1GALT1; MIM:610555) mediates the transfer of Galactose (Gal) from UDP-galactose to single O-linked GalNAc residues (Tn antigens) to form Core 1 structures on glycoproteins. C1GALT1 is active when in complex with the molecular chaperone C1GALT1C1 (aka COSMC; MIM:300611) which assists the folding and/or stability of C1GALT1. Defects in C1GALT1C1 causes somatic Tn polyagglutination syndrome (TNPS; MIM:300622), characterised by the polyagglutination of erythrocytes by naturally occurring anti-Tn antibodies following exposure of the Tn antigen on their surface. Defects in C1GALT1C1 render C1GALT1 inactive and results in the accumulation of the incompletely glycosylated Tn antigen. The Tn antigen is tumour-associated, found in a majority of human carcinomas, and is not normally expressed in peripheral tissues or blood cells (Crew et al. 2008, Ju et al. 2014). C1GALT1 and C1GALT1C1 belong to the CAZy family GT31 (www.cazy.org).
R-HSA-3359457 Defective CBLIF causes IFD Defects in cobalamin binding intrinsic factor CBLIF, aka gastric intrinsic factor GIF) cause hereditary intrinsic factor deficiency (IFD, aka congenital pernicious anemia; MIM:261000). IFD is an autosomal recessive disorder characterized by megaloblastic anemia (Tanner et al. 2005).
R-HSA-3359485 Defective CD320 causes MMATC Defects in CD320 cause methylmalonic aciduria type TCblR (MMATC aka methylmalonic aciduria; MIM:613646) resulting in elevated methylmalonic acid (MMA) and homocysteine (HCYS) in newborns (Quadros et al. 2010).
R-HSA-5678895 Defective CFTR causes cystic fibrosis Cystic fibrosis transmembrane conductance regulator (CFTR) is a low conductance chloride-selective channel that mediates the transport of chloride ions in human airway epithelial cells. Chloride ions plays a key role in maintaining homoeostasis of epithelial secretions in the lungs. Defects in CFTR can cause cystic fibrosis (CF; MIM:602421), a common generalised disorder in Caucasians affecting the exocrine glands. CF results in an ionic imbalance that impairs clearance of secretions, not only in the lung, but also in the pancreas, gastrointestinal tract and liver. Wide-ranging manifestations of the disease include chronic lung disease, exocrine pancreatic insufficiency, blockage of the terminal ileum, male infertility and salty sweat. The median survival of CF patients in North America and Western Europe is around 40 years (Davis 2006, Radlovic 2012).
R-HSA-3595174 Defective CHST14 causes EDS, musculocontractural type Carbohydrate sulfotransferase 14 (CHST14 also known as D4ST-1) mediates the transfer of sulfate to position 4 of further N-acetylgalactosamine (GalNAc) residues of dermatan sulfate (DS). Defects in CHST14 cause Ehlers-Danlos syndrome, musculocontractural type (MIM:601776). The Ehlers-Danlos syndromes (EDS) are a group of connective tissue disorders that share common features such as skin hyperextensibility, articular hypermobility and tissue fragility (Beighton et al. 1998). The musculocontractural form of EDS (MIM:601776) include distinctive characteristics such as craniofacial dysmorphism, congenital contractures of fingers and thumbs, clubfeet, severe kyphoscoliosis and muscular hypotonia (Malfait et al. 2010).
R-HSA-3595172 Defective CHST3 causes SEDCJD Carbohydrate sulfotransferase 3 (CHST3) transfers sulfate (SO4(2-)) to position 6 of N-acetylgalactosamine (GalNAc) residues of chondroitin-containg proteins resulting in chondroitin sulfate (CS), the predominant glycosaminoglycan present in cartilage. Defects in CHST3 result in spondyloepiphyseal dysplasia with congenital joint dislocations (SEDCJD; MIM:143095), a bone dysplasia clinically characterized by severe progressive kyphoscoliosis (abnormal curvature of the spine), arthritic changes with joint dislocations and short stature in adulthood (Unger et al. 2010).
R-HSA-3656225 Defective CHST6 causes MCDC1 Carbohydrate sulfotransferase 6 (CHST6) catalyzes the transfer of sulfate to position 6 of non-reducing ends of N-acetylglucosamine (GlcNAc) residues on keratan sulfate (KS). KS plays a central role in maintaining corneal transparency. Defective CHST6 (Nakazawa et al. 1984) results in unsulfated keratan deposited within the intracellular space and the extracellular corneal stroma leading to macular dystrophy, corneal type I (MCDC1; MIM:217800). MCDC1 is an early-onset, ocular disease characterized by bilateral, progressive corneal opacification, and reduced corneal sensitivity (Jones & Zimmerman 1961). MCD can be subdivided into 2 types on the basis of immunohistochemical studies and serum analysis for keratan sulfate; MCD type I, in which there is a virtual absence of sulfated KS-specific antibody response in the serum and cornea and MCD type II, in which the normal KS-specific antibody response is present in cornea and serum (Yang et al. 1988).
R-HSA-3595177 Defective CHSY1 causes TPBS Chondroitin sulfate synthases (CHSY) are involved in the synthesis of chondroitin sulfate, adding alternatingly glucuronate (GlcA) and N-acetylgalactosamine (GalNAc) to the growing chondroitin polymer (Mizumoto et al. 2013). Defects in CHSY1 cause temtamy preaxial brachydactyly syndrome (TPBS; MIM:605282), a syndrome characterized by multiple congenital anomalies, mental retardation, sensorineural deafness, growth retardation and bilateral symmetric digital anomalies mainly in the form of preaxial brachydactyly (literally, shortness of fingers and toes) and hyperphalangism (Temtamy et al. 1998, Race et al. 2010, Tian et al. 2010).
R-HSA-5619060 Defective CP causes aceruloplasminemia (ACERULOP) Ceruloplasmin (CP), synthesised in the liver and secreted into plasma, is a copper-binding (6-7 atoms per molecule) glycoprotein involved in iron trafficking in vertebrates. CP is essential for SLC40A1 (ferroportin) stability at the cell surface, the protein that mediates iron efflux from cells. CP also possesses ferroxidase activity, which oxidises ferrous iron (Fe2+) to ferric iron (Fe3+) following its transfer out of the cell. Fe3+ can then be loaded on to extracellular transferrin which transports it around the body to sites where it is required. Iron is vital for many metabolic processes such as electron transport and the transport and storage of oxygen.
Defects in CP (or indeed SLC40A1) can lead to the phenotype of iron overload as seen in the disorder aceruloplasminemia (ACERULOP; MIM:604290). It is a rare autosomal recessive disorder of iron metabolism characterised by iron accumulation mainly in the brain, but also in liver, pancreas and retina. Patients develop retinal degeneration, diabetes mellitus and neurological disturbance. ACERULOP belongs to a group of disorders known as NBIA (neurodegeneration with brain iron accumulation), distinguishing it from hereditary hemochromatosis (serum iron is high but the brain is usually not affected) and from disorders of copper metabolism such as Menkes and Wilson disease (Harris et al. 1995, Kono 2012, Musci et al. 2014).
R-HSA-5688890 Defective CSF2RA causes SMDP4 Surfactant catabolism by alveolar macrophages plays a small but critical part in surfactant recycling and metabolism. Upon ligand binding, granulocyte-macrophage colony-stimulating factor receptor (GM-CSFR), a heterodimer of alpha (CSF2RA) and beta (CSF2RB) subunits, initiates a signalling process that not only induces proliferation, differentiation and functional activation of hematopoietic cells but can also determine surfactant uptake into alveolar macrophages and its degradation via clathrin-coated vesicles. Defects in human CSF2RA can cause pulmonary surfactant metabolism dysfunction 4 (SMDP4; MIM:300770, aka congenital pulmonary alveolar proteinosis, (PAP)), a rare lung disorder due to impaired surfactant homeostasis characterised by alveoli filling with floccular material. Cellular responses to the misfolded pro-SFTPC products include ER stress, the activation of reactive oxygen species and autophagy. Excessive lipoprotein accumulation in the alveoli results in a form of respiratory distress syndrome in premature infants (RDS; MIM:267450) (Whitsett et al. 2015).
R-HSA-5688849 Defective CSF2RB causes SMDP5 Surfactant catabolism by alveolar macrophages plays a small but critical part in surfactant recycling and metabolism. Upon ligand binding, granulocyte-macrophage colony-stimulating factor receptor (GM-CSFR), a heterodimer of alpha (CSF2RA) and beta (CSF2RB) subunits, initiates a signalling process that not only induces proliferation, differentiation and functional activation of hematopoietic cells but can also determine surfactant uptake into alveolar macrophages and its degradation via clathrin-coated vesicles. Defects in human CSF2RB can cause pulmonary surfactant metabolism dysfunction 5 (SMDP5; MIM:614370, aka pulmonary alveolar proteinosis 5, PAP5), a rare lung disorder due to impaired surfactant homeostasis characterised by alveoli filling with floccular material causing respiratory failure (Greenhill & Kotton 2009, Whitsett et al. 2015).
R-HSA-3359463 Defective CUBN causes MGA1 Defects in the CUBN gene cause recessive hereditary megaloblastic anemia 1 (RH-MGA1 aka MGA1 Finnish type or Imerslund-Grasbeck syndrome, I-GS; MIM:261100). The Finnish cases described by Grasbeck et al. were caused by defects in CUBN (Grasbeck et al. 1960). The resultant malabsorption of Cbl (cobalamin, vitamin B12) leads to impaired B12-dependent folate metabolism and ultimately impaired thymine synthesis and DNA replication.
R-HSA-5579026 Defective CYP11A1 causes AICSR Cholesterol side-chain cleavage enzyme, mitochondrial (CYP11A1) normally catalyses the side-chain cleavage of cholesterol to form pregnenolone. Defects in CYP11A1 can cause Adrenal insufficiency, congenital, with 46,XY sex reversal (AICSR; MIM:613743). This is a rare disorder that can present as acute adrenal insufficiency in infancy with elevated ACTH and plasma renin activity and low or absent adrenal steroids. The severest phenotype is loss-of-function mutations associated with prematurity, complete under-androgenisation and severe, early-onset adrenal failure (Kim et al. 2008).
R-HSA-5579017 Defective CYP11B1 causes AH4 Cytochrome P450 11B1, mitochondrial (CYP11B1) possesses steroid 11-beta-hydroxylase activity which can convert 11-deoxycortisol to cortisol. 11-beta-hydroxylase deficiency is one of the main causes of congenital adrenal hyperplasia (CAH) (5-8%), second only to 21-hydroxylase deficiency which accounts for more than 90% of CAH (Zhao et al. 2008). Defects in CYP11B1 can cause Adrenal hyperplasia 4 (AH4; MIM:202010), a form of congenital adrenal hyperplasia which is a common recessive disease due to failure to convert 11-deoxycortisol to cortisol. This impaired corticosteroid biosynthesis results in androgen excess, virilization and hypertension (White et al. 1991).
R-HSA-5579009 Defective CYP11B2 causes CMO-1 deficiency Cytochrome P450 11B2, mitochondrial (CYP11B2 aka aldosterone hydroxylase) is an enzyme necessary for aldosterone biosynthesis via corticosterone (CORST) and 18-hydroxycorticosterone (18HCORST). Defects in CYP11B2 results in disorders of aldosterone synthesis. Corticosterone methyloxidase 1 and 2 deficiencies (CMO-1; MIM:203400 and CMO-2 deficiency; MIM:61060) are autosomal recessive disorders of aldosterone biosynthesis (Mitsuuchi et al. 1993, Bureik et al. 2002). In CMO-1 deficiency, aldosterone is undetectable in plasma, while its immediate precursor, 18HCORST, is low or normal. In CMO-2 deficiency, aldosterone can be low or normal, but at the expense of increased secretion of 18HCORST. Patients with CMO-2 deficiency have elevated plasma 18-hydroxycorticosterone/aldosterone ratios.
R-HSA-5579028 Defective CYP17A1 causes AH5 Steroid 17-alpha-hydroxylase/17,20 lyase (CYP17A1) mediates both 17-alpha-hydroxylase and 17,20-lyase activity, allowing the adrenal glands and gonads to synthesise both 17-alpha-hydroxylated glucocorticoids and sex steroids respectively (Kagimoto et al. 1998). Defects in CYP17A1 can cause Adrenal hyperplasia 5 (AH5), a form of congenital adrenal hyperplasia (CAH), a common recessive disease due to defective synthesis of cortisol and sex steroids. Common symptoms include mild hypocortisolism, ambiguous genitalia in genetic males or failure of the ovaries to function at puberty in genetic females, metabolic alkalosis due to hypokalemia and low-renin hypertension. CYP17A1 can have defects in either or both of 17-alpha-hydroxylase and 17,20-lyase activities thus patients can show combined partial 17-alpha-hydroxylase/17,20-lyase deficiency or isolated 17,20-lyase deficiency traits (Yanase et al. 1992, Kater & Biglieri 1994, Fluck & Miller 2006, Miller 2012).
R-HSA-5579030 Defective CYP19A1 causes AEXS Aromatase (CYP19A1) catalyses the conversion of androstenedione (ANDST) to estrone (E1). Defects in CYP19A1 can cause aromatase excess syndrome (AEXS; MIM:139300) and aromatase deficiency (AROD; MIM:613546). Affected individuals cannot synthesise endogenous estrogens. In females the lack of estrogen leads to pseudohermaphroditism and progressive virilization at puberty, whereas in males pubertal development is normal (Bulun 2014).
R-HSA-5579000 Defective CYP1B1 causes Glaucoma Cytochrome P450 1B1 (CYP1B1) can oxidise a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics as well as activating a range of procarcinogens. A specific substrate is the female sex hormone estradiol-17beta (EST17b) which is 4-hydroxylated to 4-hydroxyestradiol-17beta 4OH-EST17b). Defects in CYP1B1 can cause glaucoma disorders such as Glaucoma 3, primary congenital, A (GLC3A; MIM:231300), Glaucoma, primary open angle (POAG; MIM:137760), Glaucoma 1, open angle, A (GLC1A; MIM:137750) and Peters anomaly (PAN; MIM:604229). These disorders cause a progressive optic neuropathy characterised by visual field defects that ultimately lead to irreversible blindness (Li et al. 2011, Sarfarazi et al. 2003, Vincent et al. 2001).
R-HSA-5579021 Defective CYP21A2 causes AH3 Steroid 21-hydroxylase (CYP21A2) specifically catalyses the 21-hydroxylation of steroids which is required for the adrenal synthesis of mineralocorticoids and glucocorticoids. Defects in CYP21A2 can cause adrenal hyperplasia 3 (AH3; MIM:201910), a form of congenital adrenal hyperplasia (CAH) where cortisol synthesis is defective. This results in increased ACTH levels, causing overproduction and accumulation of cortisol precursors, particularly 17-hydroxyprogesterone (17HPROG). The resultant excessive production of androgens causes virilization. 21-hydroxylase deficiency accounts for more than 90% of CAH cases and ranges from mild to complete loss of activity (White et al. 2000, White & Bachega 2012).
R-HSA-5579010 Defective CYP24A1 causes HCAI Catabolic inactivation of the active, hormonal form of vitamin D3 (calcitriol, CALTOL, 1,25-dihydroxyvitamin D3) is initially carried out by 24-hydroxylation, mediated by 1,25-dihydroxyvitamin D3 24-hydroxylase (CYP24A1). The product formed is eventually transformed to calcitroic acid, the major water-soluble metabolite that can be excreted in bile. Defects in CYP24A1 can cause hypercalcemia infantile (HCAI; MIM:143880), a disorder characterised by abnormally high level of calcium in the blood, failure to thrive, vomiting, dehydration, and nephrocalcinosis (Schlingmann et al. 2011).
R-HSA-5579015 Defective CYP26B1 causes RHFCA Retinoic acid (RA) is a biologically active analogue of vitamin A (retinol). RA plays an important role in regulating cell growth and differentiation.CYP26A1 and B1 are involved in the metabolic breakdown of RA by 4-hydroxylation. High expression levels of CYP26B1 in the cerebellum and pons of human brain suggests a protective role of specific tissues against retinoid damage (White et al. 2000). Defects in CYP26B1 can cause radiohumeral fusions with other skeletal and craniofacial anomalies (RHFCA; MIM:614416), a disease characterised by craniofacial malformations and multiple skeletal anomalies (Laue et al. 2011).
R-HSA-5579004 Defective CYP26C1 causes FFDD4 Retinoic acid (RA) is a biologically active analogue of vitamin A (retinol). RA plays an important role in regulating cell growth and differentiation. CYP26C1 is involved in the metabolic breakdown of RA by 4-hydroxylation. While CYP26C1 can hydroxylate the trans form, it is unique in hydroxylating the 9-cis isomer of RA (9cRA) (Taimi et al. 2004). Defects in CYP26C1 can cause focal facial dermal dysplasia 4 (FFDD4; MIM:614974), a rare syndrome characterised by facial lesions.
R-HSA-5578996 Defective CYP27A1 causes CTX CYP27A1, a mitochondrial matrix sterol hydroxylase, catalyses the 27-hydroxylation of side-chains of sterol intermediates (Cali et al. 1991). In the bile acid synthesis pathway, CYP27A1 catalyses the first step in the oxidation of the side chain of sterol intermediates such as cholestane-triols (Pikuleva et al. 1998). Defects in CYP27A1 can cause Cerebrotendinous xanthomatosis (CTX; MIM:213700), a rare sterol storage disorder. Decreased bile acid production results in the accumulation of sterol intermediates in many tissues, including brain. The disorder is characterised by progressive neurologic dysfunction, premature atherosclerosis and cataracts (Gallus et al. 2006).
R-HSA-5579014 Defective CYP27B1 causes VDDR1A Vitamin D3 (cholecalciferol), synthesised in human skin by ultraviolet radiation action on 7-dehydrocholesterol, does not possess any biological activity. Vitamin D hormonal activity requires hydroxylation at the 25 and 1-alpha positions by cytochrome P450 enzymes CYP2R1 and CYP27B1 respectively. Vitamin D 25-hydroxylase (CYP2R1) catalyses the hydroxylation of vitamin D3 to calcidiol (CDL). Subsequent 1-alpha-hydroxylation of CDL by CYP27B1 produces calcitriol (CTL). CTL binds and activates the nuclear vitamin D receptor, with subsequent regulation of physiologic events such as calcium homeostasis, cellular differentiation and proliferation.
Defects in CYP27B1 can cause rickets, vitamin D-dependent 1A (VDDR1A; MIM:264700), a disorder caused by deficiency of the active form of vitamin D (CTL) resulting in defective bone mineralization and clinical features of rickets. To date, 47 mutations have been identified, the majority of them (28) being missense mutations (Kim 2011, Cui et al. 2012).
R-HSA-5579027 Defective CYP27B1 causes VDDR1B Vitamin D3 (cholecalciferol), synthesised in human skin by ultraviolet radiation action on 7-dehydrocholesterol, does not possess any biological activity. Vitamin D hormonal activity requires hydroxylation at the 25 and 1-alpha positions by cytochrome P450 enzymes CYP2R1 and CYP27B1 respectively.
Vitamin D 25-hydroxylase (CYP2R1) catalyses the hydroxylation of vitamin D3 to calcidiol (CDL). Subsequent 1-alpha-hydroxylation of CDL produces calcitriol (CTL). CTL binds and activates the nuclear vitamin D receptor, with subsequent regulation of physiologic events such as calcium homeostasis, cellular differentiation and proliferation.
Defects in CYP2R1 can cause rickets, vitamin D-dependent 1B (VDDR1B; MIM:600081), a disorder caused by a selective deficiency of the active form of vitamin D (CTL) resulting in defective bone mineralization and clinical features of rickets (Pikuleva et al. 2013).
R-HSA-5579011 Defective CYP2U1 causes SPG56 Cytochrome P450 2U1 (CYP2U1) catalyses the hydroxylation of arachidonic acid, docosahexaenoic acid and other long chain fatty acids, generating bioactive eicosanoid derivatives which may play an important physiological role in fatty acid signaling processes. Defects in CYP2U1 can cause Spastic paraplegia 56, autosomal recessive (SPG56; MIM:615030), a neurodegenerative disorder characterised by a slow, gradual, progressive weakness and spasticity of the lower limbs (Tesson et al. 2012, Fink 2013).
R-HSA-5579005 Defective CYP4F22 causes ARCI5 Cytochrome P450 4F22 (CYP4F22) is thought to 20-hydroxylate trioxilin A3 (TrXA3), an intermediary metabolite from the 12(R)-lipoxygenase pathway. This pathway is implicated in proliferative skin diseases. The major products of arachidonic acid in keratinocytes are 12- and 15-HETE which undergo biotransformation to products involved in skin hydration. CYP4F22 mutations can lead to autosomal recessive congenital ichthyosis 5 (ARCI5) (Lefevre et al. 2006, Lugassy et al. 2008).
R-HSA-5579013 Defective CYP7B1 causes SPG5A and CBAS3 Bile acids are synthesised from cholesterol via two pathways - a classic neutral pathway involving cholesterol 7-alpha-hydroxylase (CYP7A1), and an acidic pathway involving 25-hydroxycholesterol 7-alpha-hydroxylase (CYP7B1). Defects in CYP7B1 can cause spastic paraplegia 5A (SPG5A), a neurodegenerative disorder characterised by a slow, gradual, progressive weakness and spasticity of the lower limbs (Tsaousidou et al. 2008). Defects in CYP7B1 can also cause Congenital bile acid synthesis defect 3 (CBAS3; MIM:613812), a disorder resulting in severe cholestasis, cirrhosis and liver synthetic failure. Hepatic CYP7B1 activity is undetectable (Setchell et al. 1998).
R-HSA-4755609 Defective DHDDS causes RP59 The ER membrane-associated enzyme dehydrodolichyl diphosphate synthase (DHDDS) (Endo et al. 2003) normally mediates the sequential head-to-tail cis addition of multiple isopentyl pyrophosphate (IPP) molecules to farnesyl pyrophosphate (E,E-FPP) to produce polyprenol pyrophosphate (pPPP) (Shridas et al. 2003). Dolichol in humans contain homologues ranging from 17-23 isoprene units, the most common homologues contain 19 or 20 isoprene units (Freeman et al. 1980). Dolichol is an important substrate in the N-glycosylation of proteins, including rhodopsin.
Defects in DHDDS cause retinitis pigmentosa 59 (RP59; MIM:613861), a pigment retinopathy, characterised by retinal pigment deposits (visible on fundus examination) and primary loss of rod photoreceptors followed by secondary loss of cone photoreceptors. Sufferers typically have night vision blindness and loss of mid to peripheral vision. As the condition progresses, they lose far peripheral vision and eventually central vision (Zuchner et al. 2011).
R-HSA-9699150 Defective DNA double strand break response due to BARD1 loss of function Although germline mutations of BARD1 are implicated in some cases of hereditary breast and ovarian cancer (HBOC), they occur less frequently that those of the BRCA1 or BRCA2 genes (De Brakeleer et al. 2010, Alenezi et al. 2020). From animal studies, it is known that the loss of BARD1 function results in a phenotype very similar to that caused by loss of BRCA1 function, characterized by embryonic lethality (McCarthy et al. 2003), genomic instability (McCarthy et al. 2003) and defects in homology-directed repair (Lee et al. 2015). A small number of clinically-relevant BARD1 missense mutants that have been functionally characterized and shown to be impaired in BRCA1 binding (Xia et al. 2003, Lee et al. 2015) are annotated in this pathway.
R-HSA-9663199 Defective DNA double strand break response due to BRCA1 loss of function Germline mutations in the BRCA1 or BRCA2 tumor suppressor genes are implicated in up to 10% of breast cancers overall and 40% of familial breast cancers. Carriers of either BRCA1 or BRCA2 germline mutation are predisposed to hereditary breast and ovarian cancer (the HBOC syndrome), which is inherited in an autosomal dominant manner. Besides early onset breast and ovarian cancer, HBOC patients also have a modestly increased risk of developing other tumor types, including pancreatic, stomach, laryngeal, fallopian tube, and prostate cancer. The BRCA1 gene encodes a large protein of 1863 amino acids, which contains a RING finger domain at the N-terminus and two BRCT repeats at the C-terminus. The RING domain is responsible for heterodimerization with BARD1, which increases stability of BRCA1 and activates its E3 ubiquitin ligase activity. BRCA1 plays an important role in homology-directed repair of DNA double-strand breaks (DSBs). Brca1-null knockout mice die early during embryonic development and cells depleted of BRCA1 show genomic instability (reviewed by Roy et al. 2011). Cancer mutations that affect the RING domain of BRCA1 frequently result in the inability of BRCA1 to bind to BARD1 and participate in DNA DSB response (Wu et al. 1996, Ransburgh et al. 2010). Some mutations in the RING domain of BRCA1 were shown to affect the ubiquitin ligase activity of BRCA1 (Brzovic et al. 2001), but it is uncertain if the ubiquitin ligase activity is essential for the tumor suppressor role of BRCA1 (Shakya et al. 2011).
R-HSA-4755583 Defective DOLK causes DOLK-CDG Dolichol kinase (DOLK, TMEM15) normally mediates the phosphorylation of dolichol (DCHOL) to form dolichyl phosphate (DOLP) in the ER membrane (Fernandez et al. 2002). DOLP is an important substrate in the synthesis of N- and O-glycosylated proteins and GPI anchors. Defects in DOLK cause congenital disorder of glycosylation type 1m (DOLK-CDG, CDG1m, also known as dolichol kinase deficiency; MIM:610768), a severe mutisystem disorder characterised by under-glycosylated serum glycoproteins. This disorder has a very severe phenotype and death can occur in early life (Kranz et al. 2007).
R-HSA-4549356 Defective DPAGT1 causes CDG-1j, CMSTA2 UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase (DPAGT1) catalyses the initial committed step in the biosynthesis of dolichyl pyrophosphate-oligosaccharides. Defects in DPAGT1 cause congenital disorder of glycosylation 1j (DPAGT1-CDG, previously known as CDG-1j; MIM:608093), a multisystem disorder characterised by under-glycosylated serum glycoproteins (Wu et al. 2003, Timal et al. 2012). Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. Defects in DPAGT1 can also cause myasthenic syndrome, congenital, with tubular aggregates, 2 (CMSTA2; MIM:614750), characterised by muscle weakness of mainly the proximal limb muscles, with tubular aggregates present on muscle biopsy. Sufferers find walking difficult and fall frequently. Younger sufferers show hypotonia and poor head control. A disorder of neuromuscular transmission is detected on electromyography (Belaya et al. 2012, Finlayson et al. 2013).
R-HSA-4717374 Defective DPM1 causes DPM1-CDG Dolichyl-phosphate mannosyltransferase (DPM), a heterotrimeric protein embedded in the endoplasmic reticulum membrane, mediates the transfer of mannose (from cytosolic GDP-mannose) to dolichyl phosphate (DOLP) to form dolichyl-phosphate-mannose (DOLPman). The first subunit of the heterotrimer (DPM1) appears to be the actual catalyst, and the other two subunits (DPM2 and 3) appear to stabilise it (Maeda et al. 2000). Defects in DPM1 can cause congenital disorder of glycosylation 1e (DPM1-CDG, CDG-1e; MIM:608799), a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins (Kim et al. 2000, Imbach et al. 2000, Garcia-Silva et al. 2004).
R-HSA-4719377 Defective DPM2 causes DPM2-CDG Dolichyl-phosphate mannosyltransferase (DPM), a heterotrimeric protein embedded in the endoplasmic reticulum membrane, mediates the transfer of mannose (from cytosolic GDP-mannose) to dolichyl phosphate (DOLP) to form dolichyl-phosphate-mannose (DOLPman). The first subunit of the heterotrimer (DPM1) appears to be the actual catalyst, and the other two subunits (DPM2 and 3) appear to stabilise it (Maeda et al. 2000). Defects in DPM2 can cause congenital disorder of glycosylation 1u (DPM2-CDG, CDG1u; MIM:615042), a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins (Barone et al. 2012). CDG type 1 diseases result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency.
R-HSA-4719360 Defective DPM3 causes DPM3-CDG Dolichyl-phosphate mannosyltransferase (DPM), a heterotrimeric protein embedded in the endoplasmic reticulum membrane, mediates the transfer of mannose (from cytosolic GDP-mannose) to dolichyl phosphate (DOLP) to form dolichyl-phosphate-mannose (DOLPman). The first subunit of the heterotrimer (DPM1) appears to be the actual catalyst, and the other two subunits (DPM2 and 3) appear to stabilise it (Maeda et al. 2000). Defects in DPM3 can cause congenital disorder of glycosylation 1o (DPM3-CDG, CDG1o; MIM:612937), a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins. CDG type 1 diseases result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency (Lefeber et al. 2009).
Four biosynthetic pathways depend on DOLPman; N-glycosylation, O-mannosylation, C-Mannosylation and GPI-anchor biosynthesis. A defect in DPM3 strongly reduces O-mannosylation of alpha-dystroglycan, explaining the clinical phenotype of muscular dystrophy and linking the congenital disorders of glycosylation with the dystroglycanopathies (Lefeber et al. 2009).
R-HSA-3656253 Defective EXT1 causes exostoses 1, TRPS2 and CHDS Heparan sulfate (HS) is involved in regulating various body functions functions during development, homeostasis and pathology including blood clotting, angiogenesis and metastasis of cancer cells. Exostosin 1 and 2 (EXT1 and 2) glycosyltransferases are required to form HS. They are able to transfer N-acetylglucosamine (GlcNAc) and glucuronate (GlcA) to HS during its synthesis. The functional form of these enzymes appears to be a complex of the two located on the Golgi membrane. Defects in either EXT1 or EXT2 can cause hereditary multiple exostoses 1 (Petersen 1989) and 2 (McGaughran et al. 1995) respectively (MIM:133700 and MIM:133701), autosomal dominant disorders characterized by multiple projections of bone capped by cartilage resulting in deformed legs, forearms and hands. Trichorhinophalangeal syndrome, type II (TRPS2 aka Langer-Giedion syndrome, LGS) is a disorder that combines the clinical features of trichorhinophalangeal syndrome type I (TRPS1, MIM:190350) and multiple exostoses type I, caused by mutations in the TRPS1 and EXT1 genes, respectively (Langer et al. 1984, Ludecke et al. 1995). Defects in EXT1 may also be responsible for chondrosarcoma (CHDS; MIM:215300) (Schajowicz & Bessone 1967, Hecht et al. 1995).
R-HSA-3656237 Defective EXT2 causes exostoses 2 Heparan sulfate (HS) is involved in regulating various body functions during development, homeostasis and pathology including blood clotting, angiogenesis and metastasis of cancer cells. Exostosin 1 and 2 (EXT1 and 2) glycosyltransferases are required to form HS. They are able to transfer N-acetylglucosamine (GlcNAc) and glucuronate (GlcA) to HS during its synthesis. The functional form of these enzymes appears to be a complex of the two located on the Golgi membrane. Defects in either EXT1 or EXT2 can cause hereditary multiple exostoses 1 (Petersen 1989) and 2 (McGaughran et al. 1995) respectively (MIM:133700 and MIM:133701), autosomal dominant disorders characterised by multiple projections of bone capped by cartilage resulting in deformed legs, forearms and hands.
R-HSA-9672387 Defective F8 accelerates dissociation of the A2 domain Retention of A2 polypeptide is required for normal stability of activated factor VIII (FVIIIa) and dissociation of A2 correlates with FVIIIa inactivation and consequent loss of FXase activity. Hemophilia A (HA)-associated mutations (R550H, A303E, S308L, N713I, R717W and R717L) within the predicted A1-A2 and A2-A3 interface are thought to disrupt potential intersubunit hydrogen bonds and have the molecular phenotype of increased rate of inactivation of FVIIIa due to increased rate of A2 subunit dissociation (Pipe SW et al. 1999; Hakeos WH et al. 2002)
R-HSA-9672395 Defective F8 binding to the cell membrane The Reactome event describes the defective interaction between the thrombin-activated FVIIIa protein and phospholipid membrane surfaces caused by hemophilia A-associated FVIII variants, such as A2220P, A2220del and Q2330P.
R-HSA-9672393 Defective F8 binding to von Willebrand factor Upon secretion from the cell, FVIII circulates in a tight complex with the multimeric glycoprotein von Willebrand Factor (vWF), which is essential for maintaining stable levels of FVIII in the circulation (reviewed by Pipe SW et al. 2016). Genetic mutations in the F8 gene can compromise FVIII binding to vWF thus decreasing FVIII values in the plasma causing hemophilia A (HA), an X-linked recessive bleeding disorder.
R-HSA-9672391 Defective F8 cleavage by thrombin In normal human plasma, thrombin cleaves factor VIII (FVIII) after arginine residues 391 (A1-A2 domain junction) and 759 (A2-B domain junction) to yield heavy chain fragments and at R1708 (a3-A3 junction) to yield the light chain fragment (Eaton D et al. 1986; Hill-Eubanks DC et al. 1989). Mutations affecting arginine residues located at the thrombin cleavage sites of factor VIII protein result in mild/moderate hemophilia A (HA) (Pattinson JK et al. 1990; Arai M et al. 1990; Schwaab R et al. 1991). The Reactome event describes failed thrombin-mediated activation of HA-associated FVIII variants (R391C, R391H, S392L, R1708C and R1708H) due to defects at or close to thrombin cleavage sites.
R-HSA-9672397 Defective F8 secretion Hemophilia A (HA) is a bleeding disorder caused by lack of or a defective factor VIII (FVIII) protein and results from defects in the F8 gene (Peyvandi F et al. 2016).
In healthy individuals, FVIII is synthesized as a large glycoprotein of 2351 amino acids with a discrete domain structure: A1-A2-B-A3-C1-C2 (Wood WI et al. 1984; Vehar GA et al. 1984; Toole JJ et al. 1984). Upon synthesis, FVIII is translocated into the lumen of the endoplasmic reticulum (ER), where it undergoes extensive processing including cleavage of a signal peptide and N-linked glycosylation at asparagine residues (Kaufman RJ et al. 1988, 1997; Kaufman RJ 1998). In the ER lumen of mammalian cells FVIII interacts with the protein chaperones calnexin (CNX), calreticulin (CRT), and immunoglobulin-binding protein (BiP or GRP78) that facilitate proper folding of proteins prior to trafficking to the Golgi compartment (Marquette KA et al. 1995; Swaroop M et al. 1997; Pipe SW et al. 1998; Kaufman RJ et al. 1997; Kaufman RJ 1998). Trafficking from the ER to the Golgi compartment is facilitated by LMAN1 and multiple combined factor deficiency 2 (MCFD2) cargo receptor complex (Zhang B et al. 2005; Zheng, C et al. 2010, 2013). Within the Golgi apparatus, FVIII is subject to further processing, including modification of the N-linked oligosaccharides to complex-type structures, O-linked glycosylation, and sulfation of specific Tyr-residues (Kaufman RJ 1998). Upon secretion from the cell, FVIII is cleaved at two sites in the B-domain to form a heterodimer consisting of the heavy chain containing the A1-A2-B domains in a metal ion-dependent complex with the light chain consisting of the A3-C1-C2 domains (Kaufman RJ et al. 1997; Kaufman RJ 1998).
The Reactome event describes defects within the secretory pathway due to mutations in the F8 gene that can impair FVIII synthesis, folding, intracellular processing and transport which result in a lack or reduced levels of the plasma FVIII protein. The module includes also an event of defective post-translational tyrosine sulfonation of FVIII in the Golgi apparatus that is required for the optimal interaction between the secreted FVIII and the von Willebrand factor (VWF). R-HSA-9674519 Defective F8 sulfation at Y1699 Hemophilia A (HA) is a bleeding disorder caused by lack of or a defective factor VIII (FVIII) protein and results from defects in the F8 gene (Peyvandi F et al. 2016).
In healthy individuals, FVIII is synthesized as a large glycoprotein of 2351 amino acids with a discrete domain structure: A1-A2-B-A3-C1-C2 (Wood WI et al. 1984; Vehar GA et al. 1984; Toole JJ et al. 1984). Upon synthesis, FVIII is translocated into the lumen of the endoplasmic reticulum (ER), where it undergoes extensive processing including cleavage of a signal peptide and N-linked glycosylation at asparagine residues (Kaufman RJ et al. 1988, 1997; Kaufman RJ 1998). In the ER lumen of mammalian cells FVIII interacts with the protein chaperones calnexin (CNX), calreticulin (CRT), and immunoglobulin-binding protein (BiP or GRP78) that facilitate proper folding of proteins prior to trafficking to the Golgi compartment (Marquette KA et al. 1995; Swaroop M et al. 1997; Pipe SW et al. 1998; Kaufman RJ et al. 1997; Kaufman RJ 1998). Trafficking from the ER to the Golgi compartment is facilitated by LMAN1 and multiple combined factor deficiency 2 (MCFD2) cargo receptor complex (Zhang B et al. 2005; Zheng, C et al. 2010, 2013). Within the Golgi apparatus, FVIII is subject to further processing, including modification of the N-linked oligosaccharides to complex-type structures, O-linked glycosylation, and sulfation of specific Tyr-residues (Kaufman RJ 1998). Upon secretion from the cell, FVIII is cleaved at two sites in the B-domain to form a heterodimer consisting of the heavy chain containing the A1-A2-B domains in a metal ion-dependent complex with the light chain consisting of the A3-C1-C2 domains (Kaufman RJ et al. 1997; Kaufman RJ 1998).
The Reactome event describes defects within the secretory pathway due to mutations in the F8 gene that can impair FVIII synthesis, folding, intracellular processing and transport which result in a lack or reduced levels of the plasma FVIII protein. The module includes also an event of defective post-translational tyrosine sulfonation of FVIII in the Golgi apparatus that is required for the optimal interaction between the secreted FVIII and the von Willebrand factor (VWF). R-HSA-9673221 Defective F9 activation Deficiency or dysfunction of FIX leads to hemophilia B (HB), an X-linked, recessive, bleeding disorder. On a molecular basis, HB is due to a heterogeneous spectrum of mutations spread throughout the F9 gene (Rallapalli PM et al. 2013).
The Reactome event describes the defective proteolytic activation of FIX by factor XIa due to the presence of HB-associated point mutations R191C, R191H, R226Q and R226W in the cleavage sites of FIX (Liddell MB et al. 1989; Monroe DM et al. 1989; Suehiro K et al. 1989; Diuguid DL et al. 1989; Bertina RM et al.1990). In addition, naturally occurring point mutations in the FIX propeptide sequence such as N43Q, N43L or N46S are also annotated here. These FIX variants are secreted into the circulation with a mutant 18-amino acid propeptide still attached (Bentley AK et al. 1986; Galeffi P & Brownlee GG 1987). The unprocessed FIX variants were found to affect the function of the protein by destabilizing the calcium-induced conformation of FIX (Wojcik EG et al. 1997) and showed delayed activation by FXIa (Liddell MB et al. 1989; Ware J et al. 1989; de la Salle C et al. 1993; Wojcik EG et al. 1997; Bristol JA et al. 1993).
R-HSA-9673218 Defective F9 secretion A deficiency or dysfunction of factor IX (FIX) caused by mutations in the F9 gene is associated with a blood clotting disorder hemophilia B (HB). The FIX protein level may be decreased in the circulation by F9 mutations affecting FIX protein synthesis, stability, or secretion (Kurachi S et al. 1997; Enjolras N et al. 2004; Branchini A et al. 2013, 2017; Tajnik M et al. 2016; Odaira K et al. 2019).
The Reactome event describes intracellular accumulation and/or decreased secretion of FIX due to different HB-related genetic alterations spread throughout the F9 gene.
R-HSA-9673202 Defective F9 variant does not activate FX Factor IX (FIX) deficiency is associated with mild to severe bleeding in hemophilia B (HB) patients (Rallapalli PM et al. 2013). HB is caused by a wide range of mutations that can include point mutations (nonsense and missense), insertions, deletions and other complex rearrangements of the F9 gene (Rallapalli PM et al. 2013). The Reactome event describes failed generation of FXa as the functional consequence of the defective serine protease activity of hemophilia B (HB)-associated FIX variants such as G363R & G363E (Lu Q et al. 2015), G357E (Miyata T et al. 1991), A436V (Usharani P et al. 1985), I443T (Hamaguchi N et al. 1991), G409V (Bajaj SP et al. 1990), D410H and S411G (Ludwig M et al. 1992).
R-HSA-5579019 Defective FMO3 causes TMAU Trimethylamine (TMA) is present in the diet (in fish) but primarily formed in vivo from the breakdown of choline. It is N-oxidised by FMO3 in the liver, the major isoform active towards TMA. Trimethylaminuria (TMAU; MIM:602079, fish-odour syndrome) is a human genetic disorder characterised by an impaired ability to convert the malodourous TMA to its odourless N-oxide. Patients emit a foul odour, which resembles that of rotting fish and can be a psychologically disabling condition (Messenger et al. 2013).
R-HSA-5609977 Defective GALE causes EDG Cytosolic UDP-galactose 4'-epimerase (GALE) catalyses the reversible interconversion of UDP-D-galactose (UDP-Gal) and UDP-glucose (UDP-Glc), the third reacton in the Leloir pathway of galactose metabolism. GALE can also catalyse the epimerisation of UDP-N-acetylglucosamine to UDP-N-acetylgalactosamine. The active form of the enzyme is a homodimer with one molecule of bound NAD per monomer (GALE:NAD+ dimer). Defects in GALE can cause Epimerase-deficiency galactosemia (EDG; MIM:230350), or type III galactosemia (diseases of galactose metabolism) whose clinical features include early-onset cataracts, liver damage, deafness and mental retardation. Historically, it was considered that there were two forms of GALE deficidency; a benign ("peripheral") form where there is no GALE activity in red blood cells and characterised by mild symptoms (Gitzelmann 1972) and a rarer "generalised" form with no detectable GALE activity in all tissues resulting in more severe symptoms (Holton et al. 1981). The disease is now considered to be a continuum (Openo et al. 2006).
R-HSA-5609976 Defective GALK1 causes GALCT2 Cytosolic galactokinase (GALK1) catalyses the first committed step in the Leloir pathway of galactose metabolism. GALK1 catalyses the phosphorylation of D-galactose (Gal) to form D-galactose 1-phosphate (Gal1P). Defects in GALK1 can cause type II galactosemia (GALCT2; MIM:230200), an autosomal recessive deficiency characterised by congenital cataracts during infancy and presenile cataracts in the adult population. Galactitol accumulation in the lens is the cause of these cataracts (Bosch et al. 2002).
R-HSA-5083636 Defective GALNT12 causes CRCS1 The family of UDP GalNAc:polypeptide N acetylgalactosaminyltransferases (GalNAc transferases, GALNTs) carry out the addition of N acetylgalactosamine on serine, threonine or possibly tyrosine residues on a wide variety of proteins, and most commonly associated with mucins (Wandall et al. 1997). This reaction takes place in the Golgi apparatus (Rottger et al. 1998). There are 20 known members of the GALNT family, 15 of which have been characterised and 5 candidate members which are thought to belong to this family based on sequence similarity (Bennett et al. 2012). The GALNT-family is classified as belonging to CAZy family GT27. Defects in one of the GALNT family, GALNT12 (Guo et al. 2002) (MIM: 610290) can result in decreased glycosylation of mucins, mainly expressed in the digestive organs such as the stomach, small intestine and colon, and may play a role in colorectal cancer 1 (CRCS1; MIM:608812). CRCS1 is a complex disease characterised by malignant lesions arising from the inner walls of the colon and rectum (Guda et al. 2009, Clarke et al. 2012).
R-HSA-5083625 Defective GALNT3 causes HFTC The family of UDP GalNAc:polypeptide N acetylgalactosaminyltransferases (GalNAc transferases, GALNTs) carry out the addition of N acetylgalactosamine (GalNAc) on serine, threonine or possibly tyrosine residues on a wide variety of proteins, most commonly associated with mucins. This is the initial reaction in the biosynthesis of GalNAc-type O linked oligosaccharides (Wandall et al. 1997). This reaction takes place in the Golgi apparatus (Rottger et al. 1998). There are 20 known members of the GALNT family, 15 of which have been characterised and 5 candidate members which are thought to belong to this family based on sequence similarity (Bennett et al. 2012). The GALNT-family is classified as belonging to CAZy family GT27. Defects in one of the GALNT family genes, GALNT3 (MIM:601756), can cause familial hyperphosphatemic tumoral calcinosis (HFTC; MIM:211900). HFTC is a rare autosomal recessive severe metabolic disorder characterised by the progressive deposition of calcium phosphate crystals in the skin, soft tissues and sometimes bone (Chefetz et al. 2005). The biochemical observation is hyperphosphatemia, caused by increased renal absorption of phosphate (Chefetz et al. 2005, Ichikawa et al. 2005). Some patients manifest recurrent, transient, painful swellings of the long bones with radiological evidence of periosteal reaction and cortical hyperostosis (Frishberg et al. 2005).
R-HSA-5609978 Defective GALT can cause GALCT Galactose-1-phosphate uridylyltransferase (GALT) is one of the enzymes involved in galactose metabolism in the Leloir pathway. GALT catalyses the transfer of uridine monophosphate (UMP) from UDP-glucose (UDP-Glc) to galactose-1-phosphate (Gal1P) to form UDP-galactose (UDP-Gal) and glucose 1-phosphate. Defects in GALT can cause Galactosemia (GALCT; MIM:230400), an autosomal recessive disorder of galactose metabolism presenting in neonatals that causes jaundice, cataracts and mental retardation (Bosch 2006).
R-HSA-5619073 Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) Cytosolic glucokinase (GCK) (and three isoforms of hexokinase) catalyse the irreversible reaction of alpha-D-glucose (Glc) and ATP to form alpha-D-glucose-6-phosphate (G6P) and ADP, the first step in glycolysis. In the body, GCK is found only in hepatocytes and pancreatic beta cells. GCK and the hexokinase enzymes differ in that GCK has a higher Km than the hexokinases and is less readily inhibited by the reaction product. As a result, GCK should be inactive in the fasting state when glucose concentrations are low but in the fed state should have an activity proportional to glucose concentration. These features are thought to enable efficient glucose uptake and retention in the liver, and to function as a sensor of glucose concentration coupled to insulin release in pancreatic beta cells. Defects in GCK are can cause maturity-onset diabetes of the young 2 (MODY2; MIM:125851), a heritable early onset form of type II diabetes (Hussain 2010, Osbak et al. 2009).
R-HSA-5578999 Defective GCLC causes HAGGSD In mammalian cells, many antioxidant defence systems exist which protect cells from subsequent exposure to oxidant stresses. One antioxidant is glutathione (GSH), a tripeptide present in virtually all cells that regulates the intracellular redox state and protects cells from oxidative injury. It is metabolised via the gamma-glutamyl cycle, which is catalysed by six enzymes. In man, hereditary deficiencies have been found in five of the six enzymes. Gamma-glutamylcysteine ligase (GCL) catalyses the first and rate-limiting step in GSH biosynthesis. GCL is a heterodimer of a catalytic heavy chain (GCLC) and a regulatory light chain (GCLM). Defects in the catalytic GCLC can cause hemolytic anemia due to gamma-glutamylcysteine synthetase deficiency (HAGGSD; MIM:230450), a disease characterised by hemolytic anemia, glutathione deficiency, myopathy, late-onset spinocerebellar degeneration, and peripheral neuropathy (Ristoff & Larsson 2007, Aoyama & Nakaki 2013).
R-HSA-4085023 Defective GFPT1 causes CMSTA1 Glucosamine-fructose 6-phosphate aminotransferases 1 and 2 (GFPT1,2) are the first and rate-limiting enzymes in the hexosamine synthesis pathway, and thus formation of hexosamines like N-acetylglucosamine (GlcNAc). These enzymes probably play a role in limiting the availability of substrates for the N- and O-linked glycosylation of proteins. GFPT1 and 2 are required for normal functioning of neuromuscular synaptic transmission. Defects in GFPT1 lead to myasthenia, congenital, with tubular aggregates 1 (CMSTA1; MIM:610542), characterised by altered muscle fibre morphology and impaired neuromuscular junction development. Sufferers of CMSTA1 show a good response to acetylcholinesterase inhibitors (Senderek et al. 2011). The missense mutations observed do not always result in significant reduction in enzyme activity, but biopsies show reduced amounts of GFPT1 protein suggesting increased turnover or defective translation (Senderek et al. 2011).
R-HSA-5579022 Defective GGT1 causes GLUTH To be excreted in urine, glutathione conjugates undergo several hydrolysis steps to form mercapturic acids which are readily excreted. The first step is the hydrolysis of a gamma-glutamyl residue from the conjugate catalysed by gamma-glutamyltransferases (GGTs). These are membrane-bound, heterodimeric enzymes composed of light and heavy peptide chains. Extracellular glutathione (GSH) or its conjugates can be hydrolysed to give cysteinylglycine (CG, or CG conjugates) and free glutamate (L-Glu). Hydrolysis of GSH provides cells with a local cysteine supply and contributes to intracellular GSH levels (Heisterkamp et al. 2008). Defects in GGT1 can cause glutathionuria (GLUTH; MIM:231950), an autosomal recessive disorder characterised by increased GSH concentration in the plasma and urine. Mutations that cause GLUTH can occur in both chains of the GGT1 dimer (Heisterkamp et al. 2008, Aoyama & Nakaki 2013).
R-HSA-9035968 Defective GGT1 in aflatoxin detoxification causes GLUTH To be excreted in urine, glutathione conjugates undergo several hydrolysis steps to form mercapturic acids which are readily excreted. The first step is the hydrolysis of a gamma-glutamyl residue from the conjugate catalysed by gamma-glutamyltransferases (GGTs). These are membrane-bound, heterodimeric enzymes composed of light and heavy peptide chains. Extracellular glutathione (GSH) or its conjugates can be hydrolysed to give cysteinylglycine (CG, or CG conjugates) and free glutamate (L-Glu). Hydrolysis of GSH provides cells with a local cysteine supply and contributes to intracellular GSH levels (Heisterkamp et al. 2008). Defects in GGT1 can cause glutathionuria (GLUTH; MIM:231950), an autosomal recessive disorder characterised by increased GSH concentration in the plasma and urine. Mutations that cause GLUTH can occur in both chains of the GGT1 dimer (Heisterkamp et al. 2008, Aoyama & Nakaki 2013).
R-HSA-4085011 Defective GNE causes sialuria, NK and IBM2 Sialuria (MIM:269921) is caused by a metabolic defect where the UDP?N?acetylglucosamine 2?epimerase, N?acetylmannosamine kinase (GNE) gene lacks feedback inhibition resulting in constitutive overproduction of free sialic acid (Neu5Ac) (Montreuil et al. 1968, Fontaine et al. 1968). Sialuria is characterised by a large cytoplasmic accumulation and urinary excretion of Neu5Ac (Kamerling et al. 1979). Sialurias differ from sialidoses, in which there is storage and excretion of 'bound' Neu5Ac. Defects in GNE also cause Nonaka myopathy (NK; MIM:605820), an early adult-onset disorder characterised by muscle weakness and wasting of distal muscles, especially the anterior tibial muscles (Nonaka et al. 1981, Asaka et al. 2001). Defects in GNE also cause inclusion body myopathy 2 (IBM2; MIM:600737), an autosomal recessive disorder with a similar phenotype to Nonaka myopathy (NK). IBM2 is an adult-onset, proximal and distal muscle weakness and wasting disorder. Muscle biospsy reveals from sufferers shows a rimmed vacuole myopathy and the degenerating muscle fibers contained abnormal amounts of beta-amyloid protein such as that found in neurodegenerative diorders. However, there is no neurological symptoms in these patients (Argov & Yarom 1984).
R-HSA-5579006 Defective GSS causes GSS deficiency In mammalian cells, many antioxidant defence systems exist which protect cells from subsequent exposure to oxidant stresses. One antioxidant is glutathione (GSH), a tripeptide present in virtually all cells that regulates the intracellular redox state and protects cells from oxidative injury. It is metabolised via the gamma-glutamyl cycle, which is catalysed by six enzymes. In man, hereditary deficiencies have been found in five of the six enzymes. Glutathione synthetase deficiency is the most frequently recognised disorder. Defects in GSS can cause glutathione synthetase deficiency (GSSD aka 5-oxoprolinase deficiency, MIM:266130), a severe autosomal recessive disorder characterised by an increased rate of haemolysis, 5-oxoprolinuria, CNS damage and recurrent bacterial infections. In this condition, decreased levels of cellular glutathione result in overstimulation of gamma-glutamylcysteine synthesis and its subsequent conversion to 5-oxoproline. Glutathione synthetase deficiency can be classed as mild, moderate or severe (Ristoff & Larsson 2007, Aoyama & Nakaki 2013).
R-HSA-9704331 Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function Mutations in the N-terminal coiled-coil domain of PALB2 (amino acids 9-44), involved in self-interaction and BRCA1 binding, impair the interaction of PALB2 with BRCA1 (Sy et al. 2009, Foo et al. 2017, Boonen et al. 2020). Phosphorylation of PALB2 by ATR on serine residue S59 promotes BRCA1-PALB2 interaction and the localization of PALB2 to DNA damage sites (Buisson et al. 2017). Mutations in the coiled-coil domain can also affect PALB2 self-interaction, recruitment to double-strand break sites, homologous recombination repair, and RAD51 foci formation (Buisson and Masson 2012). PALB2 missense mutants that do not bind to BRCA1 can still be recruited to DNA double-strand break repair (DSBR) sites, probably through interaction with other proteins involved in DSBR, but they are unable to restore efficient gene conversion in PALB2-deficient cells and they render cells hypersensitive to the DNA damaging agent mitomycin C (Sy et al. 2009). Some variants in this region are also sensitive to PARP inhibitors (Foo et al. 2017).
R-HSA-9704646 Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function Mutations affecting the C-terminal WD40 domain of PALB2 (amino acids 853-1186) impair its ability to interact with BRCA2, RAD51 and/or RAD51C (Erkko et al. 2007, Park et al. 2014). In addition, disruption of the WD40 domain can lead to the exposure of the nuclear export signal (NES) and cytoplasmic translocation of PALB2 (Pauty et al. 2017). Mutations affecting the C-terminal domain of PALB2 are more frequent than mutations that affect the N-terminus and have been observed, as germline mutations, in familial breast cancer and in Fanconi anemia, but somatic mutations also occur in sporadic cancers. Cells that express PALB2 mutants defective in BRCA2, RAD51 and/or RAD51C binding show reduced ability to perform DSBR via homologous recombination repair, form fewer RAD51 foci at DSBR sites, and are sensitive to DNA crosslinking agents such as mitomycin C (Erkko et al. 2007, Park et al. 2014).
R-HSA-3656234 Defective HEXA causes GM2G1 Beta-hexosaminidase (HEX) cleaves the terminal N-acetyl galactosamine (GalNAc) from glycosaminoglycans (GAGs) and any other molecules containing a terminal GalNAc. There are two forms of HEX; HEXA and B. The A form is a trimer of the subunits alpha, beta A and beta B. The B form is a tetramer of 2 beta A and 2 beta B subunits (O'Dowd et al. 1988). Defects in the two subunits cause lysosomal storage diseases marked by the accumulation of GM2 gangliosides in neuronal cells. Defects in the alpha subunits are the cause of GM2-gangliosidosis type 1 (GM2G1) (MIM:272800), also known as Tay-Sachs disease (Okada & O'Brien 1969, Nakano et al. 1988). Classical Tay-Sachs disease is characterised by infant-onset neurodegeneration followed by paralysis, dementia and blindness, Death occurs by the age of 2 or 3 (Okada et al. 1971). The two other forms of Tay-Sachs disease, juvenile- and adult-onset, are less commom and severe than the infant-onset form (Suzuki et al. 1970, Johnson et al. 1982).
R-HSA-3656248 Defective HEXB causes GM2G2 Beta-hexosaminidase (HEX) cleaves the terminal N-acetyl galactosamine (GalNAc) from glycosaminoglycans (GAGs) and any other molecules containing a terminal GalNAc. There are two forms of HEX; HEXA and B. The A form is a trimer of the subunits alpha, beta A and beta B. The B form is a tetramer of 2 beta A and 2 beta B subunits (O'Dowd et al. 1988). Defects in the two subunits cause lysosomal storage diseases marked by the accumulation of GM2 gangliosides in neuronal cells.
Defects in the beta subunits are the cause of GM2-gangliosidosis type 2 (GM2G2; MIM:268800), also known as Sandhoff disease (Sandhoff et al. 1968, Banerjee et al. 1991). Sandhoff disease is an autosomal recessive lysosomal storage disease clinically indistinguishable from GM2-gangliosidosis type 1, presenting early blindness with cherry-red spots on the macula, progressive motor and mental deterioration and macrocephaly. Death usually occurs by the age of 3 years.
R-HSA-5619056 Defective HK1 causes hexokinase deficiency (HK deficiency) Cytosolic hexokinase 1 (HK1), together with isoforms HK2 and 3 and glucokinase (GCK), catalyse the irreversible reaction of alpha-D-glucose (Glc) and ATP to form alpha-D-glucose-6-phosphate (G6P) and ADP, the first step in glycolysis. HK1 is the predominant isoform of the different HKs in tissues that utilise glucose for their physiological function such as brain, lymphocytes, erythrocytes, platelets and fibroblasts. Defects in HK1 can cause hexokinase deficiency (HK deficiency; MIM:235700), a rare, autosomal recessive disease with nonspherocytic hemolytic anemia as the predominant clinical feature (Kanno 2000).
R-HSA-3371599 Defective HLCS causes multiple carboxylase deficiency Defects in HLCS causes holocarboxylase synthetase deficiency (HLCS deficiency aka early onset multiple carboxylase deficiency; MIM:253270). HLCS deficiency is an autosomal recessive disorder whereby deficient HLCS activity results in reduced activity of all five biotin-dependent carboxylases. Symptoms include metabolic acidosis, organic aciduria, lethargy, hypotonia, convulsions and dermatitis (Suzuki et al. 2005). Patients can present symptoms shortly after birth to up to early childhood and will be prescribed oral biotin supplements, typically 10-20 mg daily. Two classes of HLCS deficiency have been reported depending on whether patients respond to biotin therapy. Most patients respond favourably to treatment and show complete reversal of biochemical and clinical symptoms (Morrone et al. 2002, Dupuis et al. 1999). Here mutations in the HLCS active site cause a reduced affinity for biotin that can be overcome by pharmacological doses of the vitamin (Pendini et al. 2008). Patients who display incomplete responsiveness to biotin therapy have a poor long-term prognosis (Bailey et al. 2008). Here mutations that reside outside of the enzyme's active site have no effect on biotin binding but do compromise the protein-protein interaction between the HLCS and its substrates, resulting in reduced biotinylation of all five carboxylases thus reducing their enzymatic activity (Mayende et al. 2012).
R-HSA-9734281 Defective HPRT1 disrupts guanine and hypoxanthine salvage Normally in humans, guanine and hypoxanthine can be salvaged by conversion to GMP and IMP, catalyzed by HPRT1 (hypoxanthine guanine phosphoribosyltransferase). In the absence of HPRT1 activity, however, accumulated guanine and hypoxanthine are catabolized by XDH (xanthine dehydrogenase / oxidase) to urate (Fu & Jinnah 2012).
R-HSA-9670621 Defective Inhibition of DNA Recombination at Telomere ATRX (Alpha thalassemia mental retardation X-lined) and DAXX (Death domain-associated protein 6) chromatin remodeling factors form a complex that binds to subtelomeric regions and plays a role in inhibition of DNA recombination at telomere ends, probably by mediating loading of H3F3A histone at telomere ends and by repressing transcription of TERRA (Telomeric repeat containing RNA), a long noncoding telomeric repeats-containing RNA. Tumors positive for alternative lengthening of telomeres (ALT) markers often harbor loss-of-function mutations in ATRX, and more rarely in DAXX or missense mutations in H3F3A, implying that the impairment of function of one of these three proteins may contribute to initiation of the ALT process. Additionally, mutations in IDH, the tumor suppressor TP53 and SMARCAL1 are also observed in the context of ALT in certain types of human cancers, particularly sarcomas and tumors of the central nervous system (Jiao et al. 2012, Nicolle et al. 2019). For review, please refer to Gocha et al. 2013, Pickett and Reddel 2015, Amorim et al. 2016).
R-HSA-9670615 Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations Many tumors that are positive for markers of alternative lengthening of telomeres (ALT) harbor loss-of-function mutations in the ATRX gene, encoding a chromatin remodeling protein ATRX. ATRX is thought to act together with DAXX and histone H3F3A to inhibit DNA recombination at telomere ends. For review, please refer to Heaphy et al. 2011, Gocha et al. 2014, Pickett and Reddel 2015, Amorim et al. 2016.
R-HSA-9670613 Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations A small portion of tumors that are positive for alternative lengthening of telomeres (ALT) markers and negative for mutations in the ATRX gene harbor loss-of-function mutations in the DAXX gene, which encodes the ATRX binding partner DAXX. For review, please refer to Gocha et al. 2013, and Pickett and Reddel 2015.
R-HSA-9734009 Defective Intrinsic Pathway for Apoptosis Defects in the regulation of the intrinsic pathway for apoptosis are involved in diseases associated with increased cell loss, such as neurodegenerative diseases, as well as in diseases associated with impaired elimination of harmful cells, such as cancer and autoimmunity. For review, please refer to Reed 2001, Lavrik et al. 2009, and Tuzlak et al. 2016.
So far, Reactome has annotated apoptosis defects associated with the loss of function of the CDKN2A gene product p14ARF in cancer, loss of function of TP53 in cancer, and CDK5 dysregulation in neurodegenerative diseases.
R-HSA-9645722 Defective Intrinsic Pathway for Apoptosis Due to p14ARF Loss of Function Cancer-derived missense mutations in the CDKN2A gene that affect the C-terminal arginine-rich region of p14ARF (also known as CDKN2A transcription isoform 4, CDKN2A-4, p14 or ARF) impair p14ARF binding to the mitochondrial matrix protein C1QBP and interfere with p53-mediated apoptosis. Many mutations in the CDKN2A locus that affect C-terminal arginines of p14ARF are silent in p16INK4A (CDKN2A-1) (Itahana and Zhang 2008).
R-HSA-5083627 Defective LARGE causes MDDGA6 and MDDGB6 Glycosyltransferase-like protein LARGE (MIM:603590) is a bifunctional glycosyltransferase with both xylosyltransferase and beta-1,3-glucuronyltransferase activities involved in the biosynthesis of a phosphorylated O-mannosyl trisaccharide, a structure present in alpha-dystroglycan (DAG1; MIM:128239) which plays a key role in skeletal muscle function and regeneration. LARGE contains two substrate-specific GT-domains and belongs to the CAZy glycosyltransferase families GT8 and GT49. Defects in LARGE result in hypoglycosylation of DAG1 and cause several congenital muscular dystrophies (CMDs). Muscular dystrophy-dystroglycanopathy congenital with brain and eye anomalies A6 (MDDGA6; MIM:613154) is associated with brain anomalies, eye malformations, profound mental retardation, and death usually in the first years of life (Clement et al. 2008, Mercuri et al. 2009). Muscular dystrophy-dystroglycanopathy congenital with mental retardation B6 (MDDGB6; MIM:608840) is associated with profound mental retardation, white matter changes and structural brain abnormalities (Longman et al. 2003).
R-HSA-5083630 Defective LFNG causes SCDO3 The Fringe family (CAZy family GT31) of glycosyltransferases in mammals includes LFNG (lunatic fringe; MIM:602576), MFNG (manic fringe; MIM:602577) and RFNG (radical fringe; MIM:602578). Fringe enzymes function in the Golgi apparatus where they initiate the elongation of O-linked fucose on fucosylated peptides by the addition of a beta 1,3 N-acetylglucosaminyl group (GlcNAc) (Moloney et al. 2000). Fringe enzymes elongate conserved O fucosyl residues conjugated to EGF repeats of NOTCH, modulating NOTCH activity (Cohen et al. 1997, Johnston et al. 1997) by decreasing the affinity of NOTCH extracellular domain for JAG ligands (Bruckner et al. 2000).
The spondylocostal dysostoses (SCDs) are a group of disorders that arise during embryonic development by a disruption of somitogenesis. The Notch signalling pathway is essential for somitogenesis, the precursors of vertebra and associated musculature. Defects in one of the Fringe enzymes, beta-1,3-N-acetylglucosaminyltransferase lunatic fringe (LFNG), can cause spondylocostal dysostosis, autosomal recessive 3 (SCDO3, MIM:609813), a condition of variable severity associated with vertebral and rib segmentation defects (Sparrow et al. 2006).
R-HSA-4793950 Defective MAN1B1 causes MRT15 Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase (MAN1B1) normally trims single mannose residues from misfolded glycoproteins, targeting them for degradation and thus providing a quality control process for N-glycoyslated proteins. Defects in MAN1B1 can cause mental retardation, autosomal recessive 15 (MRT15; MIM:614202), a disorder resulting in nonsyndromic moderate to severe mental retardation. It is characterised by significantly below average intellectual functioning associated with impaired adaptative behaviour during the developmental period (Rafiq et al. 2010, Rafiq et al. 2011).
R-HSA-5579012 Defective MAOA causes BRUNS Amine oxidase (flavin-containing) A (MAOA) catalyses the oxidative deamination of biogenic and dietary amines, the regulation of which is critical for mental state homeostasis. MAOA, located on the mitochondrial outer membrane and requiring FAD as cofactor (Weyler 1989), preferentially oxidises biogenic amines such as 5-hydroxytryptamine (5HT), dopamine, noradrenaline and adrenaline. Defects in MAOA can cause Brunner syndrome (BRUNS; MIM:300615), a form of X-linked non-dysmorphic mild mental retardation. Male patients are affected by mild mental retardation and exhibit abnormal behaviour, including impulsive aggression (Brunner et al. 1993, Shih et al. 1999, Shih 2004).
R-HSA-5579024 Defective MAT1A causes MATD S-adenosylmethionine (AdoMet, SAM) is an important methyl donor in most transmethylation reactions. S-adenosylmethionine synthase isoform type-1 (MAT1A) catalyses the formation of AdoMet from methionine and ATP. Defects in MAT1A can cause methionine adenosyltransferase deficiency (MATD; MIM:250850), an inborn error of metabolism resulting in hypermethioninemia. In this condition, methionine accumulates because its conversion to AdoMet is impaired (Furujo et al. 2012, Mudd 2011).
R-HSA-4793952 Defective MGAT2 causes CDG-2a Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (MGAT2) normally catalyses the transfer of a GlcNAc moiety onto the alpha-1,6 mannose of an alpha-1,4 branch of oligomannose N-glycans to form complex N-glycans (Tan et al. 1995). Defects in MGAT2 are associated with congenital disorder of glycosylation type IIa (MGAT2-CDG, CDG-2a; MIM:212066), a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins (Tan et al. 1996, Cormier-Daire et al. 2000, Alkuraya 2010, Alazami et al. 2012). Type II CDGs refer to defects in the trimming and processing of protein-bound glycans.
R-HSA-3359475 Defective MMAA causes MMA, cblA type Defects in MMAA cause methylmalonic aciduria type cblA (cblA aka methylmalonic aciduria type A or vitamin B12-responsive methylmalonic aciduria of cblA complementation type; MIM:251100). Affected individuals accumulate methylmalonic acid in the blood and urine and are prone to potentially life threatening acidotic crises in infancy or early childhood (Dobson et al. 2002, Lerner-Ellis et al. 2004).
R-HSA-3359471 Defective MMAB causes MMA, cblB type Defects in MMAB cause methylmalonic aciduria type cblB (cblB aka methylmalonic aciduria type B or vitamin B12 responsive methylmalonicaciduria of cblB complementation type; MIM:251110). Affected individuals have methylmalonic aciduria and episodes of metabolic ketoacidosis, despite a functional methylmalonyl CoA mutase. In severe cases, newborns become severely acidotic and may die if acidosis is not treated promptly (Dobson et al. 2002).
R-HSA-3359474 Defective MMACHC causes MAHCC Defects in MMACHC cause methylmalonic aciduria and homocystinuria type cblC (MMAHCC; MIM:277400). MMAHCC is the most common disorder of cobalamin metabolism and is characterized by decreased levels of the coenzymes adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl). Affected individuals may have developmental, haematologic, neurologic, metabolic, ophthalmologic, and dermatologic clinical findings (Lerner-Ellis et al. 2006).
R-HSA-3359473 Defective MMADHC causes MMAHCD Defects in MMADHC cause methylmalonic aciduria and homocystinuria type cblD (MMAHCD; MIM:277410), a disorder of cobalamin metabolism characterized by decreased levels of the coenzymes adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl) (Coelho et al. 2008).
R-HSA-4793954 Defective MOGS causes CDG-2b After the lipid-linked oligosaccharide (LLO) precursor is attached to the protein, the outer alpha-1,2-linked glucose is removed by by mannosyl-oligosaccharide glucosidase (MOGS). This is a mandatory step for protein folding control and glycan extension. Defects in MOGS are associated with congenital disorder of glycosylation type IIb (CDGIIb), a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins (De Praeter et al. 2000, Voelker et al. 2002). Type II CDGs refer to defects in the trimming and processing of protein-bound glycans.
R-HSA-4687000 Defective MPDU1 causes CDG-1f Mannose-P-dolichol utilisation defect 1 protein (MPDU1) is required for the efficient utilisation of the mannose donor dolichyl-phospho-mannose (DOLPman) in the synthesis of both lipid-linked oligosaccharides (LLOs) and glycosylphosphatidylinositols. Defects in MPDU1 can cause congenital disorder of glycosylation 1f (MPDU1-CDG, CDG-1f; MIM:609180), a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterised by under-glycosylated serum glycoproteins. CDG type 1 diseases result in a wide phenotypic spectrum, such as poor neurological development, psychomotor retardation, dysmorphic features, hypotonia, coagulation abnormalities and immunodeficiency. In this condition, DOLPman is no longer utilised in transferase reactions extending LLOs, even as substrate levels and transferase enzyme activities appear normal (Anand et al. 2001, Schenk et al. 2001).
R-HSA-4043916 Defective MPI causes MPI-CDG Mannose 6-phosphate isomerase (MPI) normally isomerises fructose 6-phosphate (Fru6P) to mannose 6-phosphate (Man6P) in the cytosol. Man6P is a precursor in the synthesis of GDP-mannose and dolichol-phosphate-mannose, required for mannosyl transfer reactions in the N-glycosylation of proteins. Defects in MPI cause congenital disorder of glycosylation 1b (MPI-CDG, previously known as CDG1b,; MIM:602579), a multisystem disorder characterised by under-glycosylated serum glycoproteins (Schollen et al. 2000). Unlike PMM2-CDG (CDG1a), there is no neurological involvement with MPI-CDG. Instead, patients present predominantly with diarrhoea, failure to thrive and protein-losing enteropathy (Pelletier et al. 1986). MPI-CDG is one of two CDGs that can be treated with oral mannose supplementation, but can be fatal if left untreated (Marquardt & Denecke 2003).
R-HSA-3359469 Defective MTR causes HMAG Defects in MTR cause methylcobalamin deficiency type G (cblG; MIM:250940), an autosomal recessive inherited disease that causes mental retardation, macrocytic anemia, and homocystinuria (Leclerc et al. 1996, Gulati et al. 1996, Watkins et al. 2002).
R-HSA-3359467 Defective MTRR causes HMAE Defects in MTRR cause methylcobalamin deficiency type E (cblE; methionine synthase reductase deficiency; MIM:236270) (Wilson et al. 1999). Patients with cblE exhibit megaloblastic anemia and hyperhomocysteinemia. SAM is used as a methyl donor in many biological reactions and demethylation of SAM produces S-adenosylhomocysteine, which is deadenosylated to form homocysteine. Homocysteine remethylation is carried out by MTR, which requires MTRR to maintain enzyme-bound cobalamin (Cbl) in its active form; but in cblE patients, MTR becomes inactivated and thus homocysteine accumulates.
R-HSA-3359478 Defective MUT causes MMAM Defects in MUT cause methylmalonic aciduria, mut type (MMAM; MIM:251000), an often fatal disorder of organic acid metabolism (Worgan et al. 2006).
R-HSA-9608287 Defective MUTYH substrate binding For a subset of MUTYH disease variants underlying MUTYH-associated polyposis (MAP), also known as familial adenomatous polyposis 2 (FAP2), it was shown that, in addition to impaired catalytic activity, they also exhibit reduced binding to their substrate, adenine mispaired with 8-oxoguanine (OGUA:Ade, also known as 8-oxoG:A). MUTYH alpha-3 isoform (MUTYH-3) mutants with demonstrated deficient binding to OGUA:Ade include missense variants MUTYH-3 Y165C, MUTYH-3 R227W, MUTYH-3 R231L, MUTYH-3 R231H, MUTYH-3 V232F, MUTYH-3 R260Q, MUTYH-3 P281L and MUTYH-3 G382D, nonsense variants MUTYH-3 Y90*, MUTYH-3 Q377*, MUTYH-3 E466*, and frameshift variant MUTYH-3 A368fs26* (commonly known as MUTYH 1103delC) (Chmiel et al. 2003, Parker et al. 2005, Ali et al. 2008, Molatore et al. 2010, D'Agostino et al. 2010).
R-HSA-9608290 Defective MUTYH substrate processing MUTYH disease variants underlying the MUTYH-associated polyposis (MAP), also known as familial adenomatous polyposis 2 (FAP2), show impaired catalytic activity with respect to cleaving adenine mispaired with 8-oxoguanine (OGUA:Ade, also known as 8-oxoG:A). For some of the mutants, defective substrate processing is further aggravated by reduced substrate binding. MUTYH alpha-3 isoform (MUTYH-3) mutants and MUTYH gamma-3 isoform (MUTYH-6) mutants with experimentally demonstrated deficiency in catalytic activity include missense mutants MUTYH-3 Y165C (MUTYH-6 Y151C), MUTYH-3 R171W, MUTYH-3 R227W, MUTYH-3 R231H, MUTYH-3 R231L, MUTYH-3 V232F, MUTYH-3 R260Q, MUTYH-3 G272E, MUTYH-3 P281L, MUTYH-3 P391L (MUTYH-6 P377L), MUTYH-3 Q324H, MUTYH-3 Q324R,, MUTYH-3 A359V, MUTYH-3 G382D (MUTYH-6 G368D), MUTYH-3 A459D, MUTYH-6 R154H, MUTYH-6 I195V, MUTYH-6 M255V and MUTYH-3 L360P, in-frame indel mutants MUTYH-3 W138_M139insIW (also known as MUTYH 137insIW) and MUTYH-3 E466del (MUTYH-6 E452del), nonsense mutants MUTYH-3 Y90*, MUTYH-3 Q377*, and MUTYH-3 E466*, and frameshift mutant MUTYH-3 A368fs26* (commonly known as MUTYH 1103delC) (Jones et al. 2002, Chmiel et al. 2003, Wooden et al. 2004, Parker et al. 2005, Bai et al. 2005, Alhopuro et al. 2005, Bai et al. 2007, Ali et al. 2008, Yanaru-Fujisawa et al. 2008, Kundu et al. 2009, Forsbring et al. 2009, Molatore et al. 2010, D'Agostino et al. 2010, Goto et al. 2010, Raetz et al. 2012, Shinmura et al. 2012).
R-HSA-5545483 Defective Mismatch Repair Associated With MLH1 The MLH1:PMS2 complex is homologous to the E. coli MutL gene and is involved in DNA mismatch repair. Heterozygous mutations in the MLH1 gene result in hereditary nonpolyposis colorectal cancer-2 (Papadopoulos et al., 1994).
R-HSA-5632928 Defective Mismatch Repair Associated With MSH2 MSH2 is homologous to the E. coli MutS gene and is involved in DNA mismatch repair (MMR) (Fishel et al., 1994). Heterozygous mutations in the MSH2 gene result in hereditary nonpolyposis colorectal cancer-1. Variants of MSH2 are associated with hereditary nonpolyposis colorectal cancer. Alteration of MSH2 is also involved in Muir-Torre syndrome and mismatch repair cancer syndrome.
R-HSA-5632927 Defective Mismatch Repair Associated With MSH3 MSH3 forms a heterodimer with MSH2 to form the MSH3:MSH2 complex, part of the post-replicative DNA mismatch repair system. This complex initiates mismatch repair by binding to a mismatch and then forming a complex with MutL alpha heterodimer. This gene contains a polymorphic 9 bp tandem repeat sequence in the first exon. Defects in this gene are a cause of susceptibility to endometrial cancer.
R-HSA-5632968 Defective Mismatch Repair Associated With MSH6 MSH6 encodes a G/T mismatch-binding protein encoded by a gene localized to within 1 megabase of the related hMSH2 gene on chromosome 2. Unlike other mismatch repair genes, the MSH6 deficient cells showed alterations primarily in mononucleotide tracts, indicating the role MSH6 plays in maintaining the integrity of the human genome. Cells deficient in MSH6, accrue mutations in tracts of repeated nucleotides. MSH6 defects seem to be less common than MLH1 and MSH2 defects. They have been mostly observed in atypical HNPCC families and are characterized by a weaker family history of tumor development, higher age at disease onset, and low degrees of microsatellite instability (MSI) that predominantly involving mononucleotide runs.
R-HSA-5632987 Defective Mismatch Repair Associated With PMS2 PMS2 heterodimerizes with MLH1 to form the MutL alpha complex involved in DNA mismatch repair. Mutations in this PMS2 are associated with hereditary nonpolyposis colorectal cancer, Turcot syndrome, and are a cause of supratentorial primitive neuroectodermal tumors. Heterozygous truncating mutations in PMS2 play a role in a small subset of hereditary nonpolyposis colorectal carcinoma (Lynch syndrome, HNPCC-like) families. PMS2 mutations lead to microsatellite instability with carriers showing a microsatellite instability high phenotype and loss of PMS2 protein expression in all tumors.
R-HSA-4341670 Defective NEU1 causes sialidosis Sialidases have important roles in the degradation of glycoconjugates by removing terminal sialic acid residues.
Defects in sialidase 1 (NEU1) cause sialidosis, a lysosomal storage disease characterised by the progressive lysosomal storage of sialidated glycopeptides and oligosaccharides and the accumulation and excretion of N-acetylneuraminic acid (Neu5Ac) covalently-linked ('bound') glycoconjugates (Lowden & O'Brien 1979). The sialidoses are distinct from the sialurias in which there is storage and excretion of 'free' Neu5Ac. Sialidosis manifests into types I and II forms. Type I is the milder form, also known as the 'normosomatic' type or the cherry red spot-myoclonus syndrome. Sialidosis type II is the more severe form with an earlier onset, and is also known as the 'dysmorphic' type.
R-HSA-9630222 Defective NTHL1 substrate binding Several different mutations that result in truncation of NTHL1 protein have been described and associated with cancer. NTHL1 Q90TER (NTHL1 Gln90*) truncation mutant results from a nonsense mutation that replaces codon for glutamine 90 with a STOP codon. NTHL1 Q90TER has not been studied at the protein level, but is predicted to lack the DNA binding domain and the glycosylase domain, thus resulting in a complete loss of the base excision repair (BER) related DNA glycosylase function. Homozygous or compound heterozygous germline NTHL1 Q90TER mutation result in a cancer syndrome (NTHL1 associated tumor syndrome) that involves adenomatous polyposis, colorectal cancer breast cancer and multiple other types of cancer and benign tumors (Weren et al. 2015, Rivera et al. 2015, Grolleman et al. 2019). Apart from NTHL1 Q90TER, at least seven other truncating variants have been identified in patients with NTHL1 associated tumor syndrome, such as NTHL1 A79fs (NTHL1 Ala79fs), NTHL1 Y130TER (NTHL1 Tyr130*), NTHL1 W182TER (NTHL1 Trp182*), NTHL1 c.709+1G>A, NTHL1 I245fs (NTHL1 Ile245fs), NTHL1 W269TER (NTHL1 Trp269*), NTHL1 Q287TER (NTHL1 Gln287*) (Rivera et al. 2015, Broderick et al. 2017, Grolleman et al. 2019).
R-HSA-9630221 Defective NTHL1 substrate processing NTHL1 D239Y is produced as a consequence of a single nucleotide polymorphism (SNP) rs3087468 in the NTHL1 gene. The frequency of this polymorphism varies in different populations. Substitution of aspartic acid residue at position 239 with tyrosine results in an NTHL1 protein that is still able to bind to damaged DNA but appears to have impaired glycosylase activity. Expression of NTHL1 D239Y in non-transformed human and mouse mammary epithelial cells increases genomic instability and leads to neoplastic transformation, acting as a dominant negative for wild-type NTHL1, through competition for substrate binding (Galick et al. 2013). It is uncertain if heterozygosity for NTHL1 D239Y polymorphism increases predisposition to cancer.
R-HSA-9657050 Defective OGG1 Localization OGG1 splicing isoform beta contains a mitochondrial targeting sequence at the N terminus and lacks the C terminal nuclear localization signal. OGG1beta localizes to mitochondria (Nishioka et al. 1999), where it might participate in the repair of mitochondrial DNA, although its role in mitochondrial base excision repair has not been confirmed. OGG1beta G12E mutant, reported in kidney cancer, is unable to translocate to the mitochondrion as the missense mutation disrupts the mitochondrial targeting sequence (Audebert et al. 2002).
R-HSA-9656255 Defective OGG1 Substrate Binding OGG1 missense mutants reported in Alzheimer's disease, OGG1 A53T and OGG1 A288V, show decreased binding to 8 oxoguanine substrate (Mao et al. 2007).
R-HSA-9656256 Defective OGG1 Substrate Processing The majority of OGG1 mutants have been tested for their ability to excise 8-oxoguanine (8oxoG) from damaged DNA, while a small number of mutants have been tested for the ability to remove FapyG from DNA.
The following OGG1 mutants show at least a partial loss of their ability to remove 8oxoG:
OGG1 R46Q (Audebert, Chevillard et al. 2000; Audebert, Radicella et al. 2000);
OGG1 R154H (Audebert, Radicella et al. 2000, Bruner et al. 2000);
OGG1 R131Q (Chevillard et al. 1998, Bruner et al. 2000, Anderson and Dagget 2009);
OGG1 R229Q (Hyun et al. 2000, Hyun et al. 2002, Hill and Evans 2007);
OGG1 P266fs139* (Mao et al. 2007).
OGG1 R46L and OGG1 R131G have not been functionally studied but have been reported in cancer and predicted to be pathogenic. They are annotated as candidate disease variants based on their similarity with OGG1 R46Q and OGG1 R131Q, respectively.
OGG1 S326C, a frequent variant in European and Asian populations, is susceptible to oxidation, which diminishes catalytic activity under conditions of oxidative stress (Dherin et al. 1999, Yamane et al. 2004, Kershaw and Hodges 2012, Moritz et al. 2014).
The following OGG1 mutants show at least a partial loss of their ability to remove FapyG:
OGG1 R46Q (Audebert, Radicella et al. 2000);
OGG1 R154H (Audebert, Radicella et al. 2000).
OGG1 R46L has not been functionally studied but has been reported in cancer and predicted to be pathogenic. It is annotated as a candidate disease variant for FapyG excision, based on its similarity with OGG1 R46Q.
R-HSA-5578998 Defective OPLAH causes OPLAHD The gamma-glutamyl cycle is a six-enzyme cycle that represents the primary pathway for glutathione synthesis and degradation. One step is the cleavage of 5-oxo-L-proline (OPRO) to form L-glutamate, coupled to the hydrolysis of ATP. This is catalysed by 5-oxoprolinase (OPLAH) is a homodimeric, cytosolic protein. Defects in OPLAH can cause 5-oxoprolinase deficiency (OPLAHD; MIM:260005), an extremely rare disorder of the gamma-glutamyl cycle about which debate continues as to whether it is a disorder or just a biochemical condition with no adverse clinical effects apart from 5-oxoprolinuria (Calpena et al. 2013, Almaghlouth et al. 2012, Aoyama & Nakaki 2013).
R-HSA-3560796 Defective PAPSS2 causes SEMD-PA Defects in PAPSS2 cause spondyloepimetaphyseal dysplasia Pakistani type (SEMD-PA; MIM:612847), a bone disease characterized by epiphyseal dysplasia with mild metaphyseal abnormalities. Clinical features include short stature from birth, short and bowed lower limbs, mild brachydactyly, kyphoscoliosis, abnormal gait and enlarged knee joints. Some patients may manifest premature pubarche and hyperandrogenism (Ahmed et al. 1998, Noordam et al. 2009, Miyake et al. 2012).
R-HSA-5609974 Defective PGM1 causes PGM1-CDG Phosphoglucomutases 1 and 2 (PGM1, 2) are involved in the cytosolic biosynthesis of nucleotide sugars needed for glycan biosynthesis, specifically, the isomerisation of glucose-6-phosphate (G6P) into glucose-1-phosphate (G1P). Defects in PGM1 can cause congenital disorder of glycosylation 1t (CDG1t, now known as PGM1-CDG; MIM:614921), a broad spectrum disorder characterised by under-glycosylated serum glycoproteins (Timal et al. 2012, Tegtmeyer et al. 2014). CDGs result in a wide variety of clinical features such as defects in nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency.
R-HSA-4043911 Defective PMM2 causes PMM2-CDG Phosphomannomutase 2 (PMM2) normally catalyses the isomerisation of mannose 6-phosphate (Man6P) to mannose 1-phosphate (Man1P) in the cytosol of cells. Man1P is a precursor in the synthesis of GDP-mannose and dolichol-phosphate-mannose, required for critical mannosyl transfer reactions in the N-glycosylation of proteins. Mutations in the PMM2 gene are one of the causes of Jaeken syndrome, a congenital disorder of glycosylation type 1a (PMM2-CDG, previously CDG-1a) (Matthijs et al. 1997). PMM2-CDG was first described in Belgian identical twin sisters, characterized by psychomotor retardation and multiple serum glycoprotein abnormalities. Serum and CSF transferrin were found to be deficient in sialic acid (Jaeken et al. 1984). PMM2-CDG is the most common CDG disease subtype.
R-HSA-9735763 Defective PNP disrupts phosphorolysis of (deoxy)guanosine and (deoxy)inosine Normally in humans, PNP (purine nucleotide phosphorylase) catalyzes the conversion of (deoxy)guanosine and (deoxy)inosine to guanine and hypoxanthine, respectively. In the absence of PNP activity, however, these purine nucleosides accumulate, disrupting lymphoid cell function and leading to severe immunodeficiency (Aust et al. 1992; Williams et al. 1987).
R-HSA-5083628 Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 (POMGNT1; CAZy family GT61; MIM:606822) mediates the transfer of N-acetylglucosaminyl (GlcNAc) residues to mannosylated proteins such as mannose-O-serine-dystroglycan (man-O-Ser-DAG1). DAG1 is a cell surface protein that plays an important role in the assembly of the extracellular matrix in muscle, brain, and peripheral nerves by linking the basal lamina to cytoskeletal proteins. Defects in POMGNT1 (MIM:606822) result in disrupted glycosylation of DAG1 and can cause severe congenital muscular dystrophy-dystroglycanopathies ranging from a severe type A3 (MDDGA3; MIM:253280), through a less severe type B3 (MDDGB3; MIM:613151) to a milder type C3 (MDDGC3; MIM:613157) (Bertini et al. 2011, Wells 2013).
R-HSA-5083633 Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 Co-expression of both protein O-mannosyl-transferases 1 and 2 (POMT1 and POMT2; CAZy family GT39) is necessary for enzyme activity, that is mediating the transfer of mannosyl residues to the hydroxyl group of serine or threonine residues of proteins such as alpha-dystroglycan (DAG1; MIM:128239). DAG1 is a cell surface protein that plays an important role in the assembly of the extracellular matrix in muscle, brain, and peripheral nerves by linking the basal lamina to cytoskeletal proteins. Defects in POMT1 (MIM:607423) results in defective glycosylation of DAG1 and can cause severe congenital muscular dystrophy-dystroglycanopathies ranging from a severe type A, MDDGA1 (brain and eye abnormalities; MIM:236670), through a less severe type B, MDDGB1 (congenital form with mental retardation; MIM:613155) to a milder type C, MDDGC1 (limb girdle form; MIM:609308) (Bertini et al. 2011, Wells 2013).
R-HSA-5083629 Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 Co-expression of both protein O-mannosyl-transferases 1 and 2 (POMT1 and POMT2; CAZy family GT39) is necessary for enzyme activity, that is mediating the transfer of mannosyl residues to the hydroxyl group of serine or threonine residues of proteins such as alpha-dystroglycan (DAG1; MIM:128239). DAG1 is a cell surface protein that plays an important role in the assembly of the extracellular matrix in muscle, brain, and peripheral nerves by linking the basal lamina to cytoskeletal proteins. Defects in POMT2 (MIM:607439) results in defective glycosylation of DAG1 and can cause severe congenital muscular dystrophy dystroglycanopathies ranging from a severe type A, MDDGA2 (brain and eye abnormalities; MIM:613150), through a less severe type B, MDDGB2 (congenital form with mental retardation; MIM:613156) to a milder type C, MDDGC2 (limb girdle form; MIM:603158) (Bertini et al. 2011, Wells 2013).
R-HSA-4570571 Defective RFT1 causes CDG-1n The N-glycan precursor is flipped across the ER membrane, moving it from the cytosolic side to the ER lumenal side. The exact mechanism of this translocation is not well understood but protein RFT1 homolog (RFT1) is known to be involved (Helenius et al. 2002). Defects in RFT1 are associated with congenital disorder of glycosylation 1n (RFT1-CDG, CDG-1n). The disease is a multi-system disorder characterised by under-glycosylated serum glycoproteins. Early-onset developmental retardation, dysmorphic features, hypotonia, coagulation disorders and immunodeficiency are reported features of this disorder (Haeuptle et al. 2008).
R-HSA-5619042 Defective RHAG causes regulator type Rh-null hemolytic anemia (RHN) Rhesus (Rh) blood group antigens consist of several membrane-associated polypeptides including RHAG, which is required for cell-surface expression of the complex. The Rh(null) phenotype arises from missing or severely deficient Rh antigens and sufferers present a clinical syndrome of varying severity characterised by abnormalities of red cell shape, cation transport and membrane phospholipid organisation. The human gene RHAG encodes a Rhesus blood group family type A glycoprotein (belonging to the SLC42 solute transporter family) which is expressed specifically in erythroid cells. A transport function for RHAG is suggested to mediate ammonium (NH4+) export from these cells and prevent toxic build-up of NH3/NH4+ (Westhoff et al. 2002, Ripoche et al. 2004). Defects in RHAG are the cause of regulator type Rh-null hemolytic anemia (RHN, Rh-deficiency syndrome). RHN is a form of chronic hemolytic anemia (Huang & Ye 2010).
R-HSA-9693928 Defective RIPK1-mediated regulated necrosis Receptor Interacting Serine/Threonine Kinase 1 (RIPK1)-mediated regulated necrosis also called necroptosis is an important type of programmed cell death in addition to apoptosis. Necroptosis eventually leads to cell lysis and release of cytoplasmic content into the extracellular region. Necroptosis must be tightly controlled. Disregulated or defective necroptotic cell death is often associated with a tissue damage resulting in an intense inflammatory response. Defects of necroptosis may contribute to various pathological processes, including autoimmune disease, neurodegeneration, multiple cancers, and kidney injury.
R-HSA-9657689 Defective SERPING1 causes hereditary angioedema The reciprocal activation is initiated when zymogen factor XII (F12 or FXII) binds to a negatively charged surface, which induces FXII autoactivation. Activated FXII (FXIIa) converts prekallikrein (PK) to kallikrein, which proteolytically liberates bradykinin from high molecular weight kininogen (HK) (Renne T 2012; Renne T et al. 2012; Maas C et al. 2011). Kallikrein also activates FXII to produce more FXIIa (initially). FXIIa and kallikrein reciprocally activate their zymogens and thus generate a positive feedback loop. In the presence of sufficient amounts of active enzyme, FXIIa also generates active factor XI (FXIa) to potentiate the intrinsic coagulation pathway. All of these enzymatic steps are normally inhibited by C1-esterase inhibitor (C1-INH, encoded by the SERPING1 gene).
Binding of the proinflammatory peptide hormone bradykinin to the bradykinin B2 receptor (B2R) activates various proinflammatory signaling pathways that increase vascular permeability and fluid efflux. An excessive formation of bradykinin due to uncontrolled activation of the coagulation factor XII (FXII)-dependent kallikrein-kinin system causes increased vascular permeability at the level of the postcapillary venule and results in hereditary angioedema (HAE) (Bossi F et al. 2009; Kaplan AP 2010; Suffritti C et al. 2014: Zuraw BL & Christiansen SC 2016). HAE is a rare life-threatening inherited edema disorder that is characterized by recurrent episodes of localized edema of the skin or of the mucosa of the gastrointestinal tract or upper airway. Angioedema initiated by bradykinin is usually associated with SERPING1 (C1-INH) deficiency. Thus, a major role of SERPING1 (C1-INH) is to prevent the development of excessive vascular permeability. More rarely, HAE occurs in individuals with normal SERPING1 activity, linked to mutations in other proteins, including FXII, plasminogen, and angiopoietin (Magerl M et al. 2017; Zuraw BL 2018; Ivanov I et al. 2019). Patients with HAE are heterozygous for deficiency of SERPING1.The disease, therefore, has an autosomal dominant inheritance and may result from lack of expression of SERPING1 from one allele (type 1 HAE) or from expression of a nonfunctional SERPING1 protein (type 2 HAE). This classification has however been challenged by observations of intermediary HAE types, that can arise, when small amounts of dysfunctional SERPING1 is present in the blood stream (Eldering E et al. 1995; Verpy E et al. 1995; Madsen DE et al. 2014).
R-HSA-5687868 Defective SFTPA2 causes IPF One function of the pulmonary collectins, surfactant proteins A1, A2, A3 and D (SFTPAs, D), is that they influence surfactant homeostasis, contributing to the physical structures of lipids in the alveoli and to the regulation of surfactant function and metabolism. They are directly secreted from alveolar type II cells into the airway to function as part of the surfactant. The mechanism of secretion is unknown. Mutations in SFTPA2 disrupt protein structure and the defective protein is retained in the ER membrane causing idiopathic pulmonary fibrosis (IPF; MIM:178500). IPF is one of a family of idiopathic pneumonias sharing clinical features of shortness of breath, formation of scar tissue and varying degrees of inflammation and/or fibrosis on lung biopsy. IPF is typically progressive, leading to death from respiratory failure within 2-5 years of diagnosis in the majority of instances (Meltzer & Noble 2008, Noble & Barkauskas 2012).
R-HSA-5619048 Defective SLC11A2 causes hypochromic microcytic anemia, with iron overload 1 (AHMIO1) The primary site for absorption of dietary iron is the duodenum. Ferrous iron (Fe2+) is taken up from the gut lumen across the apical membranes of enterocytes and released into the portal vein circulation across basolateral membranes. The human gene SLC11A2 encodes the divalent cation transporter DCT1 (NRAMP2, Natural resistance-associated macrophage protein 2). DCT1 resides on the apical membrane of enterocytes and mediates the uptake of many metal ions, particularly ferrous iron, into these cells. Defects in SLC11A2 can cause hypochromic microcytic anemia, with iron overload 1 (AHMIO1; MIM:206100), a blood disorder characterised by high serum iron, large hepatic iron deposition, abnormal haemoglobin content in erythrocytes which are reduced in size and absence of sideroblasts and stainable bone marrow iron store (Shawki et al. 2012, Iolascon & De Falco 2009).
R-HSA-5619104 Defective SLC12A1 causes Bartter syndrome 1 (BS1) The solute carrier family 12 member 1 (SLC12A1, NKCC2) is a kidney-specific, membrane-bound protein that cotransports two Cl- ions electroneutrally into cells with a Na+ ion and a K+ ion and plays a vital role in the regulation of ionic balance and cell volume. Defects in SLC12A1 can cause Bartter’s syndrome (BS1; MIM:601678), an autosomal-recessive disease salt-wasting disorder characterised by renal tubular hypokalaemia, metabolic alkalosis and hypercalciuria. Clinical features present in infancy and include muscle weakness, anorexia, polydipsia, polyuria, failure to thrive and mental and growth retardation (Favero et al. 2011, Gagnon & Delpire 2013).
R-HSA-5619087 Defective SLC12A3 causes Gitelman syndrome (GS) The SLC12A3 gene encodes for the Thiazide-sensitive sodium-chloride cotransporter (TSC). TSC mediates sodium and chloride removal from the distal convoluted tubule of the kidney. Defects in SLC12A3 are the cause of Gitelman syndrome (GS aka familial hypokalemic hypomagnesemia; MIM:263800). GS is an autosomal recessive disorder characterised by hypokalemic metabolic alkalosis, hypomagnesemia, and hypocalciuria. Patients can present with periods of muscular weakness and tetany, usually accompanied by abdominal pain, vomiting and fever. GS has overlapping features with Bartter syndrome (caused by defects in SLC12A1). This cotransporter is the major target for thiazide-type diuretics, used in the treatment of hypertension, extracellular fluid overload and renal stone disease (Nakhoul et al. 2012).
R-HSA-5619039 Defective SLC12A6 causes agenesis of the corpus callosum, with peripheral neuropathy (ACCPN) K+/Cl- cotransport is implicated not only in regulatory volume decrease, but also in transepithelial salt absorption, renal K+ secretion, myocardial K+ loss during ischemia and regulation of neuronal Cl- concentration. Four genes (SLC12A4-7) encode the K+/Cl- cotransporters KCC1-4 respectively. Cotransport of K+ and Cl- is electroneutral with a 1:1 stoichiometry. These cotransporters function as homomultimers or heteromultimers with other K+/Cl- cotransporters. SLC12A6 encodes KCC3 which is highly expressed in heart, brain, spinal cord, kidney, muscle, pancreas and placenta. Defects in SLC12A6 are a cause of agenesis of the corpus callosum with peripheral neuropathy (ACCPN; MIM:218000), a autosomal recessive disease characterised by severe progressive sensorimotor neuropathy, mental retardation, dysmorphic features and variable degree of agenesis of the corpus callosum (Howard et al. 2002, Dupre et al. 2003, Salin-Cantegrel et al. 2011).
R-HSA-5619070 Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) Four members of the SLC16A gene family encode classical monocarboxylate transporters MCT1-4. Widely expressed, they all function as proton-dependent transporters of monocarboxylic acids such as lactate and pyruvate and ketone bodies such as acetacetate and beta-hydroxybutyrate. These processes are crucial in the regulation of energy metabolism and acid-base homeostasis.
SLC16A1 encodes MCT1, a ubiquitiously expressed protein. Heterozygous defects in SLC16A1 were found in patients with symptomatic deficiency in lactate transport (SDLT aka erythrocyte lactate transporter defect; MIM:245340), resulting in an acidic intracellular environment and muscle degeneration with the release of myoglobin and creatine kinase (Merezhinskaya et al. 2000). This defect could compromise extreme performance in otherwise healthy individuals.
SLC16A1 is essential for lactate transport in muscle cells. It is also highly enriched in astrocytes and oligodendroglia, neuroglia that support, insulate and provide energy metabolites to axons. Oligodendroglia dysfunction can lead to axon degeneration in several diseases. The cause is unknown but disruption of SLC16A1 transporter produces axon damage and neuron loss in animal and cell culture models. In humans, this transporter is reduced in patients with amyotrophic lateral sclerosis (Lee et al. 2012).
In cancer cells, a common change is the upregulation of glycolysis. The anti-cancer drug candidate 3-bromopyruvate (3-BrPA) can inhibit glycolysis through its uptake into cancer cells via SLC16A1 so it is the main determinant of 3-BrPA sensitivity in these cells (Birsoy et al. 2013).
R-HSA-5619035 Defective SLC17A5 causes Salla disease (SD) and ISSD SLC17A5 encodes a lysosomal sialic acid transporter, sialin (AST, membrane glycoprotein HP59) which exports sialic acid (N-acetylneuraminic acid, Neu5Ac) derived from the degradation of glycoconjugates from lysosomes. This export is dependent on the proton electrochemical gradient across the lysosomal membrane. SLC17A5 is present in the pathological tumor vasculature of the lung, breast, colon, and ovary, but not in the normal vasculature, suggesting that the protein may be critical to pathological angiogenesis. Sialin is not expressed in a variety of normal tissues, but is significantly expressed in human fetal lung. Defects in SLC17A5 cause Salla disease (SD) and infantile sialic acid storage disorder (ISSD aka N-acetylneuraminic acid storage disease, NSD). These diseases belong to the sialic acid storage diseases (SASDs) and are autosomal recessive neurodegenerative disorders characterised by hypotonia, cerebellar ataxia and mental retardation with patients excreting large amounts of free Neu5Ac in urine. ISSD is a severe infantile form of SASD with a more severe clinical course than SD (Verheijen et al. 1999, Aula et al. 2000).
R-HSA-5619076 Defective SLC17A8 causes autosomal dominant deafness 25 (DFNA25) There are two classes of glutamate transporters; the excitatory amino acid transporters (EAATs) which depend on an electrochemical gradient of Na+ ions and vesicular glutamate transporters (VGLUTs) which are proton-dependent. Together, these transporters uptake and release glutamate to mediate this neurotransmitter's excitatory signal and are part of the glutamate-glutamine cycle. Three members of the SLC17A gene family (7, 6 and 8) encode VGLUTs 1-3 respectively. This uptake is thought to be coupled to the proton electrochemical gradient generated by the vacuolar type H+-ATPase. They are all expressed in the CNS in neuron-rich areas but SLC17A8 (VGLUT3) is also expressed on astrocytes and in the liver and kidney. Defects in SLC17A8 can cause autosomal dominant deafness 25 (DFNA25; MIM:605583), a form of non-syndromic sensorineural hearing loss. The cochlea expresses SLC17A8 and in mice which lack this transporter are congenitally deaf. Hearing loss is due to the lack of glutamate release by inner hair cells therefore a loss of synaptic transmission at the IHC-afferent nerve synapse. Successful restoration of hearing by gene replacement in mice could be a significant advance toward gene therapy of human deafness (Ruel et al. 2008, Akil et al. 2012).
R-HSA-5619067 Defective SLC1A1 is implicated in schizophrenia 18 (SCZD18) and dicarboxylic aminoaciduria (DCBXA) There are two classes of glutamate transporters; the excitatory amino acid transporters (EAATs) which depend on an electrochemical gradient of Na+ ions and vesicular glutamate transporters (VGLUTs) which are proton-dependent. Together, these transporters uptake and release glutamate to mediate this neurotransmitter's excitatory signal and are part of the glutamate-glutamine cycle.
The SLC1 gene family includes five high-affinity glutamate transporters encoded by SLC1, 2, 3, 6 and 7. These transporters can mediate transport of L-Glutamate (L-Glu), L-Aspartate (L-Asp) and D-Aspartate (D-Asp) with cotransport of 3 Na+ ions and H+ and antiport of a K+ ion. This mechanism allows glutamate into cells against a concentration gradient. This is a crucial factor in the protection of neurons against glutamate excitotoxicity (the excitation of nerve cells to their death) in the CNS (Zhou & Danbolt 2014).
SLC1A1 encodes an excitatory amino-acid carrier 1 (EAAC1, also called EAAT3) and is abundant particularly in brain but also in kidney, liver, muscle, ovary, testis and in retinoblastoma cell lines. In the kidney, SLC1A1 is present at apical membranes of proximal tubes where it serves as a major route of glutamate and aspartate reuptake from urine. Defects in SLC1A1 are the cause of dicarboxylic aminoaciduria (DCBXA; MIM:222730), an autosomal recessive glutamate-aspartate transport defect in the kidney and intestine (Bailey et al. 2011). Mutations that can cause DCBXA are R445W and I395del (Bailey et al. 2011).
A defect in SLC1A1 is also implicated in schizophrenia 18 (SCZD18; MIM:615232). Schizophrenia (SCZD; MIM:181500) is a complex, multifactorial psychotic disorder characterised by disturbances in the form and content of thought, in mood, in sense of self and relationship to the external world and in behaviour. It ranks amongst the world's top 10 causes of long-term disability. At the neuropathological level, SCZD appears to be characterised by synaptic deficits, alterations in glutamate and dopamine neurotransmission and hypofrontality (a state of decreased cerebral blood flow (CBF) in the prefrontal cortex of the brain). Variations in the SLC1A1 gene can confer susceptibility to SCZD18 (Harris et al. 2013). In the remote Pacific island of Palau, the risk of SCZD is 2-3 times the worldwide rate. In a 5-generation Palauan family, an 84kb deletion was carried by psychosis patients and proposed to increase the disease risk more than 18-fold for family members (Myles-Worsley et al. 2013).
R-HSA-5619062 Defective SLC1A3 causes episodic ataxia 6 (EA6) There are two classes of glutamate transporters; the excitatory amino acid transporters (EAATs) which depend on an electrochemical gradient of Na+ ions and vesicular glutamate transporters (VGLUTs) which are proton-dependent. Together, these transporters uptake and release glutamate to mediate this neurotransmitter's excitatory signal and are part of the glutamate-gluatamine cycle.
The SLC1 gene family includes five high-affinity glutamate transporters encoded by SLC1, 2, 3, 6 and 7. These transporters can mediate transport of L-Glutamate (L-Glu), L-Aspartate (L-Asp) and D-Aspartate (D-Asp) with cotransport of 3 Na+ ions and H+ and antiport of a K+ ion. This mechanism allows glutamate into cells against a concentration gradient. This is a crucial factor in the protection of neurons against glutamate excitotoxicity (the excitation of nerve cells to their death) in the CNS (Zhou & Danbolt 2014).
SLC1A3 is highly expressed in the cerebellum but also found in the frontal cortex, hippocampus and basal ganglia. Defects in SLC1A3 have been shown to cause episodic ataxia type 6 (EA6; MIM:612656) where mutations in SLC1A3 can lead to decreased glutamate uptake, thus contributing to neuronal hyperexcitability to cause seizures, hemiplegia and episodic ataxia (Jen et al. 2005, de Vries et al. 2009).
R-HSA-5619111 Defective SLC20A2 causes idiopathic basal ganglia calcification 1 (IBGC1) The genes SLC20A1 and SLC20A2 encode for phosphate transporters 1 and 2 (PiT1 and PiT2 respectively). They both have a broad tissue distribution and may play a general housekeeping role in phosphate transport such as absorbing phosphate from interstitial fluid and in extracellular matrix and cartilage calcification as well as in vascular calcification.
They possess Na+-coupled phosphate (Pi) cotransporter function with a stoichiometry of 2:1 (Na+:Pi). Defects in SLC20A2 can cause idiopathic basal ganglia calcification 1 (IBGC1; MIM:213600), an autosomal dominant disorder characterised by vascular and pericapillary calcification by calcium phosphate in the basal ganglia and other brain regions. Affected individuals can either be asymptomatic or show a wide spectrum of neuropsychiatric symptoms including parkinsonism and dementia (Wang et al. 2012, Hsu et al. 2013, Ashtari et al. 2013, Forster et al. 2013).
R-HSA-5619071 Defective SLC22A12 causes renal hypouricemia 1 (RHUC1) Urate is a naturally occurring product of purine metabolism and is a scavenger of biological oxidants. Uric acid readily precipitates out of aqueous solutions causing gout and kidney stones. Due to this ability, changes in urate levels are implicated in numerous disease processes. The human gene SLC22A12 encodes urate transporter 1 (URAT1), predominantly expressed in the kidney and is involved in the regulation of blood urate levels. This transport can be trans-stimulated by organic anions such as L-lactate (LACT). Defects in SLC22A12 result in idiopathic renal hypouricaemia 1 (RHUC1; MIM:220150), a disorder characterised by impaired urate reabsorption at the apical membrane of proximal renal tubule cells and high urinary urate excretion (Wakida et al. 2005, Esparza Martin & Garcia Nieto 2011).
R-HSA-5619066 Defective SLC22A18 causes lung cancer (LNCR) and embryonal rhabdomyosarcoma 1 (RMSE1) The human gene SLC22A18 (aka TSSC5) encodes organic cation transporter-like protein 2 (ORCTL2). It is expressed at high levels in kidney, liver and colon and at lower levels in heart, brain and lung. ORCTL2 can transport organic cations such as chloroquine and quinidine with the antiport of protons.
The human chromosome region 11p15.5 is linked with Beckwith-Wiedemann syndrome (associated with susceptibility to Wilms' tumor, rhabdomyosarcoma and hepatoblastoma). SLC22A18 is located in this region (Cooper et al. 1998, Lee et al. 1998). Mutations and/or reduced expression of SLC22A18 have been found in certain tumors such as lung cancer (LNCR; MIM:211980) (Lee et al. 1998) and embryonal rhabdomyosarcoma 1 (RMSE1; MIM:268210) (Schwienbacher et al. 1998). How SLC22A18 might be involved in growth regulation is poorly understood. There is speculation that it may be involved in resistance to chemotherapy drugs and/or in the export of genotoxic substances whose retention may increase the risk of tumor formation.
R-HSA-5619053 Defective SLC22A5 causes systemic primary carnitine deficiency (CDSP) The human SLC22A5,15 and 16 genes encode for sodium-dependent, high affinity carnitine cotransporters which maintain systemic and tissue concentrations of carnitine. Carnitine is essential for beta-oxidation of long-chain fatty acids to produce ATP. SLC22A5 encodes the organic cation/carnitine transporter 2 (OCTN2). SLC22A5 is strongly expressed in the kidney, skeletal muscle, heart and placenta. Defects in SLC22A5 are the cause of systemic primary carnitine deficiency (CDSP; MIM:212140), an autosomal recessive disorder of fatty-acid oxidation caused by defective carnitine transport resulting in cardiac, skeletal, or metabolic symptoms. If diagnosed early, all clinical symptoms can be completely reversed with a carnitine supplement. However, if left untreated, patients will develop lethal heart failure (Shibbani et al. 2014, Tamai 2013).
R-HSA-5619077 Defective SLC24A1 causes congenital stationary night blindness 1D (CSNB1D) Five members of the NCKX (SLC24) family are all able to exchange one Ca2+ and one K+ for four Na+. SLC24A1 encodes an exchanger protein NCKX1 which is the most extensively studied member and is highly expressed in the eye. The light-induced lowering of calcium by efflux via this protein plays a key role in the process of light adaptation (Schnetkamp 2013). Defects in SLC24A1 can cause congenital stationary night blindness 1D (CSNB1D), an autosomal recessive, non-progressive retinal disorder characterised by impaired night vision and characterised by a Riggs-type of electroretinogram (Riazuddin et al. 2010).
R-HSA-5619055 Defective SLC24A4 causes hypomineralized amelogenesis imperfecta (AI) The five members of the NCKX (SLC24) family are all able to exchange one Ca2+ and one K+ for four Na+. SLC24A4 encodes an exchanger protein NCKX4 which may play a role in calcium transport during amelogenesis (the process of formation of tooth enamel). SLC24A4 is upregulated in ameloblasts during the maturation stage of amelogenesis (Hu et al. 2012). Defects in SLC24A4 can cause hypomineralised amelogenesis imperfecta (AI), an autosomal recessive disorder in which tooth enamel formation fails. Screening of AI families identified mutations which severely diminish or abolish transport function of SLC24A4 (Parry et al. 2013, Wang et al. 2014).
Genetic variants in SLC24A4 define the skin/hair/eye pigmentation variation locus 6 (SHEP6; MIM:210750). In a genomewide association scan of thousands of Icelanders and Dutch, Sulem et al. found a strong association between the T allele of a SNP in the SLC24A4 gene and blond versus brown hair and blue versus green eyes (Sulem et al. 2007).
R-HSA-5619036 Defective SLC24A5 causes oculocutaneous albinism 6 (OCA6) Five members of the NCKX (SLC24) family are all able to exchange one Ca2+ and one K+ for four Na+. SLC24A5 (NCKX5, located on the trans-Golgi membrane) is the prediminant K+-dependent Na+/Ca2+ exchanger in melanocytes and is one of a handful of genes thought to play a role in determining human skin colour (Wilson et al. 2013). Defects in SLC24A5 can cause oculocutaneous albinism 6 (OCA6; MIM:113750), a disorder characterised by a reduction or complete loss of melanin in the skin, hair and eyes. Patients with this condition show accompanied eye symptoms (Kamaraj & Purohit 2014, Morice-Picard et al. 2014).
R-HSA-3560792 Defective SLC26A2 causes chondrodysplasias The SLC26A1 and 2 genes encode sulfate transporter proteins that facilitate sulfate uptake into cells, critical in cartilage for sulfation of proteoglycans and extracellular matrix organization. Defects in SLC26A2 result in impaired SO4(2-) transport leading to insufficient sulfation of cartilage proteoglycans. Defective SLC26A2 is implicated in the pathogenesis of a spectrum of autosomal recessive human chondrodysplasias. Severity of symptoms range from mild (diastrophic dysplasia; MIM:222600), intermediate (atelosteogenesis type II; MIM256050) to severe (achondrogenesis type 1B; MIM:600972) (Superti-Furga et al. 1996, Dwyer et al. 2010, Dawson & Markovich 2005).
R-HSA-5619085 Defective SLC26A3 causes congenital secretory chloride diarrhea 1 (DIAR1) Solute carrier (SLC) genes that code chloride (Cl-)/bicarbonate (HCO3-) exchanger proteins are the SLC4 and SLC26 families. The chloride anion exchanger SLC26A3 (aka down-regulated in adenoma, DRA) mediates electrolyte and fluid absorption in the colon. It is also localised to the midpiece tail membrane of sperm where it plays a role in Cl-/HCO3- homeostasis during sperm epididymal maturation. Defects in SLC26A3 cause congenital chloride diarrhea 1 (DIAR1), a disease characterised by watery stools containing an excess of chloride resulting in dehydration, hypokalemia, and metabolic alkalosis (Alper & Sharma 2013, Wedenoja et al. 2011).
R-HSA-5619046 Defective SLC26A4 causes Pendred syndrome (PDS) Solute carrier (SLC) genes that code chloride (Cl-)/bicarbonate (HCO3-) exchanger proteins are in the SLC4 and SLC26 families. SLC26A4 (pendrin) is thought to act as a chloride/anion exchanger but in the thyroid and inner ear, it also contributes to the conditioning of the endolymphatic fluid by mediating iodide (I-) transport. Defects in SLC26A4 can cause Pendred syndrome (PDS; MIM:274600), an autosomal recessive disorder characterised by congenital sensorineural hearing loss in association with thyroid goiter (Choi et al. 2011, Pesce & Kopp 2014).
R-HSA-5619108 Defective SLC27A4 causes ichthyosis prematurity syndrome (IPS) The SLC27 gene family code for fatty acid transport proteins (FATPs). Long chain fatty acids (LCFAs) are critical for many physiological and cellular processes as a primary energy source. Of the six FATPs characterised, three have been shown to mediate the influx of LCFAs into cells; FATP1, 4 and 6. SLC27A4 (FATP4) is the major intestinal LCFA transporter but is also expressed at lower levels in brain, kidney, liver and heart. SLC27A4 is also expressed in skin, where it has been shown to play a major role in epidermal development, being highly expressed in neonatal keratinocytes. Defects in SLC27A4 can cause ichthyosis prematurity syndrome (IPS; MIM:604194), a keratinisation disorder which is characterised by thickened epidermis and respiratory complications. Patients suffer from a lifelong non-scaly ichthyosis (Anderson & Stahl 2013).
R-HSA-5619063 Defective SLC29A3 causes histiocytosis-lymphadenopathy plus syndrome (HLAS) The human gene SLC29A3 encodes the equilibrative nucleoside transporter 3 (ENT3). It is abundant in many tissues, especially the placenta and is localized intracellularly on the lysosomal membrane. SLC29A3 mediates the reversible transport of nucleosides as well as anticancer and antiviral agents such as cladribine, cordycepin, tubercidin and AZT. Defects in SLC29A3 can cause histiocytosis-lymphadenopathy plus syndrome (HLAS; MIM:602782), an autosomal recessive disorder characterised by combined features from 2 or more of four histiocytic disorders (Morgan et al. 2010, Colmenero et al. 2012, Young et al. 2013).
R-HSA-5619043 Defective SLC2A1 causes GLUT1 deficiency syndrome 1 (GLUT1DS1) Members of the SLC2A family encode glucose transporter (GLUT) proteins that mediate the facilitated diffusion of glucose between the extracellular space and the cytosol. While the monomeric protein can form a channel and transport glucose, kinetic studies suggest that the functional form of the protein is a homotetramer. SLC2A1 (GLUT1) is expressed by many cell types, notably endothelial cells, red blood cells and cells of the brain. Its low Km for glucose (~1 mM) relative to normal blood glucose concentration (~5 mM) allows these cells to take up glucose independent of changes in blood glucose levels. Defects in SLC2A1 can cause neurological disorders with wide phenotypic variability. The most severe 'classic' phenotype, GLUT1 deficiency syndrome 1 (GLUT1DS1; MIM:606777), comprises infantile-onset epileptic encephalopathy associated with delayed development, acquired microcephaly, motor incoordination and spasticity (Brockmann 2009, De Giorgis & Veggiotti 2013).
R-HSA-5619068 Defective SLC2A10 causes arterial tortuosity syndrome (ATS) Four class III facilitative transporters can transport glucose; SLC2A6, 8, 10 and 12 (encoding GLUT6, 8, 10 and 12 respectively). SLC2A10 (located in the Type 2 diabetes-linked region of human chromosome 20q12-13.1) encodes GLUT10, a transporter with high affinity for glucose. GLUT10 is highly expressed in liver and pancreas but is present at lower levels in most tissues. Defects in SLC2A10 are the cause of arterial tortuosity syndrome (ATS), an autosomal recessive disorder of connective tissue characterised by tortuosity and elongation of major arteries, often resulting in death at a young age (Coucke et al. 2006, Callewaert et al. 2008).
R-HSA-5619098 Defective SLC2A2 causes Fanconi-Bickel syndrome (FBS) The reversible facilitated diffusion of fructose, galactose, and glucose from the cytosol to the extracellular space is mediated by the SLC2A2 (GLUT2) transporter in the plasma membrane. In the epithelial cells of the small intestine, the basolateral localisation of SLC2A2 enables hexose sugars derived from the diet (and taken up by SLC5A1 and SLC2A5 transporters into cells) to be released into the circulation. SLC2A2 is a low affinity glucose transporter expressed mainly in the kidney, liver and pancreatic beta-cells. In beta-cells, it functions as a glucose-sensor for insulin secretion and in the liver, it allows for bi-directional glucose transport. Defects in SLC2A2 can cause Fanconi-Bickel syndrome (FBS; MIM:227810), a rare but well-defined disorder characterised by glycogen accumulation, proximal renal tubular dysfunction, and impaired utilisation of glucose and galactose (Leturque et al. 2009, Douard & Ferraris 2013).
R-HSA-5619047 Defective SLC2A9 causes hypouricemia renal 2 (RHUC2) The human SLC2A9 gene encodes the class II facilitative glucose transporter 9 (GLUT9). SLC2A9 is expressed mainly in kidney (proximal tubules of epithelial cells) and liver. SLC2A9 is a bona fide urate transporter (uric acid), but also the uptake of fructose (Fru) and glucose (Glc) at a low rate. Uric acid is the end product of purine metabolism in humans and great apes. Defects in SLC2A9 can cause renal hypouricemia 2 (RHUC2), a common inherited disorder characterised by impaired renal urate reabsorption and resultant low serum urate levels. Some patients present with severe complications, such as exercise-induced acute kidney injury (EIAKI) and nephrolithiasis (Esparza Martin & Garcia Nieto 2011, Sebesta 2012, Shen et al. 2014).
R-HSA-5619061 Defective SLC33A1 causes spastic paraplegia 42 (SPG42) The human gene SLC33A1 encodes acetyl-CoA transporter AT1. SLC33A1 transports cytosolic acetyl-CoA (Ac-CoA) to the Golgi apparatus lumen, where it serves as the substrate for acetyltransferases that O-acetylates sialyl residues of gangliosides and glycoproteins (Hirabayashi et al. 2013). Defects in SLC33A1 are the cause of spastic paraplegia autosomal dominant type 42 (SPG42; MIM:612539), a neurodegenerative disorder characterised by a variable speed of (but progressive) weakness and spasticity of the lower limbs (Lin et al. 2008, Hirabayashi et al. 2013). Defects in SLC33A1 can also cause congenital cataracts, hearing loss, and neurodegeneration (CCHLND; MIM:614482), an autosomal recessive disorder characterised by congenital cataracts, severe psychomotor retardation, and hearing loss, together with decreased serum ceruloplasmin and copper (Huppke et al. 2012).
R-HSA-5619040 Defective SLC34A1 causes hypophosphatemic nephrolithiasis/osteoporosis 1 (NPHLOP1) SLC34A1 and 2 encode Na+/Pi cotransporters, which cotransport divalent phosphate (PO4(2-), Pi) with 3 Na+ ions. SLC34A1 is an important Pi transporter mainly expressed in renal proximal tubules where it plays a major role in Pi homeostasis. Defects in SLC34A1 are the cause of hypophosphatemic nephrolithiasis/osteoporosis type 1 (NPHLOP1; MIM:612286), disease characterised by decreased renal phosphate absorption, hypophosphatemia, hyperphosphaturia, hypercalciuria, nephrolithiasis and implicated in the formation of renal calcium stones and/or bone demineralisation (Prie et al. 2002, Prie et al. 2004, Choi 2008, Boskey et al. 2013, Forster et al. 2013).
R-HSA-5687583 Defective SLC34A2 causes PALM The human gene SLC34A2 encodes NaPi-2b which is abundantly expressed in lung and to a lesser degree in epithelia of other tissues including small intestine, pancreas, prostate, and kidney. In the lung, SLC34A2 is expressed only in alveolar type II cells, which are responsible for surfactant production, so it is proposed that it uptakes liberated phosphate from the alveolar fluid for surfactant production. SLC34A2 cotransports divalent phosphate (HPO4(2-)) with three Na+ ions (electrogenic transport) from the extracellular region into alveolar type II cells. Defects in SLC34A2 can cause pulmonary alveolar microlithiasis (PALM; MIM:265100), a rare disease characterised by the deposition of calcium phosphate microliths (tiny, roundish corpuscles) throughout the lung. Most patients remain asymptomatic for years or decades, the disease following a long-term, progressive course resulting in slow deterioration of lung functions. PALM can result in a potentially lethal disease (Yin et al. 2013, Ferreira Francisco et al. 2013, Whitsett et al. 2015).
R-HSA-5619045 Defective SLC34A2 causes pulmonary alveolar microlithiasis (PALM) SLC34A1 and 2 encode Na+/Pi cotransporters, which cotransport divalent phosphate (PO4(2-), Pi) with 3 Na+ ions. SLC34A2 is abundantly expressed in lung and to a lesser extent in tissues of epithelial origin including small intestine, pancreas, prostate, and kidney. Defects in SLC34A2 are a cause of pulmonary alveolar microlithiasis (PALM; MIM:265100), a rare disease characterised by the deposition of calcium phosphate microliths throughout the lungs. The disease follows a long-term progressive course, resulting in a slow deterioration of lung function (Corut et al. 2006, Forster et al. 2013).
R-HSA-5619097 Defective SLC34A3 causes Hereditary hypophosphatemic rickets with hypercalciuria (HHRH) SLC34A3 is almost exclusively expressed at the apical membranes of kidney proximal tubules and encodes a Na+/Pi cotransporter. It cotransports 2 Na+ ions with every phosphate (Pi) (electroneutral transport). Defects in SLC34A3 are the cause of hereditary hypophosphatemic rickets with hypercalciuria (HHRH; MIM:241530), an autosomal recessive form of hypophosphatemia characterised by reduced renal phosphate reabsorption and rickets (Bergwitz et al. 2006, Segawa et al. 2013, Forster et al. 2013).
R-HSA-5619037 Defective SLC35A1 causes congenital disorder of glycosylation 2F (CDG2F) The human gene SLC35A1 encodes the CMP-sialic acid transporter which mediates the antiport of CMP-sialic acid (CMP-Neu5Ac) into the Golgi lumen in exchange for CMP (Ishida et al. 1996). Defects in SLC35A1 are the cause of congenital disorder of glycosylation type 2F (CDG2F; MIM:603585), characterised by under-glycosylated serum proteins. CDGs are a family of severe inherited diseases caused by a defect in protein N-glycosylation. These multisystem disorders present with a wide spectrum of phenotypes such as disorders of nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders and immunodeficiency (Martinez-Duncker et al. 2005, Song 2013).
R-HSA-5663020 Defective SLC35A1 causes congenital disorder of glycosylation 2F (CDG2F) The human gene SLC35A1 encodes the CMP-sialic acid transporter which mediates the antiport of CMP-sialic acid (CMP-Neu5Ac) into the Golgi lumen in exchange for CMP (Ishida et al. 1996). Defects in SLC35A1 are the cause of congenital disorder of glycosylation type 2F (CDG2F; MIM:603585), characterised by under-glycosylated serum proteins. CDGs are a family of severe inherited diseases caused by a defect in protein N-glycosylation. These multisystem disorders present with a wide spectrum of phenotypes such as disorders of nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders and immunodeficiency (Martinez-Duncker et al. 2005, Song 2013).
R-HSA-5619072 Defective SLC35A2 causes congenital disorder of glycosylation 2M (CDG2M) The human gene SLC35A2 encodes the UDP-galactose transporter. It is located on the Golgi membrane and mediates the antiport of UDP-Gal into the Golgi lumen in exchange for UMP. Nucleotide sugars such as UDP-Gal are used in protein glycosylation in the Golgi lumen. This transporter is also known to transport UDP-N-acetylgalactosamine (UDP-GalNAc) by the same antiport mechanism. Defects in SLC35A2 limit Golgi-localised pools of UDP-Gal, resulting in truncated beta-GlcNAc-terminated N-glycans and alpha-GalNAc-terminated O-glycans. Defects in SLC35A2 can cause congenital disorder of glycosylation 2M (CDG2M; MIM:300896), a disorder characterised by developmental delay, hypotonia, ocular defects and brain malformations (Ng et al. 2013). Congenital disorders of glycosylation (CDGs) are generally characterised by under-glycosylated serum glycoproteins and a wide spectrum of clinical features. Defects in SLC35A2 can also cause early infantile epileptic encephalopathy 22 (EIEE22; MIM:300896), a severe form of epilepsy characterised by by frequent tonic seizures or spasms beginning in infancy and accompanied by developmental problems (Kodera et al. 2013).
R-HSA-5619083 Defective SLC35A3 causes arthrogryposis, mental retardation, and seizures (AMRS) The human gene SLC35A3 encodes a UDP-GlcNAc transporter. It is ubiquitously expressed and resides on the Golgi membrane where it transports UDP- N-acetylglucosamine (UDP-GlcNAc) into the Golgi lumen in exchange for UMP. UDP-GlcNAc is a substrate required by Golgi-resident glycosyltransferases that generate branching of N-glycosylated proteins. Defects in SLC35A3 can cause arthrogryposis, mental retardation, and seizures (AMRS; MIM:615553) (Edvardson et al. 2013). Patient cells show a large reduction of tetraantennary N-glycans with an accumulation of abnormal lower-branched glycoproteins, although the serum N-glycome was normal.
R-HSA-5619078 Defective SLC35C1 causes congenital disorder of glycosylation 2C (CDG2C) The human gene SLC35C1 encodes a GDP-fucose transporter that resides on the Golgi membrane and mediates the transport of GDP-fucose into the Golgi lumen. Defects in SLC35C1 cause the congenital disorder of glycosylation type 2C (CDG2C aka leukocyte adhesion deficiency type II, LAD2), an autosomal recessive disorder characterised by moderate to severe psychomotor retardation, mild dysmorphism and impaired neutrophil motility (Lubke et al. 2001, Liu & Hirschberg 2013).
R-HSA-5579020 Defective SLC35D1 causes SCHBCKD The UDP-glucuronic acid/UDP-N-acetylgalactosamine transporter (SLC35D1) is an ER membrane-spanning protein that transports nucleotide-sugars from the cytosol into the ER lumen. SLC35D1 transports UDP-GlcUA and UDP-GalNAc, which are substrates for the synthesis of chondroitin sulfate disaccharide repeats, suggesting a role in chondroitin sulfate biosynthesis. Mutations in SLC35D1 can cause Schneckenbecken dysplasia (SCHBCKD; MIM:269250), a rare, autosomal recessive, lethal short-limbed skeletal dysplasia affecting cartilage and skeletal development (Liu et al. 2010, Liu & Hirschberg 2013).
R-HSA-5619041 Defective SLC36A2 causes iminoglycinuria (IG) and hyperglycinuria (HG) SLC36A2 encodes proton-coupled amino acid transporter 2 (PAT2), a high-affinity cotransporter of glycine and proline coupled with the uptake of a proton in kidney and muscles (Schweikhard & Ziegler 2012). Defects in SLC36A2 can cause iminoglycinuria (IG; MIM:242600), an autosomal recessive abnormality of renal transport of glycine and the imino acids proline and hydroxyproline. Defects can also cause hyperglycinuria (HG; MIM:138500), a related disorder to IG which is characterised by excess glycine in the urine (Broer et al. 2008). Polymorphisms in the modifiers SLC6A18, 19 and 20, contribute to these phenotypes.
R-HSA-5619088 Defective SLC39A4 causes acrodermatitis enteropathica, zinc-deficiency type (AEZ) SLC39A4 encodes the human zinc transporter hZIP4 which plays an important role in cellular zinc homeostasis. Defects in SLC39A4 result in the inherited condition acrodermatitis enteropathica, zinc deficiency type (AEZ; MIM:201100), caused by the inability to absorb dietary zinc from the duodenum and jejunum. Clinical features include growth retardation, immune system dysfunction, severe dermatitis and mental disorders (Schmitt et al. 2009).
R-HSA-5619113 Defective SLC3A1 causes cystinuria (CSNU) Neutral and basic amino acid transport protein rBAT (SLC3A1) and b(0,+)-type amino acid transporter 1 (SLC7A9) are linked by a disulfide bridge to form system b(0,+)-like activity in the high affinity transport of neutral and dibasic amino acids and cystine. The SLC7A9:SLC3A1 heterodimer mediates the electrogenic exchange of extracellular amino acids such as L-arginine (L-Arg) and L-lysine (L-lys) and cystine (CySS-, the oxidised form of L-cysteine) for intracellular neutral amino acids such as L-leucine (L-Leu). These solute carriers are mainly expressed in the kidney and small intestine where they remove dibasic amino acids and cystine from the renal tubular and intestinal lumen respectively (Schweikhard & Ziegler 2012). Defects in SLC3A1 (or SLC7A9) can cause cystinuria (CSNU; MIM:220100), an autosomal recessive disorder characterised by impaired epithelial cell transport of cystine and dibasic amino acids in the proximal renal tubule and GI tract. The build-up and low solubility of cystine causes the formation of calculi in the urinary tract, resulting in obstructive uropathy, pyelonephritis and in severe cases, renal failure (Palacin et al. 2001, Mattoo & Goldfarb 2008, Fotiadis et al. 2013, Saravakos et al. 2014). Cystinuria is subcategorized as type A (mutations on SLC3A1) and type B (mutations on SLC7A9).
R-HSA-5655799 Defective SLC40A1 causes hemochromatosis 4 (HFE4) (duodenum) The primary site for absorption of dietary iron is the duodenum. Ferrous iron (Fe2+) is taken up from the gut lumen across the apical membranes of enterocytes and released into the portal vein circulation across basolateral membranes. The human gene SLC40A1 encodes the metal transporter protein MTP1 (aka ferroportin or IREG1). This protein resides on the basolateral membrane of enterocytes and mediates ferrous iron efflux into the portal vein. SLC40A1 colocalises with hephaestin (HEPH) which stablises it and is necessary for the efflux reaction to occur.
Defects in SLC40A1 can cause hemochromatosis 4 (HFE4; MIM:606069), a disorder of iron metabolism characterised by iron overload. Excess iron is deposited in a variety of organs leading to their failure, resulting in serious illnesses including cirrhosis, hepatomas, diabetes, cardiomyopathy, arthritis and hypogonadotropic hypogonadism. Severe effects of the disease don't usually appear until after decades of progressive iron overloading (De Domenico et al. 2005, 2006, 2011, Kaplan et al. 2011).
R-HSA-5619049 Defective SLC40A1 causes hemochromatosis 4 (HFE4) (macrophages) SLC40A1 (MTP1 aka ferroportin or IREG1) is highly expressed on macrophages where it mediates iron efflux from the breakdown of haem. SLC40A1 colocalises with ceruloplasmin (CP) which stablizes SLC40A1 and is necessary for the efflux reaction to occur. Six copper ions are required by ceruloplasmin as a cofactor.
Defects in SLC40A1 can cause hemochromatosis 4 (HFE4; MIM:606069), a disorder of iron metabolism characterised by iron overload. Excess iron is deposited in a variety of organs leading to their failure, resulting in serious illnesses including cirrhosis, hepatomas, diabetes, cardiomyopathy, arthritis and hypogonadotropic hypogonadism. Severe effects of the disease don't usually appear until after decades of progressive iron overloading (De Domenico et al. 2005, 2006, 2011, Kaplan et al. 2011).
R-HSA-5619050 Defective SLC4A1 causes hereditary spherocytosis type 4 (HSP4), distal renal tubular acidosis (dRTA) and dRTA with hemolytic anemia (dRTA-HA) The proteins responsible for the exchange of Cl- with HCO3- are members of the SLC4 (1-3) and SLC26 (3, 4, 6, 7 and 9) transporter families. SLC4A1 (Band 3, AE1, anion exchanger 1) was the first bicarbonate transporter gene to be cloned and sequenced. It is ubiquitous throughout vertebrates and in humans, is the major glycoprotein present on erythrocytes and the basolateral surfaces of kidney cells. Variations in erythroid SLC4A1 determine the Diego blood group system. Mutations in the erythrocyte form of SLC4A1 can cause hereditary spherocytosis type 4 (HSP4; MIM:612653), a disorder leading to haemolytic anaemia (HA). Some mutations in SLC4A1 can cause distal (type1) renal tubular acidosis (dRTA; MIM:179800) (an inability to acidify urine) and dRTA-HA (dRTA with hemolytic anemia) (MIM:611590) (Tanner 2002, Romero et al. 2013).
R-HSA-5619054 Defective SLC4A4 causes renal tubular acidosis, proximal, with ocular abnormalities and mental retardation (pRTA-OA) Members 4, 5, 7 and 9 of the SLC4A family couple the transport of bicarbonate (HCO3-) with sodium ions (Na+). SLC4A4 (aka NBCe1) is an electrogenic Na+/HCO3- cotransporter with a stoichiometry of 1:3. SLC4A4 is expressed in the kidney and pancreas, with lesser expression in many other tissues. Mutations in SLC4A4 can cause permanent isolated proximal renal tubular acidosis with ocular abnormalities and mental retardation (pRTA-OA), a rare autosomal recessive syndrome characterised by short stature, proximal renal tubular acidosis, mental retardation, bilateral glaucoma, cataracts and bandkeratopathy. pRTA results from the failure of the proximal tubular cells to reabsorb filtered HCO3- from urine, leading to urinary HCO3- wasting and subsequent acidemia. HCO3- also needs to move out of cells in the eye, thus failure to do so can affect ocular pressure homeostasis (Horita et al. 2005, Kurtz & Zhu 2013, Kurtz & Zhu 2013b, Seki et al. 2013).
R-HSA-5656364 Defective SLC5A1 causes congenital glucose/galactose malabsorption (GGM) Sodium/glucose cotransporter 1 (SLC5A1 aka SGLT1) actively and reversibly transports glucose (Glc) into cells by Na+ cotransport with a Na+ to glucose coupling ratio of 2:1. SLC5A1 is mainly expressed in the microvilli of intestine and kidney and responsible for the absorption of sugars. Overexpressed SLC5A1 has been found in various cancers, possibly playing a role in preventing autophagic cell death by maintaining intracellular glucose levels. Defects in SLC5A1 can cause congenital glucose/galactose malabsorption (GGM; MIM:606824), an autosomal recessive disorder manifesting itself in newborns characterised by severe, life-threatening diarrhea which is usually fatal unless glucose and galactose are removed from the diet (Wright et al. 2002, Bergeron et al. 2008, Wright et al. 2007, Wright 2013).
R-HSA-5658208 Defective SLC5A2 causes renal glucosuria (GLYS1) The human gene SLC5A2 encodes a sodium-dependent glucose transporter (SGLT2), expressed in many tissues but primarily in the kidney, specifically S1 and S2 proximal tubule segments. It is a low affinity, high capacity transporter of glucose across the apical membrane, with co-transport of Na+ ions in a 1:1 ratio and is the main transporter of glucose in the kidney, responsible for approximately 98% of glucose reabsorption (reaminder by SGLT1). Defects in SLC5A2 are the cause of renal glucosuria (GLYS1; MIM:233100), an autosomal recessive renal tubular disorder characterised by glucosuria in the absence of both hyperglycemia and generalized proximal tubular dysfunction. Establishing definite genotype–phenotype correlations for GLYS1 is made difficult by variable expression of SLC5A2 and because other genes may have an impact on overall renal glucose resorption. Drugs that inhibit SLC5A2 are used to treat type 2 diabetes (T2D). The strategy to reduce hyperglycemia in T2D is to target renal glucose reabsorption by inhibiting SLC5A2 (Santer & Calado 2010, Calado et al. 2011).
R-HSA-5619096 Defective SLC5A5 causes thyroid dyshormonogenesis 1 (TDH1) Human SLC5A5 encodes the Na+/I- symporter NIS which is localised in the basolateral membrane of thyrocytes facing the bloodstream where it mediates iodide accumulation into these cells. Defects in SLC5A5 can cause hyroid dyshormonogenesis 1 (TDH1; MIM:274400), a disorder characterised by the inability of the thyroid to maintain a concentration difference of readily exchangeable iodine between the plasma and the thyroid gland (termed iodine trapping) leading to congenital hypothyroidism (Spitzweg & Morris 2010, Grasberger & Refetoff 2011).
R-HSA-5619114 Defective SLC5A7 causes distal hereditary motor neuronopathy 7A (HMN7A) The human SLC5A7 gene encodes a sodium- and chloride-dependent, high affinity choline transporter (CHT) transports choline (Cho) from the extracellular space into neuronal cells. Cho uptake is the rate-limiting step in acetylcholine synthesis, a neurotransmitter released at the neuromuscular junction (NMJ). Defects in SLC5A7 can cause distal hereditary motor neuronopathy 7A (HMN7A; MIM:158580). Distal hereditary motor neuronopathies are a group of neuromuscular disorders caused by selective degeneration of motor neurons in the anterior horn of the spinal cord, without sensory deficit in the posterior horn. The clinical picture consists of a progressive distal muscle wasting and weakness in the legs without clinical sensory loss (Barwick et al. 2012).
R-HSA-5658471 Defective SLC5A7 causes distal hereditary motor neuronopathy 7A (HMN7A) The human SLC5A7 gene encodes a sodium- and chloride-dependent, high affinity choline transporter (CHT) transports choline (Cho) from the extracellular space into neuronal cells. Cho uptake is the rate-limiting step in acetylcholine synthesis, a neurotransmitter released at the neuromuscular junction (NMJ). Defects in SLC5A7 can cause distal hereditary motor neuronopathy 7A (HMN7A; MIM:158580). Distal hereditary motor neuronopathies are a group of neuromuscular disorders caused by selective degeneration of motor neurons in the anterior horn of the spinal cord, without sensory deficit in the posterior horn. The clinical picture consists of a progressive distal muscle wasting and weakness in the legs without clinical sensory loss (Barwick et al. 2012).
R-HSA-5619079 Defective SLC6A18 may confer susceptibility to iminoglycinuria and/or hyperglycinuria SLC6A18 encodes a neutral amino acid transporter B(0)AT3 which has preference for the amino acid glycine. It is abundantly expressed in the kidney, specifically the S2/3 segments of the kidney proximal tubule (Broer & Gether 2012, Schweikhard & Ziegler 2012). Iminoglycinuria (IG; MIM:242600) or hyperglycinuria (HG; MIM:138500) can arise from defects in SLC36A2, encoding a proton-coupled amino acid transporter 2 (PAT2), a high-affinity cotransporter of glycine and proline. Mutation in SLC6A18 may contribute to both IG and HG (Broer et al. 2008).
R-HSA-5659729 Defective SLC6A18 may confer susceptibility to iminoglycinuria and/or hyperglycinuria SLC6A18 encodes a neutral amino acid transporter B(0)AT3 which has preference for the amino acid glycine. It is abundantly expressed in the kidney, specifically the S2/3 segments of the kidney proximal tubule (Broer & Gether 2012, Schweikhard & Ziegler 2012). Iminoglycinuria (IG; MIM:242600) or hyperglycinuria (HG; MIM:138500) can arise from defects in SLC36A2, encoding a proton-coupled amino acid transporter 2 (PAT2), a high-affinity cotransporter of glycine and proline. Mutation in SLC6A18 may contribute to both IG and HG (Broer et al. 2008).
R-HSA-5659735 Defective SLC6A19 causes Hartnup disorder (HND) SLC6A19 encodes the sodium-dependent neutral amino acid transporter B(0)AT1 and mediates the uptake of neutral amino acids across the plasma membrane accompanied by uptake of a sodium ion. The protein is abundantly expressed in the small intestine and kidney (Broer & Gether 2012, Schweikhard & Ziegler 2012). Defects in SLC6A19 can cause Hartnup disorder (HND; MIM:234500), an autosomal recessive abnormality of renal and gastrointestinal neutral amino acid transport characterised by increased urinary and intestinal excretion of neutral amino acids. Symptoms include transient manifestations of rashes, cerebellar ataxia and psychotic behaviour (Broer 2009, Cheon et al. 2010). Some mutations in SLC6A19 are thought to contribute to the phenotypes iminoglycinuria (IG; MIM:242600) and hyperglycinuria (HG; MIM:138500) (Broer et al. 2008).
R-HSA-5619044 Defective SLC6A19 causes Hartnup disorder (HND) SLC6A19 encodes the sodium-dependent neutral amino acid transporter B(0)AT1 and mediates the uptake of neutral amino acids across the plasma membrane accompanied by uptake of a sodium ion. The protein is abundantly expressed in the small intestine and kidney (Broer & Gether 2012, Schweikhard & Ziegler 2012). Defects in SLC6A19 can cause Hartnup disorder (HND; MIM:234500), an autosomal recessive abnormality of renal and gastrointestinal neutral amino acid transport characterised by increased urinary and intestinal excretion of neutral amino acids. Symptoms include transient manifestations of rashes, cerebellar ataxia and psychotic behaviour (Broer 2009, Cheon et al. 2010). Some mutations in SLC6A19 are thought to contribute to the phenotypes iminoglycinuria (IG; MIM:242600) and hyperglycinuria (HG; MIM:138500) (Broer et al. 2008).
R-HSA-5619109 Defective SLC6A2 causes orthostatic intolerance (OI) SLC6A2 encodes the sodium-dependent noradrenaline transporter NAT1 which terminates the action of the neurotransmitter noradrenaline by transporting it from the synapse back to its vesicles for storage and reuse (Broer & Gether 2012, Schweikhard & Ziegler 2012). SLC6A2 is expressed in the CNS and adrenal glands. Defects in SLC6A2 can cause orthostatic intolerance (OI; MIM:604715), a syndrome characterised by lightheadedness, fatigue and development of symptoms during upright standing, relieved by sitting back down again. Plasma norepinephrine concentration is abnormally high (Lambert & Lambert 2014).
R-HSA-5660724 Defective SLC6A3 causes Parkinsonism-dystonia infantile (PKDYS) The human gene SLC6A3 encodes the sodium-dependent dopamine transporter DAT which mediates the Na-dependent re-uptake of dopamine (DA) from the synaptic cleft back into cells, thereby terminating the action of DA (Broer & Gether 2012, Schweikhard & Ziegler 2012). Defects in SLC6A3 can cause Parkinsonism-dystonia infantile (PKDYS; MIM:613135), a neurodegenerative disorder characterised by infantile onset of parkinsonism and dystonia (Kurian et al. 2011).
R-HSA-5619081 Defective SLC6A3 causes Parkinsonism-dystonia infantile (PKDYS) The human gene SLC6A3 encodes the sodium-dependent dopamine transporter DAT which mediates the Na-dependent re-uptake of dopamine (DA) from the synaptic cleft back into cells, thereby terminating the action of DA (Broer & Gether 2012, Schweikhard & Ziegler 2012). Defects in SLC6A3 can cause Parkinsonism-dystonia infantile (PKDYS; MIM:613135), a neurodegenerative disorder characterised by infantile onset of parkinsonism and dystonia (Kurian et al. 2011).
R-HSA-5619089 Defective SLC6A5 causes hyperekplexia 3 (HKPX3) The amino acid glycine (Gly) plays an important role in neurotransmission. Its action is terminated by rapid re-uptake into the pre-synaptic terminal or surrounding glial cells. This re-uptake is mediated by the sodium- and chloride-dependent glycine transporters 1 and 2 (GLYT1 and GLYT2 respectively) (Broer & Gether 2012, Schweikhard & Ziegler 2012). GLYT2 is encoded by the human gene SLC6A5 and is predominantly expressed in the medulla. Defects in SLC6A5 cause startle disease (STHE or hyperekplexia (HKPX3; MIM:614618)), a neurologic disorder characterised by neonatal hypertonia, an exaggerated startle response to tactile or acoustic stimuli, and life-threatening neonatal apnea. Sometimes symptoms resolve in the first year of life (Bode & Lynch 2014, James et al. 2012).
R-HSA-5660862 Defective SLC7A7 causes lysinuric protein intolerance (LPI) SLC7A7 encodes the y+L amino acid transporter 1 (y+LAT1). As a heterodimer with SLC3A2 in the plasma membrane, SLC7A7 mediates the exchange of arginine (L-Arg) for leucine (L-Leu) and a sodium ion (Na+). The physiological concentrations of arginine and leucine are expected to favor arginine export (Schweikhard & Ziegler 2012). Defects in SLC7A7 can cause Lysinuric protein intolerance (LPI; MIM:222700), a metabolic disorder characterised by decreased cationic amino acid (CAA) transport at the basolateral membrane of epithelial cells in the intestine and kidney, increased renal excretion of CAA and orotic aciduria. There is extreme variability clinically but typical symptoms include refusal to feed, vomiting and consequent failure to thrive. Hepatosplenomegaly, hematological anomalies and neurological involvement are recurrent clinical features (Sperandeo et al. 2008, Sebastio et al. 2011).
R-HSA-5660883 Defective SLC7A9 causes cystinuria (CSNU) SLC7A9 encodes the b(0,+)-type amino acid transporter 1 BAT1. As a heterodimer with SLC3A1 in the plasma membrane, SLC7A9 mediates the high-affinity, sodium-independent transport of cystine (CySS-, the oxidised form of L-cysteine) and dibasic amino acids in exchange for neutral amino acids and is thought to be responsible for the reabsorption of CySS- and dibasic amino acids in the kidney tubule (Schweikhard & Ziegler 2012). Defects in SLC7A9 (or SLC3A1) can cause cystinuria (CSNU; MIM:220100), an autosomal disorder characterised by impaired renal reabsorption of cystine and dibasic amino acids. The low solubility of cystine causes the formation of calculi in the urinary tract resulting in obstructive uropathy, pyelonephritis, and, rarely, renal failure (Palacin et al. 2001, Mattoo & Goldfarb 2008, Fotiadis et al. 2013, Saravakos et al. 2014, Barbosa et al. 2012). Cystinuria is subcategorised as type A (mutations on SLC3A1) and type B (mutations on SLC7A9).
R-HSA-5619092 Defective SLC9A6 causes X-linked, syndromic mental retardation,, Christianson type (MRXSCH) SLC9A6 encodes the sodium/hydrogen exchanger 6 NHE6, a protein ubiquitously expressed but most abundant in mitochondria-rich tissues such as brain, skeletal muscle and heart. It is located on endosomal membranes and thought to play a housekeeping role in pH homeostasis in early endosomes. It mediates the electroneutral exchange of protons for Na+ and K+ across the early and recycling endosome membranes. Defects in SLC9A6 can cause mental retardation, X-linked, syndromic, Christianson type (MRXSCH; MIM:300243), a syndrome characterised by profound mental retardation, epilepsy, ataxia and microcephaly. MRXSCH shows phenotypic overlap with Angelman syndrome (Gilfillan et al. 2008, Schroer et al. 2010, Kondapalli et al. 2014).
R-HSA-5619052 Defective SLC9A9 causes autism 16 (AUTS16) SLC9A9 encodes the sodium/hydrogen exchanger 9 NHE9 which is expressed ubiquitously and thought to play a housekeeping role in pH homeostasis in the late endosome membrane. A defect in SLC9A9 can contribute to susceptibility to autism 16 (AUTS16; MIM:613410). Autism, the prototypic pervasive developmental disorder (PDD), is a complex, multifactorial disorder characterised by reciprocal social interaction and communication impairment, restricted and stereotyped patterns of interests and activities, and the presence of developmental abnormalities by age 3 (Morrow et al. 2008, Kondapalli et al. 2014).
R-HSA-5619110 Defective SLCO1B1 causes hyperbilirubinemia, Rotor type (HBLRR) The solute carrier organic anion transporter family member 1B1 (SLCO1B1) is expressed on the basolateral surfaces of hepatocytes and mediates the uptake of bilirubin (BIL), a breakdown product of heme degradation, to the liver where it is conjugated and excreted from the body. Defects in SLCO1B1 can cause hyperbilirubinemia, Rotor type (HBLRR; MIM:237450), an autosomal recessive form of primary conjugated hyperbilirubinemia. Mild jaundice, not associated with hemolysis, develops shortly after birth or in childhood (van de Steeg et al. 2012, Sticova & Jirsa 2013, Keppler 2014).
R-HSA-5619058 Defective SLCO1B3 causes hyperbilirubinemia, Rotor type (HBLRR) In the body, solute carrier organic anion transporter family member 1B3 (SLCO1B3) is expressed on the basolateral surfaces of hepatocytes and may play a role in the uptake of bilirubin (BIL), a breakdown product of heme that requires conjugation and excretion from the body. Defects in SLCO1B3 can cause hyperbilirubinemia, Rotor type (HBLRR; MIM:237450), an autosomal recessive form of primary conjugated hyperbilirubinemia. Mild jaundice, not associated with hemolysis, develops shortly after birth or in childhood (van de Steeg et al. 2012, Sticova & Jirsa 2013, Keppler 2014).
R-HSA-5619095 Defective SLCO2A1 causes primary, autosomal recessive hypertrophic osteoarthropathy 2 (PHOAR2) The human gene SLCO2A1 encodes prostaglandin transporter PGT. It is ubiquitously expressed and can transport the protaglandins PGD2, PGE1, PGE2 and PGF2A. This transport may be important for release of newly-formed prostaglandins (PGs) and/or their clearance of prostaglandins from the circulation. Defects in SLCO2A1 can cause hypertrophic osteoarthropathy, primary, autosomal recessive, 2 (PHOAR2; MIM:614441), a rare genodermatosis characterised by pachydermia, digital clubbing, periostosis and affecting more males than females (Castori et al. 2005, Seifert et al. 2012, Diggle et al. 2012, Madruga Dias et al. 2014).
R-HSA-4755579 Defective SRD5A3 causes SRD5A3-CDG, KHRZ Polyprenol reductase (SRD5A3), resident on the endoplasmic reticulum membrane, normally mediates the reduction of the alpha-isoprene unit of polyprenol (pPNOL) to form dolichol (DCHOL) in a NADPH-dependent manner (Cantagrel et al. 2010). DCHOLs are substrates required for the synthesis of the lipid-linked oligosaccharide (LLO) precursor used for N-glycosylation. Defects in SRD5A3 cause congenital disorder of glycosylation 1q (SRD5A3-CDG, CDG1q; MIM:612379), a neurodevelopmental disorder characterised by under-glycosylated serum glycoproteins resulting in nervous system development, psychomotor retardation, hypotonia, coagulation disorders and immunodeficiency (Cantagrel et al. 2010, Kasapkara et al. 2012). Defects in SRD5A3 can also cause Kahrizi syndrome (KHRZ; MIM:612713), a neurodevelopmental disorder characterised by mental retardation, cataracts, holes in eye structures, pathological curvature of the spine, and coarse facial features (Kahrizi et al. 2011).
R-HSA-3656243 Defective ST3GAL3 causes MCT12 and EIEE15 CMP-N-acetylneuraminate-beta-1,4-galactoside alpha-2,3-sialyltransferase (ST3GAL3) mediates the transfer of sialic acid from CMP-sialic acid to galactose-containing glycoproteins and forms the sialyl Lewis a epitope on proteins which are required for attaining and/or maintaining higher cognitive functions. Some defects in ST3GAL3 result in mental retardation, autosomal recessive 12 (MRT12; MIM:611090), a disorder characterised by below average general intellectual function and impaired adaptive behaviour (Najmabadi et al. 2007, Hu et al. 2011). Another defect of ST3GAL3 can cause early infantile epileptic encephalopathy-15 (EIEE15: MIM:615006), resulting in severe mental retardation (Edvardson et al. 2012).
R-HSA-5579032 Defective TBXAS1 causes GHDD Thromboxane-A synthase (TBXAS1), an enzyme of the arachidonic acid cascade, produces thromboxane A2 (TXA2) from prostaglandin H2 (PGH2). Together with prostacyclin (PGI2), TXA2 plays a key role in the maintenance of haemostasis. It is also a constrictor of vascular and respiratory smooth muscle and implicated in the induction of osteoclast differentiation and activation. Defects in TBXAS1 can cause Ghosal hematodiaphyseal dysplasia (GHDD; MIM:231095), a rare autosomal recessive disorder characterised by increased bone density with predominant diaphyseal involvement and aregenerative anemia, a bone marrow failure where functional marrow cells are regenerated slowly or not at all (Genevieve et al. 2008).
R-HSA-3359454 Defective TCN2 causes TCN2 deficiency Defective transcobalamin II (produced by the TCN2 gene) results in TCN2 deficiency (MIM:275350), an autosomal recessive disorder with early-onset in infancy characterized by failure to thrive, megaloblastic anemia, and pancytopenia. If left untreated, the disorder can result in mental retardation and neurologic abnormalities (Haberle et al. 2009).
R-HSA-5578995 Defective TPMT causes TPMT deficiency Methylation is a major biotransformation route of thiopurine drugs such as 6-mercaptopurine (6MP), used in the treatment of inflammatory diseases such as rheumatoid arthritis and childhood acute lymphoblastic leukemia. 6MP and its thioguanine nucleotide metabolites are principally inactivated by thiopurine methyltransferase (TPMT)-catalysed S-methylation.
Defects in TPMT can cause thiopurine S-methyltransferase deficiency (TPMT deficiency; MIM:610460). Patients with intermediate or no TPMT activity are at risk of toxicity such as myelosuppression after receiving standard doses of thiopurine drugs. Inter individual differences in response to these drugs are largely determined by genetic variation at the TPMT locus. TPMT exhibits an autosomal co dominant phenotype: About one in 300 people in Caucasian, African, African-American, and Asian populations are TPMT deficient. Approximately 6-10% of people in these populations inherit intermediate TPMT activity and are heterozygous at the TPMT locus. The rest are homozygous for the wild type allele and have high levels of TPMT activity. (Remy 1963, Weinshilboum et al. 1999, Couldhard & Hogarth 2005, Al Hadithy et al. 2005, Azimi et al. 2014).
R-HSA-5619107 Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) The nuclear pore complex (NPC) trafficks cargo across the nuclear membrane. Nucleoprotein TPR functions as a scaffolding element in the nuclear phase of the NPC essential for normal nucleocytoplasmic transport of proteins and mRNAs. The complex glucokinase (GCK1) and glucokinase regulatory protein (GKRP) can be translocated to the nucleus via the NPC. Defects in TPR may confer susceptibility towards thyroid papillary carcinona (TPC; MIM:18850), a common tumor of the thyroid that typically arises as an irregular, solid or cystic mass from otherwise normal thyroid tissue (Vriens et al. 2009, Bonora et al. 2010).
R-HSA-5579002 Defective UGT1A1 causes hyperbilirubinemia UDP-glucuronosyltransferases (UGTs) play a major role in the conjugation and therefore elimination of potentially toxic xenobiotics and endogenous compounds. The 1-1 isoform UGT1A1 is able to act upon lipophilic bilirubin, the end product of heme breakdown. Defects in UGT1A1 can cause hyperbilirubinemia syndromes ranging from mild forms such as Gilbert syndrome (GILBS; MIM:143500) and transient familial neonatal hyperbilirubinemia (HBLRTFN; MIM:237900) to the more severe Crigler-Najjar syndromes 1 and 2 (CN1, CN2; MIM:218800 and MIM:606785) (Sticova & Jirsa 2013, Strassburg 2010, Udomuksorn et al. 2007, Costa 2006, Maruo et al. 2000).
R-HSA-5579016 Defective UGT1A4 causes hyperbilirubinemia UDP-glucuronosyltransferases (UGTs) play a major role in the conjugation and therefore elimination of potentially toxic xenobiotics and endogenous compounds. The 1-4 isoform UGT1A4 is able to act upon lipophilic bilirubin, the end product of heme breakdown. Defects in UGT1A4 can cause hyperbilirubinemia syndromes ranging from mild forms such as Gilbert syndrome (GILBS; MIM:143500) to the more severe Crigler-Najjar syndromes 1 and 2 (CN1, CN2; MIM:218800 and MIM:606785) (Sticova & Jirsa 2013, Strassburg 2010, Udomuksorn et al. 2007, Costa 2006, Maruo et al. 2000).
R-HSA-9845622 Defective VWF binding to collagen type I Upon vascular injury, circulating von Willebrand factor (VWF) binds to exposed vascular collagen. This Reactome event shows defective binding of VWF to collagen type I caused by loss-of-function mutations in the A3 domain of VWF found in patients with von Willebrand disease (VWD) type 2M, which is characterized by defects in platelet adhesion and/or collagen binding with normal or subnormal VWF multimer distribution.
R-HSA-9845621 Defective VWF cleavage by ADAMTS13 variant Under normal physiological conditions, a disintegrin and metalloproteinase with thrombospondin type 1 repeats 13 (ADAMTS13) downregulates VWF procoagulant activity by cleaving the peptide bond between Tyr1605 and Met1606 within the A2 domain of VWF in a shear-dependent manner. Deficiencies in ADAMTS13 activity results in defective cleavage of ultra large VWF multimer in the plasma and are associated with excessive thrombi formation in the microvasculature in patients with thrombotic thrombocytopenic purpura (TTP) (Zheng XL 2015; Sukumar S et al. 2021). TTP is caused either by inherited mutations in the ADAMTS13 gene or by acquired inhibitory autoantibodies directed against the ADAMTS13 protein. This Reactome event describes defective cleavage of VWF by TTP-causing loss-of-function ADAMTS13 variants, A250V, P475S, Q449*, which showed normal or slightly reduced secretion (Kokame K et al., 2002; Uchida T et al., 2004; Markham-Lee Z et al., 2022).
R-HSA-9661069 Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) This pathway describes impaired binding of RB1 pocket domain mutants to activating E2Fs, E2F1, E2F2 and E2F3 (Templeton et al. 1991, Helin et al. 1993, Otterson et al. 1997, Ji et al. 2004).
R-HSA-9846298 Defective binding of VWF variant to GPIb:IX:V This Reactome event describes von Willebrand disease (VWD)-associated missense mutations in the A1 domain of VWF, namely VWF S1358N, S1387I, S1394F and Q1402P, that compromise the clot formation due to reduced binding to GPIb (Larsen DM et al., 2013).
R-HSA-9672396 Defective cofactor function of FVIIIa variant Factor VIII (FVIII) in its activated form, FVIIIa, acts as a cofactor to the serine protease FIXa, in the conversion of the zymogen FX to the active enzyme (FXa). Missense mutations within the S577-Q584 region of FVIII have been associated with mild/moderate hemophilia A (HA) (Amano K et al. 1998; Celie PH et al. 1999; Jenkins PV et al. 2002). A functional assay demonstrated that the mutations S577F, V578A, D579A, and Q584R interfere with FVIIIa:FIXa-mediated stimulation of FX activation thus the effect of the mutations is to reduce the cofactor potential of FVIII in FXa generation. The Reactome event describes failed generation of FXa as the functional consequence of the FIXa interaction with HA-associated FVIIIa variants due to reduced ability of defective FVIII to act as a cofactor for FIXa within the intrinsic tenase complex.
R-HSA-9668250 Defective factor IX causes hemophilia B The F9 gene encodes coagulation factor IX (FIX), a vitamin K-dependent plasma protease that participates in the intrinsic blood coagulation pathway. FIX circulates as a zymogen, and is proteolytically activated to FIXa by activated FXIa or tissue factor-bound FVIIa. After being activated, FIXa forms a complex with Ca2+ ions, membrane phospholipids and coagulation factor VIIIa to activate coagulation factor X. Mutations within F9 gene that lead to quantitative and/or qualitative deficiencies in the circulating FIX protein are associated with hemophilia B (HB), a rare X-linked, recessively transmitted bleeding disorder (White GC et al. 2001; Rallapalli PM et al. 2013; Goodeve AC 2015). The disease severity in hemophilia is classified according to the plasma procoagulant levels of FIX activity. The severe form is defined as a factor level <1% of normal, the moderate form as a factor level of 1-5%, and the mild form with a factor level >5 and <40%. Patients with severe hemophilia frequently develop hemorrhages into joints, muscles or soft tissues without any apparent cause. They can also suffer from life-threatening bleeding episodes such as intracranial hemorrhages. Persons with mild and moderate factor deficiency rarely experience spontaneous hemorrhages, and excessive bleeding mostly occurs only following trauma or in association with invasive procedures.
A wide range of different genetic alterations are spread throughout the F9 gene, including single nucleotide substitutions, small and large deletions (Rallapalli PM et al. 2013). However functional consequences of most F9 mutations are poorly studied. The Reactome event describes altered functions of HB-associated FIX variants such as reduced FIX protein secretion due to defective expression and/or processing, failed proteolysis of factor X to Xa by defective FIX and failed formation of a membrane complex in the presence of Ca2+ ions, phospholipid, and cofactor VIIIa. The annotated HB-associated FIX variants are supported with data from functional studies (Usharani P et al. 1985; Spitzer SG et al. 1990; Ludwig M et a. 1992; Kurachi S et al. 1997; Branchini A et al. 2013). R-HSA-9672383 Defective factor IX causes thrombophilia In healthy individuals factor IXa (FIXa), in a complex with factor VIIIa on the surfaces of activated platelets, catalyzes the formation of activated factor X with high efficiency. A substitution of leucine for arginine at residue 384 in FIX (FIX R384L, also know as FIX Padua) is a gain-of-function mutation that resulted in elevated FIX clotting activity in a patient with venous thrombosis (Simioni P et al. 2009). R-HSA-9662001 Defective factor VIII causes hemophilia A Hemophilia A is an X‐chromosome‐linked recessive bleeding disorder defined by a qualitative and/or quantitative factor VIII (FVIII, F8) deficiency (Salen P & Babiker HM 2019). Patients affected by the mild form of the disease (FVIII activity 0.05–0.4 IU/mL) suffer from bleedings occurring after trauma or surgery. In severe hemophilia A patients (FVIII activity<0.01 IU/mL) bleedings occur spontaneously, whereas moderate hemophilia A patients (FVIII activity 0.01–0.05 IU/mL present with an intermediate bleeding phenotype (White GC 2nd et al. 2001). In healthy individuals, FVIII is synthesized as an ∼ 300-kDa glycoprotein by hepatocytes, liver sinusoidal endothelial cells, and certain types of endothelial cells (Wion KL et al. 1995; Jacquemin M et al. 2006; Shahani T et al. 2009; Turner NA & Moake JL 2015). The FVIII protein contains a domain sequence A1-A2-B-ap-A3-C1-C2 and circulates as an A1-A2-B:ap-A3-C1-C2 heterodimer bound noncovalently to the von Willebrand factor (vWF) protein. vWF protects FVIII from rapid clearance (Lenting PJ et al. 2007). During the activation of FVIII by thrombin to FVIIIa, the B domain and an activation peptide (ap) are released, and cleavage between the A1 and A2 domains produces an A1:A2:A3-C1-C2 heterotrimer (Lollar P & Parker ET 1991; Nogami K et al. 2005; Newell JL & Fay PJ 2007; 2009). Once activated, FVIIIa dissociates from vWF and binds to the membrane of activated platelets to assemble with activated factor IX (FIXa) (Gilbert GE & Arena AA 1996; Ahmad SS et al. 2003; Panteleev MA et al. 2004; Ngo JC et al. 2008). At physiologic concentrations, the A2 subunit spontaneously dissociates, leading to loss of FVIIIa cofactor activity (Lollar P & Parker CG 1990).
Hemophilia A results from a broad spectrum of mutations that occur along the entire length of the F8 gene causing diverse molecular phenotypes that result in similar disease states (Peyvandi F et al. 2016). Together with missense mutations being the most common type of mutations in hemophilia A, a relatively frequent cause is ascribable to nonsense and splice site mutations, deletions/insertions and promoter mutations (Hakeos WH et al. 2002; Wei W et al. 2017; Jacquemin M et al. 2000; Amano K et al. 1998; Gilbert GE et al. 2012; Pahl S et al. 2014; Peyvandi F et al. 2016). In addition, the inversion of intron 1 or 22 in the F8 gene is responsible for approximately half of severely affected hemophilia A patients (Antonarakis SE et al. 1995). Although specific FVIII missense mutations correlate with defects including decreased secretion or stability and specific functional impairment of FVIII, the mechanisms of the majority of missense mutations are poorly understood (Hakeos WH et al. 2002; Wei W et al. 2017, 2018; Jacquemin M et al. 2000; Amano K et al. 1998; Gilbert GE et al. 2012; Pahl S et al. 2014). The Reactome module describes several molecular mechanisms underlying hemophilia A which include:(1) low-level secretion of defective FVIII molecule as a result of impaired FVIII folding and intracellular processing, (2) reduced ability of FVIII variants to bind to von Willebrand factor (VWF) that leads to instability of FVIII variants in the plasma, (3) abnormal interaction of defective FVIII with FIXa. Defects in FVIII activity may also result in potentially slowing down FVIII activation by thrombin or altering stability of activated FVIIIa.
R-HSA-9657688 Defective factor XII causes hereditary angioedema Hereditary angioedema (HAE) is a rare life-threatening inherited edema disorder that is characterized by recurrent episodes of localized edema of the skin or of the mucosa of the gastrointestinal tract or upper airway. The edema formation in patients with HAE is primarily caused by a transient increased bradykinin release from high molecular weight kininogen (HK) due to uncontrolled activation of the coagulation factor XII (FXII)-dependent kallikrein kinin system (KKS) (Bossi F et al. 2009; Kaplan AP 2010; Suffritti C et al. 2014: Zuraw BL & Christiansen SC 2016). Angioedema initiated by bradykinin is usually associated with SERPING1 (C1-INH) deficiency. SERPING1 is the major regulator of the contact system. More rarely, HAE occurs in individuals with normal SERPING1 activity, and has been linked to mutations in other proteins, including FXII, plasminogen, and angiopoietin (Magerl M et al. 2017; Zuraw BL 2018; Ivanov I et al. 2019). Substitution of threonine 328 by either a lysine or an arginine residue (T328K or T328R) in the FXII proline-rich region has been identified in several families with HAE and normal SERPING1. FXII T328K or T328R variants change protein glycosylation and introduce a new site that is sensitive to enzymatic cleavage by fibrinolytic and coagulation proteases such as plasmin, thrombin, or FXIa (de Maat S et al. 2016; Ivanov I et al. 2019). The intrinsic capacity of the truncated form of FXII (329-615) (also known as δFXII) to convert prekallikrein to kallikrein is greater than that of FXII leading to more kallikrein generated early during reciprocal activation (Ivanov I et al. 2019). Second, FXII (329-615) is a better kallikrein substrate than is FXII. The accelerated kallikrein/FXII activation with truncated FXII (329-615) appears to overwhelm the regulatory function of SERPING1 at normal plasma levels leading to uncontrolled bradykinin formation (de Maat S et al. 2016; Ivanov I et al. 2019). Binding of the proinflammatory peptide hormone bradykinin to the bradykinin B2 receptor (B2R) activates various proinflammatory signaling pathways that increase vascular permeability and fluid efflux. An excessive formation of bradykinin due to uncontrolled activation of FXII-dependent KKS causes increased vascular permeability at the level of the postcapillary venule and results in HAE (Zuraw BL & Christiansen SC 2016; de Maat S et al. 2016; Ivanov I et al. 2019).
R-HSA-9673240 Defective gamma-carboxylation of F9 Naturally occurring hemophilia B (HB)-associated point mutations in the FIX propeptide sequence reduce affinity to gamma-glutamyl carboxylase (GGCX) resulting in reduced γ-carboxylation and aberrant propeptide processing (Bentley AK et al. 1986; Rabiet MJ et al. 1987; Diuguid DL et al. 1986; Ware J et al. 1989; de la Salle C et al. 1993). Unprocessed FIX variants such as F9 N43Q/L or F9 N46S, circulate with the attached propeptide and show delayed FIX activation (Bentley AK et al. 1986; Diuguid DL et al. 1986; Ware J et al. 1989; de la Salle C et al. 1993).
R-HSA-9701192 Defective homologous recombination repair (HRR) due to BRCA1 loss of function In addition to its role in DNA double-strand break (DSB) signaling, BRCA1 plays an important role in homologous recombination repair (HRR) of DSBs by directly promoting recruitment of PALB2 and indirectly BRCA2 to DSB repair sites. In addition, BRCA1 increases the speed and processivity of DNA end resection which consists of 5′–3′ nucleolytic degradation of DSBs (Cruz-Garcia et al. 2014). The direct BRCA1 interaction with PALB2 helps to fine-tune the localization of BRCA2 and RAD51 at DSBs (Zhang et al. 2009, Sy et al. 2009). PALB2 simultaneously interacts with RAD51, BRCA2 and RAD51AP1 (Modesti et al. 2007, Wiese et al. 2007, Buisson et al. 2010, Dray et al. 2010). PALB2 and RAD51AP1 synergistically stimulate RAD51 recombinase activity, thus enhancing RAD51-mediated strand exchange (branch migration) and promoting the formation of D-loop structures (synaptic complex assembly). A D-loop structure is formed when complementary duplex DNA (sister chromatid arm) is progressively invaded by the RAD51 nucleoprotein filament, with base pairing of the invading ssDNA and the complementary sister chromatid DNA strand (Sung et al. 2003).
The N-terminal region of BRCA1 contains the RING domain (residues 7-98), required for the heterodimerization of BRCA1 with BARD1. BRCA1:BARD1 heterodimer has E3 ubiquitin ligase activity which is important for DNA repair (Drost et al. 2011). Several missense mutations within the RING domain have been linked to increased risks of developing breast/ovarian cancers (Bouwman et al. 2013; Starita et al. 2018). BRCA1 mutant proteins impaired in BARD1 binding are annotated in the pathway "Defective DNA double strand break response due to BRCA1 loss of function".
The C-terminal region of BRCA1 which contains two coiled coil domains (residues 1397-1424) and two BRCT domains (residues 1642-1736 for BRCT 1; residues 1756-1855 for BRCT 2) is involved in PALB2 binding, with the second coiled coil domain being essential (Sy et al. 2009). Several cancer-associated BRCA1 missense mutants that affect the C-terminal region were shown to have reduced ability to bind PALB2 (Sy et al. 2009). In addition, many nonsense and frameshift mutations in BRCA1 reported in cancer result in truncated proteins that lack the PALB2-binding domain.
R-HSA-9701190 Defective homologous recombination repair (HRR) due to BRCA2 loss of function BRCA2 (FANCD1) is a tumor suppressor gene located on chromosomal arm 13q. BRCA2 protein is a mediator of the core mechanism of homologous recombination repair (HRR), essential for the recruitment of RAD51 recombinase to resected DNA double-strand breaks (DSBs). Monoallelic pathogenic germline mutations in BRCA2 are one of the underlying causes of the hereditary breast and ovarian cancer (HBOC) syndrome, with carriers having close to 50% lifetime risk for development of breast cancer and about 15% lifetime risk for development of ovarian cancer. In addition, BRCA2 germline mutation carriers are predisposed to cancers of the fallopian tube, pancreas, stomach, larynx and prostate. Biallelic germline mutations in BRCA2 cause Fanconi anemia subtype characterized by brain and soft tissue tumors, including medulloblastoma and Wilms tumor. BRCA2-deficient cells are defective in the formation of RAD51 foci upon treatment with DSB-inducing DNA damaging agents and accumulate chromatid breaks and radial chromosomes.
Besides its crucial role in HRR, BRCA2 is also implicated in protection of replication forks, centrosome duplication, spindle assembly checkpoint and cytokinesis. Recently published studies show the involvement of BRCA2 in the turnover of R-loops (hybrids between RNA and single strand DNA that are generated as intermediates of gene transcription). Unscheduled accumulated R-loops may be processed into DSBs, leading to genomic instability. Finally, BRCA2 is involved in pathway choice of DSB repair by inhibiting DNA polymerase theta-mediated end-joining (TMEJ) until M-phase (reviewed in Petropoulos and Halazonetis 2021, and Llorens-Agost et al. 2021). TMEJ is the predominant pathway for microhomology-mediated end joining MMEJ/alternative-nonhomologous end joining (alt-NHEJ, a-EJ) in mammals (reviewed in Ramsden et al. 2022).
BRCA2 haploinsufficiency is frequently observed in cancers, with close to 50% of BRCA2-mutant breast cancers retaining one wild type allele, suggesting that in some tissues at least heterozygous loss of BRCA2 function is sufficient for carcinogenesis. Promoter hypermethylation is not an obvious contributor to BRCA2 gene inactivation and no pathogenic mutations in the promoter region have been identified so far.
For review, please refer to Roy et al. 2011, Nalepa and Clapp 2018, Santana dos Santos et al. 2018, Venkitaraman 2019, Le et al. 2021, and Llorens-Agost et al. 2021.
R-HSA-9701193 Defective homologous recombination repair (HRR) due to PALB2 loss of function Biallelic loss-of-function mutations in PALB2 results in Fanconi anemia subtype N (FA-N), which is phenotypically very similar to Fanconi anemia subtype D1, caused by biallelic loss-of-function of BRCA2 (Reid et al. 2007). FA-D1 and FA-N are characterized by developmental abnormalities, bone marrow failure and childhood cancer susceptibility, especially childhood solid tumors, such as Wilms tumor and medulloblastoma. Monoallelic PALB2 loss-of-function is an underlying cause of hereditary breast cancer in particular, but inactivating PALB2 mutations are also to a lesser extent found in some other cancer types, including pancreatic cancer (Erkko et al. 2007, Erkko et al. 2008, Antoniou et al. 2014, Yang et al. 2020). Germline PALB2 mutations are somewhat less frequent than those occurring in BRCA1 and BRCA2, but cause a comparably high risk of developing breast cancer. Therefore, PALB2 is a high-risk breast cancer predisposing gene (Nepomuceno et al. 2021).
PALB2 interacts with both BRCA1 and BRCA2, and serves as a bridge that connects BRCA2 with BRCA1 at sites of DNA double-strand break repair (DSBR). PALB2 also interacts directly with DNA and takes part in the regulation of RAD51-mediated homologous recombination (Buisson et al. 2010; Dray et al. 2010). PALB2 loss-of-function mutations can affect its interaction with BRCA1 when they affect the N-terminal coiled-coil domain that is necessary for BRCA1 binding (Sy et al. 2009, Foo et al. 2017). Mutations in the coiled-coil domain can also affect PALB2 self-interaction, recruitment to double-strand break sites, homologous recombination repair and RAD51 foci formation (Buisson and Masson 2012). PALB2 missense mutants that do not bind to BRCA1 can still be recruited to DSBR sites, probably through interaction with other proteins involved in DSBR, but they are unable to restore efficient gene conversion in PALB2-deficient cells and they render cells hypersensitive to the DNA damaging agent mitomycin C (Sy et al. 2009), with some variants also presenting sensitivity to PARP inhibitors (Foo et al. 2017).
Mutations evaluated so far in the central region of PALB2, which contains the ChAM motif and the MRG15-binding region, have shown no functional impact on the protein.
Mutations affecting the C-terminal WD40 domain of PALB2 impair its ability to interact with BRCA2, RAD51 and/or RAD51C (Erkko et al. 2007, Park et al. 2014, Simhadri et al. 2019). In addition, disruption of the WD40 domain can lead to the exposure of a nuclear export signal (NES), leading to cytoplasmic translocation of PALB2 (Pauty et al. 2017). Mutations affecting the C-terminal domain of PALB2 are more frequent than mutations that affect the N-terminus and have been observed, as germline mutations, in familial breast cancer and in Fanconi anemia, but somatic mutations also occur in sporadic cancers. Cells that express PALB2 mutants defective in BRCA2, RAD51 and/or RAD51C binding show reduced ability to perform DSBR via homologous recombination repair, form fewer RAD51 foci at DSBR sites, and are sensitive to DNA crosslinking agents such as mitomycin C (Erkko et al. 2007, Parker et al. 2014).
For review, please refer to Tischkowitz and Xia 2010, Pauty et al. 2014, Park et al. 2014, Nepomuceno et al. 2017, Ducy et al. 2019, Wu et al. 2020, Nepomuceno et al. 2021.
R-HSA-5688031 Defective pro-SFTPB causes SMDP1 and RDS Pulmonary surfactant-associated protein B (SFTPB), amongst other roles, is a component of surfactant, a surface-active film that helps reduce surface tension in alveoli. Defects in the SFTPB gene result in loss-of-function SFTPB proteins and accumulation of partially-processed , inactive pro-SFTPC in alveoli. Defects in SFTPB can cause pulmonary surfactant metabolism dysfunction 1 (SMDP1; MIM:265120), a rare lung disorder due to impaired surfactant homeostasis characterised by alveoli filling with floccular material. Excessive lipoprotein accumulation in the alveoli results in a form of respiratory distress syndrome in premature infants (RDS; MIM:267450) (Vorbroker et al. 1995, Li et al. 2004, Wert et al. 2009, Whitsett et al. 2015).
R-HSA-5688354 Defective pro-SFTPC causes SMDP2 and RDS Pulmonary surfactant-associated protein C (SFTPC), amongst other roles, is a component of surfactant, a surface-active film that helps reduce surface tension in alveoli. Defects in the SFTPC gene result in protein misfolding, misrouting and/or misprocessing resulting in accumulation of partially-processed, inactive pro-SFTPC in alveoli causing cell toxicity. Defects in SFTPC can cause pulmonary surfactant metabolism dysfunction 2 (SMDP2; MIM:610913), a rare lung disorder due to impaired surfactant homeostasis characterised by alveoli filling with floccular material. Cellular responses to the misfolded pro-SFTPC products include ER stress, the activation of reactive oxygen species and autophagy. Excessive lipoprotein accumulation in the alveoli results in a form of respiratory distress syndrome in premature infants (RDS; MIM:267450) (Thomas et al. 2002, Mulugeta et al. 2005, Thurm et al. 2013, Whitsett et al. 2015).
R-HSA-9710421 Defective pyroptosis Pyroptosis is a form of lytic inflammatory programmed cell death that is mediated by the pore‑forming gasdermins (GSDMs) (Shi J et al. 2017) to stimulate immune responses through the release of pro‑inflammatory interleukin (IL)‑1β, IL‑18 (mainly in GSDMD-mediated pyroptosis) as well as danger signals such as adenosine triphosphate (ATP) or high mobility group protein B1 (HMGB1) (reviewed in Shi J et al. 2017; Man SM et al. 2017; Tang D et al. 2019; Lieberman J et al. 2019). Pyroptosis protects the host from microbial infection but can also lead to pathological inflammation if overactivated or dysregulated (reviewed in Orning P et al. 2019; Tang L et al. 2020). During infections, the excessive production of cytokines can lead to a cytokine storm, which is associated with acute respiratory distress syndrome (ARDS) and systemic inflammatory response syndrome (SIRS) (reviewed in Tisoncik JR et al. 2012; Karki R et al. 2020; Ragab D et al. 2020). Pyroptosis has a close but complicated relationship to tumorigenesis, affected by tissue type and genetic background. Pyroptosis can trigger potent antitumor immune responses or serve as an effector mechanism in antitumor immunity (Wang Q et al. 2020; Zhou Z et al. 2020; Zhang Z et al. 2020), while in other cases, as a type of proinflammatory death, pyroptosis can contribute to the formation of a microenvironment suitable for tumor cell growth (reviewed in Xia X et al. 2019; Jiang M et al. 2020; Zhang Z et al. 2021).
This Reactome module describes the defective GSDME function caused by cancer‑related GSDME mutations (Zhang Z et al. 2020). It also shows epigenetic inactivation of GSDME due to hypermethylation of the GSDME promoter region (Akino K et al. 2007; Kim MS et al. 2008a,b; Croes L et al. 2017, 2018; Ibrahim J et al. 2019). Aberrant promoter methylation is considered to be a hallmark of cancer (Ehrlich M et al. 2002; Dong Y et al. 2014; Lam K et al. 2016; Croes L et al. 2018). Treatment with the DNA methyltransferase inhibitor decitabine (5‑aza‑2'‑deoxycytidine or DAC) may elevate GSDME expression in certain cancer cells (Akino K et al. 2007; Fujikane T et al. 2009; Wang Y et al. 2017). R-HSA-9824856 Defective regulation of TLR7 by endogenous ligand Activation of innate immune receptors including Toll-like receptors (TLRs) by pathogen-associated molecular patterns (PAMPs) is crucial in the host defense against microbial infections. On the other hand, these receptors are also activated by diverse molecules of host-cell origin. These molecules are known as damage-associated molecular patterns (DAMPs). This Reactome module describes defects in activation of TLRs by the endogenous ligands.
DAMPs are released from necrotic cells or secreted from activated cells in response to tissue damage to mediate tissue repair by promoting inflammatory responses (reviewed by Piccinini AM et al., 2010; Gong T et al., 2020; Zindel LJ et al., 2020). However, DAMPs have also been implicated in the pathogenesis of many inflammatory and autoimmune diseases, including rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and atherosclerosis (Duffy L & O’Reilly SC 2016; Fukuda D et al., 2019; Gong T et al., 2020; Liu J et al., 2022). There is a correlation between high level of endogenous TLR ligands and different chronic inflammatory conditions in human subjects and mouse models (Duvvuri B & Lood C et al., 2019; Negishi H et al., 2019; Punnanitinont A et al., 2022). The mechanism underlying the switch from DAMPs that initiate controlled tissue repair, to those that mediate chronic, uncontrolled inflammation is still unclear. Studies suggest that an abnormal increase in protein citrullination is involved in disease pathophysiology (Anzilotti C et al., 2010; Sanchez-Pernaute O et al., 2013; Sokolove J et al., 2011; Sharma P et al., 2012; Olsen I et al., 2018). Moreover, gene polymorphisms within TLRs may predispose to the abnormal inflammatory responses associated with chronic diseases including autoimmune diseases (Devarapu SK & Anders HJ 2018; Zhang Y et al., 2021). For example, polymorphisms that increase expression of TLR7 are associated with a higher risk of SLE (reviewed in Fillatreau S et al., 2021). Further, inherited genetic variations can promote autoimmune responses. For example, TLR7 Y264H was identified as a gain-of-function mutation in a patient with SLE (Brown GJ et al., 2022). TLR7 Y264H exhibited enhanced affinity to endogenous guanosine-containing ligands (Brown GJ et al., 2022).
R-HSA-9661070 Defective translocation of RB1 mutants to the nucleus This pathway describes impaired nuclear localization of RB1 mutants that lack the nuclear localization signal (NLS) (Zacksenhaus et al. 1993, Bremner et al. 1997).
R-HSA-9918454 Defective visual phototransduction due to ABCA4 loss of function ATP-binding cassette protein A4 (ABCA4, ABCR), expressed exclusively in retinal photoreceptors, is thought to be involved in the clearance of toxic by-products of the retinoid cycle. Defects in ABCA4 cause a diverse range of human diseases. One such disease is Stargardt's disease type 1 (STGD1, MIM:248200) (Allikmets et al. 1997), an autosomal recessive form of juvenile macular degeneration leading to progressive irreversible loss of central vision and delayed dark adaptation. STGD1 was first identified by Stargardt in 1909 (Stargardt, Arch. Klin. Exp. Ophthal. 71: 534-549, 1909), has an approximate prevalence of 1 in 10,000 (see reviews Paskowitz et al. 2006, Walia & Fishman 2009) and is usually diagnosed within the first two decades of life.
R-HSA-9918442 Defective visual phototransduction due to LRAT loss of function Normally functioning lecithin retinol acyltransferase (LRAT) mediates the transfer of an acyl group onto all-trans-retinol (atROL), forming retinyl esters (REs), the storage form of retinoids. Defects in LRAT cause Leber congenital amaurosis type 14 (LCA14, MIM:613341), an autosomal recessive juvenile-onset retinal dystrophy affecting rod and cone photoreceptors. Leber congenital amaurosis (LCA) comprises a group of early-onset retinal dystrophies characterized by vision loss, nystagmus, and severe retinal dysfunction (Chung & Traboulsi 2009).
R-HSA-9918450 Defective visual phototransduction due to OPN1LW loss of function Blue cone monochromatism (BCM) is a rare X-linked congenital cone dysfunction characterized by the absence of functional long wavelength-sensitive (red) and medium wavelength-sensitive (green) cones in the retina. Colour discrimination is severely impaired from birth, and vision is derived from the preserved short wavelength-sensitive (blue) cones and rod photoreceptors. BCM typically presents with reduced visual acuity, pendular nystagmus, photophobia and patients often have myopia. BCM affects approximately 1 in 100,000 individuals and can be caused by loss-of-function mutations in the OPN1LW gene (see review Gardner et al. 2009).
Defects in OPN1LW also cause partial colorblindness, protan series (CBP, protanopia; MIM:303900) due to non-functional red cones (Ueyama et al. 2002).
R-HSA-9918436 Defective visual phototransduction due to OPN1MW loss of function Normal human colour vision is trichromatic, based on 3 types of cones that are maximally sensitive to light at approximately 420 nm (blue cones), 530 nm (green cones), and 560 nm (red cones). Neural circuits compare light absorbed by these 3 cone types to perceive those primary colours and combinations of them. Colour vision deficiencies result from genetic mutations that affect the expression of the full complement of cone photoreceptors and are classified by severity of deficiency (see reviews Deeb 2005, Simunovic 2010).
Deutan colourblindness (DCB, deuteranopia, partial colorblindness, green colourblindness; MIM:303800) is caused by mutations in the OPN1MW gene which encodes green cones. In European populations, red-green colourblindness is prevelant in 8% of males and 0.5% of females. This frequency is lower in non-European populations (Deeb 2005).
Defects in OPN1MW also cause X-linked cone dystrophy type 5 (COD5; MIM:303700), a retinal dystrophy characterized by progressive degeneration of cone photoreceptors but with preserved rod function.
R-HSA-9918443 Defective visual phototransduction due to OPN1SW loss of function Normal human colour vision is trichromatic, based on 3 types of cones that are maximally sensitive to light at approximately 420 nm (blue cones), 530 nm (green cones), and 560 nm (red cones). Neural circuits compare light absorbed by these 3 cone types to perceive those primary colours and combinations of them. Colour vision deficiencies result from genetic mutations that affect the expression of the full complement of cone photoreceptors and are classified by severity of deficiency (see reviews Deeb 2005, Simunovic 2010).
Tritan (blue-yellow, blue colourblindness, tritanopia; MIM:190900) deficiencies are rare (1 in 500) (Went & Pronk 1985) compared to those involving green- and red-cone deficiencies. The first report of tritan defects was in 1952 (Wright 1952). Tritan deficiencies are inherited as autosomal dominant traits (Kalmus 1955) and are a result of missense mutations in the blue-cone photopigment gene OPN1SW, leading to amino-acid substitutions in the protein sequence. Tritan defects are characterized by a selective deficiency of blue spectral sensitivity (Weitz et al. 1992).
R-HSA-9918440 Defective visual phototransduction due to RDH12 loss of function Retinol dehydrogenase RDH12 mediates the reversible, NADP(H)-dependent reduction of all-trans-retinal (atRAL) or 11-cis-retinal (11cRAL) to all-trans-retinol (atROL) or 11-cis-retinol (11cROL) respectively in photoreceptor cells.
Defects in RDH12 cause Leber congenital amaurosis type 13 (LCA13; MIM:612712). LCA defects are early-onset and severe retinal degenerations that are responsible for the most common cause of congenital blindness in infants and children (Janecke et al. 2004; Perrault et al. 2004).
Defects in RDH12 cause retinitis pigmentosa type 53 (RP53; MIM:612712), an autosomal recessive retinal dystrophy characterised by retinal pigment deposits and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptor cells (Benayoun et al. 2009).
R-HSA-9918438 Defective visual phototransduction due to RDH5 loss of function 11-cis-retinol dehydrogenase (RDH5) can reversibly catalyse the oxidation of all-trans-retinol (atROL, bound to RLBP1) to all-trans-retinal (atRAL) in retinal pigment epithelium (RPE) cells using NAD+ as cofactor. Defective RDH5 causes retinitis punctata albescens (RPA, also called fundus albipunctatus, FA; MIM:136880). RPA (an autosomal recessive disorder) is a form of stationary congenital night blindness characterised by a reduced regeneration rate of rod and cone photoreceptors and yellow-white lesions within the retina or the RPE. For review, please refer to Zeitz et al. 2015.
R-HSA-9918449 Defective visual phototransduction due to STRA6 loss of function Defects in STRA6 cause microphthalmia syndromic type 9 (MCOPS9, Matthew-Wood syndrome or Spear syndrome; MIM:601186) (Chassaing et al. 2009). Mutiple systems are affected by this fatal syndrome including occular and cardiac abnormalities. Microphthalmia (also called microphthalmos, nanophthalmia or nanophthalmos) is a developmental disorder of the eye that literally means small eye and in most cases results in blindness.
R-HSA-3323169 Defects in biotin (Btn) metabolism Biotin (Btn, vitamin B7, vitamin H, coenzyme R) is an essential cofactor for five biotin-dependent carboxylase enzymes, involved in the synthesis of fatty acids, isoleucine, valine and in gluconeogenesis. Thus, Btn is necessary for cell growth, fatty acid synthesis and the metabolism of fats and amino acids. Inherited metabolic disorders characterized by deficient activities of all five biotin dependent carboxylases are termed multiple carboxylase deficiencies. Two congenital defects in biotin metabolism leading to multiple carboxylase deficiency are known, holocarboxylase synthetase deficiency (MIM 609018) and biotinidase deficiency (MIM 253260). In both scenarios symptoms include ketolactic acidosis, organic aciduria, hyperammonemia, skin rashes, hypotonia, seizures, developmental delay, alopecia, and coma. As humans are auxotrophic for Btn, the micronutrient must be obtained from external soures such as intestinal microflora and dietary forms. Accordingly, severe malnutrition can also give rise to biotin deficiency and multiple carboxylase deficiency. Biotin deficiency can also be induced by the excessive consumption of raw egg white that contains the biotin-binding protein avidin. Holocarboxylase synthetase deficiency arises when all five biotin-dependent enzymes are not biotinylated leading to their reduced activities. The defective genes causing these conditions are described here (Pendini et al. 2008, Suzuki et al. 2005). Biotinidase deficiency is caused by defects in the recycling of Btn. General symptoms include decreased appetite and growth, dermatitis and perosis. The defective genes causing these conditions are described here (Procter et al. 2013).
R-HSA-3296469 Defects in cobalamin (B12) metabolism Cobalamin (Cbl, vitamin B12) is a nutrient essential for normal functioning of the brain and nervous system and for the formation of blood. Cbl-dependent methionine synthase (MTR) is required for conversion of 5-methyltetrahydrofolate (metTHF) to tetrahydrofolate (THF), in addition to its role in conversion of homocysteine to methionine. In Cbl deficiency, and in inborn errors of Cbl metabolism that affect function of methionine synthase, inability to regenerate THF from metTHF results in decreased function of folate-dependent reactions that are involved in 2 steps of purine biosynthesis and thymidylate synthesis. Cbl deficiency results in hyperhomocysteinemia (due to defects in the conversion of homocysteine to methionine which requires Cbl as a cofactor) and increased levels of methylmalonic acid (MMA). Methionine is used in myelin production, protein, neurotransmitter, fatty acid and phospholipid production and DNA methylation. Symptoms of Cbl deficiency are bone marrow promegaloblastosis (megaloblastic anemia) due to the inhibition of DNA synthesis (specifically purines and thymidine) and neurological symptoms. The defective genes involved in Cbl deficiencies are described below (Froese & Gravel 2010, Nielsen et al. 2012, Whitehead 2006, Watkins & Rosenblatt 2011, Fowler 1998).
R-HSA-3296482 Defects in vitamin and cofactor metabolism Vitamins are essential nutrients, required in small amounts from the diet for the normal growth and development of a multicellular organism. Where there is vitamin deficiency, either by poor diet or a defect in metabolic conversion, diseases called Avitaminoses occur. Currently, cobalamin (Cbl, vitamin B12) metabolic defects are described below (Chapter 155 in The Metabolic and Molecular Bases of Inherited Disease, 8th ed, Scriver et al. 2001)
R-HSA-9651496 Defects of contact activation system (CAS) and kallikrein/kinin system (KKS) The contact activation system (CAS) is a plasma protease cascade initiated by factor XII (FXII) that activates the pro-inflammatory kallikrein‐kinin system (KKS) and the pro-coagulant intrinsic coagulation pathway (Renne T 2012; Renne T et al. 2012; Maas C et al. 2011; Schmaier AH 2016; Long AT et al. 2016). The CAS is initiated by the auto‐activation of factor XII (FXII) on charged or neutral surfaces with conversion of plasma prekallikrein (PK) to plasma kallikrein (Samuel M et al. 1992; Ivanov I et al. 2017). These events are followed by reciprocal activation of FXII by kallikrein and amplification of each other's activation. Two branches of the CAS have been identified: (i) the inflammatory branch activates contact factors FXII and PK on the surface of endothelial cells resulting in release of the peptide bradykinin (BK) and (ii) the plasma coagulation branch activates FXII and FXI on the surface of platelets. The CAS is thought to be central to crosstalk between coagulation and inflammation and the underlying cause for various disorders affecting the cardiovascular system (Wu Y 2015; Long AT et al. 2016). Physiologically, a fine balance is normally maintained between blood flow and blood clotting, the dysfunction of which yields either hemorrhage or thrombosis. Defects in the intrinsic pathway coagulation factors (FVIII, FIX, and FXI) are associated with a significant bleeding tendency. The X-linked recessive disorders, hemophilia A (FVIII deficiency) and B (FIX deficiency), are associated with spontaneous and excessive hemorrhage, especially hemarthroses and muscle hematomas (Bowen DJ 2002; Goodeve AC 2015). A deficiency in FXI, which is encoded by a gene on chromosome 4, generally results in a less severe, but still significant, bleeding tendency (James P et al. 2014; Puy C et al. 2016). Although PK and FXIIa are recognized as upstream triggers for the intrinsic coagulation system, the clinical significance of these factors on thrombosis and hemorrhage is not fully understood. The CAS blockade results in prolonged coagulation times in the activated partial thromboplastin time (aPTT) assay. However, the absence of thrombotic and hemostatic abnormalities in individuals with genetic deficiencies of PK or FXII has suggested that the CAS plays a minimal role in physiological coagulation (Müller F et al. 2011). At the same time, excessive formation of bradykinin due to abnormal FXII-dependent KKS activation causes increased vascular permeability at the level of the post capillary venule and results in hereditary angioedema (HAE). HAE initiated by bradykinin is usually associated with SERPING1 (C1-INH) deficiency (Suffritti C et al. 2014). More rarely, HAE occurs in individuals with normal SERPING1 activity, and has been linked to mutations in other proteins, including FXII, plasminogen, and angiopoietin (Cichon S et al. 2006; Magerl M et al. 2017; Zuraw BL 2016; Ivanov I et al. 2019). This Reactome module describes abnormal FXII-dependent KKS activation that leads to an excessive formation of bradykinin causing increased vascular permeability at the level of the post capillary venule and results in hereditary angioedema (HAE). HAE caused by defective function of SERPING1 is also covered here. The module also includes disorders that can cause abnormal bleeding due to a shortage (deficiency) of coagulation factor proteins, which are involved in blood clotting. This module also describes elevation of FIX activity associated with thrombophilia. Genetic variants are named following Human Genome Variation Society (HGVS) nomenclature with sequence numbering starting from the first methionine of the protein as +1.(Goodeve AC et al.2011).
R-HSA-9823587 Defects of platelet adhesion to exposed collagen This Reactome module describes dysfunctions in platelet adhesion caused by mutations in different genes, including VWF, ADAMTS13 and GP1BA.
R-HSA-1461973 Defensins The defensins are a family of antimicrobial cationic peptide molecules which in mammals have a characteristic beta-sheet-rich fold and framework of six disulphide-linked cysteines (Selsted & Ouellette 2005, Ganz 2003). Human defensin peptides have two subfamilies, alpha- and beta-defensins, differing in the length of peptide chain between the six cysteines and the order of disulphide bond pairing between them. A third subfamily, the theta defensins, is derived from alpha-defensins prematurely truncated by a stop codon between the third and fourth cysteine residues. The translated products are shortened to nonapeptides, covalently dimerized by disulfide linkages, and cyclized via new peptide bonds between the first and ninth residues. Humans have one pseudogene but no translated representatives of the theta class.
In solution most alpha and beta defensins are monomers but can form dimers and higher order structures.
The primary cellular sources of defensins are neutrophils, epithelial cells and intestinal Paneth cells.Those expressed in neutrophils and the gut are predominantly constitutive, while those in epithelial tissues such as skin are often inducible by proinflammatory stimuli such as LPS or TNF-alpha.
Defensins are translated as precursor polypeptides that include a typical signal peptide or prepiece that is cleaved in the Golgi body, and a propiece, cleaved by differing mechanisms to produce the mature defensin. Mature defensin peptides can be further processed by removal of individual N-terminal residues (Yang et al. 2004). This may be a mechanism to broaden the activity profile of defensins (Ghosh et al. 2002).
Defensins have direct antimicrobial effects and kill a wide range of Gram-positive and negative bacteria, fungi and some viruses. The primary antimicrobial action of defensins is permeabilization of microbial target membranes but several additional mechanisms have been suggested (Brogden 2005, Wilmes et al. 2011). Defensins and related antimicrobial peptides such as cathelicidin bridge the innate and acquired immune responses. In addition to their antimicrobial properties, cathelicidin and several defensins show receptor-mediated chemotactic activity for immune cells such as monocytes, T cells or immature DCs, induce cytokine production by monocytes and epithelial cells, modulate angiogenesis and stimulate wound healing (Yang et al. 1999, 2000, 2004, Rehaume & Hancock 2008, Yeung et al. 2011).
R-HSA-4641257 Degradation of AXIN AXIN is present in low concentrations in the cell and is considered to be the limiting component of the beta-catenin destruction complex in Xenopus; this may not be the case in mammalian cells, however (Lee et al, 2003; Tan et al, 2012). Cellular levels of AXIN are regulated in part through ubiquitin-mediated turnover. E3 ligases SMURF2 and RNF146 have both been shown to play a role in promoting the degradation of AXIN by the 26S proteasome (Kim and Jho, 2010; Callow et al, 2011; Zhang et al, 2011).
R-HSA-4641258 Degradation of DVL DVL protein levels are regulated by both proteasomal and lysosomal degradation (reviewed in Gao and Chen, 2010). The E3 ligases HECF1, ITCH and KLHL12:CUL3 have all been shown to contribute to the polyubiquitination and subsequent degradation of DVL (Angers et al, 2006; Miyazaki et al, 2004; Wei et al, 2012). DVL stability is also regulated by its interaction with DACT1, which promotes degradation of DVL in the lysosome (Cheyette et al, 2002; Zhang et al, 2006).
R-HSA-916853 Degradation of GABA GABA is metabolized in the mitochondrial matrix to succinate by the serial action of two enzymes, 4-aminobutyrate aminotransferase and suucinate semialdehyde dehydrogenase. Failure of the second reaction is associated with a rare human genetic disorder (Malaspina et al. 2016; Pearl et al. 2009).
R-HSA-5610780 Degradation of GLI1 by the proteasome GLI1 is the most divergent of the 3 mammalian GLI transcription factors and lacks a transcriptional repressor domain. Although GLI1 is dispensible for development, the gene is an early transcriptional target of Hh signaling and the protein contributes a minor activation function in mammals (Dai et al, 1999; Bai et al, 2002; Park et al, 2000).
In the absence of Hh signaling, GLI1 is completely degraded by the proteasome, in contrast to the partial processing that occurs with GLI3. This differential response reflects the absence in GLI1 of two of the three elements identified in GLI3 that promote partial proteolysis; these are the zinc finger region, present in all GLI proteins, and an adjacent linker sequence and the degron, neither of which are found in the GLI1 protein (Schrader et al, 2011; Pan and Wang, 2007).
R-HSA-5610783 Degradation of GLI2 by the proteasome The primary role of the GLI2 protein is as an activator of Hh-dependent signaling upon pathway stimulation; in the absence of Hh ligand, a small fraction of GLI2 appears to be processed to a repressor form, but the bulk of the protein is completely degraded by the proteasome (reviewed in Briscoe and Therond, 2013). Both the processing and the degradation of GLI2 is dependent upon sequential phosphorylation of multiple serine residues by PKA, CK1 and GSK3, analagous to the requirement for these kinases in the processing of GLI3 (Pan et al, 2009; Pan et al, 2006; Pan and Wang, 2007). The differential processing of GLI2 and GLI3 depends on the processing determinant domain (PDD) in the C-terminal of the proteins, which directs the partial proteolysis of GLI3 in the absence of Hh signal. Substitution of 2 amino-acids from GLI3 into the GLI2 protein is sufficient to promote efficient processing of GLI2 to the repressor form (Pan and Wang, 2007).
R-HSA-195253 Degradation of beta-catenin by the destruction complex The beta-catenin destruction complex plays a key role in the canonical Wnt signaling pathway. In the absence of Wnt signaling, this complex controls the levels of cytoplamic beta-catenin. Beta-catenin associates with and is phosphorylated by the destruction complex. Phosphorylated beta-catenin is recognized and ubiquitinated by the SCF-beta TrCP ubiquitin ligase complex and is subsequently degraded by the proteasome (reviewed in Kimelman and Xu, 2006).
R-HSA-1614558 Degradation of cysteine and homocysteine While in humans excess methionine is converted to homocysteine, homocysteine and its transsulfuration product cysteine can be degraded to several end products, two of which, taurine and hydrogen sulfide, have uses in other biological processes (Stipanuk & Ueki 2011).
R-HSA-1474228 Degradation of the extracellular matrix Matrix metalloproteinases (MMPs), previously referred to as matrixins because of their role in degradation of the extracellular matrix (ECM), are zinc and calcium dependent proteases belonging to the metzincin family. They contain a characteristic zinc-binding motif HEXXHXXGXXH (Stocker & Bode 1995) and a conserved Methionine which forms a Met-turn. Humans have 24 MMP genes giving rise to 23 MMP proteins, as MMP23 is encoded by two identical genes. All MMPs contain an N-terminal secretory signal peptide and a prodomain with a conserved PRCGXPD motif that in the inactive enzyme is localized with the catalytic site, the cysteine acting as a fourth unpaired ligand for the catalytic zinc atom. Activation involves delocalization of the domain containing this cysteine by a conformational change or proteolytic cleavage, a mechanism referred to as the cysteine-switch (Van Wart & Birkedal-Hansen 1990). Most MMPs are secreted but the membrane type MT-MMPs are membrane anchored and some MMPs may act on intracellular proteins. Various domains determine substrate specificity, cell localization and activation (Hadler-Olsen et al. 2011). MMPs are regulated by transcription, cellular location (most are not activated until secreted), activating proteinases that can be other MMPs, and by metalloproteinase inhibitors such as the tissue inhibitors of metalloproteinases (TIMPs). MMPs are best known for their role in the degradation and removal of ECM molecules. In addition, cleavage of the ECM and other cell surface molecules can release ECM-bound growth factors, and a number of non-ECM proteins are substrates of MMPs (Nagase et al. 2006). MMPs can be divided into subgroups based on domain structure and substrate specificity but it is clear that these are somewhat artificial, many MMPs belong to more than one functional group (Vise & Nagase 2003, Somerville et al. 2003).
R-HSA-5467343 Deletions in the AMER1 gene destabilize the destruction complex Genomic deletions of the entire AMER1/WTX gene occur in about 12% of Wilms tumors, a pediatric kidney cancer. Nonsense and missense mutations have also been identified (Ruteshouser et al, 2008; Wegert et al, 2009). AMER1 is a known component of the destruction complex and interacts directly with beta-catenin through the C-terminal half (Major et al, 2007). siRNA depletion of AMER1 in mammalian cells stabilizes cellular beta-catenin levels and increases the expression of a beta-catenin-dependent reporter gene, suggesting that AMER1 is a tumor suppressor gene (Major et al, 2007; reviewed in Huff, 2011).
R-HSA-5467345 Deletions in the AXIN1 gene destabilize the destruction complex Deletions in the AXIN1 gene have been identified in 2 hepatocellular carcinoma cell lines. These deletions, which remove the N-terminal exons of the gene, compromise AXIN1 expression and result in elevated expression of a TCF-dependent reporter (Satoh et al, 2000, reviewed in Salahshor and Woodgett, 2005).
R-HSA-4419969 Depolymerization of the Nuclear Lamina The nuclear envelope breakdown in mitotic prophase involves depolymerization of lamin filaments, the main constituents of the nuclear lamina. The nuclear lamina is located at the nuclear face of the inner nuclear membrane and plays and important role in the structure and function of the nuclear envelope (reviewed by Burke and Stewart 2012). Depolymerization of lamin filaments, which consist of lamin homodimers associated through electrostatic interactions in head-to-tail molecular strings, is triggered by phosphorylation of lamins. While CDK1 phosphorylates the N-termini of lamins (Heald and McKeon 1990, Peter et al. 1990, Ward and Kirschner 1990, Mall et al. 2012), PKCs (PRKCA and PRKCB) phosphorylate the C-termini of lamins (Hocevar et al. 1993, Goss et al. 1994, Mall et al. 2012). PKCs are activated by lipid-mediated signaling, where lipins, activated by CTDNEP1:CNEP1R1 serine/threonine protein phosphatase complex, catalyze the formation of DAG (Gorjanacz et al. 2009, Golden et al. 2009, Wu et al. 2011, Han et al. 2012, Mall et al. 2012).
R-HSA-606279 Deposition of new CENPA-containing nucleosomes at the centromere Eukaryotic centromeres are marked by a unique form of histone H3, designated CENPA in humans. In human cells newly synthesized CENPA is deposited in nucleosomes at the centromere during late telophase/early G1 phase of the cell cycle. Once deposited, nucleosomes containing CENPA remain stably associated with the centromere and are partitioned equally to daughter centromeres during S phase. A current model proposes that pre-existing CENPA at the centromere drives recruitment of new CENPA, however this has not been proved.
The deposition process requires at least 3 complexes: the Mis18 complex, HJURP complex, and the RSF complex. HJURP binds newly synthesized CENPA-H4 tetramers before deposition and brings them to the centromere for deposition in new CENPA-containing nucleosomes. The exact mechanism of deposition remains unknown.
R-HSA-73927 Depurination Depurination of a damaged nucleotide is mediated by a purine-specific DNA glycosylase. The glycosylase cleaves the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar, generating a free base and an abasic i.e. apurinic/apyrimidinic (AP) site (Slupphaug et al. 1996, Parikh et al. 1998).
R-HSA-73928 Depyrimidination Depyrimidination of a damaged nucleotide in DNA is mediated by a pyrimidine-specific DNA glycosylase. The glycosylase cleaves the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar generating a free base and an abasic i.e. apurinic/apyrimidinic (AP) site (Lindahl and Wood 1999).
R-HSA-8862803 Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models Post-mitotic neurons do not have an active cell cycle. However, deregulation of Cyclin Dependent Kinase-5 (CDK5) activity in these neurons can aberrantly activate various components of cell cycle leading to neuronal death (Chang et al. 2012). Random activation of cell cycle proteins has been shown to play a key role in the pathogenesis of several neurodegenerative disorders (Yang et al. 2003, Lopes et al. 2009). CDK5 is not activated by the canonical cyclins, but binds to its own specific partners, CDK5R1 and CDK5R2 (aka p35 and p39, respectively) (Tsai et al. 1994, Tang et al. 1995). Expression of p35 is nearly ubiquitous, whereas p39 is largely expressed in the central nervous system. A variety of neurotoxic insults such as beta-amyloid (A-beta), ischemia, excitotoxicity and oxidative stress disrupt the intracellular calcium homeostasis in neurons, thereby leading to the activation of calpain, which cleaves p35 into p25 and p10 (Lee et al. 2000). p25 has a six-fold longer half-life compared to p35 and lacks the membrane anchoring signal, which results in its constitutive activation and mislocalization of the CDK5:p25 complex to the cytoplasm and the nucleus. There, CDK5:p25 is able to access and phosphorylate a variety of atypical targets, triggering a cascade of neurotoxic pathways that culminate in neuronal death. One such neurotoxic pathway involves CDK5-mediated random activation of cell cycle proteins which culminate in neuronal death. Exposure of primary cortical neurons to oligomeric beta-amyloid (1-42) hyper-activates CDK5 due to p25 formation, which in turn phosphorylates CDC25A, CDC25B and CDC25C. CDK5 phosphorylates CDC25A at S40, S116 and S261; CDC25B at S50, T69, S160, S321 and S470; and CDC25C at T48, T67, S122, T130, S168 and S214. CDK5-mediated phosphorylation of CDC25A, CDC25B and CDC25C not only increases their phosphatase activities but also facilitates their release from 14-3-3 inhibitory binding. CDC25A, CDC25B and CDC25C in turn activate CDK1, CDK2 and CDK4 kinases causing neuronal death. Consistent with this mechanism, higher CDC25A, CDC25B and CDC25C activities were observed in human Alzheimer's disease (AD) clinical samples, as compared to age-matched controls. Inhibition of CDC25 isoforms confers neuroprotection to beta-amyloid toxicity, which underscores the contribution of this pathway to AD pathogenesis
R-HSA-2022923 Dermatan sulfate biosynthesis Dermatan sulfate (DS) consists of N-acetylgalactosamine (GalNAc) residues alternating in glycosidic linkages with glucuronic acid (GlcA) or iduronic acid (IdoA) residues. As with CS, GalNAc residues can be sulfated in CS chains but also the uronic acid
residues may be substituted with sulfate at the 2- and 4- positions. The steps below outline the synthesis of a simple DS chain (Silbert & Sugumaran 2002).
R-HSA-3299685 Detoxification of Reactive Oxygen Species Reactive oxygen species such as superoxide (O2.-), peroxides (ROOR), singlet oxygen, peroxynitrite (ONOO-), and hydroxyl radical (OH.) are generated by cellular processes such as respiration (reviewed in Murphy 2009, Brand 2010) and redox enzymes and are required for signaling yet they are damaging due to their high reactivity (reviewed in Imlay 2008, Buettner 2011, Kavdia 2011, Birben et al. 2012, Ray et al. 2012). Aerobic cells have defenses that detoxify reactive oxygen species by converting them to less reactive products. Superoxide dismutases convert superoxide to hydrogen peroxide and oxygen (reviewed in Fukai and Ushio-Fukai 2011). Catalase and peroxidases then convert hydrogen peroxide to water.
Humans contain 3 superoxide dismutases: SOD1 is located in the cytosol and mitochondrial intermembrane space, SOD2 is located in the mitochondrial matrix, and SOD3 is located in the extracellular region. Superoxide, a negative ion, is unable to easily cross membranes and tends to remain in the compartment where it was produced. Hydrogen peroxide, one of the products of superoxide dismutase, is able to diffuse across membranes and pass through aquaporin channels. In most cells the primary source of hydrogen peroxide is mitochondria and, once in the cytosol, hydrogen peroxide serves as a signaling molecule to regulate redox-sensitive proteins such as transcription factors, kinases, phosphatases, ion channels, and others (reviewed in Veal and Day 2011, Ray et al. 2012). Hydrogen peroxide is decomposed to water by catalase, decomposed to water plus oxidized thioredoxin by peroxiredoxins, and decomposed to water plus oxidized glutathione by glutathione peroxidases (Presnell et al. 2013).
R-HSA-5688426 Deubiquitination Ubiquitination, the modification of proteins by the covalent attachment of ubiquitin (Ub), is a key regulatory mechanism for many many cellular processes, including protein degradation by the 26S proteasome. Ub conjugates linked via lysine 48 (K48) target substrates to the proteasome, whereas those linked via any of the six other Ub lysines can alter the function of the modified protein without leading to degradation. Deubiquitination, the reversal of this modification, regulates the function of ubiquitin-conjugated proteins. Deubiquitinating enzymes (DUBs) catalyze the removal of Ub and regulate Ub-mediated pathways.
Given that Ub is covalently-linked to proteins destined to be degraded, it is a surprisingly long-lived protein in vivo (Haas & Bright 1987). This is due to the removal of Ub from its conjugates by DUBs prior to proteolysis. This may represent a quality control mechanism that prevents the degradation of proteins that were inappropriately tagged for degradation (Lam et al. 1997). DUBs are responsible for processing inactive Ub precursors and for keeping the 26S proteasome free of unanchored Ub chains that compete for Ub-binding sites.
DUBs can be grouped into five families based on their conserved catalytic domains (Amerik & Hochstrasser 2004). Four of these families are thiol proteases and comprise the bulk of DUBs, while the fifth family is a small group of Ub specific metalloproteases.
Thiol protease DUBs contain a Cys-His-Asp/Asn catalytic triad in which the Asp/Asn functions to polarize and orient the His, while the His serves as a general acid/base by both priming the catalytic Cys for nucleophilic attack on the (iso)peptide carbonyl carbon and by donating a proton to the lysine epsilon-amino leaving group. The nucleophilic attack of the catalytic Cys on the carbonyl carbon produces a negatively charged transition state that is stabilized by an oxyanion hole composed of hydrogen bond donors. A Cys-carbonyl acyl intermediate ensues and is then hydrolyzed by nucleophilic attack of a water molecule to liberate a protein C-terminal carboxylate and regenerate the enzyme. Ub binding often causes structural rearrangements necessary for catalysis. Many DUBs are inactivated by oxidation of the catalytic cysteine to sulphenic acid (single bond SOH) (Cotto-Rios et al. 2012, Lee et al. 2013). This can be reversed by reduction with DTT or glutathione. The sulphenic acid can be irreversibly oxidized to sulphinic acid (single bond SO2H) or sulphonic acid (single bond SO3H).
Thiol proteases are reversibly inhibited by Ub C-terminal aldehyde, forming a thio-hemiacetal between the aldehyde group and the active site thiol.
R-HSA-1266738 Developmental Biology Developmental biology seeks to understand the array of processes by which a fertilized egg gives rise to the diverse tissues of the adult body. Examples of several developmental processes have been annotated here. In the early embryo, transcriptional regulation of pluripotent stem cells, gastrulation (including NODAL signaling), and activation of HOX genes during differentiation are annotated. Annotations of later, more specialized processes include nervous system development, cardiogenesis, aspects of the roles of cell adhesion molecules in axonal guidance and myogenesis, transcriptional regulation in pancreatic beta cells, adipogenesis, transcriptional regulation of granulopoeisis, transcriptional regulation of testis differentiation, LGI-ADAM interactions, and keratinization.
Transitions between cell types and cell states in developmental and differentiation processes are annotated as developmental cell lineages.
R-HSA-9734767 Developmental Cell Lineages Our bodies are built of >30 trillion cells specialized to fulfill diverse roles within our tissues, organs, and organ systems. All these cells originate from a single cell, a zygote formed at conception. From zygote to fetus, and throughout childhood, adolescence, and adulthood, cells divide and commit to different fates in order for the organism to develop, sustain and regenerate. The series of steps that lead from an undifferentiated progenitor cell, such as a stem cell, to one of its several possible specialized descendants constitutes a cell lineage path (Burgess et al. 2018). Cell lineage paths are organized by organ systems. Each cell lineage path cross-references a Gene Ontology (GO) biological process (The Gene Ontology Consortium 2019), and consists of a series of causally connected cell development steps. Cell development steps describe the transition between cell states during development or differentiation and are characterized by regulators (molecules promoting or inhibiting the step) and, when established, “required input components” (cell state biomarkers required for the action of regulators). Each cell state is characterized by a cell type defined in Cell Ontology (Sarntivijai et al. 2014; Osumi-Sutherland 2017), anatomical location from UBERON (Haendel et al. 2014), and a unique combination of protein and/or RNA markers with references, when available, to CellMarker (Hu et al. 2023) and PanglaoDB (Franzen et al. 2019). For a more detailed data model description, please refer to Milacic et al. 2024. Recent technological advances have allowed researchers to harvest high-throughput omics data from single cells of multicellular organisms and use it to track and manipulate cell fates (Burgess 2018; Saelens et al. 2019). This opens the door to the possibility of deciphering cell lineage paths at single-cell resolution, a critical requirement for the advancement of regenerative medicine and cancer medicine.
The cell lineage path “Differentiation of keratinocytes in interfollicular epidermis in mammalian skin” describes the differentiation of keratinocytes from stem cells to corneocytes in the interfollicular epidermis, the skin surface layer in between the adnexa (hair follicles, sweat glands, and sebaceous glands).
R-HSA-9725554 Differentiation of keratinocytes in interfollicular epidermis in mammalian skin The interfollicular epidermis is the skin surface layer in between the adnexa (hair follicles, sweat glands, and sebaceous glands). Going from the dermal epidermal junction, the interfollicular epidermis strata include the basal layer (stratum basale), spinous layer (stratum spinosum), granular layer (stratum granulosum), and the cornified layer (stratum corneum). The basal layer consists of keratinocyte stem cells and transit amplifying cells. The spinous, granular, and cornified layers consist of spinous keratinocytes, granular keratinocytes, and corneocytes, respectively. Interfollicular epidermis has a high cell turnover rate. Keratinocyte stem cells self renew throughout adulthood and give rise to transit amplifying cells. Transit amplifying cells undergo several cell cycles before committing to differentiation, first into spinous layer keratinocytes, then into granular layer keratinocytes, and finally into corneocytes. Corneocytes lose their nuclei and cytoplasmic organelles, forming flattened squames that provide a physical barrier against the invasion of pathogens and loss of bodily fluids. For a detailed review, please refer to Zijl et al. 2022, and for the single cell transcriptomic and spatial transcriptomic studies that provide a higher resolution view of human interfollicular epidermis, please refer to Cheng et al. 2018, Wang et al. 2020, Aragona et al. 2020, Haensel et al. 2020, Negri et al. 2023, and Ganier et al. 2024).
The cell lineage path of keratinocytes in interfollicular epidermis is depicted through four cell differentiation steps involving five distinct cellular states: keratinocyte stem cells of epidermal basal layer, transit amplifying cells, spinous keratinocytes, granular keratinocytes, and corneocytes. Each differentiation step is regulated by a distinct combination of regulatory molecules present in the microenvironment of differentiating cells.
R-HSA-8935690 Digestion Dietary carbohydrates, fats, and proteins must be broken down to their constituent monosaccharides, fatty acids and sterols, and amino acids, respectively, before they can be absorbed in the intestine.
Dietary lipids such as long-chain triacylglycerols and cholesterol esters are hydrolyzed in the stomach and small intestine to yield long-chain fatty acids, monoacylglycerols, glycerol and cholesterol through the action of a variety of lipases, and are then absorbed into enterocytes.
Carbohydrates include starch (amylose and amylopectin) and disaccharides such as sucrose, lactose, maltose and, in small amounts, trehalose. The digestion of starch begins with the action of amylase enzymes secreted in the saliva and small intestine, which convert it to maltotriose, maltose, limit dextrins, and some glucose. Digestion of the limit dextrins and disaccharides, both dietary and starch-derived, to monosaccharides - glucose, galactose, and fructose - is accomplished by enzymes located on the luminal surfaces of enterocytes lining the microvilli of the small intestine.
Dietary protein is hydrolyzed to dipeptides and amino acids by the action of pepsin in the stomach and an array of intestinal hydrolases. All of these enzymes are released in inactive (proenzyme) forms and activated by proteolytic cleavage within the gastrointestinal lumen (Van Beers et al. 1995; Yamada 2015).
R-HSA-8963743 Digestion and absorption Fats, carbohydrates, and proteins are broken down to small molecules - fatty acids, cholesterol, and glycerol, monosaccharides, and amino acids - within the lumen of the gastrointestinal tract and absorbed into the body principally through enterocytes in the small intestine. Some of the hydrolases that catalyze these reactions are secreted into the gastrointestinal tract; others are associated with the luminal surfaces of enterocytes. Movement of the final products of digestion out of the intestinal lumen is mediated by arrays of transporters associated with the lumenal and basolateral surfaces of enterocytes (Yamada 2015).
R-HSA-189085 Digestion of dietary carbohydrate Carbohydrate is a major component of the human diet, and includes starch (amylose and amylopectin) and disaccharides such as sucrose, lactose, maltose and, in small amounts, trehalose. The digestion of starch begins with the action of amylase enzymes secreted in the saliva and small intestine, which convert it to maltotriose, maltose, limit dextrins, and some glucose. Digestion of the limit dextrins and disaccharides, both dietary and starch-derived, to monosaccharides - glucose, galactose, and fructose - is accomplished by enzymes located on the luminal surfaces of enterocytes lining the microvilli of the small intestine (Van Beers et al. 1995).
R-HSA-192456 Digestion of dietary lipid Dietary lipids such as long-chain triacylglycerols and cholesterol esters are digested in the stomach and small intestine to yield long-chain fatty acids, monoacylglycerols, glycerol and cholesterol through the action of a variety of lipases, and are then absorbed into enterocytes.
R-HSA-69416 Dimerization of procaspase-8 Procaspase-8 monomers undergo dimerization. The dimerization event occurs at death-inducing signaling complex (DISC) and results in a reposition of the procaspase-8 inter-subunit linker to become accessible for intermolecular processing by the associated procaspase-8 molecule [Keller N et al 2010; Oberst A et al 2010].
R-HSA-4641262 Disassembly of the destruction complex and recruitment of AXIN to the membrane Upon stimulation with WNT ligand, AXIN and GSK3beta are recruited to the plasma membrane through interaction with DVL (Tamai et al, 2004; Mao et al, 2001; reviewed in He et al, 2004). Polymerization of membrane-associated DVL and GSK3beta- and CSNK1-mediated phosphorylation of LRP5/6 establish a feed-forward mechanism for enhanced membrane recruitment of AXIN upon WNT signaling (Tamai et al, 2004; Cong et al, 2004; Zeng et al, 2005; Bilic et al, 2007). In Xenopus oocytes, but not necessarily all sytems, AXIN is present in limiting concentrations and is considered rate limiting for the assembly of the destruction complex (Lee et al, 2003; Benchabane et al, 2008; Tan et al, 2012; reviewed in MacDonald et al, 2009). The recruitment of AXIN away from the destruction complex upon WNT stimulation effectively destabilizes the destruction complex and contributes to the accumulation of free beta-catenin (Kikuchi, 1999; Lee et al, 2003). AXIN association with the destruction complex is also regulated by phosphorylation. In the active destruction complex, AXIN is phosphorylated by GSK3beta; dephosphorylation by protein phosphatase 1 (PP1) or protein phosphatase 2A (PP2A) destabilizes the interaction of AXIN with the other components of the destruction complex and promotes its disassembly (Luo et al, 2007; Willert et al, 1999; Jho et al, 1999). Free AXIN is also subject to degradation by the 26S proteasome in a manner that depends on the poly-ADP-ribosylating enzymes tankyrase 1 and 2 (Huang et al, 2009).
R-HSA-1643685 Disease Biological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular viewpoint, human disease pathways have three mechanistic causes: the inclusion of microbially-expressed proteins, altered functions of human proteins, or changed expression levels of otherwise functionally normal human proteins.
The first group encompasses the infectious diseases such as influenza, tuberculosis and HIV infection. The second group involves human proteins modified either by a mutation or by an abnormal post-translational event that produces an aberrant protein with a novel function. Examples include somatic mutations of EGFR and FGFR (epidermal and fibroblast growth factor receptor) genes, which encode constitutively active receptors that signal even in the absence of their ligands, or the somatic mutation of IDH1 (isocitrate dehydrogenase 1) that leads to an enzyme active on 2-oxoglutarate rather than isocitrate, or the abnormal protein aggregations of amyloidosis which lead to diseases such as Alzheimer's.
Infectious diseases are represented in Reactome as microbial-human protein interactions and the consequent events. The existence of variant proteins and their association with disease-specific biological processes is represented by inclusion of the modified protein in a new or variant reaction, an extension to the 'normal' pathway. Diseases which result from proteins performing their normal functions but at abnormal rates can also be captured, though less directly. Many mutant alleles encode proteins that retain their normal functions but have abnormal stabilities or catalytic efficiencies, leading to normal reactions that proceed to abnormal extents. The phenotypes of such diseases can be revealed when pathway annotations are combined with expression or rate data from other sources.
Depending on the biological pathway/process immediately affected by disease-causing gene variants, non-infectious diseases in Reactome are organized into diseases of signal transduction by growth factore receptors and second messengers, diseases of mitotic cell cycle, diseases of cellular response to stress, diseases of programmed cell death, diseases of DNA repair, disorders of transmembrane transporters, diseases of metabolism, diseases of immune system, diseases of neuronal system, disorders of developmental biology, disorders of extracellular matrix organization, and diseases of hemostatis.
R-HSA-3781860 Diseases associated with N-glycosylation of proteins Congenital disorders of glycosylation (CDGs) are a group of autosomal recessive disorders caused by enzymatic defects in the synthesis and processing of asparagine (N)-linked glycans or oligosaccharides on glycoproteins. These glycoconjugates play critical roles in processes such as metabolism, cell recognition and adhesion, cell migration, protease resistance, host defense, and antigenicity. CDGs are divided into 2 main groups: type I CDGs comprise defects in the assembly of the dolichol lipid-linked oligosaccharide (LLO) chain and its transfer to the nascent protein, whereas type II CDGs comprise defects in the trimming and processing of protein-bound glycans (Marquardt & Denecke 2003, Grunewald et al. 2002, Hennet 2012, Cylwik et al. 2013).
R-HSA-3906995 Diseases associated with O-glycosylation of proteins Glycosylation is the most abundant modification of proteins, variations of which occur in all living cells. Glycosylation can be further categorized into N-linked (where the oligosaccharide is conjugated to Asparagine residues) and O-linked glycosylation (where the oligosaccharide is conjugated to Serine, Threonine and possibly Tyrosine residues). Within the family of O-linked glycosylation, the oligosaccharides attached can be further categorized according to their reducing end residue: GalNAc (often described as mucin-type, due to the abundance of this type of glycosylation on mucins), Mannose and Fucose. This section reviews currently known congenital disorders of glycosylation associated with defects of protein O-glycosylation (Cylwik et al. 2013, Freeze et al. 2014).
R-HSA-3560782 Diseases associated with glycosaminoglycan metabolism A number of genetic disorders are caused by mutations in the genes encoding glycosyltransferases and sulfotransferases, enzymes responsible for the synthesis of glycosaminoglycans (GAGs) as well as hexosaminidase degradation of GAGs (Mizumoto et al. 2013).
R-HSA-5609975 Diseases associated with glycosylation precursor biosynthesis Glycosylation diseases associated with the enzymes that mediate the biosynthesis of glycosylation precursors are curated in this section (Jaeken & Matthijs 2007, Freeze et al. 2015).
R-HSA-5687613 Diseases associated with surfactant metabolism The reactions annotated here describe genetic defects in genes regulating surfactant homeostasis which are associated with severe acute and chronic lung diseases in newborns and older infants (Whitsett et al. 2015).
R-HSA-5602358 Diseases associated with the TLR signaling cascade Toll like receptors (TLRs) are sensors of the innate immune system that detect danger signals derived from pathogens (pathogen-associated molecular patterns - PAMP) or damaged cells (damage-associated molecular patterns - DAMP) (Pasare C and Medzhitov R 2005; Barton GM and Kagan JC 2009; Kawai T and Akira S 2010). Signaling by these sensors promotes the activation and nuclear translocation of transcription factors (IRFs, NFkB and AP1). The transcription factors induce secretion of inflammatory cytokines such as IL-6, TNF and pro-IL1beta that direct the adaptive immune response. Inherited or acquired abnormalities in TLR-mediated processes may lead to increased susceptibility to infection, excessive inflammation, autoimmunity and malignancy (Picard C et al. 2010; Netea MG et al. 2012; Varettoni M et al. 2013). Here we describe four primary immunodeficiency (PID) disorders associated with defective TLR-mediated responses. First, MyD88 or IRAK4 deficiency is characterized with a greater susceptibility to pyogenic bacteria in affected patients (Picard C et al. 2003; von Bernuth H et al. 2008). Second, defects in the TLR3 signaling pathway are associated with a greater susceptibility to herpes simplex virus encephalitis (Zhang SY et al. 2013). Third, imunodeficiencies due to defects in NFkB signaling components are linked to impaired TLR-mediated responses (Courtois G et al. 2003; Fusco F et al. 2004). Finally, events are annotated showing constitutive activation of a somatically mutated MyD88 gene which results in malignancy (Varettoni M et al. 2013).
R-HSA-2474795 Diseases associated with visual transduction The process of vision involves two stages; the retinoid cycle which supplies and regenerates the visual chromophore required for vision and phototransduction which propagates the light signal. Defects in the genes involved in the retinoid cycle cause degenerative retinal diseases. These defective genes are described here (for reviews see Travis et al. 2007, Palczewski 2010, Fletcher et al. 2011, den Hollander et al. 2008).
R-HSA-9605308 Diseases of Base Excision Repair Germline mutations, single nucleotide polymorphisms (SNPs) and somatic mutations in several genes involved in base excision repair (BER), a DNA repair pathway where a damaged DNA base is excised and replaced with a correct base, are involved in the development of cancer and several other oxidative stress-related diseases. For review, please refer to Fu et al. 2012, Fletcher and Houlston 2010, Brenerman et al. 2014, Patrono et al. 2014, and D'Errico et al. 2017.
R-HSA-9630747 Diseases of Cellular Senescence Cellular senescence plays an important role in normal aging, as well as in age-related diseases. Impaired cellular senescence contributes to malignant transformation and cancer development. Presence of an excessive number of senescent cells that are not cleared by the immune system, however, promotes tissue inflammation and creates a microenvironment suitable for growth of neighboring malignant cells. Besides cancer, senescence is also involved in atherosclerosis, osteoarthritis and diabetes (Childs et al. 2015, He and Sharpless 2017).
Evasion of oncogene-induced senescence, at least in cell culture, can occur due to loss-of-function (LOF) mutation in the CDKN2A gene product p16INK4A that acts as a cyclin-dependent kinase inhibitor (reviewed in Sharpless and Sherr 2015). LOF mutations in the CDKN2A gene that affect its other protein product, p14ARF, involved in stabilization of TP53 protein (p53), can contribute to evasion of oncogene-induced senescence (reviewed in Fontana et al. 2019).
LOF mutations in p16INK4A and p14ARF also contribute to evasion of oxidative stress-induced senescence (reviewed in Sharpless and Sherr 2015, and Fontana et al. 2019, respectively).
R-HSA-9675136 Diseases of DNA Double-Strand Break Repair Diseases of DNA double-strand break repair (DSBR) are caused by mutations in genes involved in repair of double strand breaks (DSBs), one of the most cytotoxic types of DNA damage. Unrepaired DSBs can lead to cell death, cellular senescence, or malignant transformation.
Germline mutations in DSBR genes are responsible for several developmental disorders associated with increased predisposition to cancer:
Ataxia telangiectasia, characterized by cerebellar neurodegeneration, hematologic malignancies and immunodeficiency, is usually caused by germline mutations in the ATM gene;
Nijmegen breakage syndrome 1, characterized by microcephaly, short stature and recurrent infections, is caused by germline mutations in the NBN (NBS1) gene;
Seckel syndrome, characterized by short stature, skeletal deformities and microcephaly, is caused by germline mutations in the ATR or RBBP8 (CtIP) genes.
Heterozygous germline mutations in BRCA1, BRCA2 or PALB2 cause the hereditary breast and ovarian cancer syndrome (HBOC), while homozygous germline mutations in BRCA2 and PALB2 cause Fanconi anemia, a developmental disorder characterized by short stature, microcephaly, skeletal defects, bone marrow failure, and predisposition to cancer.
Somatic mutations in DSBR genes are also frequently found in sporadic cancers.
The pathways "Defective DNA double strand break response due to BRCA1 loss of function" describes defects in DSB response caused by loss-of-function mutations in BRCA1 which prevent the formation of the BRCA1:BARD1 complex.
The pathway "Defective DNA double strand break response due to BARD1 loss of function" describes defects in DSB response caused by loss-of-function mutations in BARD1, the heterodimerization partner of BRCA1, which prevent the formation of the BRCA1:BARD1 complex.
The pathway "Defective homologous recombination repair (HRR) due to BRCA1 loss of function" describes defects in HRR caused by loss-of-function mutations in BRCA1 that impair its association with PALB2.
The pathway "Defective homologous recombination repair (HRR) due to BRCA2 loss of function" describes defects in HRR caused by loss-of-function mutations in BRCA2 that impair either it association with SEM1 (DSS1), its translocation to the nucleus, its binding to RAD51, or its binding to PALB2.
The pathway "Defective homologous recombination repair (HRR) due to PALB2 loss of function" describes defects in HRR caused by loss-of-function mutations in PALB2 that impair its association with BRCA2/RAD51/RAD51C.
For review, please refer to McKinnon and Caldecott 2007, Keijzers et al. 2017, and Jachimowicz et al. 2019.
R-HSA-9675135 Diseases of DNA repair Germline and somatic defects in genes that encode proteins that participate in DNA repair give rise to genetic instability that can lead to malignant transformation or trigger cellular senescence or apoptosis. Germline defects in DNA repair genes are an underlying cause of familial cancer syndromes and premature ageing syndromes. Somatic defects in DNA repair genes are frequently found in tumors. For review, please refer to Tiwari and Wilson 2019.
We have so far annotated diseases of mismatch repair, diseases of base excision repair and diseases of DNA double-strand break repair.
Defects in mammalian DNA mismatch repair (MMR) genes (MLH1, PMS2, MSH2, and MSH6) result in microsatellite instability (MSI) and reduced fidelity during replication and repair steps. Defective variants of MMR genes are associated with sporadic cancers with hypermutation phenotypes as well as hereditary cancer syndromes such as Lynch syndrome (hereditary non-polyposis colorectal cancer) and constitutional mismatch repair deficiency syndrome (CMMRD). MSI is an important predictor of sensitivity to cancer immunotherapy as the high mutational burden renders MSI tumors immunogenic and sensitive to programmed cell death-1 (PD-1) immune checkpoint inhibitors (Mandal et al. 2019). For review, please refer to Pena-Diaz and Rasmussen 2016, Sijmons and Hofstra 2016, Tabori et al. 2017, Baretti and Le 2018.
Germline mutations, single nucleotide polymorphisms (SNPs) and somatic mutations in several genes involved in base excision repair (BER), a DNA repair pathway where a damaged DNA base is excised and replaced with a correct base, are involved in the development of cancer and several oxidative stress-related diseases. For review, please refer to Fu et al. 2012, Fletcher and Houlston 2010, Brenerman et al. 2014, Patrono et al. 2014, and D'Errico et al. 2017.
Germline mutations in genes involved in repair of DNA double-strand breaks (DSBs) are the underlying cause of several cancer predisposition syndromes, some of which also encompass developmental disorders associated with immune dysfunction, radiosensitivity and neurodegeneration. Somatic mutations in genes involved in DSB repair also occur in sporadic cancers. For review, please refer to McKinnon and Caldecott 2007, Keijzers et al. 2017, and Jachimowicz et al. 2019.
R-HSA-5260271 Diseases of Immune System The immune system is a complex network of the biological processes that provide defense mechanisms during infection or in response to an intrinsic danger signal. Compromised immune response may present itself as either overactivity or underactivity of the immune system leading to a broad spectrum of clinical phenotypes that can be categorized into four main groups - autoimmunity, immunodeficiency (ID) with a greater susceptibility to infectious diseases, hypersensitivity to compounds that are usually not harmful and malignancy. Several host conditions may cause the dysfunctional immunity. Among them are inherited and somatic mutations found in the components of immune signaling pathways. In addition to genetic defects, infection with pathogen such as human immunodeficiency virus (HIV), or interaction of immune cells with immunosuppressive drugs result in non-genetic immunodeficiencies. Age-associated alterations in immunity may also contribute to pathogenesis of immunodeficiency .
The Reactome module represents selected defects of the immune system and provides a short description of their clinical phenotypes. The module also describes functional features of defective molecules by both providing a published source for experimental functional analysis data and linking to the corresponding normal process within the Reactome database.
R-HSA-5423599 Diseases of Mismatch Repair (MMR) Defects in mammalian DNA mismatch repair (MMR) genes (MLH1, PMS2, MSH2, and MSH6) are characterized by microsatellite instability and reduced fidelity during replication and repair steps. The MMR proteins interact with each other to execute steps within the mismatch repair pathway. Defective variants of these proteins are associated with nonpolyposis colorectal cancer. The MutS proteins are thought to directly contact double-stranded DNA, scanning along the genomic DNA for mismatches analogous to a "sliding clamp" until they encounter a base pair containing a mismatch. The MutS proteins interact with multiple proteins including other MLH and MutL, the later have significant amino acid identify and structural similarity to the MLH proteins, as well as RPA, EXO1, RFC, possibly HMGB1, and other less well-characterized proteins.
With respect to the mutator function, the MSH2/MutSaplha heterodimer is thought primarily to repair single-base substitutions and 1 bp insertiondeletion mutations, while MSH2/MutSbeta is thought primarily to repair 1-4 bp insertiondeletion mutations. The MLH and MutL heterodimer proteins interact with heterodimers of MutS proteins to help catalyze different functions. MLH1:MutLalpha is the primary complex that interacts with both MutS alpha and beta complex in mechanisms thought to be relevant to cancer prevention. Recent studies suggest that MLH1:MLH3 may also contributes to some of these processes as well, but in all mechanisms tested to a lesser degree than MLH1:PMS2.
Heterozygous mutations in the MLH1 gene result in hereditary nonpolyposis colorectal cancer-2 (Papadopoulos et al., 1994).
Variants of the MSH2 gene are associated with hereditary nonpolyposis colorectal cancer. Alteration of MSH2 is also involved in Muir-Torre syndrome and mismatch repair cancer syndrome (Fishel et al. 1993).
Defects in the MSH3 gene are a cause of susceptibility to endometrial cancer (Risinger et al. 1996).
Defects in the MSH6 gene are less common than MLH1 and MSH2 defects. They have been mostly observed in atypical HNPCC families and are characterized by a weaker family history of tumor development, higher age at disease onset, and low degrees of microsatellite instability (MSI) (Lucci-Cordisco et al. 2001).
Mutations in the PMS2 gene are associated with hereditary nonpolyposis colorectal cancer, Turcot syndrome, and are a cause of supratentorial primitive neuroectodermal tumors. Heterozygous truncating mutations in PMS2 play a role in a small subset of hereditary nonpolyposis colorectal carcinoma (Lynch syndrome, HNPCC-like) families. PMS2 mutations lead to microsatellite instability with carriers showing a microsatellite instability high phenotype and loss of PMS2 protein expression in all tumors (Hamilton et al. 1995, Hendriks et al. 2006).
R-HSA-9673013 Diseases of Telomere Maintenance Somatic mutations or rearrangements in genes involved in telomere maintenance enable immortalization of cancer cells either through upregulation of telomerase activity or through activation of alternative lengthening of telomeres (ALT) (Killela et al. 2013, reviewed by Gocha et al. 2013, Pickett and Reddel 2015, Amorim et al. 2016, Yuan et al. 2019). Germline mutations in telomere maintenance genes lead to telomere syndromes, such as dyskeratosis congenita (DC) and Hoyeraal-Hreidarsson (HH) syndrome, characterized by impaired ability to maintain telomere lengths during growth and development, leading to abnormally short telomere lengths and genomic instability that affects multiple organs and is associated with increased risk of certain cancers (reviewed by Sarek et al. 2015).
R-HSA-9865118 Diseases of branched-chain amino acid catabolism Mutations in the genes that encode enzymes responsible for the catabolism of the branched-chain amino acids leucine, isoleucine and valine give rise to a number of inborn errors of metabolism (IEMs). Although IEMs are individually rare, collectively they are relatively common with an estimated overall prevalence of ~1:800 live births (Mak et al, 2013). The frequency of particular IEMs is also highly variable across different populations, a result in part of founder effects in closed populations. For instance, although the overall frequency of Maple Syrup Urine disease is 1:185,000 live births (Strauss et al, 2020), the frequency rises to 1:380 in some Old Order Mennonite communities (Fisher et al, 1991).
Accumulation of toxic intermediary metabolites causes a range of clinical phenotypes in patients with IEMs including metabolic acidosis, vomiting, seizures, psychomotor and developmental delays and death (reviewed in Schrier Vergano et al, 2022; Holoček, 2018; Neinast et al, 2019).
R-HSA-5663084 Diseases of carbohydrate metabolism The processes by which dietary carbohydrate is digested to monosaccharides and these are taken up from the gut lumen into cells where they are oxidized to yield energy or consumed in biosynthetic processes are a central part of human metabolism and defects in them can lead to serious disease. Defects annotated here affect saccharide digestion in the gut lumen, fructose metabolism, and the pentose phosphate pathway. In addition, the defect in glucuronate catabolism that leads to essential pentosuria, a benign phenotype that is one of Garrod's original four inborn errors of metabolism, is annotated.
R-HSA-9675132 Diseases of cellular response to stress Cells are subject to external and internal stressors, such as foreign molecules that perturb metabolic or signaling processes, cellular respiration-generated reactive oxygen species that can cause DNA damage, oxygen and nutrient deprivation, and changes in temperature or pH. The ability of cells and tissues to respond to stress is essential to the maintenance of tissue homeostasis (Kultz 2005) and dysregulation of cellular response to stress is involved in disease.
So far, we have captured diseases of cellular senescence.
Impaired cellular senescence contributes to malignant transformation and cancer development by enabling continuous proliferation of damaged cells. On the other hand, presence of an excessive number of senescent cells that are not cleared by the immune system promotes tissue inflammation and creates a microenvironment suitable for growth of neighboring malignant cells. In addition to cancer, senescence is also involved in other age-related diseases such as atherosclerosis, osteoarthritis, chronic obstructive lung disease, and diabetes (Childs et al. 2015, He and Sharpless 2017, Hamsanathan et al. 2019, Faget et al. 2019, Gorgoulis et al. 2019, Rhinn et al. 2019). Senotherapy is a new field of pharmacology that aims to therapeutically target senescence to improve healthy aging and age-related diseases (Schmitt 2017, Gorgoulis et al. 2019).
R-HSA-3781865 Diseases of glycosylation Diseases of glycosylation, usually referred to as congenital disorders of glycosylation (CDG), are rare inherited disorders ascribing defects of nucleotide-sugar biosynthesis and transport, glycosyl transfer events and vesicular transport. Most CDGs cause neurological impairment ranging from severe psychomotor retardation to mild intellectual disability. Defects in N-glycosylation are the main cause of CDGs (Marquardt & Denecke 2003, Grunewald et al. 2002, Hennet 2012, Goreta et al. 2012) and can be identified by a characteristic abnormal isoelectric focusing profile of plasma transferrin (Jaeken et al. 1984, Stibler & Jaeken 1990). Disorders of O-glycosylation, glycosaminoglycan and glycolipid metabolism have recently been discovered and, together with N-glycosylation, represent the major pathways affected by glycan biosynthetic disorders (Freeze 2006, Jaeken 2011). In addition, glycosylation diseases associated with the enzymes that mediate the biosynthesis of glycosylation precursors are described in this section. As the number of these disorders has increased, nomenclature has been simplified so that now, the name of the mutant gene is followed by the abbreviation CDG (Jaeken et al. 2009). Effective therapies for most types of CDGs are so far not available (Thiel & Korner 2013).
R-HSA-9671793 Diseases of hemostasis Hemostasis is a complex process that leads to the formation of a blood clot at the site of vessel injury. Three phases can be distinguished: primary hemostasis or formation of a platelet plug, secondary hemostasis, or coagulation and fibrinolysis (Kriz N et al. 2009). Defects in hemostasis cause an imbalance between the coagulation and fibrinolytic systems and may lead either to hypercoagulation, which can result in thrombosis, or to hypocoagulation and increased susceptibility to bleeding (also known as hemorrhagic diathesis) (van Herrewegen F et al. 2012a,b; Kumar R & Carcao M 2013). Abnormalities can result from disorders of the platelets (primary hemostasis defect), coagulation factors defects (secondary hemostasis defect), or a combination of both (van Herrewegen F et al. 2012a,b; Kumar R & Carcao M 2013). Coagulation disorders may be inherited or acquired. Further, abnormalities of the coagulation and fibrinolytic systems are coupled to the inflammatory response, which aggravates blood vessel permeability, inflammation, and cell damage in tissues (Sandra Margetic 2012; Kaplan AP & Joseph K 2016).
This Reactome module describes abnormalities of the coagulation cascade (secondary hemostasis) due to defects of coagulation factor proteins such as factor VIII (FVIII), FIX or FXII. The module also describes an abnormal FXII- mediated activation of the pro-inflammatory kallikrein‐kinin system (KKS) that leads to an excessive formation of bradykinin causing increased vascular permeability at the level of the post capillary venule and results in hereditary angioedema (HAE).
R-HSA-5668914 Diseases of metabolism Metabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as the inactivation and elimination of toxic ones generated endogenously or present in the extracellular environment. Mutations that disrupt these processes by inactivating a required enzyme or regulatory protein, or more rarely by changing its specificity can lead to severe diseases. Metabolic diseases annotated here involve aspects of carbohydrate, glycosylation, amino acid (phenylketonuria), surfactant and vitamin metabolism, and biological oxidations. One somatic mutation that affects cytosolic isocitrate metabolism, often found in glioblastomas and some lymphoid neoplasms, is also annotated. Also described are mutated forms of adrenocorticotropic hormone (ACTH) that can lead to obesity, resulting in excessive accumulation of body fat.
R-HSA-9759774 Diseases of mitochondrial beta oxidation Of the array of known defects of mitochondrial lipid metabolism, one is annotated in Reactome, methylmalonic acidurioa due to deficiencies of the MMUT (Methylmalonyl-CoA mutase, mitochondrial) enzyme (Worgan et al. 2006)
R-HSA-9675126 Diseases of mitotic cell cycle Diseases of mitotic cell cycle are caused by mutations in cell cycle regulators (Collins and Garrett 2005, Diaz-Moralli et al. 2013), such as retinoblastoma protein RB1 (Classon and Harlow 2002), as well as proteins involved in telomere maintenance, such as ATRX and DAXX (Sarek et al. 2015). These diseases mainly include different types of cancer, hereditary syndromes such as dyskeratosis congenita that may predispose affected patients to cancer, and neurodegenerative diseases (Webber et al. 2005).
R-HSA-9735804 Diseases of nucleotide metabolism Metabolic reactions disrupted by deficiencies of ADA, APRT, HPRT1, and PNP are annotated here.
R-HSA-9645723 Diseases of programmed cell death Programmed cell death is frequently impaired in cancer and is thought to significantly contribute to resistance to chemotherapy. Mutations and perturbations in expression of different proteins involved in programmed cell death, such as TP53 (p53), BH3-only family proteins, caspases and their regulators enable malignant cells to evade apoptosis (Ghavami et al. 2009, Chao et al. 2011, Wong 2011, Fernald and Kurokawa 2013, Ichim and Tait 2016).
R-HSA-9759785 Diseases of propionyl-CoA catabolism Propionyl-CoA catabolism is the aspect of mitochondrial beta-oxidation affected by the one disease of this process annotated in Reactome.
R-HSA-5663202 Diseases of signal transduction by growth factor receptors and second messengers Signaling processes are central to human physiology (e.g., Pires-da Silva & Sommer 2003), and their disruption by either germ-line and somatic mutation can lead to serious disease. Here, the molecular consequences of mutations affecting visual signal transduction and signaling by diverse growth factors are annotated.
R-HSA-9675143 Diseases of the neuronal system Diseases of the neuronal system can affect sensory cells and transmission of signals between sensory cells and sensory neurons (Martemyanov and Sampath 2017), transmission of signals across electrical and chemical synapses in the nervous system (Picconi et al. 2012, Yin et al. 2012, Kida and Kato 2015), and transmission of signals between motor neurons and muscle cells (Sine 2012, Engel et al. 2015).
We have so far annotated diseases of visual phototransduction due to retinal degeneration caused by defects in the genes involved in the retinoid cycle (Travis et al. 2007, Palczewski 2010, Fletcher et al. 2011, den Hollander et al. 2008).
R-HSA-114516 Disinhibition of SNARE formation The SNARE (SNAp REceptor) family of proteins are critical components of the machinery required for membrane fusion (Söllner et al. 1993, Wu et al. 2017). SNAREs can be grouped into three broad subfamilies: synaptosomal-associated proteins (SNAPs), vesicle-associated membrane proteins (VAMPs) and syntaxins. SNAPs contain two SNARE motifs and lack transmembrane domains, instead they are anchored to the membrane by thioester-linked acyl groups (Hong 2005). VAMPS or R-SNAREs have two subfamilies: short VAMPs or brevins and long VAMPs or longins. Syntaxins are evolutionarily less-well conserved, but except STX11 are transmembrane proteins (Hong 2005). Several SNARE proteins including Syntaxin-2 (STX2), STX4, STX11 and Vesicle-associated membrane protein 8 (VAMP8) are thought to be involved in platelet granule secretion (Golebiewska et al. 2013).
R-HSA-9675151 Disorders of Developmental Biology Developmental disorders affect formation of body organs and organ systems. The causes of defects in human development are diverse and incompletely understood, and include environmental insults such as nutrient deficiency, exposure to toxins and infections (Gilbert 2000, National Research Council (US) Committee on Developmental Toxicology 2000, Taylor and Rogers 2005, Zilbauer et al. 2016, Izvolskaia et al. 2018), as well as genetic causes such as aneuploidy and other chromosomal abnormalities, and germline mutations in genes that regulate normal development. It is estimated that about 40% of human developmental disabilities can be attributed to genetic aberrations (Sun et al. 2015), of which at least 25% are due to mutations affecting single genes (Chong et al. 2015), and this latter group of Mendelian developmental disorders is the focus of curation in Reactome.
Disorders of nervous system development affect the function of the central nervous system (CNS) and impair motor skills, cognition, communication and/or behavior (reviewed by Ismail and Shapiro 2019). So far,we have annotated the role of loss-of-function mutations in methyl-CpG-binding protein 2 (MECP2), an epigenetic regulator of transcription, in Rett syndrome, a pervasive developmental disorder (Pickett and London 2005, Ferreri 2014).
Disorders of myogenesis are rare hereditary muscle diseases that in the case of congenital myopathies are defined by architectural abnormalities in the muscle fibres (Pelin and Wallgren-Pettersson 2019, Phadke 2019, Radke et al. 2019, Claeys 2020) and in the case of muscular dystrophies by increased muscle breakdown that progresses with age (Pasrija and Tadi 2020). Mutations in cadherin family genes are present in some types of muscular dystrophy (Puppo et al. 2015).
Disorders of pancreas development result in pancreatic agenesis, where a critical mass of pancreatic tissue is congenitally absent. For example, the PDX1 gene is a master regulator of beta cell differentiation and homozygous deletions or inactivating mutations in PDX1 gene cause whole pancreas agenesis. PDX1 gene haploinsufficiency impairs glucose tolerance and leads to development of diabetes mellitus (Hui and Perfetti 2002, Babu et al. 2007, Chen et al. 2008).
Left-right asymmetry disorders are caused by mutations in genes that regulate the characteristic asymmetry of internal organs in vertebrates. Normally, cardiac apex, stomach and spleen are positioned towards the left side, while the liver and gallbladder are on the right. Loss-of-function mutations in the CFC1 gene, whose protein product functions as a co-factor in Nodal signaling, result in heterotaxic phenotype in affected patients, manifested by randomized organ positioning (Bamford et al. 2000).
Congenital lipodystrophies are characterized by a lack of adipose tissue, which predisposes affected patient to development of insulin resistance and related metabolic disorders. The severity of metabolic complications is correlates with the extent of adipose tissue loss. Loss-of-function mutations in the PPARG gene, encoding a key transcriptional regulator of adipocyte development and function, are a well-established cause of familial partial lipodystrophy type 3 (FPLD3) (Broekema et al. 2019).
Congenital stem cell disorders are caused by mutations in genes that regulate the balance between stem cells maintenance and commitment to differentiated lineages. Loss-of-function mutations in the SOX2 gene, which encodes a transcription factor involved in the maintenance of totipotency during embryonic preimplantation period, pluripotency of embryonic stem cells, and multipotency of neural stem cells, are the cause of anophthalmia (the absence of an eye) and microphthalmia (the presence of a small eye within the orbit (Verma and Fitzpatrick 2007, Sarlak and Vincent 2016).
HOX-related structural birth defects are caused by loss-of-function mutations in HOX family genes.HOX transcription factors play a fundamental role in body patterning during embryonic development, and HOX mutation are an underlying cause of many congenital limb malformations (Goodman 2002).
Congenital keratinization disorders are caused by dominant negative mutation in keratin genes and depending on where the affected keratin gene is expressed, they affect epithelial tissues such as skin, cornea, hair and/or nails (McLean and Moore 2011).
Disorders of immune system development are caused by mutations in genes that regulate differentiation of blood cell lineages involved in immune defense, leading to immune system defects. For example, mutations in the gene encoding CSF3R, a receptor for the granulocyte-colony stimulating factor, result in congenital neutropenia, characterized by a maturation arrest of granulopoiesis at the level of promyelocytes. Patients with severe congenital neutropenia are prone to recurrent, often life-threatening infections from an early age and may be predisposed to myelodysplastic syndromes or acute myeloid leukemia (Germeshausen et al. 2008; Skokowa et al. 2017).
R-HSA-9697154 Disorders of Nervous System Development Neurodevelopmental disorders are chronic disorders that affect the function of the central nervous system (CNS) and impair motor skills, cognition, communication and/or behavior. While these disorders frequently stem from mutations in genes that directly control CNS development, they can also be a consequence of environmental insults such as hypoxic/ischemic injury, trauma, exposure to toxins, infections and nutritional deficiencies, or be indirectly caused by mutations in metabolic genes (reviewed by Ismail and Shapiro 2019). Disorders of nervous system development have been traditionally classified based on phenotypic traits (clinical presentation). Molecular genetics studies have revealed, however, that indistinguishable clinical presentations may result from pathogenic variants in different genes whose protein products function in connected biological pathways. On the other hand, distinct clinical presentations may be caused by pathogenic mutations in a single gene that functions in multiple biological pathways (Desikan and Bakrovich 2018). In the future, phenotype-based classification of neurodevelopmental disorders may be replaced by a more informative pathway-based nomenclature (Desikan and Bakrovich 2018). Biological pathways frequently impaired in neurodevelopmental disorders are signal transduction pathways such as the mTOR pathway in tuberous sclerosis complex (TSC) (Wong 2019) and the RAS/RAF/MAPK pathway in RASopathies (Kang and Lee 2019), neurotransmission pathways as in some autism spectrum disorders (ASD) (Burnashev and Szepetowski 2015, Hu et al. 2016), and pathways that regulate gene expression as in Mendelian disorders of epigenetic machinery (MDEM) (Fahrner and Bjornsson 2019).
So far,we have annotated the role of loss-of-function mutations in methyl-CpG-binding protein 2 (MECP2), an epigenetic regulator of transcription, in Rett syndrome, a pervasive developmental disorder that belongs to the MDEM category (Pickett and London 2005, Ferreri 2014).
R-HSA-5619115 Disorders of transmembrane transporters Proteins with transporting functions can be roughly classified into 3 categories: ATP hydrolysis-coupled pumps, ion channels, and transporters. Pumps utilize the energy released by ATP hydrolysis to power the movement of substrates across the membrane against their electrochemical gradient. Channels in their open state can transfer substrates (ions or water) down their electrochemical gradient at an extremely high efficiency (up to 108 s-1). Transporters facilitate the movement of a specific substrate either against or with their concentration gradient at a lower speed (about 102 -104 s-1); as generally believed, conformational change of the transporter protein is involved in the transfer process. Diseases caused by defects in these transporter proteins are detailed in this section. Disorders associated with ABC transporters and SLC transporters are annotated here (Dean 2005).
R-HSA-110357 Displacement of DNA glycosylase by APEX1 Following cleavage of the damaged base, DNA glycosylase is displaced by APEX1, an AP endonuclease (Parikh et al. 1998).
R-HSA-75205 Dissolution of Fibrin Clot The crosslinked fibrin multimers in a clot are broken down to soluble polypeptides by plasmin, a serine protease. Plasmin can be generated from its inactive precursor plasminogen and recruited to the site of a fibrin clot in two ways, by interaction with tissue plasminogen activator at the surface of a fibrin clot, and by interaction with urokinase plasminogen activator at a cell surface. The first mechanism appears to be the major one responsible for the dissolution of clots within blood vessels. The second, although capable of mediating clot dissolution, may normally play a major role in tissue remodeling, cell migration, and inflammation (Chapman 1997; Lijnen 2001).
Clot dissolution is regulated in two ways. First, efficient plasmin activation and fibrinolysis occur only in complexes formed at the clot surface or on a cell membrane - proteins free in the blood are inefficient catalysts and are rapidly inactivated. Second, both plasminogen activators and plasmin itself are inactivated by specific serpins, proteins that bind to serine proteases to form stable, enzymatically inactive complexes (Kohler and Grant 2000).
These events are outlined in the drawing: black arrows connect the substrates (inputs) and products (outputs) of individual reactions, and blue lines connect output activated enzymes to the other reactions that they catalyze.
R-HSA-212676 Dopamine Neurotransmitter Release Cycle Dopamine neurotransmitter cycle occurs in dopaminergic neurons. Dopamine is synthesized and loaded into the clathrin sculpted monoamine transport vesicles. The vesicles are docked, primed and fused with the plasmamembrane in the synapse to release dopamine into the synaptic cleft.
R-HSA-379401 Dopamine clearance from the synaptic cleft The human gene SLC6A3 encodes the sodium-dependent dopamine transporter, DAT which mediates the re-uptake of dopamine from the synaptic cleft (Vandenbergh DJ et al, 2000). Dopamine can then be degraded by either COMT or monoamine oxidase.
R-HSA-390651 Dopamine receptors Dopamine receptors play vital roles in processes such as the control of learning, motivation, fine motor control and modulation of neuroendocrine signaling (Giralt JA and Greengard P, 2004). Abnormalities in dopamine receptor signaling may lead to neuropsychiatric disorders such as Parkinson's disease and schizophrenia. Dopamine receptors are prominent in the CNS and the neurotransmitter dopamine is the primary endogenous ligand for these receptors. In humans, there are five distinct types of dopamine receptor, D1-D5. They are subdivided into two families; D1-like family (D1 and D5) which couple with the G protein alpha-s and are excitatory and D2-like family (D2,D3 and D4) which couple with the G protein alpha-i and are inhibitory (Kebabian JW and Calne DB, 1979).
R-HSA-8863795 Downregulation of ERBB2 signaling Signaling by ERBB2 can be downregulated by ubiquitination and subsequent proteasome-dependent degradation of ERBB2 or activated ERBB2 heterodimers. In addition, protein tyrosine phosphatases that dephosphorylate tyrosine residues in the C-terminus of ERBB2 prevent the recruitment of adapter proteins involved in signal transduction, thus attenuating ERBB2 signaling.
STUB1 (CHIP) and CUL5 are E3 ubiquitin ligases that can target non-activated ERBB2 for proteasome-dependent degradation (Xu et al. 2002, Ehrlich et al. 2009). RNF41 (NRDP1) is an E3 ubiquitin ligase that targets ERBB3 and activated heterodimers of ERBB2 and ERBB3 for proteasome-dependent degradation by ubiquitinating ERBB3 (Cao et al. 2007).
Two protein tyrosine phosphatases of the PEST family, PTPN12 and PTPN18, dephosphorylate tyrosine residues in the C-terminus of ERBB2, thus preventing signal transduction to RAS and PI3K effectors (Sun et al. 2011, Wang et al. 2014).
R-HSA-1358803 Downregulation of ERBB2:ERBB3 signaling Level of plasma membrane ERBB3 is regulated by E3 ubiquitin ligase RNF41 (also known as NRDP1), which binds and ubiquitinates both inactive and activated ERBB3, targeting it for degradation (Cao et al. 2007). RNF41 is subject to self-ubiquitination which keeps its levels low when ERBB3 is not stimulated, and preserves ERBB3 expression on the cell surface (Qiu et al. 2002). Self-ubiquitination of RNF41 is reversible, through the action of ubiquitin protease USP8, an enzyme stabilized by AKT-mediated phosphorylation. Therefore, activation of AKT by ERBB2:ERBB3 signaling leads to phosphorylation of USP8 (Cao et al. 2007), which increases level of RNF41 through deubiquitination, and results in degradation of activated ERBB3 (Cao et al. 2007) - a negative feedback loop of ERBB3 signaling. Downregulation of EGFR and ERBB4 signaling is explained in pathways Signaling by EGFR and Signaling by ERBB4.
R-HSA-1253288 Downregulation of ERBB4 signaling WW-domain binding motifs in the C-tail of ERBB4 play an important role in the downregulation of ERBB4 receptor signaling, enabling the interaction of intact ERBB4, ERBB4 m80 and ERBB4 s80 with NEDD4 family of E3 ubiquitin ligases WWP1 and ITCH. The interaction of WWP1 and ITCH with intact ERBB4 is independent of receptor activation and autophosphorylation. Binding of WWP1 and ITCH ubiquitin ligases leads to ubiquitination of ERBB4 and its cleavage products, and subsequent degradation through both proteasomal and lysosomal routes (Omerovic et al. 2007, Feng et al. 2009). In addition, the s80 cleavage product of ERBB4 JM-A CYT-1 isoform is the target of NEDD4 ubiquitin ligase. NEDD4 binds ERBB4 JM-A CYT-1 s80 (ERBB4jmAcyt1s80) through its PIK3R1 interaction site and mediates ERBB4jmAcyt1s80 ubiquitination, thereby decreasing the amount of ERBB4jmAcyt1s80 that reaches the nucleus (Zeng et al. 2009).
R-HSA-2173795 Downregulation of SMAD2/3:SMAD4 transcriptional activity Transcriptional activity of SMAD2/3:SMAD4 heterotrimer can be inhibited by formation of a complex with SKI or SKIL (SNO), where SKI or SKIL recruit NCOR and possibly other transcriptional repressors to SMAD-binding promoter elements (Sun et al. 1999, Luo et al. 1999, Strochein et al. 1999). Higher levels of phosphorylated SMAD2 and SMAD3, however, may target SKI and SKIL for degradation (Strochein et al. 1999, Sun et al. 1999 PNAS, Bonni et al. 2001) through recruitment of SMURF2 (Bonni et al. 2001) or RNF111 i.e. Arkadia (Levy et al. 2007) ubiquitin ligases to SKI/SKIL by SMAD2/3. Therefore,the ratio of SMAD2/3 and SKI/SKIL determines the outcome: inhibition of SMAD2/3:SMAD4-mediated transcription or degradation of SKI/SKIL. SKI and SKIL are overexpressed in various cancer types and their oncogenic effect is connected with their ability to inhibit signaling by TGF-beta receptor complex.
SMAD4 can be monoubiquitinated by a nuclear ubiquitin ligase TRIM33 (Ecto, Ectodermin, Tif1-gamma). Monoubiquitination of SMAD4 disrupts SMAD2/3:SMAD4 heterotrimers and leads to SMAD4 translocation to the cytosol. In the cytosol, SMAD4 can be deubiquitinated by USP9X (FAM), reversing TRIM33-mediated negative regulation (Dupont et al. 2009).
Phosphorylation of the linker region of SMAD2 and SMAD3 by CDK8 or CDK9 primes SMAD2/3:SMAD4 complex for ubiquitination by NEDD4L and SMURF ubiquitin ligases. NEDD4L ubiquitinates SMAD2/3 and targets SMAD2/3:SMAD4 heterotrimer for degradation (Gao et al. 2009). SMURF2 monoubiquitinates SMAD2/3, leading to disruption of SMAD2/3:SMAD4 complexes (Tang et al. 2011).
Transcriptional repressors TGIF1 and TGIF2 bind SMAD2/3:SMAD4 complexes and inhibit SMAD-mediated transcription by recruitment of histone deacetylase HDAC1 to SMAD-binding promoter elements (Wotton et al. 1999, Melhuish et al. 2001).
PARP1 can attach poly ADP-ribosyl chains to SMAD3 and SMAD4 within SMAD2/3:SMAD4 heterotrimers. PARylated SMAD2/3:SMAD4 complexes are unable to bind SMAD-binding DNA elements (SBEs) (Lonn et al. 2010).
Phosphorylated SMAD2 and SMAD3 can be dephosphorylated by PPM1A protein phosphatase, leading to dissociation of SMAD2/3 complexes and translocation of unphosphorylated SMAD2/3 to the cytosol (Lin et al. 2006).
R-HSA-2173788 Downregulation of TGF-beta receptor signaling TGF-beta receptor signaling is downregulated by proteasome and lysosome-mediated degradation of ubiquitinated TGFBR1, SMAD2 and SMAD3, as well as by dephosphorylation of TGFBR1, SMAD2 and SMAD3.
In the nucleus, SMAD2/3:SMAD4 complex stimulates transcription of SMAD7, an inhibitory SMAD (I-SMAD). SMAD7 binds phosphorylated TGFBR1 and competes with the binding of SMAD2 and SMAD3 (Hayashi et al. 1997, Nakao et al. 1997). Binding of SMAD7 to TGBR1 can be stabilized by STRAP, a protein that simultaneously binds SMAD7 and TGFBR1 (Datta et al. 2000). BAMBI simultaneously binds SMAD7 and activated TGFBR1, leading to downregulation of TGF-beta receptor complex signaling (Onichtchouk et al. 1999, Yan et al. 2009).
In addition to competing with SMAD2/3 binding to TGFBR1, SMAD7 recruits protein phosphatase PP1 to phosphorylated TGFBR1, by binding to the PP1 regulatory subunit PPP1R15A (GADD34). PP1 dephosphorylates TGFBR1, preventing the activation of SMAD2/3 and propagation of TGF-beta signal (Shi et al. 2004).
SMAD7 associates with several ubiquitin ligases, SMURF1 (Ebisawa et al. 2001, Suzuki et al. 2002, Tajima et al. 2003, Chong et al. 2010), SMURF2 (Kavsak et al. 2000, Ogunjimi et al. 2005), and NEDD4L (Kuratomi et al. 2005), and recruits them to phosphorylated TGFBR1 within TGFBR complex. SMURF1, SMURF2 and NEDD4L ubiquitinate TGFBR1 (and SMAD7), targeting TGFBR complex for proteasome and lysosome-dependent degradation (Ebisawa et al. 2001, Kavsak et al. 2000, Kuratomi et al. 2005). The ubiquitination of TGFBR1 can be reversed by deubiquitinating enzymes, UCHL5 (UCH37) and USP15, which may be recruited to ubiquitinated TGFBR1 by SMAD7 (Wicks et al. 2005, Eichhorn et al. 2012).
Basal levels of SMAD2 and SMAD3 are maintained by SMURF2 and STUB1 ubiquitin ligases. SMURF2 is able to bind and ubiquitinate SMAD2, leading to SMAD2 degradation (Zhang et al. 2001), but this has been questioned by a recent study of Smurf2 knockout mice (Tang et al. 2011). STUB1 (CHIP) binds and ubiquitinates SMAD3, leading to SMAD3 degradation (Li et al. 2004, Xin et al. 2005). PMEPA1 can bind and sequester unphosphorylated SMAD2 and SMAD3, preventing their activation in response to TGF-beta signaling. In addition, PMEPA1 can bind and sequester phosphorylated SMAD2 and SMAD3, preventing formation of SMAD2/3:SMAD4 heterotrimer complexes (Watanabe et al. 2010). A protein phosphatase MTMR4, residing in the membrane of early endosomes, can dephosphorylate activated SMAD2 and SMAD3, preventing formation of SMAD2/3:SMAD4 complexes (Yu et al. 2010).
R-HSA-202424 Downstream TCR signaling Changes in gene expression are required for the T cell to gain full proliferative competence and to produce effector cytokines. Three transcription factors in particular have been found to play a key role in TCR-stimulated changes in gene expression, namely NFkappaB, NFAT and AP-1. A key step in NFkappaB activation is the stimulation and translocation of PRKCQ. The critical element that effects PRKCQ activation is PI3K. PI3K translocates to the plasma membrane by interacting with phospho-tyrosines on CD28 via its two SH2 domains located in p85 subunit (step 24). The p110 subunit of PI3K phosphorylates the inositol ring of PIP2 to generate PIP3 (steps 25). The reverse dephosphorylation process from PIP3 to PIP2 is catalysed by PTEN (step 27). PIP3 may also be dephosphorylated by the phosphatase SHIP to generate PI-3,4-P2 (step 26). PIP3 and PI-3,4-P2 acts as binding sites to the PH domain of PDK1 (step 28) and AKT (step 29). PKB is activated in response to PI3K stimulation by PDK1 (step 30). PDK1 has an essential role in regulating the activation of PRKCQ and recruitment of CBM complex to the immune synapse. PRKCQ is a member of novel class (DAG dependent, Ca++ independent) of PKC and the only member known to translocate to this synapse. Prior to TCR stimulation PRKCQ exists in an inactive closed conformation. TCR signals stimulate PRKCQ (step 31) and release DAG molecules. Subsequently, DAG binds to PRKCQ via the C1 domain and undergoes phosphorylation on tyrosine 90 by LCK to attain an open conformation (step 32). PRKCQ is further phosphorylated by PDK1 on threonine 538 (step 33). This step is critical for PKC activity. CARMA1 translocates to the plasma membrane following the interaction of its SH3 domain with the 'PxxP' motif on PDK1 (step 34). CARMA1 is phosphorylated by PKC-theta on residue S552 (step 35), leading to the oligomerization of CARMA1. This complex acts as a scaffold, recruiting BCL10 to the synapse by interacting with their CARD domains (step 36). BCL10 undergoes phosphorylation mediated by the enzyme RIP2 (step 37). Activated BCL10 then mediates the ubiquitination of IKBKG by recruiting MALT1 and TRAF6. MALT1 binds to BCL10 with its Ig-like domains and undergoes oligomerization (step 38). TRAF6 binds to the oligomerized MALT1 and also undergoes oligomerization (step 39). Oligomerized TRAF6 acts as a ubiquitin-protein ligase, catalyzing auto-K63-linked polyubiquitination (step 40). This K-63 ubiquitinated TRAF6 activates MAP3K7 kinase bound to TAB2 (step 41) and also ubiquitinates IKBKG in the IKK complex (step 44). MAP3K7 undergoes autophosphorylation on residues T184 and T187 and gets activated (step 42). Activated MAP3K7 kinase phosphorylates IKBKB on residues S177 and S181 in the activation loop and activates the IKK kinase activity (step 43). IKBKB phosphorylates the NFKBIA bound to the NFkappaB heterodimer, on residues S19 and S23 (step 45) and directs NFKBIA to 26S proteasome degradation (step 47). The NFkappaB heterodimer with a free NTS sequence finally migrates to the nucleus to regulate gene transcription (step 46).
R-HSA-186763 Downstream signal transduction The role of autophosphorylation sites on PDGF receptors are to provide docking sites for downstream signal transduction molecules which contain SH2 domains. The SH2 domain is a conserved motif of around 100 amino acids that can bind a phosphorylated tyrosine residue. These downstream molecules are activated upon binding to, or phosphorylated by, the receptor kinases intrinsic to PDGF receptors.
Some of the dowstream molecules are themselves enzymes, such as phosphatidylinositol 3'-kinase (PI3K), phospholipase C (PLC-gamma), the Src family of tyrosine kinases, the tyrosine phosphatase SHP2, and a GTPase activating protein (GAP) for Ras. Others such as Grb2 are adaptor molecules which link the receptor with downstream catalytic molecules.
R-HSA-1168372 Downstream signaling events of B Cell Receptor (BCR) Second messengers (calcium, diacylglycerol, inositol 1,4,5-trisphosphate, and phosphatidyinositol 3,4,5-trisphosphate) trigger signaling pathways: NF-kappaB is activated via protein kinase C beta, RAS via RasGRP proteins, NF-AT via calcineurin, and AKT via PDK1 (reviewed in Shinohara and Kurosaki 2009, Stone 2006).
R-HSA-5654687 Downstream signaling of activated FGFR1 Signaling via FGFRs is mediated via direct recruitment of signaling proteins that bind to tyrosine auto-phosphorylation sites on the activated receptor and via closely linked docking proteins that become tyrosine phosphorylated in response to FGF-stimulation and form a complex with additional complement of signaling proteins.
The activation loop in the catalytic domain of FGFR maintains the PTK domain in an inactive or low activity state. The activation-loop of FGFR1, for instance, contains two tyrosine residues that must be autophosphorylated for maintaining the catalytic domain in an active state. In the autoinhibited configuration, a kinase invariant proline residue at the C-terminal end of the activation loop interferes with substrate binding while allowing access to ATP in the nucleotide binding site.
In addition to the catalytic PTK core, the cytoplasmic domain of FGFR contains several regulatory sequences. The juxtamembrane domain of FGFRs is considerably longer than that of other receptor tyrosine kinases. This region contains a highly conserved sequence that serves as a binding site for the phosphotyrosine binding (PTB) domain of FRS2. A variety of signaling proteins are phosphorylated in response to FGF stimulation, including Shc, phospholipase-C gamma and FRS2 leading to stimulation of intracellular signaling pathways that control cell proliferation, cell differentiation, cell migration, cell survival and cell shape.
R-HSA-5654696 Downstream signaling of activated FGFR2 Signaling via FGFRs is mediated via direct recruitment of signaling proteins that bind to tyrosine auto-phosphorylation sites on the activated receptor and via closely linked docking proteins that become tyrosine phosphorylated in response to FGF-stimulation and form a complex with additional complement of signaling proteins.
The activation loop in the catalytic domain of FGFR maintains the PTK domain in an inactive or low activity state. The activation-loop of FGFR1, for instance, contains two tyrosine residues that must be autophosphorylated for maintaining the catalytic domain in an active state. In the autoinhibited configuration, a kinase invariant proline residue at the C-terminal end of the activation loop interferes with substrate binding while allowing access to ATP in the nucleotide binding site.
In addition to the catalytic PTK core, the cytoplasmic domain of FGFR contains several regulatory sequences. The juxtamembrane domain of FGFRs is considerably longer than that of other receptor tyrosine kinases. This region contains a highly conserved sequence that serves as a binding site for the phosphotyrosine binding (PTB) domain of FRS2. A variety of signaling proteins are phosphorylated in response to FGF stimulation, including Shc, phospholipase-C gamma and FRS2 leading to stimulation of intracellular signaling pathways that control cell proliferation, cell differentiation, cell migration, cell survival and cell shape.
R-HSA-5654708 Downstream signaling of activated FGFR3 Signaling via FGFRs is mediated via direct recruitment of signaling proteins that bind to tyrosine auto-phosphorylation sites on the activated receptor and via closely linked docking proteins that become tyrosine phosphorylated in response to FGF-stimulation and form a complex with additional complement of signaling proteins.
The activation loop in the catalytic domain of FGFR maintains the PTK domain in an inactive or low activity state. The activation-loop of FGFR1, for instance, contains two tyrosine residues that must be autophosphorylated for maintaining the catalytic domain in an active state. In the autoinhibited configuration, a kinase invariant proline residue at the C-terminal end of the activation loop interferes with substrate binding while allowing access to ATP in the nucleotide binding site.
In addition to the catalytic PTK core, the cytoplasmic domain of FGFR contains several regulatory sequences. The juxtamembrane domain of FGFRs is considerably longer than that of other receptor tyrosine kinases. This region contains a highly conserved sequence that serves as a binding site for the phosphotyrosine binding (PTB) domain of FRS2. A variety of signaling proteins are phosphorylated in response to FGF stimulation, including Shc, phospholipase-C gamma and FRS2 leading to stimulation of intracellular signaling pathways that control cell proliferation, cell differentiation, cell migration, cell survival and cell shape.
R-HSA-5654716 Downstream signaling of activated FGFR4 Signaling via FGFRs is mediated via direct recruitment of signaling proteins that bind to tyrosine auto-phosphorylation sites on the activated receptor and via closely linked docking proteins that become tyrosine phosphorylated in response to FGF-stimulation and form a complex with additional complement of signaling proteins.
The activation loop in the catalytic domain of FGFR maintains the PTK domain in an inactive or low activity state. The activation-loop of FGFR1, for instance, contains two tyrosine residues that must be autophosphorylated for maintaining the catalytic domain in an active state. In the autoinhibited configuration, a kinase invariant proline residue at the C-terminal end of the activation loop interferes with substrate binding while allowing access to ATP in the nucleotide binding site.
In addition to the catalytic PTK core, the cytoplasmic domain of FGFR contains several regulatory sequences. The juxtamembrane domain of FGFRs is considerably longer than that of other receptor tyrosine kinases. This region contains a highly conserved sequence that serves as a binding site for the phosphotyrosine binding (PTB) domain of FRS2. A variety of signaling proteins are phosphorylated in response to FGF stimulation, including Shc, phospholipase-C gamma and FRS2 leading to stimulation of intracellular signaling pathways that control cell proliferation, cell differentiation, cell migration, cell survival and cell shape.
R-HSA-9748784 Drug ADME Pharmacokinetics (PK) is a branch of pharmacology dedicated to determining the chemical fate of substances in living organisms, from administration to elimination from the body. PK can be described as how an organism affects a drug, whereas pharmacodynamics (PD) is the study of how a drug affects the organism. Both PK and PD are described for each drug annotated in the Drug Absorption, Distribution, Metabolism and Excretion (ADME) pathways. For example, although paracetamol ADME (PK) is described in this section, the pharmacological inhibition (PD) of its targets (PTGS1 and PTGS2) is described in the relevant pathway where these enzymes perform their physiological duties. A connection is made between the two pathways to link PK and PD annotations.
The disposition of a pharmaceutical compound within an organism can be described by four main stages; absorption, distribution, metabolism, and excretion, abbreviated to ADME (Pallasch 1988, Ruiz-Garcia et al. 2008, Currie 2018). Sometimes, separate steps can be tacked on to ADME depending on what is being described. For example, where a drug is released from a pharmaceutical formulation, liberation (L) is added to ADME (LADME) or where the toxicity of a compound is described, T is added (ADMET).
ADME of various drugs is annotated in this section.
R-HSA-9665230 Drug resistance in ERBB2 KD mutants ERBB2 kinase domain (KD) mutants vary in their resistance to various tyrosine kinase inhibitors and therapeutic antibody trastuzumab (herceptin). The following ERBB2 KD mutants are resistant to the therapeutic antibody trastuzumab (herceptin):
ERBB2 L755P (Nagano et al. 2018);
ERBB2 L755S (Nagano et al. 2018);
ERBB2 I767M (Bose et al. 2013);
ERBB2 D769Y (Nagano et al. 2018);
ERBB2 V777L (Nagano et al. 2018);
ERBB2 G778_P780dup (Bose et al. 2013, Nagano et al. 2018);
ERBB2 T798M (Rexer et al. 2013);
ERBB2 V842I (Nagano et al. 2018);
ERBB2 T862A (Nagano et al. 2018);
ERBB2 L869R (Hanker et al. 2017);
For ERBB2 R896C, both resistance (Bose et al. 2013) and sensitivity (Nagano et al. 2018) to trastuzumab have been reported.
R-HSA-9665737 Drug resistance in ERBB2 TMD/JMD mutants With respect to pertuzumab, a therapeutic antibody that block ligand-driven heterodimerization of ERBB2, ERBB2 R678Q is sensitive to pertuzumab, while ERBB2 V659E, ERBB2 G660D, ERBB2 G660R and probably ERBB2 Q709L are resistant (Pahuja et al. 2018).
R-HSA-9700649 Drug resistance of ALK mutants Aberrant ALK activity arises through fusions, point mutations, overexpression or amplifications and has been shown to be an oncogenic driver in a number of cancers including anaplastic large cell lymphoma (ALCL), non-small cell lung cancer (NSCLC), inflammatory myofibroblastic tumors (IMTs) neuroblastomas and more (reviewed in Della Corte et al, 2018; Lin et al, 2017). As a result, ALK is a promising therapeutic target for inhibition with tyrosine kinase inhibitors. Crizotinib, ceritinib, brigatinib, alectinib and lorlatinib are all approved for the treatment of ALK-driven cancers, however resistance commonly develops either as a result of accumulating secondary mutations, or through activation of bypass pathways that remove the dependence on ALK signaling (reviewed in Della Corte et al, 2017; Roskoski, 2013; Lin et al, 2017).
R-HSA-9702506 Drug resistance of FLT3 mutants FLT3 is mutated in ~30% of acute myeloid leukemias (AML), with internal tandem duplications (ITDs) representing the majority of these mutations and activating point mutants occurring at lower frequency. FLT3 mutations also occur at lower rates in other cancers (reviewed in Kazi and Roonstrand, 2018; Daver et al, 2019; Larroas-Garcia and Baer, 2017). Mutation of FLT3 has been identified as a driver in progression of AML and in consequence is a promising therapeutic target. A number of first and second generation inhibitors have been demonstrated to have activity against FLT3, but accumulation of secondary mutations leads to the development of resistance. These secondary mutations further shift the equilibrium of the receptor toward the activated state, making even the second-generation type II TKIs less effective. In consequence, considerable effort is devoted to discovery of type II and, in particular, type I TKIs that are active against highly activated FLT3 alleles (reviewed in Daver et al, 2019; Staudt et al, 2018; Lim et al, 2017; Klug et al, 2018).
R-HSA-9669937 Drug resistance of KIT mutants Activating mutations in the juxtamembrane domain of KIT are common in some cancers, including gastrointestinal stromal tumors, melanoma and acute myeloid leukemia (reviewed in Roskoski, 2018). These mutations are sensitive to inhibition with imatinib, which in 2001 was the first tyrosine kinase inhibitor approved for treatment of cancer (Demetri et al, 2002; Corless et al, 2011; reviewed in Zitvogel, 2016). Although highly successful in prolonging survival, imatinib-resistance develops in most patients due to appearance of secondary mutations, often in the ATP-binding pocket or in the activation loop of the kinase domain (Gajiwala et al, 2008; Serrano et al, 2019; reviewed in Roskoski, 2018; Napolitano and Vincenzi, 2019)
R-HSA-9674415 Drug resistance of PDGFR mutants PDGFRA is mutated in ~10% of gastrointestinal stromal tumors in a mutually exclusive manner with KIT mtutations. In contrast to KIT, PDGFRA GIST mutations occur more frequently in the activation domain, rather than the juxtamembrane domain. In addition to GIST, PDGFRA is subject to missense or small in-frame deletion mutations in haematological cancers and melanoma. In contrast, missense mutations in PDGFRB are rare (Heinrich et al, 2003; Corless et al, 2005; reviewed in Corless et al, 2011). Both PDGFRA and PDGFRB are also subject to oncogenic translocation events leading to the expression of fusion proteins (Cools et al, 2003; Simon et al, 2008; Salemi et al, 2009; Ohashi et al, 2010; reviewed in Appiah-Kubi et al, 2017).
Imatinib is a type II TKIs that is approved as first-line treatment of KIT- and PDGFR-driven tumors; however secondary mutations frequently contribute to the development of imatinib resistance. These secondary mutations further shift the equilibrium of the receptor toward the activated state, making imatinib and even approved second-line type II TKIs less effective. In consequence, considerable effort is devoted to discovery of type II and, in particular, type I TKIs that are active against highly activated PDGFR alleles (Smith et al, 2019; Lierman et al, 2019; reviewed in Roskoski, 2018; Klug et al, 2018).
R-HSA-9750126 Drug-induced formation of DNA interstrand crosslinks This pathway describes how drugs commonly used in the treatment of cancer, psoriasis and severe atopic dermatitis produce DNA interstrand crosslinks that are repaired through the Fanconi anemia pathway. For review, please refer to Deans and West 2011, Fu et al. 2012, and Rycenga and Long 2018.
R-HSA-9754119 Drug-mediated inhibition of CDK4/CDK6 activity Cyclin dependent kinases CDK4 and CDK6 regulate crucial steps in the G1 phase of the cell cycle that commit cells to transition to the S phase and ultimately divide. Many growth signaling pathways, frequently perturbed in cancer, converge on CDK4/CDK6 activation, thus driving cellular proliferation. This makes CDK4 and CDK6 promising targets for anti-cancer therapy. So far, three CDK4/6 inhibitors, palbociclib, ribociclib and abemaciclib, have been approved for clinical use and many others are at different stages of clinical testing. CDK4/6 inhibitors mainly have a cytostatic effect on tumor cells, but can also influence immune response to tumor by targeting immune system cells in the tumor microenvironment. While intact RB1, the main target of CDK4/6 during cell cycle progression, is in general considered to be a prerequisite for the success of CDK4/6-targeted anti-cancer therapy, the status of other, less explored CDK4/6 targets can also affect the treatment outcome. For review, please refer to Asghar et al. 2015, Klein et al. 2018, Álvarez-Fernández and Malumbres 2020, Petroni et al. 2020).
R-HSA-9652282 Drug-mediated inhibition of ERBB2 signaling Signaling by ERBB2 can be pharmacologically inhibited with tyrosine kinase inhibitors (TKIs) (Nelson and Fry 2001, Xia et al. 2002, Wood et al. 2004, Rabindran et al. 2004, Gandreau et al. 2007, Jani et al. 2007, Li et al. 2008, Hichkinson et al. 2010, Traxler et al. 2014, Hanker et al. 2017), and therapeutic antibodies, such as trastuzumab (Hudziak et al. 1989, Carter et al. 1992, Pickl and Ries 2009, Maadi et al. 2018) and pertuzumab (Franklin et al. 2004).
R-HSA-9734091 Drug-mediated inhibition of MET activation MET receptor tyrosine kinase (RTK) is a proto-oncogene that is frequently aberrantly activated in cancer through gene amplification and/or activating mutations that result in hypersensitivity to HGF stimulation or HGF-independent activation. Oncogenic MET activation can occur as a primary mechanism of malignant transformation or be selected secondarily, as a mechanism of resistance to therapeutics that target related RTKs, such as EGFR. MET targeted anti-cancer therapeutics, either recombinant monoclonal antibodies (MAbs) or small tyrosine kinase inhibitors (TKIs), have shown promise as a first-line agents for the treatment of solid tumors with primary MET activation or as second-line agents for the treatment of solid tumors with acquired MET-mediated resistance to other RTK-targeted therapies (reviewed in Comoglio et al. 2018).
R-HSA-5696400 Dual Incision in GG-NER Double incision at the damaged DNA strand excises the oligonucleotide that contains the lesion from the open bubble. The excised oligonucleotide is ~27-30 bases long. Incision 5' to the damage site, by ERCC1:ERCC4 endonuclease, precedes the incision 3' to the damage site by ERCC5 endonuclease (Staresincic et al. 2009).
R-HSA-6782135 Dual incision in TC-NER In transcription-coupled nucleotide excision repair (TC-NER), similar to global genome nucleotide excision repair (GG-NER), the oligonucleotide that contains the lesion is excised from the open bubble structure via dual incision of the affected DNA strand. 5' incision by the ERCC1:ERCC4 (ERCC1:XPF) endonuclease precedes 3' incision by ERCC5 (XPG) endonuclease. In order for the TC-NER pre-incision complex to assemble and the endonucleases to incise the damaged DNA strand, the RNA polymerase II (RNA Pol II) complex has to backtrack - reverse translocate from the damage site. Although the mechanistic details of this process are largely unknown in mammals, it may involve ERCC6/ERCC8-mediated chromatin remodelling/ubiquitination events, the DNA helicase activity of the TFIIH complex and TCEA1 (TFIIS)-stimulated cleavage of the 3' protruding end of nascent mRNA by RNA Pol II (Donahue et al. 1994, Lee et al. 2002, Sarker et al. 2005, Vermeulen and Fousteri 2013, Hanawalt and Spivak 2008, Staresincic et al. 2009, Epshtein et al. 2014).
R-HSA-113510 E2F mediated regulation of DNA replication Progression through G1 and G1 to S-phase transition that initiates DNA synthesis involve many complexes that are regulated by RB1:E2F pathway. RB1:E2F pathway plays a key role in gene expression regulation in proliferating and differentiated cells. As a repressor, E2F remains bound to RB1; it can activate the expression of S-phase genes involved in DNA replication after the phosphorylation of RB1.
E2F proteins regulate expression of genes involved in various processes thereby forming interlinks between cell cycle, DNA synthesis, DNA damage recognition etc.
In this module, activation of replication related genes by E2F1 and two ways by which E2F1 regulates DNA replication initiation are annotated.
R-HSA-113507 E2F-enabled inhibition of pre-replication complex formation Under specific conditions, Cyclin B, a mitotic cyclin, can inhibit the functions of pre-replicative complex. E2F1 activates Cdc25A protein which regulates Cyclin B in a positive manner. Cyclin B/Cdk1 function is restored which leads to the disruption of pre-replicative complex. This phenomenon has been demonstrated by Bosco et al (2001) in Drosophila.
R-HSA-8866654 E3 ubiquitin ligases ubiquitinate target proteins E3 ubiquitin ligases catalyze the transfer of an ubiquitin from an E2-ubiquitin conjugate to a target protein. Generally, ubiquitin is transferred via formation of an amide bond to a particular lysine residue of the target protein, but ubiquitylation of cysteine, serine and threonine residues in a few targeted proteins has also been demonstrated (reviewed in McDowell and Philpott 2013, Berndsen and Wolberger 2014). Based on protein homologies, families of E3 ubiquitin ligases have been identified that include RING-type ligases (reviewed in Deshaies et al. 2009, Metzger et al. 2012, Metzger et al. 2014), HECT-type ligases (reviewed in Rotin et al. 2009, Metzger et al. 2012), and RBR-type ligases (reviewed in Dove et al. 2016). A subset of the RING-type ligases participate in CULLIN-RING ligase complexes (CRLs which include SCF complexes, reviewed in Lee and Zhou 2007, Genschik et al. 2013, Skaar et al. 2013, Lee et al. 2014).
Some E3-E2 combinations catalyze mono-ubiquitination of the target protein (reviewed in Nakagawa and Nakayama 2015). Other E3-E2 combinations catalyze conjugation of further ubiquitin monomers to the initial ubiquitin, forming polyubiquitin chains. (It may also be possible for some E3-E2 combinations to preassemble polyubiquitin and transfer it as a unit to the target protein.) Ubiquitin contains several lysine (K) residues and a free alpha amino group to which further ubiquitin can be conjugated. Thus different types of polyubiquitin are possible: K11 linked polyubiquitin is observed in endoplasmic reticulum-associated degradation (ERAD), K29 linked polyubiquitin is observed in lysosomal degradation, K48 linked polyubiquitin directs target proteins to the proteasome for degradation, whereas K63 linked polyubiquitin generally acts as a scaffold to recruit other proteins in several cellular processes, notably DNA repair (reviewed in Komander et al. 2009).
R-HSA-3000178 ECM proteoglycans Proteoglycans are major components of the extracellular matrix. In cartilage the matrix constitutes more than 90% of tissue dry weight. Proteoglycans are proteins substituted with glycosaminoglycans (GAGs), linear polysaccharides consisting of a repeating disaccharide, generally of an acetylated amino sugar alternating
with a uronic acid. Most proteoglycans are located in the extracellular
space. Proteoglycans are highly diverse, both in terms of the core proteins and the subtypes of GAG chains, namely chondroitin sulfate (CS), keratan sulfate (KS), dermatan sulfate (DS) and heparan sulfate (HS). Hyaluronan is a non-sulfated GAG whose molecular weight runs into millions of Dalton; in articular cartilage, a single hyaluronan molecule can hold upto 100 aggrecan molecules and these aggregates are stabilized by a link protein.
R-HSA-2179392 EGFR Transactivation by Gastrin Gastrin, through the action of diacylglycerol produced from downstream G alpha (q) events, transactivates EGFR via a PKC-mediated pathway by activation of MMP3 (Matrix Metalloproteinase 3) which allows formation of mature HBEGF (heparin-binding epidermal growth factor) by cleaving pro-HBEGF. Mature HBEGF is then free to bind the EGFR, resulting in EGFR activation (Dufresne et al. 2006, Liebmann 2011).
R-HSA-182971 EGFR downregulation Regulation of receptor tyrosine kinase (RTK) activity is implicated in the control of almost all cellular functions. One of the best understood RTKs is epidermal growth factor receptor (EGFR). Growth factors can bind to EGFR and activate it to initiate signalling cascades within the cell. EGFRs can also be recruited to clathrin-coated pits which can be internalised into endocytic vesicles. From here, EGFRs can either be recycled back to the plasma membrane or directed to lysosomes for destruction.This provides a mechanism by which EGFR signalling is negatively regulated and controls the strength and duration of EGFR-induced signals. It also prevents EGFR hyperactivation as commonly seen in tumorigenesis.
The proto-oncogene Cbl can negatively regulate EGFR signalling. The Cbl family of RING-type ubiquitin ligases are able to poly-ubiquitinate EGFR, an essential step in EGFR degradation. All Cbl proteins have a unique domain that recognises phosphorylated tyrosine residues on activated EGFRs. They also direct the ubiquitination and degradation of activated EGFRs by recruiting ubiquitin-conjugation enzymes. Cbl proteins function by specifically targeting activated EGFRs and mediating their down-regulation, thus providing a means by which signaling processes can be negatively regulated.
Cbl also promotes receptor internalization via it's interaction with an adaptor protein, CIN85 (Cbl-interacting protein of 85kDa). CIN85 binds to Cbl via it's SH3 domain and is enhanced by the EGFR-induced tyrosine phosphorylation of Cbl. The proline-rich region of CIN85 interacts with endophilins which are regulatory components of clathrin-coated vesicles (CCVs). Endophilins bind to membranes and induce membrane curvature, in conjunction with other proteins involved in CCV formation. The rapid recruitment of endophilin to the activated receptor complex by CIN85 is the mechanism which controls receptor internalization.
R-HSA-212718 EGFR interacts with phospholipase C-gamma Activated epidermal growth factor receptors (EGFR) can stimulate phosphatidylinositol (PI) turnover. Activated EGFR can activate phospholipase C-gamma1 (PLC-gamma1, i.e. PLCG1) which hydrolyses phosphatidylinositol 4,5-bisphosphate (PIP2) to inositol 1,4,5-triphosphate (IP3) and diacylglycerol (DAG). IP3 is instrumental in the release of calcium from intracellular stores and DAG is involved in protein kinase C activation.
R-HSA-9619665 EGR2 and SOX10-mediated initiation of Schwann cell myelination Schwann cells are glial cells of the peripheral nervous system that ensheath the peripheral nerves within a compacted lipid-rich myelin structure that is required for optimal transduction of nerve signals in motor and sensory nerves. Schwann cells develop from the neural crest in a differentiation process driven by factors derived from the Schwann cell itself, from the adjacent neuron or from the extracellular matrix (reviewed in Jessen and Mirsky, 2005). Upon peripheral nerve injury, mature Schwann cells can form repair cells that allow peripheral nerve regeneration through myelin phagocytosis and remyelination of the peripheral nerve. This process in some ways recapitulates the maturation of immature Schwann cells during development (reviewed in Jessen and Mirsky, 2016). Mature, fully myelinated Schwann cells exhibit longitudinal and radial polarization. The axon-distal abaxonal membrane interacts with elements of the basal lamina through integrins and lamins and in this way resembles the basolateral domain of polarized epithelial cells. In contrast, the axon-proximal adaxonal membrane resembles the apical domain of an epithelial cell, and is enriched with adhesion molecules and receptors that mediate interaction with ligands from the axon (reviewed in Salzer, 2015).
Schwann cells express a number of Schwann-cell specific proteins, including components of the myelin sheath such as myelin basic protein (MBP) and myelin protein zero (MPZ). In addition, Schwann cells have high lipid content relative to other membranes, and are enriched in galactosphingolipids, cholesterol and saturated long chain fatty acids (reviewed in Garbay et al, 2000). This protein and lipid profile is driven by a Schwann cell myelination transcriptional program controlled by master regulators SOX10, POU3F1 and EGR2, among others (reviewed in Svaren and Meijer, 2008; Stolt and Wegner, 2016).
R-HSA-9648025 EML4 and NUDC in mitotic spindle formation EML4 and NUDC proteins are required for mitotic spindle formation, attachment of spindle microtubule ends to kinetochores, and alignment of mitotic chromosome at the metaphase plate. EML4 is a WD40 family protein that binds to interphase microtubules and stabilizes them (Houtman et al. 2007, Adib et al. 2019). At mitotic entry, EML4 undergoes phosphorylation (Pollmann et al. 2006, Adib et al. 2019) by serine/threonine kinases NEK6 and NEK7, leading to its dissociation from microtubules, which is necessary for the assembly of a dynamic mitotic spindle (Adib et al. 2019). EML4, through its WD40 repeats, interacts with NUDC and recruits it to the kinetochores of the mitotic spindle (Chen et al. 2015). It is possible that other mitotic kinases, besides NEK6 and NEK7, also phosphorylate EML4. Phosphorylation of different residues of EML4 could reduce or increase affinity of EML4 for specific subpopulations of microtubules in mitosis.
A recurrent genomic rearrangement, reported in about 5% cases of non-small cell lung cancer (NSCLC) fuses the N-terminal portion of EML4 with the C-terminal portion of ALK (anaplastic lymphoma kinase), resulting in a constitutively active ALK (Soda et al. 2007, Richards et al. 2015).
R-HSA-2682334 EPH-Ephrin signaling During the development process cell migration and adhesion are the main forces involved in morphing the cells into critical anatomical structures. The ability of a cell to migrate to its correct destination depends heavily on signaling at the cell membrane. Erythropoietin producing hepatocellular carcinoma (EPH) receptors and their ligands, the ephrins (EPH receptors interacting proteins, EFNs), orchestrates the precise control necessary to guide a cell to its destination. They are expressed in all tissues of a developing embryo and are involved in multiple developmental processes such as axon guidance, cardiovascular and skeletal development and tissue patterning. In addition, EPH receptors and EFNs are expressed in developing and mature synapses in the nervous system, where they may have a role in regulating synaptic plasticity and long-term potentiation. Activation of EPHB receptors in neurons induces the rapid formation and enlargement of dendritic spines, as well as rapid synapse maturation (Dalva et al. 2007). On the other hand, EPHA4 activation leads to dendritic spine elimination (Murai et al. 2003, Fu et al. 2007).
EPH receptors are the largest known family of receptor tyrosine kinases (RTKs), with fourteen total receptors divided into either A- or B-subclasses: EPHA (1-8 and 10) and EPHB (1-4 and 6). EPH receptors can have overlapping functions, and loss of one receptor can be partially compensated for by another EPH receptor that has similar expression pattern and ligand-binding specificities. EPH receptors have an N-terminal extracellular domain through which they bind to ephrin ligands, a short transmembrane domain, and an intracellular cytoplasmic signaling structure containing a canonical tyrosine kinase catalytic domain as well as other protein interaction sites. Ephrins are also sub-divided into an A-subclass (A1-A5), which are tethered to the plasma membrane by a glycosylphosphatidylinositol (GPI) anchor, and a B-subclass (B1-B3), members of which have a transmembrane domain and a short, highly conserved cytoplasmic tail lacking endogenous catalytic activity. The interaction between EPH receptors and its ligands requires cell-cell interaction since both molecules are membrane-bound. Close contact between EPH receptors and EFNs is required for signaling to occur. EPH/EFN-initiated signaling occurs bi-directionally into either EPH- or EFN-expressing cells or axons. Signaling into the EPH receptor-expressing cell is referred as the forward signal and signaling into the EFN-expressing cell, the reverse signal. (Dalva et al. 2000, Grunwald et al. 2004, Davy & Robbins 2000, Cowan et al. 2004)
R-HSA-3928665 EPH-ephrin mediated repulsion of cells Despite high-affinity multimeric interaction between EPHs and ephrins (EFNs), the cellular response to EPH-EFN engagement is usually repulsion between the two cells and signal termination. These repulsive responses induce an EPH receptor-expressing cell to retract from an ephrin-expressing cell after establishing initial contact. The repulsive responses mediated by EPH receptors in the growth cone at the leading edge of extending axons and in axonal collateral branches contribute to the formation of selective neuronal connections. It is unclear how high affinity trans-cellular interactions between EPHs and ephrins are broken to convert adhesion into repulsion. Two possible mechanisms have been proposed for the repulsion of EPH-EFN bearing cells: the first one involves regulated cleavage of ephrin ligands or EPH receptors by transmembrane proteases following cell-cell contact, while the second one is rapid endocytosis of whole EPH:EFN complexes during the retraction of the interacting cells or neuronal growth cones (Egea & Klein 2007, Janes et al. 2005). RAC also plays an essential role during growth cone collapse by promoting actin polymerization that drives membrane internalization by endocytosis (Marston et al. 2003).
R-HSA-3928663 EPHA-mediated growth cone collapse EPH/Ephrin signaling is coupled to Rho family GTPases such as Rac, Rho and Cdc42 that connect bidirectional receptor-ligand interactions to changes in the actin cytoskeleton (Noren & Pasquale 2004, Groeger & Nobes 2007). RHOA regulates actin dynamics and is involved in EPHA-induced growth cone collapse. This is mediated by ephexins. Ephexin, a guanine nucleotide exchange factor for Rho GTPases, interacts with the EPHA kinase domain and its subsequent activation differentially affects Rho GTPases, such that RHOA is activated, whereas Cdc42 and Rac1 are inhibited. Activation of RHOA, and inhibition of Cdc42 and Rac, shifts actin cytoskeleton to increased contraction and reduced expansion leading to growth-cone collapse (Shamah et al. 2001, Sahin et al. 2005). The activation of EPH receptors in growing neurons typically, but not always, leads to a growth cone collapse response and retraction from an ephrin-expressing substrate (Poliakov et al. 2004, Pasquale 2005). EPHA-mediated repulsive responses prevent axons from growing into regions of excessive ephrin-A concentration, such as the posterior end of the superior colliculus (Pasquale 2005).
R-HSA-3928662 EPHB-mediated forward signaling Multiple EPHB receptors contribute directly to dendritic spine development and morphogenesis. These are more broadly involved in post-synaptic development through activation of focal adhesion kinase (FAK) and Rho family GTPases and their GEFs. Dendritic spine morphogenesis is a vital part of the process of synapse formation and maturation during CNS development. Dendritic spine morphogenesis is characterized by filopodia shortening followed by the formation of mature mushroom-shaped spines (Moeller et al. 2006). EPHBs control neuronal morphology and motility by modulation of the actin cytoskeleton. EPHBs control dendritic filopodia motility, enabling synapse formation. EPHBs exert these effects through interacting with the guanine exchange factors (GEFs) such as intersectin and kalirin. The intersectin-CDC42-WASP-actin and kalirin-RAC-PAK-actin pathways have been proposed to regulate the EPHB receptor mediated morphogenesis and maturation of dendritic spines in cultured hippocampal and cortical neurons (Irie & Yamaguchi 2002, Penzes et al. 2003). EPHBs are also involved in the regulation of dendritic spine morphology through FAK which activates the RHOA-ROCK-LIMK-1 pathway to suppress cofilin activity and inhibit cofilin-mediated dendritic spine remodeling (Shi et al. 2009).
R-HSA-901032 ER Quality Control Compartment (ERQC) Proteins that are released from the CNX or CRT complex with folding defects accumulate in a compartment of the ER called ERQC (Kamhi-Nesher et al. 2001). Here, the enzymes UGGG1 or UGGG2 are able to recognize glycoproteins with minor folding process and re-add the glucose on the alpha,1,3 branch; this is a signal for the transport of these glycoproteins back to the ER, where they can interact again with CNX or CRT in order to achieve a correct folding. At the same time that the glycoprotein is in the ERQC, the enzyme ER mannosidase I progressively removes the mannoses at positions 1A, 2A, B, C on N-glycans; when the mannose on 1A is trimmed, UDP-Glc:glycoprotein glucosyltransferases 1 and 2 (UGGT1 and 2) are no longer able to re-add the glucose, and therefore the protein is destined for ERAD. Glycoproteins subject to endoplasmic reticulum-associated degradation (ERAD) undergo reglucosylation, deglucosylation, and mannose trimming to yield Man6GlcNAc2 and Man5GlcNAc2. These structures lack the mannose residue that is the acceptor of glucose transferred by UGGT1 and 2. For years it has been thought that the removal of the mannose in position B of the N-glycan was the signal to direct proteins to degradation. However, this mechanism has been described better by Avezov et al (Avezov et al. 2008) and it has been demonstrated that even glycoproteins with Man8 or Man7 glycans can be re-glucosylated and interact again with CNX or CRT (for a review on this topic, see Lederkremer 2009 and Maattanen P et al, 2010).
R-HSA-199977 ER to Golgi Anterograde Transport Secretory cargo destined to be secreted or to arrive at the plasma membrane (PM) leaves the ER via distinct exit sites. This cargo is destined for the Golgi apparatus for further processing. About 25% of the proteome may be exported from the ER in human cells. This cargo is recognized and concentrated into COPII vesicles, which range in size from 60-90 nm, and move cargo from the ER to the ERGIC. Soluble cargo in the ER lumen is concentrated into COPII vesicles through interaction with a receptor with the receptor subsequently recycled to the ER in COPI vesicles through retrograde traffic. The ERGIC (ER-to-Golgi intermediate compartment, also known as vesicular-tubular clusters, VTCs) is a stable, biochemically distinct compartment located adjacent to ER exit sites. Retrograde traffic makes use of microtubule-directed COPI-coated vesicles, carrying ER proteins and membrane back to the ER.
R-HSA-1236974 ER-Phagosome pathway The other TAP-dependent cross-presentation mechanism in phagocytes is the endoplasmic reticulum (ER)-phagosome model. Desjardins proposed that ER is recruited to the cell surface, where it fuses with the plasma membrane, underneath phagocytic cups, to supply membrane for the formation of nascent phagosomes (Gagnon et al. 2002). Three independent studies simultaneously showed that ER contributes to the vast majority of phagosome membrane (Guermonprez et al. 2003, Houde et al. 2003, Ackerman et al. 2003). The composition of early phagosome membrane contains ER-resident proteins, the components required for cross-presentation. This model is similar to the phagosome-to-cytosol model in that Ag is translocated to cytosol for proteasomal degradation, but differs in that antigenic peptides are translocated back into the phagosome (instead of ER) for peptide:MHC-I complexes. ER fusion with phagosome introduces molecules that are involved in Ag transport to cytosol (Sec61) and proteasome-generated peptides back into the phagosome (TAP) for loading onto MHC-I.
Although the ER-phagosome pathway is controversial, the concept remains attractive as it explains how peptide-receptive MHC-I molecules could intersect with a relatively high concentration of exogenous antigens, presumably a crucial prerequisite for efficient cross-presentation (Basha et al. 2008).
R-HSA-8847993 ERBB2 Activates PTK6 Signaling PTK6 (BRK) is activated downstream of ERBB2 (HER) (Xiang et al. 2008, Peng et al. 2015) and other receptor tyrosine kinases, such as EGFR (Kamalati et al. 1996) and MET (Castro and Lange 2010). However, it is not clear if MET and EGFR activate PTK6 directly or act through ERBB2, since it is known that ERBB2 forms heterodimers with EGFR (Spivak-Kroizman et al. 1992), and MET can heterodimerize with both EGFR and ERBB2 (Tanizaki et al. 2011).
R-HSA-6785631 ERBB2 Regulates Cell Motility Activated ERBB2 heterodimers regulate cell motility through association with MEMO1. MEMO1 retains activated RHOA GTPase and its associated protein DIAPH1 at the plasma membrane, thus linking ERBB2 activation with the microtubule and actin dynamics downstream of the RHOA:GTP:DIAPH1 complex (Marone et al. 2004, Qiu et al. 2008, Zaoui et al. 2008, Zaoui et al. 2010).
R-HSA-427389 ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression About half of the rRNA genes in the genome are actively expressed, being transcribed by RNA polymerase I (reviewed in Nemeth and Langst 2008, Bartova et al. 2010, Goodfellow and Zomerdijk 2012, Grummt and Langst 2013). As inferred from mouse, those genes that are expressed are activated by ERCC6 (also known as Cockayne Syndrome protein, CSB) which interacts with TTF-I bound to the T0 terminator region (also know as the Sal Box) of rRNA genes (Yuan et al. 2007, reviewed in Birch and Zomerdijk 2008, Grummt and Langst 2013). ERCC6 recruits the histone methyltransferase EHMT2 (also known as G9a) which dimethylates histone H3 at lysine-9 in the coding region of rRNA genes. The dimethylated lysine is bound by CBX3 (also known as Heterochromatic Protein-1gamma, HP1gamma) and increases expression of the rRNA gene. Continuing dimethylation depends on continuing transcription. Mutations in CSB result in dysregulation of RNA polymerase I transcription, which plays a role in the symptoms of Cockayne Syndrome (reviewed in Hannan et al. 2013).
R-HSA-198753 ERK/MAPK targets ERK/MAPK kinases have a number of targets within the nucleus, usually transcription factors or other kinases. The best known targets, ELK1, ETS1, ATF2, MITF, MAPKAPK2, MSK1, RSK1/2/3 and MEF2 are annotated here.
R-HSA-202670 ERKs are inactivated MAP Kinases are inactivated by a family of protein named MAP Kinase Phosphatases (MKPs). They act through dephosphorylation of threonine and/or tyrosine residues within the signature sequence -pTXpY- located in the activation loop of MAP kinases (pT=phosphothreonine and pY=phosphotyrosine). MKPs are divided into three major categories depending on their preference for dephosphorylating; tyrosine, serine/threonine and both the tyrosine and threonine (dual specificity phoshatases or DUSPs). The tyrosine-specific MKPs include PTP-SL, STEP and HePTP, serine/threonine-specific MKPs are PP2A and PP2C, and many DUSPs acting on MAPKs are known. Activated MAP kinases trigger activation of transcription of MKP genes. Therefore, MKPs provide a negative feedback regulatory mechanism on MAPK signaling, by inactivating MAPKs via dephosphorylation, in the cytoplasm and the nucleus. Some MKPs are more specific for ERKs, others for JNK or p38MAPK.
R-HSA-8939211 ESR-mediated signaling Estrogens are a class of hormones that play a role in physiological processes such as development, reproduction, metabolism of liver, fat and bone, and neuronal and cardiovascular function (reviewed in Arnal et al, 2017; Haldosen et al, 2014). Estrogens bind estrogen receptors, members of the nuclear receptor superfamily. Ligand-bound estrogen receptors act as nuclear transcription factors to regulate expression of genes that control cellular proliferation and differentiation, among other processes, but also play a non-genomic role in rapid signaling from the plasma membrane (reviewed in Hah et al, 2014;Schwartz et al, 2016).
R-HSA-162594 Early Phase of HIV Life Cycle In the early phase of HIV lifecycle, an active virion binds and enters a target cell mainly by specific interactions of the viral envelope proteins with host cell surface receptors. The virion core is uncoated to expose a viral nucleoprotein complex containing RNA and viral proteins. HIV RNA genome is reverse transcribed by the viral Reverse Transcriptase to form a cDNA copy, that gets inserted into host cell DNA. The viral Integrase enzyme is vital to carry out the integration of the viral cDNA into the host genome. The host DNA repair enzymes probably repair the breaks in DNA at the sites of integration.
R-HSA-9772572 Early SARS-CoV-2 Infection Events The initial steps of SARS-CoV-2 infection involve the specific binding of the coronavirus spike (S) protein to the cellular entry receptor, angiotensin-converting enzyme 2 (ACE2). The expression and tissue distribution of entry receptors consequently influence viral tropism and pathogenicity. Besides receptor binding, the proteolytic cleavage of coronavirus S proteins by host cell-derived proteases is essential to permit fusion. SARS-CoV has been shown to use the cell-surface serine protease TMPRSS2 for priming and entry, although the endosomal cysteine proteases cathepsin B (CatB) and CatL can also assist in this process. During the intracellular life cycle SARS-CoV-2 express and replicate their genomic RNA to produce full-length copies that are incorporated into newly produced viral particles. Coronaviruses possess remarkably large RNA genomes flanked by 5' and 3' untranslated regions that contain cis-acting secondary RNA structures essential for RNA synthesis. At the 5' end, the genomic RNA features two large open reading frames (ORFs; ORF1a and ORF1b) that occupy two-thirds of the capped and polyadenylated genome. Coronavirus S proteins are homotrimeric class I fusion glycoproteins that are divided into two functionally distinct parts (S1 and S2). The surface-exposed S1 contains the receptor-binding domain (RBD) that specifically engages the host cell receptor, thereby determining virus cell tropism and pathogenicity. Besides receptor binding, the proteolytic cleavage of coronavirus S proteins by host cell-derived proteases is essential to permit fusion. SARS-CoV has been shown to use the cell-surface serine protease TMPRSS2 for priming and entry, although the endosomal cysteine proteases cathepsin B (CatB) and CatL can also assist in this process The release of the coronavirus genome into the host cell cytoplasm upon entry marks the onset of a complex programme of viral gene expression, which is highly regulated in space and time. The translation of ORF1a and ORF1b from the genomic RNA produces two polyproteins, pp1a and pp1ab, respectively. ORF1a and ORF1b encode 15-16 non-structural proteins (nsp), of which 15 compose the viral replication and transcription complex (RTC) that includes, amongst others, RNA-processing and RNA-modifying enzymes and an RNA proofreading function necessary for maintaining the integrity of the >30kb coronavirus genome. The establishment of the viral RTC is crucial for virus replication The release of the coronavirus genome into the host cell cytoplasm upon entry marks the onset of a complex programme of viral gene expression, here divided into early and late.
R-HSA-114508 Effects of PIP2 hydrolysis Hydrolysis of phosphatidyl inositol-bisphosphate (PIP2) by phospholipase C (PLC) produces diacylglycerol (DAG) and inositol triphosphate (IP3). Both are potent second messengers. IP3 diffuses into the cytosol, but as DAG is a hydrophobic lipid it remains within the plasma membrane. IP3 stimulates the release of calcium ions from the smooth endoplasmic reticulum, while DAG activates the conventional and unconventional protein kinase C (PKC) isoforms, facilitating the translocation of PKC from the cytosol to the plasma membrane. The effects of DAG are mimicked by tumor-promoting phorbol esters. DAG is also a precursor for the biosynthesis of prostaglandins, the endocannabinoid 2-arachidonoylglycerol and an activator of a subfamily of TRP-C (Transient Receptor Potential Canonical) cation channels 3, 6, and 7.
R-HSA-391903 Eicosanoid ligand-binding receptors Eicosanoids, derived from polyunsaturated 20-carbon fatty acids, are paracrine and autocrine regulators of inflammation, smooth muscle contraction, and blood coagulation. The actions of eicosanoids are mediated by eicosanoid receptors, most of which are GPCRs. There are four types of eicosanoid GPCRs in humans; leukotriene, lipoxin (Brink C et al, 2003), prostanoid (Coleman RA et al, 1994) and oxoeicosanoid (Brink C et al, 2004) receptors.
R-HSA-211979 Eicosanoids Arachidonic acid is metabolized via three major enzymatic pathways: cyclooxygenase, lipoxygenase, and cytochrome P450. The cytochrome P450 pathway metabolites are oxygenated metabolites of arachidonic acid.
R-HSA-1566948 Elastic fibre formation Elastic fibres (EF) are a major structural constituent of dynamic connective tissues such as large arteries and lung parenchyma, where they provide essential properties of elastic recoil and resilience. EF are composed of a central cross-linked core of elastin, surrounded by a mesh of microfibrils, which are composed largely of fibrillin. In addition to elastin and fibrillin-1, over 30 ancillary proteins are involved in mediating important roles in elastic fibre assembly as well as interactions with the surrounding environment. These include fibulins, elastin microfibril interface located proteins (EMILINs), microfibril-associated glycoproteins (MAGPs) and Latent TGF-beta binding proteins (LTBPs). Fibulin-5 for example, is expressed by vascular smooth muscle cells and plays an essential role in the formation of elastic fibres through mediating interactions between elastin and fibrillin (Yanigasawa et al. 2002, Freeman et al. 2005). In addition, it plays a role in cell adhesion through integrin receptors and has been shown to influence smooth muscle cell proliferation (Yanigasawa et al. 2002, Nakamura et al. 2002). EMILINs are a family of homologous glycoproteins originally identified in extracts of aortas. Found at the elastin-fibrillin interface, early studies showed that antibodies to EMILIN can affect the process of elastic fibre formation (Bressan et al. 1993). EMILIN1 has been shown to bind elastin and fibulin-5 and appears to coordinate their common interaction (Zanetti et al. 2004). MAGPs are found to co-localize with microfibrils. MAGP-1, for example, binds strongly to an N-terminal sequence of fibrillin-1. Other proteins found associated with microfibrils include vitronectin (Dahlback et al. 1990).
Fibrillin is most familiar as a component of elastic fibres but microfibrils with no elastin are found in the ciliary zonules of the eye and invertebrate circulatory systems. The addition of elastin to microfibrils is a vertebrate adaptation to high pulsatile pressures in their closed circulatory systems (Faury et al. 2003). Elastin appears to have emerged after the divergence of jawless vertebrates from other vertebrates (Sage 1982).
Fibrillin-1 is the major structural component of microfibrils. Fibrillin-2 is expressed earlier in development than fibrillin-1 and may be important for elastic fiber formation (Zhang et al. 1994). Fibrillin-3 arose as a duplication of fibrillin-2 that did not occur in the rodent lineage. It was first isolated from human brain (Corson et al. 2004).
Fibrillin assembly is not as well defined as elastin assembly. The primary structure of fibrillin is dominated by calcium binding epidermal growth factor like repeats (Kielty et al. 2002). Fibrillin may form dimers or trimers before secretion. However, multimerisation predominantly occurs outside the cell. Formation of fibrils appears to require cell surface structures suggesting an involvement of cell surface receptors. Fibrillin is assembled pericellularly (i.e. on or close to the cell surface) into microfibrillar arrays that undergo time dependent maturation into microfibrils with beaded-string appearance. Transglutaminase forms gamma glutamyl epsilon lysine isopeptide bonds within or between peptide chains. Additionally, intermolecular disulfide bond formation between fibrillins is an important contributor to fibril maturation (Reinhardt et al. 2000).
Models of fibrillin-1 microfibril structure suggest that the N-terminal half of fibrillin-1 is asymmetrically exposed in outer filaments, while the C-terminal half is buried in the interior (Kuo et al. 2007). Fibrillinopathies include Marfan syndrome, familial ectopia lentis, familial thoracic aneurysm, all due to mutations in the fibrillin-1 gene FBN1, and congenital contractural arachnodactyly which is caused by mutation of FBN2 (Maslen & Glanville 1993, Davis & Summers 2012).
In vivo assembly of fibrillin requires the presence of extracellular fibronectin fibres (Sabatier et al. 2009). Fibrillins have Arg-Gly-Asp (RGD) sequences that interact with integrins (Pfaff et al. 1996, Sakamoto et al. 1996, Bax et al., 2003, Jovanovic et al. 2008) and heparin-binding domains that interact with a cell-surface heparan sulfate proteoglycan (Tiedemann et al. 2001) possibly a syndecan (Ritty et al. 2003). Fibrillins also have a major role in binding and sequestering growth factors such as TGF beta into the ECM (Neptune et al. 2003). Proteoglycans such as versican (Isogai et al. 2002), biglycan, and decorin (Reinboth et al. 2002) can interact with the microfibrils. They confer specific properties including hydration, impact absorption, molecular sieving, regulation of cellular activities, mediation of growth factor association, and release and transport within the extracellular matrix (Buczek-Thomas et al. 2002). In addition, glycosaminoglycans have been shown to interact with tropoelastin through its lysine side chains (Wu et al. 1999), regulating tropoelastin assembly (Tu & Weiss 2008).
Elastin is synthesized as a 70kDa monomer called tropoelastin, a highly hydrophobic protein composed largely of two types of domains that alternate along the polypeptide chain. Hydrophobic domains are rich in glycine, proline, alanine, leucine and valine. These amino acids occur in characteristic short (3-9 amino acids) tandem repeats, with a flexible and highly dynamic structure (Floquet et al. 2004). Unlike collagen, glycine in elastin is not rigorously positioned every 3 residues. However, glycine is distributed frequently throughout all hydrophobic domains of elastin, and displays a strong preference for inter-glycine spacing of 0-3 residues (Rauscher et al. 2006).
Elastic fibre formation involves the deposition of tropoelastin onto a template of fibrillin rich microfibrils. Recent results suggest that the first step of elastic fiber formation is the organization of small globules of elastin on the cell surface followed by globule aggregation into microfibres (Kozel et al. 2006). An important contribution to the initial stages assembly is thought to be made by the intrinsic ability of the protein to direct its own polymeric organization in a process termed 'coacervation' (Bressan et al. 1986). This self-assembly process appears to be determined by interactions between hydrophobic domains (Bressan et al. 1986, Vrhovski et al. 1997, Bellingham et al. 2003, Cirulis & Keeley 2010) which result in alignment of the cross-linking domains, allowing the stabilization of elastin through the formation of cross-links generated through the oxidative deamination of lysine residues, catalyzed by members of the lysyl oxidase (LOX) family (Reiser et al. 1992, Mithieux & Weiss 2005). The first step in the cross-linking reaction is the oxidative formation of the delta aldehyde, known as alpha aminoadipic semialdehyde or allysine (Partridge 1963). Subsequent reactions that are probably spontaneous lead to the formation of cross-links through dehydrolysinonorleucine and allysine aldol, a trifunctional cross-link dehydromerodesmosine and two tetrafunctional cross-links desmosine and isodesmosine (Lucero & Kagan 2006), which are unique to elastin. These cross-links confer mechanical integrity and high durability. In addition to their role in self-assembly, hydrophobic domains provide elastin with its elastomeric properties, with initial studies suggesting that the elastomeric propereties of elastin are driven through changes in entropic interactions with surrounding water molecules (Hoeve & Flory 1974).
A very specific set of proteases, broadly grouped under the name elastases, is responsible for elastin remodelling (Antonicelli et al. 2007). The matrix metalloproteinases (MMPs) are particularly important in elastin breakdown, with MMP2, 3, 9 and 12 explicitly shown to degrade elastin (Ra & Parks 2007). Nonetheless, elastin typically displays a low turnover rate under normal conditions over a lifetime (Davis 1993).
R-HSA-112303 Electric Transmission Across Gap Junctions Electrical synapses are found in all nervous systems, including the human brain. The membranes of the two communicating neurons come extremely close at the synapse and are actually linked together by an intercellular specialization called a gap junction. Gap junctions contain precisely aligned, paired channels in the membrane of the pre- and postsynaptic neurons, such that each channel pair forms a pore. Electrical synapses thus work by allowing ionic current to flow passively through the gap junction pores from one neuron to another. Because passive current flow across the gap junction is virtually instantaneous, communication can occur without the delay that is characteristic of chemical synapses.
R-HSA-2395516 Electron transport from NADPH to Ferredoxin NADPH, ferredoxin reductase (FDXR, Adrenodoxin reductase), and ferredoxins (FDX1, FDX1L) comprise a short electron transport chain that provides electrons for biosynthesis of iron-sulfur clusters and steroid hormones (Sheftel et al. 2010, Shi et al. 2012, reviewed in Grinberg et al. 2000, Lambeth et al. 1982).
R-HSA-139853 Elevation of cytosolic Ca2+ levels Activation of non- excitable cells involves the agonist-induced elevation of cytosolic Ca2+, an essential process for platelet activation. It occurs through Ca2+ release from intracellular stores and Ca2+ entry through the plasma membrane. Ca2+ store release involves phospholipase C (PLC)-mediated production of inositol-1,4,5-trisphosphate (IP3), which in turn stimulates IP3 receptor channels to release Ca2+ from intracellular stores. This is followed by Ca2+ entry into the cell through plasma membrane calcium channels, a process referred to as store-operated calcium entry (SOCE). Stromal interaction molecule 1 (STIM1), a Ca2+ sensor molecule in intracellular stores, and the four transmembrane channel protein Orai1 are the key players in platelet SOCE. Other major Ca2+ entry mechanisms are mediated by the direct receptor-operated calcium (ROC) channel, P2X1 and transient receptor potential channels (TRPCs).
R-HSA-211976 Endogenous sterols A number of CYPs take part in cholesterol biosynthesis and elimination, thus playing an important role in maintaining cholesterol homeostasis. Under normal physiological conditions, cholesterol intake (diet or synthesized de novo from acetyl CoA) equals cholesterol elimination (degraded to bile salts, secreted in bile and used in steroid hormone synthesis). These processes are under tight regulatory control and any disruption leads to increased cholesterol levels resulting in cardiovacular disease. The CYPs involved in cholesterol homeostasis could serve as potential targets for cholesterol-lowering drugs (Lewis 2004, Guengerich 2006, Pikuleva 2006).
R-HSA-917729 Endosomal Sorting Complex Required For Transport (ESCRT) Many plasma membrane proteins are in a constant flux throughout the internal trafficking pathways of the cell. Some receptors are continuously internalized into recycling endosomes and returned to the cell surface. Others are sorted into intralumenal vesicles of morphologically distinctive endosomes that are known as multivesicular bodies (MVBs). These MVBs fuse with lysosomes, resulting in degradation of their cargo by lysosomal acidic hydrolases.
Endosomes can be operationally defined as being either early or late, referring to the relative time it takes for endocytosed material to reach either stage. Ultrastructural studies indicate that early endosomes are predominantly tubulovesicular structures, which constitute a major sorting platform in the cell, whereas late endosomes show the characteristics of typical MVBs and are capable of fusing with lysosomes.
A well characterized signal for shunting membrane proteins into the degradative MVB pathway is the ubiquitylation of these cargoes. At the center of a vast protein:protein and protein:lipid interaction network that underpins ubiquitin mediated sorting to the lysosome are the endosomal sorting complexes required for transport (ESCRTs), which are conserved throughout all major eukaryotic taxa.
R-HSA-1236977 Endosomal/Vacuolar pathway Some antigens are cross-presented through a vacuolar mechanism that involves generation of antigenic peptides and their loading on to MHC-I molecules within the endosomal compartment in a proteasome and TAP-independent manner. Antigens within the endosome are processed by cathepsin S and other proteases into antigenic peptides. Loading of these peptides onto MHC-I molecules occurs directly within early and late endosomal compartments. Why certain antigens are cross-presented exclusively by the cytosolic pathway while others use the vacuolar pathway is unknown. It may be because some epitopes cannot be generated by endosomal proteolysis, or are completely destroyed. Alternatively, the physical form of the antigen may influence its accessibility to the endosomal or vacuolar pathways (Shen et al. 2004).
R-HSA-380972 Energy dependent regulation of mTOR by LKB1-AMPK Upon formation of a trimeric LKB1:STRAD:MO25 complex, LKB1 phosphorylates and activates AMPK. This phosphorylation is immediately removed in basal conditions by PP2C, but if the cellular AMP:ATP ratio rises, this activation is maintained, as AMP binding by AMPK inhibits the dephosphorylation. AMPK then activates the TSC complex by phosphorylating TSC2. Active TSC activates the intrinsic GTPase activity of Rheb, resulting in GDP-loaded Rheb and inhibition of mTOR pathway.
R-HSA-9845620 Enhanced binding of GP1BA variant to VWF multimer:collagen The Reactome event describes gain-of-function variants of glycoprotein Ib α (GPIbα, encoded by GP1BA) that cause macrothrombocytopenia and mucocutaneous bleeding in patients with platelet-type von Willebrand disease (PT-VWD) due to enhanced affinity for von Willebrand factor (VWF).
R-HSA-9845619 Enhanced cleavage of VWF variant by ADAMTS13 Under normal physiological conditions, a disintegrin and metalloproteinase with thrombospondin type 1 repeats 13 (ADAMTS13) downregulates von Willebrand factor (VWF) procoagulant activity by cleaving the peptide bond between Tyr1605 and Met1606 of VWF in a shear-dependent manner. This Reactome event describes von Willebrand disease (VWD)-associated missense mutations VWF Y1584C (Bowen DJ et al., 2005; Keeney S et al., 2007; Pruss CM et al., 2012), I1568N, G1579R, G1631D, and C1099P (Jacobi PM et al., 2012), which showed enhanced susceptibility to ADAMTS13-mediated proteolysis.
R-HSA-168275 Entry of Influenza Virion into Host Cell via Endocytosis Virus particles bound to the cell surface can be internalized by four mechanisms. Most internalization appears to be mediated by clathrin-coated pits, but internalization via caveolae, macropinocytosis, and by non-clathrin, non-caveolae pathways has also been described for influenza viruses.
R-HSA-379398 Enzymatic degradation of Dopamine by monoamine oxidase Alternately dopamine is metabolized to homovanillic acid in a two-step reaction in which dopamine is first oxidized to 3,4-dihydroxypheylacetic acid (DOPAC) and then converted to homovanillic acid by catecholamine o-methyltransferase.
R-HSA-379397 Enzymatic degradation of dopamine by COMT Dopamine once taken up by the dopamine transporter from the extracellular space into the cytosol is metabolized in a two step reaction to homovanillic acid.The first reaction is catalyzed by catecholamine o-methyl transferase and the subsequent reaction is catalyzed by monoamine oxidase A.
R-HSA-3928664 Ephrin signaling The interaction between ephrin (EFN) ligands and EPH receptors results not only in forward signaling through the EPH receptor, but also in 'reverse' signaling through the EFN ligand itself. Reverse signaling through EFNB is required for correct spine morphogenesis and proper path-finding of corpus callosum and dorsal retinal axons. The molecular mechanism by which EFNBs transduce a reverse signal involves phosphorylation of multiple, conserved tyrosines on the intracellular domain of B-type ephrins, facilitating binding of the SH2/SH3 domain adaptor protein GRB4 and subsequent cytoskeletal remodeling (Bruckner et al. 1997, Cowan & Henkemeyer 2001, Lu et al. 2001). The other mechanism of reverse signaling involves the C-terminus PSD-95/Dlg/ZO-1 (PDZ)-binding motif of EFNBs which recruits various PDZ domain containing proteins. Phosphorylation and PDZ-dependent reverse signaling by ephrin-B1 have each been proposed to play important roles in multiple contexts in development and disease (Bush & Soriano 2009).
R-HSA-9917777 Epigenetic regulation by WDR5-containing histone modifying complexes
WDR5 is a component of six histone methyltransferases and three histone acetyltransferases involved in epigenetic regulation of gene expression (reviewed in Guarnaccia and Tansey 2018).
The WDR5 histone methyltransferase complexes (KMT2 complexes) include the Mixed Lineage Leukemia (MLL) 1-4, SET1A, and SET1B. All KMT2 complexes consist of a histone methyltransferase (KMT2A, KMT2B, KMT2C, KMT2D, SETD1A, or SETD1B, respectively) and the WRAD subcomplex composed of WDR5, RBBP5, ASH2L, and DPY30. The WRAD complex regulates the enzymatic activity of histone methyltransferases and enables their recruitment to chromatin. Additional transcription cofactors associate with each KMT2 histone methyltransferase complex, enabling their functional diversification. All KMT2 complexes methylate lysine K5 of histone H3 (K4 in mature histone H3 peptides, as the initiator methionine is removed), which is associated with transcriptional activation. Different KMT2 complexes preferentially monomethylate, dimethylate, or trimethylate H3K4, depending on the presence of accessory subunits, transcriptional co-factors, and posttranslational modifications. The KMT2A and KMT2B complexes preferentially methylate H3K4 at a limited number of target gene promoters, while KMT2C and KMT2D complexes preferentially methylate H3K4 at a limited number of target gene enhancers. SETD1A and SETD1B complexes are responsible for the bulk of cellular H3K4 methylation and show less target specificity. For a detailed overview, please refer to Cho et al. 2007, Song and Kingston 2008, Patel et al. 2009, Wang et al. 2009, Takahashi et al. 2011, Couture and Skiniotis 2013, van Nuland et al. 2013, Rao and Dou 2015, Klonou et al. 2021.
WDR5 is also a component of three histone acetyltransferase complexes, GCN5-ATAC, PCAF-ATAC, and MOF/KAT8-NSL. The role of WDR5 in epigenetic regulation of gene expression through histone acetylation is under investigation (reviewed in Guarnaccia and Tansey 2018).
The KMT2C (MLL3) complex, together with the related KMT2D (MLL4) complex, is most similar to Drosophila Trr (Trithorax-related) and mediates hitone H3 lysine-4 (H3K4 - lysine 5 in nascent histone H3) monomethylation, with the establishment of the H3K4me1 epigenetic marks, at transcription enhancers throughout the human genome, with estimates ranging from approximately 12,000 to over 20,000 sites, depending on the cell type and developmental stage. While H3K4 monomethylation by MLL3 and MLL4 complexes may not be essential for expression of developmental genes, it is likely important for fine tuning of transcription levels and timing, both during normal development and in cancer. For review, please refer to Hu et al. 2013, Piunti and Shilatifard 2016, Fagan and Dingwall 2019, and Klonou et al. 2021.
Based on mouse studies, MLL3 and MLL4 complexes play an important role in adipogenesis and myogenesis. During adipogenesis, the KMT2D (MLL4) complex preferentially localizes to active enhancers, marked by the presence of mono- or dimethylated histone H3 lysine-4 (H3K4me1/2, residue K4 corresponds to residue K5 in nascent histone H3), acetylated H3 lysine-27 (H3K27ac), and the presence of RNA Pol II. KMT2D localizes to these active enhancers together with the adipogenic transcription factors CEBPB, CEBPA, and PPARG, and is especially enriched at high confidence enhancers that are both CEBP and PPARG positive (Lee et al. 2013).
R-HSA-9851695 Epigenetic regulation of adipogenesis genes by MLL3 and MLL4 complexes During adipogenesis, the KMT2D (MLL4) complex preferentially localizes to active enhancers, marked by the presence of mono- or dimethylated histone H3 lysine-4 (H3K4me1/2, residue K4 corresponds to residue K5 in nascent histone H3), acetylated H3 lysine-27 (H3K27ac), and the presence of RNA Pol II. KMT2D localizes to these active enhancers together with the adipogenic transcription factors CEBPB, CEBPA, and PPARG, and is especially enriched at high confidence enhancers that are both CEBP and PPARG positive (Lee et al. 2013). Single Kmt2c (Mll3) knockout in mouse brown preadipocytes led to a modest decrease of H3K4me1, while double Kmt2c;Kmt2d (Mll4) knockout led to a global decrease of H3K4me1/2 (Lee et al. 2013). Most MLL4-binding sites are marked by both H3K4me1 and H3K4me2 during adipogenesis (Lee et al. 2013). Double knockout of Kmt2c and Kmt2d in differentiating mouse adipocytes prevented increase in H3K4me1/2, H3K27ac, Mediator complex and RNA Pol II on adipogenic enhancers, specifically on Cebpa and Pparg gene loci (Lee et al. 2013). KMT2D-dependent deposition of H3K4me1/2 marks was also detected on some adipogenic promoters, but was less pronounced than on adipogenic enhancers (Lee et al. 2013). Deletion of Kmt2d significantly decreased expression of genes associated with Kmt2d+ adipogenic enhancers (Lee et al. 2013). The expression of KMT2C, the catalytic subunit of the MLL3 complex, is upregulated during brown adipocyte differentiation (Son et al. 2016).Cytosolic enzymes capable of oxidizing acetaldehyde to acetate have also been identified and characterized in vitro (Inoue et al. 1979) so a purely cytosolic pathway for ethanol oxidation to acetate and conversion to acetyl-CoA can be annotated. The role of this pathway in vivo is unclear, though limited attempts to correlate deficiencies in the cytosolic enzyme with alcohol intolerance have yielded suggestive data (Yoshida et al. 1989). Additional peroxisomal and microsomal pathways for the oxidation of ethanol to acetaldehyde have been described; their physiological significance is unclear and they are not annotated here.
R-HSA-156842 Eukaryotic Translation Elongation The translation elongation cycle adds one amino acid at a time to a growing polypeptide according to the sequence of codons found in the mRNA. The next available codon on the mRNA is exposed in the aminoacyl-tRNA (aa-tRNA) binding site (A site) on the 30S subunit.
A: Ternary complexes of aa -tRNA:eEF1A:GTP enter the ribosome and enable the anticodon of the tRNA to make a codon/anticodon interaction with the A-site codon of the mRNA. B: Upon cognate recognition, the eEF1A:GTP is brought into the GTPase activating center of the ribosome, GTP is hydrolyzed and eEF1A:GDP leaves the ribosome. C: The peptidyl transferase center of ribosome catalyses the formation of a peptide bond between the incoming amino acid and the peptide found in the peptidyl-tRNA binding site (P site). D: In the pre-translocation state of the ribosome, the eEF2:GTP enters the ribosome, physically translocating the peptidyl-tRNA out of the A site to P site and leaves the ribosome eEF2:GDP. This action of eEF2:GTP accounts for the precise movement of the mRNA by 3 nucleotides.Consequently, deacylated tRNA is shifted to the E site. A ribosome associated ATPase activity is proposed to stimulate the release of deacylated tRNA from the E site subsequent to translocation (Elskaya et al., 1991). In this post-translocation state, the ribosome is now ready to receive a new ternary complex.
This process is illustrated below with: an amino acyl-tRNA with an amino acid, a peptidyl-tRNA with a growing peptide, a deacylated tRNA with an -OH, and a ribosome with A,P and E sites to accommodate these three forms of tRNA.
R-HSA-72613 Eukaryotic Translation Initiation Initiation of translation in the majority of eukaryotic cellular mRNAs depends on the 5'-cap (m7GpppN) and involves ribosomal scanning of the 5' untranslated region (5'-UTR) for an initiating AUG start codon. Therefore, this mechanism is often called cap-dependent translation initiation. Proximity to the cap, as well as the nucleotides surrounding an AUG codon, influence the efficiency of the start site recognition during the scanning process. However, if the recognition site is poor enough, scanning ribosomal subunits will ignore and skip potential starting AUGs, a phenomenon called leaky scanning. Leaky scanning allows a single mRNA to encode several proteins that differ in their amino-termini. Merrick (2010) provides an overview of this process and hghlights several features of it that remain incompletely understood.
Several eukaryotic cell and viral mRNAs initiate translation by an alternative mechanism that involves internal initiation rather than ribosomal scanning. These mRNAs contain complex nucleotide sequences, called internal ribosomal entry sites, where ribosomes bind in a cap-independent manner and start translation at the closest downstream AUG codon.
Initiation on several viral and cellular mRNAs is cap-independent and is mediated by binding of the ribosome to internal ribosome entry site (IRES) elements. These elements are often found in characteristically long structured regions on the 5'-UTR of an mRNA that may or may not have regulatory upstream open reading frames (uORFs). Both of these features on the 5'-end of the mRNA hinder ribosomal scanning, and thus promote a cap-independent translation initiation mechanism. IRESs act as specific translational enhancers that allow translation initiation to occur in response to specific stimuli and under the control of different trans-acting factors, as for example when cap-dependent protein synthesis is shut off during viral infection. Such regulatory elements have been identified in the mRNAs of growth factors, protooncogenes, angiogenesis factors, and apoptosis regulators, which are translated under a variety of stress conditions, including hypoxia, serum deprivation, irradiation and apoptosis. Thus, cap-independent translational control might have evolved to regulate cellular responses in acute but transient stress conditions that would otherwise lead to cell death, while the same mechanism is of major importance for viral mRNAs to bypass the shutting-off of host protein synthesis after infection. Encephalomyocarditis virus (EMCV) and hepatitis C virus exemplify two distinct mechanisms of IRES-mediated initiation. In contrast to cap-dependent initiation, the eIF4A and eIF4G subunits of eIF4F bind immediately upstream of the EMCV initiation codon and promote binding of a 43S complex. Accordingly, EMCV initiation does not involve scanning and does not require eIF1, eIF1A, and the eIF4E subunit of eIF4F. Nonetheless, initiation on some EMCV-like IRESs requires additional non-canonical initiation factors, which alter IRES conformation and promote binding of eIF4A/eIF4G. Initiation on the hepatitis C virus IRES is simpler: a 43S complex containing only eIF2 and eIF3 binds directly to the initiation codon as a result of specific interaction of the IRES and the 40S subunit.
R-HSA-72764 Eukaryotic Translation Termination The arrival of any of the three stop codons (UAA, UAG and UGA) into the ribosomal A-site triggers the binding of a release factor (RF) to the ribosome and subsequent polypeptide chain release. In eukaryotes, the RF is composed of two proteins, eRF1 and eRF3. eRF1 is responsible for the hydrolysis of the peptidyl-tRNA, while eRF3 provides a GTP-dependent function. The ribosome releases the mRNA and dissociates into its two complex subunits, which can reassemble on another molecule to begin a new round of protein synthesis. It should be noted that at present, there is no factor identified in eukaryotes that would be the functional equivalent of the bacterial ribosome release (or recycling) factor, RRF, that catalyzes dissociation of the ribosome from the mRNA following release of the polypeptide
R-HSA-9833109 Evasion by RSV of host interferon responses Infection with human respiratory syncytial virus (hRSV) is typically associated with low to undetectable levels of type I interferons (IFNs). Several hRSV proteins interact with host innate immune system factors that support the type I interferon response. Nonstructural proteins NS1 and NS2 localize to mitochondria and nucleus where they bind MAVS, DDX58, TRIM25, IRF3, and CREBBP, affecting DDX58/IFIH1-mediated interferon induction (reviewed by Thornhill & Verhoeven, 2020). Additionally, hRSV nucleoprotein interacts with MDA5 downregulating the interferon response and with PKR (EIF2AK2) blocking the innate immune system signal for shutting down protein translation. Further interactions of the M, SH, and G proteins are reviewed by van Royen et al, 2022.
R-HSA-9630791 Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 Missense mutations and small indels in the CDKN2A gene, which result in amino acid changes in p16INK4A that impair its ability to bind to CDK4, interfere with p16INK4A-mediated induction of cellular senescence in response to oncogenic signaling (Jones et al. 2007).
Loss-of-function mutations in p16INK4A can also contribute to cancer by interfering with p16INK4A-mediated inhibition of NFKB signaling (Becker et al. 2005).
R-HSA-9630794 Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 Missense and nonsense mutations in the CDKN2A gene that result in amino acid substitutions in p16INK4A or p16INK4A truncations, impairing its ability to bind to CDK4 and CDK6, interfere with p16INK4A-mediated induction of cellular senescence in response to oncogenic signaling (Haferkamp et al. 2008).
Loss-of-function mutations in p16INK4A can also contribute to cancer by interfering with p16INK4A-mediated inhibition of NFKB signaling (Becker et al. 2005).
R-HSA-9646303 Evasion of Oncogene Induced Senescence Due to p14ARF Defects In cell culture, p14ARF (CDKN2A transcript 4, CDKN2A-4, ARF), one of the two main protein products of the CDKN2A gene, contributes to oncogene induced senescence by stabilizing TP53 (p53). The function of p14ARF in p53 stabilization through sequestration of MDM2, a p53 ubiquitin ligase, depends on the nuclear localization of p14ARF and its ability to interact with MDM2. The nuclear localization signal and the MDM2 interaction domain map to the first 15 amino acids of the N-terminus of p14ARF. This region is encoded by the p14ARF-specific exon 1beta of CDKN2A. An independent MDM2-binding domain localized to the C-terminus of p14ARF (Lohrum et al. 2000). Insertion of 16 nucleotides in exon 1beta results in a frameshift truncation of p14ARF, responsible for a familial melanoma syndrome in which the p16INK4A product of the CDKN2A gene is unaffected. This mutation is rare and has so far been reported in one family only. The mutant protein, p14ARF V22Pfs*46 has the nucleotide localization signal and the N-terminal MDM2 interaction region preserved, but is unable to translocate from the cytosol to the nucleus, possibly due to aberrant conformation (Rizos, Puig et al. 2001), and also lacks the C-terminal MDM2 interaction region. Relocation of wild type p14ARF to the cytosol has been observed in melanoma (Rizos, Darmanian et al. 2001) and aggressive thyroid papillary carcinoma (Ferru et al. 2006). Genomic deletion of exon 1beta, with exons 1alpha, 2 and 3 intact, has been reported in about 30% of melanoma cases with genomic deletions involving the CDKN2A locus (Freedberg et al. 2008). Several different familial melanoma germline mutations map to the exon 1beta splice donor site (Harland et al. 2005).
The ability of p14ARF to localize to the nucleolus also plays a role in p14ARF-mediated stabilization of p53. Mutations in exon 2 of the CDKN2A gene can lead to missense mutations in p14ARF that affect its nucleolar localization and p53 stabilization, but the exact mechanism has not been fully elucidated (Zhang and Xiong 1999, reviewed by Fontana et al. 2019).
R-HSA-9630750 Evasion of Oncogene Induced Senescence Due to p16INK4A Defects The CDKN2A gene consists of four exons, exon 1beta, exon 1alpha, exon 2 and exon 3, going from the proximal to the distal gene end. There are two promoters in the CDKN2A gene locus. The promoter located between exons 1beta and 1alpha regulates transcription of the p16INK4A mRNA, which consists of exon 1alpha, exon 2 and exon 3 (only partially translated), and encodes a cyclin-dependent kinase inhibitor p16INK4A (also known as CDKN2A isoform 1, p16, INK4A, CDKN2A, CDK4I or MTS-1). The promoter located upstream of exon 1beta regulates transcription of the p14-ARF mRNA, which consists of exon 1beta, exon 2 (partially translated) and exon 3 (untranslated). The p14ARF mRNA is translated in a different reading frame from the p16INK4A mRNA and produces the tumor suppressor ARF (also known as p14ARF or CDKN2A isoform 4), an inhibitor of MDM2 E3 ubiquitin ligase-mediated degradation of TP53 (p53).
Wild type p16INK4A is able to form a complex with either CDK4 or CDK6 and prevent formation of catalytically active CDK complexes consisting of CDK4 or CDK6 and D-type cyclins (CCND). Thus, p16INK4A prevents hyperphosphorylation of RB-family proteins, required for initiation of DNA replication in RB1-competent cells. Expression of p16INK4A increases in response to strong oncogenic signaling, leading to accelerated cellular senescence (programmed cell cycle arrest). Expression of p16INK4A also increases after excessive proliferation, including that following oncogene activation by mutation in vivo. Loss-of-function of p16INK4A frequently occurs in cancer, usually through loss of p16INK4A protein expression due to promoter hypermethylation or CDKN2A gene deletion (Merlo et al. 1995, Herman et al. 1995, Gonzalez-Zulueta et al. 1995, Wong et al. 1997, Witkiewicz et al. 2011, Shima et al. 2011, Tamayo-Orrego et al. 2016). Missense, nonsense and frameshift mutations in the CDKN2A locus can also impair p16INK4A function through expression of non-functional substitution mutants or truncated proteins (Kamb et al. 1994, Bartsch et al. 1995, Castellano et al. 1997). Germline intronic CDKN2A mutations that create aberrant splicing sites and result in expression of non-functional splicing variants of p16INK4A have been reported in familial melanoma (Harland et al. 2001, Harland et al. 2005). A CDKN2A gene mutation in the region encoding the 5'UTR of p16INK4A, reported in familial melanoma, creates a novel translation start codon and diminishes translation from the wild type start codon (Liu et al. 1999). However, mutations in the non-coding regions of the CDKN2A gene are rare (Pollock et al. 2001).
Based on cell culture studies, p16INK4A defects enable precancerous and cancerous cells to delay or evade senescence under oncogenic signaling stress (Ruas et al. 1999, Haferkamp et al. 2008, Rayess et al. 2012, Jeanblanc et al. 2012, LaPak and Burd 2014, Sharpless and Sherr 2015). Establishment of an in vivo role of oncogene induced senescence, and thus an in vivo role of p16INK4A in this context, have been difficult owing to lack of specific biomarkers and interconnectedness of various senescence triggers (Baek and Ryeom 2017, reviewed in Sharpless and Sherr 2015).
Genomic deletions in the CDKN2A locus affect p14ARF, unless they are limited to exon 1alpha. The p14ARF promoter can also be hypermethylated in cancer, leading to loss of p14ARF expression. Some missense mutations occurring in exon 2 of the CDKN2A gene affect the p14ARF protein sequence. However, p14ARF mutants usually appear to be less functionally compromised than their p16INK4A counterparts. Most functional tests on p14ARF mutants examine the effect of mutations on MDM2 binding and TP53-mediated transcription of CDKN1A (p21), as well as sub-nuclear localization of p14ARF (Zhang and Xiong 1999, Schmitt et al. 1999, Eischen et al. 1999, Pinyol et al. 2000, Bostrom et al. 2001, Laud et al. 2006). Still, there are poorly explored functions of p14ARF that may be significantly affected in mutant p14ARF proteins detected in cancer (Itahana and Zhang 2008, Dominguez-Brauer et al. 2010).
R-HSA-9632697 Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 Missense mutations and small indels in the CDKN2A gene, which result in amino acid changes in p16INK4A that impair its ability to bind to CDK4, interfere with p16INK4A-mediated, oxidative stress-induced, cellular senescence (Chen 2000, Vurusaner et al. 2012).
Loss-of-function mutations in p16INK4A can also contribute to cancer by interfering with p16INK4A-mediated inhibition of NFKB signaling (Becker et al. 2005).
R-HSA-9632700 Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 Missense and nonsense mutations in the CDKN2A gene that result in amino acid substitutions in p16INK4A or p16INK4A truncations, respectively, impairing its ability to bind to CDK4 and CDK6, interfere with p16INK4A-mediated induction of cellular senescence in response to oxidative stress (Chen 2000, Vurusaner et al. 2012).
Loss-of-function mutations in p16INK4A can also contribute to cancer by interfering with p16INK4A-mediated inhibition of NFKB signaling (Becker et al. 2005).
R-HSA-9646304 Evasion of Oxidative Stress Induced Senescence Due to p14ARF Defects One of the two main protein products of the CDKN2A gene, p14ARF (CDKN2A transcript 4, CDKN2A-4, ARF), contributes to oxidative stress induced cellular senescence by stabilizing TP53 (p53). The function of p14ARF in p53 stabilization through sequestration of MDM2, a p53 ubiquitin ligase, depends on the nuclear localization of p14ARF and its ability to interact with MDM2. The nuclear localization signal and the MDM2 interaction domain map to the first 15 amino acids of the N-terminus of p14ARF. This region is encoded by the p14ARF-specific exon 1beta of CDKN2A. An independent MDM2-binding domain is localized at the C-terminus of p14ARF (Lohrum et al. 2000). Insertion of 16 nucleotides in exon 1beta results in a frameshift truncation of p14ARF, responsible for a familial melanoma syndrome in which the p16INK4A product of the CDKN2A gene is unaffected. This mutation is rare and has so far been reported in one family only. The mutant protein, p14ARF V22Pfs*46 has the nucleotide localization signal and the N-terminal MDM2 interaction region preserved, but is unable to translocate from the cytosol to the nucleus, possibly due to aberrant conformation (Rizos, Puig et al. 2001), and also lacks the C-terminal MDM2 interaction region. Relocation of wild type p14ARF to the cytosol has been observed in melanoma (Rizos, Darmanian et al. 2001) and aggressive thyroid papillary carcinoma (Ferru et al. 2006). Genomic deletion of exon 1beta, with exons 1alpha, 2 and 3 intact, has been reported in about 30% of melanoma cases with genomic deletions involving the CDKN2A locus (Freedberg et al. 2008). Several different familial melanoma germline mutations map to the exon 1beta splice donor site (Harland et al. 2005).
The ability of p14ARF to localize to the nucleolus also plays a role in p14ARF-mediated stabilization of p53. Mutations in exon 2 of the CDKN2A gene can lead to missense mutations in p14ARF that affect its nucleolar localization and p53 stabilization, but the exact mechanism has not been fully elucidated (Zhang and Xiong 1999, reviewed by Fontana et al. 2019).
R-HSA-9632693 Evasion of Oxidative Stress Induced Senescence Due to p16INK4A Defects The CDKN2A gene consists of four exons, exon 1beta, exon 1alpha, exon 2 and exon 3, going from the proximal to the distal gene end. There are two promoters in the CDKN2A gene locus. The promoter located between exons 1beta and 1alpha regulates transcription of the p16INK4A mRNA, which consists of exon 1alpha, exon 2 and exon 3 (only partially translated), and encodes a cyclin-dependent kinase inhibitor p16INK4A (also known as CDKN2A isoform 1, p16, INK4A, CDKN2A, CDK4I or MTS-1). The promoter located upstream of exon 1beta regulates transcription of the p14ARF mRNA, which consists of exon 1beta, exon 2 (partially translated) and exon 3 (untranslated). The p14ARF mRNA is translated in a different reading frame from the p16INK4A mRNA and produces the tumor suppressor ARF (also known as p14ARF or CDKN2A isoform 4), an inhibitor of MDM2 E3 ubiquitin ligase-mediated degradation of TP53 (p53).
Wild type p16INK4A is able to form a complex with either CDK4 or CDK6 and prevent formation of catalytically active CDK complexes consisting of CDK4 or CDK6 and D-type cyclins (CCND). Thus, p16INK4A prevents hyperphosphorylation of RB-family proteins, required for initiation of DNA replication in RB1-competent cells. Expression of p16INK4A increases in response to oxidative stress, leading to cellular senescence (programmed cell cycle arrest) under conditions of prolonged oxidative stress. Loss-of-function of p16INK4A frequently occurs in cancer, usually through loss of p16INK4A protein expression due to promoter hypermethylation or CDKN2A gene deletion (Merlo et al. 1995, Herman et al. 1995, Gonzalez-Zulueta et al. 1995, Wong et al. 1997, Witkiewicz et al. 2011, Shima et al. 2011, Tamayo-Orrego et al. 2016). Missense, nonsense and frameshift mutations in the CDKN2A locus can also impair p16INK4A function through expression of non-functional substitution mutants or truncated proteins (Kamb et al. 1994, Bartsch et al. 1995, Castellano et al. 1997). Germline intronic CDKN2A mutations that create aberrant splicing sites and result in expression of non-functional splicing variants of p16INK4A have been reported in familial melanoma (Harland et al. 2001, Harland et al. 2005). A CDKN2A gene mutation in the region encoding the 5'UTR of p16INK4A, reported in familial melanoma, creates a novel translation start codon and diminishes translation from the wild type start codon (Liu et al. 1999). However, mutations in the non coding regions of the CDKN2A gene are rare (Pollock et al. 2001).
p16INK4A defects enable cancerous cells to evade cell cycle arrest and senescence under prolonged oxidative stress (Tanaka et al. 1999, Chen 2000, Chen et al. 2004, Vurusaner et al. 2012, Rayess et al. 2012, LaPak and Burd 2014, Sharpless and Sherr 2015, Zhang et al. 2017). A cell cycle-independent role of p16INK4A in regulation of intracellular oxidative stress has been reported (Jenkins et al. 2011, Vurusaner et al. 2012, Jenkins et al. 2013).
Genomic deletions in the CDKN2A locus affect p14ARF, unless they are limited to exon 1alpha. The p14ARF promoter can also be hypermethylated in cancer, leading to loss of p14ARF expression. Some missense mutations occurring in exon 2 of the CDKN2A gene affect the p14ARF protein sequence. However, p14ARF mutants usually appear to be less functionally compromised than their p16INK4A counterparts. Most functional tests on p14ARF mutants examine the effect of mutations on MDM2 binding and TP53-mediated transcription of CDKN1A (p21), as well as sub-nuclear localization of p14ARF (Zhang and Xiong 1999, Schmitt et al. 1999, Eischen et al. 1999, Pinyol et al. 2000, Bostrom et al. 2001, Laud et al. 2006). Still, there are poorly explored functions of p14ARF that may be significantly affected in mutant p14ARF proteins detected in cancer (Itahana and Zhang 2008, Dominguez-Brauer et al. 2010).
R-HSA-8941413 Events associated with phagocytolytic activity of PMN cells When neutrophils engulf bacteria they enclose them in small vacuoles (phagosomes) into which superoxide is released by activated NADPH oxidase (NOX2) on the internalized neutrophil membrane. The directional nature of NOX2 activity creates a charge imbalance that must be counteracted to prevent depolarization of the membrane and the shutdown of activity (Winterbourn CC et al. 2016). Also, protons are produced in the cytosol and consumed in the external compartment (for example, the phagosome) through the dismutation of superoxide. Both situations are largely overcome by a balancing flow of protons transported by voltage-gated proton channels, primarily VSOP/HV1, which are activated in parallel with the oxidase (Demaurex N & El Chemaly A 2010; El Chemaly A et al. 2010; Petheo GL et al. 2010; Kovacs I et al. 2014; Henderson LM et al. 1987, 1988). The pH of the phagosome is regulated by these activities. In contrast to the phagosomes of macrophages, in which pH drops following particle ingestion, neutrophil phagosomes remain alkaline during the period that the oxidase is active. Until recently, their pH has been accepted to lie between 7.5 and 8. However, in a 2015 study using a probe that is more sensitive at higher pH, an average pH closer to 9 was measured in individual phagosomes (Levine AP et al. 2015).
The superoxide dismutates to hydrogen peroxide, which is used by myeloperoxidase (MPO) to generate other oxidants, including the highly microbicidal species such as hypochlorous acid (Winterbourn CC et al. 2013, 2016).
R-HSA-168274 Export of Viral Ribonucleoproteins from Nucleus Influenza genomic RNA (vRNA), synthesized in the nucleus of the infected host cell, is packaged into ribonucleoprotein (RNP) complexes containing viral polymerase proteins and NP (nucleocapsid). NP trimers bind the sugar phosphate backbone of the vRNA. As influenza viral RNP complexes are too large for passive diffusion out of the nucleus, utilization of the cellular nuclear export machinery is achieved by viral adaptor proteins. Matrix protein (M1) is critical for export of the complex from the nucleus, mediating the interaction of the RNP complex with the viral NEP/NS2 protein, which in turn interacts with host cell CRM1/exportin-1 nuclear export protein (Martin, 1991; O'Neill, 1998; Neumann et al., 2000; Elton, 2001; Cros, 2003; Ye, 2006; reviewed in Boulo, 2006).
R-HSA-9036866 Expression and Processing of Neurotrophins Neurotrophins function as ligands for receptor tyrosine kinases of the NTRK (TRK) family, as well as the death receptor NGFR (p75NTR). While all four neurotrophins, NGF, BDNF, NTF3 (NT-3) and NTF4 (NT-4, NT-5, NTF5) can bind to and activate NGFR, they show different specificity for NTRKs. NGF exclusively activates NTRK1 (TRKA). BDNF and NTF4 are high affinity ligands for NTRK2 (TRKB). NTF3 is a high affinity ligand for NTRK3 (TRKC) and a low affinity ligand for NTRK2. Neurotrophins play pivotal roles in survival, differentiation, and plasticity of neurons in the peripheral and central nervous system. They are produced, and secreted in minute amounts, by a variety of tissues. For review, please refer to Lessmann et al. 2003, Chao 2003, and Park and Poo 2013.
Human NGF, also knowns as the nerve growth factor, is encoded by a gene on chromosome 1, which produces a single transcript. Nascent NGF protein, pre-pro-NGF, is 241 amino acids long. As pre-pro-NGF enters the endoplasmic reticulum (ER), the signal peptide, consisting of eighteen amino acids at the N-terminus, is cleaved, producing pro-NGF. Two molecules of pro-NGF form homodimers in the ER. After transport of pro-NGF homodimers to the Golgi, 103 amino acids at the N-terminus of pro-NGF are cleaved, producing mature NGF homodimers. Both pro-NGF homodimers and mature NGF homodimers are secreted to the extracellular space. Mature NGF homodimers activate NTRK1 signaling, while NGFR signaling can be activated by both mature and pro-NGF homodimers. Secreted pro-NGF homodimers may be cleaved by extracellular matrix proteases to produce mature NGF homodimers. For review, please refer to Poo 2001, Lu et al. 2005, Skaper et al. 2012, Bradshaw et al. 2015.
Human BDNF, also known as brain-derived neurotrophic factor, is encoded by a gene on chromosome 11, which, through the use of 9 alternative promoters and alternative splicing, produces 17 protein-coding transcripts. Most BDNF transcripts result in the same pre-pro-BDNF protein of 247 amino acids, but alternative promoters and different 5' and 3’UTRs allow to fine-tune regulation of BDNF expression at different developmental stages and at different levels of neuronal activity. Similar to NGF, pre-pro-BDNF is processed by proteolytic cleavage in the ER to produce pro-BDNF homodimers. It is unclear whether proteolytic processing of pro-BDNF, to produce mature BDNF homodimers, occurs in the Golgi or in the secretory granules. Extracellular matrix proteases can also cleave secreted pro-BDNF to produce mature BDNF homodimers. Secreted mature BDNF homodimers can activate NTRK2 signaling, while secreted pro-BDNF homodimers can activate NGFR signaling. For review, please refer to Poo 2001, Lu et al. 2005, Skaper et al. 2012, Park and Poo 2013.
Human NTF4, also known as neurotrophin-4, is transcribed from a gene on chromosome 19. A single experimentally confirmed transcript produces a pre-pro-NTF4 protein of 210 amino acids. After proteolytic processing in the ER and Golgi, mature NTF4 homodimers are secreted and can activate NTRK2 signaling (Hibbert et al. 2003). For review, please refer to Poo 2001, Skaper et al. 2012.
Human NTF3, also known as neurotrophin-3, is transcribed from a gene on chromosome 12. Two NTF3 transcripts have been experimentally confirmed, but only the longer NTF3 splice variant of 270 amino acids has been studied. After proteolytic processing in the ER and Golgi, mature NTF3 homodimers are secreted and can activate NTRK3 signaling (Seidah et al. 1996, Farhadi et al. 2000). For review, please refer to Poo 2001, Skaper et al. 2012.
R-HSA-9752946 Expression and translocation of olfactory receptors Olfactory receptors (ORs) are 7-pass transmembrane G protein-coupled receptors (GPCRs) located on dendritic cilia of olfactory sensory neurons (OSNs) of the olfactory epithelium (reviewed in Persuy et al. 2015). ORs are also located on cells of some other tissues (reviewed in Oh 2015). ORs bind ligands, called odorants, and activate downstream signaling through a heterotrimeric G-protein leading to opening of olfactory cyclic nucleotide-gated channels (CNG channels) and depolarization of the OSN. The human genome contains about 857 OR genes of which about 394 appear to be capable of encoding a functional OR. The remaining putative OR genes appear to be pseudogenes functionally inactivated by mutations.
Each OR binds a particular odorant or family of odorants. In order to provide odor discrimination, each OSN expresses only one OR gene and connects to specific olfactory bulb glomeruli according to the specific OR expressed (reviewed in Monahan and Lomvardas 2015, McClintock et al. 2020, Sakano et al. 2020). The choice of which OR gene to express is made by an epigenetic mechanism (reviewed in Bashkirova and Lomvardas 2019). Initially during OSN development, OR genes are heterochromatic. A few OR genes become weakly expressed and one then becomes dominant while all other OR genes remain silenced by heterochromatin. During activation of an OR gene, LHX2, LDB1, and EBF1 bind several (~60) intergenic enhancers located between OR genes on 18 chromosomes. The LHX2:LDB1:EBF1:enhancer complexes assemble into an interchromosomal super-enhancer that associates with the expressed OR gene and drives transcription.
Accumulation of OR protein in the endoplasmic reticulum membrane activates the unfolded protein response (UPR) that activates translation of ADCY3, which downregulates the histone methyltransferase KDM1A (LSD1) thereby preventing activation of any other OR genes (Lyons et al. 2013, Dalton et al. 2013).
Most OR proteins are inefficiently translocated from the endoplasmic reticulum membrane to the plasma membrane when they are expressed in heterologous cells. OSNs contain specific proteins that act as chaperones to increase subcellular translocation of at least some ORs (reviewed in Mainland and Matsunami 2012). The short isoform of RTP1 (RTP1S) and RTP2 bind the OR in the endoplasmic reticulum, are translocated with the OR to the plasma membrane, and remain at the plasma membrane. REEP1 more weakly increases translocation of ORs by an uncharacterized mechanism.
R-HSA-180786 Extension of Telomeres Telomerase acts as reverse transcriptase in the elongation of telomeres (Smogorzewska and de Lange 2004).
R-HSA-9009391 Extra-nuclear estrogen signaling In addition to its well-characterized role in estrogen-dependent transcription, estrogen (beta-estradiol, also known as E2) also plays a rapid, non-genomic role through interaction with receptors localized at the plasma membrane by virtue of dynamic palmitoylation. Estrogen receptor palmitoylation is a prerequisite for the E2-dependent activation of extra-nuclear signaling both in vitro and in animal models (Acconcia et al, 2004; Acconcia et al, 2005; Marino et al, 2006; Marino and Ascenzi, 2006). Non-genomic signaling through the estrogen receptor ESR1 also depends on receptor arginine methylation by PMRT1 (Pedram et al, 2007; Pedram et al, 2012; Le Romancer et al, 2008; reviewed in Arnal, 2017; Le Romancer et al, 2011 ).
E2-evoked extra-nuclear signaling is independent of the transcriptional activity of estrogen receptors and occurs within seconds to minutes following E2 administration to target cells. Extra-nuclear signaling consists of the activation of a plethora of signaling pathways including the RAF/MAP kinase cascade and the PI3K/AKT signaling cascade and governs processes such as apoptosis, cellular proliferation and metastasis (reviewed in Hammes et al, 2007; Handa et al, 2012; Lange et al, 2007; Losel et al, 2003; Arnal et al, 2017; Le Romancer et al, 2011). ESR-mediated signaling also cross-talks with receptor tyrosine kinase, NF- kappa beta and GPCR signaling pathways by modulating the post-translational modification of enzymes and other proteins and regulating second messengers (reviewed in Arnal et al, 2017; Schwartz et al, 2016; Boonyaratanakornkit, 2011; Biswas et al, 2005). In the nervous system, E2 affects neural functions such as cognition, behaviour, stress responses and reproduction in part by inducing such rapid extra-nuclear responses (Farach-Carson and Davis, 2003; Losel et al, 2003), while in endothelial cells, non-genomic ESR-dependent signaling also regulates vasodilation through the eNOS pathway (reviewed in Levin, 2011).
Extra-nuclear signaling additionally cross-talks with nuclear estrogen receptor signaling and is required to control ER protein stability (La Rosa et al, 2012)
Recent data have demonstrated that the membrane ESR1 can interact with various endocytic proteins to traffic and signal within the cytoplasm. This receptor intracellular trafficking appears to be dependent on the phyical interaction of ESR1 with specific trans-membrane receptors such as IGR-1R and beta 1-integrin (Sampayo et al, 2018)
R-HSA-1474244 Extracellular matrix organization The extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded in a viscoelastic gel of anionic proteoglycan polymers. It performs many functions in addition to its structural role; as a major component of the cellular microenvironment it influences cell behaviours such as proliferation, adhesion and migration, and regulates cell differentiation and death (Hynes 2009).
ECM composition is highly heterogeneous and dynamic, being constantly remodeled (Frantz et al. 2010) and modulated, largely by matrix metalloproteinases (MMPs) and growth factors that bind to the ECM influencing the synthesis, crosslinking and degradation of ECM components (Hynes 2009). ECM remodeling is involved in the regulation of cell differentiation processes such as the establishment and maintenance of stem cell niches, branching morphogenesis, angiogenesis, bone remodeling, and wound repair. Redundant mechanisms modulate the expression and function of ECM modifying enzymes. Abnormal ECM dynamics can lead to deregulated cell proliferation and invasion, failure of cell death, and loss of cell differentiation, resulting in congenital defects and pathological processes including tissue fibrosis and cancer.
Collagen is the most abundant fibrous protein within the ECM constituting up to 30% of total protein in multicellular animals. Collagen provides tensile strength. It associates with elastic fibres, composed of elastin and fibrillin microfibrils, which give tissues the ability to recover after stretching. Other ECM proteins such as fibronectin, laminins, and matricellular proteins participate as connectors or linking proteins (Daley et al. 2008).
Chondroitin sulfate, dermatan sulfate and keratan sulfate proteoglycans are structural components associated with collagen fibrils (Scott & Haigh 1985; Scott & Orford 1981), serving to tether the fibril to the surrounding matrix. Decorin belongs to the small leucine-rich repeat proteoglycan family (SLRPs) which also includes biglycan, fibromodulin, lumican and asporin. All appear to be involved in collagen fibril formation and matrix assembly (Ameye & Young 2002).
ECM proteins such as osteonectin (SPARC), osteopontin and thrombospondins -1 and -2, collectively referred to as matricellular proteins (reviewed in Mosher & Adams 2012) appear to modulate cell-matrix interactions. In general they induce de-adhesion, characterized by disruption of focal adhesions and a reorganization of actin stress fibers (Bornstein 2009). Thrombospondin (TS)-1 and -2 bind MMP2. The resulting complex is endocytosed by the low-density lipoprotein receptor-related protein (LRP), clearing MMP2 from the ECM (Yang et al. 2001).
Osteopontin (SPP1, bone sialoprotein-1) interacts with collagen and fibronectin (Mukherjee et al. 1995). It also contains several cell adhesive domains that interact with integrins and CD44.
Aggrecan is the predominant ECM proteoglycan in cartilage (Hardingham & Fosang 1992). Its relatives include versican, neurocan and brevican (Iozzo 1998). In articular cartilage the major non-fibrous macromolecules are aggrecan, hyaluronan and hyaluronan and proteoglycan link protein 1 (HAPLN1). The high negative charge density of these molecules leads to the binding of large amounts of water (Bruckner 2006). Hyaluronan is bound by several large proteoglycans proteoglycans belonging to the hyalectan family that form high-molecular weight aggregates (Roughley 2006), accounting for the turgid nature of cartilage.
The most significant enzymes in ECM remodeling are the Matrix Metalloproteinase (MMP) and A disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS) families (Cawston & Young 2010). Other notable ECM degrading enzymes include plasmin and cathepsin G. Many ECM proteinases are initially present as precursors, activated by proteolytic processing. MMP precursors include an amino prodomain which masks the catalytic Zn-binding motif (Page-McCawet al. 2007). This can be removed by other proteinases, often other MMPs. ECM proteinases can be inactivated by degradation, or blocked by inhibitors. Some of these inhibitors, including alpha2-macroglobulin, alpha1-proteinase inhibitor, and alpha1-chymotrypsin can inhibit a large variety of proteinases (Woessner & Nagase 2000). The tissue inhibitors of metalloproteinases (TIMPs) are potent MMP inhibitors (Brew & Nagase 2010).
R-HSA-140834 Extrinsic Pathway of Fibrin Clot Formation Factor VII, the protease that initiates the normal blood clotting cascade, circulates in the blood in both its proenzyme (factor VII) and its activated (factor VIIa) forms. No clotting occurs, however, because neither form of the protein has any catalytic activity when free in solution. Blood clotting is normally initiated when tissue factor (TF), an intrinsic plasma membrane protein, is exposed to the blood by injury to the wall of a blood vessel. TF is then able to bind factor VIIa from plasma, and possibly also factor VII, to form complexes capable of catalyzing the conversion of factor X, from plasma, into its activated form, factor Xa. Factor Xa catalyzes the conversion of additional factor VII molecules to their activated form, increasing the amount of tissue factor:factor VIIa complex available at the site of injury, accelerating the generation of factor Xa, and allowing the activation of factor IXa as well. This process is self-limiting because as levels of factor Xa increase, tissue factor:factor VIIa complexes become trapped in the form of catalytically inactive heterotetramers with factor Xa and the protein TFPI (tissue pathway factor inhibitor). At this point the intinsic pathway, as an independent source of activated factor X, is thought to become critical for the continuation of clot formation (Broze 1995; Mann et al. 2003).
The nature of the initial tissue factor:factor VII complexes formed is controversial. One model, building on the observation that the complex of factor VII and TF has low but measurable proteolytic activity on factor X, suggests that this complex begins the activation of factor X, and that as factor VIIa accumulates, tissue factor:factor VIIa complexes also form, accelerating the process (Nemerson 1988). A second model, building on the observation that normal plasma contains low levels of activated factor VII constitutively, suggests that complexes with factor VIIa form immediately at the onset of clotting (Rapaport and Rao 1995). The two models are not mutually exclusive, and in any event, the central roles of tissue factor and factor VIIa in generating an initial supply of factors IXa and Xa, and the self-limiting nature of the process due to the action of TFPI, are all well-established.
R-HSA-9837092 FASTK family proteins regulate processing and stability of mitochondrial RNAs Fas-activated serine/threonine kinase (FASTK) and its homologs FASTKD1-5 each contain three conserved domains (FAST_1, FAST_2, and RAP) that bind RNA (Castello et al. 2012, Baltz et al. 2012). FASTKD1-5 and the short isoform of FASTK localize to mitochondria where they participate in regulating the processing and stability of RNA (Simarro et al. 2010, reviewed in Jourdain et al. 2017).
FASTK interacts with the 3' end of the MT-ND6 mRNA and protects the mRNA from degradation by the degradosome, SUPV3L1:PNPT1 (Jourdain et al. 2015). The MT-ND6 mRNA is unusual in being processed from the large L-strand precursor without flanking tRNA genes and thus without canonical processing by RNAse P and RNase Z. FASTK may, therefore, participate in an uncharacterized non-canonical mechanism of RNA processing or protect 3' ends produced by such a mechanism.
FASTKD1 acts to reduce the abundance of the MT-ND3 mRNA by an uncharacterized mechanism (Boehm et al. 2017).
FASTKD2 binds the 16S rRNA and the MT-ND6 mRNA and participates in their processing and expression (Antonicka and Shoubridge 2015, Popow et al. 2015). FASTKD2 interacts with several mitochondrial proteins including MTERFD1, TRUB2, WBSCR16, and NGRN (Antonicka et al. 2017).
FASTKD3 increases levels of five mitochondrial mRNAs (MT-ND2, MT-ND3, MT-CYB, MT-CO2, and the MT-ATP8/6 bicistronic mRNA) and increases translation of MT-CO1 mRNA through uncharacterized mechanisms (Boehm et al. 2016, Ohkubo et al. 2021).
TBRG4 (FASTKD4) binds most RNAs transcribed from the H-strand and enhances the expression levels of MT-ATP8/6, MT-CO1, MT-CO2, MT-CO3, MT-ND3, MT-CYB, and MT-ND5 mRNAs (Wolf and Mootha 2014, Boehm et al. 2017, Ohkubo et al. 2021). TBRG4 stabilizes MT-CO1, MT-ND3, and MT-CO2 mRNAs and assists the processing of MT-ND5 and MT-CYB mRNAs (Boehm et al. 2017, Ohkubo et al. 2021).
FASTKD5 binds 12S rRNA and all mRNAs except MT-ND3 and reduces levels of MT-ATP8/6, MT-CO1, MT-CO3, MT-ND5, and MT-CYB mRNAs (Antonicka and Shoubridge 2015, Ohkubo et al. 2021). .
R-HSA-8854050 FBXL7 down-regulates AURKA during mitotic entry and in early mitosis The protein levels of aurora kinase A (AURKA) during mitotic entry and in early mitosis can be reduced by the action of the SCF-FBXL7 E3 ubiquitin ligase complex consisting of SKP1, CUL1, RBX1 and FBXL7 subunits. FBXL7 is the substrate recognition subunit of the SCF-FBXL7 complex that associates with the centrosome-bound AURKA, promoting its ubiquitination and proteasome-mediated degradation. Overexpression of FBXL7 results in G2/M cell cycle arrest and apoptosis (Coon et al. 2011).
FBXL7 protein levels are down-regulated by the action of the SCF-FBXL18 E3 ubiquitin ligase complex, consisting of SKP1, CUL1, RBX1 and the substrate recognition subunit FBXL18. FBXL18 binds to the FQ motif of FBXL7, targeting it for ubiquitination and proteasome-mediated degradation, counteracting its pro-apoptotic activity (Liu et al. 2015). Cell cycle stage-dependency of down-regulation of FBXL7 by FBXL18 is unknown.
R-HSA-2644605 FBXW7 Mutants and NOTCH1 in Cancer FBXW7 (FBW7) is a component of the SCF (SKP1, CUL1, and F-box protein) ubiquitin ligase complex SCF-FBW7 which is involved in the degradation of NOTCH1 (Oberg et al. 2001, Wu et al. 2001, Fryer et al. 2004). Loss of function mutations in FBXW7 are frequently found in T-cell acute lymphoblastic leukemia (Akhoondi et al. 2007, Thompson et al. 2007, O'Neil et al. 2007) and are mutually exclusive with NOTCH1 PEST domain mutations (Thompson et al. 2007, O'Neil et al. 2007).
R-HSA-2871809 FCERI mediated Ca+2 mobilization Increase of intracellular calcium in mast cells is most crucial for mast cell degranulation. Elevation of intracellular calcium is achieved by activation of PLC-gamma. Mast cells express both PLC-gamma1 and PLC-gamma2 isoforms and activation of these enzymes leads to conversion of phosphatidylinositol 4,5-bisphosphate (PIP2) into inositol triphosphate (IP3) and diacylglycerol (DAG). The production of IP3 leads to mobilization of intracellular Ca+2, which later results in a sustained Ca+2 flux response that is maintained by an influx of extracellular Ca+2. In addition to degranulation, an increase in intracellular calcium concentration also activates the Ca2+/calmodulin-dependent serine phosphatase calcineurin. Calcineurin dephosphorylates the nuclear factor for T cell activation (NFAT) which exposes nuclear-localization signal sequence triggering translocation of the dephosphorylated NFAT-CaN complex to the nucleus. Once in the nucleus, NFAT regulates the transcription of several cytokine genes (Kambayashi et al. 2007, Hoth & Penner 1992, Ebinu et al. 2000, Siraganian et al).
R-HSA-2871796 FCERI mediated MAPK activation Formation of the LAT signaling complex leads to activation of MAPK and production of cytokines. The sequence of events that leads from LAT to cytokine production has not been as clearly defined as the sequence that leads to degranulation. However, the pathways that lead to cytokine production require the guanine-nucleotide-exchange factors SOS and VAV that regulate GDP-GTP exchange of RAS. After its activation, RAS positively regulates the RAF-dependent pathway that leads to phosphorylation and, in part, activation of the mitogen-activated protein kinases (MAPKs) extracellular-signal-regulated kinase 1 (ERK1) and ERK2 (Gilfillan & Tkaczyk 2006).
R-HSA-2871837 FCERI mediated NF-kB activation The increase in intracellular Ca+2 in conjunction with DAG also activates PKC and RasGRP, which inturn contributes to cytokine production by mast cells (Kambayashi et al. 2007). Activation of the FCERI engages CARMA1, BCL10 and MALT1 complex to activate NF-kB through PKC-theta (Klemm et al. 2006, Chen et al. 2007). FCERI stimulation leads to phosphorylation, and degradation of IkB which allows the release and nuclear translocation of the NF-kB proteins. Activation of the NF-kB transcription factors then results in the synthesis of several cytokines. NF-kB activation by FCERI is critical for proinflammatory cytokine production during mast cell activation and is crucial for allergic inflammatory diseases (Klemm et al. 2006).
R-HSA-2029481 FCGR activation Cross-linking of FCGRs with IgG coated immune complexes results in tyrosine phosphorylation of the immuno tyrosine activation motif (ITAMs) of the rececptor by membrane-bound tyrosine kinases of the SRC family. The phosphorylated ITAM tyrosines serve as docking sites for Src homology 2 (SH2) domain-containing SYK kinase. Recruitment and activation of SYK is critical for FCGR-mediated signaling in phagocytosis, but the exact role of SYK in this process is unclear. Activated SYK then transmits downstream signals leading to actin polymerization and particle internalization.
R-HSA-9664323 FCGR3A-mediated IL10 synthesis Interleukin 10 (IL-10) is an important immunoregulatory cytokine produced by many cell populations; in macrophages it is induced after the stimulation of TLRs, Fcγ receptors or by the TLR-FcγR crosstalk (Vogelpoel et al. 2014 & Saninet al. 2015). Classically, its function is considered to be the limitation and termination of inflammatory responses and the regulation of differentiation of several immune cells (Asadullah et al. 2003). There is increasing evidence of the role of IL-10 in parasite infection outcomes either as a protective or a pathological mediator (Asadullah et al. 2003). In the context of the parasitic disease cutaneous leishmaniasis, Leishmania amastigotes opsonized by IgG induce IL-10 response through FcγRs, which in turn supresses the killing mechanisms in phagocytic cells. (Chu et al. 2010).
R-HSA-9664422 FCGR3A-mediated phagocytosis The Fc gamma receptors (FCGRs) have been reported to facilitate Leishmania internalization, especially when in its amastigote form (Ueno et al. 2012). Following cell-to-cell propagation within an established infection or reinfection of a previously infected host, the IgG produced by the host covers the surface of Leishmania amastigote parasites, making them more susceptible to phagocytosis through FCGRs (Polando et al. 2013).
Classically, phagocytosis via FCGRs has been associated with the subsequent activation of Rac GTPases and Cdc42 which in turn activate the phagocyte's NADPH oxidase, contributing to the activation of killing mechanisms (Ueno et al. 2012).
R-HSA-190242 FGFR1 ligand binding and activation The vertebrate fibroblast growth factor receptor 1 (FGFR1) is alternatively spliced generating multiple variants that are differentially expressed during embryo development and in the adult body. The restricted expression patterns of FGFR1 isoforms, together with differential expression and binding of specific ligands, leads to activation of common FGFR1 signal transduction pathways, but may result in distinctively different biological responses as a result of differences in cellular context. FGFR1 isoforms are also present in the nucleus in complex with various fibroblast growth factors where they function to regulate transcription of target genes.
FGFR is probably activated by NCAM very differently from the way by which it is activated by FGFs, reflecting the different conditions for NCAM-FGFR and FGF-FGFR interactions. The affinity of FGF for FGFR is approximately 10e6 times higher than that of NCAM for FGFR. Moreover, in the brain NCAM is constantly present on the cell surface at a much higher (micromolar) concentration than FGFs, which only appear transiently in the extracellular environment in the nanomolar range.
R-HSA-1839124 FGFR1 mutant receptor activation The FGFR1 gene has been shown to be subject to activating mutations, chromosomal rearrangements and gene amplification leading to a variety of proliferative and developmental disorders depending on whether these events occur in the germline or arise somatically (reviewed in Webster and Donoghue, 1997; Burke, 1998; Cunningham, 2007; Wesche, 2011; Greulich and Pollock, 2011). Many of the resulting mutant FGFR1 proteins can dimerize and promote signaling in a ligand-independent fashion, although signal transduction may still be amplified in the presence of ligand (reviewed in Turner and Gross, 2010; Greulich and Pollock, 2011; Wesche et al, 2011).
R-HSA-190370 FGFR1b ligand binding and activation This pathway depicts the binding of an experimentally-verified range of ligands to FGFR1b. While binding affinities may vary considerably within this set, the ligands listed have been established to bring about receptor activation at their reported physiological concentrations.
R-HSA-190374 FGFR1c and Klotho ligand binding and activation FGF23 is a member of the endocrine subfamily of FGFs. It is produced in bone tissue and regulates kidney functions. Klotho is essential for endogenous FGF23 function as it converts FGFR1c into a specific FGF23 receptor.
R-HSA-190373 FGFR1c ligand binding and activation This pathway depicts the binding of an experimentally-verified range of ligands to FGFR1c. While binding affinities may vary considerably within this set, the ligands listed have been established to bring about receptor activation at their reported physiological concentrations.
R-HSA-6803529 FGFR2 alternative splicing Alternative splicing of the FGFR2 nascent mRNA generates an epithelial specific isoform (FGFR2 IIIb) and a mesenchymal specific isoform (FGFR2 IIIc). The inclusion of exon 8 in FGFR2 IIIb or exon 9 in FGFR2 IIIc alters the C-terminal half of the D3 loop of the receptor and is responsible for the different ligand-binding specificities of the two isoforms (reviewed in Eswarakumar et al, 2005). In recent years, a number of cis- and trans-acting elements have been identified that regulate the alternative splicing event. Exon IIIb repression is mediated by the presence of weak splice sites flanking the exon, an exonic silencing sequence (ESS) within the IIIb exon and both intronic silencing sequences (ISS) upstream and downstream (Carstens et al, 2000; Del Gatto and Breathnach, 1995; Del Gatto et al, 1996; Wagner et al 2005; Wagner and Garcia-Blanco, 2001). Binding of hnRNPA1, PTB1, SR family proteins and other factors to these elements represses the IIIb exon and promotes FGFR2 IIIc expression in mesenchymal cells (Del Gatto-Konczak et al, 1999; Carstens et al, 2000; Wagner et al, 2005; Wagner and Garcia-Blanco, 2001; Wagner and Garcia-Blanco, 2002). In epithelial cells, recruitment of epithelial specific factors shifts the splicing events to favour inclusion of exon 8. ESPN1 and ESPN2 are epithelial-specific factors that bind to an ISE/ISS-3 (intronic splicing enhancer/intronic splicing silencer-3) region within intron 8 to promote FGFR2 IIIb-specific splicing (Warzecha et al, 2009). A complex of RBFOX2, hnRNPH1 and hnRNPF also contribute to epithelial-specific splicing by competing for binding to a site that is occupied by the SR proteins ASF/SF2 in mesenchymal cells (Baraniak et al, 2006; Mauger et al, 2008). Other proteins and sequences have also been identified that appear to contribute to the regulated expression of FGFR2b and FGFR2c, but the full details of the alternative splicing event remain to be worked out (Muh et al, 2002; Newman et al, 2006; Del Gatto et al, 2000; Hovhannisyan and Carstens, 2007).
R-HSA-190241 FGFR2 ligand binding and activation Dominant mutations in the fibroblast growth factor receptor 2 (FGFR2) gene have been identified as causes of four phenotypically distinct craniosynostosis syndromes, including Crouzon, Jackson- Weiss, Pfeiffer, and Apert syndromes. FGFR2 binds a number of different FGFs preferentially, as illustrated in this pathway.
FGFR is probably activated by NCAM very differently from the way by which it is activated by FGFs, reflecting the different conditions for NCAM-FGFR and FGF-FGFR interactions. The affinity of FGF for FGFR is approximately 10e6 times higher than that of NCAM for FGFR. Moreover, in the brain NCAM is constantly present on the cell surface at a much higher (micromolar) concentration than FGFs, which only appear transiently in the extracellular environment in the nanomolar range.
R-HSA-1839126 FGFR2 mutant receptor activation Autosomal dominant mutations in FGFR2 are associated with the development of a range of skeletal disorders including Beare-Stevensen cutis gyrata syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome, Crouzon syndrome and Apert Syndrome (reveiwed in Burke, 1998; Webster and Donoghue 1997; Cunningham, 2007). Activating point mutations have also been identified in FGFR2 in ~15% of endometrial cancers, as well as to a lesser extent in ovarian and gastric cancers (Dutt, 2008; Pollock, 2007; Byron, 2010; Jang, 2001). Activating mutations in FGFR2 are thought to contribute to receptor activation through diverse mechanisms, including constitutive ligand-independent dimerization (Robertson, 1998), expanded range and affinity for ligand (Ibrahimi, 2004b; Yu, 2000) and enhanced kinase activity (Byron, 2008; Chen, 2007). FGFR2 amplifications have been identified in 10% of gastric cancers, where they are associated with poor prognosis diffuse cancers (Hattori, 1996; Ueda, 1999; Shin, 2000; Kunii, 2008) , and in ~1% of breast cancers (Turner, 2010; Tannheimer, 2000). FGFR2 amplification often occur in conjunction with deletions of C-terminal exons, resulting in expression of a internalization- and degradation-resistant form of the receptor (Takeda, 2007; Cha, 2008, 2009). Signaling through overexpressed FGFR2 shows evidence of being ligand-independent and sensitive to FGFR inhibitors (Lorenzi, 1997; Takeda, 2007; Cha, 2009). More recently, FGFR2 fusion proteins have been identified in a number of cancers; these are thought to form constitutive ligand-independent dimers based on the dimerization domains of the 3' fusion partners and contribute to cellular proliferation and tumorigenesis in a kinase-inhibitor sensitive manner (Wu, 2013; Arai, 2013; Seo, 2012; reviewed in Parker, 2014).
R-HSA-190377 FGFR2b ligand binding and activation This pathway depicts the binding of an experimentally-verified range of ligands to FGFR2b. While binding affinities may vary considerably within this set, the ligands listed have been established to bring about receptor activation at their reported physiological concentrations.
R-HSA-190375 FGFR2c ligand binding and activation This pathway depicts the binding of an experimentally-verified range of ligands to FGFR2c. While binding affinities may vary considerably within this set, the ligands listed have been established to bring about receptor activation at their reported physiological concentrations.
R-HSA-190239 FGFR3 ligand binding and activation FGFR3 is a receptor tyrosine kinase of the FGF receptor family, known to have a negative regulatory effect on long bone growth. Somatically, some of the same activating mutations are associated with hypochondroplasia, multiple myeloma, and cervical and vesical carcinoma.
R-HSA-2033514 FGFR3 mutant receptor activation The FGFR3 gene has been shown to be subject to activating mutations and gene amplification leading to a variety of proliferative and developmental disorders depending on whether these events occur in the germline or arise somatically. As is the case for the other receptors, many of the activating mutations that are seen in FGFR3-related cancers mimic the germline FGFR3 mutations that give rise to autosomal skeletal disorders and include both ligand-dependent and independent mechanisms (reviewed in Webster and Donoghue, 1997; Burke et al, 1998; Wesche et al, 2011). In addition to activating mutations, the FGFR3 gene is subject to a translocation event in 15% of multiple myelomas (Avet-Loiseau et al, 1998; Chesi et al, 1997). This chromosomal rearrangement puts the FGFR3 gene under the control of the highly active IGH promoter and promotes overexpression and constitutive activation of FGFR3 (Otsuki et al, 1999). In a small proportion of multiple myelomas, the translocation event is accompanied by activating mutations in the FGFR3 coding sequence (Chesi et al, 1997; Onwuazor et al, 2003; Ronchetti et al, 2001).
Finally, FGFR3 is subject to fusion events in a number of cancers, including lung, bladder and glioblastoma (Singh et al, 2012; Parker et al, 2013; Williams et al, 2013; Wu et al, 2013; Capelletti et al, 2014; Yuan et al, 2014; Wang et al, 2014; Carneiro et al, 2015; reviewed in Parker et al, 2014). These fusions are constitutively active based on dimerization domains provided by the fusion partners and support transformation and proliferation through downstream signaling pathways such as ERK and AKT (Singh et al, 2012; Williams et al, 2013; Parker et al, 2013; reviewed in Parker et al, 2014).
R-HSA-190371 FGFR3b ligand binding and activation This pathway depicts the binding of an experimentally-verified range of ligands to FGFR3b. While binding affinities may vary considerably within this set, the ligands listed have been established to bring about receptor activation at their reported physiological concentrations.
R-HSA-190372 FGFR3c ligand binding and activation This pathway depicts the binding of an experimentally-verified range of ligands to FGFR3c. While binding affinities may vary considerably within this set, the ligands listed have been established to bring about receptor activation at their reported physiological concentrations.
R-HSA-190322 FGFR4 ligand binding and activation FGFR4 is expressed mainly in mature skeletal muscle, and disruption of FGFR4 signaling interrupts limb muscle formation in vertebrates.
R-HSA-1839128 FGFR4 mutant receptor activation FGFR4 is perhaps the least well studied of the FGF receptors, and unlike the case for the other FGFR genes, mutations in FGFR4 are not known to be associated with any developmental disorders. Recently, however, somatically arising mutations in the FGFR4 coding sequence have begun to be identified in some cancers. (Taylor, 2009; Ruhe, 2007; Roidl, 2010). The resulting mutant versions of FGFR4 promote aberrant signaling through ligand-independent dimerization and enhanced autophosphorylation, among other mechanisms (Roidl, 2009; Taylor, 2009).
R-HSA-5658623 FGFRL1 modulation of FGFR1 signaling FGFRL1 is a fifth member of the FGFR family of receptors. The extracellular region has 40% sequence similarity with FGFR1-4, but FGFRL1 lacks the internal kinase domain of the other FGF receptors and how it acts in FGFR signaling is unclear. Some models suggest FGFRL1 restricts canonical FGFR signaling by sequestering ligand away from kinase-active receptors, while other models suggest that FGFRL1 may promote canonical signaling by nucleating signaling complexes or enhancing ERK1/2 activation (reviewed in Trueb, 2011; Trueb et al, 2013).
R-HSA-9607240 FLT3 Signaling Feline McDonough Sarcoma-like tyrosine kinase (FLT3) (also known as FLK2 (fetal liver tyrosine kinase 2), STK-1 (stem cell tyrosine kinase 1) or CD135) is a member of the class III receptor tyrosine kinase family involved in the differentiation, proliferation and survival of hematopoietic progenitor cells and of dendritic cells. Upon FLT3 ligand (FL) binding, the receptor forms dimers and is phosphorylated. Consequently, adapter and signaling molecules bind with the active receptor and trigger the activation of various pathways downstream including PI3K/Akt and MAPK cascades (Grafone T et al. 2012).
R-HSA-9702509 FLT3 mutants bind TKIs Aberrant signaling by activated forms of FLT3 can be inhibited by tyrosine kinase inhibitors (TKIs). FLT3 receptors are class III receptor tyrosine kinase receptors, also known as dual-switch. Dual-switch receptors are activated through a series of phosphorylation and conformational changes that move the receptor from the inactive form to the fully activated form. Type II TKIs bind to the inactive form of the receptor at a site adjacent to the ATP-binding cleft, while type I TKIs bind to the active form (reviewed in Klug et al, 2018; Daver et al, 2019).
FLT3 internal tandem duplications (ITDs) are found in ~25-30% of acute myeloid leukemias, and are present at lower frequencies in other cancers (reviewed in Kazi and Roostrand, 2019; Patnaik et al, 2018). These ITDs generally occur in a tyrosine-rich region of exon 14, encoding the juxtamembrane domain region of the protein; at a lower frequency, ITDs are found in the first tyrosine kinase domain (TKD1). In addition to ITDs, a number of point mutations in the juxtamembrane domain have also been identified. Juxtamembrane domain mutations affect an autoinhibitory loop, shifting the equilibrium of the receptor towards the activated state; despite this, however, juxtamembrane domain mutants remain predominantly in the inactive state and as such are susceptible to inhibition by type II TKIs (reviewed in Patnaik et al, 2018; Kazi and Roonstrand et al, 2019).
Activation loop mutations more strongly favor the active conformation of the receptor and are susceptible to inhibition by both type II and type I TKIs. The most prevalent FLT3 mutation, D835Y, promotes the active conformation strongly enough to be resistant to type II TKIs (Patnaik et al, 2017; Klug et al, 2018; Daver et al, 2019).
R-HSA-9706377 FLT3 signaling by CBL mutants Missense and splicing mutants have been identified in the E3 ubiquitin ligase CBL in a number of cancers including acute and chronic myeloid leukemias, among others. These cancers show elevated signaling through FLT3 as a result of impaired CBL-mediated downregulation of the receptor (Sargin et al, 2007; Reindl et al, 2009; Caligiuri et al, 2007; Abbas et al, 2008).
R-HSA-9682385 FLT3 signaling in disease FLT3 is a type III receptor tyrosine kinase (RTK). The extracellular domain consists of 5 immunoglobulin (Ig) domains that contribute to dimerization and ligand binding. The intracellular region has a juxtamembrane domain that plays a role in autoinhibiting the receptor in the absence of ligand, and a bi-lobed kinase region with an activation loop and the catalytic cleft (reviewed in Klug et al, 2018). Signaling through FLT3 occurs after ligand-induced dimerization and transautophosphorylation, and promotes signaling through the MAP kinase, PI3K and STAT5 pathways, among others. FLT3 signaling promotes cellular proliferation and differentiation and contributes to haematopoeisis. FLT3 is mutated in up to 30% of acute myeloid leukemias. ~25% of the FLT3 mutations in AML cases occur as internal tandem duplications (ITDs) either in the juxtamembrane domain region encoded by exon 14 or the tyrosine kinase domain (TKD), while ~7-10% of AML cases contain FLT3 missense mutations in the TKD (reviewed in Klug et al, 2018; Daver et al, 2019). These mutations all support ligand-independent activation of the receptor and result in constitutive activation and signaling (Zheng et al, 2004; reviewed in Klug et al, 2018; Kazi and Roonstrand, 2019). In rare cases, the FLT3 locus is also subject to translocations that generate constitutively active fusion proteins (reviewed in Kazi and Roonstrand, 2019). Oncogenic FLT3 activity can be targeted with tyrosine kinase inhibitors, although resistance often arises due to secondary mutations or activation of bypass pathways (reviewed in Staudt et al, 2018; Daver et al, 2019).
R-HSA-9706374 FLT3 signaling through SRC family kinases Several SRC family kinases (SFKs) have been shown to interact with active FLT3 to modulate downstream signaling. These include FYN, HCK, LCK and SYK (Heiss et al, 2006; Mitina et al, 2007; Chougule et al, 2016; Dosil et al, 1993; Marhall et al, 2017; Puissant et al, 2014; reviewed in Kazi and Ronnstrand, 2019a,b). The role of SFKs downstream of FLT3 is complex and not fully elucidated. Some family members appear to contribute positively to signaling, as assessed by elevated STAT5 signaling, while others may contribute to ubiquitin ligation and downregulation of the receptor through interaction with CBL (Chougule et al, 2016; Heiss et al, 2006; Marhall et al, 2017; reviewed in Kazi and Ronnstrand, 2019a,b).
R-HSA-217271 FMO oxidises nucleophiles Flavin-containing monooxygenases (FMOs) are the second family of microsomal oxidative enzymes with broad and overlapping specificity. The major reactions FMOs catalyze are nucleophilic hetero-atom compounds such as nitrogen, sulfur or phosphorus as the hetero-atom to form N-oxides, S-oxides or P-oxides respectively. Despite the functional overlap with cytochrome P450s, the mechanism of action differs. FMOs bind and activate molecular oxygen before the substrate binds to the enzyme (picture). They also require flavin adenosine dinucleotide (FAD) as a cofactor. Unlike cytochrome P450 enzymes, FMOs are heat-labile, a useful way to distinguish which enzyme system is at work for researchers studying metabolism. Also, FMOs are not inducible by substrates, unlike the P450 enzymes.\n(1) NADPH binds to the enzyme and reduces the prosthetic group FAD to FADH2. NADP+ remains bound to the enzyme.\n(2) Incorporation of molecular oxygen to form a hydroperoxide.\n(3) A peroxide oxygen is transferred to the substrate.\n(4) Water is released.\n(5) NADP+ dissociates returning the enzyme to its initial state.\n\nTo date, there are 6 isozymes of FMO (FMO1-6) in humans, the most prominent and active one being FMO3. The FMO6 gene does not encode for a functional enzyme although it has the greatest sequence similarity with FMO3 (71%), whilst the others range from 50-58% sequence similarity with FMO3. FMO1-3 are the ones that exhibit activity towards nucleophiles, the others are insignificant in this respect (Cashman 2003, Krueger & Williams 2005).
R-HSA-9614085 FOXO-mediated transcription The family of FOXO transcription factors includes FOXO1, FOXO3, FOXO4 and FOXO6. FOXO transcription factors integrate pathways that regulate cell survival, growth, differentiation and metabolism in response to environmental changes, such as growth factor deprivation, starvation and oxidative stress (reviewed by Accili and Arden 2004, Calnan and Brunet 2008, Eijkelenboom and Burgering 2013).
R-HSA-9617828 FOXO-mediated transcription of cell cycle genes FOXO transcription factors induce expression of several genes that negatively regulate proliferation of different cell types, such as erythroid progenitors (Bakker et al. 2004, Wang et al. 2015) and neuroepithelial progenitor cells in the telencephalon (Seoane et al. 2004).
Transcription of cyclin-dependent kinase (CDK) inhibitors CDKN1A (p21Cip1) is directly stimulated by FOXO1, FOXO3 and FOXO4 (Seoane et al. 2004, Tinkum et al. 2013). FOXO transcription factors can cooperate with the SMAD2/3:SMAD4 complex to induce CDKN1A transcription in response to TGF-beta signaling (Seoane et al. 2004).
FOXO transcription factors FOXO1, FOXO3 and FOXO4 stimulate transcription of the CDKN1B (p27Kip1) gene, but direct binding of FOXOs to the CDKN1B gene locus has not been demonstrated (Dijkers et al. 2000, Medema et al. 2000, Lees et al. 2008).
FOXO3 and FOXO4, and possibly FOXO1, directly stimulate transcription of the GADD45A gene (Tran et al. 2002, Furukawa Hibi et al. 2002, Hughes et al. 2011, Sengupta et al. 2011, Ju et al. 2014).
Transcription of the retinoblastoma family protein RBL2 (p130), involved in the maintenance of quiescent (G0) state, is directly stimulated by FOXO1, FOXO3 and FOXO4 (Kops et al. 2002, Chen et al. 2006).
Transcription of the anti-proliferative protein CCNG2 is directly stimulated by FOXO1 and FOXO3, and possibly FOXO4 (Martinez Gac et al. 2004, Chen et al. 2006). Transcription of the anti-proliferative protein BTG1 is directly stimulated by FOXO3 (Bakker et al. 2004, Bakker et al. 2007, Wang et al. 2015).
Transcription of CAV1, encoding caveolin-1, involved in negative regulation of growth factor receptor signaling and establishment of quiescent cell phenotype, is directly stimulated by FOXO1 and FOXO3 (van den Heuvel et al. 2005, Roy et al. 2008, Nho et al. 2013, Sisci et al. 2013).
FOXO1 and FOXO3 promote transcription of the KLF4 gene, encoding a transcription factor Krueppel-like factor 4, which inhibits proliferation of mouse B cells (Yusuf et al. 2008).
FOXO1, together with the p-2S-SMAD2/3:SMAD4 complex, stimulates transcription of the MSTN gene, encoding myostatin, a TGF-beta family member that stimulates differentiation of myoblasts (Allen and Unterman 2007).
R-HSA-9614657 FOXO-mediated transcription of cell death genes FOXO transcription factors promote expression of several pro-apoptotic genes, such as FASLG (Brunet et al. 1999, Ciechomska et al. 2003, Chen et al. 2013, Li et al. 2015), PINK1 (Mei et al. 2009, Sengupta et al. 2011), BCL2L11 (BIM) (Gilley et al. 2003, Urbich et al. 2005, Chuang et al. 2007, Hughes et al. 2011, Chen et al. 2013, Wang et al. 2016), BCL6 (Tang et al. 2002, Fernandez de Mattos et al. 2004, Shore et al. 2006) and BBC3 (PUMA) (Dudgeon et al. 2010, Hughes et al. 2011, Liu et al. 2015, Wu et al. 2016, Liu et al. 2017, Fitzwalter et al. 2018). FOXO-mediated induction of cell death genes is important during development, for example during nervous system development, where FOXO promotes neuronal death upon NGF withdrawal (Gilley et al. 2003), and also contributes to the tumor-suppressive role of FOXO factors (Arimoto Ishida et al. 2004). FOXO1 transcriptional activity is implicated in the cell death of enteric nervous system (ENS) precursors. RET signaling, which activates PI3K/AKT signaling, leading to inhibition of FOXO mediated transcription, ensures survival of ENS precursors (Srinivasan et al. 2005).
Transcription of the STK11 (LKB1) gene, encoding Serine/threonine-protein kinase STK11 (also known as Liver kinase B1), which regulates diverse cellular processes, including apoptosis, is directly stimulated by FOXO3 and FOXO4 (Lutzner et al. 2012).
R-HSA-9615017 FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes FOXO6, the least studied member of the FOXO family, directly stimulates transcription of PLXNA4 gene, encoding a co-factor for the semaphorin SEMA3A receptor. FOXO6-mediated regulation of PLXNA4 expression plays an important role in radial glia migration during cortical development (Paap et al. 2016).
FOXO-mediated up-regulation of genes involved in reduction of the oxidative stress burden is not specific to neurons, but plays an important role in neuronal survival and neurodegenerative diseases. FOXO3 and FOXO4, and possibly FOXO1, directly stimulate transcription of the SOD2 gene, encoding mitochondrial manganese-dependent superoxide dismutase, which converts superoxide to the less harmful hydrogen peroxide and oxygen (Kops et al. 2002, Hori et al. 2013, Araujo et al. 2011, Guan et al. 2016). FOXO4 stimulates SOD2 gene transcription in collaboration with ATXN3, a protein involved in spinocerebellar ataxia type 3 (SCA3) (Araujo et al. 2011). FOXO3 and FOXO6, and possibly FOXO1, directly stimulate transcription of the CAT gene, encoding catalase, an enzyme that converts hydrogen peroxide to water and oxygen, thus protecting cells from the oxidative stress (Awad et al. 2014, Kim et al. 2014, Rangarajan et al. 2015, Song et al. 2016, Liao et al. 2016, Guo et al. 2016).
FOXO transcription factors regulate transcription of several genes whose protein products are secreted from hypothalamic neurons to control appetite and food intake: NPY gene, AGRP gene and POMC gene. At low insulin levels, characteristic of starvation, FOXO transcription factors bind to insulin responsive elements (IRES) in the regulatory regions of NPY, AGRP and POMC gene. FOXO1 directly stimulates transcription of the NPY gene, encoding neuropeptide-Y (Kim et al. 2006, Hong et al. 2012), and the AGRP gene, encoding Agouti-related protein (Kitamura et al. 2006, Kim et al. 2006), which both stimulate food intake. At the same time, FOXO1 directly represses transcription of the POMC gene, encoding melanocyte stimulating hormone alpha , which suppresses food intake (Kitamura et al. 2006, Kim et al. 2006). When, upon food intake, blood insulin levels rise, insulin-mediated activation of PI3K/AKT signaling inhibits FOXO transcriptional activity.
In liver cells, FOXO transcription factors regulate transcription of genes involved in gluconeogenesis: G6PC gene, encoding glucose-6-phosphatase and PCK1 gene, encoding phosphoenolpyruvate carboxykinase. Actions of G6PC and PCK1 enable steady glucose blood levels during fasting. FOXO1, FOXO3 and FOXO4 directly stimulate PCK1 gene transcription (Hall et al. 2000, Yang et al. 2002, Puigserver et al. 2003), while all four FOXOs, FOXO1, FOXO3, FOXO4 and FOXO6 directly stimulate G6PC gene transcription (Yang et al. 2002, Puigserver et al. 2003, Onuma et al. 2006, Kim et al. 2011). FOXO-mediated induction of G6PC and PCK1 genes is negatively regulated by insulin-induced PI3K/AKT signaling.
FOXO1, FOXO3 and FOXO4 directly stimulate transcription of the IGFBP1 gene, encoding insulin growth factor binding protein 2 (Tang et al. 1999, Kops et al. 1999, Hall et al. 2000, Yang et al. 2002), which increases sensitivity of cells to insulin.
FOXO1 and FOXO3 directly stimulate transcription of the ABCA6 (ATP-binding cassette sub-family A member 6) gene, encoding a putative transporter protein that is thought to be involved in lipid homeostasis (Gai et al. 2013). The GCK (glucokinase) gene is another gene involved in lipid homeostasis that is regulated by FOXOs. FOXO1, acting with the SIN3A:HDAC complex, directly represses the GCK gene transcription, thus repressing lipogenesis in the absence of insulin (Langlet et al. 2017). The SREBF1 (SREBP1) gene, which encodes a transcriptional activator required for lipid homeostasis, is directly transcriptionally repressed by FOXO1 (Deng et al. 2012). Transcription of the RETN gene, encoding resistin, an adipocyte specific hormone that suppresses insulin-mediated uptake of glucose by adipose cells, is directly stimulated by FOXO1 (Liu et al. 2014).
Transcription of two genes encoding E3 ubiquitin ligases FBXO32 (Atrogin-1) and TRIM63 (MURF1), involved in degradation of muscle proteins and muscle wasting during starvation, is positively regulated by FOXO transcription factors (Sandri et al. 2004, Waddell et al. 2008, Raffaello et al. 2010, Senf et al. 2011, Bollinger et al. 2014, Wang et al. 2017).
R-HSA-5654693 FRS-mediated FGFR1 signaling The FRS family of scaffolding adaptor proteins has two members, FRS2 (also known as FRS2 alpha) and FRS3 (also known as FRS2beta or SNT-2). Activation of FGFR tyrosine kinase allows FRS proteins to become phosphorylated on tyrosine residues and then bind to the adaptor GRB2 and the tyrosine phosphatase PPTN11/SHP2. Subsequently, PPTN11 activates the RAS-MAP kinase pathway and GRB2 activates the RAS-MAP kinase , PI-3-kinase and ubiquitinations/degradation pathways by binding to SOS, GAB1 and CBL, respectively, via the SH3 domains of GRB2. FRS2 acts as a central mediator in FGF signaling mainly because it induces sustained levels of activation of ERK with ubiquitous expression.
R-HSA-5654700 FRS-mediated FGFR2 signaling The FRS family of scaffolding adaptor proteins has two members, FRS2 (also known as FRS2 alpha) and FRS3 (also known as FRS2beta or SNT-2). Activation of FGFR tyrosine kinase allows FRS proteins to become phosphorylated on tyrosine residues and then bind to the adaptor GRB2 and the tyrosine phosphatase PPTN11/SHP2. Subsequently, PPTN11 activates the RAS-MAP kinase pathway and GRB2 activates the RAS-MAP kinase , PI-3-kinase and ubiquitinations/degradation pathways by binding to SOS, GAB1 and CBL, respectively, via the SH3 domains of GRB2. FRS2 acts as a central mediator in FGF signaling mainly because it induces sustained levels of activation of ERK with ubiquitous expression.
R-HSA-5654706 FRS-mediated FGFR3 signaling The FRS family of scaffolding adaptor proteins has two members, FRS2 (also known as FRS2 alpha) and FRS3 (also known as FRS2beta or SNT-2). Activation of FGFR tyrosine kinase allows FRS proteins to become phosphorylated on tyrosine residues and then bind to the adaptor GRB2 and the tyrosine phosphatase PPTN11/SHP2. Subsequently, PPTN11 activates the RAS-MAP kinase pathway and GRB2 activates the RAS-MAP kinase , PI-3-kinase and ubiquitinations/degradation pathways by binding to SOS, GAB1 and CBL, respectively, via the SH3 domains of GRB2. FRS2 acts as a central mediator in FGF signaling mainly because it induces sustained levels of activation of ERK with ubiquitous expression.
R-HSA-5654712 FRS-mediated FGFR4 signaling The FRS family of scaffolding adaptor proteins has two members, FRS2 (also known as FRS2 alpha) and FRS3 (also known as FRS2beta or SNT-2). Activation of FGFR tyrosine kinase allows FRS proteins to become phosphorylated on tyrosine residues and then bind to the adaptor GRB2 and the tyrosine phosphatase PPTN11/SHP2. Subsequently, PPTN11 activates the RAS-MAP kinase pathway and GRB2 activates the RAS-MAP kinase , PI-3-kinase and ubiquitinations/degradation pathways by binding to SOS, GAB1 and CBL, respectively, via the SH3 domains of GRB2. FRS2 acts as a central mediator in FGF signaling mainly because it induces sustained levels of activation of ERK with ubiquitous expression.
R-HSA-983231 Factors involved in megakaryocyte development and platelet production Megakaryocytes (MKs) give rise to circulating platelets (thrombocytes) through terminal differentiation of MKs which release cytoplasmic fragments as circulating platelets. As MKs mature they undergo endoreduplication (polyploidisation) and expansion of cytoplasmic mass to cell sizes larger than 50-100 microns, and ploidy ranges up to 128 N. As MKs mature, the polyploid nucleus becomes horseshoe-shaped, the cytoplasm expands, and platelet organelles and the demarcation membrane system are amplified. Proplatelet projections form which give rise to de novo circulating platelets (Deutsch & Tomer 2006).
The processes of megakaryocytopoiesis and platelet production occur within a complex microenvironment where chemokines, cytokines and adhesive interactions play major roles (Avecilla et al. 2004). Megakaryocytopoiesis is regulated at several levels including proliferation, differentiation and platelet release (Kaushansky 2003). Thrombopoietin (TPO/c-Mpl ligand) is the most potent cytokine stimulating proliferation and maturation of MK progenitors (Kaushansky 2005) but many other growth factors are involved. MK development is controlled by the action of multiple transcription factors. Many MK-specific genes are co-regulated by GATA and friend of GATA (FOG), RUNX1 and ETS proteins. Nuclear factor erythroid 2 (NF-E2), which has an MK-erythroid specific 45-kDa subunit, controls terminal MK maturation, proplatelet formation and platelet release (Schulze & Shivdasani 2004). NF-E2 deficient mice have profound thrombocytopenia (Shiraga et al. 1999). MYB (c-myb) functions with EP300 (p300) as a negative regulator of thrombopoiesis (Metcalf et al. 2005). During MK maturation, internal membrane systems, granules and organelles are assembled. Cytoplasmic fragmentation requires changes in the MK cytoskeleton and formation of organelles and channels. Individual organelles migrate from the cell body to the proplatelet ends, with approximately 30 percent of organelles/granules in motion at any given time (Richardson et al. 2005).
R-HSA-6783310 Fanconi Anemia Pathway Fanconi anemia (FA) is a genetic disease of genome instability characterized by congenital skeletal defects, aplastic anemia, susceptibility to leukemias, and cellular sensitivity to DNA damaging agents. Patients with FA have been categorized into at least 15 complementation groups (FA-A, -B, -C, -D1, -D2, -E, -F, -G, -I, -J, -L, -M, -N, -O and -P). These complementation groups correspond to the genes FANCA, FANCB, FANCC, FANCD1/BRCA2, FANCD2, FANCE, FANCF, FANCG, FANCJ/BRIP1, FANCL, FANCM, FANCN/PALB2, FANCO/RAD51C and FANCP/SLX4. Eight of these proteins, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL, and FANCM, together with FAAP24, FAAP100, FAAP20, APITD1 and STRA13, form a nuclear complex termed the FA core complex. The FA core complex is an E3 ubiquitin ligase that recognizes and is activated by DNA damage in the form of interstrand crosslinks (ICLs), triggering monoubiquitination of FANCD2 and FANCI, which initiates repair of ICL-DNA.
FANCD2 and FANCI form a complex and are mutually dependent on one another for their respective monoubiquitination. After DNA damage and during S phase, FANCD2 localizes to discrete nuclear foci that colocalize with proteins involved in homologous recombination repair, such as BRCA1 and RAD51. The FA pathway is regulated by ubiquitination and phosphorylation of FANCD2 and FANCI. ATR-dependent phosphorylation of FANCI and FANCD2 promotes monoubiquitination of FANCD2, stimulating the FA pathway (Cohn and D'Andrea 2008, Wang 2007). The complex of USP1 and WDR48 (UAF1) is responsible for deubiquitination of FANCD2 and negatively regulates the FA pathway (Cohn et al. 2007).
Monoubiquitinated FANCD2 recruits DNA nucleases, including SLX4 (FANCP) and FAN1, which unhook the ICL from one of the two covalently linked DNA strands. The DNA polymerase nu (POLN) performs translesion DNA synthesis using the DNA strand with unhooked ICL as a template, thereby bypassing the unhooked ICL. The unhooked ICL is subsequently removed from the DNA via nucleotide excision repair (NER). Incision of the stalled replication fork during the unhooking step generates a double strand break (DSB). The DSB is repaired via homologous recombination repair (HRR) and involves the FA genes BRCA2 (FANCD1), PALB2 (FANCN) and BRIP1 (FANCJ) (reviewed by Deans and West 2011, Kottemann and Smogorzewska 2013). Homozygous mutations in BRCA2, PALB2 or BRIP1 result in Fanconi anemia, while heterozygous mutations in these genes predispose carriers to primarily breast and ovarian cancer. Well established functions of BRCA2, PALB2 and BRIP1 in DNA repair are BRCA1 dependent, but it is not yet clear whether there are additional roles for these proteins in the Fanconi anemia pathway that do not rely on BRCA1 (Evans and Longo 2014, Jiang and Greenberg 2015). Heterozygous BRCA1 mutations predispose carriers to breast and ovarian cancer with high penetrance. Complete loss of BRCA1 function is embryonic lethal. It has only recently been reported that a partial germline loss of BRCA1 function via mutations that diminish protein binding ability of the BRCT domain of BRCA1 result in a FA-like syndrome. BRCA1 has therefore been designated as the FANCS gene (Jiang and Greenberg 2015).
The FA pathway is involved in repairing DNA ICLs that arise by exposure to endogenous mutagens produced as by-products of normal cellular metabolism, such as aldehyde containing compounds. Disruption of the aldehyde dehydrogenase gene ALDH2 in FANCD2 deficient mice leads to severe developmental defects, early lethality and predisposition to leukemia. In addition to this, the double knockout mice are exceptionally sensitive to ethanol consumption, as ethanol metabolism results in accumulated levels of aldehydes (Langevin et al. 2011).
R-HSA-75157 FasL/ CD95L signaling The Fas family of cell surface receptors initiate the apototic pathway through interaction with the external ligand, FasL. The cytoplasmic domain of Fas interacts with a number of molecules in the transduction of the external signal to the cytoplasmic side of the cell membrane. The most notable cytoplasmic domain is the Death Domain (DD) that is involved in recruiting the FAS-associating death domain-containing protein (FADD). This interaction drives downstream events.
R-HSA-434316 Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion Fatty acids augment the glucose triggered secretion of insulin through two mechanisms: intracellular metabolism and activation of FFAR1 (GPR40), a G-protein coupled receptor. Based on studies with inhibitors of G proteins such as pertussis toxin FFAR1 is believed to signal through Gq/11. Binding of free fatty acids by FFAR1 activates the heterotrimeric Gq complex which then activates Phospholipase C, producing inositol 1,4,5-trisphosphate and eventually causing the release of intracellular calcium into the cytosol. From experiments in knockout mice it is estimated that signaling through FFAR1 is responsible for about 50% of the augmentation of insulin secretion produced by free fatty acids.
R-HSA-8978868 Fatty acid metabolism The synthesis and breakdown of fatty acids are a central part of human energy metabolism, and the eicosanoid class of fatty acid derivatives regulate diverse processes in the body (Vance & Vance 2008 - URL). Processes annotated in this module include the synthesis of fatty acids from acetyl-CoA, mitochondrial and peroxisomal breakdown of fatty acids, and the metabolism of eicosanoids and related molecules.
R-HSA-211935 Fatty acids The CYP4 family are the main CYPs involved in the metabolism of long-chain fatty acids.
R-HSA-75105 Fatty acyl-CoA biosynthesis Fatty acyl-CoA biosynthesis involves following steps:
-Palmitate synthesis catalyzed by Acetyl-CoA carboxylase and Fatty acid synthase
-Conversion of palmitic acid to long chain fatty acids and
-Conversion of long chain fatty acids to fatty acyl-CoA by acyl-CoA synthases.
R-HSA-2454202 Fc epsilon receptor (FCERI) signaling Mast cells (MC) are distributed in tissues throughout the human body and have long been recognized as key cells of type I hypersensitivity reactions. They also play important roles in inflammatory and immediate allergic reactions. Activation through FCERI-bound antigen-specific IgE causes release of potent inflammatory mediators, such as histamine, proteases, chemotactic factors, cytokines and metabolites of arachidonic acid that act on the vasculature, smooth muscle, connective tissue, mucous glands and inflammatory cells (Borish & Joseph 1992, Amin 2012, Metcalfe et al. 1993). FCERI is a multimeric cell-surface receptor that binds the Fc fragment of IgE with high affinity. On mast cells and basophils FCERI exists as a tetrameric complex consisting of one alpha-chain, one beta-chain, and two disulfide-bonded gamma-chains, and on dendritic cells, Langerhans cells, macrophages, and eosinophils it exists as a trimeric complex with one alpha-chain and two disulfide-bonded gamma-chains (Wu 2011, Kraft & Kinet 2007). FCERI signaling in mast cells includes a network of signaling molecules and adaptor proteins. These molecules coordinate ultimately leading to effects on degranulation, eicosanoid production, and cytokine and chemokine production and cell migration and adhesion, growth and survival.
The first step in FCERI signaling is the phosphorylation of the tyrosine residues in the ITAM of both the beta and the gamma subunits of the FCERI by LYN, which is bound to the FCERI beta-chain. The phosphorylated ITAM then recruits the protein tyrosine kinase SYK (spleen tyrosine kinase) which then phosphorylates the adaptor protein LAT. Phosphorylated LAT (linker for activation of T cells) acts as a scaffolding protein and recruits other cytosolic adaptor molecules GRB2 (growth-factor-receptor-bound protein 2), GADS (GRB2-related adaptor protein), SHC (SRC homology 2 (SH2)-domain-containing transforming protein C) and SLP76 (SH2-domain-containing leukocyte protein of 76 kDa), as well as the exchange factors and adaptor molecules VAV and SOS (son of sevenless homologue), and the signalling enzyme phospholipase C gamma1 (PLC-gamma1). Tyrosoine phosphorylation of enzymes and adaptors, including VAV, SHC GRB2 and SOS stimulate small GTPases such as RAC, RAS and RAF. These pathways lead to activation of the ERK, JNK and p38 MAP kinases, histamine release and cytokine production. FCERI activation also triggers the phosphorylation of PLC-gamma which upon membrane localisation hydrolyse PIP2 to form IP3 and 1,2-diacylglycerol (DAG) - second messengers that release Ca2+ from internal stores and activate PKC, respectively. Degranulation or histamine release follows the activation of PLC-gamma and protein kinase C (PKC) and the increased mobilization of calcium (Ca2+). Receptor aggregation also results in the phosphorylation of adaptor protein NTAL/LAT2 which then recruits GAB2. PI3K associates with phosphorylated GAB2 and catalyses the formation of PIP3 in the membrane, which attracts many PH domain proteins like BTK, PLC-gamma, AKT and PDK. PI3K mediated activation of AKT then regulate the mast cell proliferation, development and survival (Gu et al. 2001).
R-HSA-2029480 Fcgamma receptor (FCGR) dependent phagocytosis Phagocytosis is one of the important innate immune responses that function to eliminate invading infectious agents. Monocytes, macrophages, and neutrophils are the professional phagocytic cells. Phagocytosis is a complex process involving the recognition of invading foreign particles by specific types of phagocytic receptors and the subsequent internalization of the particles. Fc gamma receptors (FCGRs) are among the best studied phagocytic receptors that bind to Fc portion of immunoglobulin G (IgG). Through their antigen binding F(ab) end, antibodies bind to specific antigen while their constant (Fc) region binds to FCGRs on phagocytes. The clustering of FCGRs by IgG antibodies on the phagocyte initiates a variety of signals, which lead, through the reorganisation of actin cytoskeleton and membrane remodelling, to the formation of pseudopod and phagosome. Fc gamma receptors are classified into three classes: FCGRI, FCGRII and FCGRIII. Each class of these FCGRs consists of several individual isoforms. Among all these isoforms FCGRI, FCGRIIA and FCGRIIIA, are able to mediate phagocytosis (Joshi et al. 2006, Garcia Garcia & Rosales 2002, Nimmerjahn & Ravetch 2006).
R-HSA-1187000 Fertilization Mammalian fertilization comprises sperm migration through the female reproductive tract, biochemical and morphological changes to sperm, and sperm-egg interaction in the oviduct. Although the broad concepts of fertilization are well defined, our understanding of the biochemical mechanisms underlying sperm-egg binding is limited.
R-HSA-1566977 Fibronectin matrix formation Fibronectin (FN1) is found in the extracellular matrix (ECM) of all cells as linear and branched networks that surround and connect neighbouring cells (Singh et al. 2010). Prior to matrix formation FN1 exists as a protein dimer. Often the two peptide chains represent differentially-spliced variants. The chains are linked by a pair of C-terminal disulfide bonds which are essential for subsequent multimerization (Schwarzbaur 1991). FN1 monomers have a molecular weight of 230-270 kDa depending on alternative splicing and contain three types of repeating unit, I, II, and III. I and II are stabilized by intra-chain disulfide bonds. The absence of disulfide bonds in type III modules allows them to partially unfold under applied force (Erickson 2002). Three regions of variable splicing occur along the length of the FN1 monomer (Mao & Schwarzbauer 2005). One or both of the 'extra' type III modules EIIIA and EIIIB may be present in cellular FN1, but never in plasma FN1. A variable (V) region exists between the 14th and 15th type III module. This contains the binding site for alpha4 beta1 and alpha4beta7 integrins. It is present in most cellular FN1, occasionally in plasma FN1. The modules are arranged into several functional and protein-binding domains. There are four FN1-binding domains (Mao & Schwarzbauer 2005). One of these domains (I1-5), referred to as the 'assembly domain', is required for the initiation of FN1 matrix assembly. Modules III9-10 correspond to the 'cell-binding domain' of FN1. The Arg-Gly-Asp (RGD) integrin binding sequence located in III10 is the primary site of FN1 to cell attachment, mediated predominantly by alpha5 beta1 and alphaV beta3 integrins. The 'synergy site' in III9 modulates FN1's association with alpha5 beta1 integrins. FN1 also contains interaction domains for fibrin (I1-5, I10-12), collagen (I6-9, II1-2), fibulin-1 (III13-14), heparin, syndecan (III12-14) and fibrillin-1 (I6-9) (Mao & Schwartzbauer 2005, Sabatier et al. 2009).
FN1 dimer binding to alpha5beta1 integrin stimulates self-association. Binding is thought to lead to a conformational change in FN1 that triggers the addition of further FN1 dimers (Singh et al. 2010). I1-5 functions as a unit that is the primary FN1 matrix assembly domain (Sottile et al. 1991) but other units are likely to be involved (Singh et al. 2010), the process is not fully understood.
Several ECM proteins appear to require the FN1 matrix for their own assembly. Fibrillin-1 containing microfibrils are formed when fibrillin-1 multimers bind to the FN1 matrix (Sabatier et al. 2009). FN1 polymerization promotes the deposition of type I and type III collagen (Sottile and Hocking 2002, Velling et al. 2002). Inhibition of FN1 polymerization increases its turnover and a concomitant loss of collagen types I and III from the ECM (Sottile and Hocking 2002, Sottile et al. 2007). FN1 is regulated by matrix metalloproteinases, particularly MMP14 (Shi & Sottile 2011).
R-HSA-2855086 Ficolins bind to repetitive carbohydrate structures on the target cell surface Ficolins are recognition molecules in the lectin pathway of complement activation. Three types of ficolin have been identified in humans: M-ficolin (ficolin-1, FCN1), L-ficolin (ficolin-2, FCN2) and H-ficolin (ficolin-3, FCN3). FCN2 and 3 circulate in blood plasma whereas FCN1 is locally secreted by immune response cells (Teh et al. 2000, Liu et al. 2005, Matsushita et al. 2002). Plasma ficolins circulate as complexes with MBL-associated serine proteases (MASPs). Upon binding of ficolins to carbohydrates on the target cell surface, MASPs are activated and subsequently activate the complement cascade (Matsushita et al. 2002, Gout et al. 2009). Ficolins function as trimers and larger oligomers. Ficolin peptide sequences contain an amino-terminal cysteine-rich region, a collagen-like domain, a neck region and a carboxy-terminal fibrinogen-like domain. The fibrinogen-like domain binds to pathogen- or apoptotic cell-associated molecular patterns. Different ficolins have distinct recognition specificities (Endo et al. 2007, Thiel and Gadjeva 2009, Garlatti et al. 2010).
R-HSA-390450 Folding of actin by CCT/TriC Nucleotide-independent transfer of beta-actin from prefoldin to CCT occurs when prefoldin binds to CCT (Vainberg et al., 1998). Following ATP- dependent folding within CCT (Gao et al., 1992), beta-actin is released as a soluble, monomeric protein.
R-HSA-163210 Formation of ATP by chemiosmotic coupling The re-entry of protons into the mitochondrial matrix through Complex V causes conformational changes which result in ATP synthesis. Complex V (ATP synthase) is composed of 3 parts; an F1 catalytic core (approx 5 subunits), an F0 membrane proton channel (approx 9 subunits) and two stalks linking F1 to F0. F1 contains three alpha subunits, three beta subunits, and one each of gamma, delta, and epsilon subunits. Each beta subunit contains an active site for ATP synthesis. F0 has at least 9 subunits (a-g, A6L and F6; see Lai et al., 2023; reviewed in Jonckheere et al., 2011).
The mechanism of ATP synthesis by Complex V was predicted by Boyer et al in 1973: ADP and Pi bind to the enzyme resulting in a conformational change. ATP is then synthesized, still bound to the enzyme. Another change in the active site results in the release of free ATP into the matrix. The overall reaction is:
ADP + Pi + H+ + nH+ (intermemb. space) = ATP + H2O + nH+ (matrix)
Mutations in several ATP synthase subunits can lead to different types of mitochondrial complex V deficiency (MC5D; reviewed in Garone et al., 2022; Del Dotto et al., 2024).
R-HSA-140877 Formation of Fibrin Clot (Clotting Cascade) The formation of a fibrin clot at the site of an injury to the wall of a normal blood vessel is an essential part of the process to stop blood loss after vascular injury. The reactions that lead to fibrin clot formation are commonly described as a cascade, in which the product of each step is an enzyme or cofactor needed for following reactions to proceed efficiently. The entire clotting cascade can be divided into three portions, the extrinsic pathway, the intrinsic pathway, and the common pathway. The extrinsic pathway begins with the release of tissue factor at the site of vascular injury and leads to the activation of factor X. The intrinsic pathway provides an alternative mechanism for activation of factor X, starting from the activation of factor XII. The common pathway consists of the steps linking the activation of factor X to the formation of a multimeric, cross-linked fibrin clot. Each of these pathways includes not only a cascade of events that generate the catalytic activities needed for clot formation, but also numerous positive and negative regulatory events.
R-HSA-167152 Formation of HIV elongation complex in the absence of HIV Tat During the formation of the HIV elongation complex in the absence of HIV Tat, eongation factors are recruited to form the HIV-1 elongation complex (Hill and Sundquist 2013) and P-TEFb complex hyperphosphorylates RNA Pol II CTD (Hermann and Rice, 2005, Zhou et al., 2000).
R-HSA-167200 Formation of HIV-1 elongation complex containing HIV-1 Tat This HIV-1 event was inferred from the corresponding human RNA Poll II transcription event in Reactome. The details relevant to HIV-1 are described below. For a more detailed description of the general mechanism, see the link to the corresponding RNA Pol II transcription event below. The formation of the HIV-1 elongation complex involves Tat mediated recruitment of P-TEFb(Cyclin T1:Cdk9) to the TAR sequence (Wei et al, 1998) and P-TEFb(Cyclin T1:Cdk9) mediated phosphorylation of the RNA Pol II CTD as well as the negative transcriptional elongation factors DSIF and NELF (Herrmann, 1995; Ivanov et al. 2000; Fujinaga et al. 2004; Zhou et al., 2004).
R-HSA-5696395 Formation of Incision Complex in GG-NER After the XPC complex and the UV-DDB complex bind damaged DNA, a basal transcription factor TFIIH is recruited to the nucleotide excision repair (NER) site (Volker et al. 2001, Riedl et al. 2003). DNA helicases ERCC2 (XPD) and ERCC3 (XPB) are subunits of the TFIIH complex. ERCC2 unwinds the DNA around the damage in concert with the ATPase activity of ERCC3, creating an open bubble (Coin et al. 2007). Simultaneously, the presence of the damage is verified by XPA (Camenisch et al. 2006). The recruitment of XPA is partially regulated by PARP1 and/or PARP2 (King et al. 2012).
Two DNA endonucleases, ERCC5 (XPG) and the complex of ERCC1 and ERCC4 (XPF), are recruited to the open bubble structure to form the incision complex that will excise the damaged oligonucleotide from the affected DNA strand (Dunand-Sauthier et al. 2005, Zotter et al. 2006, Riedl et al. 2003, Tsodikov et al. 2007, Orelli et al. 2010). The RPA heterotrimer coats the undamaged DNA strand, thus protecting it from the endonucleolytic attack (De Laat et al. 1998).
R-HSA-112382 Formation of RNA Pol II elongation complex TFIIS is a transcription factor involved in different phases of transcription, occurring in a major ubiquitous form and other tissue specific forms. TFIIS stimulates RNA Pol II complex out of elongation arrest.
Other transcription factors like ELL, Elongin family members and TFIIF interact directly with elongating Pol II and increase its elongation rate. These factors have been observed to act on naked DNA templates by suppressing transient pausing by the enzyme at all or most steps of nucleotide addition. In Drosophila, ELL is found at a large number of transcriptionally active sites on polytene chromosomes. In general, ELL is suspected to have more unidentified functions.
Elongin is a heterotrimeric protein complex that stimulates the overall rate of elongation. In addition, Elongin may act as an E3 Ubiquitin ligase. Ubiquitylation of RNA Pol II occurs rapidly after genotoxic assault by UV light or chemicals, and results in degradation by proteasome. The FACT complex appears to promote elongation by facilitating passage of polymerase through chromatin.
All these factors contribute to the formation of a processive elongation complex centered around the RNA Pol II complex positioned on the DNA:RNA hybrid. This enables the RNA Pol II elongation complex to function as a platform that coordinates mRNA processing and export (Reviewed by Shilatifard et al., 2003).
R-HSA-2559584 Formation of Senescence-Associated Heterochromatin Foci (SAHF) The process of DNA damage/telomere stress induced senescence culminates in the formation of senescence associated heterochromatin foci (SAHF). These foci represent facultative heterochromatin that is formed in senescent cells. They contribute to the repression of proliferation promoting genes and play an important role in the permanent cell cycle exit that characterizes senescence (Narita et al. 2003 and 2006). SAHF appear as compacted, punctate DAPI stained foci of DNA. Each chromosome is condensed into a single SAH focus, with telomeric and centromeric chromatin located predominantly at its periphery (Funayama et al. 2006, Zhang et al. 2007).
An evolutionarily conserved protein complex of HIRA, ASF1A, UBN1 and CABIN1 plays a crucial role in the SAHF formation. As cells approach senescence, HIRA, ASF1A, UBN1 and CABIN1 accumulate at the PML bodies (Zhang et al. 2005, Banumathy et al. 2009, Rai et al. 2011). PML bodies are punctate nuclear structures that contain PML protein and numerous other proteins and are proposed to be the sites of assembly of macromolecular regulatory complexes and protein modification (Fogal et al. 2000, Guo et al. 2000, Pearson et al. 2000). Recruitment of HIRA to PML bodies coincides with altered chromatin structure and deposition of macroH2A histone H2A variant onto chromatin. As cells become senescent, HIRA, ASF1A, UBN1 and CABIN1 relocate from PML bodies to SAHF. HIRA accumulation at PML bodies is RB1 and TP53 independent, but may require phosphorylation of HIRA serine S697 by GSK3B (Ye, Zerlanko, Kennedy et al. 2007). SAHF formation itself, however, requires functional RB1 and TP53 pathways (Ye, Zerlanko, Zhang et al. 2007).
SAHF contain H3K9Me mark, characteristic of trancriptionally silent chromatin, and HP1, marcoH2A histone H2A variant and HMGA proteins are also components of SAHF (Narita et al. 2006), besides the HIRA:ASF1A:UBN1:CABIN1 complex. A yet unidentified H3K9Me histone methyltransferase may be recruited to SAHF by UBN1 (Banumathy et al. 2009). One of the functions of the HIRA:ASF1A:UBN1:CABIN1 complex is to deposit histone H3.3. variant to chromatin, which influences gene expression (Zhang et al. 2007, Rai et al. 2011).
Further studies are needed to fully elucidate the mechanism of SAHF formation and mechanism by which SAHF promote cell senescence.
R-HSA-6781823 Formation of TC-NER Pre-Incision Complex Formation of TC-NER pre-incision complex is initiated when the RNA polymerase II (RNA Pol II) complex stalls at a DNA damage site. The stalling is caused by misincorporation of a ribonucleotide opposite to a damaged base (Brueckner et al. 2007). Cockayne syndrome protein B (ERCC6, CSB) binds stalled RNA Pol II and recruits Cockayne syndrome protein A (ERCC8, CSA). ERCC8 is part of an ubiquitin ligase complex that also contains DDB1, CUL4A or CUL4B and RBX1. This complex is implicated in the regulation of TC-NER progression probably by ubiquitinating one or more factors involved in this pathway, which may include RNA Pol II and ERCC6 at the later stages of repair (Bregman et al. 1996, Fousteri et al. 2006, Groisman et al. 2006). XPA is recruited to the TC-NER site through its interaction with the TFIIH complex (Furuta et al. 2002, Ziani et al. 2014). The XAB2 complex, which probably regulates the accessibility of the DNA damage site through its RNA-DNA helicase activity, binds the TC-NER site via the interaction of its XAB2 subunit with RNA Pol II, ERCC6, ERCC8 and XPA (Nakatsu et al. 2000, Sollier et al. 2014). TCEA1 (TFIIS) is a transcription elongation factor that may facilitate backtracking of the stalled RNA Pol II, enabling access of repair proteins to the DNA damage site and promotes partial digestion of the 3' protruding end of the nascent mRNA transcript by the backtracked RNA Pol II, allowing resumption of RNA synthesis after damage removal (Donahue et al. 1994). Access to DNA damage sites in TC-NER was suggested to be facilitated by a chromatin remodeler HMGN1 (Birger et al. 2003), but another sudy found that HMGN1 was not needed for human TC-NER (Apelt et al. 2020). UVSSA protein interacts with ubiquitinated ERCC6 and RNA Pol II, recruiting ubiquitin protease USP7 to the TC-NER site and promoting ERCC6 stabilization (Nakazawa et al. 2012, Schwertman et al. 2012, Zhang et al. 2012, Fei and Chen 2012).
R-HSA-9772755 Formation of WDR5-containing histone-modifying complexes WDR5 is a component of six mammalian histone methyltransferase KMT2 complexes: Mixed Lineage Leukemia (MLL) 1-4, SET1A, and SET1B. All KMT2 complexes consist of a histone methyltransferase (KMT2A, KMT2B, KMT2C, KMT2D, SETD1A, or SETD1B, respectively) and the WRAD subcomplex composed of WDR5, RBBP5, ASH2L, and DPY30. The WRAD complex regulates the enzymatic activity of histone methyltransferases and enables their recruitment to chromatin. Additional transcription cofactors associate with each KMT2 histone methyltransferase complex, enabling their functional diversification. For a detailed overview, please refer to Cho et al. 2007, Song and Kingston 2008, Takahashi et al. 2011, Couture and Skiniotis 2013, van Nuland et al. 2013, Klonou et al. 2021.
The KMT2 complexes are evolutionarily conserved. While a single SET1/COMPASS complex is present in yeast, three distinct complexes are present in Drosophila: trithorax (Trx), trithorax-related (Trr), and Set1. In mammals, due to gene duplication, two Trx-like complexes (one with KMT2A and another with KMT2B as the catalytic subunit), as well as two Trr-like complexes (one with KMT2C and another with KMT2D as the catalytic subunit), and two Set1-like complexes (one with SETD1A and another with SETD1B as the catalytic subunit) are formed. For review, please refer to Rao and Dou 2015.
All KMT2 complexes methylate lysine K5 of histone H3 (K4 in mature histone H3 peptides, as the initiator methionine is removed), which is associated with transcriptional activation. Different KMT2 complexes preferentially monomethylate, dimethylate, or trimethylate H3K4, depending on the presence of accessory subunits, transcriptional co-factors, and posttranslational modifications. The catalytic activity of KMT2 complexes may differ between endogenous complexes and complexes reconstituted in vitro by mammalian proteins expressed and produced in bacterial or insect cells. The KMT2A and KMT2B complexes preferentially methylate H3K4 at a limited number of target gene promoters, while KMT2C and KMT2D complexes preferentially methylate H3K4 at a limited number of target gene enhancers. SETD1A and SETD1B complexes are responsible for the bulk of cellular H3K4 methylation and show less target specificity. For overview, please refer to Patel et al. 2009, Wang et al. 2009, Rao and Dou 2015.
In both Drosophila and vertebrates, KMT2 complexes control the expression of evolutionarily conserved Hox genes which serve as master regulators of embryonic patterning (reviewed in Soshnikova and Duboule 2009).
Germline mutations in human KMT2 complexes are the underlying cause of several chromatinopathies. Germline loss-of-function (LOF) mutations in KMT2A cause Weideman-Steiner syndrome, a rare autosomal-dominant disorder characterized by intellectual disability, developmental delay, pre- and post-natal growth delay, hypertrichosis, short stature, hypotonia, distinctive facial features, skeletal abnormalities, feeding problems and behavioral difficulties (reviewed in Castiglioni et al. 2022). Germline LOF mutations in KMT2B cause dystonia-28 (DYT28) and intellectual developmental, autosomal dominant disorder-68 (MRD68). DYT28 is an autosomal dominant neurologic disorder characterized by onset of progressive dystonia in the first decade of life (reviewed in Zech et al. 2019), while MRD68 is an autosomal dominant disorder characterized by developmental delay/intellectual disability, microcephaly, poor growth, feeding difficulties, and dysmorphic features (Cif et al. 2020). Germline LOF mutations in KMT2C cause Kleefstra syndrome-2 (KLEFS2), an autosomal dominant neurodevelopmental disorder characterized by delayed psychomotor development, variable intellectual disability, and mild dysmorphic features (reviewed in Lavery et al. 2020). Germline LOF mutations in KMT2D cause Kabuki syndrome 1, a congenital mental retardation syndrome with postnatal dwarfism, a facial dysmorphism and skeletal abnormalities (reviewed in Lavery et al. 2020). Germline LOF mutations in SETD1A cause early-onset epilepsy with or without developmental delay (EPEDD), an autosomal dominant neurologic disorder (Yu et al. 2019), and neurodevelopmental disorder with speech impairment and dysmorphic facies (NEDSID) (Kummeling et al. 2021). Germline LOF mutations in SETD1B cause intellectual developmental disorder with seizures and language delay (IDDSELD) (Roston et al. 2021).
Somatic mutations in KMT2 genes contribute to cancer development. They were first discovered in Mixed Lineage Leukemia (MLL), characterized by chromosomal translocations that involve the KMT2A gene locus on chromosome 11 (chromosomal band 11q23) and result in the expression of fusion proteins with oncogenic properties. Besides gene fusions, other types of KMT2A mutations are also present in blood cancers (most frequently in high-grade B-cell lymphoma, T-cell lymphoblastic leukemia, and acute myeloid leukemia) and solid tumors (most often reported in lung adenocarcinoma, colon adenocarcinoma, and bladder urothelial carcinoma). Somatic cancer mutations in other KMT2 genes (KMT2B, KMT2C, KMT2D, SETD1A and SETD1B) are less characterized but most frequently affect the catalytic SET domain and show different distributions between different cancer types. For review, please refer to Rao and Dou 2015, Castiglioni et al. 2022. Several anti-cancer therapeutics are being developed that affect the association of KMT2 enzymes with components of the WRAD complex, in particular WDR5 (reviewed in Vedadi et al. 2017; Siladi et al. 2022).
WDR5 is also a component of three histone acetyltransferase complexes, GCN5-ATAC, PCAF-ATAC, and MOF/KAT8-NSL. The role of WDR5 in epigenetic regulation of gene expression through histone acetylation is under investigation (reviewed in Guarnaccia and Tansey 2018).
The function of WDR5-containing histone modifying complexes is currently depicted in the following Reactome pathways: "Transcriptional regulation of granulopoiesis" (MLL1 complex), "Transcriptional regulation by RUNX1" (MLL1 complex), "Activation of anterior HOX genes in hindbrain development during early embryogenesis" (MLL3 complex and MLL4 complex), "TCF dependent signaling in response to WNT" (MLL4 complex), and "Chromatin organization" (MLL1 complex, MLL2 complex, MLL3 complex, MLL4 complex, SET1A complex, SET1B complex, GCN5-ATAC complex, PCAF-ATAC complex, and MOF/KAT8-NSL complex). Please note that there is an inconsistency in naming of MLL2 and MLL4 complexes in the literature and in Reactome pathways, as MLL2 and MLL4 have been used as synonyms for both KMT2B and KMT2D, depending on whether the numbering of MLLs referred to order of cloning or whether it referred to similarity to founding MLL1 (MLL, KMT2A) enzyme. The current UniProt standard is for MLL2 to be used as the preferred synonym of KMT2B, and for MLL4 to be used as the preferred synonym of KMT2D.
R-HSA-72689 Formation of a pool of free 40S subunits The 80S ribosome dissociates into free 40S (small) and 60S (large) ribosomal subunits. Each ribosomal subunit is constituted by several individual ribosomal proteins and rRNA.
R-HSA-196025 Formation of annular gap junctions Gap junction plaque internalization and the disruption cell communication requires a reorganization of Cx molecular interactions. Proteins including Dab-2, AP-2, Dynamin and Myosin VI associate with gap junction plaques permitting the internalisation of plaques after clathrin association (Piehl et al., 2007). Until now, two kinds of annular gap junctions have been described. The first is a small vesicle like structure which permits gap junction plaque renewal without arrest of functionality (Jordan et al., 2001). The second is a large annular structure, composed primarily of the junctional plaques of two adjacent cells (Jordan et al., 2001; Segretain et al., 2004).
R-HSA-111458 Formation of apoptosome The apoptosome is a cytoplasmic protein complex of two major components ‑ the adapter protein apoptotic protease activating factor 1 (APAF1) and the protease caspase‑9 (CASP9) which interact with each other through their caspase recruitment domains (CARD) (Qin et al. 1999; Yuan S et al. 2010; Yuan S & Akey CW 2013). The function of the apoptosome is to assemble a multimeric complex between APAF1 and procaspase-9 CARDs to facilitate CASP9 activation (Jiang X and Wang X 2000; Srinivasrula SM et al. 2001; Shiozaki EN et al. 2002). The apoptosome is assembled upon APAF1 interaction with cytochrome c (CYCS), which is released from the mitochondrial intermembrane space during apoptosis (Zou H et al. 1997; Yuan S et al. 2013; Shakeri R et al. 2017). CYCS‑bound APAF1 undergoes ATP-mediated conformational changes and in the presence of CARD of CASP9 oligomerizes into a heptameric complex, which activates procaspase 9 (Zou H et al. 1997; Bratton SB et al. 2010; Acehan D et al. 2002; Yu X et al. 2005; Yuan S et al. 2010; Su TW et al. 2017). In the apoptosome, recruitment of caspase-9 may occur before oligomerization in the CARD disk, which presumably brings the caspase domain into proximity for their dimerization and activation (Su TW et al. 2017; Hu Q et al. 2014; Cheng TC et al. 2016). Once activated, CASP9 activates downstream effector caspases‑3 and ‑7. The activated effector caspases then cleave various cellular proteins.
Different models have been proposed to explain CASP9 activation: the “proximity‑driven dimerization model” and the “induced conformation model”. The first models states that upon binding to heptameric APAF1, monomers of procaspase‑9 are brought into close proximity at a high concentration (Acehan et al. 2002; Renatus et al. 2001). This induces dimerization which is sufficient for CASP9 activation whereas autoprocessing within the apoptosome complex merely stabilizes CASP9 dimer (Boatright KM et al. 2003; Pop C et al. 2006). The “induced conformation model” is based on the observation that CASP9 has a much higher level of catalytic activity when it's bound to the apoptosome. The model suggests that a conformational change occurs at the active site of CASP9 upon binding to APAF1 thus inducing CASP9 homodimerization and stabilizing it in the catalytically active conformation (Shiozaki EN et al. 2002). CASP9 activation may also involve formation of a multimeric CARD:CARD assembly between APAF1 and procaspase‑9 (Hu Q et al. 2014).
R-HSA-9796292 Formation of axial mesoderm Axial mesoderm, also called chordamesoderm, is formed by cells ingressing at the anterior end of the primitive streak. The axial mesoderm produces three types of cells, namely (from anterior to posterior) prechordal plate, anterior head process, and node-derived notochord precursors (reviewed in Balmer et al. 2016). In mouse and rat, the prechordal plate gives rise to cells in the foregut endoderm, oral endoderm, and ventral cranial mesoderm (Aoto et al. 2009); the anterior head process gives rise to the anterior portion of the notochord; notochord precursors give rise to the remaining posterior region of the notochord. Contribution of axial mesoderm in humans is less well characterized (Muller and O'Rahilly 2003). (
All these cells initially form a single columnar epithelium, the notochordal plate, that is contiguous with the endoderm. The notochordal plate then submerges into the embryo to form the tubular notochord structure. During embryogenesis the notochord not only provides physical stiffness but also produces signaling molecules such as Sonic Hedgehog (SHH) that pattern surrounding tissues. After the notochord forms, it regresses in regions where vertebrae form and expands in the perichordal disc to form the nuclei pulposi, cartilage-like discs that are interspersed with the vertebrae (reviewed in Williams et al. 2019).
Formation of the axial mesoderm is initiated by NODAL signaling via SMAD2,3 proteins that interact with the FOXH1 pioneer transcription factor (inferred from the activities of mouse homologs, as described by Hoodless et al. 2001, Yamamoto et al. 2001). TEAD proteins (inferred from mouse homologs as described by Sawada et al. 2005), which are negatively regulated by the HIPPO signaling pathway, and TBXT (T, BRACHURY) (inferred from mouse homologs, as described by Lolas et al. 2014), whose expression is initiated prior to primitive streak formation, act with the SMADs and FOXH1 to activate FOXA2, which then participates in activating downstream targets such as NOTO and SHH.
R-HSA-9823730 Formation of definitive endoderm The endoderm in mammalian embryos originates from two different populations of cells: the visceral endoderm, which is present before gastrulation as the hypoblast underlying the epiblast, and the definitive endoderm, which is derived from epiblast cells ingressing through the anterior-most region of the primitive streak. After ingression, the cells of the definitive endoderm then intercalate with the cells of the visceral endoderm to form the embryonic endoderm that will give rise to the gut and visceral organs associated with the gut such as the pancreas and liver (reviewed in Lewis and Tam 2006, Nowotschin et al. 2019). In the discoid human gastrula (differs from the rodent gastrula which acquires a cup shape), the endoderm initially is organized in a flat epithelial sheet that later rolls into a tube to form the gut. Due to ethical considerations, research on gastrulation is undertaken primarily in non-human primate species (for example Bergmann et al. 2022) and stem cells (D'Amour et al. 2005, reviewed in Salehin et al. 2022), which have provided insight into germ layer formation in human embryos.
The definitive endoderm originates in the anterior region of the primitive streak where there are high levels of NODAL signaling (inferred from mouse embryos in Vincent et al. 2003) and lower levels of BMP signaling (inferred from mouse embryos in Bachiller et al. 2000) and Wnt signaling (inferred from mouse embryos in Mukhopadhyay et al. 2001). In mouse, Eomesodermin (EOMES), whose expression is activated by NODAL signaling via SMAD2 and SMAD3 in the primitive streak, is required for formation of both mesoderm and endoderm (Arnold et al. 2008). Experiments in human embryonic stem cells and mouse embryos indicate that EOMES is a core element of a gene regulatory network that specifies definitive endoderm by activating expression of transcription factors such as FOXA2 and SOX17 which then activate sets of endodermally expressed genes (Teo et al. 2011, Chia et al. 2019). As endoderm progenitors enter the primitive streak they redistribute E-cadherin (CDH1) on their surface, which may play a role in sorting the cells into an epithelial layer (inferred from mouse homologs in Viotti et al. 2014). Unlike mesoderm, endoderm progenitors do not undergo a complete epithelial to mesenchymal transition (EMT) (inferred from mouse embryos and stem cells in Scheibner et al. 2021). They do not switch cadherin expression from E-cadherin (CDH1) to N-cadherin (CDH2) and do not require the EMT transcription factor SNAI1 (in ferred from mouse homologs in Scheibner et al. 2021). The endodermal transcription factor FOXA2 may repress EMT activity (in ferred from the mouse homolog in Scheibner et al. 2021).
Though no single marker gene is expressed exclusively in definitive endoderm, the definitive endoderm is characterized by the expression of a combination of genes, including FOXA2, SOX17, GATA4, GATA6, CXCR4, GSC, and E-cadherin (CDH1). CDH1, a general marker of epithelial cells, and the chemokine receptor CXCR4 are often used together as surface markers of definitive endoderm (inferred from mouse homologs in Yasunaga et al. 2005).
R-HSA-77042 Formation of editosomes by ADAR proteins It is still unclear how ADAR 1 and ADAR 2 proteins form the editosomes with the target RNA. Other components of these editosomes for A to I editing are unknown.
R-HSA-9761174 Formation of intermediate mesoderm Intermediate mesoderm gives rise to the urogenital system including the gonads and all components of the kidney, with the anterior intermediate mesoderm giving rise to the ureteric epithelium and the posterior intermediate epithelium giving rise to the metanephric mesenchyme. Intermediate mesoderm, is induced by a graded level of BMP signaling between the lateral plate mesoderm (high BMP activity) and the paraxial mesoderm (low BMP activity) (inferred from mouse embryos: James and Schultheiss 2005, reviewed by Davidson et al. 2019). Specification of the intermediate mesoderm in the anterior-posterior dimension is influenced by the caudal-rostral gradient Wnt and FGF signaling and rostral-caudal gradient retinoic acid signaling (inferred from mouse embryos: Cartry et al. 2006, reviewed by Davidson et al. 2019).
In mouse, the first observed markers of intermediate mesoderm are Osr1 and Lhx1, which are also expressed in the lateral plate mesoderm. Later, Pax2 and Pax8 are expressed specifically in the intermediate mesoderm. In mouse embryos, knockout experiments indicate that Osr1 activates Lhx1 and Pax2 (Wang et al. 2005), Lhx1 activates Pax2 (Tsang et al. 2000), and Pax2 activates Lhx1 and Osr1 (Boualia et al. 2013, Ranghini and Dressler 2015, reviewed in Marcotte et al. 2013). Foxc1 and Foxc2 produced in the paraxial mesoderm repress Lhx1 and Osr1 and thereby restrict the expansion of intermediate mesoderm (Wilm et al. 2004).
In vitro, human pluripotent stem cells can be induced to form intermediate mesoderm by treatment with a Wnt agonist (CHIR99021) followed by treatment with FGF2 and retinoic acid (Lam et al. 2014).
R-HSA-9758920 Formation of lateral plate mesoderm Subsets of mesoderm that have different developmental fates are produced along the primitive streak from posterior to anterior (reviewed in Arnold and Robertson 2009, Ferretti and Hadjantonakis 2019, Prummel et al. 2020, Zhai et al. 2021). In mice these subsets are (from posterior to anterior): extraembryonic mesoderm; lateral mesoderm that will form heart, limbs, and blood; presomitic mesoderm that will form somites; axial mesoderm that will form the notochord; and, finally, definitive endoderm. In humans and other primates, extraembryonic mesoderm appears to form from the hypoblast prior to gastrulation so lateral plate mesoderm is the first type of mesoderm to form at the primitive streak.
In the lateral plate mesoderm, a self-reinforcing transcription loop is initiated by Hedgehog signaling from the adjacent primitive endoderm (inferred from mouse homologs in Astorga and Carlsson 2007, Becker et al. 1997). Hedgehog proteins SHH and IHH activate expression of FOXF1, a marker of the lateral plate mesoderm following its induction (inferred from mouse homologs in Rojas et al. 2005, Astorga and Carlsson 2007). BMP4 may also activate FOXH1 in the primitive streak and lateral plate mesoderm (inferred from Xenopus homologs in Tseng et al. 2004). FOXF1 activates expression of BMP4 and BMP4 together with FOXF1 activate GATA4 (inferred from mouse homologs in Rojas et al. 2005).. BMP4 maintains the expression of FOXF1. GATA4 maintains its own expression and the expression of BMP4. FOXF1 and GATA4 then activate expression of downstream genes that further differentiate the lateral plate mesoderm. In zebrafish, the combined activity of Eomesodermin, FoxH1, and Mixl1, together with Smad proteins induces lateral plate mesoderm and this mechanism may be shared across chordates (Prummel et al. 2019).
R-HSA-9793380 Formation of paraxial mesoderm Skeletal tissues originate from paraxial mesoderm, lateral plate mesoderm, and neural crest. Paraxial mesoderm is produced by invagination of cells through the primitive streak and is the precursor of somites, which are spheres of mesenchyme bounded by epithelium that bud at fixed intervals from the anterior paraxial mesoderm in a process termed somitogenesis (reviewed in Tam and Trainor 1994, Pourquie 2003). Somites give rise to the axial skeleton and skeletal muscles.
Paraxial mesoderm becomes specified at a lower level of BMP signaling (Xi et al. 2017) that results from the interaction of BMP4, produced by the lateral plate mesoderm, with NOGGIN (NOG), a negative regulator of BMP signaling produced by the notochord (reviewed in Tani et al. 2020). WNT signaling by WNT3A that activates beta‑catenin (CTNNB1), FGF signaling that acts though FGFR1, and TBXT activate expression of TBX6 and Mesogenin 1 (MSGN1). MSGN1 binds and activates SNAI1 to promote epithelial-mesenchymal transitions (EMT). TBX6 activates MSGN1, and MSGN1 activates TBX6, to establish a positive feedback loop that ensures commitment to the paraxial mesoderm lineage. TBX6 and MSGN1 act with WNT signaling to activate expression of MSGN1, and the NOTCH ligand Delta‑like 1 (DLL1), which enhances NOTCH signaling. MSGN1 binds and activates expression of DLL1, DLL3, NOTCH1, and NOTCH2, and binds to Clock enhancers that regulate periodic expression of LFNG during somitogenesis in the anterior paraxial mesoderm. The counterbalancing DLL3 protein inhibits NOTCH signaling by binding NOTCH1 in endosomes and targeting NOTCH1 for lysosomal degradation.
TBX6 alone is capable of reprogramming pluripotent stem cells to paraxial mesoderm (Sadahiro et al. 2018) and acts in a regulatory loop with MESP2 to create the boundaries of nascent somites (Oginuma et al. 2011): TBX6 activates expression of MESP2 which then represses TBX6 by targeting TBX6 for degradation, leaving MESP2 alone at the segmental boundary.
R-HSA-2408499 Formation of selenosugars for excretion Selenite (SeO3(2-)), potentially formed from oxidised H2Se, combines with glutathione (GSH) and 1beta-methylseleno-N-acetyl-D-galactosamine derivative to form selonosugars which are further metabolised and then excreted.
R-HSA-113418 Formation of the Early Elongation Complex Transcription elongation by RNA polymerase II (RNAPII) is controlled by a number of trans-acting transcription elongation factors as well as by cis-acting elements. Transcription elongation is a rate-limiting step for proper mRNA production in which the phosphorylation of Pol II CTD is a crucial biochemical event. The role of CTD phosphorylation in transcription by Pol II is greatly impaired by protein kinase inhibitors such as 5,6-dichloro-1- ribofuranosylbenzimidazole (DRB), which block CTD phosphorylation and induce arrest of elongating Pol II. DRB-sensitive activation Pol II CTD during elongation has enabled the isolation of two sets of factors -Negative Elongation Factors (NELF) and DRB sensitivity inducing factor (DSIF). P-Tefb is a DRB-sensitive, cyclin-dependent CTD kinase composed of Cdk9 that carries out Serine-2 phosphorylation of Pol II CTD during elongation.
The mechanism by which DSIF, NELF and P-TEFb act together in Pol II-regulated elongation is yet to be fully understood. Various biochemical evidences point to a model in which DSIF and NELF negatively regulate elongation through interactions with polymerase containing a hypophosphorylated CTD. Subsequent phosphorylation of the Pol II CTD by P-Tefb might promote elongation by inhibiting interactions of DSIF and NELF with the elongation complex.
R-HSA-75094 Formation of the Editosome The editosome for C to U editing in mammals consist of a member of cytidine deaminase family of enzymes, apoB mRNA editig catalytic polypeptide 1 (APOBEC-1) and a complementing specificity factor (ACF) in addition to the target mRNA.
R-HSA-167158 Formation of the HIV-1 Early Elongation Complex This HIV-1 event was inferred from the corresponding human RNA Poll II transcription event. The details relevant to HIV-1 are described below. Formation of the early elongation complex involves hypophosphorylation of RNA Pol II CTD by FCP1P protein, association of the DSIF complex with RNA Pol II, and formation of DSIF:NELF:HIV-1 early elongation complex as described below (Mandal et al 2002; Kim et al 2003; Yamaguchi et al 2002).
R-HSA-173599 Formation of the active cofactor, UDP-glucuronate Glucose 1-phosphate and UTP are the precursors to UDP-glucuronate formation. After oxidation of the resultant complex, UDP-glucuronate is transported to the ER lumen.
R-HSA-9823739 Formation of the anterior neural plate The neural plate is a thickened layer of cells on the dorsal surface of the gastrula rostral to the node and primitive streak. As development proceeds, the neural plate folds to form a tube that will generate the brain and spinal cord (reviewed in Massarwa et al. 2013). Failure to completely form a neural tube causes neural tube defects, such as spina bifida, which are the most common birth anomaly of the central nervous system (reviewed in Lee and Gleeson 2020). Though a single structure, the neural plate actually contains two regions formed from different progenitors and regulated by distinct gene expression programs: the anterior neural plate (ANP) gives rise to the forebrain and midbrain (reviewed in Wilson and Houart 2004, Kondoh et al. 2016) and the posterior neural plate (PNP) gives rise to the hindbrain and anterior part of the spinal cord (reviewed in Kondoh et al. 2016).
The ANP arises directly from the epiblast, requires inhibition of BMP signaling by secreted inhibitors from the anterior visceral endoderm (reviwed in Andoniadou and Martinez-Barbera 2013), and expresses SOX2 driven by OTX2, ZIC2, and POU5F1/POU3F1 bound to the N2 enhancer upstream of the SOX2 gene (inferred from mouse homologs in Iwafuchi-Doi et al. 2012). The posterior part of the PNP arises from neuromesodermal cells that express SOX2 driven by WNT and FGF acting through the N1 enhancer downstream of the SOX2 gene (inferred from mouse homologs in Takemoto et al. 2006).
Both the ANP and PNP express ZEB2 and SOX1, however the ANP is characterized by high OTX2 expression (Simeone et al. 1992), while the anterior PNP expresses higher levels of GBX2 (inferred from mouse homologs in Simeone et al. 1992). The boundary between the ANP and the PNP is partly determined by a mutual antagonism between OTX2 and GBX2. OTX2 from the ANP represses expression of GBX2 and GBX2 from the PNP represses expression of OTX2 (inferred from mouse homologs in Wassarman et al. 1997, Martinez‑Barbera et al. 2001, Li et al. 2001).
R-HSA-201722 Formation of the beta-catenin:TCF transactivating complex Once in the nucleus, beta-catenin is recruited to WNT target genes through interaction with TCF/LEF transcription factors. This family, which consists of TCF7 (also known as TCF1), TCF7L1 (also known as TCF3), TCF7L2 (also known as TCF4) and TCF7L3 (also known as LEF1), are HMG-containing transcription factors that bind to the WNT responsive elements in target gene promoters (reviewed in Brantjes et al, 2002). In the absence of WNT signal, TCF/LEF proteins recruit Groucho/TLE repressors to inhibit transcription; upon WNT stimulation, beta-catenin can displace Groucho/TLE from TCF/LEF proteins to initiate transcriptional activation (reviewed in Chen and Courey, 2000). Although this model for WNT-dependent activation of target genes is widely accepted, it is important to note that TCF/LEF proteins are not redundant and can contribute to WNT target gene expression in a number of different ways (reviewed in Brantjes et al, 2002; MacDonald et al, 2009). In particular, TCF7L1 (TCF3) is thought to have a more pronounced repressor function than other TCF/LEF family members. A couple of recent studies in Xenopus and mammalian cells show that WNT- and beta-catenin-dependent phosphorylation of TCF7L1(TCF3) promotes its dissociation from the promoter of target genes and allows gene expression through relief of this repression activity (Hikasa et al, 2010; Hikasa et al, 2011).
The role of beta-catenin at WNT promoters hinges upon its ability to act as a scaffold for the recruitment of other proteins. The structure of beta-catenin consists of 12 imperfect ARM repeats (R1-12) flanked by an N-terminal and C-terminal extension (NTD and CTD respectively), with a conserved Helix C located between R12 and the CTD. Nuclear beta-catenin interacts with TCF/LEF at WNT target genes through ARM domains 3-9 (Graham et al, 2000; Poy et al, 2001; Xing et al, 2008). The N and the C terminal regions are important for the recruitment of transcriptional activator and repressors that contribute to WNT target gene expression (reviewed in Mosimann et al, 2009; Valenta et al, 2012). The N-terminal ARM domains 1-4 recruit the WNT-pathway specific activators BCL9:PYGO while the C-terminal region (R11-CTD) interacts with a wide range of general transcriptional activators that are involved in chromatin remodelling and transcription initiation. These include HATs such as P300, CBP and TIP60, histone methyltransferases such as MLL1 and 2, SWI/SNF factors BRG1 and ISWI and components of the PAF complex (reviewed in Mosimann et al, 2009; Valenta et al, 2012). Although many binding partners have been identified for the C-terminal region of beta-catenin, in many cases the timing and relationship of these interactions and indeed, the exact complex composition remains to be elucidated. Moreover, because many of the interacting partners appear to bind to overlapping regions of beta-catenin, it is unlikely that they all bind simultaneously. For simplicity, the interactions have been depicted as though they occur independently of one another; more accurately they are likely to cycle successively on and off beta-catenin to promote an active chromatin structure (reviewed in Willert and Jones, 2006; Valenta et al, 2012).
R-HSA-6809371 Formation of the cornified envelope As keratinocytes progress towards the upper epidermis, they undergo a unique process of cell death termed cornification (Eckhart et al. 2013). This involves the crosslinking of keratinocyte proteins such as loricrin and involucrin by transglutaminases and the breakdown of the nucleus and other organelles by intracellular and secreted proteases (Eckhart et al. 2000, Denecker et al. 2008). This process is strictly regulated by the Ca2+ concentration gradient in the epidermis (Esholtz et al. 2014). Loricrin and involucrin are encoded in ‘Epidermal Differentiation Complex’ linked to a large number of genes encoding nonredundant components of the CE (Kypriotou et al. 2012, Niehues et al. 2016). Keratinocytes produce specialized proteins and lipids which are used to construct the cornified envelope (CE), a heavily crosslinked submembranous layer that confers rigidity to the upper epidermis, allows keratin filaments to attach to any location in the cell membrane (Kirfel et al. 2003) and acts as a water-impermeable barrier. The CE has two functional parts: covalently cross-linked proteins (10 nm thick) that comprise the backbone of the envelope and covalently linked lipids (5 nm thick) that coat the exterior (Eckert et al. 2005). Desmosomal components are crosslinked to the CE to form corneodesmosomes, which bind cornified cells together (Ishida-Yamamoto et al. 2011). Mature terminally differentiated cornified cells consist mostly of keratin filaments covalently attached to the CE embedded in lipid lamellae (Kalinin et al. 2002). The exact composition of the cornified envelope varies between epithelia (Steinert et al. 1998); the relative amino-acid composition of the proteins used may determine differential mechanical properties (Kartasova et al. 1996).
R-HSA-9830364 Formation of the nephric duct The nephric duct originates from nephrogenic cords of intermediate mesoderm by a transition of the cells to epithelium in response to signals from somites and overlying ectoderm (reviewed in Reidy and Rosenblum 2009, Little and McMahon 2012, Khoshdel Rad et al. 2020). Initially, the nephric duct forms within in the pronephros, the first kidney structure, which comprises the nephric duct (the pronephric duct at this time) and connected tubules that empty into it. The second kidney structure, the mesonephros, then forms at the caudal end of the pronephros and contains a segment of the nephric duct, the mesonephric duct (also called the Wolffian duct), with connected proximal and distal tubules attached to nephrons and vascular glomeruli. The mesonephros fuses with the cloaca and contributes to the urinary bladder.
The metanephros then forms and persists as the functional adult kidney. The metanephros originates by the initiation of the ureteric bud from of the caudal end of the mesonephric duct, a process that is driven by molecular interactions between the nephric duct and the adjacent metanephric mesenchyme. The ureteric bud then branches and about a million nephrons, the functional filtration units of the kidney, are formed at the ureteric bud tips by an interaction between the ureteric bud and the metanephric mesenchyme.
The position of kidney formation is determined by the retinoic acid gradient acting through the HOXB4 homeobox transcription factor (inferred from mouse embryos in Preger-Ben Noon et al.2009, reviewed in Marcotte et al. 2014). PAX2, PAX8, and LHX1 are expressed early during the formation of the intermediate mesoderm. Subsequently, expression of LHX1 becomes restricted to the developing renal progenitors and is maintained by PAX2 and PAX8 (inferred from mouse homologs in Boualia et al. 2013). In the developing nephric duct, LHX1 acts with PAX2 and GATA3 to form a self-reinforcing regulatory module based on the mutual activation of LHX1 and GATA3 that drives formation of the nephric duct of the pronephros and mesonephros (inferred from mouse homologs in Boualia et al. 2013, reviewed in Marcotte et al. 2014). LHX1, GATA3, PAX2, and PAX8 then activate several genes involved in differentiation of the nephric duct including EMX2, EVI1, ID4, PLAC8, WFDC2, PCDH19, Nephronectin (NPNT), and the receptor tyrosine kinase RET (reviewed in Marcotte et al. 2014). Subsequent formation of the ureteric bud is regulated by the interaction between GDNF from the metanephric mesenchyme and RET (inferred from mouse homologs in Majumdar et al. 2003) and the interaction between integrin alpha8/beta1 (ITGA8) from the metanephric mesenchyme and NPNT (inferred from mouse homologs in Brandenberger et al. 2001).
R-HSA-9832991 Formation of the posterior neural plate The neural plate is a thickened layer of cells on the dorsal surface of the gastrula rostral to the node and primitive streak. As development proceeds, the neural plate folds to form a tube that will generate the brain and spinal cord (reviewed in Massarwa et al. 2013). Failure to completely form a neural tube causes neural tube defects, such as spina bifida, which are the most common birth anomaly of the central nervous system (reviewed in Lee and Gleeson 2020). Though a single structure, the neural plate actually contains two regions formed from different progenitors and regulated by distinct gene expression programs: the anterior neural plate (ANP) gives rise to the forebrain and midbrain (reviewed in Wilson and Houart 2004, Kondoh et al. 2016) and the posterior neural plate (PNP) gives rise to the hindbrain and anterior part of the spinal cord (reviewed in Kondoh et al. 2016).
The ANP arises directly from the epiblast, requires inhibition of BMP signaling by secreted inhibitors from the anterior visceral endoderm (reviwed in Andoniadou and Martinez-Barbera 2013), and expresses SOX2 driven by OTX2, ZIC2, and POU5F1/POU3F1 bound to the N2 enhancer upstream of the SOX2 gene (inferred from mouse homologs in Iwafuchi-Doi et al. 2012). The posterior part of the PNP arises from neuromesodermal cells that express SOX2 driven by WNT and FGF acting through the N1 enhancer downstream of the SOX2 gene (inferred from mouse homologs in Takemoto et al. 2006).
Both the ANP and PNP express ZEB2 and SOX1, however the ANP is characterized by high OTX2 expression (Simeone et al. 1992), while the anterior PNP expresses higher levels of GBX2 (inferred from mouse homologs in Simeone et al. 1992). The boundary between the ANP and the PNP is partly determined by a mutual antagonism between OTX2 and GBX2. OTX2 from the ANP represses expression of GBX2 and GBX2 from the PNP represses expression of OTX2 (inferred from mouse homologs in Wassarman et al. 1997, Martinez‑Barbera et al. 2001, Li et al. 2001).
R-HSA-72695 Formation of the ternary complex, and subsequently, the 43S complex Binding of the methionyl-tRNA initiator to the active eIF2:GTP complex results in the formation of the ternary complex. Subsequently, this Met-tRNAi:eIF2:GTP (ternary) complex binds to the complex formed by the 40S subunit, eIF3 and eIF1A, to form the 43S complex.
R-HSA-9830674 Formation of the ureteric bud Visible kidney development initiates with the formation of the pronephros and then the mesonephros (reviewed in McMahon 2016). In amniotes these are transitory structures that are superseded by formation of the metanephros, the functional kidney that persists into adulthood. The nephric duct appears during development of the pronephros and then extends caudally in the mesonephros, inducing the formation of mesonephric tubules that drain into the nephric duct and provide blood filtration in the embryo. (The mesonephric duct is also called the Wolffian duct.)
Subsequently, the metanephros is initiated by formation of the ureteric bud in the nephric duct due to the interaction between the nephric duct and the adjacent metanephric mesenchyme. The ureteric bud will grow to become the ureter, branch further, and induce the formation of nephrons and collecting ducts at the termini of the branches (reviewed in Costantini 2012). Development of the ureteric bulge is regulated by reciprocal signals passed between the nephric duct and the metanephric mesenchyme (reviewed in Marcotte et al. 2014). Nephronectin (NPNT) secreted by the nephric duct interacts with Integrin alpha8/beta1 (ITGA8) on the metanephric mesenchyme to activate expression of GDNF in the metanephric mesenchyme (Brandenberger et al. 2001, Linton et al. 2007). GDNF secreted by the metanephric mesenchyme then binds and activates the RET tyrosine kinase located in the plasma membrane of nephric duct cells (Trupp et al. 1996, Majumdar et al. 2003). RET activates expression of WNT11 in the nephric duct to regulate differentiation (Majumdar et al. 2003). The extent of kidney development is circumscribed by inhibitory signals provided by ROBO2:SLIT at the duct-mesenchyme interface (Wainwright et al. 2015) and by FOXC1,2 from the paraxial mesoderm.
R-HSA-389960 Formation of tubulin folding intermediates by CCT/TriC TriC/CCT forms a binary complex with unfolded alpha- or beta-tubulin (Frydman et al., 1992; Gao et al., 1993). The tubulin folding intermediates produced by TriC are unstable (Gao et al., 1993). Five additional protein cofactors (cofactor A-E) are required for the generation of properly folded alpha- and beta-tubulin and for the formation of alpha/beta-tubulin heterodimers (Gao et al., 1993) (Tian et al., 1997, Cowan and Lewis 2001).
R-HSA-5661270 Formation of xylulose-5-phosphate The conversion of D-glucuronate to D-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway, proceeds via L-gulonate, 3-dehydro-L-gulonate, L-xylulose, xylitol, and D-xylulose (Wamelink et al. 2008). D-glucuronate can be generated via the degradation of glucuronidated proteins. This pathway would have the effect of returning it to the pentose phosphate pathway or glycolysis.
R-HSA-444473 Formyl peptide receptors bind formyl peptides and many other ligands The formyl peptide receptor (FPR) was defined pharmacologically in 1976 as a high affinity binding site on the surface of neutrophils for the peptide N-formyl-methionine-leucine-phenylalanine (fMLF). FPR was cloned in 1990 and the cDNA used as a probe to identify two additional genes, FPRL1 and FPRL2. The three genes for a cluster on 19q13.3. All are coupled to the Gi family of G proteins.
All 3 receptors can be activated by formyl peptides but also display affinities for a range of structurally diverse ligands.
R-HSA-444209 Free fatty acid receptors Fatty acids are the ligands for a small family of G-protein-coupled receptors, the Free Fatty Acid receptors, and an unrelated receptor GPR120.
Free fatty acid receptor 1 (FFAR1/GPR40) is activated by both saturated and unsaturated medium to long-chain fatty acids while FFAR2 (GPR43) and FFAR3 (GPR41) are activated by short-chain fatty acids (carboxylates) with six or fewer carbon molecules. A fourth highly homologous receptor GPR42 is believed to be a pseudogene with intact open reading frame, but could be a functional gene in a significant fraction of the human population.
GPR120 is activated by long chain (C16-22) fatty acids.
R-HSA-400451 Free fatty acids regulate insulin secretion Free fatty acids augment the glucose-triggered secretion of insulin. The augmentation is believed to be due to the additive effects of the activation of the free fatty acid receptor 1 (FFAR1 or GPR40) and the metabolism of free fatty acids within the pancreatic beta cell. This module describes each pathway.
R-HSA-170968 Frs2-mediated activation The adaptor protein Frs2 (Fibroblast growth factor receptor substrate 2) can mediate the prolonged activation of the MAPK (ERK) cascade.
R-HSA-5652227 Fructose biosynthesis The conversion of glucose to fructose via sorbitol was demonstrated by Hers (1960) in the seminal vesicles of sheep, has since been demonstrated as well in human epidydimal tissue (Frenette et al. 2006), and appears to be the physiological source of the abundant fructose found in seminal fluid. The enzymes of the pathway are likewise abundant in the eye lens and in neurons, where their physiological role is less clear but where they appear to play a central role in diabetic tissue damage (Oates 2008).
R-HSA-70350 Fructose catabolism Fructose occurs naturally in foods as a free monosaccharide and as a component of the disaccharide sucrose. It is also widely used as a sweetener. In the body, fructose catabolism occurs in the liver and to a lesser extent in the kidney and small intestine. In these tissues, it is converted to dihydroxyacetone phosphate and D-glyceraldehyde 3-phosphate, two intermediates in the glycolytic pathway, in a sequence of three reactions. It is phosphorylated to form fructose 1-phosphate, which is cleaved by aldolase to yield dihydroxyacetone phosphate and D-glyceraldehyde, and the latter compound is phosphorylated to yield D-glyceraldehyde 3-phosphate. Other pathways exist for the conversion of D-glyceraldehyde to intermediates of glycolysis, but these appear to play only a minor role in normal fructose metabolism (Sillero et al. 1969).
R-HSA-5652084 Fructose metabolism Fructose is found in fruits, is one of the components of the disaccharide sucrose, and is a widely used sweetener in processed foods. Dietary fructose is catabolized in the liver via fructose 1-phosphate to yield dihydroxyacetone phosphate and glyceraldehyde 3-phosphate, which then are converted to pyruvate via steps of canonical glycolysis (Hers & Kusaka 1953; Sillero et al. 1969). Excessive dietary intake of fructose and its metabolism have been associated with major disease risks in humans, although this issue remains controversial (Kolderup & Svihus 2015; DiNicolantonio et al. 2015; Bray 2013; Mayes 1993; Rippe & Angelopoulos 2013; van Buul et al. 2013). Fructose can also be synthesized from glucose via the polyol pathway (Hers 1960; Oates 2008). This synthetic process provides the fructose found in seminal fluid and, in other tissues, can contribute to pathologies of diabetes.
R-HSA-168270 Fusion and Uncoating of the Influenza Virion Uncoating of viral particles takes place in the host cell endosome. Acidification of the endosome promotes fusion of the viral and endosomal membranes, causing a structural change in the viral hemagglutinin (HA) and freeing the fusion peptide of its HA2 subunit to interact with the endosome membrane. The concerted structural change of several HA molecules opens up a pore through which the viral RNP passes into the cytosol of the cell. The precise timing and the location of uncoating (early vs. late endosomes) depends on the pH-mediated transition of the specific HA molecule involved. The virus-associated M2 ion channel protein allows the influx of H+ ions into the virion, which disrupts protein-protein interactions, resulting in the release of RNP free of the viral M1 matrix protein. Thus the HA mediated fusion of the viral membrane with the endosomal membrane and the M2-mediated release of the RNP results in the release of the RNP complex into the cytosol. Amantadine and rimantadine have been shown to block the ion channel activity of the M2 protein and thus interfere with uncoating.
R-HSA-168288 Fusion of the Influenza Virion to the Host Cell Endosome After the virus binds to the target cell surface and is endocytosed, the low pH of the endosome causes the viral HA (hemagglutinin) to undergo a structural change which frees the fusion peptide of its HA2 subunit allowing it to interact with the endosome membrane. The transmembrane domain of the HA2 (inserted into the viral membrane) and the fusion peptide (inserted into the endosomal membrane) are in juxtaposition in the acidic pH structure of HA. The concerted structural change of several hemagglutinin molecules then opens a pore through which the viral RNP will be able to pass into the host cell cytosol.
R-HSA-416482 G alpha (12/13) signalling events The G12/13 family is probably the least well characterized subtype, partly because G12/13 coupling is difficult to determine when compared with the other subtypes which predominantly rely on assay technologies that measure intracellular calcium. The G12/13 family are best known for their involvement in the processes of cell proliferation and morphology, such as stress fiber and focal adhesion formation. Interactions with Rho guanine nucleotide exchange factors (RhoGEFs) are thought to mediate many of these processes. (Buhl et al.1995, Sugimoto et al. 2003). Activation of Rho or the regulation of events through Rho is often taken as evidence of G12/13 signaling. Receptors that are coupled with G12/13 invariably couple with one or more other G protein subtypes, usually Gq.
R-HSA-418594 G alpha (i) signalling events The classical signalling mechanism for G alpha (i) is inhibition of the cAMP dependent pathway through inhibition of adenylate cyclase (Dessauer C W et al. 2002). Decreased production of cAMP from ATP results in decreased activity of cAMP-dependent protein kinases. Other functions of G alpha (i) includes activation of the protein tyrosine kinase c-Src (Ma Y C et al. 2000). Regulator of G-protein Signalling (RGS) proteins can regulate the activity of G alpha (i) (Soundararajan et al. 2008).
R-HSA-416476 G alpha (q) signalling events The classic signalling route for G alpha (q) is activation of phospholipase C beta thereby triggering phosphoinositide hydrolysis, calcium mobilization and protein kinase C activation. This provides a path to calcium-regulated kinases and phosphatases, GEFs, MAP kinase cassettes and other proteins that mediate cellular responses ranging from granule secretion, integrin activation, and aggregation in platelets. Gq participates in many other signalling events including direct interaction with RhoGEFs that stimulate RhoA activity and inhibition of PI3K. Both in vitro and in vivo, the G-protein Gq seems to be the predominant mediator of the activation of platelets. Moreover, G alpha (q) can stimulate the activation of Burton tyrosine kinase (Ma Y C et al. 1998). Regulator of G-protein Signalling (RGS) proteins can regulate the activity of G alpha (z) (Soundararajan M et al. 2008).
R-HSA-418555 G alpha (s) signalling events The general function of the G alpha (s) subunit (Gs) is to activate adenylate cyclase (Tesmer et al. 1997), which in turn produces cAMP, leading to the activation of cAMP-dependent protein kinases (often referred to collectively as Protein Kinase A). The signal from the ligand-stimulated GPCR is amplified because the receptor can activate several Gs heterotrimers before it is inactivated. Another downstream effector of G alpha (s) is the protein tyrosine kinase c-Src (Ma et al. 2000).
R-HSA-418597 G alpha (z) signalling events The heterotrimeric G protein G alpha (z), is a member of the G (i) family. Unlike other G alpha (i) family members it lacks an ADP ribosylation site cysteine four residues from the carboxyl terminus and is thus pertussis toxin-insensitive. It inhibits adenylyl cyclase types I, V and VI (Wong Y H et al. 1992). G alpha (z) interacts with the Rap1 GTPase activating protein (Rap1GAP) to attenuate Rap1 signaling. Like all G-proteins G alpha (z) has an intrinsic GTPase activity, but this activity tends to be lower for the pertussis toxin insensitive G-proteins, most strikingly so for G alpha (z), whose kcat value for GTP hydrolysis is 200-fold lower than those of G alpha (s) or G alpha (i) (Grazziano et al. 1989). G alpha (z) knockout mice have disrupted platelet aggregation at physiological concentrations of epinephrine and responses to several neuroactive drugs are altered (Yang et al. 2000). Regulator of G-protein Signalling (RGS) proteins can regulate the activity of G alpha (z) (Soundararajan M et al. 2008).
R-HSA-8964315 G beta:gamma signalling through BTK G-Protein Coupled Receptors (GPCR) sense extracellular signals and activate different Guanine nucleotide binding proteins (G-proteins) that have alpha, beta and gamma subunits. Upon activation, the alpha subunit of G-proteins dissociates from beta-gamma and the both are then free to regulate downstream effectors. G-protein beta-gamma complex, along with phosphatidylinositol 3,4,5-trisphosphate (PIP3), recruits the non-receptor Tyrosine-protein kinase BTK to the cell membrane. Here, the G-protein beta-gamma complex activates BTK. Subsequently, active BTK dissociates from the complex to phosphorylate downstream substrates. Physiologically, BTK plays a key role in B lymphocyte development, differentiation and signalling.
R-HSA-8964616 G beta:gamma signalling through CDC42 G-Protein Coupled Receptors (GPCR) sense extracellular signals and activate different Guanine nucleotide binding proteins (G-proteins) that have alpha, beta and gamma subunits. Upon activation, the alpha subunit of G-proteins dissociates from beta-gamma and the both are then free to regulate downstream effectors. Serine/threonine-protein kinase PAK 1 binds with Rho guanine nucleotide exchange factor 6 (ARHGEF6, PIX-Alpha) in the cytosol and is subsequently translocated by the G-protein beta-gamma complex to the plasma membrane. Here, ARHGEF6 activates Cell division control protein 42 homolog (CDC42) by acting as a GEF. Once active, CDC42 can facilitate the activation of PAK1. CDC42 is known to be involved in epithelial cell polarization processes.
R-HSA-392451 G beta:gamma signalling through PI3Kgamma PI3K gamma (PI3KG) is a heterodimer consisting of a p110 catalytic subunit associated with a regulatory p101 or p84 subunit. PI3KG is most highly expressed in neutrophils, where the p101 form predominates (approximately 95%). G beta:gamma recruits PI3KG to the plasma membrane, both activating PI3KG and providing access to its substrate PIP2, which is converted to PIP3.
R-HSA-418217 G beta:gamma signalling through PLC beta Phospholipase C beta (PLCbeta) isoforms are activated by G-protein beta:gamma in the order PLCB3 > PLCB2 > PLCB1. Gbeta:gamma binds to the pleckstrin homology domain of PLC beta, increasing phospholipase activity and leading to increased hydrolysis of PIP2 to DAG and IP3.
R-HSA-1296059 G protein gated Potassium channels Inwardly rectifying G protein activated K+ channels (GIRK) are tetrameric assemblies of Ki3 3 family subunits (Kir 3.1, 3.2 3.3 and 3.4). The activation of G protein coupled receptor by ligand results in the liberation of G alpha and G beta gamma subunits. Gbeta gamma subunits interact and activate GIRK channels.
R-HSA-202040 G-protein activation Receptor activated heterotrimeric G proteins consist of the Galpha and the tightly associated Gbeta-gamma subunits. When a ligand binds to a G protein-coupled receptor, it stabilises a conformation with an high affinity for the G-protein bound to GDP. GDP is then exchanged for GTP on the Galpha subunit. This exchange triggers the dissociation of the Galpha subunit from the Gbeta-gamma dimer and the receptor. Galpha-GTP and Gbeta-gamma, can then modulate different signalling cascades and effector proteins, while the receptor is able to activate another G protein, resulting in an amplification cascade. The Galpha subunit will eventually hydrolyze the attached GTP to GDP by its inherent enzymatic activity, allowing it to reassociate with Gbeta-gamma and start a new cycle.
R-HSA-397795 G-protein beta:gamma signalling The classical role of the G-protein beta/gamma dimer was believed to be the inactivation of the alpha subunit, Gbeta/gamma was viewed as a negative regulator of Galpha signalling. It is now known that Gbeta/gamma subunits can directly modulate many effectors, including some also regulated by G alpha.
R-HSA-112040 G-protein mediated events When dissociated Galpha-GTP and Gbeta-gamma can activate or inhibit different signalling cascades and effector proteins. The precise pathways depends on the identity of the alpha and beta/gamma subtypes.
R-HSA-1538133 G0 and Early G1 In G0 and early G1 in quiescent cells, p130 (RBL2) bound to E2F4 or E2F5 and either DP1 or DP2, associates with the MuvB complex, forming an evolutionarily conserved DREAM complex, that represses transcription of cell cycle genes. During early G1 phase in actively cycling cells, p107 (RBL1) forms a complex with E2F4 and DP1 or DP2 and represses transcription of E2F target genes. Both p130 (RBL2) and p107 (RBL1) repress transcription of E2F targets through recruiting histone deacetylase HDAC1, possibly in complex with other chromatin modifying enzymes, to E2F-regulated promoters. Expression of p107 (RBL1) is cell cycle regulated, with its levels peaking in late G1 and S phase. Although p107 (RBL1) is phosphorylated by cyclin D assocaited kinases during late G1 phase, a small pool of p107 (RBL1) is thought to be present throughout G1 and S phase, and could be involved in fine tuning the transcription of S-phase genes. This is supported by studies showing that unlike RB1 and p130 (RBL2), which are able to induce G1 arrest when over-expressed, p107 (RBL1) over-expression can arrest the cell cycle in both G1 and S phase. For recent reviews on the function of p107, p130 and pocket proteins in general, please refer to Wirt and Sage, 2010, MacPherson 2008 and Cobrinik 2005.
R-HSA-69236 G1 Phase Early cell cycle progression in G1 is under the control of the D-type cyclins together with Cdk4 and Cdk6. An important target for these CDKs is the Retinoblastoma (Rb) protein, which when phosphorylated promotes cell cycle progression by releasing E2F transcription factors that transactivate several important genes for later cell cycle events. The formation of Cyclin D - Cdk4/6 complexes is promoted by two proteins, p21Cip1/Waf1 and p27kip1, and their activity can be inhibited by the binding of several small CDK-inhibitory proteins (CKIs): p15INK4B, p16INK4A, p18INK4C and p19INK4D.
R-HSA-69615 G1/S DNA Damage Checkpoints In the G1 phase there are two types of DNA damage responses, the p53-dependent and the p53-independent pathways. The p53-dependent responses inhibit CDKs through the up-regulation of genes encoding CKIs mediated by the p53 protein, whereas the p53-independent mechanisms inhibit CDKs through the inhibitory T14Y15 phosphorylation of Cdk2. Failure of DNA damage checkpoints in G1 leads to mutagenic replication of damaged templates and other replication defects.
R-HSA-69206 G1/S Transition Cyclin E - Cdk2 complexes control the transition from G1 into S-phase. In this case, the binding of p21Cip1/Waf1 or p27kip1 is inhibitory. Important substrates for Cyclin E - Cdk2 complexes include proteins involved in the initiation of DNA replication. The two Cyclin E proteins are subjected to ubiquitin-dependent proteolysis, under the control of an E3 ubiquitin ligase known as the SCF. Cyclin A - Cdk2 complexes, which are also regulated by p21Cip1/Waf1 and p27kip1, are likely to be important for continued DNA synthesis, and progression into G2. An additional level of control of Cdk2 is reversible phosphorylation of Threonine-14 (T14) and Tyrosine-15 (Y15), catalyzed by the Wee1 and Myt1 kinases, and dephosphorylation by the three Cdc25 phosphatases, Cdc25A, B and C.
R-HSA-69205 G1/S-Specific Transcription The E2F family of transcription factors regulate the transition from the G1 to the S phase in the cell cycle. E2F activity is regulated by members of the retinoblastoma protein (pRb) family, resulting in the tight control of the expression of E2F-responsive genes. Phosphorylation of pRb by cyclin D:CDK complexes releases pRb from E2F, inducing E2F-targeted genes such as cyclin E.
E2F1 binds to E2F binding sites on the genome activating the synthesis of the target proteins. For annotation purposes, the reactions regulated by E2F1 are grouped under this pathway and information about the target genes alone are displayed for annotation purposes.
Cellular targets for activation by E2F1 include thymidylate synthase (TYMS) (DeGregori et al. 1995), Rir2 (RRM2) (DeGregori et al. 1995, Giangrande et al. 2004), Dihydrofolate reductase (DHFR) (DeGregori et al. 1995, Wells et al. 1997, Darbinian et al. 1999), Cdc2 (CDK1) (Furukawa et al. 1994, DeGregori et al. 1995, Zhu et al. 2004), Cyclin A1 (CCNA1) (DeGregori et al. 1995, Liu et al. 1998), CDC6 (DeGregori et al. 1995, Yan et al. 1998; Ohtani et al. 1998), CDT1 (Yoshida and Inoue 2004), CDC45 (Arata et al. 2000), Cyclin E (CCNE1) (Ohtani et al. 1995), Emi1 (FBXO5) (Hsu et al. 2002), and ORC1 (Ohtani et al. 1996, Ohtani et al. 1998). The activation of TK1 (Dnk1) (Dou et al. 1994, DeGregori et al. 1995, Giangrande et al. 2004) and CDC25A (DeGregori et al. 1995, Vigo et al. 1999) by E2F1 is conserved in Drosophila (Duronio and O'Farrell 1994, Reis and Edgar 2004).
RRM2 protein is involved in dNTP level regulation and activation of this enzyme results in higher levels of dNTPs in anticipation of S phase. E2F activation of RRM2 has been shown also in Drosophila by Duronio and O'Farrell (1994). E2F1 activation of CDC45 is shown in mouse cells by using human E2F1 construct (Arata et al. 2000). Cyclin E is also transcriptionally regulated by E2F1. Cyclin E protein plays important role in the transition of G1 in S phase by associating with CDK2 (Ohtani et al. 1996). E2F1-mediated activation of PCNA has been demonstrated in Drosophila (Duronio and O'Farrell 1994) and in some human cells by using recombinant adenovirus constructs (DeGregori et al. 1995). E2F1-mediated activation of the DNA polymerase alpha subunit p180 (POLA1) has been demonstrated in some human cells. It has also been demonstrated in Drosophila by Ohtani and Nevins (1994). It has been observed in Drosophila that E2F1 induced expression of Orc1 stimulates ORC1 6 complex formation and binding to the origin of replication (Asano and Wharton 1999). ORC1 6 recruit CDC6 and CDT1 that are required to recruit the MCM2 7 replication helicases. E2F1 regulation incorporates a feedback mechanism wherein Geminin (GMNN) can inhibit MCM2 7 recruitment of ORC1 6 complex by interacting with CDC6/CDT1. The activation of CDC25A and TK1 (Dnk1) by E2F1 has been inferred from similar events in Drosophila (Duronio RJ and O'Farrell 1994; Reis and Edgar 2004). E2F1 activates string (CDC25) that in turn activates the complex of Cyclin B and CDK1. A similar phenomenon has been observed in mouse NIH 3T3 cells and in Rat1 cells.
R-HSA-68911 G2 Phase This is one of two 'gap' phases in the standard eukaryotic mitotic cell cycle. It is the interval between the completion of DNA synthesis and the beginning of mitosis. Protein synthesis occurs in this phase, following DNA replication in the S phase. This is the time when the cell stockpiles on the cytoplasmic contents, before mitosis and cytokinesis occur (Mitchison 2003, Kaldis 2016).
R-HSA-69481 G2/M Checkpoints G2/M checkpoints include the checks for damaged DNA, unreplicated DNA, and checks that ensure that the genome is replicated once and only once per cell cycle. If cells pass these checkpoints, they follow normal transition to the M phase. However, if any of these checkpoints fail, mitotic entry is prevented by specific G2/M checkpoint events.
The G2/M checkpoints can fail due to the presence of unreplicated DNA or damaged DNA. In such instances, the cyclin-dependent kinase, Cdc2(Cdk1), is maintained in its inactive, phosphorylated state, and mitotic entry is prevented. Events that ensure that origins of DNA replication fire once and only once per cell cycle are also an example of a G2/M checkpoint.
In the event of high levels of DNA damage, the cells may also be directed to undergo apopotosis (not covered). R-HSA-69473 G2/M DNA damage checkpoint Throughout the cell cycle, the genome is constantly monitored for damage, resulting either from errors of replication, by-products of metabolism or through extrinsic sources such as ultra-violet or ionizing radiation. The different DNA damage checkpoints act to inhibit or maintain the inhibition of the relevant CDK that will control the next cell cycle transition. The G2 DNA damage checkpoint prevents mitotic entry solely through T14Y15 phosphorylation of Cdc2 (Cdk1). Failure of the G2 DNA damage checkpoint leads to catastrophic attempts to segregate unrepaired chromosomes. R-HSA-69478 G2/M DNA replication checkpoint The G2/M DNA replication checkpoint ensures that mitosis is not initiated until DNA replication is complete. If replication is blocked, the DNA replication checkpoint signals to maintain Cyclin B - Cdc2 complexes in their T14Y15 phosphorylated and inactive state. This prevents the phosphorylation of proteins involved in G2/M transition, and prevents mitotic entry.
Failure of these checkpoints results in changes of ploidy: in the case of mitosis without completion of DNA replication, aneuploidy of <2C will result, and the opposite is true if DNA replication is completed more than once in a single cell cycle with an overall increase in ploidy. The mechanism by which unreplicated DNA is first detected by the cell is unknown.
R-HSA-69275 G2/M Transition Together with two B-type cyclins, CCNB1 and CCNB2, Cdc2 (CDK1) regulates the transition from G2 into mitosis. CDK1 can also form complexes with Cyclin A (CCNA1 and CCNA3). CDK1 complexes with A and B type cyclins are activated by dephosphorylation of CDK1 threonine residue T14 and tyrosine residue Y15. Cyclin A:CDK1 and Cyclin B:CDK1 complexes phosphorylate several proteins involved in mitotic spindle formation and function, the breakdown of the nuclear envelope, and chromosome condensation that is necessary for the ~2 meters of DNA to be segregated at mitosis (Nigg 1998, Nilsson and Hoffmann 2000, Salaun et al. 2008, Fisher et al. 2012).
R-HSA-180292 GAB1 signalosome GAB1 is recruited to the activated EGFR indirectly, through GRB2. GAB1 acts as an adaptor protein that enables formation of an active PIK3, through recruitment of PIK3 regulatory subunit PIK3R1 (also known as PI3Kp85), which subsequently recruits PIK3 catalytic subunit PIK3CA (also known as PI3Kp110). PIK3, in complex with EGFR, GRB2 and GAB1, catalyzes phosphorylation of PIP2 and its conversion to PIP3, which leads to the activation of the AKT signaling.
R-HSA-977444 GABA B receptor activation Functional GABA B receptors are heteromers of GABA B1 and B2 subunits, complexed with G protein alpha-i, 0, beta, and gamma subunits. They function as metabotropic receptors. When GABA is bound to the B1 sub-unit, the B2 subunit undergoes a conformational change that releases the G alpha-i G0 dimer (which binds and inactivates cytosolic adenylate cyclase) and the G beta G gamma dimer (which activates the GIRK (KIR3) potassium channel) (Pinard et al. 2010).
R-HSA-977443 GABA receptor activation Gamma aminobutyric acid (GABA) receptors are the major inhibitory receptors in human synapses. They are of two types. GABA A receptors are fast-acting ligand gated chloride ion channels that mediate membrane depolarization and thus inhibit neurotransmitter release (G Michels et al Crit Rev Biochem Mol Biol 42, 2007, 3-14). GABA B receptors are slow acting metabotropic Gprotein coupled receptors that act via the inhibitory action of their Galpha/Go subunits on adenylate cyclase to attenuate the actions of PKA. In addition, their Gbeta/gamma subunits interact directly with N and P/Q Ca2+ channels to decrease the release of Ca2+. GABA B receptors also interact with Kir3 K+ channels and increase the influx of K+, leading to cell membrane hyperpolarization and inhibition of channels such as NMDA receptors (A Pinard et al Adv Pharmacol, 58, 2010, 231-55).
R-HSA-888568 GABA synthesis GABA synthesized uniquely by two forms of glutamate decarboxylases, GAD65 and GAD67, that are functionally distinct and have different co-factor requirements. GAD65 is functionally linked to VGAT, the GABA transporter and selectively GABA synthesized by GAD65 is preferably loaded into the synaptic vesicles. GABA synthesized by GAD67 may be used for functions other than nuerotransmission.
R-HSA-888590 GABA synthesis, release, reuptake and degradation GABA is a major inhibitory neurotransmitter in the mammalian central nervous system. GABA modulates neuronal excitability throughout the nervous system. Disruption of GABA neurotransmission leads to many neurological diseases including epilepsy and a general anxiety disorder. GABA is synthesized by two distinct enzymes GAD67 and GAD65 that differ in their cellular localization, functional properties and co-factor requirements. GABA synthesized by GAD65 is used for neurotransmission whereas GABA synthesized by GAD67 is used for processes other than neurotransmission such as synaptogenesis and protection against neuronal injury. GABA is loaded into synaptic vesicle with the help of vesicular inhibitory amino acid transporter or VGAT. GAD65 and VGAT are functionally linked at the synaptic vesicle membrane and GABA synthesized by GAD65 is preferentially loaded into the synaptic vesicle over GABA synthesized in cytoplasm by GAD67.The GABA loaded synaptic vesicles are docked at the plasma membrane with the help of the SNARE complexes and primed by interplay between various proteins including Munc18, complexin etc. Release of GABA loaded synaptic vesicle is initiated by the arrival of action potential at the presynaptic bouton and opening of N or P/Q voltage gated Ca2+ channels. Ca2+ influx results in Ca2+ binding by synaptobrevin, which is a part of the SNARE complex that also includes SNAP25 and syntaxin, leading to synaptic vesicle fusion. Release of GABA in the synaptic cleft leads to binding of GABA by the GABA receptors and post ligand binding events.
R-HSA-6787639 GDP-fucose biosynthesis Fucose-containing glycans play important roles in immunity and signalling. Fucosylated glycans are created by fucosyltransferases, which require the high-energy donor substrate GDP-fucose. Two pathways for the synthesis of GDP-fucose exist in mammalian cells; the GDP-mannose-dependent de novo pathway provides the majority of GDP-fucose whereas a minor contribution comes from the free fucose-dependent salvage pathway (Becker & Lowe 2003).
R-HSA-5635851 GLI proteins bind promoters of Hh responsive genes to promote transcription GLI proteins are bifunctional DNA-binding proteins that recognize consensus GLI sites 5'-GACCACCC-3' in the promoters of target genes (Kinzler and Vogelstein, 1990). Pathway induction upon ligand-binding diverts the GLI proteins from the processing/degradation pathway that generates the truncated repressor form and promotes the formation of the full-length transcriptional activator (reviewed in Hui and Angers, 2011; Briscoe and Therond, 2013). GLI-dependent target genes have been identified by a number of ChIP based screens, and well-established, direct targets include a number of Hh pathway members including PTCH1, PTCH2, GLI1, HHIP and BOC (Lee et al, 2010; Vokes et al, 2007; Vokes et al, 2008; Agren et al, 2004; Bai et al, 2004; Bai et al, 2002; Dai et al, 1999). Full-length GLI proteins nucleate the assembly of a transcriptional activation complex at target gene promoters, but the details of interacting partners are not well known. The C-terminus of GLI3 has been shown to interact with a number of transcriptional activators including the histone acetyltransferase CBP, the Mediator component Med12 and the TATA-box recognition protein TAF31, but the detail of how and when these binding partners interact is not known (Dai et al, 1999; Zhou et al, 2006; Yoon et al, 1998; reviewed in Hui and Angers, 2011). Each of the GLI proteins has been shown to bind to CDC 73, a component of the PAF complex that has roles in RNA polymerase II-mediated transcription (Mosimann et al, 2009; reviewed in Tomson and Arndt, 2013).
R-HSA-5610785 GLI3 is processed to GLI3R by the proteasome In the absence of Hh signaling, the majority of full-length GLI3 is partially processed by the proteasome to a shorter form that serves as the principal repressor of Hh target genes (Wang et al, 2000). Processing depends on phosphorylation at 6 sites by PKA, which primes the protein for subsequent phosphorylation at adjacent sites by CK1 and GSK3. The hyperphosphorylated protein is then a direct target for betaTrCP-dependent ubiquitination and proteasome-dependent processing (Wang and Li, 2006; Tempe et al, 2006; Wen et al, 2010; Schrader et al, 2011; Pan and Wang, 2007).
R-HSA-430116 GP1b-IX-V activation signalling The platelet GPIb complex (GP1b-IX-V) together with GPVI are primarily responsible for regulating the initial adhesion of platelets to the damaged blood vessel and platelet activation. The importance of GPIb is demonstrated by the bleeding problems in patients with Bernard-Soulier syndrome where this receptor is either absent or defective. GP1b-IX-V binds von Willebrand Factor (vWF) to resting platelets, particularly under conditions of high shear stress. This transient interaction is the first stage of the vascular repair process. Activation of GP1b-IX-V on exposure of the fibrous matrix following atherosclerotic plaque rupture, or in occluded arteries, is a major contributory factor leading to thrombus formation leading to heart attack or stroke. GpIb also binds thrombin (Yamamoto et al. 1986), at a site distinct from the site of vWF binding, acting as a docking site for thrombin which then activates Proteinase Activated Receptors leading to enhanced platelet activation (Dormann et al. 2000).
R-HSA-388396 GPCR downstream signalling G protein-coupled receptors (GPCRs) are classically defined as the receptor, G-protein and downstream effectors, the alpha subunit of the G-protein being the primary signaling molecule. However, it has become clear that this greatly oversimplifies the complexities of GPCR signaling (Gurevich & Gurevich 2008). The beta:gamma G-protein dimer is also involved in downstream signaling (Smrcka 2008) and some receptors form metastable complexes with accessory proteins such as the arrestins. GPCRs are involved in many diverse signaling events (Kristiansen 2004), using a variety of pathways that include modulation of adenylyl cyclase, phospholipase C, the mitogen activated protein kinases (MAPKs), extracellular signal regulated kinase (ERK) c-Jun-NH2-terminal kinase (JNK) and p38 MAPK. Regulator of G-protein Signalling (RGS) proteins can directly inhibit the activity of the G-alpha subunit (Soundararajan et al. 2008). The general function of the G alpha-s subunit (Gs) is to activate adenylate cyclase (Tesmer et al. 1997), which in turn produces cyclic-AMP (cAMP), leading to the activation of cAMP-dependent protein kinases (often referred to collectively as Protein Kinase A). The signal from the ligand-stimulated GPCR is amplified because the receptor can activate several Gs heterotrimers before it is inactivated. The classical signalling mechanism for G alpha-i (Gi) is inhibition of the cAMP dependent pathway through inhibition of adenylate cyclase (Dessauer et al. 2002). Decreased production of cAMP results in decreased activity of cAMP-dependent protein kinases. G alpha-z (Gz) is a member of the Gi family. Unlike other Gi family members it is pertussis toxin-insensitive. Gz interacts with Rap1 GTPase activating protein (RAP1GAP) to attenuate Rap1 signaling. The classic signalling route for G alpha-q (Gq) is activation of phospholipase C beta, leading to phosphoinositide hydrolysis, calcium mobilization and protein kinase C activation. This provides a path to calcium-regulated kinases and phosphatases, GEFs, MAP kinases and many other proteins. The G-alpha-12/13 (G12/13) family is probably the least well characterized, at least in part because G12/13 coupling is more difficult to determine than for other subtypes, G12/13 is best known for involvement in the processes of cell proliferation and morphology, such as stress fiber and focal adhesion formation. Interactions with Rho guanine nucleotide exchange factors (RhoGEFs) are thought to mediate many of these processes. (Buhl et al.1995, Sugimoto et al. 2003). Activation of Rho or the regulation of events through Rho is often taken as evidence of G12/13 signaling. Receptors that are coupled with G12/13 invariably couple with one or more other G protein subtypes, usually Gq.
R-HSA-500792 GPCR ligand binding There are more than 800 G-protein coupled receptor (GPCRs) in the human genome, making it the largest receptor superfamily. GPCRs are also the largest class of drug targets, involved in virtually all physiological processes (Frederiksson 2003). GPCRs are receptors for a diverse range of ligands from large proteins to photons (Kristiansen et al. 2004) and have an equal diversity of ligand-binding mechanisms (Gether et al. 2002). Classical GPCR signaling involves signal transduction via heterotrimeric G-proteins, though G-protein independent mechanisms have been reported. Rhodopsin-like receptors (class A/1) are by far the largest group of GPCRs and the best studied, though a large proportion of the functional and structural studies have focused on a very few members; many remain functionally uncharacterized. This large family can be subdivided into at least 19 subfamilies (Subfamily A1-19) based on phylogenetic analysis (Joost & Methner 2002). Family A includes receptors for a wide variety of ligands including hormones, light and neurotransmitters, encompassing a wide range of functions including many autocrine, paracrine and endocrine processes. The secretin-like family B/2 GPCRs includes receptors for many hormone-like peptides, such as secretin, calcitonin, parathyroid hormone/parathyroid hormone-related peptides and vasoactive intestinal peptide, which activate adenylyl cyclase and the phosphatidyl-inositol-calcium pathway (Harmar 2001). The class C/3 GPCRs include the metabotropic glutamate receptors and taste receptors (Brauner-Osborne et al. 2007). All have a large extracellular N-terminus that structurally resembles a clamshell and has an important role in ligand binding.
R-HSA-9634597 GPER1 signaling GPER1 (also known as GPR30) is an orphan G-protein coupled receptor that has been suggested to act as an alternate estrogen receptor (Revankar et al, 2005; Filardo et al, 2007; reviewed in Prossnitz and Barton, 2011; Gaudet et al, 2015). In support of this, a number of studies have shown that GPER1 stimulates MAPK and cAMP activation in response to estrogen in ESR1 negative breast cancer cells. Similar to classical ESR1-mediated signaling, this estrogen-responsive GPER1 is suggested to act through G beta gamma and to involve EGFR transactivation (Filardo et al, 2000; Filardo et al, 2002; reviewed in Filardo and Thomas, 2012).
R-HSA-114604 GPVI-mediated activation cascade The GPVI receptor is a complex of the GPVI protein with Fc epsilon R1 gamma (FcR). The Src family kinases Fyn and Lyn constitutively associate with the GPVI-FcR complex in platelets and initiate platelet activation through phosphorylation of the immunoreceptor tyrosine-based activation motif (ITAM) in the FcR gamma chain, leading to binding and activation of the tyrosine kinase Syk. Downstream of Syk, a series of adapter molecules and effectors lead to platelet activation.
The GPVI receptor signaling cascade is similar to that of T- and B-cell immune receptors, involving the formation of a signalosome composed of adapter and effector proteins. At the core of the T-cell receptor signalosome is the transmembrane adapter LAT and two cytosolic adapters SLP-76 and Gads. While LAT is essential for signalling to PLCgamma1 downstream of the T-cell receptor, the absence of LAT in platelets only impairs the activation of PLCgamma2, the response to collagen and GPVI receptor ligands remains sufficient to elicit a full aggregation response. In contrast, GPVI signalling is almost entirely abolished in the absence of SLP-76.
R-HSA-179812 GRB2 events in EGFR signaling Autophosphorylated EGFR tyrosine residues are docking sites for many downstream effectors in EGFR signaling. The adaptor protein GRB2 binds to phosphotyrosine residues in the C-tail of EGFR through its SH2 domain. GRB2 is constitutively associated with SOS, a guanine nucleotide exchange factor of RAS. GRB2 binding to phosphorylated EGFR results in the recruitment of SOS to the plasma membrane where it comes in proximity to RAS. This mechanism has been seen to be the model for RAS activation.
R-HSA-1963640 GRB2 events in ERBB2 signaling ERBB2:EGFR and ERBB2:ERBB4 can directly recruit GRB2:SOS1 complex through phosphorylated C-tail tyrosines of EGFR (Y1068 and Y1086) and ERBB2 (Y1139) that serve as docking sites for GRB2 (Xie et al. 1995, Sepp-Lorenzino et al. 1996), which, again, results in SOS1-mediated guanyl-nucleotide exchange on RAS and activation of RAF and MAP kinases (Janes et al. 1994, Sepp-Lorenzino et al. 1996).
R-HSA-354194 GRB2:SOS provides linkage to MAPK signaling for Integrins Integrin signaling is linked to the MAP kinase pathway by recruiting Grb2 to the FADK1/SRC activation complex.
R-HSA-1306955 GRB7 events in ERBB2 signaling Heterodimers of ERBB2 and ERBB3 are able to bind GRB7 (Fiddes et al. 1998) through phosphorylated tyrosine residues in the C-tail of ERBB3 (Y1199 and Y1262) (Fiddes et al. 1998), but the exact downstream signaling of this complex has not been elucidated. GRB7 can recruit SHC1 to the active ERBB2 complex, and contributes to ERBB2 signaling-induced RAS activation, which promotes cellular proliferation, but the exact mechanism has not been elucidated (Pradip et al. 2013). In addition, GRB7 can be phosphorylated by the integrin-activated PTK2 (FAK), leading to VAV2-dependent activation of RAC1 and promotion of cell migration. The exact mechanistic details of GRB7-induced RAC1 activation are not known (Pradip et al. 2013).
R-HSA-9762114 GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 In addition to KEAP1:CUL3-mediated degradation in the cytosol, NFE2L2 appears to also be subject to degradation by a BTRC:CUL1 E3 ligase (reviewed in Cuadrado, 2015; Baird and Yamamoto, 2020; Yamamoto et al, 2018). Degradation by the BTRC:CUL1 pathway is mediated by interaction with the NFE2L2 Neh6 domain, and is stimulated by GSK3B-mediated phosphorylation of the Neh6 DSGIS motif. GSK3B-dependent Neh6 phosphorylation is primed by the phosphorylation of a cluster of adjacent serines by unknown kinase(s) (Salazar et al, 2006; Rada et al, 2011; Rada et L, 2012; Rojo et al, 2012; Chen et al, 2017; reviewed in Baird and Yamamoto, 2020). Inhibitory phosphorylation of GSK3B by activated PI3K/AKT signaling relieves BTRC:CUL1-mediated NFE2L2 degradation and provides a biochemical link between activated PI3K signaling and increased NFE2L2 pathway activity (reviewed in Cuadrado, 2015; Baird and Yamamoto, 2020; Yamamoto et al, 2018).
R-HSA-72706 GTP hydrolysis and joining of the 60S ribosomal subunit Hydrolysis of eIF2-GTP occurs after the Met-tRNAi has recognized the AUG. This reaction is catalyzed by eIF5 (or eIF5B) and is thought to cause dissociation of all other initiation factors and allow joining of the large 60S ribosomal subunit. The 60S subunit joins - a reaction catalyzed by eIF5 or eIF5B - resulting in a translation-competent 80S ribosome. Following 60S subunit joining, eIF5B hydrolyzes its GTP and is released from the 80S ribosome, which is now ready to start elongating the polypeptide chain.
R-HSA-9726842 Gain-of-function MRAS complexes activate RAF signaling This pathway describes the effect of activating mutations of MRAS-complex components on RAF activation (reivewed in Simanshu et al, 2017).
R-HSA-70370 Galactose catabolism The main sources of galactose in the human diet are milk and milk products. The disaccharide lactose from these sources is hydrolyzed in the intestine to its constituent monosaccharides, glucose and galactose. Galactose is metabolized primarily in the liver in a sequence of three reactions that yield one molecule of glucose 1-phosphate per molecule of galactose. First, it is phosphorylated to yield galactose 1-phosphate. Then, galactose 1-phosphate and UDP-glucose react to form UDP-galactose and glucose 1-phosphate, and UDP-galactose undergoes epimerization to form UDP-glucose. In a reaction shared with other pathways, glucose 1-phosphate can be converted into glucose 6-phosphate (Holton et al. 2001; Elsas and Lai 2001).
R-HSA-163841 Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation After translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the body. These modifications include the vitamin K-dependent attachment of carboxyl groups to glutamate residues and the conversion of a lysine residue in eIF5A to hypusine, the conversion of a histidine residue in EEF to diphthamide, and the hydrxylation of various amino acid side chains.
R-HSA-159740 Gamma-carboxylation of protein precursors Gamma-carboxylation of a cluster of glutamate residues near the amino termini of thrombin, factor VII, factor IX, factor X, protein C, protein S, protein Z, and Gas 6 is required for these proteins to bind Ca++ and function efficiently in blood clotting. A single enzyme, vitamin K-dependent gamma-carboxylase, catalyzes the gamma-carboxylation of all eight proteins involved in clotting (Morris et al. 1995; Brenner et al. 1998; Spronk et al. 2000). In the carboxylation reaction, the enzyme binds its substrate protein via a sequence motif on the amino terminal side of the glutamate residues to be carboxylated (Furie et al. 1999), then processively carboxylates all glutamates in the cluster before releasing the substrate (Morris et al. 1995; Berkner 2000; Stenina et al. 2001). The reaction occurs in the endoplasmic reticulum (Bristol et al. 1996).
R-HSA-159854 Gamma-carboxylation, transport, and amino-terminal cleavage of proteins A number of proteins, including eight required for normal blood clot formation and its regulation (Prothrombin (factor II), factor VII, factor IX, factor X, protein C, protein S, protein Z, and Gas6) share a sequence motif rich in glutamate residues near their amino termini. Carboxylation of the glutamate residues within this motif followed by removal of an aminoterminal propeptide is required for each of these proteins to function. These modifications occur as the proteins move through the endoplasmic reticulum and Golgi apparatus.
R-HSA-190861 Gap junction assembly The assembly of gap junctions involves (1) synthesis of connexin polypeptides at endoplasmic reticulum membranes, (2) oligomerization into homomeric- and heteromeric gap junction connexons (hemi-channels), (3) passage through the Golgi stacks, (4) intracellular storage within Trans Golgi membranes, (5) trafficking along microtubules, (6) insertion of connexons into the plasma membrane, (7) lateral diffusion of connexons in the plasma membrane, (8) aggregation of individual gap junction channels into plaques, and (9) stabilization of peripheral microtubule plus-ends by binding to Cx43-based gap junctions (see Segretain and Falk, 2004.)
R-HSA-190873 Gap junction degradation The half-life of Cx is very short (1 to 5h) compared to other junctional proteins (Laird et al., 1995 ; Fallon and Goudenough, 1981). Connexins are targeted for degradation by the proteasome and the lysosome. Degradation appears to involve the phosphorylation of Connexins as well as their interactions with other proteins (Piehl et al., 2007).
R-HSA-190828 Gap junction trafficking Gap junctions are intercellular communication channels formed from Cx (connexin) protein subunits (see Segretain and Falk 2004 and Evans et al. 2006 for comprehensive reviews). Connexins are transported to the plasma membrane after oligomerizing into hexameric assemblies called hemichannels (CxHcs) or connexons. Connexons dock head-to-head in the extracellular space with opposing hexameric channels located in the plasma membranes of neighbouring cells. The double membrane channel or gap junction generated directly links the cytoplasms of interacting cells and facilitates the integration and co-ordination of cellular signalling, metabolism, secretion and contraction. In addition to their role in intercellular communication, connexon hemichannels coordinate the release of ATP, glutamate, NAD+ and prostaglandin E2 from the cells. CxHcs open in response to various types of external changes, including mechanical, shear, ionic and ischaemic stress.
The trafficking of gap junctions involves (1) synthesis of connexin polypeptides at endoplasmic reticulum membranes, (2) oligomerization into homomeric- and heteromeric gap junction connexons (hemi-channels), (3) passage through the Golgi stacks, (4) intracellular storage within Trans Golgi membranes, (5) trafficking along microtubules, (6) insertion of connexons into the plasma membrane, (7) lateral diffusion of connexons in the plasma membrane, (8) aggregation of individual gap junction channels into plaques, (9) stabilization of peripheral microtubule plus-ends by binding to Cx43-based gap junctions, (10) internalization of the channel plaque leading to cytoplasmic annular junctions, and (11) complete degradation via lysosomal and proteasomal pathways (see Segretain and Falk 2004). Aspects of gap assembly are described here.
R-HSA-157858 Gap junction trafficking and regulation Gap junctions are clusters of intercellular channels connecting adjacent cells and permitting the direct exchange of ions and small molecules between cells. These channels are composed of two hemichannels, or connexons, one located on each of the two neighboring cells. Each connexon is composed of 6 trans-membrane protein subunits of the connexin (Cx) family. A gap of approximately 3 nm remains between the adjacent cell membranes, but two connexons interact and dock head-to-head in the extra-cellular space forming a tightly sealed, double-membrane intercellular channel (see Segretain and Falk, 2004). The activity of these intercellular channels is regulated, particularly by intramolecular modifications such as phosphorylation which appears to regulate connexin turnover, gap junction assembly and the opening and closure (gating) of gap junction channels.
R-HSA-5696397 Gap-filling DNA repair synthesis and ligation in GG-NER Global genome nucleotide excision repair (GG-NER) is completed by DNA repair synthesis that fills the single stranded gap created after dual incision of the damaged DNA strand and excision of the ~27-30 bases long oligonucleotide that contains the lesion. DNA synthesis is performed by DNA polymerases epsilon or delta, or the Y family DNA polymerase kappa (POLK), which are loaded to the repair site after 5' incision (Staresincic et al. 2009, Ogi et al. 2010). DNA ligases LIG1 or LIG3 ligate the newly synthesized stretch of oligonucleotides to the incised DNA strand (Arakawa et al. 2012, Paul-Konietzko et al. 2015).
R-HSA-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER In transcription-coupled nucleotide excision repair (TC-NER), similar to global genome nucleotide excision repair (GG-NER), DNA polymerases delta or epsilon, or the Y family DNA polymerase kappa, fill in the single stranded gap that remains after dual incision. DNA ligases LIG1 or LIG3, subsequently seal the single stranded nick by ligating the 3' end of the newly synthesized patch with the 5' end of incised DNA (Staresincic et al. 2009, Ogi et al. 2010, Arakawa et al. 2012, Paul-Konietzko et al. 2015).
R-HSA-881907 Gastrin-CREB signalling pathway via PKC and MAPK Gastrin is a hormone whose main function is to stimulate secretion of hydrochloric acid by the gastric mucosa, which results in gastrin formation inhibition. This hormone also acts as a mitogenic factor for gastrointestinal epithelial cells. Gastrin has two biologically active peptide forms, G34 and G17.Gastrin gene expression is upregulated in both a number of pre-malignant conditions and in established cancer through a variety of mechanisms. Depending on the tissue where it is expressed and the level of expression, differential processing of the polypeptide product leads to the production of different biologically active peptides. In turn, acting through the classical gastrin cholecystokinin B receptor CCK-BR, its isoforms and alternative receptors, these peptides trigger signalling pathways which influence the expression of downstream genes that affect cell survival, angiogenesis and invasion (Wank 1995, de Weerth et al. 1999, Grabowska & Watson 2007)
R-HSA-9758941 Gastrulation Gastrulation is the reorganization of the blastula to form the multilayered gastrula. During gastrulation, a portion of cells from the exterior of the epithelial epiblast layer migrate to the interior, where they form mesoderm and endoderm which, together with the outer layer of ectoderm (arising from epiblast cells that have not migrated), comprise the three cell layers that are characteristic of triploblastic metazoans (reviewed in Technau and Scholz 2003). In the human peri-implantation embryo, epiblast cells ingress through the primitive streak located in the posterior region of the embryonic disc to form the mesoderm and endoderm of the embryo proper (reviewed in Bardot and Hadjantonakis 2020, Ghimire et al. 2021, Zhai et al. 2021, Rossant and Tam 2022). In the mouse, a mammalian model organism, the embryo is cup-shaped instead of being disc-shaped (reviewed in Kojima et al. 2014). However, the morphogenetic process of germ layer formation is broadly conserved in both species.
The primitive streak forms at the posterior region of the epiblast where there is high signaling activity of NODAL, BMP, FGF and WNT pathways, which drive the allocation of cells to the mesoderm and endoderm lineages. In the primitive streak, the ingressing cells undergo epithelial-to-mesenchymal transition (reviewed in Amack 2021). Cells allocated to the mesoderm acquire a mesenchymal phenotype. Endodermal cells are reputed to revert back to an epithelial architecture through a mesenchymal-to-epithelial transition as they are integrated into the pre-existing layer of hypoblast. A recent study in mouse, however, revealed that ingressing cells that are destined for the endoderm undergo an incomplete or partial-EMT and retain some epithelial features prior to re-acquiring epithelialization (Scheibner et al. 2021).
During gastrulation in mice, extraembryonic mesoderm is formed first and is followed by mesoderm that populates the anterior structures, the head, face and heart of the embryo and next the mesoderm to the trunk. Endoderm is also formed in an anterior to posterior sequence, with endoderm emerging early in gastrulation populating the foregut, followed by the mid- and hind-gut. Along the anterior-posterior axis of the primitive streak, endoderm and axial mesoderm emerge from the anterior region, whereas mesoderm emerging from the mid- to posterior regions is allocated in a medial-lateral order to paraxial, intermediate and lateral plate mesoderm. Cells remaining in the overlying epiblast contribute to the ectoderm. Cells of the ectoderm are allocated to the neural ectoderm and to the surface ectoderm and the neural border cells that give rise to the neural crest cells. Patterning of the neuroectoderm is facilitated by the inductive interaction with prechordal plate and the notochord derived from the axial mesoderm.
Before ingression, cells of the primitive streak express genes such as TBXT (T, BRACHYURY) and EOMES that are characteristic of nascent mesoderm and endoderm. It is not known if there are common progenitors that give rise to all types of mesodermal derivatives, such as lateral plate mesoderm and paraxial mesoderm. The knowledge to this date indicates that the different types of mesodermal derivatives are allocated in accordance to the timing and locality of emergence from the primitive streak. The existence of bipotential mesendoderm progenitors in the gastrulating embryo is unresolved but unlikely (Probst et al. 2021), though a bipotential cell population may be derived from mouse embryonic stem cells in vitro.
R-HSA-211000 Gene Silencing by RNA In this module, the biology of various types of regulatory non-coding RNAs are described. Biogenesis and functions of small interfering RNAs (siRNAs) and microRNAs (miRNAs) are annotated. Biogenesis of PIWI-interacting small RNAs (piRNAs) and tRNA-derived small RNAs (tsRNAs) are also annotated.
R-HSA-8950505 Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation Experiments using human cord blood CD4(+) T cells show 22 protein spots and 20 protein spots, upregulated and downregulated proteins respectively, following Interleukin-12 stimulation (Rosengren et.al, 2005). The identified upregulated proteins are: BOLA2, PSME2, MTAP, CA1, GSTA2, RALA, CNN2, CFL1, TCP1, HNRNPDL, MIF, AIP, SOD1, PPIA and PDCD4.
And the identified downregulated proteins are:
ANXA2, RPLP0, CAPZA1, SOD2, SNRPA1, LMNB1, LCP1, HSPA9, SERPINB2, HNRNPF, TALDO1, PAK2, TCP1, HNRNPA2B1, MSN, PITPNA, ARF1, SOD2, ANXA2, CDC42, RAP1B and GSTO1.
R-HSA-74160 Gene expression (Transcription) Gene expression encompasses transcription and translation and the regulation of these processes. RNA Polymerase I Transcription produces the large preribosomal RNA transcript (45S pre-rRNA) that is processed to yield 18S rRNA, 28S rRNA, and 5.8S rRNA, accounting for about half the RNA in a cell. RNA Polymerase II transcription produces messenger RNAs (mRNA) as well as a subset of non-coding RNAs including many small nucleolar RNAs (snRNA) and microRNAs (miRNA). RNA Polymerase III Transcription produces transfer RNAs (tRNA), 5S RNA, 7SL RNA, and U6 snRNA. Transcription from mitochondrial promoters is performed by the mitochondrial RNA polymerase, POLRMT, to yield long transcripts from each DNA strand that are processed to yield 12S rRNA, 16S rRNA, tRNAs, and a few RNAs encoding components of the electron transport chain. Regulation of gene expression can be divided into epigenetic regulation, transcriptional regulation, and post-transcription regulation (comprising translational efficiency and RNA stability). Epigenetic regulation of gene expression is the result of heritable chemical modifications to DNA and DNA-binding proteins such as histones. Epigenetic changes result in altered chromatin complexes that influence transcription. Gene Silencing by RNA mostly occurs post-transcriptionally but can also affect transcription. Small RNAs originating from the genome (miRNAs) or from exogenous RNA (siRNAs) are processed and transferred to the RNA-induced silencing complex (RISC), which interacts with complementary RNA to cause cleavage, translational inhibition, or transcriptional inhibition.
R-HSA-202433 Generation of second messenger molecules In addition to serving as a scaffold via auto-phosphorylation, ZAP70 also phosphorylates a restricted set of substrates following TCR stimulation - including LAT (step 13) and LCP2. These substrates have been recognized to play pivotal role in TCR signaling by releasing second messengers. When phosphorylated, LAT and SLP-76 act as adaptor proteins which serve as nucleation points for the construction of a higher order signalosome: PLC-gamma1 (step 14) and GRAP2 (step 15) bind to the LAT on the phosphorylated tyrosine residues. LCP2 is then moved to the signalosome by interacting with the SH3 domains of GRAP2 using their proline rich sequences (step 16). Once LCP2 binds to GRAP2, three LCP2 acidic domain N-term tyrosine residues are phosphorylated by ZAP70 (step 17). These phospho-tyrosine residues act as binding sites to the SH2 domains of ITK (steps 18) and PLC-gamma1 (step 19). PLC-gamma1 is activated by dual phosphorylation on the tyrosine residues at positions 771, 783 and 1254 by ITK (step 20) and ZAP70 (step 21). Phosphorylated PLC-gamma1 subsequently detaches from LAT and LCP2 and translocates to the plasma membrane by binding to phosphatidylinositol-4,5-bisphosphate (PIP2) via its PH domain (step 22). PLC-gamma1 goes on to hydrolyse PIP2 to second messengers DAG and IP3 (step 23). These second messengers are involved in PKC and NF-kB activation and calcium mobilization.
R-HSA-212436 Generic Transcription Pathway OVERVIEW OF TRANSCRIPTION REGULATION:
Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or tissue-specific regulation of differential gene transcription is mediated (reviewed in Naar, 2001. Kadonaga, 2004, Maston, 2006, Barolo, 2002; Roeder, 2005, Rosenfeld, 2006). Of the three major classes of DNA polymerase involved in eukaryotic gene transcription, Polymerase II generally regulates protein-encoding genes. Figure 1 shows a diagram of the various components involved in cell-specific regulation of Pol-II gene transcription.
Core Promoter: Pol II-regulated genes typically have a Core Promoter where Pol II and a variety of general factors bind to specific DNA motifs:
i: the TATA box (TATA DNA sequence), which is bound by the "TATA-binding protein" (TBP).
ii: the Initiator motif (INR), where Pol II and certain other core factors bind, is present in many Pol II-regulated genes.
iii: the Downstream Promoter Element (DPE), which is present in a subset of Pol II genes, and where additional core factors bind.
The core promoter binding factors are generally ubiquitously expressed, although there are exceptions to this.
Proximal Promoter: immediately upstream (5') of the core promoter, Pol II target genes often have a Proximal Promoter region that spans up to 500 base pairs (b.p.), or even to 1000 b.p.. This region contains a number of functional DNA binding sites for a specific set of transcription activator (TA) and transcription repressor (TR) proteins. These TA and TR factors are generally cell- or tissue-specific in expression, rather than ubiquitous, so that the presence of their cognate binding sites in the proximal promoter region programs cell- or tissue-specific expression of the target gene, perhaps in conjunction with TA and TR complexes bound in distal enhancer regions.
Distal Enhancer(s): many or most Pol II regulated genes in higher eukaryotes have one or more distal Enhancer regions which are essential for proper regulation of the gene, often in a cell or tissue-specific pattern. Like the proximal promoter region, each of the distal enhancer regions typically contain a cluster of binding sites for specific TA and/or TR DNA-binding factors, rather than just a single site.
Enhancers generally have three defining characteristics:
i: They can be located very long distances from the promoter of the target gene they regulate, sometimes as far as 100 Kb, or more.
ii: They can be either upstream (5') or downstream (3') of the target gene, including within introns of that gene.
iii: They can function in either orientation in the DNA.
Combinatorial mechanisms of transcription regulation: The specific combination of TA and TR binding sites within the proximal promoter and/or distal enhancer(s) provides a "combinatorial transcription code" that mediates cell- or tissue-specific expression of the associated target gene. Each promoter or enhancer region mediates expression in a specific subset of the overall expression pattern. In at least some cases, each enhancer region functions completely independently of the others, so that the overall expression pattern is a linear combination of the expression patterns of each of the enhancer modules.
Co-Activator and Co-Repressor Complexes: DNA-bound TA and TR proteins typically recruit the assembly of specific Co-Activator (Co-A) and Co-Repressor (Co-R) Complexes, respectively, which are essential for regulating target gene transcription. Both Co-A's and Co-R's are multi-protein complexes that contain several specific protein components.
Co-Activator complexes generally contain at lease one component protein that has Histone Acetyl Transferase (HAT) enzymatic activity. This functions to acetylate Histones and/or other chromatin-associated factors, which typically increases that transcription activation of the target gene. By contrast, Co-Repressor complexes generally contain at lease one component protein that has Histone De-Acetylase (HDAC) enzymatic activity. This functions to de-acetylate Histones and/or other chromatin-associated factors. This typically increases the transcription repression of the target gene.
Adaptor (Mediator) complexes: In addition to the co-activator complexes that assemble on particular cell-specific TA factors, - there are at least two additional transcriptional co-activator complexes common to most cells. One of these is the Mediator complex, which functions as an "adaptor" complex that bridges between the tissue-specific co-activator complexes assembled in the proximal promoter (or distal enhancers). The human Mediator complex has been shown to contain at least 19 protein distinct components. Different combinations of these co-activator proteins are also found to be components of specific transcription Co-Activator complexes, such as the DRIP, TRAP and ARC complexes described below.
TBP/TAF complex: Another large Co-A complex is the "TBP-associated factors" (TAFs) that assemble on TBP (TATA-Binding Protein), which is bound to the TATA box present in many promoters. There are at least 23 human TAF proteins that have been identified. Many of these are ubiquitously expressed, but TAFs can also be expressed in a cell or tissue-specific pattern.
Specific Coactivator Complexes for DNA-binding Transcription Factors.
A number of specific co-activator complexes for DNA-binding transcription factors have been identified, including DRIP, TRAP, and ARC (reviewed in Bourbon, 2004, Blazek, 2005, Conaway, 2005, and Malik, 2005). The DRIP co-activator complex was originally identified and named as a specific complex associated with the Vitamin D Receptor member of the nuclear receptor family of transcription factors (Rachez, 1998). Similarly, the TRAP co-activator complex was originally identified as a complex that associates with the thyroid receptor (Yuan, 1998). It was later determined that all of the components of the DRIP complex are also present in the TRAP complex, and the ARC complex (discussed further below). For example, the DRIP205 and TRAP220 proteins were show to be identical, as were specific pairs of the other components of these complexes (Rachez, 1999).
In addition, these various transcription co-activator proteins identified in mammalian cells were found to be the orthologues or homologues of the Mediator ("adaptor") complex proteins (reviewed in Bourbon, 2004). The Mediator proteins were originally identified in yeast by Kornberg and colleagues, as complexes associated with DNA polymerase (Kelleher, 1990). In higher organisms, Adapter complexes bridge between the basal transcription factors (including Pol II) and tissue-specific transcription factors (TFs) bound to sites within upstream Proximal Promoter regions or distal Enhancer regions (Figure 1). However, many of the Mediator homologues can also be found in complexes associated with specific transcription factors in higher organisms. A unified nomenclature system for these adapter / co-activator proteins now labels them Mediator 1 through Mediator 31 (Bourbon, 2004). For example, the DRIP205 / TRAP220 proteins are now identified as Mediator 1 (Rachez, 1999), based on homology with yeast Mediator 1.
Example Pathway: Specific Regulation of Target Genes During Notch Signaling:
One well-studied example of cell-specific regulation of gene transcription is selective regulation of target genes during Notch signaling. Notch signaling was first identified in Drosophila, where it has been studied in detail at the genetic, molecular, biochemical and cellular levels (reviewed in Justice, 2002; Bray, 2006; Schweisguth, 2004; Louvri, 2006). In Drosophila, Notch signaling to the nucleus is thought always to be mediated by one specific DNA binding transcription factor, Suppressor of Hairless. In mammals, the homologous genes are called CBF1 (or RBPJkappa), while in worms they are called Lag-1, so that the acronym "CSL" has been given to this conserved transcription factor family. There are at least two human CSL homologues, which are now named RBPJ and RBPJL.
In Drosophila, Su(H) is known to be bifunctional, in that it represses target gene transcription in the absence of Notch signaling, but activates target genes during Notch signaling. At least some of the mammalian CSL homologues are believed also to be bifunctional, and to mediate target gene repression in the absence of Notch signaling, and activation in the presence of Notch signaling.
Notch Co-Activator and Co-Repressor complexes: This repression is mediated by at least one specific co-repressor complexes (Co-R) bound to CSL in the absence of Notch signaling. In Drosophila, this co-repressor complex consists of at least three distinct co-repressor proteins: Hairless, Groucho, and dCtBP (Drosophila C-terminal Binding Protein). Hairless has been show to bind directly to Su(H), and Groucho and dCtBP have been shown to bind directly to Hairless (Barolo, 2002). All three of the co-repressor proteins have been shown to be necessary for proper gene regulation during Notch signaling in vivo (Nagel, 2005).
In mammals, the same general pathway and mechanisms are observed, where CSL proteins are bifunctional DNA binding transcription factors (TFs), that bind to Co-Repressor complexes to mediate repression in the absence of Notch signaling, and bind to Co-Activator complexes to mediate activation in the presence of Notch signaling. However, in mammals, there may be multiple co-repressor complexes, rather than the single Hairless co-repressor complex that has been observed in Drosophila.
During Notch signaling in all systems, the Notch transmembrane receptor is cleaved and the Notch intracellular domain (NICD) translocates to the nucleus, where it there functions as a specific transcription co-activator for CSL proteins. In the nucleus, NICD replaces the Co-R complex bound to CSL, thus resulting in de-repression of Notch target genes in the nucleus (Figure 2). Once bound to CSL, NICD and CSL proteins recruit an additional co-activator protein, Mastermind, to form a CSL-NICD-Mam ternary co-activator (Co-A) complex. This Co-R complex was initially thought to be sufficient to mediate activation of at least some Notch target genes. However, there now is evidence that still other co-activators and additional DNA-binding transcription factors are required in at least some contexts (reviewed in Barolo, 2002).
Thus, CSL is a good example of a bifunctional DNA-binding transcription factor that mediates repression of specific targets genes in one context, but activation of the same targets in another context. This bifunctionality is mediated by the association of specific Co-Repressor complexes vs. specific Co-Activator complexes in different contexts, namely in the absence or presence of Notch signaling.
R-HSA-9754189 Germ layer formation at gastrulation Due to ethical considerations, most research on mammalian gastrulation has been performed on mouse embryos. Therefore most of the reactions described in this section are the results of research in mouse embryos. Significant research has also been performed on non-human primates such as cynomolgus monkeys (Macaca fascicularis) (Nakamura et al. 2016, Sasaki et al. 2016). More recently, human gastrula-like cell assemblages ("gastruloids") generated from pluripotent stem cells have been developed (Moris et al. 2020) and are now being compared with mouse embryos (reviewed in Rossant and Tam 2021, Ghimire et al. 2021).
At the beginning of gastrulation in the mouse, the primitive streak forms in a region of BMP, WNT, FGF, and NODAL signaling. In the mouse embryo, NODAL is expressed throughout the epiblast before anterior-posterior axis induction and is required for pluripotency (reviewed in Robertson 2014). NODAL signaling is restricted to the posterior side of the embryo by the secretion of NODAL and WNT antagonists (CER1, LEFTY1) from the anterior visceral endoderm (AVE) (reviewed in Stower and Srinivas 2014). In human embryonic stem cells (hESCs) NODAL is also crucial for maintenance of pluripotency (James et al. 2005, Vallier et al. 2004). In mouse embryos, NODAL and WNT3 are required for formation of the primitive streak (Conlon et al. 1994, Brennan et al. 2001, Liu et al. 1999) and NODAL expression subsequently becomes restricted to the node at the anterior end of the primitive streak (Zhou et al. 1993). Pro-NODAL secreted by the epiblast in response to BMP4 signalling from the extraembryonic ectoderm is converted to mature NODAL by furin (PCSK3) secreted from the extraembryonic ectoderm. NODAL maintains BMP4 expression in the extraembryonic ectoderm which then activates WNT3 in the posterior epiblast. WNT signaling, in turn, amplifies NODAL expression (Brennan et al. 2001). The order of events in this signaling cascade may be different in human embryos due to differences in early embryo architecture.
NODAL, BMP, and WNT show similar effects on human 2D gastruloids (Martyn et al. 2019). Mesoderm and definitive endoderm progenitors appear to be already separate and distinct in the primitive streak, therefore bipotential mesendoderm progenitors may be transitory if they exist (Probst et al. 2021). This is an area of ongoing research.
Mesoderm is formed by an epithelial-mesenchymal transition that produces an ingression of cells through the primitive streak. Endoderm does not show a complete epithelial-mesenchymal transition and instead forms by cell plasticity (a partial epithelial-mesenchymal transition in which both E-cadherin and N-Cadherin are expressed) (inferred from mouse embryos in Scheibner et al. 2021). However, in mouse embryos endoderm progenitors still ingress through the anterior region of the primitive streak, migrate with mesoderm cells, and eventually integrate into the visceral endoderm layer to give rise to the definitive endoderm (Viotti et al. 2014).
Specific types of mesoderm are formed sequentially according to the time and position of ingression of cells through the primitive streak. This patterning is caused by gradients of NODAL, WNT, and BMP signaling that activate transcriptional programs in the mesoderm progenitors.
T-box transcription factor T (TBXT, T, Brachyury) and Eomesodermin (EOMES) are two of the first transcription factors expressed in mesoderm and endoderm progenitors in the primitive streak (reviewed in Probst and Arnold 2016). The two factors combined are required for formation of all mesoderm and endoderm (Arnold et al. 2008, Tosic et al. 2019).
TBXT is activated by WNT signaling (via beta-catenin acting with LEF1 or TCF1) and BMP4 and is expressed in mesodermal and axial mesodermal progenitors and in the primitive streak during gastrulation, later becoming localized to the notochord and tailbud. TBXT is an early marker of mesodermal differentiation and is often used in studies of embryonic stem cells. In hESCs TBXT is expressed in both mesodermal and endodermal progenitors, it regulates different sets of target genes depending on the signaling environment (Faial et al. 2015).
Expression of EOMES is activated by NODAL via SMAD2 and SMAD3 and is observed in the posterior epiblast prior to formation of the primitive streak and in mesoderm and endoderm progenitors during the first day of gastrulation. EOMES in combination with SMAD2,3 is crucial for the activation of definitive endoderm genes (Teo et al. 2011). TBXT and EOMES generally activate expression of mesoderm genes and repress expression of genes associated with pluripotency such as SOX2 and NANOG.
Some transcription factors are particularly important for regulating gastrulation and are also used as markers for particular stages and morphological features. For example, Goosecoid (GSC) expression marks the onset of gastrulation, is first observed in the primitive streak, and becomes localized to the anterior end of the primitive streak and then the axial mesoderm (Blum et al. 1992). SMAD2 and SMAD3 activated by NODAL are recruited to the GSC promoter by FOXH1, which is already located at the promoter. MIXL1 also binds the GSC promoter and activates expression. In mice, GSC is a regulator of head development.
MIXL1 is required for formation of both mesoderm and definitive endoderm (Hart et al. 2002) and is expressed early throughout the primitive streak and in nascent mesoderm cells exiting the streak. Expression of MIXL1 is mediated downstream by NODAL through SMAD2 and SMAD3 binding to the promoter of MIXL1. EOMES also plays a direct role in activating MIXL1 and GSC expression in hESCs (Teo et al. 2011) and in mouse embryos (Tosic et al. 2019)..
Developing mesoderm becomes specified by expression of transcription factors such as MESP1, a marker of cardiac progenitors. (See the Reactome pathway "Cardiogenesis".)
R-HSA-5696399 Global Genome Nucleotide Excision Repair (GG-NER) The DNA damage in GG-NER is recognized by the joint action of two protein complexes. The first complex is composed of XPC, RAD23A or RAD23B and CETN2. The second complex, known as the UV-DDB complex, is an ubiquitin ligase composed of DDB1, CUL4A or CUL4B, RBX1 and a GG-NER specific protein DDB2. In vitro, the UV-DDB complex is onlynecessary for GG-NER mediated repair of UV-induced pyrimidine dimers. In vivo, however, where DNA repair occurs in the chromatin context, the UV-DDB complex likely facilitates GG-NER mediated repair irrespective of the DNA damage type.
After DNA damage recognition, the TFIIH complex, together with XPA, verifies the DNA damage and unwinds the DNA helix around the damage, creating an open bubble. Two DNA endonucleases, ERCC5 (XPG) and the complex of ERCC1 and ERCC4 (XPF), excise the oligonucleotide that contains damaged base(s) from the affected DNA strand. DNA polymerases delta, epsilon and/or kappa perform DNA repair synthesis, followed by DNA ligation, thus completing GG-NER.
For a recent review, please refer to Marteijn et al. 2014.
R-HSA-163359 Glucagon signaling in metabolic regulation Glucagon and insulin are peptide hormones released from the pancreas into the blood, that normally act in complementary fashion to stabilize blood glucose concentration. When blood glucose levels rise, insulin release stimulates glucose uptake from the blood, glucose breakdown (glycolysis), and glucose storage as glycogen. When blood glucose levels fall, glucagon release stimulates glycogen breakdown and de novo glucose synthesis (gluconeogenesis), while inhibiting glycolysis and glycogen synthesis.
At a molecular level, the binding of glucagon to the extracellular face of its receptor causes conformational changes in the receptor that allow the dissociation and activation of subunits Gs and Gq. The activation of Gq leads to the activation of phospholipase C, production of inositol 1,4,5-triphosphate, and subsequent release of intracellular calcium. The activation of Gs leads to activation of adenylate cyclase, an increase in intracellular cAMP levels, and activation of protein kinase A (PKA). Active PKA phosphorylates key enzymes of glycogenolysis, glycogenesis, gluconeogenesis, and glycolysis, modifying their activities. These signal transduction events, and some of their downstream consequences, are illustrated below (adapted from Jiang and Zhang, 2003).
R-HSA-381676 Glucagon-like Peptide-1 (GLP1) regulates insulin secretion Glucagon-like Peptide-1 (GLP-1) is secreted by L-cells in the intestine in response to glucose and fatty acids. GLP-1 circulates to the beta cells of the pancreas where it binds a G-protein coupled receptor, GLP-1R, on the plasma membrane. The binding activates the heterotrimeric G-protein G(s), causing the alpha subunit of G(s) to exchange GDP for GTP and dissociate from the beta and gamma subunits.
The activated G(s) alpha subunit interacts with Adenylyl Cyclase VIII (Adenylate Cyclase VIII, AC VIII) and activates AC VIII to produce cyclic AMP (cAMP). cAMP then has two effects: 1) cAMP activates Protein Kinase A (PKA), and 2) cAMP activates Epac1 and Epac2, two guanyl nucleotide exchange factors.
Binding of cAMP to PKA causes the catalytic subunits of PKA to dissociate from the regulatory subunits and become an active kinase. PKA is known to enhance insulin secretion by closing ATP-sensitive potassium channels, closing voltage-gated potassium channels, releasing calcium from the endoplasmic reticulum, and affecting insulin secretory granules. The exact mechanisms for PKA's action are not fully known. After prolonged increases in cAMP, PKA translocates to the nucleus where it regulates the PDX-1 and CREB transcription factors, activating transcription of the insulin gene.
cAMP produced by AC VIII also activates Epac1 and Epac2, which catalyze the exchange of GTP for GDP on G-proteins, notably Rap1A. Rap1A regulates insulin secretory granules and is believed to activate the Raf/MEK/ERK mitogenic pathway leading to proliferation of beta cells. The Epac proteins also interact with RYR calcium channels on the endoplasmic reticulum, the SUR1 subunits of ATP-sensitive potassium channels, and the Piccolo:Rim2 calcium sensor at the plasma membrane.
R-HSA-420092 Glucagon-type ligand receptors The glucagon hormone family regulates the activity of GPCRs from the secretin receptor subfamily in Class II/B (Mayo KE et al, 2003).
R-HSA-194002 Glucocorticoid biosynthesis Cortisol, the major human glucocorticoid, is synthesized in the zona fasciculata of the adrenal cortex from pregnenolone. Pregnenolone is converted to 17alpha-hydoxyprogesterone in two reactions, both catalyzed by 3-beta-hydroxysteroid dehydrogenase/isomerase. 17Alpha-hydroxyprogesterone is hydroxylated by CYP21A2 to form 11-deoxycortisol, which in turn is converted to cortisol by CYP11B1. The conversion of the active steroid hormone, cortisol, to inactive cortisone occurs in many tissues, notably the liver (Payne and Hales 2004).
R-HSA-70263 Gluconeogenesis Gluconeogenesis converts mitochondrial pyruvate to cytosolic glucose 6 phosphate which in turn can be hydrolyzed to glucose and exported from the cell. Gluconeogenesis is confined to cells of the liver and kidney and enables glucose synthesis from molecules such as lactate and alanine and other amino acids when exogenous glucose is not available (reviewed, e.g., by Chourpiliadis & Mohiuddin 2022). Gluconeogenesis occurs in two parts: a network of reactions converts mitochondrial pyruvate to cytosolic phosphoenolpyruvate; then phosphoenolpyruvate is converted to glucose 6 phosphate in a single sequence of cytosolic reactions.
Three variants of the first part of the process are physiologically important. 1) A series of transport and transamination reactions convert mitochondrial oxaloacetate to cytosolic oxaloacetate which is converted to phosphoenolpyruvate by a hormonally regulated, cytosolic isoform of phosphoenolpyruvate carboxykinase. This variant allows regulated glucose synthesis from lactate. 2) Mitochondrial oxaloacetate is reduced to malate, which is exported to the cytosol and re oxidized to oxaloacetate. This variant provides reducing equivalents to the cytosol, needed for glucose synthesis from amino acids such as alanine and glutamine. 3) Constitutively expressed mitochondrial phosphoenolpyruvate carboxykinase catalyzes the conversion of mitochondrial oxaloacetate to phosphoenolpyruvate which may then be transported to the cytosol. The exact path followed by any one molecule of pyruvate through this reaction network is determined by the tissue in which the reactions are occurring, the source of the pyruvate, and the physiological stress that triggered gluconeogenesis.
In the second part of gluconeogenesis, cytosolic phosphoenolpyruvate, however derived, is converted to fructose 1,6 bisphosphate by reactions that are the reverse of steps of glycolysis. Hydrolysis of fructose 1,6 bisphosphate to fructose 6 phosphate is catalyzed by fructose 1,6 bisphosphatase, and fructose 6 phosphate is reversibly isomerized to glucose 6 phosphate.
In all cases, the synthesis of glucose from two molecules of pyruvate requires the generation and consumption of two reducing equivalents as cytosolic NADH + H+. For pyruvate derived from lactate (variants 1 and 3), NADH + H+ is generated with the oxidation of lactate to pyruvate in the cytosol (a reaction of pyruvate metabolism not shown in the diagram). For pyruvate derived from amino acids (variant 2), mitochondrial NADH + H+ generated by glutamate dehydrogenase (a reaction of amino acid metabolism, not shown) is used to reduce oxaloacetate to malate, which is transported to the cytosol and re oxidized, generating cytosolic NADH + H+. The synthesis of glucose from pyruvate also requires the consumption of six high energy phosphates, four from ATP and two from GTP. R-HSA-70326 Glucose metabolism Glucose is the major form in which dietary sugars are made available to cells of the human body. Its breakdown is a major source of energy for all cells, and is essential for the brain and red blood cells. Glucose utilization begins with its uptake by cells and conversion to glucose 6-phosphate, which cannot traverse the cell membrane. Fates open to cytosolic glucose 6-phosphate include glycolysis to yield pyruvate, glycogen synthesis, and the pentose phosphate pathway. In some tissues, notably the liver and kidney, glucose 6-phosphate can be synthesized from pyruvate by the pathway of gluconeogenesis. R-HSA-156588 Glucuronidation Glucuronidation conjugation utilizes UDP-glucuronosyltransferases (UGTs; EC 2.4.1.17) to catalyze a wide range of diverse endogenous and xenobiotic compounds. Glucuronidation is the major pathway in phase II metabolism and accounts for approximately 35% of drug conjugation. UGTs are microsomal membrane-bound and catalyze the transfer of a glucuronate group of uridine diphosphoglucuronate (UDPGA, a co-substrate) to the functional group of specific substrates. UDPGA is synthesized from glucose-1-phosphate (G1P). G1P is required for glycolysis and is present in high concentrations in the cell, making it is unlikely to be a limiting factor in UDPGA synthesis. UDP is added to G1P to form UDP-glucose which is then dehydrogenated to form UDPGA. The basic reaction is
UDP-Glucuronate + acceptor -> UDP + acceptor-beta-D-glucuronide
The effect of this conjugation is to confer polarity to the substrate which can then be easily excreted in urine or bile. Functional groups acted on include hydroxyl, carboxylate, amino and sulfate groups. There are 2 families of UGTs, UGT1 and UGT2 which are further sub-divided into 3 subfamilies, UGT1A, UGT2A and UGT2B. There are more than 26 different isozymes in humans, of which 18 are functional proteins. They are composed of 527-530 residues and have a molecular weight of 50-57KDa.RX + GSH -> HX + GSR
Glutathione conjugates are excreted in bile and converted to cysteine and mercapturic acid conjugates in the intestine and kidneys. GSH is the major, low molecular weight, non-protein thiol synthesized de novo in mammalian cells. As well as taking part in conjugation reactions, GSH also has antioxidant ability and can metabolize endogenous and exogenous compounds. The nucleophilic GSH attacks the electrophilic substrate forming a thioether bond between the cysteine residue of GSH and the electrophile. The result is generally a less reactive and more water-soluble conjugate that can be easily excreted. In some cases, GSTs can activate compounds to reactive species such as certain haloalkanes and haloalkenes. Substrates for GSTs include epoxides, alkenes and compounds with electrophilic carbon, sulfur or nitrogen centres. There are two types of conjugation reaction with glutathione: displacement reactions where glutathione displaces an electron-withdrawing group and addition reactions where glutathione is added to activated double bond structures or strained ring systems. R-HSA-174403 Glutathione synthesis and recycling The combination of glutamate, cysteine and ATP is required to form glutathione. The steps involved in the synthesis and recycling of glutathione are outlined (Meister, 1988). R-HSA-1483206 Glycerophospholipid biosynthesis Glycerophospholipids are important structural and functional components of biological membranes and constituents of serum lipoproteins and the pulmonary surfactant. In addition, glycerophospholipids act as precursors of lipid mediators such as platelet-activating factor and eicosanoids. Cellular membranes contains a distinct composition of various glycerophospholipids such as phosphatidic acid (PA), phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), phosphatidylglycerol (PG), phosphatidylinositol (PI), cardiolipin (CL), lysophosphatidic acid (LPA) and lysobisphosphatidic acid (also known as bis(monoacylglycerol) hydrogen phosphate - BMP).Glycogen can also be taken up into lysosomes, where it is normally broken done by the action of a single enzyme, lysosomal alpha-glucosidase (GAA).
Enzymes in liver generate 1,5-anhydro-D-fructose from glycogen, which in turn can be reduced to 1,5-anhydro-D-glucitol, a sequence of events that may represent a novel minor pathway for glycogen breakdown (Kametani et al. 1996).
R-HSA-8982491 Glycogen metabolism Glycogen, a highly branched glucose polymer, is formed and broken down in most human tissues, but is most abundant in liver and muscle, where it serves as a major stored fuel. Glycogen metabolism has been studied in most detail in liver and skeletal muscle. Glycogen metabolism in other tissues has not been studied as extensively, and is thought to resemble the muscle process.
Glycogen synthesis involves five reactions. The first two, conversion of glucose 6-phosphate to glucose 1-phosphate and synthesis of UDP-glucose from glucose 1-phosphate and UTP, are shared with several other pathways. The next three reactions, the auto-catalyzed synthesis of a glucose oligomer on glycogenin, the linear extension of the glucose oligomer catalyzed by glycogen synthase, and the formation of branches catalyzed by glycogen branching enzyme, are unique to glycogen synthesis. Repetition of the last two reactions generates large, extensively branched glycogen polymers. The catalysis of glycogenin glucosylation and oligoglucose chain extension by distinct isozymes in liver and nonhepatic tissues allows them to be regulated independently (Agius 2008; Bollen et al. 1998; Roach et al. 2012).
Cytosolic glycogen breakdown occurs via the same chemical steps in all tissues but is separately regulated via tissue specific isozymes and signaling pathways that enable distinct physiological fates for glycogen in liver and other tissues. Glycogen phosphorylase, which can be activated by phosphorylase kinase, catalyzes the removal of glucose residues as glucose 1-phosphate from the ends of glycogen branches. The final four residues of each branch are removed in two steps catalyzed by debranching enzyme, and further glycogen phosphorylase activity completes the process of glycogen breakdown. The first glucose residue in each branch is released as free glucose; all other residues are released as glucose 1-phosphate. The latter molecule can be converted to glucose 6-phosphate in a step shared with other pathways (Villar-Palasi & Larner 1970; Hers 1976).
Glycogen can also be taken up into lysosomes, where it is normally broken done by the action of a single enzyme, lysosomal alpha-glucosidase (GAA) (Brown et al. 1970).
R-HSA-3858516 Glycogen storage disease type 0 (liver GYS2) Glycogen synthase 2 (GYS2 "liver") normally catalyzes the addition of glucose residues to a growing glycogen molecule. In its absence, glycogen synthesis fails. Expression of GYS2 is confined to the liver and its deficiency is most prominently associated with fasting hypoglycemia (Gitzelmann et al. 1996; Orho et al. 1998).
R-HSA-3828062 Glycogen storage disease type 0 (muscle GYS1) Glycogen synthase 1 (GYS1 "muscle") is widely expressed in the body. It normally catalyzes the addition of glucose residues to a growing glycogen molecule. In its absence, glycogen synthesis fails. This deficiency is most prominently associated with exercise intolerance and cardiomyopathy (Kolberg et al. 2007; Cameron et al. 2009).
R-HSA-5357609 Glycogen storage disease type II (GAA) Glycogen storage disease type II (GSD II - Pompe's disease) is caused by mutations that reduce or eliminate the activity of lysosomal alpha-glucosidase (GAA) (Hers 1963). The presentation of GSD II varies with the severity of the mutation: patients with little or no GAA activity are affected shortly after birth and multiple tissues are severely affected. Patients with higher levels of GAA activity present later in life, often with symptoms restricted tocardiac and skeletal muscle (Leslie & Tinkle). At a cellular level, symptoms of the disease are due to accumulation of structurally normal glycogen in lysosomes. Glycogen, thought to enter lysosomes via autophagy, is fully degraded by GAA (Brown et al. 1970), but accumulates if the enzyme is absent or reduced in activity.
The two mutant alleles annotated here are associated with near-complete loss of enzyme activity and early onset of disease (Hermans et al. 1991; Zhong et al. 1991). Many other mutant alleles have been described and their residual activities correlated with disease presentation (e.g., Kroos et al. 2012).
R-HSA-3878781 Glycogen storage disease type IV (GBE1) Normally, cytosolic glycogen branching enzyme (GBE1) associated with glycogen granules transfers terminal alpha(1,4) glucose blocks to form alpha(1,6) branches on growing glycogen molecules of both liver and muscle types. In the absence of GBE1 activity, abnormal amylopectin-like glycogen with longer alpha(1,4) chains and fewer branch points forms in all tissues where glycogen is normally found. Presentation of the disease is clinically heterogeneous: missense and nonsense mutations associated with little or no enzyme activity can lead to progressive liver disease or neuromuscuolar disease (Bao et al. 1996; Bruno et al. 2004).
R-HSA-3274531 Glycogen storage disease type Ia (G6PC) Glucose-6-phosphatase (G6PC) associated with the inner face of the endoplasmic reticulum membrane normally catalyzes the hydrolysis of glucose-6-phosphate to glucose and orthophosphate. Defects in glucose-6-phosphatase are the cause of glycogen storage disease type Ia (Lei et al. 1993, 1995, Chou and Mansfield 2008).
R-HSA-3229133 Glycogen storage disease type Ib (SLC37A4) The SLC37A4 transport protein in the endoplasmic reticulum membrane normally mediates the exchange of cytosolic glucose-6-phosphate and orthophosphate from the endoplasmic reticulum lumen. Defects in this transporter are associated with glycogen storage disease type Ib (Gerin et al. 1997; Chen et al. 2008; Veiga-da-Cunha et al. 1998).
R-HSA-3814836 Glycogen storage disease type XV (GYG1) Glycogen synthesis is normally initiated by the autoglycosylation of glycogenin (GYG) to form oligo (1,4)-alpha-D-glucosyl GYG. A missense mutation of GYG1 yields a protein that cannot undergo glucosylation, leading to failure of glycogen synthesis, associated with muscle weakness and other abnormalities (Moslemi et al. 2010).
R-HSA-3229121 Glycogen storage diseases The regulated turnover of glycogen plays a central, tissue-specific role in the maintenance of blood glucose levels and in the provision of glucose to tissues such as muscle and brain in response to stress. Defects in the enzymes involved in glycogen turnover are associated with abnormal responses to fasting and exercise that can differ widely in their presentation and severity. Additional symptoms can be the result of accumulation of abnormal products of glycogen metabolism (Hauk et al. 1959; Hers 1964; Shin 2006). Annotations are provided here for diseases due to deficiencies of GYS1 and GYS1 (glycogen synthase 1 and 2; glycogen storage disease type 0 (GSD type 0), of G6PC (glucose-6-phosphatase, GSD type Ia) and the SLC37A4 transporter (GSD type Ib), of GAA (lysosomal acid alpha-glucosidase, GSD type II), of GBE1 (glycogen branching enzyme, GSD type IV), and of GYG1 (glycogenin 1, GSD XV). Two additional diseases, myoclonic epilepsy of Lafora (Roach et al. 2012) and severe congenital neutropenia type 4 (Boztug et al. 2009), are included as they are due to defects in enzymes of glycogen metabolism.
R-HSA-3322077 Glycogen synthesis Glycogen, a highly branched glucose polymer, is formed and broken down in most human tissues, but is most abundant in liver and muscle, where it serves as a major stored fuel. Glycogen metabolism has been studied in most detail in muscle, although considerable experimental data are available concerning these reactions in liver as well. Glycogen metabolism in other tissues has not been studied as extensively, and is thought to resemble the muscle process. Glycogen synthesis involves five reactions. The first two, conversion of glucose 6-phosphate to glucose 1-phosphate and synthesis of UDP-glucose from glucose 1-phosphate and UTP, are shared with several other pathways. The next three reactions, the auto-catalyzed synthesis of a glucose oligomer on glycogenin, the linear extension of the glucose oligomer catalyzed by glycogen synthase, and the formation of branches catalyzed by glycogen branching enzyme, are unique to glycogen synthesis. Repetition of the last two reactions generates large, extensively branched glycogen polymers. The catalysis of glycogenin glucosylation and oligoglucose chain extension by distinct isozymes in liver and nonhepatic tissues allows them to be regulated independently (Agius 2008; Bollen et al. 1998; Roach et al. 2012).
R-HSA-70171 Glycolysis The reactions of glycolysis (e.g., van Wijk and van Solinge 2005) convert glucose 6-phosphate to pyruvate. The entire process is cytosolic. Glucose 6-phosphate is reversibly isomerized to form fructose 6-phosphate. Phosphofructokinase 1 catalyzes the physiologically irreversible phosphorylation of fructose 6-phosphate to form fructose 1,6-bisphosphate. In six reversible reactions, fructose 1,6-bisphosphate is converted to two molecules of phosphoenolpyruvate and two molecules of NAD+ are reduced to NADH + H+. Each molecule of phosphoenolpyruvate reacts with ADP to form ATP and pyruvate in a physiologically irreversible reaction. Under aerobic conditions the NADH +H+ can be reoxidized to NAD+ via electron transport to yield additional ATP, while under anaerobic conditions or in cells lacking mitochondria NAD+ can be regenerated via the reduction of pyruvate to lactate.
R-HSA-209822 Glycoprotein hormones More complex protein hormones have carbohydrate side chains and are called glycoprotein hormones. Hormones in this class are Follicle-stimulating hormone (FSH; follitropin), Luteinizing hormone (LH), Thyroid-stimulating hormone (TSH; thyrotropin) and human chorionic gonadotropin (hCG). The alpha subunit of glycoprotein hormones is a 92 aa peptide and serves as the alpha subunit for FSH, LH, hCG and TSH (Fiddes JC and Goodman HM, 1981). The beta subunits for these hormones are unique and confer biological specificity to them. These two subunits combine via disulphide bonding to produce the mature glycoprotein hormone dimer.
R-HSA-1630316 Glycosaminoglycan metabolism Glycosaminoglycans (GAGs) are long, unbranched polysaccharides containing a repeating disaccharide unit composed of a hexosamine (either N-acetylgalactosamine (GalNAc) or N-acetylglucosamine (GlcNAc)) and a uronic acid (glucuronate or iduronate). They can be heavily sulfated. GAGs are located primarily in the extracellular matrix (ECM) and on cell membranes, acting as a lubricating fluid for joints and as part of signalling processes. They have structural roles in connective tissue, cartilage, bone and blood vessels (Esko et al. 2009). GAGs are degraded in the lysosome as part of their natural turnover. Defects in the lysosomal enzymes responsible for the metabolism of membrane-associated GAGs lead to lysosomal storage diseases called mucopolysaccharidoses (MPS). MPSs are characterised by the accumulation of GAGs in lysosomes resulting in chronic, progressively debilitating disorders that in many instances lead to severe psychomotor retardation and premature death (Cantz & Gehler 1976, Clarke 2008). The biosynthesis and breakdown of the main GAGs (hyaluronate, keratan sulfate, chondroitin sulfate, dermatan sulfate and heparan sulfate) is described here.
R-HSA-9840309 Glycosphingolipid biosynthesis The steps involved in the synthesis of glycosphingolipids (sphingolipids with one or more sugars attached) are annotated here (the topic is reviewed by Sandhoff & Sandhoff, 2018; Sandhoff et al, 2018).
R-HSA-9840310 Glycosphingolipid catabolism Gangliosides (GGs) are glycosphingolipids in which oligosaccharide chains containing N-acetylneuraminic acid (NeuNAc) are attached to a ceramide. Produced in the Golgi, they locate to the plasma membrane, where they contribute to Ca2+ and protein-ligand binding and to the ability of patches of the membrane to experience high curvature topologies, which is essential in many neuronal cells. Degradation of complex polysialylgangliosides starts during endocytosis producing GM1. Inward budding of the late endosomal membrane yields intralysosomal luminal vesicles (ILV) that carry the GGs on the outside of their membranes for final degradation and release to the cytosol. Essential cofactors for lysosomal ganglioside catabolism are the saposins, small carrier proteins which make GGs soluble by providing lipid anchors to move GGs from ILV membranes to the lysosome lumen. Another cofactor is the Ganglioside GM2 activator (GM2A, GM2AP), which is essential for beta-hexosaminidase activity in the degradation of GM2, GA2, and SM2A. Further cofactors appear to be membrane lipids including cholesterol. Lack of any participating enzyme or cofactor leads to the accumulation of glycosphingolipids in lysosomes and sphingolipidoses, including Gaucher's and Niemann–Pick diseases (reviewed in Kolter & Sandhoff, 2010; Sandhoff, 2016; Sandhoff & Sandhoff, 2018; Sandhoff et al., 2018; Breiden & Sandhoff, 2020).
R-HSA-1660662 Glycosphingolipid metabolism The steps involved in the synthesis and degradation of glycosphingolipids (sphingolipids with one or more sugars attached) are annotated here (the topic is reviewed by Gault et al. 2010; Sandhoff & Sandhoff, 2018; Sandhoff et al, 2018).
R-HSA-9845576 Glycosphingolipid transport After biosynthesis on the Golgi membrane, gangliosides localize to other membranes via vesicle transport, endocytosis, and exocytosis. To decouple transport from vesicular transport of proteins, gangliosides are additionally transported via non-vesicular processes (reviewed by Perry & Ridgway, 2005; Funato et al., 2020).
R-HSA-389661 Glyoxylate metabolism and glycine degradation Glyoxylate is generated in the course of glycine and hydroxyproline catabolism and can be converted to oxalate. In humans, this process takes place in the liver. Defects in two enzymes of glyoxylate metabolism, alanine:glyoxylate aminotransferase (AGXT) and glycerate dehydrogenase/glyoxylate reductase (GRHPR), are associated with pathogenic overproduction of oxalate (Danpure 2005). The reactions that interconvert glycine, glycolate, and glyoxylate and convert glyoxylate to oxalate have been characterized in molecular detail in humans. A reaction sequence for the conversion of hydroxyproline to glyoxylate has been inferred from studies of partially purified extracts of rat and bovine liver but the enzymes involved in the corresponding human reactions have not been identified.
R-HSA-432722 Golgi Associated Vesicle Biogenesis Proteins that have been synthesized, processed and sorted eventually reach the final steps of the secretory pathway. This pathway is responsible not only for proteins that are secreted from the cell but also enzymes and other resident proteins in the lumen of the ER, Golgi, and lysosomes as well as integral proteins transported in the vesicle membranes.
R-HSA-162658 Golgi Cisternae Pericentriolar Stack Reorganization The pericentriolar stacks of Golgi cisternae undergo extensive fragmentation and reorganization in mitosis.
In mammalian cells, Golgi apparatus consists of stacked cisternae that are connected by tubules to form a ribbon-like structure in the perinuclear region, in vicinity of the centrosome. Reorganization of the Golgi apparatus during cell division allows both daughter cells to inherit this organelle, and may play additional roles in the organization of the mitotic spindle.
First changes in the structure of the Golgi apparatus likely start in G2 and are subtle, involving unlinking of the Golgi ribbon into separate stacks. These changes are required for the entry of mammalian cells into mitosis (Sutterlin et al. 2002). This initial unlinking of the Golgi ribbon depends on GRASP proteins and on CTBP1 (BARS) protein, which induces the cleavage of the tubular membranes connecting the stacks (Hidalgo Carcedo et al. 2004, Colanzi et al. 2007), but the exact mechanism is not known. Activation of MEK1/2 also contributes to unlinking of the Golgi ribbon in G2 (Feinstein and Linstedt 2007).
From prophase to metaphase, Golgi cisternae undergo extensive fragmentation that is a consequence of unstacking of Golgi cisternae and cessation of transport through Golgi. At least three mitotic kinases, CDK1, PLK1 and MEK1, regulate these changes. CDK1 in complex with cyclin B phosphorylates GOLGA2 (GM130) and GORASP1 (GRASP65), constituents of a cis-Golgi membrane complex (Lowe et al. 1998, Preisinger et al. 2005). Phosphorylation of GOLGA2 prevents binding of USO1 (p115), a protein localizing to the membrane of ER (endoplasmic reticulum) to Golgi transport vesicles and cis-Golgi, thereby impairing fusion of these vesicles with cis-Golgi cisternae and stopping ER to Golgi transport (Lowe et al. 1998, Seeman et al. 2000, Moyer et al. 2001). Phosphorylation of GORASP1 by CDK1 enables further phosphorylation of GORASP1 by PLK1 (Sutterlin et al. 2001, Preisinger et al. 2005). Phosphorylation of GORASP1 by CDK1 and PLK1 impairs stacking of Golgi cisternae by interfering with formation of GORASP1 trans-oligomers that would normally link the Golgi cisternae together (Wang et al. 2003, Wang et al. 2005, Sengupta and Linstedt 2010).
In the median Golgi, GORASP2 (GRASP55), a protein that forms a complex with BLFZ1 (Golgin-45) and RAB2A GTPase and contributes to cisternae stacking and Golgi trafficking (Short et al. 2001), is also phosphorylated in mitosis. Phosphorylation of GORASP2 by MEK1/2-activated MAPK1 (ERK2) and/or MAPK3-3 (ERK1b in human, Erk1c in rat) contributes to Golgi unlinking in G2 and fragmentation of Golgi cisternae in mitotic prophase (Acharya et al. 1998, Jesch et al. 2001, Colanzi et al. 2003, Shaul and Seger 2006, Duran et al. 2008, Feinstein and Linstedt 2007, Feinstein and Linstedt 2008, Xiang and Wang 2010).
R-HSA-8856688 Golgi-to-ER retrograde transport Retrograde traffic from the cis-Golgi to the ERGIC or the ER occurs through either COPI-coated vesicles or through a less well characterized RAB6-dependent route that makes use of tubular carriers (reviewed in Lord et al, 2013; Spang et al, 2013; Heffernan and Simpson, 2014). The balance between these two pathways may be influenced cargo type and concentration and membrane composition, though the details remain to be worked out (reviewed in Heffernan and Simpson, 2014).
R-HSA-982772 Growth hormone receptor signaling Growth hormone (Somatotropin or GH) is a key factor in determining lean body mass, stimulating the growth and metabolism of muscle, bone and cartilage cells, while reducing body fat. It has many other roles; it acts to regulate cell growth, differentiation, apoptosis, and reorganisation of the cytoskeleton, affecting diverse processes such as cardiac function, immune function, brain function, and aging. GH also has insulin-like effects such as stimulating amino acid transport, protein synthesis, glucose transport, and lipogenesis. The growth hormone receptor (GHR) is a a member of the cytokine receptor family. When the dimeric receptor binds GH it undergoes a conformational change which leads to phosphorylation of key tyrosine residues in its cytoplasmic domains and activation of associated tyrosine kinase JAK2. This leads to recruitment of signaling molecules such as STAT5 and Src family kinases such as Lyn leading to ERK activation. The signal is attenuated by association of Suppressor of Cytokine Signaling (SOCS) proteins and SHP phosphatases which bind to or dephosphorylate specific phosphorylated tyrosines on GHR/JAK. The availability of GHR on the cell surface is regulated by at least two processes; internalization and cleavage from the suface by metalloproteases.
R-HSA-9912529 H139Hfs13* PPM1K causes a mild variant of MSUD PPM1K is a mitochondrial protein phosphatase that removes the inhibitory phosphorylation from the E1 beta subunit of branched-chain ketoacid dehydrogenase (BCKDH) to restore BCKDH activity (Lu et al, 2007; Lu et al, 2009 a, b; Wynn et al, 2012; Zhou et al, 2012).
BCKDH is responsible for the oxidative decarboxylation of branched-chain amino acid (BCAA) derivatives of leucine, valine and isoleucine, providing acetyl CoA and succinyl CoA intermediates for the Krebs Cycle (reviewed in Strauss et al, 2020; Zhang et al, 2023). Loss-of-function mutations in subunits of BCKDH cause accumulation of toxic BCAAs in the urine, neurological defects and are the cause of Maple Syrup Urine disease (MSUD). More recently, a frameshift mutation in PPM1K was identified as the probable cause of a mild variant of MSUD (Oyarzabal et al, 2012). This frameshift introduces a stop codon at residue 151, destabilizing the protein, and transfection of PPM1K-deficient fibroblast lines with WT PPM1K restores BCKDH activity (Oyarzabal et al, 2012).
R-HSA-3214847 HATs acetylate histones Histone acetyltransferases (HATs) involved in histone modifications are referred to as A-type or nuclear HATs. They can be grouped into at least four families based on sequence conservation within the HAT domain: Gcn5/PCAF, MYST, p300/CBP and Rtt109. The p300/CBP and Rtt109 families are specific to metazoans and fungi respectively (Marmorstein & Trievel 2009). Gcn5/PCAF and MYST family members have no significant sequence homology but share a globular alpha/beta fold with a common structure involved in acetyl-Coenzyme A (ACA) binding. Both use a conserved glutamate residue for the acetyl transfer reaction but may not share a common catalytic mechanism (Trievel et al. 1999, Tanner et al. 1999, Yan et al. 2002, Berndsen et al. 2007). The p300/CBP HAT domain has no homology with the other families but some structural conservation within theACA-binding core (Liu et al. 2008). In addition to histone acetylation, members of all 3 human HAT families have been shown to acetylate non-histones (Glozak et al. 2005).
HATs and histone deacetylase (HDAC) enzymes generally act not alone but as part of multiprotein complexes. There are numerous examples in which subunits of HAT or HDAC complexes influence their substrate specificity and lysine preference, which in turn, affect the broader functions of these enzymes (Shahbazian & Grunstein 2007).
N.B. The coordinates of post-translational modifications represented and described here follow UniProt standard practice whereby coordinates refer to the translated protein before any further processing. Histone literature typically refers to coordinates of the protein after the initiating methionine has been removed. Therefore the coordinates of post-translated residues in the Reactome database and described here are frequently +1 when compared with the literature.
R-HSA-9609690 HCMV Early Events Once in the cytoplasm the capsid and tegument proteins are free to interact with host proteins. The capsid travels to the nucleus, where the genome is delivered and circularized. Tegument proteins regulate host cell responses and initiate the expression of viral I immediate early genes. This is followed by the expression of delayed early genes.
R-HSA-9609646 HCMV Infection Herpesviruses have a unique four-layered structure: a core containing the large, double-stranded DNA genome is enclosed by an icosapentahedral capsid which is composed of capsomers. The capsid is surrounded by an amorphous protein coat called the tegument. It is encased in a glycoprotein-bearing lipid bilayer envelope.
Herpesviruses are divided into three groups: alpha-herpesviruses, beta-herpesviruses, and gamma-herpesviruses. The beta herpesviruses have a restricted host range. Their reproductive life cycle is long (days), with infection progressing slowly in cell culture systems. These viruses cause their host cells to enlarge, as exemplified by a human cytomegalovirus (HCMV) infection. These viruses can establish latent infection in secretory glands, cells of the reticuloendothelial system, and the kidneys.
Human Cytomegalovirus, or HCMV, is a common virus that infects people of all ages. In the United States, nearly one in three children are already infected with HCMV by age 5 years. Over half of adults by age 40 have been infected with HCMV. Once HCMV is in a person’s body, it stays there for life and can reactivate.
Cytomegalovirus causes three clinical syndromes:
(1) Congenital cytomegalovirus infection (when symptomatic) causes hepatosplenomegaly, retinitis, rash, and central nervous system involvement.
(2) In about 10 per cent of older children and adults, primary cytomegalovirus infection causes a mononucleosis syndrome with fever, malaise, atypical lymphocytosis, and pharyngitis.
(3) Immunocompromised hosts (transplant recipients and human immunodeficiency virus [HIV]-infected individuals) may develop life-threatening disseminated disease involving the lungs, gastrointestinal tract, liver, retina, and central nervous system.
Experimentally HCMV can be propagated in multiple cell lines. When propagated in human fibroblasts, HCMV clinical isolates acquire mutations in a manner that suggests a process of adaptation. Two strains of HCMV AD169 (grown from cultures of adenoid tissue taken from a 7-year-old girl) and Towne (developed as an attenuated vaccine by passaging 125 times in vitro) were initially used as the primary clinical strains. As only 26 % of HCMV canonical genes (45/171) are essential for viral replication in vitro it became important that a model strain be developed.
The Merlin BAC was derived for this use. Produced using a bacterial artificial chromosome (BAC) cloning system (to avoid adaptation/degradation of the genome with each passage) the Merlin strain contains a complete HCMV genome that is thought to accurately to represent the original clinical agent from which it was derived. It is also a reproducible source of clonal virus (via transfection) and is capable of reconstituting phenotypically wild-type virus.
The lifecycle represented here uses the Merlin strain where possible.Infectious Human Cytomegalovirus (HCMV) particles enter the cell through interaction with cellular receptors. Once in the cytoplasm capsid and tegument proteins are delivered to the cytosol. The capsid travels to the nucleus, where the genome is delivered and circularized. Tegument proteins regulate host cell responses and initiate the expression of viral I immediate early genes. This is followed by delayed early genes, which initiate viral genome replication, then late genes. Late gene expression initiates capsid assembly in the nucleus, followed by nuclear egress to the cytosol. Capsids associate with tegument proteins in the cytosol and are trafficked to the viral assembly complex that contains components from the endoplasmic reticulum, Golgi apparatus, and endosomal machinery. The capsids acquire additional tegument proteins and a viral envelope by budding into intracellular vesicles. These vesicles fuse with the plasma membrane to release enveloped infectious particles along with non-infectious dense bodies.
R-HSA-9610379 HCMV Late Events Once Human Cytomegalovirus (HCMV) Immediate Early (IE) and Delayed Early (DE) gene products begin to appear the processes driving DNA replication, Late (L) gene expression, and virion assembly begin.
R-HSA-1296061 HCN channels Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are nonselective ligand-gated cation channels in the plasma membranes of heart and brain cells. HCN channels are sometimes referred to as “pacemaker channels” because they help to generate rhythmic activity within groups of heart and brain cells. They are highly expressed in spontaneously active cardiac regions, such as the sinoatrial node (SAN, the natural pacemaker region), the atrioventricular node (AVN) and the Purkinje fibres of conduction tissue. HCN channels are encoded by four genes (HCN1, 2, 3, 4) and are widely expressed throughout the heart and the central nervous system. HCN channels are homotetramers of four subunits and conduct a Na+ and K+ current with a permeability of 1:4. The mixed sodium–potassium current activates upon hyperpolarization at voltages in the diastolic range (normally from −60/−70 mV to −40 mV). At the end of a sinoatrial action potential, the membrane repolarizes below −40/−50 mV, the "funny current" is activated and supplies inward current, which is responsible for starting the diastolic depolarization phase (DD); by this mechanism, the funny current controls the rate of spontaneous activity of sinoatrial myocytes, hence the cardiac rate. HCN channels are involved in controlling the rhythmic activity of pacemaker current in autorythymic cells in heart and neuronal processes such as dendritic integration and synaptic transmission.
R-HSA-3214815 HDACs deacetylate histones Lysine deacetylases (KDACs), historically referred to as histone deacetylases (HDACs), are divided into the Rpd3/Hda1 metal-dependent 'classical HDAC family' (de Ruijter et al. 2003, Verdin et al. 2003) and the unrelated sirtuins (Milne & Denu 2008). Phylogenetic analysis divides human KDACs into four classes (Gregoretti et al. 2004): Class I includes HDAC1, 2, 3 and 8; Class IIa includes HDAC4, 5, 7 and 9; Class IIb includes HDAC6 and 10; Class III are the sirtuins (SIRT1-7); Class IV has one member, HDAC11 (Gao et al. 2002). Class III enzymes use an NAD+ cofactor to perform deacetylation (Milne & Denu 2008, Yang & Seto 2008), the others classes use a metal-dependent mechanism (Gregoretti et al. 2004) to catalyze the hydrolysis of acetyl-L-lysine side chains in histone and non-histone proteins yielding L-lysine and acetate. X-ray crystal structures are available for four human HDACs; these structures have conserved active site residues, suggesting a common catalytic mechanism (Lombardi et al. 2011). They require a single transition metal ion and are typically studied in vitro as Zn2+-containing enzymes, though in vivo HDAC8 exhibits increased activity when substituted with Fe2+ (Gantt et al. 2006). The structurally-related enzyme acetylpolyamine amidohydrolase (APAH) (Leipe & Landsman 1997) exhibits optimal activity with Mn2+, followed closely by Zn2+ (Sakurada et al. 1996).
HDACs are often part of multi-protein transcriptional complexes that are recruited to gene promoters, regulating transcription without direct DNA binding. With the exception of HDAC8, all class I members can be catalytic subunits of multiprotein complexes (Yang & Seto 2008). HDAC1 and HDAC2 interact to form the catalytic core of several multisubunit complexes including Sin3, nucleosome remodeling deacetylase (NuRD) and corepressor of REST (CoREST) complexes (Grozinger & Schreiber 2002). HDAC3 is part of the silencing mediator of retinoic acid and thyroid hormone receptor (SMRT) complex or the homologous nuclear receptor corepressor (NCoR) (Li et al. 2000, Wen et al. 2000, Zhang et al. 2002, Yoon et al. 2003, Oberoi et al. 2011) which are involved in a wide range of processes including metabolism, inflammation, and circadian rhythms (Mottis et al. 2013).
Class IIa HDACs (HDAC4, -5, -7, and -9) shuttle between the nucleus and cytoplasm (Yang & Seto 2008, Haberland et al. 2009). The nuclear export of class IIa HDACs requires phosphorylation stimulated by calcium or other stimuli. They appear to have been evolutionarily inactivated as enzymes, having acquired a histidine substitution of the tyrosine residue in the active site of the mammalian deacetylase domain (H976 in humans) (Lahm et al. 2007, Schuetz et al. 2008). Instead they function as transcriptional corepressors for the MEF2 family of transcription factors (Yang & Gregoire 2005) .
Histones are the primary substrate for most HDACs except HDAC6 which is predominantly cytoplasmic and acts on alpha-tublin (Hubbert et al. 2002, Zhang et al. 2003, Boyault et al. 2007). HDACs also deacetylate proteins such as p53, E2F1, RelA, YY1, TFIIE, BCL6 and TFIIF (Glozak et al. 2005).
Histone deacetylases are targeted by structurally diverse compounds known as HDAC inhibitors (HDIs) (Marks et al. 2000). These can induce cytodifferentiation, cell cycle arrest and apoptosis of transformed cells (Marks et al. 2000, Bolden et al. 2006). Some HDIs have significant antitumor activity (Marks and Breslow 2007, Ma et al. 2009) and at least two are approved anti-cancer drugs.
The coordinates of post-translational modifications represented and described here follow UniProt standard practice whereby coordinates refer to the translated protein before any further processing. Histone literature typically refers to coordinates of the protein after the initiating methionine has been removed. Therefore the coordinates of post-translated residues in the Reactome database and described here are frequently +1 when compared with the literature.
R-HSA-8963896 HDL assembly HDL particles play a central role in the reverse transport of cholesterol, the process by which cholesterol in tissues other than the liver is returned to the liver for conversion to bile salts and excretion from the body and provided to tissues such as the adrenals and gonads for steroid hormone synthesis (Tall et al. 2008).
HDL particles are heterogeneous and can be fractionated into sub-populations based on their electrophoretic mobility, their density, or their content of various apolipoproteins (Kontush and Chapman 2006). All HDL particles share two key features: they are assembled on a protein scaffold provided by apolipoprotein A-I (apoA-I), and they are recycled to allow a net flow of lipids from peripheral tissues to the liver and steroidogenic tissues while allowing apoA-I molecules to be re-used.
Here, the assembly of nascent (discoidal) HDL particles on newly synthesized apoA-I, a process that in the body occurs primarily in the liver, and the loading of discoidal HDL with additional lipid through interaction with cells carrying excess cholesterol (transformation to spherical HDL) are annotated.
R-HSA-8964011 HDL clearance Clearance of circulating HDL particles involves particle binding to cell-surface SR-BI receptors, particle disassembly with rlease of pre-beta HDL (Silver & Tall 2001), and uptake of the latter mediated by cell-surface CUBN:AMN complex (Kozyraki et al. 1999).
R-HSA-8964058 HDL remodeling HDL (high-density lipoprotein) particles play a central role in the reverse transport of cholesterol, the process by which cholesterol in tissues other than the liver is returned to the liver for conversion to bile salts and excretion from the body and provided to tissues such as the adrenals and gonads for steroid hormone synthesis (Tall et al. 2008).
ABCG1 mediates the movement of intracellular cholesterol to the extracellular face of the plasma membrane where it is accessible to circulating HDL (Vaughan & Oram 2005). Spherical (mature) HDL particles can acquire additional molecules of free cholesterol (CHOL) and phospholipid (PL) from cell membranes.
At the HDL surface, LCAT (lecithin-cholesterol acyltransferase) associates strongly with HDL particles and, activated by apoA-I, catalyzes the reaction of cholesterol and phosphatidylcholine to yield cholesterol esterified with a long-chain fatty acid and 2-lysophosphatidylcholine. The hydrophobic cholesterol ester reaction product is strongly associated with the HDL particle while the 2-lysophosphatidylcholine product is released. Torcetrapib associates with a molecule of CETP and a spherical HDL particle to form a stable complex, thus trapping CETP and inhibiting CETP-mediated lipid transfer between HDL and LDL (Clark et al. 2006).
Spherical HDL particles can bind apoC-II, apoC-III and and apoE proteins.
R-HSA-3214842 HDMs demethylate histones Histone lysine demethylases (KDMs) are able to reverse N-methylations of histones and probably other proteins. To date KDMs have been demonstrated to catalyse demethylation of N-epsilon methylated lysine residues. Biochemically there are two distinct groups of N-epsilon methylated lysine demethylases with different catalytic mechanisms, both of which result in methyl group oxidation to produce formaldhyde. KDM1A, formerly known as Lysine Specific Demethylase 1 (LSD1), belongs to the flavin adenine dinucleotide (FAD)-dependent amino oxidase family. The KDM1A reaction mechanism requires a protonatable lysine epsilon-amine group, not available in trimethylated lysines, which consequently are not KDM1 substrates. Other KDMs belong to the Jumonji C (JmjC) -domain containing family. These are members of the Cupin superfamily of mononuclear Fe (II)-dependent oxygenases, which are characterised by the presence of a double-stranded beta-helix core fold. They require 2-oxoglutarate (2OG) and molecular oxygen as co-substrates, producing, in addition to formaldehyde, succinate and carbon dioxide. This hydroxylation-based mechanism does not require a protonatable lysine epsilon-amine group and consequently JmjC-containing demethylases are able to demethylate tri-, di- and monomethylated lysines.
The coordinates of post-translational modifications represented and described here follow UniProt standard practice whereby coordinates refer to the translated protein before any further processing. Histone literature typically refers to coordinates of the protein after the initiating methionine has been removed. Therefore the coordinates of post-translated residues in the Reactome database and described here are frequently +1 when compared with the literature.
In general, methylation at histone H3 lysine-5 (H3K4) and lysine-37 (H3K36), including di- and trimethylation at these sites, has been linked to actively transcribed genes (reviewed in Martin & Zhang 2005). In contrast, lysine-10 (H3K9) promoter methylation is considered a repressive mark for euchromatic genes and is also one of the landmark modifications associated with heterochromatin (Peters et al. 2002).
The first reported JmjC-containing demethylases were KDM2A/B (JHDM1A/B, FBXL11/10). These catalyse demethylation of histone H3 lysine-37 when mono- or di-methylated (H3K36Me1/2) (Tsukada et al. 2006). They were found to contain a JmjC catalytic domain, previously implicated in chromatin-dependent functions (Clissold & Ponting 2001). Subsequently, many other JmjC enzymes have been identified and discovered to have lysine demethylase activities with distinct methylation site and state specificities.
KDM3A/B (JHDM2A/B) are specific for mono or di-methylated lysine-10 on histone H3 (H3K9Me1/2) (Yamane et al. 2006, Kim et al. 2012). KDM4A-C (JMJD2A-C/JHDM3A-C) catalyse demethylation of di- or tri-methylated histone H3 at lysine-10 (H3K9Me2/3) (Cloos et al. 2006, Fodor et al. 2006), with a strong preference for Me3 (Whetstine et al. 2007). KDM4D (JMJD2D) also catalyses demethylation of H3K9Me2/3 (Whetstine et al. 2007). KDM4A-C (JHDM3A-C) can also catalyse demethylation of lysine-37 of histone H3 (H3K36Me2/3) (Klose et al. 2006). KDM5A-D (JARID1A-D) catalyses demethylation of di- or tri-methylated lysine-5 of histone H3 (H3K4Me2/3) (Christensen et al. 2007, Klose et al. 2007, Lee et al. 2007, Secombe et al. 2007, Seward et al. 2007, Iwase et al. 2007). KDM6A and KDM6B (UTX/JMJD3) catalyse demethylation of di- or tri-methylated lysine-28 of histone H3 (H3K27Me2/3) (Agger et al. 2007, Cho et al. 2007, De Santra et al. 2007, Lan et al. 2007, Lee et al. 2007).
KDM7A (KIAA1718/JHDM1D) catalyses demethylation of mono- or di-methylated lysine-10 of histone H3 (H3K9Me1/2) and mono- and di-methylated lysine-28 of histone H3 (H3K27Me1/2) (Horton et al. 2010, Huang et al. 2010). PHF8 (JHDM1E) catalyses demethylation of mono- or di-methylated lysine-10 of histone H3 (H3K9Me1/2) and mono-methylated lysine-21 of histone H4 (H4K20Me1) (Loenarz et al. 2010, Horton et al. 2010, Feng et al. 2010, Kleine-Kohlbrecher et al. 2010, Fortschegger et al. 2010, Qi et al. 2010, Liu et al. 2010). PHF2 (JHDM1E) catalyses demethylation of mono- or di-methylated lysine-10 of histone H3 (H3K9Me1/2) (Wen et al, 2010, Baba et al. 2011). JMJD6 was initially characterized as an arginine demethylase that catalyses demethylation of mono or di methylated arginine 3 of histone H3 (H3R2Me1/2) and arginine 4 of histone H4 (H4R3Me1/2) (Chang et al. 2007) although it was subsequently also characterized as a lysine hydroxylase (Webby et al. 2009). N.B. The coordinates of post-translational modifications represented and described here follow UniProt standard practice whereby coordinates refer to the translated protein before any further processing. Histone literature typically refers to coordinates of the protein after the initiating methionine has been removed. Therefore the coordinates of post-translated residues in the Reactome database and described here are frequently +1 when compared with the literature.
R-HSA-5685942 HDR through Homologous Recombination (HRR) Homology directed repair (HDR) through homologous recombination is known as homologous recombination repair (HRR). HRR occurs after extensive resection of DNA double-strand break (DSB) ends, which creates long 3'-ssDNA overhangs. RAD51 coats 3'-ssDNA overhangs in a BRCA2-controlled fashion, creating invasive RAD51 nucleofilaments. The RAD51 nucleofilament invades a sister chromatid DNA duplex, leading to D-loop formation. After the D-loop is extended by DNA repair synthesis, the resulting recombination intermediates in the form of extended D-loops or double Holliday junctions can be resolved through crossover- or non-crossover-generating processes (reviewed by Ciccia and Elledge 2010).
R-HSA-5693567 HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA) Homology directed repair (HDR) of replication-independent DNA double-strand breaks (DSBs) via homologous recombination repair (HRR) or single strand annealing (SSA) requires the activation of ATM followed by ATM-mediated phosphorylation of DNA repair proteins. ATM coordinates the recruitment of DNA repair and signaling proteins to DSBs and formation of the so-called ionizing radiation induced foci (IRIF). While IRIFs include chromatin regions kilobases away from the actual DSB, this Reactome pathway represents simplified foci and shows events that happen at the very ends of the broken DNA.
For both HRR and SSA to occur, the ends of the DNA DSB must be processed (resected) to generate lengthy 3' ssDNA tails, and the resulting ssDNA coated with RPA complexes, triggering ATR activation and signaling.
After the resection step, BRCA2 and RAD51 trigger HRR, a very accurate process in which the 3'-ssDNA overhang invades a sister chromatid, base pairs with the complementary strand of the sister chromatid DNA duplex, creating a D-loop, and uses the complementary sister chromatid strand as a template for DNA repair synthesis that bridges the DSB.
The SSA is triggered when 3'-ssDNA overhangs created in the resection step contain highly homologous direct repeats. In a process involving RAD52, the direct repeats in each 3'-ssDNA overhang become annealed, the unannealed 3'-flaps excised, and structures then processed by DNA repair synthesis. SSA results in the loss of one of the annealed repeats and the DNA sequence between the two repeats. Therefore, SSA is error-prone and is probably used as a backup for HRR, with RAD52 loss-of-function mutations being synthetically lethal with mutations in HRR genes, such as BRCA2 (reviewed by Ciccia and Elledge 2010). R-HSA-5685939 HDR through MMEJ (alt-NHEJ) Homology directed repair (HDR) through microhomology-mediated end joining (MMEJ) is an error prone process also known as alternative nonhomologous end joining (alt-NHEJ), although it does not involve proteins that participate in the classical NHEJ. Contrary to the classical NHEJ and other HDR pathways, homologous recombination repair (HRR) and single strand annealing (SSA), MMEJ does not require ATM activation. In fact, ATM activation inhibits MMEJ. Therefore, MMEJ may be triggered when the amount of DNA double strand breaks (DSBs) overwhelms DNA repair machinery of higher fidelity or when cells are deficient in components of high fidelity DNA repair.
MMEJ is initiated by a limited resection of DNA DSB ends by the MRN complex (MRE11A:RAD50:NBN) and RBBP8 (CtIP), in the absence of CDK2-mediated RBBP8 phosphorylation and related BRCA1:BARD1 recruitment (Yun and Hiom 2009). Single strand DNA (ssDNA) at resected DNA DSB ends recruits PARP1 or PARP2 homo- or heterodimers, together with DNA polymerase theta (POLQ) and FEN1 5'-flap endonuclease. In a poorly studied sequence of events, POLQ promotes the annealing of two 3'-ssDNA overhangs through microhomologous regions that are optimally 10-19 nucleotides long. Using analogy with POLB-mediated long patch base excision repair (BER), it is plausible that PARP1 (or PARP2) dimers coordinate the extension of annealed 3'-ssDNA overhangs via POLQ-mediated strand displacement synthesis with FEN1-mediated cleavage of the resulting 5'-flaps (Liang et al. 2005, Mansour et al. 2011, Sharma et al. 2015, Kent et al. 2015, Ciccaldi et al. 2015, Mateos-Gomez et al. 2015). The MRN complex subsequently recruits DNA ligase 3 (LIG3) bound to XRCC1 (LIG3:XRCC1) to ligate the remaining single strand nicks (SSBs) at MMEJ sites (Della-Maria et al. 2011).
Similar to single strand annealing (SSA), MMEJ leads to deletion of one of the microhomology regions used for annealing and the DNA sequence in between two annealed microhomology regions. MMEJ, just like classical NHEJ, can result in genomic translocations (Ghezraoui et al. 2014). In addition, since POLQ is an error-prone DNA polymerase, MMEJ introduces frequent base substitutions (Ceccaldi et al. 2015). R-HSA-5685938 HDR through Single Strand Annealing (SSA) Homology directed repair (HDR) through single strand annealing (SSA), similar to HDR through homologous recombination repair (HRR), involves extensive resection of DNA double-strand break ends (DSBs), preceded by ATM activation and formation of the so-called ionizing radiation induced foci (IRIF) at DNA DSB sites. Following ATM activation and foci formation, the two-step resection is initiated by the MRN complex (MRE11A:RAD50:NBN) and RBBP8 (CtIP) associated with BRCA1:BARD1, and completed by EXO1 or DNA2 in cooperation with DNA helicases BLM, WRN and BRIP1 (BACH1) (Sartori et al. 2007, Yun and Hiom 2009, Eid et al. 2010, Nimonkar et al. 2011, Suhasini et al. 2011, Sturzenegger et al. 2014). Long 3'-ssDNA overhangs produced by extensive resection are coated by the RPA heterotrimer (RPA1:RPA2:RPA3), triggering ATR signaling. ATR signaling is needed for SSA, probably because of the related phosphorylation of RPA2 (Zou and Elledge 2003, Anantha et al. 2007, Liu et al. 2012).
RAD52 is the key mediator of SSA. Activated ATM phosphorylates and activates ABL1, and activated ABL1 subsequently phosphorylates pre-formed RAD52 heptameric rings, increasing their affinity for ssDNA (Honda et al. 2011). Phosphorylated RAD52 binds phosphorylated RPA heterotrimers on 3'-ssDNA overhangs at resected DNA DSBs. RAD52 also binds RAD51 and prevents formation of invasive RAD51 nucleofilaments involved in HRR (Chen et al. 1999, Van Dyck et al. 1999, Parsons et al. 2000, Jackson et al. 2002, Singleton et al. 2002).
RAD52 promotes annealing of two 3'-ssDNA overhangs when highly homologous directed repeats are present in both 3'-ssDNA overhangs. Nonhomologous regions lying 3' to the annealed repeats are displaced as 3'-flaps (Parsons et al. 2000, Van Dyck et al. 2001, Singleton et al. 2002, Stark et al. 2004, Mansour et al. 2008). The endonuclease complex composed of ERCC1 and ERCC4 (XPF) is subsequently recruited to SSA sites through direct interaction between RAD52 and ERCC4, leading to cleavage of 3' flaps (Motycka et al. 2004, Al-Minawi et al. 2008). The identity of a DNA ligase that closes the remaining single strand nicks (SSBs) to complete SSA-mediated repair is not known.
SSA results in deletion of one of the annealed repeats and the intervening DNA sequence between the two annealed repeats and is thus mutagenic.
R-HSA-5658034 HHAT G278V doesn't palmitoylate Hh-Np A loss-of-function mutation in HHAT that abrogates palmitoylation of Hh ligand is associated with Syndromic 46, XY Disorder of Sex Development, which results in testis dysgenesis (Callier et al, 2014).
R-HSA-162906 HIV Infection The global pandemic of Human Immunodeficiency Virus (HIV) infection has resulted in tens of millions of people infected by the virus and millions more affected. UNAIDS estimates around 40 million HIV/AIDS patients worldwide with 75% of them living in sub-Saharan Africa. The primary method of HIV infection is by sexual exposure while nonsexual HIV transmission also can occur through transfusion with contaminated blood products, injection drug use, occupational exposure,accidental needlesticks or mother-to-child transmission. HIV damages the immune system, leaving the infected person vulnerable to a variety of "opportunistic" infections arising from host immune impairment (Hare, 2004).
HIV-1 and the less common HIV-2 belong to the family of retroviruses. HIV-1 contains a single-stranded RNA genome that is 9 kilobases in length and contains 9 genes that encode 15 different proteins. These proteins are classified as: structural proteins (Gag, Pol, and Env), regulatory proteins (Tat and Rev), and accessory proteins (Vpu, Vpr, Vif, and Nef) (Frankel and Young,1998).
HIV infection cycle can be divided into two phases:
1. An Early phase consisting of early events occuring after HIV infection of a susceptible target cell and a
2. Late phase comprising the later events in the HIV-infected cell resulting in the assembly of new infectious virions. The section titled HIV lifecycle consists of annotations of events in these two phases.
The virus has developed various molecular strategies to suppress the antiviral immune responses (innate, cellular and humoral) of the host. HIV-1 viral auxiliary proteins (Tat, Rev, Nef, Vif, Vpr and Vpu) play important roles in these host-pathogen interactions (Li et al.,2005). The section titled Host interactions of HIV factors highlights these complex post-infection processes.
R-HSA-162587 HIV Life Cycle The life cycle of HIV-1 is divided into early and late phases, shown schematically in the figure. In the early phase, an HIV-1 virion binds to receptors and co-receptors on the human host cell surface (a), viral and host cell membranes fuse and the viral particle is uncoated (b), the viral genome is reverse transcribed and the viral preintegration complex (PIC) forms (c), the PIC is transported through the nuclear pore into the nucleoplasm (d), and the viral reverse transcript is integrated into a host cell chromosome (e). In the late phase, viral RNAs are transcribed from the integrated viral genome and processed to generate viral mRNAs and full-length viral genomic RNAs (f), the viral RNAs are exported through the nuclear pore into the cytosol (g), viral mRNAs are translated and the resulting viral proteins are post-translationally processed (h), core particles containing viral genomic RNA and proteins assemble at the host cell membrane and immature viral particles are released by budding. The released particles mature to become infectious (j), completing the cycle (Frankel and Young 1998; Miller and Bushman 1997).
Most of the crucial concepts used to describe these processes were originally elucidated in studies of retroviruses associated with tumors in chickens, birds, and other animal model systems, and the rapid elucidation of the basic features of the HIV-1 life cycle was critically dependent on the intellectual framework provided by these earlier studies. This earlier work has been very well summarized (e.g., Weiss et al. 1984; Coffin et al. 1997); here for brevity and clarity we focus on experimental studies specific to the HIV-1 life cycle.
R-HSA-167169 HIV Transcription Elongation In the absence of the HIV-1 protein Tat, transcription of the proviral DNA is inefficient and results in the production of truncated transcripts (Kao et al., 1987). While initiation of transcription from the HIV-1 LTR and formation of the early elongation complex occurs normally, transcription elongation is incomplete with non-processive polymerases disengaging from the proviral DNA template prematurely (reviewed in Karn 1999). The mechanism of Tat-mediated elongation is described below.
R-HSA-167161 HIV Transcription Initiation Formation of the open complex exposes the template strand to the catalytic center of the RNA polymerase II enzyme. This facilitates formation of the first phosphodiester bond, which marks transcription initiation. As a result of this, the TFIIB basal transcription factor dissociates from the initiation complex.
The open transcription initiation complex is unstable and can revert to the closed state. Initiation at this stage requires continued (d)ATP-hydrolysis by TFIIH. Dinucleotide transcripts are not stably associated with the transcription complex. Upon dissociation they form abortive products. The transcription complex is also sensitive to inhibition by small oligo-nucleotides.
Dinucleotides complementary to position -1 and +1 in the template can also direct first phosphodiester bond formation. This reaction is independent on the basal transcription factors TFIIE and TFIIH and does not involve open complex formation. This reaction is sensitive to inhibition by single-stranded oligonucleotides. R-HSA-167287 HIV elongation arrest and recovery RNA Pol II arrest is believed to be a result of irreversible backsliding of the enzyme by ~7-14 nucleotides. TFIIS reactivates arrested RNA Pol II by promoting the excision of nascent transcript ~7-14 nucleotides upstream of the 3' end. R-HSA-2022928 HS-GAG biosynthesis Heparan sulfate (HS) and heparin (sometimes collectively called HS-GAG) consist of the disaccharide unit GlcNAc-GlcA (N-acetylglucosamine-glucuronic acid) connected by a beta1,4 linkage. Heparin is exclusively made in mast cells whereas HS is made by virtually every type of cell in the body. As the chain length increases, the polysaccharides can undergo modifcations such as epimerisation of glucuronic acid to iduronic acid and deacetylation and sulfation of GlcNAc to form sulfated glucosamine (Stringer & Gallagher 1997, Sasisekharan & Venkataraman 2000). R-HSA-2024096 HS-GAG degradation Lysosomal degradation of glycoproteins is part of the cellular homeostasis of glycosylation (Winchester 2005). The steps outlined below describe the degradation of heparan sulfate/heparin. Complete degradation of glycoproteins is required to avoid build up of glycosaminoglycan fragments which can cause lysosomal storage diseases. The proteolysis of the core protein of the glycoprotein is not shown here. R-HSA-3371511 HSF1 activation Heat shock factor 1 (HSF1) is a transcription factor that activates gene expression in response to a variety of stresses, including heat shock, oxidative stress, as well as inflammation and infection (Shamovsky I and Nudler E 2008; Akerfelt et al. 2010; Bjork and Sistonen 2010; Anckar and Sistonen 2011).
HSF1 is constitutively present in the cell. In the absence of stress HSF1 is found in both the cytoplasm and the nucleus as an inactive monomer (Sarge KD et al. 1993; Mercier PA et al. 1999; Vujanac M et al. 2005). A physical or chemical proteotoxic stress rapidly induces HSF1 activation, which occurs through a multi?step process, involving HSF1 monomer-to-homotrimer transition, nuclear accumulation, and binding to a promoter element, called the heat shock element (HSE), which leads to the increase in the stress-inducible gene expression (Sarge KD et al. 1993; Baler R et al. 1998; Sonna LA et al. 2002; Shamovsky I and Nudler E 2008; Sakurai H and Enoki Y 2010; Herbomel G et al. 2013). Depending on the type of stress stimulus, the multiple events associated with HSF1 activation might be affected differently (Holmberg CI et al 2000; Bjork and Sistonen 2010). R-HSA-3371571 HSF1-dependent transactivation Acquisition of DNA binding activity by HSF1 is necessary but insufficient for transcriptional activation (Cotto JJ et al. 1996; Trinklein ND et al. 2004). In addition to having a sequence-specific DNA binding domain, HSF1 contains a C-terminal region which is involved in activating the transcription of the target genes (Green M et al. 1995). However, the transactivating ability of the transactivation domain itself is not stress sensitive. Rather, it's controled by a regulatory domain of HSF1 (amino acids 221-310), which represses the transactivating ability under normal physiological conditions (Green M et al. 1995; Zuo J et al. 1995; Newton EM et al. 1996). The HSF1 transactivation domain can be divided into two distinct regions, activation domain 1 (AD1) and activation domain 2 (AD2) (Brown SA et al. 1998). AD1 and AD2 each contain residues that are important for both transcriptional initiation and elongation. Mutations in acidic residues in both AD1 and AD2 preferentially affect the ability of HSF1 to stimulate transcriptional initiation, while mutations in phenylalanine residues preferentially affect stimulation of elongation (Brown SA et al. 1998).
Activation of the DNA-bound but transcriptionally incompetent HSF1 is thought to occur upon stress induced HSF1 phosphorylation at several serine residues (Ding XZ et al. 1997; Holmberg CI et al. 2001; Guettouche T et al. 2005). In cells exposed to heat, acquisition of HSE DNA-binding activity was observed to precede phosphorylation of HSF1 (Cotto JJ et al. 1996; Kline MP & Morimoto RI 1997). While there is a sufficient evidence to suggest that phosphorylation of HSF1 is essential to modulate HSF1 transactiviting capacity, mechanisms behind stress stimuli and kinases/phosphatases involved have not been clearly established. R-HSA-3371497 HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand Steroid hormone receptors (SHR) are transcription factors that become activated upon sensing steroid hormones such as glucocorticoids, mineralocorticoids, progesterone, androgens, or estrogen (Escriva et al 2000; Griekspoor A et al. 2007; Eick GN & Thornton JW. 2011). Depending on SHR type and the presence of ligand, they show different subcellular localizations. Whereas both unliganded and liganded estrogen receptors (ERalpha and ERbeta) are predominantly nuclear, unliganded glucocorticoid (GR) and androgen receptors (AR) are mostly located in the cytoplasm and completely translocate to the nucleus only after binding hormone (Htun H et al. 1999; Stenoien D et al. 2000; Tyagi RK et al. 2000; Cadepond F et al. 1992; Jewell CM et al. 1995; Kumar S et al. 2006). The unliganded mineralocorticoid receptor (MR) is partially cytoplasmic but can be found in nucleus in the ligand-bound or ligand-free form (Nishi M & Kawata M 2007). The progesterone receptor (PR) exists in two forms (PRA and PRB) with different ratios of nuclear versus cytoplasmic localization of the unliganded receptor. In most cell contexts, the PRA isoform is a repressor of the shorter PRB isoform, and without hormone induction it is mostly located in the nucleus, whereas PRB distributes both in the nucleus and in the cytoplasm (Lim CS et al. 1999; Griekspoor A et al. 2007). In the absence of ligand, members of the steroid receptor family remain sequestered in the cytoplasm and/or nucleus in the complex with proteins of HSP70/HSP90 chaperone machinery (Pratt WB & Dittmar KD1998). The highly dynamic ATP-dependent interactions of SHRs with HSP90 complexes regulate SHR cellular location, protein stability, competency to bind steroid hormones and transcriptional activity (Echeverria PC & Picard D 2010). Understanding the mechanism of ATPase activity of HSP90 is mostly based on structural and functional studies of the Saccharomyces cerevisiae Hsp90 complexes (Meyer P et al. 2003, 2004; Ali MM et al. 2006; Prodromou C et al. 2000; Prodromou C 2012). The ATPase cycle of human HSP90 is less well understood, however several studies suggest that the underlying enzymatic mechanisms and a set of conformational changes that accompany the ATPase cycle are highly similar in both species (Richter K et al. 2008; Vaughan CK et al. 2009). Nascent SHR proteins are chaperoned by HSP70 and HSP40 to HSP90 cycle via STIP1 (HOP) (and its TPR domains) (Hernández MP et al. 2002a,b; EcheverriaPC & Picard D 2010; Li J et al. 2011). The ATP-bound form of HSP90 leads to the displacement of STIP1 by immunophilins FKBP5 or FKBP4 resulting in conformational changes that allow efficient hormone binding (Li J et al. 2011). PTGES3 (p23) binds to HSP90 complex finally stabilizing it in the conformation with a high hormone binding affinity. After hydrolysis of ATP the hormone bound SHR is released from HSP90 complex. The cytosolic hormone-bound SHR can be transported to the nucleus by several import pathways such as the dynein-based nuclear transport along microtubules involving the transport of the entire HSP90 complex or nuclear localization signals (NLS)-mediated nuclear targeting by importins (Tyagi RK et al. 2000; Cadepond F et al. 1992; Jewell CM et al. 1995; Kumar S et al. 2006). It is worth noting that GR-importin interactions can be ligand-dependent or independent (Freedman & Yamamoto 2004; Picard & Yamamoto 1987). In the nucleus ligand-activated SHR dimerizes, binds specific sequences in the DNA, called Hormone Responsive Elements (HRE), and recruits a number of coregulators that facilitate gene transcription. Nuclear localization is essential for SHRs to transactivate their target genes, but the same receptors also possess non-genomic functions in the cytoplasm.
The Reactome module describes the ATPase-driven conformational cycle of HSP90 that regulates ligand-dependent activation of SHRs.
R-HSA-5610787 Hedgehog 'off' state Hedgehog is a secreted morphogen that has evolutionarily conserved roles in body organization by regulating the activity of the Ci/Gli transcription factor family. In Drosophila in the absence of Hh signaling, full-length Ci is partially degraded by the proteasome to generate a truncated repressor form that translocates to the nucleus to represses Hh-responsive genes. Binding of Hh ligand to the Patched (PTC) receptor allows the 7-pass transmembrane protein Smoothened (SMO) to be activated in an unknown manner, disrupting the partial proteolysis of Ci and allowing the full length activator form to accumulate (reviewed in Ingham et al, 2011; Briscoe and Therond, 2013).
While many of the core components of Hh signaling are conserved from flies to humans, the pathways do show points of significant divergence. Notably, the human genome encodes three Ci homologues, GLI1, 2 and 3 that each play slightly different roles in regulating Hh responsive genes. GLI3 is the primary repressor of Hh signaling in vertebrates, and is converted to the truncated GLI3R repressor form in the absence of Hh. GLI2 is a potent activator of transcription in the presence of Hh but contributes only minimally to the repression function. While a minor fraction of GLI2 protein is processed into the repressor form in the absence of Hh, the majority is either fully degraded by the proteasome or sequestered in the full-length form in the cytosol by protein-protein interactions. GLI1 lacks the repression domain and appears to be an obligate transcriptional activator (reviewed in Briscoe and Therond, 2013).
Vertebrate but not fly Hh signaling also depends on the movement of pathway components through the primary cilium. The primary cilium is a non-motile microtubule based structure whose construction and maintenance depends on intraflagellar transport (IFT). Anterograde IFT moves molecules from the ciliary base along the axoneme to the ciliary tip in a manner that requires the microtubule-plus-end directed kinesin KIF3 motor complex and the IFT-B protein complex, while retrograde IFT back to the ciliary base depends on the minus-end directed dynein motor and the IFT-A complex. Genetic screens have identified a number of cilia-related proteins that are required both to maintain Hh in the 'off' state and to transduce the signal when the pathway is activated (reviewed in Hui and Angers, 2011; Goetz and Anderson, 2010).
R-HSA-5632684 Hedgehog 'on' state Hedgehog is a secreted morphogen that has evolutionarily conserved roles in body organization by regulating the activity of the Ci/Gli transcription factor family. In Drosophila in the absence of Hh signaling, full-length Ci is partially degraded by the proteasome to generate a truncated repressor form that translocates to the nucleus to represses Hh-responsive genes. Binding of Hh ligand to the Patched (PTC) receptor allows the 7-pass transmembrane protein Smoothened (SMO) to be activated in an unknown manner, disrupting the partial proteolysis of Ci and allowing the full length activator form to accumulate (reviewed in Ingham et al, 2011; Briscoe and Therond, 2013).
While many of the core components of Hh signaling are conserved from flies to humans, the pathways do show points of significant divergence. Notably, the human genome encodes three Ci homologues, GLI1, 2 and 3 that each play slightly different roles in regulating Hh responsive genes. GLI3 is the primary repressor of Hh signaling in vertebrates, and is converted to the truncated GLI3R repressor form in the absence of Hh. GLI2 is a potent activator of transcription in the presence of Hh but contributes only minimally to the repression function. While a minor fraction of GLI2 protein is processed into the repressor form in the absence of Hh, the majority is either fully degraded by the proteasome or sequestered in the full-length form in the cytosol by protein-protein interactions. GLI1 lacks the repression domain and appears to be an obligate transcriptional activator (reviewed in Briscoe and Therond, 2013).
Vertebrate but not fly Hh signaling also depends on the movement of pathway components through the primary cilium. The primary cilium is a non-motile microtubule based structure whose construction and maintenance depends on intraflagellar transport (IFT). Anterograde IFT moves molecules from the ciliary base along the axoneme to the ciliary tip in a manner that requires the microtubule-plus-end directed kinesin KIF3 motor complex and the IFT-B protein complex, while retrograde IFT back to the ciliary base depends on the minus-end directed dynein motor and the IFT-A complex. Genetic screens have identified a number of cilia-related proteins that are required both to maintain Hh in the 'off' state and to transduce the signal when the pathway is activated (reviewed in Hui and Angers, 2011; Goetz and Anderson, 2010).
R-HSA-5358346 Hedgehog ligand biogenesis Mammalian genomes encode three Hedgehog ligands, Sonic Hedgehog (SHH), Indian Hedgehog (IHH) and Desert Hedgehog (DHH). These secreted morphogens can remain associated with lipid rafts on the surface of the secreting cell and affect developmental processes in adjacent cells. Alternatively, they can be released by proteolysis or packaging into vesicles or lipoprotein particles and dispersed to act on distant cells. SHH activity is required for organization of the limb bud, notochord and neural plate, IHH regulates bone and cartilage development and is partially redundant with SHH, and DHH contributes to germ cell development in the testis and formation of the peripheral nerve sheath (reviewed in Pan et al, 2013).
Despite divergent biological roles, all Hh ligands are subject to proteolytic processing and lipid modification during transit to the surface of the secreting cell (reviewed in Gallet, 2011). Precursor Hh undergoes autoproteolytic cleavage mediated by the C-terminal region to yield an amino-terminal peptide Hh-Np (also referred to as Hh-N) (Chen et al, 2011). No other well defined role for the C-terminal region of Hh has been identified, and the secreted Hh-Np is responsible for all Hh signaling activity. Hh-Np is modified with cholesterol and palmitic acid during transit through the secretory system, and both modifications contribute to the activity of the ligand (Porter et al, 1996; Pepinsky et al, 1998; Chamoun et al, 2001).
At the cell surface, Hh-Np remains associated with the secreting cell membrane by virtue of its lipid modifications, which promote clustering of Hh-Np into lipid rafts (Callejo et al, 2006; Peters et al, 2004). Long range dispersal of Hh-Np depends on the untethering of the ligand from the membrane through a variety of mechanisms. These include release of monomers through the combined activity of the transmembrane protein Dispatched (DISP2) and the secreted protein SCUBE2, assembly into soluble multimers or apolipoprotein particles or release on the surface of exovesicles (Vyas et al, 2008; Tukachinsky et al, 2012; Chen 2004; Zeng et al, 2001; reviewed in Briscoe and Therond, 2013).
R-HSA-189451 Heme biosynthesis Although heme is synthesised in virtually all tissues, the principal sites of synthesis are erythroid cells (~85%) and hepatocytes (most of the remainder). Eight enzymes are involved in heme biosynthesis, four each in the mitochondria and the cytosol (Layer et al. 2010). The process starts in the mitochondria with the condensation of succinyl CoA (from the TCA cycle) and glycine to form 5-aminolevulinate (ALA). The next four steps take place in the cytosol. Two molecules of ALA are condensed to form the monopyrrole porphobilinogen (PBG). The next two steps convert four molecules of PBG into the cyclic tetrapyrrole uroporphyringen III, which is then decarboxylated into coproporphyrinogen III. The last three steps occur in the mitochondria and involve modifications to the tetrapyrrole side chains and finally, insertion of iron. In addition to these synthetic steps, a spontaneous cytosolic reaction allows the formation of uroporphyringen I which is then enzymatically decarboxylated to coproporphyrinogen I, which cannot be metabolized further in humans. Also, lead can inactivate ALAD, the enzyme that catalyzes PBG synthesis, and ferrochelatase, the enzyme that catalyzes heme synthesis (Ponka et al. 1999, Aijoka et al. 2006).
The porphyrias are disorders that arise from defects in the enzymes of heme biosynthesis. Defective pathway enzymes after ALA synthase result in accumulated substrates which can cause either skin problems, neurological complications, or both due to their toxicity in higher concentrations. They are broadly classified as hepatic porphyrias or erythropoietic porphyrias, based on the site of the overproduction of the substrate. Each defect is described together with the reaction it affects (Peoc'h et al. 2016).
R-HSA-189483 Heme degradation Most of the heme degraded in humans comes from hemoglobin. Approximately 6-8 grams of hemoglobin is degraded daily which is equivalent to approximately 300 milligrams of heme per day. Heme is not recycled so it must be degraded and excreted. The iron, however, is conserved. There are two steps to heme degradation;
1. cleavage of the heme ring by a microsomal heme oxygenase producing biliverdin
2. biliverdin is reduced to bilirubin.
Bilirubin can then be conjugated with glucuronic acid and excreted.
R-HSA-9707616 Heme signaling Extracellular hemoglobin, a byproduct of hemolysis, can release its prosthetic heme groups upon oxidation. Blood plasma contains proteins that scavenge heme. It is estimated that about 2–8% of the heme released in plasma becomes ‘bioavailable’, being internalized by bystander cells. If the heme degradation capacity of a cell, represented by heme oxidase 1 and 2, cannot be ramped up sufficiently then heme signaling and reactivity puts cells under stress. Platelets are activated by heme, and macrophages switch to the inflammatory type (Donegan et al, 2019; Gouveia et al, 2019).
Free (labile) heme accumulates in the blood stream in great amounts under pathological conditions like viral infections and malaria, but also ARDS amd COPD. The locally affected cells' primary reaction is to upregulate heme oxidase 1 (HMOX1) expression. HMOX1 induction in these cells not only removes heme from circulation but also triggers a functional switch toward the anti-inflammatory phenotype (Vijayan et al, 2018). However, heme scavenging and degradation systems may get overwhelmed by the sheer amount of heme present.
Heme promotes platelet activation, complement activation, vasculitis, and thrombosis (Bourne et al, 2020; Merle et al, 2018). Heme was recognized to act as a danger signal, damage-associated molecular pattern (DAMP), or alarmin (Soares and Bozza, 2016) and was shown to activate Toll-like receptor 4 (TLR4) signaling (Figueiredo et al, 2007; Janciauskiene et al, 2020). It also has a role as corepressor in the circadian clock system (Ko and Takahashi, 2006). BACH1 is regulated by heme in a cell, thus placing heme as a signaling molecule in gene expression in higher eukaryotes. The regulation of BACH1 by heme may be important for the stress response in general (Suzuki et al, 2004).
Extracellular hemoglobin, a byproduct of hemolysis, can release its prosthetic heme groups uponoxidation. Due to the reactive nature of free heme, the blood plasma contains proteins that scavenge heme. It is estimated that about 2–8% of the heme released in plasma becomes ‘bioavailable’, being internalized by bystander cells. Failure of nearby cells to sufficientlymetabolize free heme can incite platelet activation, macrophage differentiation, and oxidative stress (Donegan et al, 2019; Gouveia et al, 2019).
R-HSA-109582 Hemostasis Hemostasis is a physiological response that culminates in the arrest of bleeding from an injured vessel. Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhesion and activation, suppresses coagulation, enhances fibrin cleavage and is anti-inflammatory in character. Under acute vascular trauma, vasoconstrictor mechanisms predominate and the endothelium becomes prothrombotic, procoagulatory and proinflammatory in nature. This is achieved by a reduction of endothelial dilating agents: adenosine, NO and prostacyclin; and by the direct action of ADP, serotonin and thromboxane on vascular smooth muscle cells to elicit their contraction (Becker et al. 2000). The chief trigger for the change in endothelial function that leads to the formation of a haemostatic thrombus is the loss of the endothelial cell barrier between blood and extracellular matrix components (Ruggeri 2002). Circulating platelets identify and discriminate areas of endothelial lesions; here, they adhere to the exposed sub endothelium. Their interaction with the various thrombogenic substrates and locally generated or released agonists results in platelet activation. This process is described as possessing two stages, firstly, adhesion - the initial tethering to a surface, and secondly aggregation - the platelet-platelet cohesion (Savage & Cattaneo et al. 2001). Three mechansism contribute to the loss of blood following vessel injury. The vessel constricts, reducing the loss of blood. Platelets adhere to the site of injury, become activated and aggregate with fibrinogen into a soft plug that limits blood loss, a process termed primary hemostasis. Proteins and small molecules are released from granules by activated platelets, stimulating the plug formation process. Fibrinogen from plasma forms bridges between activated platelets. These events initiate the clotting cascade (secondary hemostasis). Negatively-charged phospholipids exposed at the site of injury and on activated platelets interact with tissue factor, leading to a cascade of reactions that culminates with the formation of an insoluble fibrin clot.
R-HSA-1638091 Heparan sulfate/heparin (HS-GAG) metabolism The acronym HS-GAG is used to describe both heparin and heparan sulfate. HS-GAG is a member of the glycosaminoglycan family and consists of a variably sulfated repeating disaccharide unit, the most common one (50% of the total) being glucuronic acid (GlcA) linked to N-acetylglucosamine (GlcNAc). GlcA can be epimerized to iduronic acid. Higher degrees of sulfation and iduronic acid content in the polysaccharide chain confers the name heparin rather than heparan sulfate to the chain. HS-GAG, like the majority of GAGs in the body, are linked to core proteins, forming proteoglycans (mucopolysaccharides). Two or three HS-GAG chains attach to a core protein on the cell surface or in the extracellular matrix (Sasisekharan & Venkataraman 2000). HS-GAG bound to a core protein can regulate many biological processes such as angiogenesis, blood coagulation and tumour metastasis (Stringer & Gallagher 1997, Tumova et al. 2000). Degradation of HS-GAG is required to maintain a natural turnover of GAGs. Defects in the degradative enzymes result in lysosomal storage diseases, where GAGs build up rather than being broken down and having pathological effects (Ballabio & Gieselmann 2009).
R-HSA-5657560 Hereditary fructose intolerance Deficiencies in aldolase B arising from mutations in the aldolase B gene (ALDOB) prevent the cleavage of fructose 1-phosphate to glyceraldehyde (GA) and dihydroxyacetone phosphate (DHAP), leading to hereditary fructose intolerance (HFI). This autosomal recessive disorder is potentially fatal, but can be managed by exclusion of fructose from the diet (Cox et al. 1988; Tolan 1995).
R-HSA-5387390 Hh mutants abrogate ligand secretion Hh signaling is required for a number of developmental processes, and mutations that disrupt the normal processing and biogenesis of Hh ligand can result in neonatal abnormalities. SHH is one of a number of genes that have been associated with the congenital disorder holoprosencephaly, which causes abnormalities in brain and craniofacial development (Roessler et al, 2009; reviewed in Roessler and Muenke, 2011). SHH variants associated with the condition affect the autocatalytic processing of the precursor and dramatically impair the production of the secreted active Hh-Np, abrogating signaling (reviewed in Pan et al, 2013). Aberrant Hh signaling is also associated with gondal dysgenesis syndromes in which palmitoylation of DHH is abrogated by mutation of the acyltransferase HHAT (Callier et al, 2014).
R-HSA-5362768 Hh mutants are degraded by ERAD Hh signaling is required for a number of developmental processes, and mutations that disrupt the normal processing and biogenesis of Hh ligand can result in neonatal abnormalities. SHH is one of a number of genes that have been associated with the congenital disorder holoprosencephaly, which causes abnormalities in brain and craniofacial development (Roessler et al, 2009; reviewed in Roessler and Muenke, 2011). SHH variants associated with the condition affect the autocatalytic processing of the precursor and dramatically impair the production of the secreted active Hh-Np, abrogating signaling (reviewed in Pan et al, 2013).
R-HSA-9856530 High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells Laminar shear stress produced by high fluid flow across endothelial cells causes the cells to produce vasodilatory nitric oxide (NO) and to elongate from polygonal to ellipsoid such that their long axes become parallel with direction of the flow (Nerem et al. 1981, Dewey et al. 1981, reviewed in Tamargo et al. 2023). Nitric oxide produced by endothelial cells modulates soluble guanylyl cyclase and cGMP-dependent kinase in surrounding smooth muscle cells to cause vasodilation (reviewed in Feletou et al. 2008, 2012). By optimizing blood flow without inflammation, the response to laminar shear stress is atheroprotective.
Laminar shear stress on endothelial cells is detected by the glycocalyx, caveolae, cilia, the mechanosensitive ion channel PIEZO1 located on the apex of the cell, and the PECAM1:CDH5:KDR (PECAM1:VE-cadherin:VEGFR2) complex located on the lateral surfaces between adjacent cells (reviewed in Tanaka et al. 2021). The active molecular components, mechanisms of activation, and downstream events related to the glycocalyx, caveolae, and cilia are incompletely characterized so the annotation here focuses more on PIEZO1 and the PECAM1:CDH5:KDR complex.
The force of the flow on the membrane of the endothelial cell activates the mechanosensitive ion channel PIEZO1 and, indirectly, the ion channel TRPV4 to transport cations, notably calcium, from the extracellular region to the cytosol (reviewed in Li et al. 2014, Ranade et al. 2014, Fang et al. 2021, Xiao et al. 2023). Cytosolic calcium activates the protease complex Calpain2 to cleave the cytoskeletal proteins TALIN1 and VINCULIN, resulting in changes to the cytoskeleton that alter the shape of the endothelial cell (Miyazaki et al. 2007).
Flow-sensitive potassium channels (which may include Kir2.1 and TREK1) and chloride channels (which may include LRRC8A) are also observed to open, however their mechanisms of activation and downstream events are incompletely characterized (reviewed in Tanaka et al. 2021).
Cytosolic calcium activates Pannexin channels to release ATP (Wang et al. 2016), which binds the P2RY2 (P2Y2) receptor on the cell surface in an autocrine and paracrine manner and thereby activates Galpha(q/11)-PI3K-AKT1 signaling. Both signaling by P2RY2 and signaling by a mechanosensitive complex containing PECAM1 and KDR (VEGFR2) (inferred from mouse homologs in Tzima et al. 2005) produce phosphatidylinositol 3,4,5-trisphosphate (PIP3), which binds AKT1 and enhances the phosphorylation of AKT1 on serine-475 by the mTORC2 complex.
Through a PI3K-independent mechanism, P2RY2 signaling and cytosolic calcium activate the kinase PDPK1, which phosphorylates the kinase PKN2 (PRK2) (Jin et al. 2021). Phospho-PKN2 then phosphorylates AKT1 on threonine-308 (Jin et al. 2021). Phospho-T308,S475-AKT1 phosphorylates serine-1177 of NOS3 (eNOS) while phospho-PKN2 also phosphorylates serine-1179 of NOS3 (Jin et al. 2021), causing increased nitric oxide production (reviewed in Cabou and Martinez 2022).
Laminar shear stress increases secretion of Adrenomedullin (ADM), a vasodilator, by endothelial cells through an uncharacterized mechanism (Iring et al. 2019). ADM binds the AM1 receptor and signals through G-alpha(s), adenylate cyclase, and resultant cAMP to activate protein kinase A (PKA) to phosphorylate serine-633 of NOS3, further increasing nitric oxide production (Iring et al. 2019).
The sphingosine 1-phosphate receptor S1PR1, which couples to Galpha(i1) and Galpha(i3), contributes in a ligand-independent manner to activation of AKT and NOS3, however the intermediate steps are incompletely characterized (reviewed in Tanaka et al. 2021). Other GPCRs such as GPR68 also become activated, possibly through flow-induced deformation of the extracellular domain (reviewed in Tanaka et al. 2021).
R-HSA-629597 Highly calcium permeable nicotinic acetylcholine receptors Nicotinic acetylcholine receptors exhibit high influx of Ca2+, the degree of Ca2+ permeability is dependent on the subunit composition; homomeric acetylcholine receptors containing aplha 7 subunits allow maximum Ca2+ influx followed by receptors containing alpha3 beta2 alpha5 or alpha3 beta4 alpha5.
R-HSA-629594 Highly calcium permeable postsynaptic nicotinic acetylcholine receptors Postsynaptic acetylcholine receptors mediate Ca2+ currents that may be involved in the facilitation of long term potentiation (LTP).
R-HSA-629587 Highly sodium permeable postsynaptic acetylcholine nicotinic receptors Nicotinic acetylcholne receptors that have low Ca2+ permeability allow the influx of Na+ which causes depolarization of the membrane initiating voltage dependent responses such as activation of voltage dependent opening of Ca2+ channels and thus eliciting an increase in Ca2+ and downstream signaling. These receptors could be found in both presynaptic and postsynaptic terminals.
R-HSA-390650 Histamine receptors Histamine is a biogenic amine involved in local immune responses, regulation of gut function and neurotransmission. It exerts its actions by binding to histamine receptors. There are four receptors in humans, H1-H4 (Hill SJ et al, 1997).
R-HSA-70921 Histidine catabolism The major pathway of histidine catabolism, annotated here, proceeds in four steps to yield glutamate and, in the process, convert one molecule of tetrahydrofolate to 5-formiminotetrahydrofolate (Morris et al. 1972). Histidine can also be decarboxylated to form histamine. Histidine can also be used to form carnosine (beta-alanyl-L-histidine), an abundant dipeptide in skeletal muscle and brain of most vertebrates.
R-HSA-5693579 Homologous DNA Pairing and Strand Exchange The presynaptic phase of homologous DNA pairing and strand exchange begins with the displacement of RPA from 3'-ssDNA overhangs created by extensive resection of DNA double-strand break (DSB) ends. RPA is displaced by the joint action of RAD51 and BRCA2. BRCA2 nucleates RAD51 on 3'-ssDNA overhangs, leading to formation of invasive RAD51 nucleofilaments which are stabilized by the BCDX2 complex (RAD51B:RAD51C:RAD51D:XRCC2). Stable synaptic pairing between recombining DNA molecules involves the invasion of the homologous sister chromatid duplex DNA by the RAD51 nucleofilament and base-pairing between the invading ssDNA and the complementary sister chromatid DNA strand, while the non-complementary strand of the sister chromatid DNA duplex is displaced. This results in the formation of a D-loop structure (Sung et al., 2003). PALB2 and RAD51AP1 synergistically stimulate RAD51 recombinase activity and D-loop formation. PALB2 simultaneously interacts with RAD51, BRCA2 and RAD51AP1 (Modesti et al. 2007, Wiese et al. 2007, Buisson et al. 2010, Dray et al. 2010). PALB2 also interacts with BRCA1, and this interaction fine-tunes the localization of BRCA2 and RAD51 at DNA DSBs (Zhang et al. 2009, Sy et al. 2009). The CX3 complex, composed of RAD51C and XRCC3, binds D-loop structures through interaction with PALB2 and may be involved in the resolution of Holliday junctions (Chun et al. 2013, Park et al. 2014).
While RAD52 promotes formation of invasive RAD51 nucleofilaments in yeast, human BRCA2 performs this function, while human RAD52 regulates single strand annealing (SSA) (reviewed by Ciccia and Elledge 2010). R-HSA-5693538 Homology Directed Repair Homology directed repair (HDR) of DNA double strand breaks (DSBs) requires resection of DNA DSB ends. Resection creates 3'-ssDNA overhangs which then anneal with a homologous DNA sequence. This homologous sequence can then be used as a template for DNA repair synthesis that bridges the DSB. HDR preferably occurs through the error-free homologous recombination repair (HRR), but can also occur through the error-prone single strand annealing (SSA), or the least accurate microhomology-mediated end joining (MMEJ).
HRR and SSA share the initial steps that involve ATM signaling, formation of the so-called ionizing radiation-induced foci (IRIF), extensive resection of DNA DSB ends and activation of ATR signaling. In homologous recombination, 3'-ssDNA overhangs anneal with complementary sister chromatid strands. In SSA, 3'-ssDNA overhangs anneal with each other through homologous direct repeats contained in each overhang, resulting in deletions of one of the repeats and the DNA sequence in between the repeats during DNA repair synthesis.
Contrary to HRR and SSA, which both involve annealing of long stretches of highly homologous DNA sequences, MMEJ entails annealing of short regions of two 3'-ssDNA overhangs (up to 20 nucleotides) and is therefore more promiscuous and more likely to join unrelated DNA molecules. The error rate of MMEJ is additionally increased by the low fidelity of the DNA polymerase theta (POLQ), which performs DNA repair synthesis in MMEJ.
For reviews of this topic, please refer to Khanna 2001, Thompson and Schild 2001, Thompson and Schild 2002, Thompson and Limoli 2003, Ciccia and Elledge 2010.
R-HSA-375281 Hormone ligand-binding receptors The class A (rhodopsin-like) GPCRs that bind to hormone ligands are annotated here. The hormones follicle-stimulating hormone (FSH), luteinizing hormone (LH), thyroid-stimulating hormone (TSH) and human chorionic gonadotrophin (hCG) are dimeric glycoproteins, sharing an identical alpha subunit and varying beta subunits. Their actions are mediated by the respective GPCRs, influencing reproductive processes and thyroid hormone release.
R-HSA-162909 Host Interactions of HIV factors Like all viruses, HIV-1 must co-opt the host cell macromolecular transport and processing machinery. HIV-1 Vpr and Rev proteins play key roles in this co-optation. Efficient HIV-1 replication likewise requires evasion of APOBEC3G-mediated mutagenesis of reverse transcripts, a process mediated by the viral Vif protein.
R-HSA-450520 HuR (ELAVL1) binds and stabilizes mRNA HuR (ELAVL1) is a ubiquitous protein that binds AU-rich elements in mRNAs and acts to stabilize the mRNAs. HuR activity is controlled by phosphorylation, with PKC alpha and PCK delta enhancing the ability of HuR to bind and stabilize mRNAs. Binding of mRNAs occurs in the nucleus and HuR then interacts with the CRM1 export pathway to transfer the mRNA to the cytoplasm. The mechanism by which HuR shields the mRNA from degradation is unknown.
HuR also regulates translation of some mRNAs, in some cases repressing translation and in some cases enhancing translation of bound mRNAs by recruiting them to polysomes.
HuR binds and regulates mRNAs encoding Cyclooxygenase-2 (COX2, PTGS2), Cyclin A (CCNA, CCNA2), Cyclin D1 (CCND1), Cyclin B1 (CCNB1), CD83 antigen (CD83), and proto-oncogene c-Fos (FOS).
HuR is a member of a family of proteins that also contains HuD (ELAVL4), HuB (ELAVL2), and HuC (ELAVL3). HuB, HuC, and HuD are specifically expressed in neural tissue.
HuR participates in apoptosis. During lethal stress HuR becomes mostly cytoplasmic and is a target of Caspase-3 and Caspase-7. The cleavage products of HuR in turn promote apoptosis.
R-HSA-2142850 Hyaluronan biosynthesis and export Hyaluronan (hyaluronic acid, HA) is composed of repeating disaccharide units of glucuronic acid and N-acetylglucosamine [-4GlcAb1-3GlcNAcb1-]. It is synthesized in the cell membrane by adding monosaccharides to the reducing end of the chain using the precursors UDP-glucuronic acid and UDP-N-acetylglucosamine in the presence of Mg2+. The integral membrane dual-action glycosyltransferase proteins hyaluronan synthases, of which vertebrates have three types (HAS1-3), catalyze these monosaccharide additions. Unlike other GAGs, HA is synthesized as a free glycan, not attached to a protein (Laurent 1987, Weigel & DeAngelis, 2007). As HA is synthesised it is extruded from the cell by an ABC-type transporter into the extracellular medium.
R-HSA-2142845 Hyaluronan metabolism Hyaluronan (hyaluronic acid, hyaluronate or HA) is an anionic glycosaminoglycan (GAG) distributed widely throughout connective, epithelial, and neural tissues and most abundant in the extracellular matrix and skin. HA is unique among the GAGs in that it is not sulfated and is not found covalently attached to proteins as a proteoglycan. HA polymers are very large (they can reach molecular weights of 10 million Da) and can displace a large volume of water making them excellent lubricators and shock absorbers. Another unique feature of HA is that it is synthesized at the plasma membrane unlike other GAGs which are formed in the Golgi. HA is a polymer of the disaccharide unit D-glucuronic acid and D-N-acetylglucosamine, linked via alternating beta-1,4 and beta-1,3 glycosidic bonds (Toole 2000, 2004, Volpi et al. 2009).
R-HSA-2160916 Hyaluronan uptake and degradation Hyaluronan (HA) turnover can occur locally at the tissue of origin, where it is taken up by cells to be degraded, or released into the lymphatic and vascular systems, where it can be eliminated by the liver and kidneys. Uptake of HA into cells for degradation involves receptor-mediated processes. Once HA enters lysosomes, the acidic conditions favour hyaluronidases to cleave it into small oligosaccharides, the most common size being a tetrasaccharide. Beta-glucuronidases participate in degrading the small oligosaccharides in the lysosome. Ultimately, HA is degraded into its constituent sugars (glucuronic acid and N-acetylglucosamine) which can be used to reform many glycosaminoglycans (GAGs) when released from the lysosome.
A third of the total HA content in humans is turned over daily and it has a short half life of minutes in circulation up to days in many tissues. The reasons why the body eliminates HA so rapidly are unknown but one possible explanation could be HA's role as a reactive oxygen species (ROS) scavenger. Removing these toxic compounds could explain the rapid elimination of HA (Lepperdinger et al. 2004, Menzel & Farr 1998, Erickson & Stern 2012, Stern 2003).
R-HSA-1483115 Hydrolysis of LPC Lysophosphatidylcholine (LPC) is hydrolyzed by phospholipases to produce glycerophosphocholine (GPCho) which is in turn hydrolyzed by glycerophosphocholine phosphodiesterase to produce choline (Cho) and glycerol-3-phosphate (G3P) (Yamashita et al. 2009, Yamashita et al. 2005, Ghomashchi et al. 2010).
R-HSA-1483152 Hydrolysis of LPE Lysophosphatidylethanolamine (LPE) is hydrolyzed by phospholipases to produce glycerophosphoethanolamine (GPETA) which is in turn hydrolyzed by glycerophosphocholine phosphodiesterase to produce ethanolamine (ETA) and glycerol-3-phosphate (G3P) (Yamashita et al. 2009, Yamashita et al. 2005).
R-HSA-3296197 Hydroxycarboxylic acid-binding receptors The G-protein-coupled receptors Hydroxy-carboxylic acid receptor 1 (HCAR1, GPR81), HCAR2 (GPR109A), and HCAR3 (GPR109B) have significant sequence homology and are encoded by clustered genes. Their endogenous ligands are hydroxy-carboxylic acid metabolites. HCAR1 is activated by lactate (2-hydroxy-propanoic acid). HCAR2 is a receptor for 3-hydroxy-butyric acid. HCAR3 is activated by 3-hydroxy-octanoic acid. HCAR1 and HCAR2 are found in most mammalian species; HCA3 is found only in higher primates. All three receptors are expressed in adipocytes and are coupled to Gi-type G-proteins, mediating antilipolytic effects in fat cells. HCAR2 and HCAR3 are also expressed in a variety of immune cells. HCAR2 is a receptor for the antidyslipidemic drug nicotinic acid (niacin) and related natural and synthetic compounds.
R-HSA-204626 Hypusine synthesis from eIF5A-lysine Cytosolic eukaryotic translation initiation factor 5A (eIF5A) undergoes a unique two-step post-translational modification at Lys 50 via deoxyhypusine (Dhp) to hypusine (Hyp). In the first step deoxyhypusine synthase transfers the aminobutyl group of spermidine to the epsilon-amino group of lysine 50, using NAD+ as a cofactor. Hydroxylation of the C2 of the newly added moiety in the second step is catalyzed by deoxyhypusine hydroxylase/monooxygenase with molecular oxygen as the source. The molecular function of eIF5A is unknown, but the protein is required for viability in eukaryotic cells and its normal function requires hypusinylation. eIF5A is the only protein known to undergo hypusinylation (Park 2006).
R-HSA-9732724 IFNG signaling activates MAPKs Interferon-gamma (IFNG) signaling results in transient activation of MAPK1 (ERK2) and MAPK3 (ERK1) (Sakatsume et al. 1998, Ulloa et al. 1999). IFNG-mediated MAPK (ERK) activation is JAK1-dependent and RAS-independent (Sakatsume et al. 1998). It is thought to occur through JAK1-meidated phosphorylation of RAF1 (Sakatsume et al. 1998).
R-HSA-2428924 IGF1R signaling cascade After autophosphorylation the type 1 insulin-like growth factor receptor (IGF1R) binds and phosphorylates scaffold proteins, IRS1/2/4 and SHC1, which in turn bind effectors possessing enzymatic activity (recently reviewed in Pavelic et al. 2007, Chitnis et al. 2008, Maki et al. 2010, Parrella et al. 2010, and Siddle et al. 2012). IRS1/2/4 can bind both PI3K (via the p85 subunit of PI3K) and the GRB2:SOS complex. PI3K activates PKB (AKT, AKT1) signaling. GRB:SOS stimulates RAS to exchange GDP for GTP leading to activation of RAF and MAPK.
R-HSA-5602636 IKBKB deficiency causes SCID Four patients with early-onset, life-threatening microbial infections and failure to thrive were found to carry a homozygous duplication c.1292dupG in exon 13 of IKBKB gene that results in a lack of expression of IKBKB (Pannicke U et al. 2013). IKBKB deficiency is associated with severe combined immunodeficiency (SCID), a health condition characterized by low levels of immunoglobulins (hypogammaglobulinemia). Further phenotype assessment revealed that patients peripheral-blood B cells and T cells had normal counts but were almost exclusively of naive phenotype. Regulatory T cells and gamma delta T cells were absent.
R-HSA-5603027 IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) Many signaling pathways rely on the activation of nuclear factor kappa B (NFkB), which is critical for the induction of the appropriate cellular function in response to various stimuli such as inflammatory cytokines, microbial products or various types of stress (Lawrence T 2009; Hoesel B and Schmid JA 2013). The NFkB family of transcription factors is kept inactive in the cytoplasm by inhibitor of kappa B (IkB) family members (Oeckinghaus A and Ghosh S 2009). Canonical NFkB activation depends on the phosphorylation of IkB by the I kappa B kinase (IKK) complex, which contains two catalytic subunits named IKK alpha, IKK beta and a regulatory subunit named NFkB essential modulator (NEMO or IKBKG) (Rothwarf DM et al. 1998). Phosphorylation of IkB leads to K48-linked ubiquitination and proteasomal degradation of IkB, allowing translocation of NFkB factor to the nucleus, where it can activate transcription of a variety of genes participating in the immune and inflammatory response, cell adhesion, growth control, and protection against apoptosis (Collins T et al. 1995; Kaltschmidt B et al. 2000; Lawrence T 2009).
IKBKG is encoded by an X-linked gene. Null alleles of the gene are lethal in hemizygous males, whereas hypomorphic alleles typically result in the impaired NFkB signaling in patients with a broad spectrum of clinical phenotypes in terms of both developmental defects and immunodeficiency (Döffinger R et al. 2001; Hanson EP et al. 2008). Several categories of mutations affecting IKBKG have been reported in humans (Döffinger R et al. 2001; Vinolo E et al. 2006; Fusko F et al. 2008). The first category of these mutations consists of hypomorphic mutations typically involving the zinc finger domain and nearby C-terminal regions and causing hypohidrotic ectodermal dysplasia with immune deficiency (HED-ID) in males (Jain A et al. 2001; Shifera AS 2010). The second category consists of amorphic mutations causing incontinentia pigmenti (IP) in females and, generally, prenatal death in males (Aradhya S et al. 2001; Fusco F et al. 2004). The third category is composed of hypomorphic mutations involving the stop codon causing anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID), osteopetrosis and lymphedema (OL-EDA-ID) in males (Döffinger R et al. 2001). Also some patients with a defective IKBKG gene can develop immunodeficiency without ectodermal dysplasia (Orange JS et al. 2004). This module describes several EDA-ID-associated hypomorphic IKBKG mutations that have been reported to affect inflammatory responses initiated by toll like receptors (TLR). R-HSA-937041 IKK complex recruitment mediated by RIP1 Receptor-interacting protein 1 (RIP1) mediates the activation of proinflammatory cytokines via intermediate induction of IKK complex in NFkB pathways [Ea et al. 2006]. Poly(I-C) treatment stimulated the recruitment of RIP1, TRAF6, and TAK1 to the TLR3 receptor complex in human embryonic kidney HEK293 transfected with FLAG-tagged TLR3 [Cusson-Hermance et al. 2005]. RIP1 was shown to be dispensable for TRIF-dependent activation of IRF3, which occurs in a TRIF/TBK1/IKKi-dependent manner [Cusson-Hermance et al. 2005, Sato et al. 2003] R-HSA-6788467 IL-6-type cytokine receptor ligand interactions The members involved in (interleukin)-6-type cytokine signalling are the IL-6, IL-11, LIF (leukaemia inhibitory factor), OSM (oncostatin M), ciliary neurotrophic factor (CNTF), cardiotrophin-1 (CTF1) and cardiotrophin-like cytokine factor 1 (CLCF1). Receptors involved in recognition of the IL-6-type cytokines can be subdivided in the non-signalling alpha-receptors (IL6R, IL 11R, and CNTFR) and the signal transducing receptors (gp130, LIFR, and OSMR). The latter associate with JAKs and become tyrosine phosphorylated in response to cytokine stimulation (Heinrich et al. 1998, 2003). IL27 and IL35 belongs to IL12 cytokine family but they share gp130 as a component of signalling receptor, along with IL-6, IL-11, LIF, OSM, CNTF, CTF1 and CLCF1. R-HSA-1855196 IP3 and IP4 transport between cytosol and nucleus Inositol trisphosphate (IP3) and tetrakisphosphate (IP4) molecules are exported from the cytosol to the nucleus (Dewaste et al. 2003, Nalaskowski et al. 2002). It is unknown whether this occurs by diffusion or is mediated by a transporter. R-HSA-1855229 IP6 and IP7 transport between cytosol and nucleus The inositol phosphates IP6 and IP7 are exported from the cytosol to the nucleus (Saiardi et al. 2001, Mulugu et al. 2007). The molecular details of these transport processes remain uncertain. R-HSA-1855215 IPs transport between ER lumen and cytosol Inositol phosphates IP3 and IP5 are imported into the cytosol from the endoplasmic reticulum (ER) lumen (Caffrey et al. 1999, Chi et al. 1999, Nalaskowski et al. 2002, Ho et al. 2002, Brehm et al. 2007). The molecular details of these transport processes remain uncertain. R-HSA-1855156 IPs transport between ER lumen and nucleus Inositol phosphates IP4 and IP5 are exported from the endoplasmic reticulum (ER) lumen to the nucleus (Caffrey et al. 1999, Chi et al. 1999, Nalaskowski et al. 2002, Verbsky et al. 2002, Brehm et al. 2007, Choi et al. 2007). The molecular details of these transport processes remain uncertain. R-HSA-1855184 IPs transport between cytosol and ER lumen Inositol phosphates IP4, IP5, and IP6 are exported from the cytosol to the endoplasmic reticulum (ER) lumen (Caffrey et al. 1999, Chi et al. 1999). The molecular details of these transport processes remain uncertain. R-HSA-1855192 IPs transport between nucleus and ER lumen Inositol phosphate IP6 is imported to the endoplasmic reticulum (ER) lumen from the nucleus (Caffrey et al. 1999). The molecular details of these transport processes remain uncertain. R-HSA-1855170 IPs transport between nucleus and cytosol Inositol phosphates (IPs) synthesised in the nucleus are imported into the cytosol from the nucleus. The molecular details of these transport processes remain uncertain (Nalaskowski et al. 2002; Ho et al. 2002, Brehm et al. 2007, Saiardi et al. 2001, Saiardi et al. 2000, Fridy et al. 2007, Leslie et al. 2002). R-HSA-937039 IRAK1 recruits IKK complex The role of IRAK1 kinase activity in the activation of NF-kappa-B by IL-1/TLR is still uncertain. It has been shown that a kinase-dead IRAK1 mutants can still activate NF-kappa-B. Furthermore, stimulation of IRAK1-deficient I1A 293 cells with LMP1 (latent membrane protein 1- a known viral activator of NF-kappa-B) leads to TRAF6 polyubiquitination and IKKbeta activation [Song et al 2006]. On the other hand, IRAK1 enhances p65 Ser536 phosphorylation [Song et al 2006] and p65 binding to the promoter of NF-kappa-B dependent target genes [Liu G et al 2008].
IRAK1 has also been shown to be itself Lys63-polyubiquitinated (probably by Pellino proteins, which have E3 ligase activity). Mutation of the ubiquitination sites on IRAK1 prevented interaction with the NEMO subunit of IKK complex and subsequent IL-1/TLR-induced NF-kappa-B activation [Conze et al 2008]. These data suggest that kinase activity of IRAK1 is not essential for its ability to activate NF-kappa-B, while its Lys63-polyubuquitination allows IRAK1 to bind NEMO thus facilitating association of TRAF6 and TAK1 complex with IKK complex followed by induction of NF-kappa-B.
Upon IL-1/TLR stimulation IRAK1 protein can undergo covalent modifications including phosphorylation [Kollewe et al 2004], ubiquitination [Conze DB et al 2008] and sumoylation [Huang et al 2004]. Depending upon the nature of its modification, IRAK1 may perform distinct functions including activation of IRF5/7 [Uematsu et al 2005, Schoenemeyer et al 2005], NF-kappa-B [Song et al 2006], and Stat1/3 [Huang et al 2004, Nguyen et al 2003]. R-HSA-975144 IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation The role of IRAK1 kinase activity in the activation of NF-kappa-B by IL-1/TLR is still uncertain. It has been shown that a kinase-dead IRAK1 mutants can still activate NF-kappa-B. Furthermore, stimulation of IRAK1-deficient I1A 293 cells with LMP1 (latent membrane protein 1- a known viral activator of NF-kappa-B) leads to TRAF6 polyubiquitination and IKKbeta activation [Song et al 2006]. On the other hand, IRAK1 enhances p65 Ser536 phosphorylation [Song et al 2006] and p65 binding to the promoter of NF-kappa-B dependent target genes [Liu G et al 2008].
IRAK1 has also been shown to be itself Lys63-polyubiquitinated (probably by Pellino proteins, which have E3 ligase activity). Mutation of the ubiquitination sites on IRAK1 prevented interaction with the NEMO subunit of IKK complex and subsequent IL-1/TLR-induced NF-kappa-B activation [Conze et al 2008]. These data suggest that kinase activity of IRAK1 is not essential for its ability to activate NF-kappa-B, while its Lys63-polyubuquitination allows IRAK1 to bind NEMO thus facilitating association of TRAF6 and TAK1 complex with IKK complex followed by induction of NF-kappa-B.
Upon IL-1/TLR stimulation IRAK1 protein can undergo covalent modifications including phosphorylation [Kollewe et al 2004], ubiquitination [Conze DB et al 2008] and sumoylation [Huang et al 2004]. Depending upon the nature of its modification, IRAK1 may perform distinct functions including activation of IRF5/7 [Uematsu et al 2005, Schoenemeyer et al 2005], NF-kappa-B [Song et al 2006], and Stat1/3 [Huang et al 2004, Nguyen et al 2003]. R-HSA-937042 IRAK2 mediated activation of TAK1 complex Although IRAK-1 was originally thought to be a key mediator of TRAF6 activation in the IL1R/TLR signaling (Dong W et al. 2006), recent studies showed that IRAK-2, but not IRAK-1, led to TRAF6 polyubiquitination (Keating SE et al 2007). IRAK-2 loss-of-function mutants, with mutated TRAF6-binding motifs, could no longer activate NF-kB and could no longer stimulate TRAF-6 ubiquitination (Keating SE et al 2007). Furthermore, the proxyvirus protein A52 - an inhibitor of all IL-1R/TLR pathways to NF-kB activation, was found to interact with both IRAK-2 and TRAF6, but not IRAK-1. Further work showed that A52 inhibits IRAK-2 functions, whereas association with TRAF6 results in A52-induced MAPK activation. The strong inhibition effect of A52 was also observed on the TLR3-NFkB axis and this observation led to the discovery that IRAK-2 is recruited to TLR3 to activate NF-kB (Keating SE et al 2007). Thus, A52 possibly inhibits MyD88-independent TLR3 pathways to NF-kB via targeting IRAK-2 as it does for other IL-1R/TLR pathways, although it remains unclear how IRAK-2 is involved in TLR3 signaling.
IRAK-2 was shown to have two TRAF6 binding motifs that are responsible for initiating TRAF6 signaling transduction (Ye H et al 2002). R-HSA-975163 IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation Although IRAK-1 was originally thought to be a key mediator of TRAF6 activation in the IL1R/TLR signaling (Dong W et al. 2006), recent studies showed that IRAK-2, but not IRAK-1, led to TRAF6 polyubiquitination (Keating SE et al 2007). IRAK-2 loss-of-function mutants, with mutated TRAF6-binding motifs, could no longer activate NF-kB and could no longer stimulate TRAF-6 ubiquitination (Keating SE et al 2007). Furthermore, the proxyvirus protein A52 - an inhibitor of all IL-1R/TLR pathways to NF-kB activation, was found to interact with both IRAK-2 and TRAF6, but not IRAK-1. Further work showed that A52 inhibits IRAK-2 functions, whereas association with TRAF6 results in A52-induced MAPK activation. The strong inhibition effect of A52 was also observed on the TLR3-NFkB axis and this observation led to the discovery that IRAK-2 is recruited to TLR3 to activate NF-kB (Keating SE et al 2007). Thus, A52 possibly inhibits MyD88-independent TLR3 pathways to NF-kB via targeting IRAK-2 as it does for other IL-1R/TLR pathways, although it remains unclear how IRAK-2 is involved in TLR3 signaling.
IRAK-2 was shown to have two TRAF6 binding motifs that are responsible for initiating TRAF6 signaling transduction (Ye H et al 2002). R-HSA-5603041 IRAK4 deficiency (TLR2/4) Interleukin-1 receptor-associated kinase 4 (IRAK4) is a serine/threonine kinase, that mediates activation of transcriptional factors such as NFkB and AP1 downstream of IL-1 receptors and all toll like receptors (TLR) except for TLR3 (Suzuki N et al. 2002). IRAK4 is recruited to the TLR receptor complex through a homophilic interaction of the death domains of IRAK4 and adaptor myeloid differentiation factor 88 protein (MyD88) (Motshwene PG et al. 2009; Lin SC et al. 2010). Studies have identified patients with an autosomal recessive (AR) form of IRAK4 deficiency, a health condition with clinical manifestation in infancy or early childhood, that predisposes affected patients to recurrent pyogenic bacterial infection (e.g., Streptococcus pneumoniae and Staphylococcus aureus) (Picard C et al. 2003; Ku CL et al. 2007; Picard C et al. 2010; Picard C et al. 2011). Leukocytes derived from IRAK4-deficient patients display a lack of production of inflammatory cytokines such as TNF alpha, IL-6 and IL-1 beta by whole blood or a lack of CD62 ligand (CD62L) shedding from granulocytes following activation with the most TLR agonists including those of TLR1/2 (Pam3CSK4), TLR2/6 (Pam2CSK4) and TLR4 (LPS) (Picard C et al. 2003; McDonald DR et al. 2006; Ku CL et al. 2007). However, LPS-induced TLR4-mediated production of some cytokines (IL8 and MIP-1beta) was reduced but not abolished (Ku CL et al. 2007). LPS-stimulated induction of type I IFN via MyD88-IRAK4 independent signaling axis was normal or weakly affected suggesting that TLR4 could induce some responses in IRAK4 deficient patients(Yang K et al. 2005).
Patients with AR IRAK4 deficiency were found to bear homozygous or compound heterozygous mutations in the IRAK4 gene (Picard C et al. 2003; Ku CL et al. 2007; McDonald DR et al. 2006). Here we describe selected mutations, that have been functionally characterized. Cell-based assay as well as in vitro protein-interaction analyses with IRAK4 variants showed that the loss-of-function of defective IRAK4 is caused by either loss of protein production (reported for IRAK4 Q293* and E402*) or an impaired interaction with MyD88 as shown for missense mutation IRAK4 R12C (Ku CL et al. 2007; Yamamoto T et al. 2014).
Besides defective TLR2/4 mediated signaling, the Reactome module describes the impact of functional deficiency of IRAK4 on TLR5 pathways. The module does not include defective TLR7, TLR8 and TLR9 signaling events, which are associated mostly with viral infections, although studies using patient-derived blood cells showed abolished cytokine production by peripheral blood mononuclear cells (PBMCs) and lack of CD62 ligand (CD62L) shedding from granulocytes in response to TLR7-9 agonists (McDonald DR et al. 2006; von Bernuth H et al. 2006; Ku CL et al. 2007). In addition to the TLR-NFkappaB signaling axis, endosomic TLR7-9 activates IFN-alpha/beta and IFN-gamma responses and these are also impaired in IRAK4-deficient PBMC (Yang K et al. 2005). Nevertheless, IFN-alpha/beta and -gamma production in IRAK-4-deficient blood cells in response to 9 of 11 viruses was normal or weakly affected, suggesting that IRAK-4-deficient patients may control viral infections by TLR7-9-independent production of IFNs such as IRAK4-independent antiviral RIGI and MDA5 pathways (Yang K et al. 2005). So it is not yet possible to annotate a definitive molecular pathway between IRAK-4 deficiency and changes in TLR7-9 signaling. R-HSA-5603037 IRAK4 deficiency (TLR5) Toll like receptor 5 (TLR5) specifically recognizes bacterial infection through binding of flagellin from pathogenic bacteria. Upon ligand binding, TLR5 dimers recruit MyD88 through their TIR domains. Then, MyD88 oligomerizes via its death domain (DD) and TIR domain and interacts with the interleukin-1 receptor-associated kinases (IRAKs) to form the Myddosome complex (MyD88:IRAK4:IRAK1/2) (Motshwene PG et al. 2009; Lin SC et al. 2010). The Myddosome complex transmits the signal leading to activation of transcription factors such as nuclear factor-kappaB (NFkB) and activator protein 1 (AP1). Studies have identified patients with autosomal recessive (AR) form of IRAK4 deficiency, a health condition with clinical manifestation in infancy or early childhood, that predisposes affected patients to recurrent pyogenic bacterial infection (e.g., Streptococcus pneumoniae and Staphylococcus aureus) (Picard C et al. 2003; Ku CL et al. 2007; Picard C et al. 2010; Picard C et al. 2011). Leukocytes derived from IRAK4-deficient patients display a lack of production of inflammatory cytokines such as TNF alpha, IL-6 and IL-1beta or a lack of CD62 ligand (CD62L) shedding from granulocytes following activation with flagellin, the TLR5 agonist (Picard C et al. 2003; McDonald DR et al. 2006; Ku CL et al. 2007). Patients with AR IRAK4 deficiency were found to bear homozygous or compound heterozygous mutations in the IRAK4 gene (Picard C et al. 2003; Ku CL et al. 2007; McDonald DR et al. 2006). Here we describe selective mutations, that have been functionally characterized. Cell-based assays as well as in vitro protein-interaction analyses with IRAK4 variants showed that the loss-of-function of defective IRAK4 can be caused by either an abolished protein production as a result of nonsense mutations (e.g.,Q293* and E402*) or an impaired interaction with MyD88 due to missense mutations (e.g., R12C) (Ku CL et al. 2007; Yamamoto T et al. 2014).
IRAK4 mediates immune responses downstream of all TLRs except for TLR3. Besides defective TLR5 signaling, the Reactome module describes the impact of functional deficiency of IRAK4 on TLR2/4 signaling pathways. We did not include defective TLR7, TLR8 and TLR9 signaling events, which are stimulated by nucleic acids upon viral infections, although studies using patients-derived blood cells have showed abolished cytokines production by peripheral blood mononuclear cells (PBMCs) and lack of CD62 ligand (CD62L) shedding from granulocytes in response to TLR7-9 agonists, i.e.,3M-13 (TLR7), 3M-2 (TLR8), R848 (TLR7 and 8) and CpG (TLR9) (McDonald DR et al. 2006; von Bernuth H et al. 2006; Ku CL et al. 2007). In addition to TLR-NFkB signaling axis the endosomic TLR7-9 activate IFN-alpha/beta and IFN-gamma responses, which have been also impaired in IRAK4-deficient PBMC (Yang K et al. 2005). However, IFN-alpha/beta and IFN-gamma production in response to 9 of 11 viruses tested was normal or weakly affected in IRAK-4-deficient blood cells, suggesting that IRAK-4-deficient patients may control viral infections by TLR7-9-independent production of IFNs (Yang K et al. 2005). So it is not yet possible to annotate a definitive molecular pathway between IRAK-4 deficiency and changes in TLR7-9 signaling. R-HSA-381070 IRE1alpha activates chaperones IRE1-alpha is a single-pass transmembrane protein that resides in the endoplasmic reticulum (ER) membrane. The C-terminus of IRE1-alpha is located in the cytosol; the N-terminus is located in the ER lumen. In unstressed cells IRE1-alpha exists in an inactive heterodimeric complex with BiP such that BiP in the ER lumen binds the N-terminal region of IRE1-alpha. Upon accumulation of unfolded proteins in the ER, BiP binds the unfolded protein and the IRE1-alpha:BiP complex dissociates. The dissociated IRE1-alpha then forms homodimers. Initially the luminal N-terminal regions pair. This is followed by trans-autophosphorylation of IRE1-alpha at Ser724 in the cytosolic C-terminal region. The phosphorylation causes a conformational change that allows the dimer to bind ADP, causing a further conformational change to yield back-to-back pairing of the cytosolic C-terminal regions of IRE1-alpha. The fully paired IRE1-alpha homodimer has endoribonuclease activity and cleaves the mRNA encoding Xbp-1. A 26 residue polyribonucleotide is released and the 5' and 3' fragments of the original Xbp-1 mRNA are rejoined. The spliced Xbp-1 message encodes Xbp-1 (S), a potent activator of transcription. Xbp-1 (S) together with the ubiquitous transcription factor NF-Y bind the ER Stress Responsive Element (ERSE) in a number of genes encoding chaperones. Recent data suggest that the IRE1-alpha homodimer can also cleave specific subsets of mRNAs, including the insulin (INS) mRNA in pancreatic beta cells. R-HSA-1606341 IRF3 mediated activation of type 1 IFN Interferon regulatory factors (IRF) IRF-3 and IRF-7 are the major modulators of IFN gene expression in response to pathogenic molecules. The relative contribution of IRF3 and IRF7 depends on the signaling pathway that is activated. Type I IFN production in cytosolic DNA-sensing pathway is mediated predominantly by IRF3 and partially by IRF7, since DNA-stimulated IFN-beta and IFN-alpha4 mRNA induction was strongly inhibited in IRF3-deficient mouse embryonic fibroblasts (MEFs), while remained normal (IFN-beta) or reduced (IFN-alpha4) in IRF7-deficient MEFs (Takaoke A et al 2007). IRF3 activation in response to B-DNA stimulation occurs via its co-recruitment with serine/threonine kinase TANK-binding kinase 1 (TBK1) or inducible IkB kinase (IKKi/IKKepsilon) to the C-terminal region of DAI. R-HSA-3270619 IRF3-mediated induction of type I IFN TANK-binding kinase 1 (TBK1) and interferon regulatory factor 3 (IRF3) are central regulators of type-I interferon induction during bacterial or viral infection. TBK1 was found to form complexes with distinct scaffolding proteins that appeared to target TBK1 to different subcellular compartments [Hemmi H et al 2004; Oganesyan G et al 2006; Chariot A et al 2002; Huang J et al 2005]. STING interacted with both TBK1 and IRF3. Once STING is stimulated, its C-terminus served as a signaling scaffold to recruit IRF3 anhd TBK1, which led to TBK1-dependent phosphorylation of IRF3. Phosphorylation of IRF3 promoted its dimerization and translocation to the nucleus, where it triggered the transcription of interferon stimulated genes (ISGs) (Tanaka Y and Chen ZJ 2012). R-HSA-74713 IRS activation IRS is one of the mediators of insulin signalling events. It is activated by phosphorylation and triggers a cascade of events involving PI3K, SOS, RAF and the MAP kinases. The proteins mentioned under IRS are examples of IRS family members acting as indicated. More family members are to be confirmed and added in the future. Using receptor mutagenesis studies it is known that IRS1 via its PTB domain binds to the insulin receptor at the juxtamembrane region at tyrosine 972. The interaction is further stabilized by the PH domain of IRS1 which interacts with the phospholipids of the plasma membrane. This allows the receptor to phosphorylate IRS1 on up to 13 of its tyrosine residues. Once phosphorylated the IRS1 falls away from the receptor. Now in a tyrosine phosphorylated and hence activated state other proteins can interact with the IRS proteins. R-HSA-112399 IRS-mediated signalling Release of phospho-IRS from the insulin receptor triggers a cascade of signalling events via PI3K, SOS, RAF and the MAP kinases. R-HSA-2428928 IRS-related events triggered by IGF1R The phosphorylated type 1 insulin-like growth factor receptor phosphorylates IRS1, IRS2, IRS4 and possibly other IRS/DOK family members (reviewed in Pavelic et al. 2007, Chitnis et al. 2008, Maki et al. 2010, Parrella et al. 2010, Siddle et al. 2012). The phosphorylated IRS proteins serve as scaffolds that bind the effector molecules PI3K and GRB2:SOS. PI3K then activates PKB (AKT) signaling while GRB2:SOS activates RAS-RAF-MAPK signaling. R-HSA-1169408 ISG15 antiviral mechanism Interferon-stimulated gene 15 (ISG15) is a member of the ubiquitin-like (Ubl) family. It is strongly induced upon exposure to type I Interferons (IFNs), viruses, bacterial LPS, and other stresses. Once released the mature ISG15 conjugates with an array of target proteins, a process termed ISGylation. ISGylation utilizes a mechanism similar to ubiquitination, requiring a three-step enzymatic cascade. UBE1L is the ISG15 E1 activating enzyme which specifically activates ISG15 at the expense of ATP. ISG15 is then transfered from E1 to the E2 conjugating enzyme UBCH8 and then to the target protein with the aid of an ISG15 E3 ligase, such as HERC5 and EFP. Hundreds of target proteins for ISGylation have been identified. Several proteins that are part of antiviral signaling pathways, such as RIG-I, MDA5, Mx1, PKR, filamin B, STAT1, IRF3 and JAK1, have been identified as targets for ISGylation. ISG15 also conjugates some viral proteins, inhibiting viral budding and release. ISGylation appears to act either by disrupting the activity of a target protein and/or by altering its localization within the cell. R-HSA-5603029 IkBA variant leads to EDA-ID The nuclear factor kappa B (NFkB) family of transcription factors is kept inactive in the cytoplasm by the inhibitor of kappa B (IkB) family members IKBA (IkB alpha, NFKBIA), IKBB (IkB beta, NFKBIB) and IKBE (IkB epsilon, NFKBIE) (Oeckinghaus A and Ghosh S 2009). Multiple stimuli such as inflammatory cytokines, microbial products or various types of stress activate NFkB signaling leading to stimuli-induced phosphorylation of IkB molecule (Scherer DC et al. 1995; Alkalay I et al. 1995; Lawrence T 2009; Hoesel B and Schmid JA 2013). The phosphorylation of IkB proteins triggers their polyubiquitination and subsequent degradation by 26S proteasome, allowing free NFkB dimer to translocate to the nucleus where it directs the expression of target genes. Studies have identified an autosomal dominant form of ectodermal dysplasia with immunodeficiency (AD-EDA-ID) caused by a hypermorphic heterozygous mutation of NFKBIA/IKBA gene. The IKBA defects prevent the phosphorylation and degradation of IKBA protein resulting in gain-of-function condition with the enhanced inhibitory capacity of IKBA in sequestering NF?B dimers in the cytoplasm (Courtois G et al. 2003; Lopes-Granados E et al. 2008; Schimke LF et al. 2013). R-HSA-9669917 Imatinib-resistant KIT mutants Imatinib is approved for treatment of cancers carrying primary mutations in the KIT receptor. Imatinib binds and inhibits the inactive state of the receptor, including the conformation promoted by exon 11 mutations that relieve the auto-inhibition of the WT protein. Resistance to imatinib arises due to the polyclonal expansion of subpopulations bearing secondary KIT mutations in the ATP binding pocket or the activation loop of the protein (Serrano et al, 2019; reviewed in Roskoski, 2018; Klug et al, 2018; Corless et al, 2011). R-HSA-9674396 Imatinib-resistant PDGFR mutants A number of PDGFRA mutations found in GIST and other cancers are resistant to inhibition with imatinib (reviewed in Corless et al, 2011). These include the most common allele D842V, which occurs in the activation loop of the receptor, as well as S601P and the gatekeeper mutation T674I (reviewed in Roskoski, 2018; Klug et al, 2018). R-HSA-168256 Immune System Humans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first critical hours and days of exposure to a new pathogen, our innate immune system. R-HSA-198933 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell A number of receptors and cell adhesion molecules play a key role in modifying the response of cells of lymphoid origin (such as B-, T- and NK cells) to self and tumor antigens, as well as to pathogenic organisms.
Molecules such as KIRs and LILRs form part of a crucial surveillance system that looks out for any derangement, usually caused by cancer or viral infection, in MHC Class I presentation. Somatic cells are also able to report internal functional impairment by displaying surface stress markers such as MICA. The presence of these molecules on somatic cells is picked up by C-lectin NK immune receptors.
Lymphoid cells are able to regulate their location and movement in accordance to their state of activation, and home in on tissues expressing the appropriate complementary ligands. For example, lymphoid cells may fine tune the presence and concentration of adhesion molecules belonging to the IgSF, Selectin and Integrin class that interact with a number of vascular markers of inflammation.
Furthermore, there are a number of avenues through which lymphoid cells may interact with antigen. This may be presented directly to a specific T-cell receptor in the context of an MHC molecule. Antigen-antibody complexes may anchor to the cell via a small number of lymphoid-specific Fc receptors that may, in turn, influence cell function further. Activated complement factor C3d binds to both antigen and to cell surface receptor CD21. In such cases, the far-reaching influence of CD19 on B-lymphocyte function is tempered by its interaction with CD21.
R-HSA-9709603 Impaired BRCA2 binding to PALB2 This pathway describes BRCA2 missense mutations that affect the N-terminus of BRCA2 and impair the ability of BRCA2 to bind PALB2, which is a crucial step in homologous recombination repair (HRR) of DNA double-strand breaks (DSBs) (Xia et al. 2006).
R-HSA-9709570 Impaired BRCA2 binding to RAD51 A critical function of BRCA2 is to bind RAD51 and nucleate RAD51 filament formation on single-stranded DNA. BRCA2 has two regions that interact with RAD51: 8 BRC repeats encoded by exon11 (Bork et al. 1996, Wong et al. 1997) and a C-terminal RAD51 binding domain called TR2 (Sharan et al. 1997).
R-HSA-9763198 Impaired BRCA2 binding to SEM1 (DSS1) This pathway describes BRCA2 cancer mutations that affect the ability of BRCA2 to bind to SEM1 (DSS1), a small protein of 70 amino acids that regulates BRCA2 stability and its nuclear localization (reviewed in Le et al. 2021).
R-HSA-9709275 Impaired BRCA2 translocation to the nucleus This pathway describes truncating mutations in BRCA2 that result in mutant proteins lacking nuclear localization signals (NLSs) in the C-terminal domain. These truncated BRCA2 proteins mainly localize to the cytosol, impairing the ability of BRCA2 mutants to participate in homologous recombination repair (HRR) in the nucleus. Truncating mutations are the most frequent BRCA2 mutations detected in cancer (Spain et al. 1999, Yano et al. 2000, Ma et al. 2017).
R-HSA-141430 Inactivation of APC/C via direct inhibition of the APC/C complex In the direct inhibition model, the cytosolic Mitotic Checkpoint Complex, consisting of hBUBR1, hBUB3, Cdc20 and Mad2, directly inhibits APC/C by binding to it.
R-HSA-428543 Inactivation of CDC42 and RAC1 Rho family GTPases, including RAC1, RHOA, and CDC42, are ideal candidates to regulate aspects of cytoskeletal dynamics downstream of axon guidance receptors. Biochemical and genetic studies have revealed an important role for CDC42 and RAC1 in ROBO repulsion. ROBO controls the activity of Rho GTPases by interacting with a family of SLIT/ROBO-specific GAPs (SrGAPs) and Vilse/CrossGAP. SrGAPs inactivate CDC42 and Vilse/CrossGAP specifically inactivates RAC1.
It was recently implicated that SRGAP3 may inactivate RAC1 downstream of SLIT1-activated ROBO2, which promotes neurite outgrowth in mammalian dorsal root ganglion (DRG) neurons (Zhang et al. 2014).
R-HSA-9705462 Inactivation of CSF3 (G-CSF) signaling Signaling by CSF3 causes its own inactivation, thereby preventing overproliferation of neutrophils (reviewed in Beekman and Touw 2010, Palande et al. 2013). Activated CSF3R recruits and activates JAK2, which phosphorylates STAT1, STAT3, and STAT5. The phosphorylated STATs transit to the nucleus and enhance the expression of SOCS1 and SOCS3, inhibitors of CSF3R signaling (inferred from mouse homologs). SOCS3, the principle negative regulator, binds the phosphorylated C-terminal region of CSF3R (Hörtner et al. 2002, van de Geijn et al. 2004, and inferred from mouse homologs) and acts in two ways: direct inhibition of the phosphorylation activity of JAK2 (van de Geijn et al. 2004) and promotion of endocytosis (Ward et al. 1999, Aarts et al. 2004, Irandoust et al. 2007) and ubiquitination (Irandoust et al. 2007, Wölfler et al. 2009) of CSF3R.
R-HSA-2514859 Inactivation, recovery and regulation of the phototransduction cascade To terminate the single photon response and restore the system to its basal state, the three activated intermediates in phototransduction, rhodopsin (MII), transducin alpha subunit with GTP bound (GNAT1-GTP) and phosphodiesterase 6 (PDE6) all need to be efficiently deactivated. In addition, the cGMP concentrations must be restored to support reopening of the CNG channels. This section describes the inactivation and recovery events of the activated intermediates involved in phototransduction (Burns & Pugh 2010, Korenbrot 2012).
R-HSA-400508 Incretin synthesis, secretion, and inactivation Incretins are peptide hormones produced by the gut that enhance the ability of glucose to stimulate insulin secretion from beta cells in the pancreas. Two incretins have been identified: Glucagon-like Peptide-1 (GLP-1) and Glucose-dependent Insulinotropic Polypeptide (GIP, initially named Gastric Inhibitory Peptide). Both are released by cells of the small intestine, GLP-1 from L cells and GIP from K cells.
The control of incretin secretion is complex. Fatty acids, phospholipids, glucose, acetylcholine, leptin, and Gastrin-releasing Peptide all stimulate secretion of GLP-1. Fatty acids and phospholipids are the primary stimulants of secretion of GIP in humans (carbohydrates have more effect in rodents).
Incretins secreted into the bloodstream are subject to rapid inactivation by Dipeptidyl Peptidase IV (DPP IV), which confers half-lives of only a few minutes onto GLP-1 and GIP. Inhibitors of DPP IV, for example sitagliptin, are now being used in the treatment of Type 2 diabetes.
R-HSA-9733458 Induction of Cell-Cell Fusion Many enveloped viruses induce multinucleated cells (syncytia) in later stages of viral infection. The membrane fusion that drives these cell-cell fusion events are caused by the same machinery that underlies viral entry. The presence of infected syncytial pneumocytes in severe COVID-19 patients is well established (Zhang et al., 2021). However, it is currently unclear if syncytia formation is also a feature of milder or asymptomatic SARS-CoV-2 infections. These syncytia are also thought to facilitate replication and evasion of the host immune response (for a recent review on Spike-mediated fusion and syncytia formation see Rajah et al, 2022). Experiments that utilize co-cultures of human cells expressing the receptor ACE2 with cells expressing SARS-CoV-2 spike protein, result in synapse-like intercellular contacts that initiate cell-cell fusion, producing syncytia resembling those we identify in lungs of COVID-19 patients (Sanders et al., 2021). Studies on SARS-CoV-2 identified similar syncytia (Buchrieser et al., 2020; Hoffmann et al., 2020a; Ou et al., 2020; Xia et al., 2020). Formation of the ACE2/spike protein complex drives fusion events that proceed from finger-like projections, forming synapses between cells to development of a fusion pore and subsequent membrane fusion (reviewed in Rajah et al, 2022; Rey, 2021). Notably cleaving the spike protein into S1 and S2 sub-fragments appears to increase the probability of S1/ACE2 fusion (Hoffmann et al., 2020a).
The Alpha, Beta, and Delta variants of SARS-CoV-2 display enhanced syncytia formation (Cheng et al, 2021; Rajah et al, 2021). An additional phenomenon with SARS-CoV-2 syncytia is their targeting of lymphocytes for internalization and cell-in-cell mediated elimination, potentially contributing to lymphopenia and pathogenesis in COVID-19 patients (Zhang et al, 2021).
R-HSA-9635486 Infection with Mycobacterium tuberculosis Infection with Mycobacterium tuberculosis (Mtb) is soon countered by the host's immune system, the organism is however almost never eradicated; ten per cent of infections will develop into "open tuberculosis", while the other ninety per cent become "latent", a state that can persist for decades until loss of immune control. Approximately 25% of the world's population is estimated to harbour latent tuberculosis. Latent infection involves the bacterium being internalized by phagocytes where it stops and counters the innate immune answer (Russell 2011, Russell et al. 2010). When a status-quo is reached, Mtb enters a non-replicating persistent state (Barry et al. 2009, Boshoff & Barry 2005). Weakening of the immune defense sooner or later enables the waking up and multiplication of the bacterium inside the phagocyte, necrosis of the cell, and escape, analogous to the burst of lytic viruses (Repasy 2013).
R-HSA-5663205 Infectious disease Infectious diseases are ones due to the presence of pathogenic microbial agents in human host cells. Processes annotated in this category include bacterial, viral and parasitic infection pathways.
Bacterial infection pathways currently include some metabolic processes mediated by intracellular Mycobacterium tuberculosis, the actions of clostridial, anthrax, and diphtheria toxins, and the entry of Listeria monocytogenes into human cells.
Viral infection pathways currently include the life cycles of SARS-CoV viruses, influenza virus, HIV (human immunodeficiency virus), and human cytomegalovirus (HCMV).
Parasitic infection pathways currently include Leishmania infection-related pathways.
Fungal infection pathways and prion diseases have not been annotated.
R-HSA-622312 Inflammasomes In contrast to NOD1/2 some NLRPs function as large macromolecular complexes called 'Inflammasomes'. These multiprotein platforms control activation of the cysteinyl aspartate protease caspase-1 and thereby the subsequent cleavage of pro-interleukin 1B (pro-IL1B) into the active proinflammatory cytokine IL1B. Activation of caspase-1 is essential for production of IL1B and IL18, which respectively bind and activate the IL1 receptor (IL1R) and IL18 receptor (IL18R) complexes. IL1R and IL18R activate NFkappaB and other signaling cascades.
As the activation of inflammasomes leads to caspase-1 activation, inflammasomes can be considered an upstream step of the IL1R and IL18R signaling cascades, linking intracellular pathogen sensing to immune response pathways mediated by Toll-Like Receptors (TLRs). Monocytes and macrophages do not express pro-IL1B until stimulated, typically by TLRs (Franchi et al. 2009). The resulting pro-IL1B is not converted to IL1B unless a second stimulus activates an inflammasome. This requirement for two distinct stimuli allows tight regulation of IL1B/IL18 production, necessary because excessive IL-1B production is associated with numerous inflammatory diseases such as gout and rheumatoid arthritis (Masters et al. 2009).
There are at least four subtypes of the inflammasome, characterized by the NLRP. In addition the protein AIM2 can form an inflammasome. All activate caspase-1. NLRP1 (NALP1), NLRP3 (Cryopyrin, NALP3), IPAF (CARD12, NLRC4) and AIM2 inflammasomes all have clear physiological roles in vivo. NLRP2, NLRP6, NLRP7, NLRP10 and NLRP12 have been demonstrated to modulate caspase-1 activity in vitro but the significance of this is unclear (Mariathasan and Monack, 2007).
NLRP3 and AIM2 bind the protein 'apoptosis-associated speck-like protein containing a CARD' (ASC, also called PYCARD), via a PYD-PYD domain interaction. This in turn recruits procaspase-1 through a CARD-CARD interaction. NLRP1 and IPAF contain CARD domains and can bind procaspase-1 directly, though both are stimulated by ASC. Oligomerization of NLRPs is believed to bring procaspases into close proximity, leading to 'induced proximity' auto-activation (Boatright et al. 2003). This leads to formation of the active caspase tetramer. NLRPs are generally considered to be cytoplasmic proteins, but there is evidence for cytoplasmic-nuclear shuttling of the family member CIITA (LeibundGut-Landmann et al. 2004) and tissue/cell dependent NALP1 expression in the nucleus of neurons and lymphocytes (Kummer et al. 2007); the significance of this remains unclear.
R-HSA-168255 Influenza Infection For centuries influenza epidemics have plagued man; with influenza probably being the disease described by Hippocrates in 412 BC. Today it remains a major cause of morbidity and mortality worldwide with large segments of the human population affected every year. Many animal species can be infected by influenza viruses, often with catastrophic consequences. An influenza pandemic is a continuing global level threat. The 1918 influenza pandemic is a modern example of how devastating such an event could be with an estimated 50 million deaths worldwide.
Influenza viruses belong to the family of Orthomyxoviridae; viruses with segmented RNA genomes that are negative sense and single-stranded (Baltimore 1971). Influenza virus strains are named according to their type (A, B, or C), the species from which the virus was isolated (omitted if human), location of isolate, the number of the isolate, the year of isolation, and in the case of influenza A viruses, the hemagglutinin (H) and neuraminidase (N) subtype. For example, the virus of H5N1 subtype isolated from chickens in Hong Kong in 1997 is: influenza A/chicken/Hong Kong/220/97(H5N1) virus. Currently 16 different hemagglutinin (H1 to H16) subtypes and 9 different neuraminidase (N1 to N9) subtypes are known for influenza A viruses. Most human disease is due to influenza viruses of the A type. The events of influenza infection have been annotated in Reactome primarily use protein and genome references to the Influenza A virus A/Puerto Rico/8/1934 H1N1 strain. The influenza virus particle initially associates with a human host cell by binding to sialic acid receptors on the host cell surface. Sialic acids are found on many vertebrate cells and numerous viruses make use of this ubiquitous receptor. The bound virus is endocytosed by one of four distinct mechanisms. Once endocytosed the low endosomal pH sets in motion a number of steps that lead to viral membrane fusion mediated by the viral hemagglutinin (HA) protein, and the eventual release of the uncoated viral ribonucleoprotein complex into the cytosol of the host cell. The ribonucleoprotein complex is transported through the nuclear pore into the nucleus. Once in the nucleus, the incoming negative-sense viral RNA (vRNA) is transcribed into messenger RNA (mRNA) by a primer-dependent mechanism. Replication occurs via a two step process. A full-length complementary RNA (cRNA), a positive-sense copy of the vRNA, is first made and this in turn is used as a template to produce more vRNA. The viral proteins are expressed and processed and eventually assemble with vRNAs at what will become the budding sites on the host cell membrane. The viral protein and ribonucleoprotein complexes are assembled into complete viral particles and bud from the host cell, enveloped in the host cell's membrane.
Infection of a human host cell with influenza virus triggers an array of defensive host processes. This coevolution has driven the development of host processes that interfere with viral replication, notably the production of type I interferon. At the some time the virus counters these responses with the viral NS1 protein playing a central role in the viral response to the host cells defense.
R-HSA-168273 Influenza Viral RNA Transcription and Replication In the host cell nucleus, the viral negative-strand RNA (vRNA) serves as a template for the synthesis both of capped, polyadenylated viral messenger RNA and of full-length positive-strand RNA or complementary RNA (cRNA). The cRNA is associated with the same viral proteins as the vRNA. It serves as a template for the synthesis of new vRNA molecules, which in turn serve as a template for mRNA particularly early in infection, and cRNA. Viral RNA polymerase subunits (PB1, PB2, and PA) and nucleoprotein (NP) enter the host cell nucleus and catalyze all three of these reactions. During initial infection, these proteins enter the nucleus as part of the viral RNP complex. After the first round of viral mRNA synthesis (primary transcription) and translation, newly synthesized viral polymerase proteins and NP localize to the nucleus to catalyze further mRNA transcription and vRNA/cRNA replication. Late in the infection process, the synthesis of vRNA and nuclear export of newly synthesized vRNP (vRNA complexed with NP and viral polymerase) is increased relative to transcription (Krug, 1981; Braam, 1983; Kawakami, 1983; Huang, 1990; Cros, 2003; Fodor, 2004; Deng, 2005; Amorim, 2006; reviewed in Neumann, 2004; Engelhardt, 2006; Buolo, 2006).
R-HSA-168277 Influenza Virus Induced Apoptosis Influenza A virus induces apoptosis in a variety of ways including activation of host TGF-beta by expression of viral NA, M1 and M2 proteins, and by the binding of viral PB1-F2 to host mitochondrial adenine nucleotide translocator 3 (ANT3).
R-HSA-997272 Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits GABA B receptors are coupled to Gproteins and function by increasing the K+ and decreasing the Ca2+ inside the cell. The increase in K+ increases the negative membrane potential of the cell thereby hyper polarizing the cell which inhibits the release of neurotransmitters. The decrease in Ca2+ also inhibits neurotransmitter in two ways; first by preventing the fusion of synaptic vesicles containing the neurotransmitter with the plasma membrane and second by decreasing the Ca2+ dependent recruitment of synaptic vesicles to the plasma membrane. In particular GABA B receptors inhibit voltage gated Ca2+ channels via the activity of Gbeta/Ggamma subunits of G proteins.
R-HSA-9670095 Inhibition of DNA recombination at telomere Telomeres resemble double strand DNA breaks (DSBs) and, if not properly packaged and protected, are recognized by the DNA double strand break repair (DSBR) machinery. Initiation of DSB signaling at telomeres due to replicative shortening of telomeres is one of the triggers of cellular senescence, which can also be triggered by other cellular stressors, such as oxidative stress, and oncogenic signaling-induced mitotic arrest. The loss of telomere protection can result in telomere fusions via non-homologous end joining (NHEJ) of microhomology-mediated end joining (MMEJ). Loss of telomere protection accompanied by changes in the organization of telomeric chromatin (O'Sullivan et al. 2014) can trigger extension of telomeres via homologous recombination repair-mediated alternative lengthening of telomeres (ALT). ALT occurs in about 5-15% of cancers and is a telomerase-independent mechanism of replicative immortality. For review, please refer to Arnoult and Karlseder 2015 and Pickett and Reddel 2015.
R-HSA-168315 Inhibition of Host mRNA Processing and RNA Silencing The Influenza Virus NS1 protein inhibits the cleavage and polyadenylation specificity factor CPSF and the PABII components of the host cell 3' end processing machinery, preventing efficient 3' end processing of host pre-mRNAs. NS1 also inhibits the splicing of pre-mRNAs, resulting in their retention within the host cell nucleus.
R-HSA-168888 Inhibition of IFN-beta Since the presence of intracellular dsRNA serves as the signal for virus infection and triggers host interferon (IFN) synthesis the simplest model for viral NS1 protein function is that it sequesters dsRNA and thus prevents the downstream signaling required to activate IRF-3, NF-kB and AP-1. These findings are strongly supported by mutational analyses of NS1 that indicate that the IFN antagonist properties of NS1 depend on its ability to bind dsRNA. However, a compensatory mutation (S42G), which was acquired during the passaging of the mutant RNA-binding virus, results in partial restoration of wild-type phenotype but does not restore RNA binding. This indicates that the ability of NS1 to inhibit IFN synthesis is not solely dependent on dsRNA binding and that additional mechanisms may be involved.
R-HSA-168305 Inhibition of Interferon Synthesis Interferon Synthesis is inhibited.
R-HSA-169131 Inhibition of PKR The key role played by PKR in the innate response to virus infection is emphasized by the large number of viruses that encode PKR inhibitors.
R-HSA-5638303 Inhibition of Signaling by Overexpressed EGFR Recombinant monoclonal antibody Cetuximab acts as an antagonist of EGFR ligand binding, and is approved for the treatment of tumors that over-express wild-type EGFR receptor (Cunningham et al. 2004, Li et al. 2005, Burtness et al. 2005). Effective concentrations of covalent tyrosine kinase inhibitors (TKIs) inhibit wild-type EGFR, causing severe side effects (Zhou et al. 2009). Hence, covalent TKIs have not shown much promise in clinical trials (Reviewed by Pao and Chmielecki in 2010).
R-HSA-165181 Inhibition of TSC complex formation by PKB Phosphorylation of TSC2 by PKB disrupts TSC1/TSC2 heterodimer formation (Hay & Sonenberg 2004). TSC2 function is affected in at least two ways: first, phosphorylation decreases the activity of TSC2; second, phosphorylation destabilizes the TSC2 protein. This destabilization is achieved by disrupting complex formation between TSC1 and TSC2 and inducing ubiquination of the free TSC2 (Inoki et al. 2002). Phosphorylation of complexed TSC2 by PKB may result in the dissociation of the TSC1:TSC2 complex (Proud 2002).
R-HSA-9635644 Inhibition of membrane repair When the phagosomal membrane is injured, this is sensed and acted upon both by the host phagocyte and Mtb. While the host repair system is activated, the bacterium is secreting proteins that block host repair components, effectively inhibiting repair (Mittal et al. 2018).
R-HSA-9636249 Inhibition of nitric oxide production Phagocytes produce nitric oxide to damage interned bacteria before fusion of the phagosome with lysosomes. While Mtb has several pathways to neutralize NO it also attempts to block the host enzymes used for NO production (Fang 2004, Bhat 2017).
R-HSA-113501 Inhibition of replication initiation of damaged DNA by RB1/E2F1 During S phase of the cell cycle, RB1 is dephosphorylated by the PP2A protein phosphatase complex. Unphosphorylated RB1 associates with DNA damage sites in S phase, preventing initiation of DNA replication from these sites (Knudsen et al. 2000, Avni et al. 2003).
R-HSA-141405 Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components The target of the mitotic checkpoint is the Anaphase Promoting Complex/Cyclosome (APC/C) an E3 ubiquitin ligase that targets proteins whose destruction is essential for mitotic exit. Currently, there are two proposed mechanism by which inhibition of the APC/C is achieved. These mechanisms differ depending on the mechanism of signal transduction. The APC/C may be inhibited directly by association with the Mitotic Checkpoint Complex (MCC) or through the sequestration of its activator, Cdc20.
R-HSA-166663 Initial triggering of complement Complement activation is due to a cascade of proteolytic steps, performed by serine protease domains in some of the components. Three different pathways of activation are distinguished triggered by target-bound antibody (the classical pathway); microbial polysaccharide structures (the lectin pathway); or recognition of other "foreign" surface structures (the alternative pathway) by C3b. All three merge in the pivotal activation of C3 and, subsequently, of C5 by highly specific enzymatic complexes, the so-called C3/C5 convertases. A complement system with three C3 activation pathways and a common lytic pathway is found only in jawed vertebrates.
R-HSA-2995383 Initiation of Nuclear Envelope (NE) Reformation Reassembly of the nuclear envelope (NE) is initiated at late anaphase/early telophase when BANF1 (BAF), which is dispersed throughout the cytoplasm during metaphase, accumulates on the surfaces of coalesced chromosomes. This is coordinated with the chromatin association of membranes and inner nuclear membrane proteins that include EMD (emerin), TMPO (LAP2beta), LEMD3 (MAN1) and LEMD2 (LEM2), and lamins (Haraguchi et al. 2008, reviewed by Wandke and Kutay 2013). The DNA-cross-bridging activity of BANF1 is required for individual chromosomes to properly coalesce for enclosure in a single nucleus (Samwer et al. 2017).
R-HSA-8876493 InlA-mediated entry of Listeria monocytogenes into host cells The pathogenic bacteria Listeria monocytogenes can enter host cells through endocytosis triggered by binding of the bacterial cell wall protein internalin (InlA) to the E-cadherin (CDH1) complex at the host cell plasma membrane (Mengaud et al. 1996, Lecuit et al. 1999). Binding of InlA to CDH1, similar to CDH1 engagement during normal cell-to-cell adhesion, triggers activation of the SRC protein tyrosine kinase and phosphorylation of CDH1 and CDH1-bound beta-catenin (CTNNB1) (Fujita et al. 2002, McLachlan et al. 2007, Sousa et al. 2007, Bonazzi et al. 2008). Integrins likely contribute to CDH1-triggered SRC activation, and ERKs (MAPK1 and MAPK3), ROCKs and MLCK may also be involved (Avizienyte et al. 2002, Avizienyte et al. 2004, Martinez-Rico et al. 2010). FAK1 (PTK2), a SRC-regulated protein tyrosine kinase, may contribute to SRC-mediated regulation of CDH1 (Avizienyte et al. 2002).
Phosphorylation of CDH1 and CTNNB1 by SRC creates docking sites for a CBL-like ubiquitin protein ligase Hakai (CBLL1). CBLL1 ubiquitinates SRC-phosphorylated CDH1 and CTNNB1 upon InlA binding, as well as in the context of CDH1-mediated cell-to-cell adhesion, thus triggering CDH1 endocytosis (Fujita et al. 2002, Bonazzi et al. 2008, Mukherjee et al. 2012).
CBLL1 may also undergo SRC-mediated phosphorylation and subsequent autoubiquitination (Fujita et al. 2002).
Both clathrin-mediated and caveolin-mediated endocytosis are implicated in the InlA-mediated entry of Listeria monocytogenes to host cells (Veiga et al. 2007). SRC-mediated phosphorylation of cortactin and the ARP2/3 complex involved in actin polymerization is implicated in CDH1 endocytosis and Listeria monocytogenes internalization (Sousa et al. 2007, Ren et al. 2009).
R-HSA-8875360 InlB-mediated entry of Listeria monocytogenes into host cell InlB, a cell wall protein of Listeria monocytogenes, binds MET receptor, acting as an HGF agonist (Shen et al. 2000, Veiga and Cossart 2005). Listeria monocytogenes InlB proteins dimerize through their leucine-rich repeat regions (LRRs), promoting dimerization of MET receptors that they are bound to (Ferraris et al. 2010). InlB-induced MET receptor dimerization is followed by MET trans-autophosphorylation and activation of downstream RAS/RAF/MAPK signaling and PI3K/AKT signaling (Niemann et al. 2007, Ferraris et al. 2010). InlB-bound phosphorylated MET receptor recruits the E3 ubiquitin ligase CBL through GRB2. CBL-mediated monoubiquitination of InlB-bound MET promotes endocytosis and entry of Listeria monocytogenes to host cells (Veiga and Cossart 2005). CIN85 is necessary for endocytosis-mediated entry of Listeria monocytogenes triggered by CBL-mediated monoubiquitination of MET (Veiga and Cossart 2005). Proteins involved in clathrin-mediated endocytosis EPS15 and HGS (Hrs) are both necessary for CBL and MET-mediated entry of Listeria monocytogenes into host cells (Veiga and Cossart 2005).
A potential coreceptor role of CD44 in InlB-mediated MET activation is contradictory (Jung et al. 2009, Dortet et al. 2010).
R-HSA-168249 Innate Immune System Innate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
R-HSA-1483249 Inositol phosphate metabolism Inositol phosphates (IPs) are molecules involves in signalling processes in eukaryotes. myo-Inositol consists of a six-carbon cyclic alcohol with an axial 2-hydroxy and five equatorial hydroxyls. Mono-, di-, and triphosphorylation of the inositol ring generates a wide variety of stereochemically distinct signalling entities. Inositol 1,4,5-trisphosphate (I(1,4,5)P3), is formed when the phosphoinositide phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is hydrolysed by a phospholipase C isozyme. An array of inositol trisphosphate (IP3) and tetrakisphosphate (IP4) molecules are synthesised by the action of various kinases and phosphatases in the cytosol. These species then transport between the cytosol and the nucleus where they are acted on by inositol polyphosphate multikinase (IPMK), inositol-pentakisphosphate 2-kinase (IPPK), inositol hexakisphosphate kinase 1 (IP6K1) and 2 (IP6K2), to produce IP5, IP6, IP7, and IP8 molecules. Some of these nuclear produced IPs transport back to the cytosol where they are converted to an even wider variety of IPs, by kinases and phosphatases, including the di- and triphospho inositol phosphates aka pyrophosphates (Irvine & Schell 2001, Bunney & Katan 2010, Alcazar-Romain & Wente 2008, York 2006, Monserrate and York 2010).
R-HSA-429593 Inositol transporters Myo-Inositol is a neutral cyclic polyol, abundant in mammalian tissues. It plays important roles; it is a precursor to phosphatidylinositols (PtdIns) and to the inositol phosphates (IP), which serve as second messengers and as key regulators of many cell functions. It can also serve as a compatible osmolyte during volume regulation in many tissues where cells are exposed to hyperosmotic conditions. Three members of the glucose transporter families are inositol transporters. Two (SMIT1 and SMIT2) couple myo-inositol transport with two Na+ ions. Unlike SMIT1, SMIT2 also transports D-chiro_inositol. The third transporter (HMIT), couples myo-inositol transport with a proton.
R-HSA-9609523 Insertion of tail-anchored proteins into the endoplasmic reticulum membrane Tail-anchored (TA) proteins have a hydrophobic transmembrane domain (TMD) located near the C-terminus ("tail") of the protein. Depending on the nature of the TMD, TA proteins can be inserted into the endoplasmic reticulum (ER) membrane by at least 4 mechanisms: cotranslational insertion by the signal recognition particle (SRP), post-translational insertion by ASNA1 (TRC40), post-translational insertion by the SRP, and post-translational insertion by a SRP-independent mechanism (SND) (Casson et al. 2017, reviewed in Borgese and Fasana 2011, Casson et al. 2016, Aviram et al. 2016, Chio et al. 2017). Much of the information about the mammalian system of insertion by ASNA1 (TRC40) has been inferred from the Saccharomyces cerevisiae homologue Get3.
Prior to post-translational insertion by ASNA1, SGTA binds the transmembrane domain of the substrate TA protein immediately after translation (Leznicki et al. 2011, Leznicki and High 2012, Xu et al. 2012, Wunderly et al. 2014, Shao et al. 2017), the SGTA:TA protein complex then binds the BAG6 complex (BAG6:GET4:UBL4A) via UBL4A (Winnefeld et al. 2006, Chartron et al. 2012, Xu et al. 2012, Leznicki et al. 2013, Mock et al. 2015, Kuwabara et al. 2015, Shao et al. 2017), and the TA protein is transferred to ASNA1 (Mariappan et al. 2010, Leznicki et al. 2011, Shao et al. 2017), also bound by the BAG6 complex via UBL4A. The ASNA1:TA protein complex then docks at the WRB:CAMLG (WRB:CAML) complex located in the ER membrane and the TA protein is inserted into the ER membrane by an uncharacterized mechanism that involves ATP and the transmembrane domain insertase activity of the WRB:CAML complex (Vilardi et al. 2011, Vilardi et al. 2014, Vogl et al. 2016, and inferred from yeast in Wang et al. 2014).
Misfolded TA proteins, overexpressed TA proteins, and membrane proteins mislocalized in the cytosol bind SGTA but are not efficiently transferred to ASNA1 and, instead, are retained by BAG6 which recruits RNF126 to ubiquitinate them, targeting them for degradation by the proteasome (Wang et al. 2011, Leznicki and High 2012, Xu et al. 2012, Rodrigo-Brenni et al. 2014, Wunderly et al. 2014, Shao et al. 2017, reviewed in Lee and Ye 2013, Casson et al. 2016, Krysztofinska et al. 2016, Guna and Hegde 2018).
R-HSA-163754 Insulin effects increased synthesis of Xylulose-5-Phosphate One of the downstream effects of insulin, mediated via protein phosphatase 2A (PP2A), is increased synthesis of Fructose-2,6-bisphosphate, an allosteric activator of phosphofructokinase 1 (PFK1). PFK1 in turn catalyzes the committed step of glycolysis so the net effect of this whole sequence of events set off by insulin is to increase cytosolic concentrations of the small molecules formed in the course of glycolysis. This in turn drives the increased synthesis of Xylulose-5-phosphate, itself a positive regulator of PP2A.
R-HSA-264876 Insulin processing Generation of insulin containing secretory granules from newly synthesized proinsulin in the lumen of the endoplasmic reticulum (ER) involves formation of proinsulin intramolecular disulfide bonds, formation of proinsulin zinc calcium complexes, proteolytic cleavage of proinsulin to yield insulin and C peptide, and translocation of the granules across the cytosol to the plasma membrane (Dodson & Steiner 1998).
Transcription of the human insulin gene INS is annotated as part of the pathway “Regulation of gene expression in beta cells” (see reaction R-HSA-211289). The preproinsulin mRNA is translated by ribosomes at the rough endoplasmic reticulum (ER) and the preproinsulin enters the secretion pathway by virtue of its signal peptide, which is co-translationally cleaved to yield proinsulin.
In the process annotated here, within the ER, three intramolecular disulfide bonds form in proinsulin, mediated by P4HD (PDI1A) and ERO1B proteins. Correctly folded, disulfide-bonded proinsulin then moves via vesicles from the ER to the Golgi Complex where it forms complexes with zinc and calcium.
Proinsulin zinc calcium complexes bud in vesicles from the trans Golgi to form immature secretory vesicles (secretory granules) in the cytosol. Within the immature granules, endoproteases PCKS1 and PCKS2 (Prohormone Convertases 1 and 2) cleave proinsulin at two sites and CPE (Carboxypeptidase E) removes additional amino acid residues to yield the cystine bonded A and B chains of mature insulin and the C peptide, which will be secreted with the insulin. The insulin zinc calcium complexes form insoluble crystals within the granule.
The insulin containing secretory granules are then translocated across the cytosol to the inner surface of the plasma membrane. Translocation occurs initially by attachment of the granules to Kinesin 1, which motors along microtubules, and then by attachment to Myosin Va, which motors along the microfilaments of the cortical actin network.
A pancreatic beta cell contains about 10,000 insulin granules of which about 1,000 are docked at the plasma membrane and 50 are readily releasable in immediate response to stimulation by glucose or other secretogogues. Docking is due to interaction between the Exocyst proteins EXOC3 on the granule membrane and EXOC4 on the plasma membrane. Exocytosis is accomplished by interaction between SNARE type proteins Syntaxin 1A and Syntaxin 4 on the plasma membrane and Synaptobrevin 2/VAMP2 on the granule membrane. Exocytosis is a calcium dependent process due to interaction of the calcium binding membrane protein Synaptotagmin V/IX with the SNARE type proteins.
R-HSA-77387 Insulin receptor recycling Triggered by acidification of the endosome, insulin dissociates from the receptor and is degraded. The receptor is dephosphorylated and re-integrated into the plasma membrane, ready to be activated again by the binding of insulin molecules.
R-HSA-74751 Insulin receptor signalling cascade Autophosphorylation of the insulin receptor triggers a series of signalling events, mediated by SHC or IRS, and resulting in activation of the Ras/RAF and MAP kinase cascades. A second effect of the autophosphorylation of the insulin receptor is its internalisation into an endosome, which downregulates its signalling activity.
R-HSA-428359 Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs) bind specific sets of RNA and regulate their translation, stability, and subcellular localization. IGF2BP1, IGF2BP2, and IGF2BP3 bind about 8400 protein-coding transcripts. The target RNAs contain the sequence motif CAUH (where H is A, U, or, C) and binding of IGFBPs increases the stability of the target RNAs.
R-HSA-163685 Integration of energy metabolism Many hormones that affect individual physiological processes including the regulation of appetite, absorption, transport, and oxidation of foodstuffs influence energy metabolism pathways. While insulin mediates the storage of excess nutrients, glucagon is involved in the mobilization of energy resources in response to low blood glucose levels, principally by stimulating hepatic glucose output. Small doses of glucagon are sufficient to induce significant glucose elevations. These hormone-driven regulatory pathways enable the body to sense and respond to changed amounts of nutrients in the blood and demands for energy.
Glucagon and Insulin act through various metabolites and enzymes that target specific steps in metabolic pathways for sugar and fatty acids. The processes responsible for the long-term control of fat synthesis and short-term control of glycolysis by key metabolic products and enzymes are annotated in this module as seven specific pathways:
Pathway 1. Regulation of insulin secretion.
Pathway 2. Glucagon signalling in metabolic pathways: In response to low blood glucose, pancreatic alpha-cells release glucagon. The binding of glucagon to its receptor results in increased cAMP synthesis, and Protein Kinase A (PKA) activation.
Pathway 3. PKA mediated phosphorylation:PKA phosphorylates key enzymes, e.g., 6-Phosphofructo-2-kinase /Fructose-2,6-bisphosphatase (PF2K-Pase) at serine 36, and regulatory proteins, e.g., Carbohydrate Response Element Binding Protein (ChREBP) at serine 196 and threonine 666.
In brief, the binding of insulin to its receptor leads to increased protein phosphatase activity and to hydrolysis of cAMP by cAMP phosphodiesterase. These events counteract the regulatory effects of glucagon.
Pathway 4: Insulin stimulates increased synthesis of Xylulose-5-phosphate (Xy-5-P). Activation of the insulin receptor results indirectly in increased Xy-5-P synthesis from Glyceraldehyde-3-phosphate and Fructose-6-phosphate. Xy-5-P, a metabolite of the pentose phosphate pathway, stimulates protein phosphatase PP2A.
Pathway 5: AMP Kinase (AMPK) mediated response to high AMP:ATP ratio: In response to diet with high fat content or low energy levels, the cytosolic AMP:ATP ratio is increased. AMP triggers a complicated cascade of events. In this module we have annotated only the phosphorylation of ChREBP by AMPK at serine 568, which inactivates this transcription factor.
Pathway 6: Dephosphorylation of key metabolic factors by PP2A: Xy-5-P activated PP2A efficiently dephosphorylates phosphorylated PF2K-Pase resulting in the higher output of F-2,6-P2 that enhances PFK activity in the glycolytic pathway. PP2A also dephosphorylates (and thus activates) cytosolic and nuclear ChREBP.
Pathway 7: Transcriptional activation of metabolic genes by ChREBP: Dephosphorylated ChREBP activates the transcription of genes involved in glucose metabolism such as pyruvate kinase, and lipogenic genes such as acetyl-CoA carboxylase, fatty acid synthetase, acyl CoA synthase and glycerol phosphate acyl transferase.
R-HSA-162592 Integration of provirus For retroviral DNA to direct production of progeny virions it must become covalently integrated into the host cell chromosome (reviewed in Coffin et al. 1997; Hansen et al. 1998). Analyses of mutants have identified the viral integrase coding region (part of the retroviral pol gene) as essential for the integration process (Donehower 1988; Donehower and Varmus 1984; Panganiban and Temin 1984; Quinn and Grandgenett 1988; Schwartzberg et al. 1984). Also essential are regions at the ends of the viral long terminal repeats (LTRs) that serve as recognition sites for integrase protein (Colicelli and Goff 1985, 1988; Panganiban and Temin 1983).
The viral genomic RNA is reverse transcribed to form a linear double-stranded DNA molecule, the precursor to the integrated provirus (Brown et al. 1987, 1989; Fujiwara and Mizuuchi 1988). The provirus is colinear with unintegrated linear viral DNA (Dhar et al. 1980; Hughes et al. 1978) but differs from the reverse transcription product in that it is missing two bases from each end (Hughes et al. 1981). Flanking the integrated HIV provirus are direct repeats of the cellular DNA that are 5 base pairs in length (Vincent et al. 1990). This duplication of cellular sequences flanking the viral DNA is generated as a consequence of the integration mechanism (Coffin et al., 1997).
Linear viral DNA is found in a complex with proteins in the cytoplasm of infected cells. These complexes (termed "preintegration complexes", PICs) can be isolated and have been shown to mediate integration of viral DNA into target DNA in vitro (Bowerman et al. 1989; Brown et al. 1987; Ellison et al. 1990; Farnet and Haseltine 1990, 1991).
The development of in vitro assays with purified integrase has allowed its enzymatic functions to be elucidated. The provirus is formed by two reactions catalyzed by the viral integrase: terminal cleavage and strand transfer. Studies with purified integrase have shown that it is sufficient for both 3' end cleavage (Bushman and Craigie 1991; Craigie et al. 1990; Katzman et al. 1989; Sherman and Fyfe 1990) and joining of the viral DNA to the cellular chromosome or naked target DNA (Bushman et al. 1990; Craigie et al. 1990; Katz et al. 1990). HIV integrase catalyze the removal of two bases from the 3' end of each viral DNA strand, leaving recessed 3' hydroxyl groups (Brown et al. 1989; Fujiwara and Mizuuchi 1988; Roth et al. 1989; Sherman and Fyfe 1990). This terminal cleavage reaction is required for proper integration. It may allow the virus to create a standard end from viral DNA termini that can be heterogeneous due to the terminal transferase activity of reverse transcriptase (Miller et al. 1997; Patel and Preston 1994). In addition, the terminal cleavage step is coupled to the formation of a stable integrase-DNA complex (Ellison and Brown 1994; Vink et al. 1994). Following terminal cleavage, a recessed hydroxyl is exposed that immediately follows a CA dinucleotide. More internal LTR sites are also important for integration (Balakrishnan and Jonsson 1997; Bushman and Craigie 1990; Leavitt et al. 1992). After end processing, integrase catalyzes the covalent attachment of hydroxyl groups at the viral DNA termini to protruding 5' phosphoryl ends of the host cell DNA (Brown et al. 1987; Brown et al. 1989; Fujiwara and Mizuuchi 1988). The DNA cleavage and joining reactions involved in integration are shown in the figure below. Both the viral DNA 3' end cleavage and strand transfer reactions are mediated by single-step transesterification chemistry as shown by stereochemical analysis of reaction products (Engelman et al. 1991). Biochemical analysis of purified integrase revealed that it requires a divalent metal - either Mg2+ or Mn2+ - to carry out reactions with model substrates, that probably mediate the reaction chemistry (Bushman and Craigie 1991; Craigie et al. 1990; Katzman et al. 1989; Sherman and Fyfe 1990; Gao et al. 2004). R-HSA-175567 Integration of viral DNA into host genomic DNA Following nuclear entry, the viral preintegration complex (PIC) must select a site for integration in a host cell chromosome, and then carry out the chemical steps of the reaction.
At the chromosomal level, HIV has been found to favor active transcription units for integration. Subsequent studies established that the cellular PSIP1/LEDGF/p75 protein is important in this reaction. PSIP1/LEDGF/p75 binds tightly to HIV integrase, and also to chromatin. Knocking down PSIP1/LEDGF/p75 in cells resulted in several perturbations of integration targeting in vivo, including reduced integration in transcription units. Thus PSIP1/LEDGF/p75 has been hypothesized to act as a tethering factor that dictates at least in part the placement of HIV integration sites.
The integration target DNA is also expected to be coated with nucleosomes. Tests of integration into mononucleosomes in vitro have shown that wrapping integration target DNA actually boosts integration activity. Kinked positions on the DNA gyre are particularly favored for integration.
Integration does not take place at a unique sequence in the integration target DNA (i.e. it is not like a restriction enzyme). However, favored and disfavored primary sequences can be detected when many integration sites are aligned. Synthesis and testing of favored HIV integration sites showed that they were favored for integration by PICs in vitro.
After a target DNA is bound, the integration reactions take place via a single-step transesterification.
Integration of both ends of the viral DNA, followed by melting of the target DNA segments between the points of joining, yields single stranded gaps at each host-virus DNA junction, and a two base overhang derived from the viral DNA. The manner by which this intermediate is subsequently repaired to yield the fully integrated provirus is unclear. For many parasitic DNA replication reactions, the parasite carries out reaction steps only up to a point that the host cannot easily reverse, forcing the host to complete the job (Bushman 2001; Craig et al. 2002). For retroviral integration, it is reasonable to infer that host DNA repair enzymes complete provirus formation. DNA gap repair enzymes are known to be involved in a variety of DNA repair pathways, so their recruitment to gaps at host-virus DNA junctions is readily envisioned. Consistent with this, known gap repair enzymes have been shown to act on model host-virus DNA junctions in vitro (Yoder and Bushman, 2000).
R-HSA-216083 Integrin cell surface interactions The extracellular matrix (ECM) is a network of macro-molecules that underlies all epithelia and endothelia and that surrounds all connective tissue cells. This matrix provides the mechanical strength and also influences the behavior and differentiation state of cells in contact with it. The ECM are diverse in composition, but they generally comprise a mixture of fibrillar proteins, polysaccharides synthesized, secreted and organized by neighboring cells. Collagens, fibronectin, and laminins are the principal components involved in cell matrix interactions; other components, such as vitronectin, thrombospondin, and osteopontin, although less abundant, are also important adhesive molecules.
Integrins are the receptors that mediate cell adhesion to ECM. Integrins consists of one alpha and one beta subunit forming a noncovalently bound heterodimer. 18 alpha and 8 beta subunits have been identified in humans that combine to form 24 different receptors.
The integrin dimers can be broadly divided into three families consisting of the beta1, beta2/beta7, and beta3/alphaV integrins. beta1 associates with 12 alpha-subunits and can be further divided into RGD-, collagen-, or laminin binding and the related alpha4/alpha9 integrins that recognise both matrix and vascular ligands. beta2/beta7 integrins are restricted to leukocytes and mediate cell-cell rather than cell-matrix interactions, although some recognize fibrinogen. The beta3/alphaV family members are all RGD receptors and comprise aIIbb3, an important receptor on platelets, and the remaining b-subunits, which all associate with alphaV. It is the collagen receptors and leukocyte-specific integrins that contain alpha A-domains.
R-HSA-354192 Integrin signaling Integrins are a major family of cell surface receptors that modulate cell adhesion, migration, proliferation and survival through interaction with the extracellular matrix (ECM) and the actin cytoskeleton. Integrins are type 1 transmembrane proteins that exist at the cell surface as heterodimers of alpha and beta subunits, of which there are 18 and 8 different isoforms, respectively, in human cells. In addition to their mechanical role in mediating contact between the ECM and the cytoskeleton, integrins also modulate intracellular signaling pathways governing cytoskeletal rearrangements and pro-survival and mitogenic signaling (reviewed in Hehlgans et al, 2007; Harburger and Calderwood, 2009; Ata and Antonescu, 2017).
In this pathway, we describe signaling through integrin alphaIIb beta3 as a representative example.
At the sites of vascular injury bioactive molecules such as thrombin, ADP, collagen, fibrinogen and thrombospondin are generated, secreted or exposed. These stimuli activate platelets, converting the major platelet integrin alphaIIbbeta3 from a resting state to an active conformation, in a process termed integrin priming or 'inside-out signalling'. Integrin activation refers to the change required to enhance ligand-binding activity. The activated alphaIIbbeta3 interacts with the fibrinogen and links platelets together in an aggregate to form a platelet plug. AlphaIIbbeta3 bound to fibrin generates more intracellular signals (outside-in signalling), causing further platelet activation and platelet-plug retraction.
In the resting state the alpha and beta tails are close together. This interaction keeps the membrane proximal regions in a bent conformation that maintains alphaIIbbeta3 in a low affinity state.
Integrin alphaIIbbeta3 is released from its inactive state by interaction with the protein talin. Talin interacts with the beta3 cytoplasmic domain and disrupts the salt bridge between the alpha and beta chains. This separation in the cytoplasmic regions triggers the conformational change in the extracellular domain that increases its affinity to fibrinogen.
Much of talin exists in an inactive cytosolic pool, and the Rap1 interacting adaptor molecule (RIAM) is implicated in talin activation and translocation to beta3 integrin cytoplasmic domain.
R-HSA-2534343 Interaction With Cumulus Cells And The Zona Pellucida A typical mammalian egg is surrounded by an outer layer of about 3,000 cumulus cells embedded in an extracellular matrix rich in hyaluronic acid. It is suggested that the fertilizing sperm with it's acrosome intact, passes through the cumulus cell layer. The zona pellucida (ZP), a glycoproteinaceous matrix surrounding the mammalian oocyte plays an important role in species specific sperm-egg binding, induction of acrosome reaction in the ZP bound spermatozoa, avoidance of polyspermy and protection of the embryo prior to implantation. The human ZP matrix is composed of 4 glycoproteins designated as ZP1, ZP2, ZP3 and ZP4.
R-HSA-445095 Interaction between L1 and Ankyrins Ankyrins are a family of adaptor proteins that couple membrane proteins such as voltage gated Na+ channels and the Na+/K+ anion exchanger to the spectrin actin cytoskeleton. Ankyrins are encoded by three genes (ankyrin-G, -B and -R) of which ankyrin-G and -B are the major forms expressed in the developing nervous system. Ankyrins bind to the cytoplasmic domain of L1 CAMs and couple them and ion channel proteins, to the spectrin cytoskeleton. This binding enhances the homophilic adhesive activity of L1 and reduces its mobility within the plasma membrane. L1 interaction with ankyrin mediates branching and synaptogenesis of cortical inhibitory neurons.
R-HSA-8854521 Interaction between PHLDA1 and AURKA PHLDA1 (TDAG51), the product of a gene involved in breast cancer progression, interacts with aurora kinase A (AURKA). While unphosphorylated PHLDA1 promotes AURKA ubiquitination and degradation, AURKA-mediated phosphorylation of PHLDA1 results in down-regulation of PHLDA1 protein levels. Ectopic expression of PHLDA1 strongly antagonizes AURKA-triggered oncogenic phenotypes, suggesting PHLDA1 downregulation as one of the key mechanisms by which AURKA promotes breast cancer (Johnson et al. 2011).
R-HSA-177243 Interactions of Rev with host cellular proteins In order to facilitate the transport of incompletely spliced HIV-1 transcripts, Rev shuttles between the cytoplasm and nucleus using host cell transport mechanisms (reviewed in Li et al. 2005). Nuclear import appears to be achieved by the association of Rev with importin-beta and B23 and docking at the nuclear pore through interactions between importin-beta and nucleoporins. The dissociation of Rev with the import machinery and the subsequent export of Rev-associated HIV-1 mRNA complex requires Ran-GTP. Ran GTP associates with importin-beta, displacing its cargo. Crm1 associates with the Rev:RNA complex and Ran:GTP and is believed to interact with nucleoporins facilitating docking of the RRE-Rev-CRM1-RanGTP complex to the nuclear pore and the translocation of the complex across the nuclear pore complex. In the cytoplasm, RanBP1 associates with Ran-GTP causing the Crm1-Rev-Ran-GTP complex to disassemble. The Ran GAP protein promotes the hydrolysis of RanGTP to Ran GDP. The activities of Ran GAP in the cytoplasm and Ran-GEF, which converts RAN-GDP to Ran-GTP in the nucleus, produce a gradient of Ran-GTP/GDP required for this shuttling of Rev and other cellular transport proteins.
R-HSA-176034 Interactions of Tat with host cellular proteins The elongation of HIV-1 mRNA depends upon the interaction of Tat with the host P-TEFb complex (Hermann and Rice, 1995; Wei et al., 1998).
R-HSA-176033 Interactions of Vpr with host cellular proteins Vpr has been implicated in multiple processes during HIV-1 replication, including nuclear import of the pre-integration complex (PIC)(Heinzinger et al., 1994), apoptosis (Stewart et al., 1997) and induction of cell cycle G2/M arrest (He et al., 1995; Re et al., 1995; Zhao et al., 1996).
Interactions between Vpr and host nucleoporins (importin) appear to facilitate the nuclear import of the PIC (Popov et al., 1998; Vodicka et al., 1998) while interactions between Vpr the adenine nucleotide transporter (ANT) protein at the inner mitochondrial membrane may contribute to release of apoptosis factors by promoting permeabilization of the mitochondrial outer membrane (Jacotot et al., 2000).
Vpr induces cell cycle G2/M arrest by promoting hyperphosphorylation of Cdk1/Cdc2 (Re et al., 1995; Zhao et al., 1996). However, it is unclear which protein(s) Vpr interacts with to cause this effect. For recent reviews, see, (Li et al., 2005; Zhao, Bukrinsky, and Elder, 2005). Progression of cells from G2 phase of the cell cycle to mitosis is a tightly regulated cellular process that requires activation of the Cdk1/Cdc2 kinase, which determines onset of mitosis in all eukaryotic cells. The activity of Cdk1/Cdc2 is regulated in part by the phosphorylation status of tyrosine 15 (Tyr15) on Cdk1/Cdc2, which is phosphorylated by Wee1 kinase during late G2 and is rapidly dephosphorylated by the Cdc25 tyrosine phosphatase to trigger entry into mitosis. These Cdk1/Cdc2 regulators are the downstream targets of two well-characterized G2/M checkpoint pathways which prevent cells from entering mitosis when cellular DNA is damaged or when DNA replication is inhibited. It is clear that Vpr induces cell cycle G2/M arrest by promoting Tyr15 phosphorylation of Cdk1/Cdc2 both in human and fission yeast cells (Elder et al., 2000; Re et al., 1995; Zhao et al., 1996), which modulates host cell cycle machinery to benefit viral survival or replication. Although some aspects of Vpr-induced G2/M arrest resembles induction of host cellular checkpoints, increasing evidence suggests that Vpr induces cell cycle G2 arrest through a mechanism that is to some extent different from the classic G2/M checkpoints. One the unique features distinguishing Vpr-induced G2 arrest from the classic checkpoints is the role of phosphatase 2A (PP2A) in Vpr-induced G2 arrest (Elder, Benko, and Zhao, 2002; Elder et al., 2001; Masuda et al., 2000). Interestingly, PP2A is targeted by a number of other viral proteins including SV40 small T antigen, polyomavirus T antigen, HTLV Tax and adenovirus E4orf4. Thus an in-depth understanding of the molecular mechanisms underlying Vpr-induced G2 arrest will provide additional insights into the basic biology of cell cycle G2/M regulation and into the biological significance of this effect during host-pathogen interactions.
R-HSA-880009 Interconversion of 2-oxoglutarate and 2-hydroxyglutarate The two stereoisomers of 2-hydroxyglutarate are normally converted to 2-oxoglutarate in the mitochondrial matrix, and can then be metabolized by the citric acid cycle. The physiological sources of 2-hydroxyglutarate have not been established although plausible hypotheses are that it is generated by lysine breakdown or as a byproduct of delta-aminolevulinate metabolism. The stereoisomers are oxidized to 2-oxoglutarate in FAD-dependent reactions catalyzed by the enzymes D2HGDH (specific for R(-)-2-hydroxyglutarate) and L2HGDH (specific for S(-)-2-hydroxyglutarate). An inherited deficiency in either enzyme is associated with accumulation of 2-hydroxyglutarate and variable neurological symptoms. R(-)-2-hydroxyglutarate also reacts reversibly with succinate semialdehyde to form 4-hydroxybutyrate and 2-oxoglutarate, catalyzed by ADHFE1. No deficiencies of this enzyme have been found in patients with elevated 2-hydroxyglutarate levels (Struys 2006).
R-HSA-499943 Interconversion of nucleotide di- and triphosphates An array of kinases catalyze the reversible phosphorylation of nucleotide monophosphates to form nucleotide diphosphates and triphosphates.
Nucleoside monophosphate kinases catalyze the reversible phosphorylation of nucleoside and deoxynucleoside 5'-monophosphates to form the corresponding nucleoside 5'-diphosphates. Most appear to have restricted specificities for nucleoside monophosphates, and to use ATP preferentially (Van Rompay et al. 2000; Anderson 1973; Noda 1973). The total number of human enzymes that catalyze these reactions in vivo is not clear. In six cases, a well-defined biochemical activity has been associated with a purified protein, and these are annotated here. However, additional nucleoside monophosphate kinase-like human proteins have been identified in molecular cloning studies whose enzymatic activities are unknown, and several distinctive nucleoside monophosphate kinase activities detected in cell extracts, e.g., a GTP-requiring adenylate kinase activity (Wilson et al. 1976) and one or more guanylate kinase activities (Jamil et al. 1975) have not been unambiguously associated with specific human proteins.
The nucleoside monophosphates against which each of the six well-characterized enzymes is active is shown in the table (Van Rompay et al. 2000). All six efficiently use ATP as a phosphate donor, but have some activity with other nucleoside triphosphates as well in vitro. The high concentrations of ATP relative to other nucleoside triphosphates in vivo makes it the likely major phosphate donor in these reactions under most conditions.
All of these phosphorylation reactions are freely reversible in vitro when carried out with purified enzymes and substrates, having equilibrium constants near 1. In vivo, high ratios of ATP to ADP are likely to favor the forward direction of these reactions, i.e., the conversion of (d)NMP and ATP to (d)NDP and ADP. At the same time, the reversibility of the reactions and the overlapping substrate specificities of the enzymes raises the possibility that this group of reactions can buffer the intracellular nucleotide pool and regulate the relative concentrations of individual nucleotides in the pool: if any one molecule builds up to unusually high levels, multiple routes appear to be open not only to dispose of it but to use it to increase the supply of less abundant nucleotides.
Ribonucleotide reductase catalyzes the synthesis of deoxyribonucleotide diphosphates from ribonucleotide diphosphates.
R-HSA-351200 Interconversion of polyamines The reactions catalyzed by aminopropyl-transferases annotated above are generally irreversible. But spermine and spermidine can be recycled respectively into spermidine and putrescine. These events require the formation of N-acetylated intermediates, N1-acetylspermine and N1-acetylspermidine catalyzed by a cytosolic acetyl-CoA:spermidine/spermine N1-acetyl-tranferase (SSAT) enzyme.
Subsequently, polyamine-oxidase (PAO), a FAD enzyme present in the peroxysomes, yields a polyamine with release of an aldehyde (3-acetamindopropanal) and H2O2.
In addition, SMOX, a FAD-dependent, polyamine oxidase (PAOh1/SMO) that can efficiently use spermine as a substrate and is involved in interconversion reactions.
R-HSA-913531 Interferon Signaling Interferons (IFNs) are cytokines that play a central role in initiating immune responses, especially antiviral and antitumor effects. There are three types of IFNs:Type I (IFN-alpha, -beta and others, such as omega, epsilon, and kappa), Type II (IFN-gamma) and Type III (IFN-lamda). In this module we are mainly focusing on type I IFNs alpha and beta and type II IFN-gamma. Both type I and type II IFNs exert their actions through cognate receptor complexes, IFNAR and IFNGR respectively, present on cell surface membranes. Type I IFNs are broadly expressed heterodimeric receptors composed of the IFNAR1 and IFNAR2 subunits, while the type II IFN receptor consists of IFNGR1 and IFNGR2. Type III interferon lambda has three members: lamda1 (IL-29), lambda2 (IL-28A), and lambda3 (IL-28B) respectively. IFN-lambda signaling is initiated through unique heterodimeric receptor composed of IFN-LR1/IF-28Ralpha and IL10R2 chains.
Type I IFNs typically recruit JAK1 and TYK2 proteins to transduce their signals to STAT1 and 2; in combination with IRF9 (IFN-regulatory factor 9), these proteins form the heterotrimeric complex ISGF3. In nucleus ISGF3 binds to IFN-stimulated response elements (ISRE) to promote gene induction.
Type II IFNs in turn rely upon the activation of JAKs 1 and 2 and STAT1. Once activated, STAT1 dimerizes to form the transcriptional regulator GAF (IFNG activated factor) and this binds to the IFNG activated sequence (GAS) elements and initiate the transcription of IFNG-responsive genes.
Like type I IFNs, IFN-lambda recruits TYK2 and JAK1 kinases and then promote the phosphorylation of STAT1/2, and induce the ISRE3 complex formation.
R-HSA-909733 Interferon alpha/beta signaling Type I interferons (IFNs) are composed of various genes including IFN alpha (IFNA), beta (IFNB), omega, epsilon, and kappa. In humans the IFNA genes are composed of more than 13 subfamily genes, whereas there is only one IFNB gene. The large family of IFNA/B proteins all bind to a single receptor which is composed of two distinct chains: IFNAR1 and IFNAR2. The IFNA/B stimulation of the IFNA receptor complex leads to the formation of two transcriptional activator complexes: IFNA-activated-factor (AAF), which is a homodimer of STAT1 and IFN-stimulated gene factor 3 (ISGF3), which comprises STAT1, STAT2 and a member of the IRF family, IRF9/P48. AAF mediates activation of the IRF-1 gene by binding to GAS (IFNG-activated site), whereas ISGF3 activates several IFN-inducible genes including IRF3 and IRF7.
R-HSA-877300 Interferon gamma signaling Interferon-gamma (IFN-gamma) belongs to the type II interferon family and is secreted by activated immune cells-primarily T and NK cells, but also B-cells and APC. INFG exerts its effect on cells by interacting with the specific IFN-gamma receptor (IFNGR). IFNGR consists of two chains, namely IFNGR1 (also known as the IFNGR alpha chain) and IFNGR2 (also known as the IFNGR beta chain). IFNGR1 is the ligand binding receptor and is required but not sufficient for signal transduction, whereas IFNGR2 do not bind IFNG independently but mainly plays a role in IFNG signaling and is generally the limiting factor in IFNG responsiveness. Both IFNGR chains lack intrinsic kinase/phosphatase activity and thus rely on other signaling proteins like Janus-activated kinase 1 (JAK1), JAK2 and Signal transducer and activator of transcription 1 (STAT-1) for signal transduction. IFNGR complex in its resting state is a preformed tetramer and upon IFNG association undergoes a conformational change. This conformational change induces the phosphorylation and activation of JAK1, JAK2, and STAT1 which in turn induces genes containing the gamma-interferon activation sequence (GAS) in the promoter.
R-HSA-912526 Interleukin receptor SHC signaling Phosphorylation of Shc at three tyrosine residues, 239, 240 (Gotoh et al. 1996) and 317 (Salcini et al. 1994) involves unidentified tyrosine kinases presumed to be part of the activated receptor complex. These phosphorylated tyrosines subsequently bind SH2 signaling proteins such as Grb2, Gab2 and SHIP that are involved in the regulation of different signaling pathways. Grb2 can associate with the guanosine diphosphate-guanosine triphosphate exchange factor Sos1, leading to Ras activation and regulation of cell proliferation. Downstream signals are mediated via the Raf-MEK-Erk pathway.Grb2 can also associate through Gab2 with PI3K and with SHIP.
Figure reproduced from Gu, H. et al. 2000. Mol. Cell. Biol. 20(19):7109-7120
Copyright American Society for Microbiology. All Rights Reserved.
R-HSA-446652 Interleukin-1 family signaling The Interleukin-1 (IL1) family of cytokines comprises 11 members, namely Interleukin-1 alpha (IL1A), Interleukin-1 beta (IL1B), Interleukin-1 receptor antagonist protein (IL1RN, IL1RA), Interleukin-18 (IL18), Interleukin-33 (IL33), Interleukin-36 receptor antagonist protein (IL36RN, IL36RA), Interleukin-36 alpha (IL36A), Interleukin-36 beta (IL36B), Interleukin-36 gamma (IL36G), Interleukin-37 (IL37) and Interleukin-38 (IL38). The genes encoding all except IL18 and IL33 are on chromosome 2. They share a common C-terminal three-dimensional structure and with apart from IL1RN they are synthesized without a hydrophobic leader sequence and are not secreted via the classical reticulum endoplasmic-Golgi pathway. IL1B and IL18, are produced as biologically inactive propeptides that are cleaved to produce the mature, active interleukin peptide. The IL1 receptor (IL1R) family comprises 10 members: Interleukin-1 receptor type 1 (IL1R1, IL1RA), Interleukin-1 receptor type 2 (IL1R2, IL1RB), Interleukin-1 receptor accessory protein (IL1RAP, IL1RAcP, IL1R3), Interleukin-18 receptor 1 (IL18R1, IL18RA) , Interleukin-18 receptor accessory protein (IL18RAP, IL18RB), Interleukin-1 receptor-like 1 (IL1RL1, ST2, IL33R), Interleukin-1 receptor-like 2 (IL1RL2, IL36R), Single Ig IL-1-related receptor (SIGIRR, TIR8), Interleukin-1 receptor accessory protein-like 1 (IL1RAPL1, TIGGIR2) and X-linked interleukin-1 receptor accessory protein-like 2 (IL1RAPL2, TIGGIR1). Most of the genes encoding these receptors are on chromosome 2. IL1 family receptors heterodimerize upon cytokine binding. IL1, IL33 and IL36 bind specific receptors, IL1R1, IL1RL1, and IL1RL2 respectively. All use IL1RAP as a co-receptor. IL18 binds IL18R1 and uses IL18RAP as co-receptor. The complexes formed by IL1 family cytokines and their heterodimeric receptors recruit intracellular signaling molecules, including Myeloid differentiation primary response protein MyD88 (MYD88), members of he IL1R-associated kinase (IRAK) family, and TNF receptor-associated factor 6 (TRAF6), activating Nuclear factor NF-kappa-B (NFκB), as well as Mitogen-activated protein kinase 14 (MAPK14, p38), c-Jun N-terminal kinases (JNKs), extracellular signal-regulated kinases (ERKs) and other Mitogen-activated protein kinases (MAPKs).
R-HSA-448706 Interleukin-1 processing The IL-1 family of cytokines that interact with the Type 1 IL-1R include IL-1α (IL1A), IL-1β (IL1B) and the IL-1 receptor antagonist protein (IL1RAP). IL1RAP is synthesized with a signal peptide and secreted as a mature protein via the classical secretory pathway. IL1A and IL1B are synthesised as cytoplasmic precursors (pro-IL1A and pro-IL1B) in activated cells. They have no signal sequence, precluding secretion via the classical ER-Golgi route (Rubartelli et al. 1990). Processing of pro-IL1B to the active form requires caspase-1 (Thornberry et al. 1992), which is itself activated by a molecular scaffold termed the inflammasome (Martinon et al. 2002). Processing and release of IL1B are thought to be closely linked, because mature IL1B is only seen inside inflammatory cells just prior to release (Brough et al. 2003). It has been reported that in monocytes a fraction of cellular IL1B is released by the regulated secretion of late endosomes and early lysosomes, and that this may represent a cellular compartment where caspase-1 processing of pro-IL1B takes place (Andrei et al. 1999). Shedding of microvesicles from the plasma membrane has also been proposed as a mechanism of secretion (MacKenzie et al. 2001). These proposals superceded previous models in which non-specific release due to cell lysis and passage through a plasma membrane pore were considered. However, there is evidence in the literature that supports all of these mechanisms and there is still controversy over how IL1B exits from cells (Brough & Rothwell 2007). A calpain-like potease has been reported to be important for the processing of pro-IL1A, but much less is known about how IL1A is released from cells and what specific roles it plays in biology.
R-HSA-9020702 Interleukin-1 signaling Interleukin 1 (IL1) signals via Interleukin 1 receptor 1 (IL1R1), the only signaling-capable IL1 receptor. This is a single chain type 1 transmembrane protein comprising an extracellular ligand binding domain and an intracellular region called the Toll/Interleukin-1 receptor (TIR) domain that is structurally conserved and shared by other members of the two families of receptors (Xu et al. 2000). This domain is also shared by the downstream adapter molecule MyD88. IL1 binding to IL1R1 leads to the recruitment of a second receptor chain termed the IL1 receptor accessory protein (IL1RAP or IL1RAcP) enabling the formation of a high-affinity ligand-receptor complex that is capable of signal transduction. Intracellular signaling is initiated by the recruitment of MyD88 to the IL-1R1/IL1RAP complex. IL1RAP is only recruited to IL1R1 when IL1 is present; it is believed that a TIR domain signaling complex is formed between the receptor and the adapter TIR domains. The recruitment of MyD88 leads to the recruitment of Interleukin-1 receptor-associated kinase (IRAK)-1 and -4, probably via their death domains. IRAK4 then activates IRAK1, allowing IRAK1 to autophosphorylate. Both IRAK1 and IRAK4 then dissociate from MyD88 (Brikos et al. 2007) which remains stably complexed with IL-1R1 and IL1RAP. They in turn interact with Tumor Necrosis Factor Receptor (TNFR)-Associated Factor 6 (TRAF6), which is an E3 ubiquitin ligase (Deng et al. 2000). TRAF6 is then thought to auto-ubiquinate, attaching K63-polyubiquitin to itself with the assistance of the E2 conjugating complex Ubc13/Uev1a. K63-pUb-TRAF6 recruits Transforming Growth Factor (TGF) beta-activated protein kinase 1 (TAK1) in a complex with TAK1-binding protein 2 (TAB2) and TAB3, which both contain nuclear zinc finger motifs that interact with K63-polyubiquitin chains (Ninomiya-Tsuji et al. 1999). This activates TAK1, which then activates inhibitor of NF-kappaB (IkappaB) kinase 2 (IKK2 or IKKB) within the IKK complex, the kinase responsible for phosphorylation of IkappaB. The IKK complex also contains the scaffold protein NF-kappa B essential modulator (NEMO). TAK1 also couples to the upstream kinases for p38 and c-jun N-terminal kinase (JNK). IRAK1 undergoes K63-linked polyubiquination; Pellino E3 ligases are important in this process. (Butler et al. 2007; Ordureau et al. 2008). The activity of these proteins is greatly enhanced by IRAK phosphorylation (Schauvliege et al. 2006), leading to K63-linked polyubiquitination of IRAK1. This recruits NEMO to IRAK1, with NEMO binding to polyubiquitin (Conze et al. 2008).
TAK1 activates IKKB (and IKK), resulting in phosphorylation of the inhibitory IkB proteins and enabling translocation of NFkB to the nucleus; IKKB also phosphorylates NFkB p105, leading to its degradation and the subsequent release of active TPL2 that triggers the extracellular-signal regulated kinase (ERK)1/2 MAPK cascade. TAK1 can also trigger the p38 and JNK MAPK pathways via activating the upstream MKKs3, 4 and 6. The MAPK pathways activate a number of downstream kinases and transcription factors that co-operate with NFkB to induce the expression of a range of TLR/IL-1R-responsive genes. There are reports suggesting that IL1 stimulation increases nuclear localization of IRAK1 (Bol et al. 2000) and that nuclear IRAK1 binds to the promoter of NFkB-regulated gene and IkBa, enhancing binding of the NFkB p65 subunit to NFkB responsive elements within the IkBa promoter. IRAK1 is required for IL1-induced Ser-10 phosphorylation of histone H3 in vivo (Liu et al. 2008). However, details of this aspect of IRAK1 signaling mechanisms remain unclear. Interleukin-18 is another Interleukin-1 related cytokine which signals through IL18R and IL18RAP subunit receptors (which share homology with IL1R and IL1RAP in the cytokine signaling cascade). Later it follows a MYD88/IRAK1/TRAF6 cascade signaling until reach the NFKB activation (Moller et al. 2002). Interleukin 33, 36, 37 and 38 are relatively recently discovered Interleukin-1 related citokines which are also able to signal through IL1 receptor subunits or other as IL18R, IL37R (Schmitz et al. 2005, Yi et al. 2016, Lunding et al. 2015, van de Veendorck et al. 2012, Lin et al. 2001).
R-HSA-6783783 Interleukin-10 signaling Interleukin-10 (IL10) was originally described as a factor named cytokine synthesis inhibitory factor that inhibited T-helper (Th) 1 activation and Th1 cytokine production (Fiorentino et al. 1989). It was found to be expressed by a variety of cell types including macrophages, dendritic cell subsets, B cells, several T-cell subpopulations including Th2 and T-regulatory cells (Tregs) and Natural Killer (NK) cells (Moore et al. 2001). It is now recognized that the biological effects of IL10 are directed at antigen-presenting cells (APCs) such as macrophages and dendritic cells (DCs), its effects on T-cell development and differentiation are largely indirect via inhibition of macrophage/dendritic cell activation and maturation (Pestka et al. 2004, Mocellin et al. 2004). T cells are thought to be the main source of IL10 (Hedrich & Bream 2010). IL10 inhibits a broad spectrum of activated macrophage/monocyte functions including monokine synthesis, NO production, and expression of class II MHC and costimulatory molecules such as IL12 and CD80/CD86 (de Waal Malefyt et al. 1991, Gazzinelli et al. 1992). Studies with recombinant cytokine and neutralizing antibodies revealed pleiotropic activities of IL10 on B, T, and mast cells (de Waal Malefyt et al. 1993, Rousset et al. 1992, Thompson-Snipes et al. 1991) and provided evidence for the in vivo significance of IL10 activities (Ishida et al. 1992, 1993). IL10 antagonizes the expression of MHC class II and the co-stimulatory molecules CD80/CD86 as well as the pro-inflammatory cytokines IL1Beta, IL6, IL8, TNFalpha and especially IL12 (Fiorentino et al. 1991, D'Andrea et al. 1993). The biological role of IL10 is not limited to inactivation of APCs, it also enhances B cell, granulocyte, mast cell, and keratinocyte growth/differentiation, as well as NK-cell and CD8+ cytotoxic T-cell activation (Moore et al. 2001, Hedrich & Bream 2010). IL10 also enhances NK-cell proliferation and/or production of IFN-gamma (Cai et al. 1999).
IL10-deficient mice exhibited inflammatory bowel disease (IBD) and other exaggerated inflammatory responses (Kuhn et al. 1993, Berg et al. 1995) indicating a critical role for IL10 in limiting inflammatory responses. Dysregulation of IL10 is linked with susceptibility to numerous infectious and autoimmune diseases in humans and mouse models (Hedrich & Bream 2010).
IL10 signaling is initiated by binding of homodimeric IL10 to the extracellular domains of two adjoining IL10RA molecules. This tetramer then binds two IL10RB chains. IL10RB cannot bind to IL10 unless bound to IL10RA (Ding et al. 2001, Yoon et al. 2006); binding of IL10 to IL10RA without the co-presence of IL10RB fails to initiate signal transduction (Kotenko et al. 1997).
IL10 binding activates the receptor-associated Janus tyrosine kinases, JAK1 and TYK2, which are constitutively bound to IL10R1 and IL10R2 respectively. In the classic model of receptor activation assembly of the receptor complex is believed to enable JAK1/TYK2 to phosphorylate and activate each other. Alternatively the binding of IL10 may cause conformational changes that allow the pseudokinase inhibitory domain of one JAK kinase to move away from the kinase domain of the other JAK within the receptor dimer-JAK complex, allowing the two kinase domains to interact and trans-activate (Waters & Brooks 2015).
The activated JAK kinases phosphorylate the intracellular domains of the IL10R1 chains on specific tyrosine residues. These phosphorylated tyrosine residues and their flanking peptide sequences serve as temporary docking sites for the latent, cytosolic, transcription factor, STAT3. STAT3 transiently docks on the IL10R1 chain via its SH2 domain, and is in turn tyrosine phosphorylated by the receptor-associated JAKs. Once activated, it dissociates from the receptor, dimerizes with other STAT3 molecules, and translocates to the nucleus where it binds with high affinity to STAT-binding elements (SBEs) in the promoters of IL-10-inducible genes (Donnelly et al. 1999).
R-HSA-447115 Interleukin-12 family signaling Interleukin-12 (IL-12) is a heterodimer of interleukin-12 subunit alpha (IL12A, IL-12p35) and interleukin-12 subunit beta (IL12B, IL-12p40). It is a potent immunoregulatory cytokine involved in the generation of cell mediated immunity to intracellular pathogens. It is produced by antigen presenting cells, including dendritic cells, macrophages/monocytes, neutrophils and some B cells (D'Andrea et al. 1992, Kobayashi et al.1989, Heufler et al.1996). It enhances the cytotoxic activity of natural killer (NK) cells and cytotoxic T cells, stimulating proliferation of activated NK and T cells and induces production of interferon gamma (IFN gamma) by these cells (Stern et al. 1990). IL-12 also plays an important role in immunomodulation by promoting cell mediated immunity through induction of a class 1 T helper cell (Th1) immune response. IL-12 may contribute to immunopathological conditions such as rheumatoid arthritis (McIntyre et al. 1996). The receptor for IL-12 is a heterodimer of IL-12Rbeta1 (IL12RB1) and IL-12Rbeta2 (IL12RB2), both highly homologous to Interleukin-6 receptor subunit beta (IL6ST,gp130). Each has an extracellular ligand binding domain, a transmembrane domain and a cytosolic domain containing box 1 and box 2 sequences that mediate binding of Janus family tyrosine kinases (JAKs). IL-12 binding is believed to bring about the heterodimerization and generation of a high affinity receptor complex capable of signal transduction. In this model, receptor dimerization leads to juxtaposition of the cytosolic domains and subsequent tyrosine phosphorylation and activation of JAK2 and TYK2. These activated kinases, in turn, tyrosine phosphorylate and activate several members of the signal transducer and activator of transcription (STAT) family, mainly STAT4, while also STAT1, STAT3 and STAT5 have been reported to be activated (Bacon et al. 1995, Jacobson et al. 1995, Yu et al. 1996, Gollob et al.1995). The STATs translocate to the nucleus to activate transcription of several genes, including IFN gamma. The production of IFN gamma has a pleiotropic effect in the cell, stimulating production of molecules important to cell mediated immunity. In particular, IFN gamma stimulates production of more IL-12 and sets up a positive regulation loop between IL-12 signaling and IFN gamma (Chan et al. 1991). The importance of IL-12 for this loop is demonstrated by IL-12 and STAT4 knockout mice that are severely compromised in IFN-gamma production (Kaplan et al. 1996; Magram et al. 1996), as well as by patients with IL12B mutations that are severely compromised in IFN-gamma production (Altare et al.1998).
R-HSA-9020591 Interleukin-12 signaling Interleukin 12 (IL-12) is heterodimeric cytokine produced by dendritic cells, macrophages and neutrophils. It is encoded by the genes Interleukin-12 subunit alpha (IL12A) and Interleukin-12 subunit beta (IL12B), which encode a 35-kDa light chain (p35) and a 40-kDa heavy chain (p40), respectively. The active IL12 heterodimer is sometimes referred to as p70. The p35 component has homology to single-chain cytokines, while p40 is homologous to the extracellular domains of members of the haematopoietic cytokine-receptor family. The IL12 heterodimer therefore resembles a cytokine linked to a soluble receptor. IL12 is involved in the differentiation of naive T cells into Th1 cells and sometimes known as T cell-stimulating factor. IL12 enhances the cytotoxic activity of Natural Killer cells and CD8+ cytotoxic T lymphocytes. IL12 also has anti-angiogenic activity, mediated by increased production of CXCL10 via interferon gamma. The IL12 receptor is a heterodimer formed by Interleukin-12 receptor subunit beta-1 (IL12RB1) and Interleukin-12 receptor subunit beta-2 (IL12RB2), both of which have extensive homology to IL6ST (gp130), the signal transducing receptor subunit of the IL6-like cytokine superfamily. IL-12RB2 is considered to play the key role in IL12 function, in part because its expression on activated T cells is stimulated by cytokines that promote Th1 cell development and inhibited by those that promote Th2 cells development. In addition, IL12 binding leads to IL12RB2 tyrosine phosphorylation, which provides binding sites for the kinases Non-receptor tyrosine-protein kinase TYK2 and Tyrosine-protein kinase JAK2. These activate transcription factor proteins in the Signal transducer and activator of transcription (STAT) family, particularly STAT4.
R-HSA-8983432 Interleukin-15 signaling The high affinity Interleukin-15 receptor is a heterotrimer of Interleukin-15 receptor subunit alpha (IL15RA), Interleukin-2 receptor subunit beta (IL2RB, CD122) and Cytokine receptor common subunit gamma (IL2RG, CD132). IL2RB and IL2RG are also components of the Interleukin-2 (IL2) receptor. Treatment of human T cells with Interleukin-15 (IL15) results in tyrosine phosphorylation of Tyrosine-protein kinase JAK1 (JAK1, Janus kinase 1) and Tyrosine-protein kinase JAK3 (JAK3, Janus kinase 3) (Johnston et al. 1995, Winthrop 2017). IL15 can signal by a process termed 'trans presentation', where IL15 bound by IL15 on one cell is trans-presented to IL2RB:IL2RG on another cell (Dubois et al. 2002) but can also participate in more 'traditional' cis signaling (Wu et al. 2008, Mishra et al. 2014) where all the three receptors are present on the same cell. Stimulation of lymphocytes by IL15 release MAPK activation through GAB2/SHP2/SHC (GRB2-associated-binding protein 2/Tyrosine-protein phosphatase non-receptor type 11/SHC transforming protein 1 or 2) cascade activation (Gadina et al. 2000).
R-HSA-448424 Interleukin-17 signaling Interleukin-17 (IL17) is a family of cytokines (Kawaguchi et al. 2004, Gu et al. 2013). IL17A, the founding member of the family is able to induce the production of other cytokines and chemokines, such as IL6, IL8, and granulocyte colony-stimulating factor (G-CSF) in a variety of cell types, including activated T-cells. It plays a pivotal role in host defenses in response to microbial infection and is involved in the pathogenesis of autoimmune diseases and allergic syndromes. IL17 activates several downstream signaling pathways including NFkB, MAPKs and C/EBPs, inducing the expression of antibacterial peptides, proinflammatory chemokines and cytokines and matrix metalloproteases (MMPs). IL17 can stabilize the mRNA of genes induced by TNF-alpha. IL17 signal transduction is mediated by the cytosolic adaptor molecule ACT1 (also known as CIKS).
The receptor for IL17D is unknown (Gu et al. 2013).
R-HSA-9012546 Interleukin-18 signaling Interleukin-18 (IL18, pro-IL18) is a pleiotropic and pro inflammatory cytokine. It belongs to the Interleukin-1 (IL1 superfamily (Alboni et al. 2010, Krumm et al. 2017, Dinarello 1999). IL18 is synthesized as an inactive 24-kDa precursor protein that is cleaved by extracellular proteases such as caspase-1, protease 3, serine protease, elastase or cathepsin G (Fantuzzi & Dinarello 1999, Gracie et al. 2004, Sugawara et al. 2001), forming an 18-kDa mature protein (Arend et al. 2008, Akita et al. 1997, Fantuzzi et al. 1998, Ghayur et al. 1997, Gu et al. 1997, Ushio et al. 1996).
IL18 also occurs as a short isoform, the result of an alternative splicing event that removes 57 bp/19 aa (IL18alpha) (Conti et al. 1997, Yang et al. 2005). This short isoform has a modest synergistic action with the IL18 canonical active form. The IL18 receptor (IL18R) belongs to the Interleukin-1 receptor/Toll like receptor superfamily. It consists of two subunits, Interleukin-18 receptor 1 (IL18R1, IL-18Rα, IL1Rrp1, IL18R1, IL-1R5) and Interleukin-18 receptor accessory protein (IL18RAP, IL18RB, IL-18Rβ,IL-18RacP, IL-18RII or IL-1R7). Both subunits have three extracellular immunoglobulin-like domains and one intracellular Toll/IL-1 receptor (TIR) domain (O'Neill & Dinarello 2000, Sims 2002). It is believed that IL18 binds first to IL18R1 and later recruits IL18RAP to form a high-affinity heterotrimeric complex (Sims 2002, Sergi & Pentilla 2004, Alboni et al. 2009). A short isoform of IL18R1 lacks the TIR domain (IL18R1 type II) (Alboni et al. 2009), which is required for signaling, leading to the suggestion that IL18R1 type II is a decoy receptor (Colotta et al. 1994). A truncated form of IL18RAP containing only one of the three immunoglobulin domains stabilizes IL18 binding to IL18R1 but prevents signaling.
IL-18 binding protein (IL18BP), a 38-kDa soluble protein, is another negative regulator of IL18 signaling. It has some sequence homology with IL18R1 (Im et al. 2002 , Kim et al. 2002, Novick et al. 1999). IL18BP binds with high affinity to mature IL18, preventing its interaction with IL18R1. Several isoforms IL18BP have been described (Kim et al. 2000). Interleukin-37 (IL37, IL-1F7), another negative regulator of IL18 signaling, is able to bind IL18BP and IL18RAP preventing signaling (Bufler et al.2002, Pan et al. 2001, Kumar et al. 2002).
IL18 stimulates Interferon gamma (IFNG, IFN-γ) production from T-helper lymphocytes cells (Th1) and macrophages and enhances the cytotoxicity of natural killer (NK) cells. IL18 stimulated IFNG production is synergistically amplified by other Th1-related cytokines such as IL2, IL15, IL12 and IL23 (Boraschi & Dinarello 2006, Park et al. 2007, Dinarello 2007, Dinarello & Fantuzzi 2003).
R-HSA-451927 Interleukin-2 family signaling The interleukin-2 family (also called the common gamma chain cytokine family) consists of interleukin (IL)2, IL9, IL15 and IL21. Although sometimes considered to be within this family, the IL4 and IL7 receptors can form complexes with other receptor chains and are represented separately in Reactome. Receptors of this family associate with JAK1 and JAK3, primarily activating STAT5, although certain family members can also activate STAT1, STAT3 or STAT6.
R-HSA-9020558 Interleukin-2 signaling Interleukin-2 (IL-2) is a cytokine that is produced by T cells in response to antigen stimulation. Originally, IL-2 was discovered because of its potent growth factor activity on activated T cells in vitro and was therefore named 'T cell growth factor' (TCGF). However, the generation of IL-2- and IL-2 receptor-deficient mice revealed that IL-2 also plays a regulatory role in the immune system by suppressing autoimmune responses. Two main mechanisms have been identified that explain this suppressive function: (1) IL-2 sensitizes activated T cells for activation-induced cell death (AICD) and (2) IL-2 is critical for the survival and function of regulatory T cells (Tregs), which possess potent immunosuppressive properties.
IL-2 signaling occurs when IL-2 binds to the heterotrimeric high-affinity IL-2 receptor (IL-2R), which consists of alpha, beta and gamma chains. The IL-2R was identified in 1981 via radiolabeled ligand binding (Robb et al. 1981). The IL-2R alpha chain was identified in 1982 (Leonard et al.), the beta chain in 1986/7 (Sharon et al. 1986, Teshigawara et al. 1987) and the IL-2R gamma chain in 1992 (Takeshita et al.). The high affinity of IL-2 binding to the IL-2R is created by a very rapid association rate to the IL-2R alpha chain, combined with a much slower dissociation rate contributed by the combination of the IL-2R beta and gamma chains (Wang & Smith 1987). After antigen stimulation, T cells upregulate the high-affinity IL-2R alpha chain; IL-2R alpha captures IL-2 and this complex then associates with the constitutively expressed IL-2R beta and gamma chains. The IL-2R gamma chain is shared by several other members of the cytokine receptor superfamily including IL-4, IL-7, IL-9, IL-15 and IL-21 receptors, and consequently is often referred to as the Common gamma chain (Gamma-c). The tyrosine kinases Jak1 and Jak3, which are constitutively associated with IL-2R beta and Gamma-c respectively, are activated resulting in phosphorylation of three critical tyrosine residues in the IL-2R beta cytoplasmic tail. These phosphorylated residues enable recruitment of the adaptor molecule Shc, activating the MAPK and PI3K pathways, and the transcription factor STAT5. After phosphorylation, STAT5 forms dimers that translocate to the nucleus and initiate gene expression. While STAT5 activation is critical for IL-2 function in most cell types, the contribution of the PI3K/Akt pathway differs between distinct T cell subsets. In Tregs for example, PI3K/Akt is not involved in IL-2 signaling and this may explain some of the different functional outcomes of IL-2 signaling in Tregs vs. effector T cells.
R-HSA-8854691 Interleukin-20 family signaling The interleukin 20 (IL20) subfamily comprises IL19, IL20, IL22, IL24 and IL26. They are members of the larger IL10 family, but have been grouped together based on their usage of common receptor subunits and similarities in their target cell profiles and biological functions. Members of the IL20 subfamily facilitate the communication between leukocytes and epithelial cells, thereby enhancing innate defence mechanisms and tissue repair processes at epithelial surfaces. Much of the understanding of this group of cytokines is based on IL22, which is the most studied member (Rutz et al. 2014, Akdis M et al. 2016, Longsdon et al. 2012).
R-HSA-9020958 Interleukin-21 signaling Interleukin-21 (IL21) is a pleiotropic cytokine with four alpha-helical bundles. It is produced primarily by natural killer T cells, T follicular helper cells and TH17 cells, with lower levels of production by numerous other populations of lymphohaematopoietic cells (Spolski & Leonard 2014). IL21 binds Interleukin-21 receptor (IL21R, NILR) and Cytokine receptor common subunit gamma (IL2RG, GammaC).
IL21R has significant homology with the class I cytokine receptors Interleukin-2 receptor subunit beta (IL2RB) and Interleukin-4 receptor subunit alpha (IL4R) and was predicted to similarly form a complex with IL2RG. IL21R dimers can weakly bind and signal in response to IL21 but IL21 generates a much stronger response when IL21R is combined with IL2RG, which is required for a fully signaling capable IL21 receptor complex (Ozaki et al. 2000, Asao et al. 2001, Habib et al. 2002). IL21R can bind Janus kinase 1 (JAK1) (Ozaki et al. 2000) but IL2RG is required for IL21 induced signaling (Asao et al. 2001). The heteromeric IL21 receptor complex can activate JAK1, JAK3, Signal transducer and activator of transcription 1 (STAT1), STAT3, STAT4 and STAT5, depending on the cell type. In cultured T-cells IL21 induced phosphorylation of JAK1, JAK3, STAT1, STAT3 and weakly STAT5 (Asao et al. 2001). In primary CD4+ T cells IL21 induced the phosphorylation of STAT1 and STAT3 but not STAT5, whereas IL2 induced the phosphorylation of STAT5 and STAT1 but not STA3 (Bennet et al. 2003). IL21 stimulation of primary splenic B cells and the pro-B-cell line Ba-F3 induced the activation of JAK1, JAK3 and STAT5 (Habib et al. 2002). In primary human NK cells or the NK cell line NK-92, IL21 induced the activation of STAT1, STAT3, and STAT4 but not STAT5 (Strengell et al. 2002, 2003). IL21 activated STAT1 and STAT3 in human monocyte-derived macrophages (Vallières & Girard 2017).
R-HSA-9020933 Interleukin-23 signaling Interleukin-23 (IL23) is a heterodimer of Interleukin-12 subunit beta (IL12B, IL-12p40), which is shared with IL12, and Interleukin-23 subunit alpha IL23A (IL-23p19) subunit. The functional receptor for IL23 consists of Interleukin-12 receptor subunit beta-1 (IL12RB1), which is shared with the IL12 receptor, and Interleukin-23 receptor (IL23R). IL23R is mainly expresed on activated memory T cells, Natural Killer cells, monocytes/macrophage and at low levels on dendritic cells (DCs). IL23 is mainly secreted by activated macrophages and DCs in peripheral tissues such as skin, intestinal mucosa and lung. IL23 is proinlflammatory and implicated in several autoimmune inflammatory disorders such as colitis, gastritis, psoriasis and arthritis. It is similar to IL-12 both in structure and its ability to memory T cells to increase interferon-γ (IFN-γ) production and proliferation, the ability of IL-23 to induce IL-17. IL23 activates the Janus kinases JAK2 and TYK2, resulting in phosphorylation of the receptor complex, which forms the docking sites for Signal transducer and activator of transcription 3 (STAT3) and STAT4 to bind and become phosphorylated.
R-HSA-9020956 Interleukin-27 signaling Interleukin-27 (IL27) is a heterodimeric cytokine that contains Epstein-Barr virus–induced gene 3 (EBI3) and IL27p28 (IL27). It signals through a receptor composed of Interleukin-6 receptor subunit beta (IL6ST, gp130), which is utilized by many cytokines, and Interleukin-27 receptor subunit alpha (IL27RA, WSX-1, TCCR) (Yoshida & Hunter 2015).
R-HSA-512988 Interleukin-3, Interleukin-5 and GM-CSF signaling The Interleukin-3 (IL-3), IL-5 and Granulocyte-macrophage colony stimulating factor (GM-CSF) receptors form a family of heterodimeric receptors that have specific alpha chains but share a common beta subunit, often referred to as the common beta (Bc). Both subunits contain extracellular conserved motifs typical of the cytokine receptor superfamily. The cytoplasmic domains have limited similarity with other cytokine receptors and lack detectable catalytic domains such as tyrosine kinase domains.
IL-3 is a 20-26 kDa product of CD4+ T cells that acts on the most immature marrow progenitors. IL-3 is capable of inducing the growth and differentiation of multi-potential hematopoietic stem cells, neutrophils, eosinophils, megakaryocytes, macrophages, lymphoid and erythroid cells. IL-3 has been used to support the proliferation of murine cell lines with properties of multi-potential progenitors, immature myeloid as well as T and pre-B lymphoid cells (Miyajima et al. 1992). IL-5 is a hematopoietic growth factor responsible for the maturation and differentiation of eosinophils. It was originally defined as a T-cell-derived cytokine that triggers activated B cells for terminal differentiation into antibody-secreting plasma cells. It also promotes the generation of cytotoxic T-cells from thymocytes. IL-5 induces the expression of IL-2 receptors (Kouro & Takatsu 2009). GM-CSF is produced by cells (T-lymphocytes, tissue macrophages, endothelial cells, mast cells) found at sites of inflammatory responses. It stimulates the growth and development of progenitors of granulocytes and macrophages, and the production and maturation of dendritic cells. It stimulates myeloblast and monoblast differentiation, synergises with Epo in the proliferation of erythroid and megakaryocytic progenitor cells, acts as an autocrine mediator of growth for some types of acute myeloid leukemia, is a strong chemoattractant for neutrophils and eosinophils. It enhances the activity of neutrophils and macrophages. Under steady-state conditions GM-CSF is not essential for the production of myeloid cells, but it is required for the proper development of alveolar macrophages, otherwise, pulmonary alvelolar proteinosis (PAP) develops. A growing body of evidence suggests that GM-CSF plays a key role in emergency hematopoiesis (predominantly myelopoiesis) in response to infection, including the production of granulocytes and macrophages in the bone marrow and their maintenance, survival, and functional activation at sites of injury or insult (Hercus et al. 2009).
All three receptors have alpha chains that bind their specific ligands with low affinity (de Groot et al. 1998). Bc then associates with the alpha chain forming a high affinity receptor (Geijsen et al. 2001), though the in vivo receptor is likely be a higher order multimer as recently demonstrated for the GM-CSF receptor (Hansen et al. 2008).
The receptor chains lack intrinsic kinase activity, instead they interact with and activate signaling kinases, notably Janus Kinase 2 (JAK2). These phosphorylate the common beta subunit, allowing recruitment of signaling molecules such as Shc, the phosphatidylinositol 3-kinases (PI3Ks), and the Signal Transducers and Activators of Transcription (STATs). The cytoplasmic domain of Bc has two distinct functional domains: the membrane proximal region mediates the induction of proliferation-associated genes such as c-myc, pim-1 and oncostatin M. This region binds multiple signal-transducing proteins including JAK2 (Quelle et al. 1994), STATs, c-Src and PI3 kinase (Rao and Mufson, 1995). The membrane distal domain is required for cytokine-induced growth inhibition and is necessary for the viability of hematopoietic cells (Inhorn et al. 1995). This region interacts with signal-transducing proteins such as Shc (Inhorn et al. 1995) and SHP and mediates the transcriptional activation of c-fos, c-jun, c-Raf and p70S6K (Reddy et al. 2000).
Figure reproduced by permission from Macmillan Publishers Ltd: Leukemia, WL Blalock et al. 13:1109-1166, copyright 1999. Note that residue numbering in this diagram refers to the mature Common beta chain with signal peptide removed.
R-HSA-9014843 Interleukin-33 signaling Interleukin-33 (IL33) cytokine is a member of the Interleukin-1 family. It can be classified as an alarmin because it is released into the extracellular space during cell damage. It acts as an endogenous danger signal (Liew et al. 2010).] The gene product is biologically active (full-length IL33). Its potency has been reported to increase significantly (up to 30x) after cleavage at the N-terminus by inflammatory proteases such as Cathepsin G (CTSG) and Neutrophil elastase (ELANE) (Lefrançais et al. 2012, Lefrançais et al. 2014) but others have suggested that processing inactivates IL33 (Cayrol & Girard 2009). IL33 can act as an extracellular ligand and an intracellular signaling molecule (Martin et al. 2013, 2016). Full-length IL33 has a nuclear localization sequence and can translocate to the nucleus, where it binds heterochromatin (Moussion et al. 2008, Carriere et al. 2007, Roussel et al. 2008, Kuchler et al. 2008, Sundlisaeter et al. 2012, Baekkevold et al. 2003). IL33 that has undergone proteolytic processing is unable to translocate to the nucleus (Martin et al. 2013, Ali et al. 2010). Binding of extracellular IL33 to its receptor Interleukin-1 receptor-like 1 (IL1RL1, suppression of tumorigenicity 2, ST2) initiates several cellular signaling pathways. Cell injury or death are the dominant mechanisms by which IL33 reaches the extracellular environment, IL33 is not actively secreted by cells (Martin et al. 2016, Kaczmarek et al. 2013, Vancamelbeke et al. 2017). Because IL33 is expressed constitutively by endothelial and epithelial cells it is immediately available to the extracellular microenvironment after cell injury and necrosis (Lefrançais et al. 2012). Increases in extracellular ATP or mechanical stress correlate with increased IL33 secretion by mast cells or cardiomyocytes, respectively (Shimokawa et al. 2017, Kakkar et al. 2012, Zhao et al. 2012, Sanada et al. 2007, Chen et al. 2015). Soluble IL1RL1 (IL1RL1 Isoform C, ST2V) (Iwahana et al. 2005, Tominaga et al. 1999) shares the extracellular components of IL1RL1, including the ligand binding domain, but lacks the transmembrane and intracellular components of IL1RL1 (Kakkar et al. 2008, Iwahana et al. 1999). The IL33-IL1RL1 complex recruits a co-receptor, most commonly IL1 receptor accessory protein (IL1RAP, IL-1RAcP) (Schmitz et al. 2005, Lingel et al. 2009, Palmer et al. 2008, Liu et al. 2013).
R-HSA-8984722 Interleukin-35 Signalling Interleukin 35 (IL35) is an IL12 family cytokine produced by regulatory but not effector T-cells. It is a dimeric protein composed of IL-12RB2 and IL27RA chains. IL35 suppresses inflammatory responses of immune cells.
R-HSA-9014826 Interleukin-36 pathway Interleukin-36 alpha (IL36A), IL36B and IL36G are collectively known as IL36. They are members of the Interlukin-1 family that signal through a receptor composed of Interleukin-1 receptor-like 2 (IL1RL2, IL36R) and Interleukin-1 receptor accessory protein (IL1RAP, IL-1R/AcP) to promote inflammatory responses. Interleukin-36 receptor antagonist protein (IL36RN, IL36Ra) is a natural antagonist. IL36 is expressed predominantly by epithelial cells and is implicated strongly through functional and genetic evidence in the pathology of psoriatic disorders.
R-HSA-9008059 Interleukin-37 signaling Interleukins (IL) are immunomodulatory proteins that elicit a wide array of responses in cells and tissues. Interleukin 37 (IL37), also known as IL 1F7, is a member of the IL 1 family (Sharma et al. 2008). Isoform b of IL37 (referred just as IL37) is synthesized as a precursor that requires processing (primarily by caspase 1) to attain full receptor agonist or antagonist function (Kumar et al. 2002). Both full length and processed IL37 can bind to the IL 18 binding protein (IL 18BP) and the Interleukin 18 receptor 1 (IL 18R1) (Shi et al. 2003). Upon binding to the IL18R1, IL37 recruits Single Ig IL 1 related receptor (SIGIRR) (Nold-Petry et al. 2015). The IL37:IL18R1 complex can activate phosphorylation of Signal transducer and activator of transcription 3 (STAT3), Tyrosine protein kinase Mer and Phosphatidylinositol 3,4,5 trisphosphate 3 phosphatase and dual specificity protein phosphatase PTEN and can also inhibit Nuclear factor NF kappa B p105 subunit (NFKB) (Nold-Petry et al. 2015). Processed IL37 can be secreted from the cytosol to the extracellular space or translocated into the nucleus (Bulau et al. 2014). Full length IL37 can also be secreted from the cytosol to the extracellular space (Bulau et al. 2014). Processed IL37 can bind with Mothers against decapentaplegic homolog 3 (SMAD3) in the cytosol and then translocate to the nucleus, where it facilitates transcription of Tyrosine protein phosphatase non receptors (PTPNs) (Nold et al. 2010, Luo et al. 2017). These events ultimately lead to suppression of cytokine production in several types of immune cells resulting in reduced inflammation.
R-HSA-9007892 Interleukin-38 signaling Interleukins are immunomodulatory proteins that elicit a wide array of responses in cells and tissues. Interleukin 1 family member 10 (IL1F10, IL 38) is a member of the IL1 family (Lin et al. 2001, Bensen et al. 2001). IL1F10 is selectively produced by human apoptotic cells (Mora et al. 2016) and human epidermal keratinocytes (based on mRNA studies) (Boutet M A et al. 2016). IL1F10 can bind to interleukin 1 receptor like 2 (IL1RL2) and may result in the suppression of IL 17 and IL 22 and induction of IL 6 production (van de Veerdonk et al. 2012, Mora et al. 2016). IL1F10 is synthesized as precursors that require N terminal processing to attain full receptor agonist or antagonist function (Mora et al. 2016). Both full length (1 – 152 amino acids) and N terminal truncated (20 – 152 amino acids) IL1F10 can bind Interleukin 1 receptor accessory protein like 1 (IL1RAPL1) (Mora et al. 2016). The binding affinity of truncated IL1F10 is much higher than that of the full length. However, binding of the full length or truncated forms has distinct outcomes; the former induces IL6 and the latter suppresses IL6 via JNK and AP1 signaling (Mora et al. 2016).
R-HSA-6785807 Interleukin-4 and Interleukin-13 signaling Interleukin-4 (IL4) is a principal regulatory cytokine during the immune response, crucially important in allergy and asthma (Nelms et al. 1999). When resting T cells are antigen-activated and expand in response to Interleukin-2 (IL2), they can differentiate as Type 1 (Th1) or Type 2 (Th2) T helper cells. The outcome is influenced by IL4. Th2 cells secrete IL4, which both stimulates Th2 in an autocrine fashion and acts as a potent B cell growth factor to promote humoral immunity (Nelms et al. 1999).
Interleukin-13 (IL13) is an immunoregulatory cytokine secreted predominantly by activated Th2 cells. It is a key mediator in the pathogenesis of allergic inflammation. IL13 shares many functional properties with IL4, stemming from the fact that they share a common receptor subunit. IL13 receptors are expressed on human B cells, basophils, eosinophils, mast cells, endothelial cells, fibroblasts, monocytes, macrophages, respiratory epithelial cells, and smooth muscle cells, but unlike IL4, not T cells. Thus IL13 does not appear to be important in the initial differentiation of CD4 T cells into Th2 cells, rather it is important in the effector phase of allergic inflammation (Hershey et al. 2003). IL4 and IL13 induce “alternative activation” of macrophages, inducing an anti-inflammatory phenotype by signaling through IL4R alpha in a STAT6 dependent manner. This signaling plays an important role in the Th2 response, mediating anti-parasitic effects and aiding wound healing (Gordon & Martinez 2010, Loke et al. 2002) There are two types of IL4 receptor complex (Andrews et al. 2006). Type I IL4R (IL4R1) is predominantly expressed on the surface of hematopoietic cells and consists of IL4R and IL2RG, the common gamma chain. Type II IL4R (IL4R2) is predominantly expressed on the surface of nonhematopoietic cells, it consists of IL4R and IL13RA1 and is also the type II receptor for IL13. (Obiri et al. 1995, Aman et al. 1996, Hilton et al. 1996, Miloux et al. 1997, Zhang et al. 1997). The second receptor for IL13 consists of IL4R and Interleukin-13 receptor alpha 2 (IL13RA2), sometimes called Interleukin-13 binding protein (IL13BP). It has a high affinity receptor for IL13 (Kd = 250 pmol/L) but is not sufficient to render cells responsive to IL13, even in the presence of IL4R (Donaldson et al. 1998). It is reported to exist in soluble form (Zhang et al. 1997) and when overexpressed reduces JAK-STAT signaling (Kawakami et al. 2001). It's function may be to prevent IL13 signalling via the functional IL4R:IL13RA1 receptor. IL13RA2 is overexpressed and enhances cell invasion in some human cancers (Joshi & Puri 2012).
The first step in the formation of IL4R1 (IL4:IL4R:IL2RB) is the binding of IL4 with IL4R (Hoffman et al. 1995, Shen et al. 1996, Hage et al. 1999). This is also the first step in formation of IL4R2 (IL4:IL4R:IL13RA1). After the initial binding of IL4 and IL4R, IL2RB binds (LaPorte et al. 2008), to form IL4R1. Alternatively, IL13RA1 binds, forming IL4R2. In contrast, the type II IL13 complex (IL13R2) forms with IL13 first binding to IL13RA1 followed by recruitment of IL4R (Wang et al. 2009).
Crystal structures of the IL4:IL4R:IL2RG, IL4:IL4R:IL13RA1 and IL13:IL4R:IL13RA1 complexes have been determined (LaPorte et al. 2008). Consistent with these structures, in monocytes IL4R is tyrosine phosphorylated in response to both IL4 and IL13 (Roy et al. 2002, Gordon & Martinez 2010) while IL13RA1 phosphorylation is induced only by IL13 (Roy et al. 2002, LaPorte et al. 2008) and IL2RG phosphorylation is induced only by IL4 (Roy et al. 2002).
Both IL4 receptor complexes signal through Jak/STAT cascades. IL4R is constitutively-associated with JAK2 (Roy et al. 2002) and associates with JAK1 following binding of IL4 (Yin et al. 1994) or IL13 (Roy et al. 2002). IL2RG constitutively associates with JAK3 (Boussiotis et al. 1994, Russell et al. 1994). IL13RA1 constitutively associates with TYK2 (Umeshita-Suyama et al. 2000, Roy et al. 2002, LaPorte et al. 2008, Bhattacharjee et al. 2013).
IL4 binding to IL4R1 leads to phosphorylation of JAK1 (but not JAK2) and STAT6 activation (Takeda et al. 1994, Ratthe et al. 2007, Bhattacharjee et al. 2013).
IL13 binding increases activating tyrosine-99 phosphorylation of IL13RA1 but not that of IL2RG. IL4 binding to IL2RG leads to its tyrosine phosphorylation (Roy et al. 2002). IL13 binding to IL4R2 leads to TYK2 and JAK2 (but not JAK1) phosphorylation (Roy & Cathcart 1998, Roy et al. 2002).
Phosphorylated TYK2 binds and phosphorylates STAT6 and possibly STAT1 (Bhattacharjee et al. 2013).
A second mechanism of signal transduction activated by IL4 and IL13 leads to the insulin receptor substrate (IRS) family (Kelly-Welch et al. 2003). IL4R1 associates with insulin receptor substrate 2 and activates the PI3K/Akt and Ras/MEK/Erk pathways involved in cell proliferation, survival and translational control. IL4R2 does not associate with insulin receptor substrate 2 and consequently the PI3K/Akt and Ras/MEK/Erk pathways are not activated (Busch-Dienstfertig & González-Rodríguez 2013).
R-HSA-6783589 Interleukin-6 family signaling The interleukin-6 (IL6) family of cytokines includes IL6, IL11, IL27, leukemia inhibitory factor (LIF), oncostatin M (OSM), ciliary neurotrophic factor (CNTF), cardiotrophin 1 and 2 (CT-1) and cardiotrophin-like cytokine (CLC) (Heinrich et al. 2003, Pflanz et al. 2002). The latest addition to this family is IL31, discovered in 2004 (Dillon et al. 2004). The family is defined largely by the shared use of the common signal transducing receptor Interleukin-6 receptor subunit beta (IL6ST, gp130). The IL31 receptor uniquely does not include this subunit, instead it uses the related IL31RA. The members of the IL6 family share very low sequence homology but are structurally highly related, forming anti-parallel four-helix bundles with a characteristic “up-up-down-down” topology (Rozwarski et al. 1994, Cornelissen et al. 2012).
Although each member of the IL6 family signals through a distinct receptor complex, their underlying signaling mechanisms are similar. Assembly of the receptor complex is followed by activation of receptor-associated Janus kinases (JAKs), believed to be constitutively associated with the receptor subunits.Activation of JAKs initiates downstream cytoplasmic signaling cascades that involve recruitment and phosphorylation of transcription factors of the Signal transducer and activator of transcription (STAT) family, which dimerize and translocate to the nucleus where they bind enhancer elements of target genes leading to transcriptional activation (Nakashima & Taga 1998).
Negative regulators of IL6 signaling include Suppressor of cytokine signals (SOCS) family members and PTPN11 (SHP-2).
IL6 is a pleiotropic cytokine with roles in processes including immune regulation, hematopoiesis, inflammation, oncogenesis, metabolic control and sleep.
IL6 and IL11 bind their corresponding specific receptors IL6R and IL11R respectively, resulting in dimeric complexes that subsequently associate with IL6ST, leading to IL6ST homodimer formation (in a hexameric or higher order complex) and signal initiation. IL6R alpha exists in transmembrane and soluble forms. The transmembrane form is mainly expressed by hepatocytes, neutrophils, monocytes/macrophages, and some lymphocytes. Soluble forms of IL6R (sIL6R) are also expressed by these cells. Two major mechanisms for the production of sIL6R have been proposed. Alternative splicing generates a transcript lacking the transmembrane domain by using splicing donor and acceptor sites that flank the transmembrane domain coding region. This also introduces a frameshift leading to the incorporation of 10 additional amino acids at the C terminus of sIL6R.A second mechanism for the generation of sIL6R is the proteolytic cleavage or 'shedding' of membrane-bound IL-6R. Two proteases ADAM10 and ADAM17 are thought to contribute to this (Briso et al. 2008). sIL6R can bind IL6 and stimulate cells that express gp130 but not IL6R alpha, a process that is termed trans-signaling. This explains why many cells, including hematopoietic progenitor cells, neuronal cells, endothelial cells, smooth muscle cells, and embryonic stem cells, do not respond to IL6 alone, but show a remarkable response to IL6/sIL6R. It is clear that the trans-signaling pathway is responsible for the pro-inflammatory activities of IL6 whereas the membrane bound receptor governs regenerative and anti-inflammatory IL6 activities
LIF, CNTF, OSM, CTF1, CRLF1 and CLCF1 signal via IL6ST:LIFR heterodimeric receptor complexes (Taga & Kishimoto 1997, Mousa & Bakhiet 2013). OSM signals via a receptor complex consisting of IL6ST and OSMR. These cytokines play important roles in the regulation of complex cellular processes such as gene activation, proliferation and differentiation (Heinrich et al. 1998).
Antibodies have been developed to inhibit IL6 activity for the treatment of inflammatory diseases (Kopf et al. 2010).
R-HSA-1059683 Interleukin-6 signaling Interleukin-6 (IL-6) is a pleiotropic cytokine with roles in processes including immune regulation, hematopoiesis, inflammation, oncogenesis, metabolic control and sleep. It is the founding member of a family of IL-6-related cytokines such as IL-11, IL-27 leukemia inhibitory factor (LIF), cilliary neurotrophic factor (CNTF) and oncostatin M.
The IL-6 receptor (IL6R) consists of an alpha subunit that specifically binds IL-6 and a beta subunit, IL6RB or gp130, which is the signaling component of all the receptors for cytokines related to IL-6. IL6R alpha exists in transmembrane and soluble forms. The transmembrane form is mainly expressed by hepatocytes, neutrophils, monocytes/macrophages, and some lymphocytes. Soluble forms of IL6R (sIL6R) are also expressed by these cells. Two major mechanisms for the production of sIL6R have been proposed. Alternative splicing generates a transcript lacking the transmembrane domain by using splicing donor and acceptor sites that flank the transmembrane domain coding region. This also introduces a frameshift leading to the incorporation of 10 additional amino acids at the C terminus of sIL6R.A second mechanism for the generation of sIL6R is the proteolytic cleavage or 'shedding' of membrane-bound IL-6R. Two proteases ADAM10 and ADAM17 are thought to contribute to this (Briso et al. 2008). sIL6R can bind IL6 and stimulate cells that express gp130 but not IL6R alpha, a process that is termed trans-signaling. This explains why many cells, including hematopoietic progenitor cells, neuronal cells, endothelial cells, smooth muscle cells, and embryonic stem cells, do not respond to IL6 alone, but show a remarkable response to IL6/sIL6R. It is clear that the trans-signaling pathway is responsible for the pro-inflammatory activities of IL-6 whereas the membrane bound receptor governs regenerative and anti-inflammatory IL-6 activities
IL6R signal transduction is mediated by two pathways:the JAK-STAT (Janus family tyrosine kinase-signal transducer and activator of transcription) pathway and the Ras-MAPK (mitogen-activated protein kinase) pathway. Negative regulators of IL-6 signaling include SOCS (suppressor of cytokine signals) and SHP2. Within the last few years different antibodies have been developed to inhibit IL-6 activity, and the first such antibodies have been introduced into the clinic for the treatment of inflammatory diseases (Kopf et al. 2010).
R-HSA-1266695 Interleukin-7 signaling Interleukin-7 (IL7) is produced primarily by T zone fibroblastic reticular cells found in lymphoid organs, and also expressed by non-hematopoietic stromal cells present in other tissues including the skin, intestine and liver. It is an essential survival factor for lymphocytes, playing a key anti-apoptotic role in T-cell development, as well as mediating peripheral T-cell maintenance and proliferation. This dual function is reflected in a dose-response relationship that distinguishes the survival function from the proliferative activity; low doses of IL7 (<1 ng/ml) sustain only survival, higher doses (>1 ng/ml) promote survival and cell cycling (Kittipatarin et al. 2006, Swainson et al. 2007).
The IL7 receptor is a heterodimeric complex of the the common cytokine-receptor gamma chain (IL2RG, CD132, or Gc) and the IL7-receptor alpha chain (IL7R, IL7RA, CD127). Both chains are members of the type 1 cytokine family. Neither chain is unique to the IL7 receptor as IL7R is utilized by the receptor for thymic stromal lymphopoietin (TSLP) while IL2RG is shared with the receptors for IL2, IL4, IL9, IL15 and IL21. IL2RG consists of a single transmembrane region and a 240aa extracellular region that includes a fibronectin type III (FNIII) domain thought to be involved in receptor complex formation. It is expressed on most lymphocyte populations. Null mutations of IL2RG in humans cause X-linked severe combined immunodeficiency (X-SCID), which has a phenotype of severely reduced T-cell and natural killer (NK) cell populations, but normal numbers of B cells. In addition to reduced T- and NK-cell numbers, Il2rg knockout mice also have dramatically reduced B-cell populations suggesting that Il2rg is more critical for B-cell development in mice than in humans. Patients with severe combined immunodeficiency (SCID) phenotype due to IL7R mutations (see Puel & Leonard 2000), or a partial deficiency of IL7R (Roifman et al. 2000) have markedly reduced circulating T cells, but normal levels of peripheral blood B cells and NK cells, similar to the phenotype of IL2RG mutations, highlighting a requirement for IL7 in T cell lymphopoiesis. It has been suggested that IL7 is essential for murine, but not human B cell development, but recent studies indicate that IL7 is essential for human B cell production from adult bone marrow and that IL7-induced expansion of the progenitor B cell compartment is increasingly critical for human B cell production during later stages of development (Parrish et al. 2009).
IL7 has been shown to induce rapid and dose-dependent tyrosine phosphorylation of JAKs 1 and 3, and concomitantly tyrosine phosphorylation and DNA-binding activity of STAT5a/b (Foxwell et al. 1995). IL7R was shown to directly induce the activation of JAKs and STATs by van der Plas et al. (1996). Jak1 and Jak3 knockout mice displayed severely impaired thymic development, further supporting their importance in IL7 signaling (Rodig et al. 1998, Nosaka et al. 1995).
The role of STAT5 in IL7 signaling has been studied largely in mouse models. Tyr449 in the cytoplasmic domain of IL7RA is required for T-cell development in vivo and activation of JAK/STAT5 and PI3k/Akt pathways (Jiang et al. 2004, Pallard et al. 1999). T-cells from an IL7R Y449F knock-in mouse did not activate STAT5 (Osbourne et al. 2007), indicating that IL7 regulates STAT5 activity via this key tyrosine residue. STAT5 seems to enhance proliferation of multiple cell lineages in mouse models but it remains unclear whether STAT5 is required solely for survival signaling or also for the induction of proliferative activity (Kittipatarin & Khaled, 2007).
The model for IL7 receptor signaling is believed to resemble that of other Gc family cytokines, based on detailed studies of the IL2 receptor, where IL2RB binds constitutively to JAK1 while JAK3 is pre-associated uniquely with the IL2RG chain. Extending this model to IL7 suggests a similar series of events: IL7R constitutively associated with JAK1 binds IL7, the resulting trimer recruits IL2RG:JAK3, bringing JAK1 and JAK3 into proximity. The association of both chains of the IL7 receptor orients the cytoplasmic domains of the receptor chains so that their associated kinases (Janus and phosphatidylinositol 3-kinases) can phosphorylate sequence elements on the cytoplasmic domains (Jiang et al. 2005). JAKs have low intrinsic enzymatic activity, but after mutual phosphorylation acquire much higher activity, leading to phosphorylation of the critical Y449 site on IL7R. This site binds STAT5 and possibly other signaling adapters, they in turn become phosphorylated by JAK1 and/or JAK3. Phosphorylated STATs translocate to the nucleus and trigger the transcriptional events of their target genes.
The role of the PI3K/AKT pathway in IL7 signaling is controversial. It is a potential T-cell survival pathway because in many cell types PI3K signaling regulates diverse cellular functions such as cell cycle progression, transcription, and metabolism. The ERK/MAPK pathway does not appear to be involved in IL7 signaling (Crawley et al. 1996).
It is not clear how IL7 influences cell proliferation. In the absence of a proliferative signal such as IL7 or IL3, dependent lymphocytes arrest in the G0/G1 phase of the cell cycle. To exit this phase, cells typically activate specific G1 Cyclin-dependent kinases/cyclins and down regulate cell cycle inhibitors such as Cyclin-dependent kinase inhibitor 1B (Cdkn1b or p27kip1). There is indirect evidence suggesting a possible role for IL7 stimulated activation of PI3K/AKT signaling, obtained from transformed cell lines and thymocytes, but not confirmed by observations using primary T-cells (Kittipatarin & Khaled, 2007). IL7 withdrawal results in G1/S cell cycle arrest and is correlated with loss of cdk2 activity (Geiselhart et al. 2001), both events which are known to be regulated by the dephosphorylating activity of Cdc25A. Expression of a p38 MAPK-resistant Cdc25A mutant in an IL-7-dependent T-cell line as well as in peripheral, primary T-cells was sufficient to sustain cell survival and promote cell cycling for several days in the absence of IL7 (Khaled et al. 2005). Cdkn1b is a member of the CIP/KIP family of cyclin-dependent cell cycle inhibitors (CKIs) that negatively regulates the G1/S transition. In IL7 dependent T-cells, the expression of Cdkn1b was sufficient to cause G1 arrest in the presence of IL7. Withdrawal of IL7 induced the upregulation of Cdkn1b and arrested cells in G1 while siRNA knockout of Cdkn1b enhanced cell cycle progression. However, adoptive transfer of Cdkn1b-deficient lymphocytes into IL7 deficient mice indicated that loss of Cdkn1b could only partially compensate for the IL7 signal needed by T-cells to expand in a lymphopenic environment (Li et al. 2006), so though Cdkn1b may be involved in negative regulation of the cell cycle through an effect on cdk2 activity, its absence is not sufficient to fully induce cell cycling under lymphopenic conditions.
R-HSA-8985947 Interleukin-9 signaling Interleukin 9 (IL9) binds interleukin 9 receptor a chain (IL9R) and the interleukin 2 receptor common gamma chain (IL2RG) to initiate IL9 signaling downstream cascade. IL9R colocalize with Interleukin 2 receptor α chain and MHC molecules in lipid rafts of human T lymphoma cells (Nizsalóczki et al. 2014). IL2RG is essential for IL9 dependent growth signal transduction (Kimura et al. 1995). IL9R (glycoprotein of 64 kDa) has saturable and specific binding sites with a Kd of 100 pM (Renauld et al. 1992). The activated IL9R complex recruits tyrosine kinase proteins from the Janus kinase (JAK) family: JAK1 (JAK1) and JAK3 (JAK3) for subsequent activation of the Signal transducer and activator of transcription (STAT) factors STAT1, STAT3 and STAT5. The activated STATs form STAT5 dimers and STAT1:STAT3 heterodimers (Neurath & Finotto 2016, Li & Rostami 2010).
R-HSA-8963676 Intestinal absorption Nutrient absorption occurs mostly in the small intestine. Processes annotated here include the uptake of dietary cholesterol and phytosterols, and of monosaccharides. Movement of the final products of digestion out of the intestinal lumen is mediated by arrays of transporters associated with the apical and basolateral surfaces of enterocytes (Yamada 2015).
R-HSA-8981373 Intestinal hexose absorption Hexoses, notably fructose, glucose, and galactose generated in the lumen of the small intestine by breakdown of dietary carbohydrate, are taken up by enterocytes lining the microvilli of the small intestine and released from them into the blood. Uptake into enterocytes is mediated by two transporters localized on the luminal surfaces of the cells. SLC5A1, also known as SGLT1, mediates the co-transport of sodium ions and glucose and galactose, and SLC2A5, also known as GLUT5, mediates fructose uptake (Wright 1998). Tetrameric SLC2A2, also known as GLUT2, localized on the basolateral surfaces of enterocytes, mediates the release of these hexoses into the blood (Kellett & Brot-Laroche 2005; Wright et al. 2004).
R-HSA-8942233 Intestinal infectious diseases Gastroenteritis, also known as infectious diarrhea, is an inflammatory disease of the stomach and small intestine caused by infections by viruses, bacteria, parasites and fungi. Signs and symptoms include diarrhea, vomiting, abdominal pain, fever, lack of energy, and dehydration. Gastroenteritis is usually an acute and self-limiting disease that does not require medication but the preferred method of treatment is oral rehydration therapy. Enterotoxigenic Escherichia coli (ETEC) is one of the leading bacterial causes of gastroenteritis worldwide (Kopic & Geibel 2010, Gonzales-Siles & Sjoling 2016).
R-HSA-8963678 Intestinal lipid absorption Niemann-Pick C1 Like 1 (NPC1L1) protein in enterocytes is critical for intestinal cholesterol and phytosterol absorption, and is the target of the drug ezetimibe (Davis et al. 2004).
R-HSA-5659898 Intestinal saccharidase deficiencies Defects in in two enzymes required for intestinal digestion of dietary carbohydrate, lactase (LCT, a domain of lactase-phlorizin hydrolase protein) and sucrase-isomaltase (SI), are annotated here. The first affects nursing infants; the second affects individuals after weaning.
The disaccharide lactose is a major constituent of human breast milk. To be taken up from the gut in the nursing infant, this sugar must first be hydrolyzed by LCT present on the external face of enterocytes in microvilli of the small intestine. Mutations that disrupt LCT activity are associated with acute illness in newborn children as lactose fermentation by gut bacteria leads to severe diarrhea. The condition is effectively treated by feeding affected infants a lactose-free formula. This congenital disease is distinct from the down-regulation of LCT expression after weaning in many human populations that is associated with a milder form of lactose intolerance in adults (Jarvela et al. 2009).
The starch in a post-weaning diet is digested by amylases to di- and oligosaccharides that must be further digested to monosaccharides in order to be taken up from the lumen of the small intestine into endothelial cells of the intestinal brush border. If they are not digested, a process in which enterocyte-associated SI plays a central role, they remain in the gut lumen and are fermented by gut bacteria, leading to osmotic and fermentative diarrhea (Naim et al. 2012; Van Beers et al. 1995).
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic The mammalian Golgi complex, a central hub of both anterograde and retrograde trafficking, is a ribbon of stacked cisterna with biochemically distinct compartments (reviewed in Glick and Nakano, 2009; Szul and Sztul, 2011). Anterograde cargo from the ERGIC and ER is received at the cis-Golgi, trafficked through the medial- and trans-Golgi and released through the trans-Golgi network (TGN) to the endolysosomal system and the plasma membrane. Although still under debate, current models of Golgi trafficking favour the cisternal maturation model, where anterograde cargo remain associated with their original lipid membrane during transit through the Golgi and are exposed to sequential waves of processing enzymes by the retrograde movement of Golgi resident proteins. In this way, cis-cisterna mature to medial- and trans-cisterna as the early acting Golgi enzymes are replaced by later acting ones (reviewed in Pelham, 2001; Storrie, 2005; Glick and Nakano, 2009; Szul and Sztul, 2011). More recently. a kiss-and-run (KAR) model for intra-Golgi trafficking has been proposed, which marries aspects of the cisternal maturation model with a diffusion model of transport (reviewed in Mironov et al, 2103).
Like the anterograde ERGIC-to Golgi transport step, intra-Golgi trafficking between the cisterna appears to be COPI-dependent (Storrie and Nilsson, 2002; Szul and Sztul, 2011). Numerous snares and tethering complexes contribute to the targeting and fusion events that are required to maintain the specificity and directionality of these trafficking events (reviewed in Chia and Gleeson, 2014). Golgi tethers include long coiled coiled proteins like the Golgins, as well as multisubunit tethers like the COG complex. These tethers make numerous interactions with other components of the secretory system including RABs, SNAREs, motor and coat proteins as well as components of the cytoskeleton (reviewed in Munro, 2011; Willet et al, 2013).
Retrograde traffic from the cis-Golgi back to the ERGIC and ER depends on both the COPI-dependent pathway, which appears to be important for recyling of KDEL receptors, and a more recently described COPI-independent pathway that relies on RAB6 (reviewed in Szul and Sztul, 2011; Heffernan and Simpson, 2014). RAB6 and RAB9 also play roles at the TGN side of the Golgi, where they are implicated in the docking of vesicles derived from the endolysosomal system and the plasma membrane (reviewed in Pfeffer, 2011)
R-HSA-6811438 Intra-Golgi traffic The mammalian Golgi consists of at least three biochemically distinct cisternae, cis-, medial- and trans (reviewed in Szul and Sztul, 2011; Day et al, 2013). The structure and function of the Golgi are tightly interconnected, such that proteins that are required for protein transport through the Golgi are often also required for the organization of the Golgi stacks, and vice versa (reviewed in Liu and Storrie, 2012; Liu and Storrie, 2015; Chia and Gleeson, 2014; Munro, 2011). Newly synthesized proteins from the ER and ERGIC are received at the cis face of the Golgi and flow through to the trans-Golgi before being released to the trans-Golgi network (TGN) for further secretion to the endolysosomal system, plasma membrane or extracellular region. Retrograde flow from the trans- to cis-cisternae moves endocytosed cargo from the extracellular region, the plasma membrane and the endolysosomal system back towards the ER. Intra-Golgi retrograde traffic also returns resident Golgi proteins to their appropriate cisternae, in this way facilitating cisternal remodeling or maturation (reviewed in Boncompain and Perez, 2013; Day et al, 2013). Intra-Golgi traffic in both directions is mediated by COPI carriers, with specificity of transport being determined at least in part by the complement of SNAREs, RABs and tethering proteins involved (reviewed in Szul and Sztul, 2011; Spang 2013; Willet et al, 2013; Chia and Gleeson, 2014).
R-HSA-434313 Intracellular metabolism of fatty acids regulates insulin secretion Fatty acids augment the glucose triggered secretion of insulin through two mechanisms: activation of FFAR1 (GPR40) and intracellular metabolism of fatty acids. Fatty acids are transported into the cell by CD36 (FAT) (Noushmehr et al. 2005) and metabolized by ligation to coenzyme A (Ansari et al. 2017), transport into mitochondria, and beta oxidation which generates ATP. The ATP increases the intracellular ratio of ATP:ADP and thereby closes potassium channels (K(ATP) channels) at the plasma membrane (reviewed in Acosta-Montano and Garcia-Gonzalez 2018). The enzymes that metabolize fatty acids in beta cells also metabolize fatty acids in other tissues however their combinations and subcellular locations may differ.
R-HSA-8981607 Intracellular oxygen transport Globins are heme-containing proteins that reversibly bind molecular oxygen. Humans contain at least 5 types of globins: hemoglobins, myoglobin, cytoglobin, neuroglobin, and androglobin (reviewed in Burmester et al. 2014). Myoglobin, neuroglobin, and cytoglobin are cytosolic globins with similar affinities for oxygen (reviewed in Hankeln et al. 2005). Androglobin is a more distantly related globin of uncertain function that is expressed in testes (Hoogewijs et al. 2012). Myoglobin is predominantly expressed in muscle tissue (reviewed in Helbo et al. 2013), neuroglobin is expressed in neurons, and cytoglobin is expressed in connective tissue fibroblasts and smooth muscle cells (reviewed in Pesce et al. 2002, Hankeln et al. 2004, Ascenzi et al. 2016). Whereas myoglobin contains pentacoordinated heme iron, neuroglobin and cytoglobin contain hexacoordinated heme iron: the iron atom is bound by 4 nitrogen atoms of heme and 2 histidine residues of the globin. Binding by one of the histidines is reversible, which allows the iron atom to bind various ligands such as molecular oxygen, carbon monoxide, and nitric oxide (reviewed in Kakar et al. 2010). Neuroglobin may function in oxygen homeostasis, however the importance of its oxygen-binding activity is unclear (reviewed in Pesce et al. 2002, Hankeln et al. 2005). Cytoglobin may function in nitric oxide metabolism (Thuy et al. 2016, Liu et al. 2017). Globins can also regulate oxygen homeostasis via reactions with nitric oxide (NO), a vasodilator. Oxygenated globins scavenge NO by oxidation while deoxygenated globins can act as a nitrite reductase to produce NO (reviewed in Hendgen-Cotta et al. 2014, Tejero and Gladwin 2014).
R-HSA-9006925 Intracellular signaling by second messengers Second messengers are generated within the cell as a downstream step in signal transduction cascades initiated by the interaction of an external stimulus with a cell surface receptor. Common second messengers include DAG, cAMP, cGMP, IP3, Ca2+ and phosphatidylinositols (reviewed in Kang et al, 2015; Raker et al, 2016; Li and Marshall, 2015; Pinto et al, 2015; Ahmad et al, 2015).
R-HSA-5620924 Intraflagellar transport Intraflagellar transport (IFT) is a motor-based process that controls the anterograde and retrograde transport of large protein complexes, ciliary cargo and structural components along the ciliary axoneme (reviewed in Cole and Snell, 2009). IFT particles contain two multiprotein IFT subcomplexes, IFT A and IFT B, with ~6 and ~15 subunits, respectively. Linear arrays of IFT A and IFT B 'trains' assemble at the ciliary base along with the active plus-end directed kinesin-2 motors and the inactive dynein motors and traffic along the microtubules at a rate of ~2 micrometers per second. At the ciliary tip, the IFT trains disassemble, releasing cargo and motors, and smaller IFT trains are subsequently reassembled for retrograde traffic driven by the now active minus-end directed dynein-2 motors. Retrograde trains travel down the length of the axoneme at a rate of ~3 micrometers per second and are disassembled and recycled for further rounds of transport at the ciliary base (reviewed in Taschner et al, 2012; Bhogaraju et al, 2013; Ishikawa et al, 2011). Mutations in kinesin-2 motors or IFT B complex members tend to abrogate cilium formation, while mutations in dynein-2 motor or in IFT A complex members generally result in short, bulging cilia that abnormally accumulate IFT particles. These observations are consistent with a primary role for IFT B and IFT A complexes in anterograde and retrograde transport, respectively (see for instance, Huangfu et al, 2005; Follit et al, 2006; May et al, 2005; Tran et al, 2008; reviwed in Ishikawa et al, 2011). In addition to the IFT A and B complexes, the IFT particles may also contain the multi-protein BBSome complex, which displays typical IFT-like movement along the ciliary axoneme and which is required for cilium biogenesis and delivery and transport of some ciliary cargo (Blaque et al, 2004; Nachury et al, 2007; Ou et al, 2005; Ou et al, 2007; reviewed in Sung and Leroux, 2013; Bhorgaraju et al, 2013).
R-HSA-109606 Intrinsic Pathway for Apoptosis The intrinsic (Bcl-2 inhibitable or mitochondrial) pathway of apoptosis functions in response to various types of intracellular stress including growth factor withdrawal, DNA damage, unfolding stresses in the endoplasmic reticulum and death receptor stimulation. Following the reception of stress signals, proapoptotic BCL-2 family proteins are activated and subsequently interact with and inactivate antiapoptotic BCL-2 proteins. This interaction leads to the destabilization of the mitochondrial membrane and release of apoptotic factors. These factors induce the caspase proteolytic cascade, chromatin condensation, and DNA fragmentation, ultimately leading to cell death. The key players in the Intrinsic pathway are the Bcl-2 family of proteins that are critical death regulators residing immediately upstream of mitochondria. The Bcl-2 family consists of both anti- and proapoptotic members that possess conserved alpha-helices with sequence conservation clustered in BCL-2 Homology (BH) domains. Proapoptotic members are organized as follows:
1. "Multidomain" BAX family proteins such as BAX, BAK etc. that display sequence conservation in their BH1-3 regions. These proteins act downstream in mitochondrial disruption.
2. "BH3-only" proteins such as BID,BAD, NOXA, PUMA,BIM, and BMF have only the short BH3 motif. These act upstream in the pathway, detecting developmental death cues or intracellular damage. Anti-apoptotic members like Bcl-2, Bcl-XL and their relatives exhibit homology in all segments BH1-4. One of the critical functions of BCL-2/BCL-XL proteins is to maintain the integrity of the mitochondrial outer membrane. R-HSA-140837 Intrinsic Pathway of Fibrin Clot Formation The intrinsic pathway of blood clotting connects interactions among kininogen (high molecular weight kininogen, HK), prekallikrein (PK), and factor XII to the activation of clotting factor X by a series of reactions that is independent of the extrinsic pathway and that is not subject to inhibition by TFPI. It is thus essential for the prolongation of the clotting cascade: while the reactions of the extrinsic pathway appear to be sufficient to initiate clot formation, those of the intrinsic pathway are required to maintain it (Broze 1995; Davie et al. 1991; Monroe et al. 2002). The intrinsic pathway can be divided into three parts: 1) reactions involving interactions of kininogen, prekallikrein, and factor XII, leading to the activation of factor XII, 2) reactions involving factor XI, factor IX, factor VIII, and von Willebrand factor (vWF) leading to the activation of factors VIII and IX, and 3) reactions that inactivate factor XIIa and kallikrein.
Kininogen, prekallikrein, and factor XII were first identified as proteins needed for the rapid formation of clots when whole blood is exposed to negatively charged surfaces in vitro. Early studies in vitro identified several possible sets of interactions, in which small quantities of one or more of these proteins 'autoactivate' and then catalyze the formation of larger quantities of activated factors. Subsequent work, however, suggests that these factors form complexes on endothelial cell surfaces mediated by C1q binding protein (C1q bp), that the first activation event is the cleavage of prekallikrein by prolylcarboxypeptidase, and that the resulting kallikrein catalyzes the activation of factor XII (Schmaier 2004).
The second group of events, occurs in vivo on the surfaces of activated platelets (although most biochemical characterization of the reactions was originally done with purified proteins in solution). Factor XI binds to the platelet glycoprotein (GP) Ib:IX:V complex, where it can be activated by cleavage either by thrombin (generated by reactions of the common pathway) or by activated factor XII (generated in the first part of the intrinsic pathway). Activated factor XI in turn catalyzes the activation of factor IX. Simultaneously, factor VIII, complexed with vWF, is cleaved by thrombin, activating it and causing its release from vWF. Activated factors VIII and IX form a complex on the platelet surface that very efficiently converts factor X to activated factor X. (Activated factors X and V then form a complex that efficiently activates thrombin.)
While these two groups of events can be viewed as forming a single functional pathway (e.g., Davie et al. 1991), human clinical genetic data cast doubt on this view. Individuals deficient in kininogen, prekallikrein, or factor XII proteins exhibit normal blood clot formation in vivo. In contrast, deficiencies of factor XI can be associated with failure of blood clotting under some conditions, and deficiencies of vWF, factor VIII, or factor IX cause severe abnormalities - von Willebrand disease, hemophilia A, and hemophilia B, respectively. These data suggest that while the second group of events is essential for normal clot formation in vivo, the first group has a different function (e.g., Schmaier 2004).
Finally, reactions neutralize proteins activated in the first part of the intrinsic pathway. Kallikrein forms stable complexes with either C1 inhibitor (C1Inh) or with alpha2-macroglobulin, and factor XIIa forms stable complexes with C1Inh. The relevance of these neutralization events to the regulation of blood clotting is unclear, however. The physiological abnormalities observed in individuals who lack C1Inh appear to be due entirely to abnormalities of complement activation; blood clotting appears to proceed normally. This observation is consistent with the hypothesis, above, that factor XIIa plays a limited role in normal blood clotting under physiological conditions.
R-HSA-8941237 Invadopodia formation Podosomes and invadopodia are actin-based dynamic protrusions of the plasma membrane of metazoan cells that represent sites of attachment to and degradation of the extracellular matrix (Linder & Kopp 2005, Murphy & Courtneidge 2011). They are characteristically composed of an actin-rich core surrounded by adhesion and scaffolding proteins. Current convention is to use the term podosome for the structures found in normal cells (such as monocytic cells, endothelial cells and smooth muscle cells) and in Src-transformed fibroblasts, and invadopodium for the structures found in cancer cells. The maturation process for podosomes and invadopodia involves the recruitment and activation of multiple pericellular proteases, which facilitates ECM degradation (Artym et al. 2006).
R-HSA-1296065 Inwardly rectifying K+ channels Inwardly rectifying K+ channels (Kir channels) show an inward rather than outward (like the voltage gated K+ channels) flow of K+ thereby contributing to maintenance of resting membrane potential and regulation of action potential in excitable tissue. Kir channels are found in a variety of cell types such as cardiac myocytes, neurons, blood cells, osteoblasts, glial cells, epithelial cells, and oocytes. Kir channels can be functionally divided into ATP sensitive K+ channels (Kir 6.1 and Kir 6.2), classical kir channels (Kir 2.1, 2.2, 2.3, 2.4, 5.1) G protein gated K+ channels (Kir 3.1, 3.2, 3.3, 3.4) and K+ transport channels (Kir1.1, 7.1, 4.2, 4.1).
R-HSA-983712 Ion channel transport Ion channels mediate the flow of ions across the plasma membrane of cells. They are integral membrane proteins, typically a multimer of proteins, which, when arranged in the membrane, create a pore for the flow of ions. There are different types of ion channels. P-type ATPases undergo conformational changes to translocate ions. Ligand-gated ion channels operate like a gate, opened or closed by a chemical signal. Voltage-gated ion channels are activated by changes in electrical potential difference at the membrane (Purves, 2001; Kuhlbrandt, 2004).
R-HSA-5578775 Ion homeostasis Ion channels and ion homeostasis in relation to cardiac conduction is described in this section (Couette et al. 2006, Bartos et al. 2015).
R-HSA-6803544 Ion influx/efflux at host-pathogen interface Essential metal ions act as co-factors that enable enzymes to catalyse a wider range of chemical transformations than would be achievable using solely organic catalysts. The precise metal requirements of organisms vary between species, environmental niches, metabolic states and circadian rhythms.
Metals are required cofactors for numerous processes that are essential to both pathogen and host. They are coordinated in enzymes responsible for DNA replication and transcription, relief from oxidative stress, and cellular respiration. However, excess transition metals can be toxic due to their ability to cause spontaneous redox cycling and disrupt normal metabolic processes. Vertebrates have evolved intricate mechanisms to limit the availability of some crucial metals while concurrently flooding sites of infection with antimicrobial concentrations of other metals.
Both pathogens and hosts have complex regulatory systems for metal homeostasis. Understanding these provides strategies for fighting pathogens, either by excluding essential metals from the microbes, by delivery of excess metals to cause toxicity, or by complexing metals in microorganisms.
R-HSA-936837 Ion transport by P-type ATPases The P-type ATPases (E1-E2 ATPases) are a large group of evolutionarily related ion pumps that are found in bacteria, archaea and eukaryotes. They are referred to as P-type ATPases because they catalyze auto-phosphorylation of a key conserved aspartate residue within the pump. They all appear to interconvert between at least two different conformations, E1 and E2. Most members of this transporter family pump a large variety of cations (Kuhlbrandt W, 2004).
R-HSA-451306 Ionotropic activity of kainate receptors Kainate receptors are either Ca2+ permeable or impermeable depending on the composition of the receptor and the editing status of subunits GluR5 and GluR6 (GRIK1 and 2).
R-HSA-917937 Iron uptake and transport The transport of iron between cells is mediated by transferrin. However, iron can also enter and leave cells not only by itself, but also in the form of heme and siderophores. When entering the cell via the main path (by transferrin endocytosis), its goal is not the (still elusive) chelated iron pool in the cytosol nor the lysosomes but the mitochondria, where heme is synthesized and iron-sulfur clusters are assembled (Kurz et al,2008, Hower et al 2009, Richardson et al 2010).
R-HSA-9914355 Isovaleric acidemia Isovaleric acidemia is an inborn error of metabolism that arises due to mutations in isovaleryl-CoA dehydrogenase (IVD), a mitochondrial enzyme that catalyzes the third step in the catabolic pathway for leucine, the conversion of isovaleryl-CoA and FAD to beta-methylcrotonyl-CoA and FADH2 (Tanaka et al, 1966; Finocchiaro et al. 1978; Rhead and Tanaka 1980). Isovaleric acidemia has variable clinical presentation and lacks a clear correspondence between genotypic alterations and phenotypic outcome (Vockley and Ensenauer, 2006). Symptoms include vomiting, seizures, low energy, and a characteristic sweaty foot odor due to presence of isovaleric acid, 3-hydroxyisovaleric acid, isovarleryl-glycine and isovaleryl-carnitine in blood and urine (Vockley et al, 1991; Mohsen et al, 1998; Zaki et al, 2017; Dercksen et al, 2012; D'Annibale et al, 2021).
R-HSA-450321 JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 C-Jun NH2 terminal kinases (JNKs) are an evolutionarily conserved family of serine/threonine protein kinases, that belong to mitogen activated protein kinase family (MAPKs - also known as stress-activated protein kinases, SAPKs). The JNK pathway is activated by heat shock, or inflammatory cytokines, or UV radiation.
The JNKs are encoded by at least three genes: JNK1/SAPK-gamma, JNK2/SAPK-alpha and JNK3/ SAPK-beta. The first two are ubiquitously expressed, whereas the JNK3 protein is found mainly in brain and to a lesser extent in heart and testes. As a result of alternative gene splicing all cells express distinct active forms of JNK from 46 to 55 kDa in size. Sequence alignment of these different products shows homologies of >80%. In spite of this similarity, the multiple JNK isoforms differ in their ability to bind and phosphorylate different target proteins, thus leading to the distinctive cellular processes: induction of apoptosis, or enhancment of cell survival, or proliferation.
Activation of JNKs is mediated by activated TAK1 which phosphorylates two dual specificity enzymes MKK4 (MAPK kinase 4) and MKK7(MAPK kinase 7).
R-HSA-5689877 Josephin domain DUBs The Josephin domain is present in four human DUBs: Ataxin-3 (ATXN3), ATXN3L, Josephin-1 (JOSD1) and JOSD2. All have been shown to possess DUB activity (Tzveltkov & Breuer 2007, Weeks et al. 2011). Josephin domain DUBs may specialize in distinguishing between polyubiquitin chains of different lengths (Eletr & Wilkinson 2014).
R-HSA-9755511 KEAP1-NFE2L2 pathway The KEAP1:NFE2L2 (KEAP1-NRF2, Kelch-like ECH-associated protein 1-Nuclear Factor (erythroid-derived 2)-like 2) regulatory pathway plays a central role in protecting cells against multiple homeostatic responses including adaptation to oxidative, inflammatory, metabolic, proteotoxic and xenobiotic stresses. The NFE2L2 transcriptome has been implicated in protection against many chronic diseases including cardiovascular, metabolic, neurodgenerative and respiratory diseases (reviewed in Cuadrado et al, 2018; Baird and Yamamoto, 2020). In cancer, NFE2L2 plays a critical role in the metabolic reprogramming, directing metabolic intermediates into the Warburg and pentose phosphate pathways to support proliferative growth and redox homeostasis (reviewed in He et al, 2020; Ge et al, 2020; Hayes et al, 2020; Kitamura and Hotomashi, 2018)
KEAP1 is a redox sensor that together with CUL3/RBX1 forms part of an E3 ubiquitin ligase, which tightly regulates the activity of the transcription factor NFE2L2 by targeting it for ubiquitination and proteasome-dependent degradation. Oxidative modifications or electrophile adduct formation with redox-sensitive cysteines within KEAP1 renders this protein unable to target bound NFE2L2 for ubiquitination and allows newly translated NFE2L2 to accumulate within the cell and translocate to the nucleus where it can promote its transcriptional program (reviewed in Cuadrado et al, 2019; Baird and Yamamoto, 2020).
R-HSA-9669921 KIT mutants bind TKIs Aberrant signaling by activated forms of KIT can be inhibited by tyrosine kinase inhibitors. Primary mutations in KIT are frequently found in exon 11, encoding the juxtamembrane domain responsible for autoinhibition of the kinase. These mutations are generally sensitive to tyrosine kinase inhibitors such as imatinib. Accumulation of secondary mutations in the ATP-binding pocket and the activation loop of the kinase domain contributes to resistance to first line tyrosine kinase inhibitors. KIT receptors with in these regions are sensitive to a panel of additional tyrosine kinase inhibitors such as sunitinib and regorafenib (Serrano et al, 2019; reviewed in Roskoski, 2018; Klug et al, 2018; Serrano et al, 2017).
R-HSA-450604 KSRP (KHSRP) binds and destabilizes mRNA KSRP binds to AU-rich sequences in the 3' untranslated regions of mRNAs. KSRP causes the bound mRNA to be targeted for hydrolysis by recruiting exonucleases and decapping enzymes. The activity of KSRP is regulated by phosphorylation. Protein kinase B/Akt phosphorylates KSRP at serine193. The phosphorylation inhibits the ability of KSRP to destabilize mRNA. KSRP phosphorylated at serine193 binds 14-3-3zeta (YWHAZ) which causes KSRP to be retained in the nucleus.
R-HSA-9702569 KW2449-resistant FLT3 mutants KW-2449 is a second generation, type I aurora kinase and FLT3 tyrosine kinase inhibitor, Despite effectiveness against a number of FLT3 mutant alleles, it has been withdrawn from development due to poor pharmacodynamics (reviewed in Larrosa-Garcia and Baer, 2017; Kazi and Roonstrand, 2019). This pathway describes FLT3 mutants that are resistant to inhibition by KW-2449.
R-HSA-2022854 Keratan sulfate biosynthesis Keratan sulfate (KSI) is the best characterised keratan sulfate. It is 10 times more abundant in cornea than cartilage. KSI is attached to an asparagine (Asn) residue on the core protein via an N-linked branched oligosaccharide (an N-glycan core structure used as a precursor in N-glycan biosynthesis). KSI is elongated by the alternate additions of galactose (Gal) and N-acetylglucosamine (GlcNAc), mediated by glycosyltransferases. Elongation is terminated by the addition of a single N-acetylneuraminic acid (sialyl) residue. KSI is also sulfated on Gal and GlcNAc residues by at least two sulfotransferases (Funderburgh 2000, Funderburgh 2002, Quantock et al. 2010). KSI can be attached to asparagine residues on core proteins, creating so called proteoglycans (PGs). Seven common core proteins found in corneal and skeletal tissues are used as examples here.
R-HSA-2022857 Keratan sulfate degradation Keratan sulfate proteoglycans (KSPGs) are degraded in lysosomes as part of normal homeostasis of glycoproteins. Glycoproteins must be completely degraded to avoid undigested fragments building up and causing a variety of lysosomal storage diseases. KSPGs are Asn-linked glycoproteins and are acted upon by exo-glycosidases to release sugar monomers. The main steps of degradation are shown representing the types of cleavage reactions that occur so the full degradation of KS is not shown to avoid repetition. The proteolysis of the core protein of the glycoprotein is not shown here (Winchester 2005, Aronson & Kuranda 1989).
R-HSA-1638074 Keratan sulfate/keratin metabolism Keratan sulfate (KS) (a glycosaminoglycan, GAG) is a linear polysaccharide that consists of the repeating disaccharide unit GlcNAc-Gal (N-acetylglucosamine-galactose). KS can perform a structural function and is found in bone, cartilage and the cornea. In joints, it also acts as a shock absorber due to its highly hydrated nature. There are several classes of KS, KSI, II and III. KSI is N-linked to asparagine (Asn) residues in the core protein and is predominantly found in the cornea. KSII is O-linked to serine (Ser) or Thr (threonine) residues in the core protein and is found predominantly in cartilage linked to the protein aggrecan, forming the most abundant proteoglycan in cartilage. A third class of KS, KSIII, are proteoglycans in the brain. KSIII chains are linked to Ser/Thr residues in the core protein via mannose (Funderburgh 2000, Funderburgh 2002).
Normally, the body degrades GAGs as a natural turnover. Defects in the degradative enzymes cause the autosomal recessive mucopolysaccharide storage disease Morquio's syndrome (also called mucopolysaccharidosis IV). This involves the build up of KS in lysosomes, manifesting clinically as skeletal, dental and corneal abnormalities (Tomatsu et al. 2005).
R-HSA-6805567 Keratinization Keratins are the major structural protein of vertebrate epidermis, constituting up to 85% of a fully differentiated keratinocyte (Fuchs 1995). Keratins belong to a superfamily of intermediate filament (IF) proteins that form alpha-helical coiled-coil dimers, which associate laterally and end-to-end to form approximately 10 nm diameter filaments. Keratin filaments are heteropolymeric, formed from equal amounts of acidic type I and basic /neutral type 2 keratins. Humans have 54 keratin genes (Schweitzer et al. 2006). They have highly specific expression patterns, related to the epithelial type and stage of differentiation. Roughly half of human keratins are specific to hair follicles (Langbein & Schweizer 2005). Keratin filaments bundle into tonofilaments that span the cytoplasm and bind to desmosomes and other cell membrane structures (Waschke 2008). This reflects their primary function, maintaining the mechanical stability of individual cells and epithelial tissues (Moll et al. 2008).
R-HSA-74182 Ketone body metabolism Acetoacetate, beta-hydroxybutyrate, and acetone collectively are called ketone bodies. The first two are synthesized from acetyl-CoA, in the mitochondria of liver cells; acetone is formed by spontaneous decarboxylation of acetoacetate. Ketone body synthesis in liver is effectively irreversible because the enzyme that catalyzes the conversion of acetoacetate to acetoacetyl-CoA is not present in liver cells.
Ketone bodies, unlike fatty acids and triglycerides, are water-soluble. They are exported from the liver, and are taken up by other tissues, notably brain and skeletal and cardiac muscle. There, they are broken down to acetyl-CoA which is oxidized via the TCA cycle to yield energy. In a normal person, this pathway of ketone body synthesis and utilization is most active during extended periods of fasting. Under these conditions, mobilization and breakdown of stored fatty acids generates abundant acetyl-CoA acetyl-CoA in liver cells for synthesis of ketone bodies, and their utilization in other tissues minimizes the demand of these tissues for glucose (Sass 2011).
R-HSA-9830369 Kidney development Kidney development begins at embryonic day 8.5 (E8.5) in mouse embryos, a time after gastrulation and formation of the intermediate mesoderm (reviewed in Marcotte et al. 2014, Smyth 2021, Schnell et al. 2022). Renal progenitors are specified within the intermediate mesoderm in the region between the 6th and 8th somites. The nephric duct then begins to form by mesenchymal to epithelial transitions of the renal progenitors and grows caudally to fuse with the bladder and urethra primordium (cloaca). The nephric duct induces the formation of mesonephric tubules in the adjacent nephric cord which form the mesonephros, an embryonic kidney in mammals that regresses and is supplanted by the metanephros. (In anamniotes such as frogs and fish, the mesonephros is the adult kidney and no metanephros forms.)
In mammals, the metanephros is initiated as the caudal region of the nephric cord forms metanephric mesenchyme which then interacts with the nephric duct to induce formation of the ureteric bud, the progenitor of the ureter. Branching of the ureteric bud forms ureter tips which induce nephron formation in the surrounding metanephric mesenchyme (reviewed in El-Dahr et al. 2008, O'Brien and McMahon 2014, Desgrange and Cereghini 2015, Chambers and Wingert 2020, Schnell et al. 2022).
Induction of kidney development in the intermediate mesoderm occurs by incompletely characterized signals from the adjacent ectoderm and lateral plate mesoderm. Notably, BMP activity from the lateral plate mesoderm can induce expression of the renal markers Pax2 and Lhx1.
Foxc1 and Foxc2 expressed in the paraxial mesoderm repress Lhx1 and prevent over-expansion of the intermediate mesoderm (Wilm et al. 2004). Conversely, Nodal signaling maintains Pax2 expression and prevents over-expansion of the paraxial mesoderm (Fleming et al. 2013). The rostral-caudal position of renal development appears to specified by the rostral-caudal gradient of retinoic acid acting through HoxB4 (Preger-Ben Noon et al. 2009) and limited caudally by HoxA6.
The combined expression of Pax2, Pax8, Lhx1, and Gata3 is the earliest observed marker of the renal lineage and these transcription factors, together with Emx2, form a self-reinforcing module that drives formation of the nephric duct. Nephronectin (Npnt) from the nephric duct interacts with integrin alpha8/beta1 (Itga8) on the metanephric mesenchyme and Ret located on the nephric duct interacts with Gdnf secreted by the metanephric mesenchyme to regulate formation and branching of the ureteric bud (reviewed in Marcotte et al. 2014). Signals from the tips of the ureteric bud then induce epithelialization of the metanephric mesenchyme and formation of nephrons, the basic filtration units of the kidney comprising the glomerulus, the proximal tubule, the loop of Henle, and the distal tubule (reviewed in Desgrange and Cereghini 2015). Canonical Wnt signaling from the ureteric bud appears to be the main inductive event: Wnt9b activates Wnt4 expression to epithelialize mesenchymal pre-tubular aggregates and Wnt9b also supports expression of Six2 to maintain a nephron progenitor pool in the cap mesenchyme.
Congenital anomalies of the kidney and urinary tract (CAKUT) comprise about 30% of antnatal congenital abnormalities and cause the majority of chronic kidney disease in children (reviewed in Costigan and Rosenblum 2022). Knowledge gained from studying kidney development is being used to generate kidney organoids in vitro with a goal of producing transplantable kidney tissue (reviewed in Kalejaiye et al. 2022, Safi et al. 2022, Trush and Takasato 2022, Shi et al. 2023).
R-HSA-9664420 Killing mechanisms The long-lasting Leishmania infection is established within macrophages in which the most effective killing response is the production of reactive oxygen species (ROS) and reactive nitrogen species (RNS). (Rossi and Fasel 2018). Additionally, autophagy has been described as an innate immune mechanism for eliminating intracellular pathogens, although its role in restricting Leishmania replication is unclear (Veras et al. 2019)
R-HSA-983189 Kinesins Kinesins are a superfamily of microtubule-based motor proteins that have diverse functions in transport of vesicles, organelles and chromosomes, and regulate microtubule dynamics. There are 14 families of kinesins, all reprsented in humans. A standardized nomenclature was published in 2004 (Lawrence et al.).
R-HSA-156827 L13a-mediated translational silencing of Ceruloplasmin expression While circularization of mRNA during translation initiation is thought to contribute to an increase in the efficiency of translation, it also appears to provide a mechanism for translational silencing. This might be achieved by bringing inhibitory 3' UTR-binding proteins into a position in which they interfere either with the function of the translation initiation complex or with the assembly of the ribosome (Mazumder et al 2001). Translational silencing of Ceruloplasmin (Cp) occurs 16 hrs after its induction by INF-gamma (Mazumder et al., 1997). Although the mechanism by which silencing occurs has not yet been determined, this process is mediated by the L13a subunit of the 60s ribosome and thought to require circularization of the Cp mRNA (Sampath et al., 2003; Mazumder et al., 2001; Mazumder et al., 2003). Between 14 and 16 hrs after INF gamma induction, the L13a subunit of the 60s ribosome is phosphorylated and released from the 60s subunit. Phosphorylated L13a then associates with the GAIT element in the 3' UTR of the Cp mRNA inhibiting its translation.
R-HSA-373760 L1CAM interactions The L1 family of cell adhesion molecules (L1CAMs) are a subfamily of the immunoglobulin superfamily of transmembrane receptors, comprised of four structurally related proteins: L1, Close Homolog of L1 (CHL1), NrCAM, and Neurofascin. These CAMs contain six Ig like domains, five or six fibronectin like repeats, a transmembrane region and a cytoplasmic domain. The L1CAM family has been implicated in processes integral to nervous system development, including neurite outgrowth, neurite fasciculation and inter neuronal adhesion.
L1CAM members are predominately expressed by neuronal, as well as some nonneuronal cells, during development. Except CHL1 all the other members of L1 family contain an alternatively spliced 12-nclueotide exon, encoding the amino acid residues RSLE in the neuronal splice forms but missing in the non-neuronal cells. The extracellular regions of L1CAM members are divergent and differ in their abilities to interact with extracellular, heterophilic ligands. The L1 ligands include other Ig-domain CAMs (such as NCAM, TAG-1/axonin and F11), proteoglycans type molecules (neurocan), beta1 integrins, and extra cellular matrix protein laminin, Neuropilin-1, FGF and EGF receptors. Some of these L1-interacting proteins also bind to other L1CAM members. For example TAG-1/axonin interact with L1 and NrCAM; L1, neurofascin and CHL1 binds to contactin family members. The cytoplasmic domains of L1CAM members are most highly conserved. Nevertheless, they have different cytoplasmic binding partners, and even those with similar binding partners may be involved in different signaling complexes and mechanisms. The most conserved feature of L1CAMs is their ability to interact with the actin cytoskeletal adapter protein ankyrin. The cytoplasmic ankyrin-binding domain, exhibits the highest degree of amino acid conservation throughout the L1 family.
R-HSA-8964038 LDL clearance LDL (low-density lipoproteins) are complexes of a single molecule of apoprotein B-100 (apoB-100) non-covalently associated with triacylglycerol, free cholesterol, cholesterol esters, and phospholipids.Clearance of LDL from the blood involves binding to LDL receptors associated with coated pits at the cell surface, forming complexes that are internalized and passed via clathrin-coated vesicles to endosomes, where they dissociate. The LDL particles move into lysosomes and are degraded while the LDL receptors are returned to the cell surface. This process occurs in most cell types but is especially prominent in hepatocytes. It plays a major role in returning cholesterol from peripheral tissues to the liver (Hobbs et al. 1990).
R-HSA-8964041 LDL remodeling LDL (low density lipoproteins) are complexes of a single molecule of apoprotein B-100 (apoB-100) non-covalently associated with triacylglycerol, free cholesterol, cholesterol esters, and phospholipids. CETP (cholesterol ester transfer protein) complexed with cholesterol esters interacts with an LDL (low density lipoprotein) particle, acquiring triacylglycerol molecules and donating cholesterol ester to the LDL (Swenson et al. 1988; Morton & Zilversmit 1983), a key step in the transport of tissue cholesterol to the liver.
As an alternative to LDLR-mediated uptake and degradation, a LDL particle can bind a single molecule of LPA (apolipoprotein A), forming a Lp(a) lipoprotein particle (Lobentanz et al. 1998).
R-HSA-5682910 LGI-ADAM interactions Synapse formation and maturation require multiple interactions between presynaptic and postsynaptic neurons. These interactions are mediated by a diverse set of synaptogenic proteins (Kegel et al. 2013, Siddiqui & Craig 2011). Initial synapse formation needs both the binding of secreted proteins to presynaptic and postsynaptic receptors, and the direct binding between presynaptic and postsynaptic transmembrane proteins. One class of molecules that plays an important role in cellular interactions in nervous system development and function is the leucine-rich glioma inactivated (LGI) protein family. These are secreted synaptogenic proteins consisting of an LRR (leucine-rich repeat) domain and a epilepsy-associated or EPTP (epitempin) domain (Gu et al. 2002). Both protein domains are generally involved in protein-protein interactions. Genetic and biochemical evidence suggests that the mechanism of action of LGI proteins involves binding to a subset of cell surface receptors belonging to the ADAM (a disintegrin and metalloproteinase) family, i.e. ADAM11, ADAM22 and ADAM23. These interactions play crucial role in the development and function of the vertebrate nervous system mainly mediating synaptic transmission and myelination (Kegel et al. 2013, Novak 2004, Seals & Courtneidge 2003).
R-HSA-5340573 LGK974 inhibits PORCN Aberrant WNT signaling is associated with the development of numerous cancers, and strategies for targeting this pathway are under intense investigation (reviewed in Polakis, 2012; Polakis, 2000; Yao et al, 2011). Secretion of WNT ligand depends on its PORCN-dependent palmitoleoylation in the ER, making PORCN a attractive therapeutic target in cases where WNT is aberrantly over-expressed (reviewed in MacDonald et al, 2009). LGK974 is a PORCN-inhibitor that was identified in a screen for compounds that abrogate the secretion of WNT ligands, and is in Phase I clinical trials for the treatment of WNT-dependent cancers (Liu et al, 2013)
R-HSA-3134973 LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production Leucine-rich repeat flightless-interacting protein 1 (LRRFIP1) can bind exogenous double-stranded RNA and double-stranded DNA (Wilson SA et al. 1998; Yang P et al. 2010). LRRFIP1 was shown to mediate Listeria monocytogenes- and vesicular stomatitis virus (VSV)-induced IFN-beta production in mouse primary macrophages by regulating beta-catenin activity. Beta-catenin possibly functions as a transcriptional cofactor of IRF3 to initiate Ifnb1 transcription (Yang P et al. 2010).
R-HSA-9664535 LTC4-CYSLTR mediated IL4 production The Leukotriene C4 (LTC4) is a metabolite of arachidonic acid that can be produced intracellularly or extracellularly. LTC4 binds an unidentified, intracellular cysLTR. Signalling downstream LTC4 cysLTR binding has been associated with the production of IL4, independent of the GPCR associated heterotrimeric protein Gq (Bandeira Melo et al. 2002).
R-HSA-5653890 Lactose synthesis Synthesis of the disaccharide lactose takes place within the Golgi apparatus of epithelial cells of the lactating mammary gland. The synthesis itself is a single chemical reaction of free glucose and UDP-galactose to form lactose and UDP. For this reaction to occur, glucose is transported from the cytosol into the Golgi lumen, and B4GALT1 interacts with LALBA (alpha-lactalbumin) to modulate its substrate specificity (Brew and Hill 1975).
R-HSA-69186 Lagging Strand Synthesis Due to the antiparallel nature of DNA, DNA polymerization is unidirectional, and one strand is synthesized discontinuously. This strand is called the lagging strand. Although the polymerase switching on the lagging strand is very similar to that on the leading strand, the processive synthesis on the two strands proceeds quite differently. Short DNA fragments, about 100 bases long, called Okazaki fragments are synthesized on the RNA-DNA primers first. Strand-displacement synthesis occurs, whereby the primer-containing 5'-terminus of the adjacent Okazaki fragment is folded into a single-stranded flap structure. This flap structure is removed by endonucleases, and the adjacent Okazaki fragments are joined by DNA ligase.
R-HSA-3000157 Laminin interactions Laminins are a large family of conserved, multidomain trimeric basement membrane proteins. There are many theoretical trimer combinations but only 18 have been described (Domogatskaya et al. 2012, Miner 2008, Macdonald et al. 2010) and the existence of isoforms laminin-212 and/or laminin-222 (Durbeej et al. 2010) awaits further confirmation. The chains assemble through coiled-coil domains at their C-terminal end. Alpha chains additionally have a large C-terminal globular domain containing five LG subdomains (LG1-5). The N termini are often referred to as the short arms. These have varying numbers of laminin-type epidermal growth factor-like (LE) repeats. Trimer assembly is controlled by highly specific coiled-coil interactions (Domogatskaya et al. 2012). Some laminin isoforms are modified extracellularly by proteolytic processing at the N- or C-terminal ends prior to their binding to cellular receptors or other matrix molecules (Tzu & Marinkovitch 2008).
The cell adhesion properties of laminins are mediated primarily through the alpha chain G domain to integrins, dystroglycan, Lutheran glycoprotein, or sulfated glycolipids. The N-terminal globular domains of the alpha-1 (Colognato-Pyke et al. 1995) and alpha-2 chains (Colognato et al. 1997) and globular domains VI (Nielsen & Yamada 2001) and IVa (Sasaki & Timpl 2001) of the alpha-5 chain can bind to several integrin isoforms (alpha1beta1, alpha2beta1, alpha3beta1, and alphaVbeta3), which enables cell binding at both ends of laminins with these alpha chains.
R-HSA-162599 Late Phase of HIV Life Cycle The late phase of the HIV-1 life cycle includes the regulated expression of the HIV gene products and the assembly of viral particles. The assembly of viral particles will be covered in a later release of Reactome. HIV-1 gene expression is regulated by both cellular and viral proteins. Although the initial activation of the HIV-1 transcription is facilitated by cellular transcription factors including NF-kappa B (Nabel and Baltimore, 1987), this activation results in the production of primarily short transcripts (Kao et al., 1987). Expression of high levels of the full length HIV-1 transcript requires the function of the HIV-1 Tat protein which promotes elongation of the HIV-1 transcript (reviewed in Karn, 1999; Taube et al. 1999; Liou et al., 2004; Barboric and Peterlin 2005). The HIV-1 Rev protein is required post-transcriptionally for the expression of the late genes. Rev functions by promoting the nuclear export of unspliced and partially spliced transcripts that encode the major structural proteins Gag, Pol and Env, and the majority of the accessory proteins (Malim et al., 1989; reviewed in Pollard and Malim 1998 .
R-HSA-9772573 Late SARS-CoV-2 Infection Events The coronavirus virion consists of structural proteins, namely spike (S), envelope (E), membrane (M), nucleocapsid (N) and, for some betacoronaviruses, haemagglutinin-esterase. The positive-sense, single-stranded RNA genome (+ssRNA) is encapsidated by N, whereas M and E ensure its incorporation in the viral particle during the assembly process. S trimers protrude from the host-derived viral envelope and provide specificity for cellular entry receptors. SARS-CoV-2 particles bind to angiotensin-converting enzyme 2 (ACE2) cellular receptors and together with host factors (such as the cell surface serine protease TMPRSS2), promote viral uptake and fusion at the cellular or endosomal membrane. Following entry, the release and uncoating of the incoming genomic RNA subject it to the immediate translation of two large open reading frames, ORF1a and ORF1b. ORF1a and ORF1b encode 1516 non-structural proteins (nsp), of which 15 compose the viral replication and transcription complex (RTC) that includes, amongst others, RNA-processing and RNA-modifying enzymes and an RNA proofreading function necessary for maintaining the integrity of the >30kb coronavirus genome. ORFs that encode structural proteins and interspersed ORFs that encode accessory proteins are transcribed from the 3' one-third of the genome to form a nested set of subgenomic mRNAs (sg mRNAs). The resulting polyproteins pp1a and pp1ab are co-translationally and post-translationally processed into the individual non-structural proteins (nsps) that form the viral replication and transcription complex. Concordant with the expression of nsps, the biogenesis of viral replication organelles consisting of characteristic perinuclear double-membrane vesicles (DMVs), convoluted membranes (CMs) and small open double-membrane spherules (DMSs) create a protective microenvironment for viral genomic RNA replication and transcription of subgenomic mRNAs comprising the characteristic nested set of coronavirus mRNAs. Translated structural proteins translocate into endoplasmic reticulum (ER) membranes and transit through the ER-to-Golgi intermediate compartment (ERGIC), where interaction with N-encapsidated, newly produced genomic RNA results in budding into the lumen of secretory vesicular compartments. Finally, virions are secreted from the infected cell by exocytosis. A successful intracellular coronavirus life cycle invariably relies on critical molecular interactions with host proteins that are repurposed to support the requirements of the virus. This includes host factors required for virus entry (such as the entry receptor and host cell proteases), factors required for viral RNA synthesis and virus assembly (such as ER and Golgi components and associated vesicular trafficking pathways) and factors required for the translation of viral mRNAs (such as critical translational initiation factors)
R-HSA-9615710 Late endosomal microautophagy Microautophagy (MI) is a non-selective autophagic pathway that involves internalisation of cytosolic cargo through invaginations of the lysosomal membrane. MI can be induced by nitrogen starvation and complements other related self-eating processes such as Macroautophagy (MA) and Chaperone Mediated Autophagy (CMA). MI can degrade cell organelles and bulk cytosolic proteins directly via the lysosome and late endosome. MI can also target substrates with KFERQ motifs with the help of HSPA8 (Li W W et al. 2012).
R-HSA-1222499 Latent infection - Other responses of Mtb to phagocytosis Mtb encounters a vastly changed environment, soon after it gets internalized by macrophages. The compartment it resides in, the phagosome, is acidified and devoid of important metal ions. It is flooded with reactive oxygen and nitrogen species. And steps will be soon taken by the macrophage to "mature" the phagosome with all kinds of lysosomal digestive enzymes. However, unlike most other bacteria species Mtb. has evolved solutions to each of these threats and, after making sure these are installed, it soon will enter a dormant state (de Chastellier, 2009; Flannagan et al, 2009). A combination of the host defense and the response of the infecting bacillus (active and passive) ensure suppression of bacterial metabolic activity and replication, resulting in a non-replicating state (Russell 2011, Russell et al. 2010).
R-HSA-69109 Leading Strand Synthesis The processive complex is responsible for synthesizing at least 5-10 kb of DNA in a continuous manner during leading strand synthesis. The incorporation of nucleotides by pol delta is quite accurate. However, incorporation of an incorrect nucleotide does occur occasionally. Misincorporated nucleotides are removed by the 3' to 5' exonucleolytic proofreading capability of pol delta.
R-HSA-166662 Lectin pathway of complement activation Activation of the lectin pathway (LP) is initiated by Mannose-binding lectin (MBL), the hetero-complex CL-LK formed from COLEC11 (Collectin liver 1, CL-L1) and COLEC10 (Collectin kidney 1, CL-K1), and the ficolins (FCN1, FCN2, FCN3). All are Ca-dependent (C-type) lectins that initiate the complement cascade after binding to specific carbohydrate patterns on the target cell surface. All form trimers and larger oligomers (Jensen et al. 2005, Dommett et al. 2006, Garlatti et al. 2010). MBL and ficolins circulate in plasma as complexes with homodimers of MBL-associated serine proteases (MASP) (Fujita et al. 2004, Hajela et al. 2002). MASP1, MASP2 and MASP3 have all been reported to mediate complement activation. Upon binding of human lectin to the target surface, the complex of lectin:MASP undergoes conformational changes that result in MASP cleavage and activation (Matsushita M et al. 2000, Fujita et al. 2004). Active MASP2 cleaves C4 to generate C4a and C4b. C4b binds to the target cell surface via its thioester bond, then binds circulating C2 (Law and Dodds 1997). Bound C2 is cleaved by MASP2 to yield the C3 convertase C4b:C2a. The active form of MASP1 was reported to cleave C2 in a manner similar to MASP2 (Matsushita et al. 2000, Chen & Wallis 2004). MASP1 can cleave proenzyme MASP2, leading to complement activation (Heja et al. 2012). MASP1 can also cleave fibrinogen to yield fibrinopeptide B, and activates factor XIII. MASP1 may have a role in removal of 'dead C3', i.e. C3(H2O) (Hajela et al. 2002). In addition to MASP1 to 3, two alternatively-slpiced forms of MASP1 (MAp44) and MASP2 (sMAP) have been implicated in complement cascade signaling (Takahashi et al. 1999, Degn et al. 2010). The functions of MASP3, sMAP and MAp44 in the lectin pathway remain to be clarified.
R-HSA-9658195 Leishmania infection Intracellular parasites of the genus Leishmania constitute the etiologic agent of a disease complex called Leishmaniasis. Leishmania parasites alternate between two distinct developmental stages: the insect-adapted, flagellated, extracellular “promastigote” and the mammal-adapted, non flagellated, intracellular “amastigote” form, where the later resides within phagolysosomal vesicles of the phagocytic cell (Liu et al. 2012a). Paradoxically, the macrophage, which is the main host cell where the parasite replicates and grows, is at the same time the main cell responsible for its elimination.
The uptake of Leishmania promastigotes by host cells is a receptor mediated process that initiates phagocytosis (Ueno et al. 2012). Some parasites differentiate and survive within the macrophage phagolysosomes; others are killed by the acidic and higher temperature environment (Rossi et al. 2018). In the end, it is the balance between the host and parasitic factors that control the activation/deactivation of macrophages that determines the fate of the parasites as well as the infection outcome (Liu et al. 2012b).
The pathways curated here summarize the major steps of parasite internalization by the macrophage, the defence mechanisms that are turned on and the mechanisms of evasion of the parasite to counteract them.
R-HSA-9664433 Leishmania parasite growth and survival Leishmania parasites infecting macrophages are considered a good model to study successful evolutionary mechanisms of evasion of the macrophage mediated immune response (Olivier et al. 2005). To evade killing by the host, Leishmania parasites manipulate the host's cellular signaling mechanisms, to prevent the production of microbicidal molecules and stimulating the activation of protective signaling pathways or to interfere with effective antigen presentation (Liu et al. 2012a). In most natural infections or after the resolution of the disease, a few Leishmania parasites remain in the host, perhaps as a product of a balance between forces favouring parasite persistence and those favouring destruction (Mandell et al. 2017).
R-HSA-9664417 Leishmania phagocytosis The internalization mechanism of leishmania parasites depends on not only the dynamic nature of the parasite's surface, but whether it is a non infective (procyclic) or infective (metacyclic) promastigote or infective amastigote, and also its virulent nature (Ueno et al. 2012 & Lee et al. 2018). Host receptors reported to facilitate Leishmania internalization include the third complement receptor (CR3), first complement receptor (CR1), mannose receptor (MR), Fc gamma receptors (FCGRs) and fibronectin receptors (FNRs) (Ueno et al 2012). The route of entry to the macrophage can affect the fate of the Leishmania parasite (Ueno et al. 2012).
R-HSA-391906 Leukotriene receptors Leukotriene receptors bind leukotriene ligands. There are four types of receptor in humans; two for leukotriene B4 and two for cysteinyl leukotrienes (Brink C et al, 2003).
R-HSA-9037629 Lewis blood group biosynthesis The Lewis antigen system is a human blood group system based upon genes on chromosome 19 p13.3 (the FUT3 gene aka the Le gene) and 19q13.3, (FUT2 gene aka the Se gene). Both genes are expressed in glandular epithelia and have dominant alleles (Le and Se, respectively) coding for enzymes with fucosyltransferase activity and recessive alleles (le and se, respectively) that are non-functional. There are two main Lewis antigens, Lewis A and Lewis B which can result in three common phenotypes: Le(A+B-), Le(A-B+) and Le(A-B-). Lewis antigens are components of exocrine epithelial secretions, and can be adsorbed onto the surfaces of red blood cells (RBCs), therefore are not produced directly by RBCs themselves (Ewald & Sumner 2016).
The same two oligosaccharides (Type 1 and Type 2) used to determine ABO blood types are also utilised by the Lewis system. Fucosyltransferase 3 (FUT3, Le) adds fucose to Type 1 chains to form the Lewis A antigen (LeA). IF the individual is a non-secretor (lacks the Se gene, homozygous sese), LeA is adsorbed onto the red cell, and that individual is LeA type. Approximately 80% of the population has the Se gene. Functional fucosyltransferase 2 (FUT2, Se) adds a fucose to LeA to form LeB. Both LeA and LeB present in the plasma of secretors but LeA preferentially adsorbs onto the RBC and therefore, the individual types as LeB. Other FUTs, especially FUT4, can add a fucose to Type 2 chains to form the Lewis X antigen (LeX). Further fucosylation of LeX by FUT2 produces the Lewis Y antigen (LeY). LeX and LeY are structural isomers of LeA and LeB. The formation of LeY is controlled by Se/se as in the case for LeB. LeA and LeX antigens can also undergo sialation to produce sialated forms of these antigens.
Aberrant glycosylation of tumour cells is recognised as a feature of cancer pathogenesis. Overexpression of fucosylated and sialated Lewis antigens frequently occurs on the surfaces of cancer cells and is mainly attributed to upregulated expression of the relevant fucosyltransferases (FUTs). The sialyl-Lewis A antigen (sLeA), also known as the CA19-9 antigen, is the most common tumour marker used primarily in the management of pancreatic and gastrointestinal cancers worldwide (Magnani 2004, Blanas et al. 2018).
Selectins (L-, E- and P-selectin) are type I membrane proteins composed of long N-terminus C-type lectin domains protruding into the extracellular space and with a short cytoplasmic tail. They bind carbohydrate structures through a Ca2+-dependent domain, the minimal sugar structure recognised fulfilled by sLeA and sLeX. Selectins are found on endothelial cells, platelets and leukocytes and are involved in trafficking of cells of the innate immune system, T lymphocytes and platelets, thereby playing important roles in chronic and acute inflammation and haemostasis. Selectins also play a role in cancer progression. Metastasis is facilitated by cell-cell interactions between cancer cells and endothelial cells in distant tissues. In addition, cancer cell interactions with platelets and leukocytes contribute to cancer cell adhesion, extravasation, and the establishment of metastatic lesions. Targeting selectins and their ligands as well as the enzymes involved in their generation, in particular sialyl transferases, could be a useful strategy in cancer treatment (Ley 2003, Laubli & Borsig 2010, Cheung et al. 2011, Natoli et al. 2016, Trinchera et al. 2017).
R-HSA-5632681 Ligand-receptor interactions Repression of Hh signaling in the absence of ligand depends on the transmembrane receptor protein Patched (PTCH), which inhibits Smoothened (SMO) activity by an unknown mechanism. This promotes the proteolytic processing and/or degradation of the GLI family of transcription factors and maintains the pathway in a transcriptionally repressed state (reviewed in Briscoe and Therond, 2013). In the absence of ligand, PTCH is localized in the cilium, while SMO is largely concentrated in intracellular compartments. Upon binding of Hh to the PTCH receptor, PTCH is endocytosed, relieving SMO inhibition and allowing it to accumulate in the primary cilium (Marigo et al, 1996; Chen and Struhl, 1996; Stone et al, 1996; Rohatgi et al, 2007; Corbit et al, 2005; reviewed in Goetz and Anderson, 2010). In the cilium, SMO is activated by an unknown mechanism, allowing the full length transcriptional activator forms of the GLI proteins to accumulate and translocate to the nucleus, where they bind to the promoters of Hh-responsive genes (reviewed in Briscoe and Therond, 2013).
In addition to PTCH, three additional membrane proteins have been shown to bind Hh and to be required for Hh-dependent signaling in vertebrates: CDON (CAM-related/downregulated by oncogenes), BOC (brother of CDO) and GAS1 (growth arrest specific 1) (Yao et al, 2006; Okada et al, 2006; Tenzen et al, 2006; McLellan et al, 2008; reviewed in Kang et al, 2007; Beachy et al, 2010; Sanchez-Arrones et al, 2012). CDON and BOC, homologues of Drosophila Ihog and Boi respectively, are evolutionarily conserved transmembrane glycoproteins that have been shown to bind both to Hh ligand and to the canonical receptor PTCH to promote Hh signaling (Okada et al, 2006; Yao et al, 2006; Tenzen et al, 2006, McLellan et al, 2008; Izzi et al, 2011; reviewed in Sanchez-Arrones et al, 2012). Despite the evolutionary conservation, the mode of ligand binding by CDON/Ihog and BOC/Boi is distinct in vertebrates and invertebrates. High affinity ligand-binding by CDON and BOC requires Ca2+, while invertebrate ligand-binding is heparin-dependent (Okada et al, 2006; Tenzen et al, 2006; McLellan et al, 2008; Yao et al, 2006; Kavran et al, 2010). GAS1 is a vertebrate-specific GPI-anchored protein that similarly binds both to Hh ligand and to the PTCH receptor to promote Hh signaling (Martinelli and Fan, 2007; Izzi et al, 2011; reviewed in Kang et al, 2007). CDON, BOC and GAS1 have partially overlapping but not totally redundant roles, and knock-out of all three is required to abrogate Hh signaling in mice (Allen et al, 2011; Izzi et al, 2011; reviewed in Briscoe and Therond, 2013).
R-HSA-2046105 Linoleic acid (LA) metabolism Linoleic acid (LA, 18:2(n-6)) is an omega-6 fatty acid obtained through diet, mainly from vegetable oils. Omega-6 fatty acids helps stimulate skin and hair growth, maintain bone health, regulate metabolism, and maintain the reproductive system. All the desaturation and elongation steps occur in the endoplasmic reticulum (ER) except for the final step which requires translocation to peroxisomes for partial beta-oxidation. The linoleic acid pathway involves the following steps: 18:2(n-6)-->18:3(n-6)--> 20:3(n-6)-->20:4(n-6)-->22:4(n-6)-->24:4(n-6)-->24:5(n-6)-->22:5(n-6). Two desaturation enzymes are involved in this process: delta-6 desaturase which converts 18:2(n-6) to 18:3 (n-6) and 24:4(n-6) to 24:5(n-6) respectively, and delta-5 desaturase which converts 20:3(n-6) to 20:4(n-6). (Sprecher 2002).
R-HSA-8964572 Lipid particle organization Lipid droplets (LDs) are cytosolic structures found in cells of all eukaryotes, comprising a monolayer of phospholipids surrounding a core of uncharged lipids such as triglyceride (TAG) and sterol esters. CIDEA, CIDEB and CIDEC were first studied for their roles in promotion of apoptosis but they are also known to play a role in energy metabolism. CIDEA and C bind to lipid droplets and regulate their enlargement, thereby restricting lipolysis and favouring storage (by promoting net neutral lipid transfer from smaller to larger lipid droplets) (Gao & Goodman 2015). LD formation involves the partitioning of neutral lipids from their site of synthesis at the endoplasmic reticulum (ER) to the cytosol. The fat storage-inducing transmembrane proteins 1 and 2 (FITM1 and FITM2), associated with the ER membrane, mediate binding and partitioning of TAGs into LDs. The short-chain dehydrogenases/reductases (SDR) family is a large family of NAD- or NADP-dependent oxidoreductase enzymes. 17-beta-hydroxysteroid dehydrogenase 13 (HSD17B13) is a recently-discovered enzyme of unknown physiological function that is associated with lipid droplets and significantly upregulated in patients with nonalcoholic fatty liver disease. Hypoxia-inducible lipid droplet-associated protein (HILPDA) is a lipid droplet protein and stimulates intracellular lipid accumulation.
R-HSA-9613354 Lipophagy Triglycerides stored in lipid droplets are hydrolysed under nutrient starvation to release fatty acids for energy. The content of lipid droplets may vary but they are all coated with a protective protein called perilipin. When this protein is degraded, lipid droplets associate with autophagic components and breakdown into fatty acids (Ward C et al. 2016, Schulze R J et al. 2017). This process is termed as lipophagy (Singh R et al. 2009).
R-HSA-8876384 Listeria monocytogenes entry into host cells Listeria monocytogenes is a short, gram-positive, nonspore-forming motile rod. Serotypes 1/2a, 1/2b and 4b make up more than 95% of isolates from humans, with serotype 4b causing most of the food-borne outbreaks. Listeria monocytogenes enters the body through the gastrointestinal tract after ingestion of contaminated food. The bacteria can survive food preservation procedures, such as refrigeration, low pH and high salt.
Listeria monocytogenes expresses several adhesin proteins at the cell surface that facilitate bacterial binding and entry to host cells. The bacteria can enter host cells through endocytosis mediated by binding of the bacterial InlA (internalin) protein to CDH1 (E-cadherin) at the host cell plasma membrane. Listeria monocytogenes can also enter host cells through endocytosis mediated by binding of the bacterial InlB protein to MET receptor tyrosine kinase at the host cell plasma membrane. Listeria monocytogenes proliferates inside the host cells and triggers formation of filopods, elongated protrusions of the host plasma membrane that contain bacteria. Filopods are ingested by adjacent cells, allowing Listeria monocytogenes to spread from cell to cell, invisible to the immune system of the host.
Listeria monocytogenes can cross the intestinal, blood-brain and placental barriers. In immunocompetent adults Listeria monocytogenes infection usually causes gastroenteritis. In infants infected in utero and in immunocompromised adults Listeria monocytogenes infection can result in meningoencephalitis and bacteremia (sepsis).
InlA is critical for crossing the intestinal barrier while both InlA and InlB are needed for crossing the placental barrier (Gessain et al. 2015) and, based on in vitro studies, the blood-cerebrospinal fluid barrier (Grundler et al. 2013). It seems that the intrinsic level of PI3K activity in Listeria-targeted host cells determines whether the entry depends on InlA only or InlA and InlB. The interaction of InlA with E-cadherin does not activate PI3K/AKT signaling while the interaction of InlB with the MET receptor activated the PI3K/AKT signal transduction cascade. Therefore, InlB-MET interaction may be important in tissues with low intrinsic PI3K activity (Gessain et al. 2015). Even if InlA-E-cadherin route is sufficient for bacterial entry, InlB may accelerate bacterial invasion (Pentecost et al. 2010). Cholesterol levels in host cell plasma membrane may also influence the preferred route for bacterial endocytosis (Seveau et al. 2004). In addition to InlA and InlB, many other virulence factors are involved in the Listeria monocytogenes infection cycle (Camejo et al. 2011) and will be annotated as mechanistic details become available.
For review, please refer to Bonazzi et al. 2009, Brooks et al. 2010, Camejo et al. 2011, Pizarro-Cerda et al. 2012.
R-HSA-446343 Localization of the PINCH-ILK-PARVIN complex to focal adhesions The interactions among ILK, PINCH, and parvins are necessary but not sufficient for localization of ILK to cell-ECM adhesions (Zhang et al., 2002). Additional proteins that interact with PINCH-ILK-parvin complex components likely participate in mediating its localization (reviewed in Wu, 2004).
R-HSA-9620244 Long-term potentiation In long-term potentiation (LTP), involved in learning and memory, a brief period of synaptic activity induces a lasting increase in the strength of the synapse. LTP is initiated by NMDA receptor-mediated activation of calcium/calmodulin-dependent protein kinase II (CaMKII), followed by binding of CaMKII to the NMDA receptor and CaMKII-mediated phosphorylation of AMPA receptor subunits (reviewed by Lisman et al. 2012 and Luscher and Malenka 2012).
R-HSA-2644607 Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling Loss of function mutations found in FBXW7 in T-cell acute lymphoblastic leukemia are predominantly dominant negative missense mutations that target one of the three highly conserved arginine residues in the WD repeats of FBXW7 (Thompson et al. 2007, O'Neil et al. 2007). These three arginine residues are part of the FBXW7 substrate binding pocket and each one of them contacts the phosphorylated threonine residue in the conserved substrate phosphodegron region (Orlicky et al. 2003). Specifically, FBXW7 interacts with the PEST domain of NOTCH1 upon phosphorylation of the PEST domain by CDK8 (Fryer et al. 2004). FBXW7 mutants are therefore unable to bind and promote ubiquitination of the NOTCH1 intracellular domain (NICD1), leading to prolonged NICD1 transcriptional activity (Thompson et al. 2007, O'Neil et al. 2007).
R-HSA-3304349 Loss of Function of SMAD2/3 in Cancer Loss-of-function of SMAD2 and SMAD3 in cancer occurs less frequently than the loss of SMAD4 function and was studied in most detail in colorectal cancer (Fleming et al. 2013).
Similarly to SMAD4, coding sequence mutations in SMAD2 and SMAD3 in cancer cluster in the MH2 domain, involved in the formation of transcriptionally active heterotrimers with SMAD4. Another region of SMAD2 and SMAD3 that is frequently mutated in cancer is the phosphorylation motif Ser-Ser-X-Ser at the very C-terminus (Fleming et al. 2013). The phosphorylation of this conserved motif by the activated TGF-beta receptor complex is an essential step in SMAD2 and SMAD3 activation and a prerequisite for the formation of heterotrimers with SMAD4 (Chacko et al. 2001, Chacko et al. 2004).
Smad2 knockout mice die at embryonic day 8.5, with impaired visceral endoderm function and deficiency in mesoderm formation. Smad2+/- heterozygotes appear normal and are fertile (Hamamoto et al. 2002). While polyps of compound Smad2+/-;Apc+/- mice show no difference in the number, size or histopathology from the polyps of Apc+/- mice (Takaku et al. 2002, Hamamoto et al. 2002), Smad2+/-;Apc+/- mice develop extremely large intestinal tumors and multiple invasive cancers not observed in Apc+/- mice. Therefore, loss of Smad2 does not contribute to initiation of intestinal tumorigenesis, but accelerates malignant progression (Hamamoto et al. 2002). Smad3 knockout mice are viable and fertile but die between 4 and 6 months of age from colorectal adenocarcinoma (Zhu et al. 1998), indicating that the loss of Smad3 initiates intestinal tumorigenesis.
R-HSA-3304347 Loss of Function of SMAD4 in Cancer SMAD4 was identified as a gene homozygously deleted in ~30% of pancreatic cancers and was named DPC4 (DPC stands for deleted in pancreatic cancer). SMAD4 maps to the chromosomal band 18q21.1, and about 90% of pancreatic carcinomas show allelic loss at chromosomal arm 18q (Hahn et al. 1996), while ~50% of pancreatic cancers show some alteration of the SMAD4 gene (reviewed by Schutte et al. 1999).
Based on COSMIC database (Catalogue Of Somatic Mutations In Cancer) (Forbes et al. 2011), mutations in the coding sequence of SMAD4 gene are frequently found in pancreatic cancer, biliary duct carcinoma and colorectal cancer (reviewed by Schutte et al. 1999). Germline SMAD4 mutations are the cause of juvenile polyposis, an autosomal dominant disease that predisposes affected individuals to hamartomatous polyps and gastrointestinal cancer (Howe et al. 1998). Homozygous Smad4 loss is embryonic lethal in mice (Takaku et al. 1998). Smad4 +/- heterozygotes appear normal but develop intestinal polyps between 6 and12 months of age and these polyps can progress to cancer. Loss of the remaining wild-type Smad4 allele is detectable only at later stages of tumor progression in Smad4+/- mice (Xu et al. 2000). Compound Apc+/-;Smad4+/- mice develop malignant tumors from intestinal polyps more rapidly than Apc+/- mice (Takaku et al. 1998).
SMAD4 coding sequence mutations are most frequently found in the MH2 domain and impair the formation of SMAD4 heterotrimers with phosphorylated SMAD2 and SMAD3 (Shi et al. 1997, Fleming et al. 2013), thereby impairing SMAD4:SMAD2/3 heterotrimer-mediated transcriptional regulation of TGF-beta responsive genes. MH2 domain is also involved in the formation of SMAD4 homotrimers which may play a role in SMAD4 protein stability (Shi et al. 1997).
Coding sequence mutations are also found in the MH1 domain of SMAD4. MH1 domain is involved in DNA binding (Dai et al. 1999) and it is also involved in the formation of SMAD4 homotrimers (Hata et al. 1997).
R-HSA-3656534 Loss of Function of TGFBR1 in Cancer TGF-beta receptor 1 (TGFBR1) loss-of-function is a less frequent mechanism for inactivation of TGF-beta signaling in cancer compared to SMAD4 and TGFBR2 inactivation. Genomic deletion of TGFBR1 locus has been reported in pancreatic cancer (Goggins et al. 1998), biliary duct cancer (Goggins et al. 1998) and lymphoma (Schiemann et al. 1999), while loss-of-function mutations have been reported in breast (Chen et al. 1998) and ovarian cancer (Chen et al. 2001), metastatic head-and-neck cancer (Chen et al. 2001), and in Ferguson-Smith tumors (multiple self-healing squamous epithelioma - MSSE) (Goudie et al. 2011). Loss-of-function mutations mainly affect the ligand-binding extracellular domain of TGFBR1 and the kinase domain of TGFBR1 (Goudie et al. 2011). In the mouse model of colorectal cancer, Tgfbr1 haploinsufficiency cooperates with Apc haploinsufficiency in the development of intestinal tumors (Zeng et al. 2009).
R-HSA-3642278 Loss of Function of TGFBR2 in Cancer Loss-of-function of transforming growth factor-beta receptor II (TGFBR2) is most prevalent in colorectal cancer. Over 60% of colorectal cancers with microsatellite instability (MSI) harbor inactivating mutations in both alleles of TGFBR2, mostly 1 or 2 bp deletions in the 10 bp adenine repeat that codes for three lysine residues in the extracellular domain of TGFBR2. These small deletions result in a frameshift and a premature stop codon (Markowitz et al. 1995). TGFBR2 kinase domain (KD) mutations are found in ~20% of microsatellite stable (MSS) colorectal cancers and these are mostly missense mutations that results in substitution of conserved amino acids in the kinase domain (Grady et al. 1999), likely impairing the catalytic activity of TGFBR2 KD mutants. The silencing of TGFBR2 gene via promoter methylation has been reported in B-cell lymphoma (Chen et al. 2007). Knockout of murine Tgfbr2 in colonic epithelium promotes azoxymethane-induced colon cancer formation (Biswas et al. 2004) and increases the number of adenomas and adenocarcinomas in Apc+/- mice (Munoz et al. 2006).
R-HSA-9723907 Loss of Function of TP53 in Cancer TP53 is the most frequently mutated tumor suppressor gene, with mutations present in more than 50% of human tumors and germline mutation in TP53 being underlying cause of the cancer-predisposing Li-Fraumeni syndrome (reviewed in Monti et al. 2020). The TP53 gene maps to chromosomal band 17p13 and encodes a transcription factor that contains four functional domains. A transactivation domain (TAD) involves amino acid residues 1-61 and is involved in interaction with components of the transcription machinery. A DNA binding domain (DBD) involves amino acid residues 94-290 and interacts with specific DNA target sequences called p53 response elements. A C-terminal domain (CTD) involves residues 357-393 and regulates DNA binding (reviewed in Monti et al. 2020). A tetramerization domain (TD) involves amino acids 325-355 and is needed for the formation of TP53 homotetramers. TP53 is considered the “guardian of the genome” (Lane 1992) as it is activated by DNA damage to initiate, depending on the amount of damage, cell cycle arrest, senescence or apoptosis (reviewed in Reinhardt and Schumacher 2012). In addition, TP53 regulates the expression of DNA repair genes, and is involved in the regulation of metabolism and autophagy (reviewed in Monti et al. 2020).
Most cancer-derived TP53 mutations are missense mutations that affect the central DNA binding domain of TP53 (amino acid residues 94-312). Eight hotspot amino acid substitutions in this region (R175H, G245S, R248Q, R248W, R249S, R273H, R273S and R282W) are found in close to 30% of TP53-mutated cancers. Based on their functional impact, TP53 mutations can be classified as 1) loss-of-function (LOF), 2) partial LOF (which may involve temperature sensitivity); 3) wild type-like (WT-L) or super-transactivating (ST) mutants; 4) mutants with altered specificity (AS), which are active or partially active on some but inactive on other TP53 target genes; 5) dominant-negative (DN) mutants, able to tetramerize with and inhibit the activity of the wild type TP53 protein. Some of the TP53 mutants, especially in the category of ST and AS mutants, are gain-of-function (GOF) mutants, able to interact with novel target genes and/or novel components of the transcriptional machinery (reviewed in Monti et al. 2020, and Gencel-Augusto and Lozano 2020).
Due to the complex function of WT-L, ST, AS and DN mutants of TP53, we have so far focused on annotating LOF mutants of TP53 which are unable to oligomerize due to mutations in the TD. Although accounting for a small percent of TP53 mutants, TD mutant are therefore considered to be completely defective in transcriptional activity, with no possibility of AS, DN and GOF effects (Chène and Bechter 1999, reviewed in Chène 2001, and Kamada et al. 2016). However, when overexpressed, some missense TD mutants of TP53 can form homotetramers and heterotetramers with the wild type TP53 which are partially functional and some extent of AS, DN and GOF effects may not be excluded for those mutants (Atz et al. 2000, reviewed in Chène 2001). In addition, the synthetic mutant p153(1-320) which consists of the first 320 amino acids and lacks the TD and CTD, while unable to tetramerize, can form stacked oligomers at the recombinant target gene promoter and induce transcription at a low level. Stacked oligomers are formed through interactions that involve amino acid residues outside the TD, which are facilitated by the presence of a target DNA sequence (Stenger et al. 1994).
R-HSA-9022534 Loss of MECP2 binding ability to 5hmC-DNA Missense mutations in the methyl-CpG binding domain (MBD) of MECP2, spanning amino acids 90 to 162, negatively affect the binding ability of MECP2 to hydroxymethylated DNA (Mellen et al. 2012).
R-HSA-9022538 Loss of MECP2 binding ability to 5mC-DNA Missense mutations in the methyl-CpG binding domain (MBD) of methyl-CpG-binding protein 2 (MECP2), spanning amino acids 90 to 162, negatively affect the binding ability of MECP2 to methylated DNA (Ghosh et al. 2008, Ho et al. 2008, Goffin et al. 2012, Mellen et al. 2012).
R-HSA-9022537 Loss of MECP2 binding ability to the NCoR/SMRT complex Missense mutations in the transcriptional repression domain of methyl-CpG-binding protein 2 (MECP2) can negatively affect binding of MECP2 to the nuclear receptor co-repressor (NCoR/SMRT) complex (Lyst et al. 2013, Ebert et al. 2013).
R-HSA-380259 Loss of Nlp from mitotic centrosomes During interphase, Nlp interacts with gamma-tubulin ring complexes (gamma-TuRC), and is thought to contribute to the organization of interphase microtubules (Casenghi et al.,2003). Plk1 is activated at the onset of mitosis and phosphorylates Nlp triggering its displacement from the centrosome (Casenghi et al.,2003). Removal of Nlp appears to contribute to the establishment of a mitotic scaffold with enhanced microtubule nucleation activity.
R-HSA-9005891 Loss of function of MECP2 in Rett syndrome Loss of function mutations in methyl-CpG-binding protein 2 (MECP2), an epigenetic regulator of transcription, are the major cause of Rett syndrome, a neurodevelopmental disorder that affects 1 in 10,000-15,000 female births. The symptoms of Rett syndrome appear after 6-18 months of apparently normal postnatal development and include regression of acquired language and motor skills, stereotypic hand movements, intellectual disability, epileptic seizures and respiratory disturbances. Besides Rett syndrome, aberrant MECP2 expression is implicated as an underlying cause of other neuropsychiatric disorders (reviewed by Banerjee et al. 2012, Ebert and Greenberg 2013, Lyst and Bird 2015). Only functionally characterized MECP2 mutations are annotated. For a comprehensive list of MECP2 mutations reported in Rett syndrome, please refer to the RettBASE (http://mecp2.chw.edu.au), a database dedicated to curation of disease variants of MECP2, CDKL5 and FOXG1 in Rett syndrome (Krishnaraj et al. 2017).
The pathway "Loss of MECP2 binding ability to the NCoR/SMRT complex" describes MECP2 loss-of-function mutations reported in Rett syndrome that impair its ability to associate with the NCoR/SMRT complex.
The pathway "Loss of phosphorylation of MECP2 at T308" describe loss-of-function mutations in MECP2 reported in Rett syndrome that impair its ability to undergo phosphorylation at threonine residue 308 in response to neuronal activity.
The pathway "Loss of MECP2 binding ability to 5hmC-DNA" describes MECP2 loss-of-function mutations reported in Rett syndrome that impair the ability of MECP2 to bind to hydroxymethylated DNA.
The pathway "Loss of MECP2 binding ability to 5mC-DNA" describes MECP2 loss-of-function mutations reported in Rett syndrome that impair the ability of MECP2 to bind to methylated DNA.
R-HSA-9723905 Loss of function of TP53 in cancer due to loss of tetramerization ability The physiologically active form of TP53 is homotetramer, which represents a dimer of dimers (Lee et al. 1994, Clore et al. 1994, Jeffrey et al. 1995), with the dimer considered to represent a transient intermediate (Mateau et al. 1998, Mateau et al. 1999, Natan et al. 2009). The tetramerization domain (TD) of TP53 localizes to the C-terminal region and involves amino acid residues 325-355 and is connected to the DNA binding domain (DBD) via a short unstructured region (reviewed in Wang et al 1993). The destabilizing effects of some of the DBD mutations in TP53 can only be observed in the context of the TP53 tetramer, but not in monomeric TP53 (Lubin et al. 2010). A number of nonsense and frameshift truncations result in mutant TP53 proteins that lack the tetramerization domain. In addition, several missense mutations affect the tetramerization domain, some of which, like R342P and L344P, have been shown to impede tetramerization (Chène and Bechter 1999; Lubin et al. 2010). Oligomerization-defective TP53 TD mutants are considered to be complete loss-of-function mutants in terms of their transcriptional activity, without altered specificity, dominant-negative or gain-of-function effects (Chène and Bechter 1999, reviewed in Chène 2001). However, when overexpressed, some missense TD mutants of TP53 can form homotetramers and heterotetramers with the wild type TP53 which are partially functional and some extent of AS, DN and GOF effects may not be excluded for those mutants (Atz et al. 2000, reviewed in Chène 2001). In addition, the synthetic mutant p153(1-320) which consists of the first 320 amino acids and lacks the TD and the C-terminal domain (CTD), while unable to tetramerize, can form stacked oligomers at the recombinant target gene promoter and induce transcription at a low level. Stacked oligomers are formed through interactions that involve amino acid residues outside the TD, which are facilitated by the presence of a target DNA sequence (Stenger et al. 1994). Recombinant TP53 that consists of amino acid residues 83-323 also predominantly exists as a monomer (reviewed in Wang et al. 1994).
R-HSA-9022535 Loss of phosphorylation of MECP2 at T308 Missense mutations of methyl-CpG-binding protein 2 (MECP2) in the vicinity of its threonine T308 phosphorylation site can negatively affect the ability of MECP2 to be phosphorylated at T308 in response to neuronal membrane depolarization (neuronal activity) (Ebert et al. 2013).
R-HSA-380284 Loss of proteins required for interphase microtubule organization from the centrosome In addition to recruiting proteins and complexes necessary for increased microtubule nucleation, centrosomal maturation involves the loss of proteins involved in interphase microtubule organization and centrosome cohesion (Casenghi et al., 2003; Mayor et al., 2002).
R-HSA-9865125 Loss-of-function mutations in BCKDHA or BCKDHB cause MSUD Mutations in either of the protein subunits of the E1 decarboxylase subcomplex of BCKDH are associated with Maple Syrup Urine Disease 1 (MSUD1).
Mutations of residues in BCKDHA that participate in subunit associations or that form part of the hydrophobic core destabilize the overall assembly of BCKDH and are associated with classic Maple Syrup Urine Disease 1A (Aevarsson et al, 2000; reviewed in Straus et al, 2020; Biswas et al, 2019). Mutations of BCKDHA with less drastic effects on structural stability of the overall BCKDH complex are generally associated with intermediate or intermittent forms of MSUD, and are not annotated in this pathway (reviewed in Strauss et al, 2020)
Mutations in BCKDHB appear to be causative in 35% of MSUD cases(reviewed in Strauss et al, 2020). Classic Maple Syrup Disease 1B is associated with severe loss-of-function mutations in BCKDHB that destabilize the protein interaction interfaces and compromise structural integrity of the complex (reviewed in Straus et al, 2020; Biswas et al, 2019). Less detrimental mutations in BCKDHB are not annotated in this pathway and are generally associated with intermediate or intermittent forms of MSUD (reviewed in Strauss et al, 2020).
R-HSA-9865113 Loss-of-function mutations in DBT cause MSUD2 Loss-of-function mutations in DBT disrupt the integrity of the E2 subunit of BCKDH, resulting in MSUD2 (reviewed in Strauss et al, 2020; Biswas et al, 2019).
R-HSA-9907570 Loss-of-function mutations in DLD cause MSUD3/DLDD Mutations in the dihydrolipoyl dehydrogenase (DLD) gene are associated with dihydrolipoyl dehydrogenase deficiency (DLDD), an autosomal recessive disorder characterized by lactic acidosis and neurological deterioration (reviewed in Quinonez et al, 2021). DLDD is sometimes referred to as Maple Syrup Urine Disease 3 due to its effects on BCKDH function, but the phenotype is distinct due to the involvement of DLD in multiple protein complexes (reviewed in Strauss et al, 2020).
DLD encodes the shared E3 component of the multiprotein mitochondrial enzymes BCKDH (branched-chain amino acid dehydrogenase), KGDH (alpha-ketoglutarate deydrogenase) and PDH (pyruvate dehydrogenase). In consequence mutations in DLD have pleiotropic effects and manifest with a range of clinical outcomes, including increased urinary excretion of alpha-keto acids and accumulation of pyruvate and plasma branched-chain amino acids in plasma (reviewed in Quinonez and Thoene, 2021). Mutations in DLD often occur as compound heterozygotes complicating the assignment of pathogenic effect. Moreover, the severity of phenotypic effects displayed in vivo does not correlate linearly with the extent of residual DLD enzymatic activity in vitro (Shany et al, 1999; Cameron et al, 2006; Quinonez et al, 2013; reviewed in Quinonez and Thoene, 2021).
R-HSA-71064 Lysine catabolism In humans, most catabolism of L-lysine normally proceeds via a sequence of seven reactions which feeds into the pathway for fatty acid catabolism. In the first two reactions, catalyzed by a single enzyme complex, lysine is combined with alpha-ketoglutarate to form saccharopine, which in turn is cleaved and oxidized to yield glutamate and alpha-ketoadipic semialdehyde. The latter molecule is further oxidized to alpha-ketoadipate. Alpha-ketoadipate is oxidatively decarboxylated by the alpha-ketoglutarate dehydrogenase complex (the same enzyme complex responsible for the conversion of alpha-ketoglutarate to succinyl-CoA in the citric acid cycle), yielding glutaryl-CoA. Glutaryl-CoA is converted to crotonyl-CoA, crotonyl-CoA is converted to beta-hydroxybutyryl-CoA, and beta-hydroxybutyryl-CoA is converted to acetoacetyl-CoA. The products of lysine catabolism are thus exclusively ketogenic; i.e., under starvation conditions they can be used for the synthesis of ketone bodies, beta-hydroxybutyrate and acetoacetate, but not for the net synthesis of glucose (Cox 2001; Goodman and Freeman 2001).
R-HSA-8853383 Lysosomal oligosaccharide catabolism N-Glycosylation is one of the most common co- and posttranslational modifications of eukaryotic proteins occurring in the ER lumen. N-glycosylation plays pivotal roles in protein folding and intra- or inter-cellular trafficking of N-glycosylated proteins. Quality control mechanisms in the ER sift out incorrectly-folded proteins from correctly-folded proteins, the former then destined for degradation. Incorrectly-folded N-glycans are exported to the cytosol where the process of degradation begins. Once the unfolded protein is cleaved from the oligosaccharide (forming free oligosaccharides, fOS), step-wise degradation of mannose moieties, both in the cytosol (Suzuki & Harada 2014) and then in the lysosome (Aronson & Kuranda 1989, Winchester 2005), results in complete degradation. Breakdown must be complete to avoid lysosomal storage diseases that occur when fragments as small as dimers are left undigested.
R-HSA-432720 Lysosome Vesicle Biogenesis Proteins that have been synthesized, processed and sorted eventually reach the final steps of the secretory pathway. This pathway is responsible not only for proteins that are secreted from the cell but also enzymes and other resident proteins in the lumen of the ER, Golgi, and lysosomes as well as integral proteins transported in the vesicle membranes. Here the proteins in this secretory pathway are ultimately found in lysososmes.
R-HSA-419408 Lysosphingolipid and LPA receptors The Lysophospholipid receptor (LPLR) group are members of the G protein-coupled receptor family of integral membrane proteins that are important for lipid signaling. In humans there are eight LPL receptors, each encoded by a separate gene (these genes also sometimes referred to as "Edg" or endothelial differentiation gene). The ligands for LPLRs are the lysophospholipid extracellular signaling molecules, lysophosphatidic acid (LPA) and sphingosine 1-phosphate (S1P). The primary effects are inhibition of adenylyl cyclase and release of calcium from the endoplasmic reticulum, as well as secondary effects of preventing apoptosis and increasing cell proliferation (Contos JJ et al, 2000; An S et al, 1998; Fukushima N and Chun J, 2001).
R-HSA-68886 M Phase Mitosis, or the M phase, involves nuclear division and cytokinesis, where two identical daughter cells are produced. Mitosis involves prophase, prometaphase, metaphase, anaphase, and telophase. Finally, cytokinesis leads to cell division. The phase between two M phases is called the interphase; it encompasses the G1, S, and G2 phases of the cell cycle.
R-HSA-9820841 M-decay: degradation of maternal mRNAs by maternally stored factors Maternal transcripts are transcribed from the maternal genome and accumulate in the oocyte during oogenesis. A subset of these maternal transcripts is degraded during later development of the unfertilized oocyte and after fertilization of the oocyte. Maternal decay of maternal transcripts (M-decay, reviewed in Jian and Fan 2022) refers to the degradation of maternal transcripts by maternally provided factors such as ZFP36L2 (inferred from the mouse homolog in Chousal et al. 2018, Sha et al. 2018), BTG4 (inferred from the mouse homolog in Liu et al. 2016, Yu et al. 2016, Pasternak et al. 2016, Zhao et al. 2020), and AGO2 (inferred from the mouse homolog in Zhang et al. 2020). ZFP36L2 acting before fertilization and BTG4 acting after fertilization recruit the CCR4-NOT deadenylation complex to the mRNA to initiate degradation. AGO2 is primed with endogenous small interfering RNAs (endosiRNAs) produced from double-stranded RNAs that originate from specific loci. The resulting AGO2:endosiRNA complexes bind and hydrolyze complementary maternal mRNAs. Similar patterns of mRNA decay are observed in human and mouse zygotes (Sha et al. 2020).
R-HSA-450294 MAP kinase activation The mitogen activated protein kinase (MAPK) cascade, one of the most ancient and evolutionarily conserved signaling pathways, is involved in many processes of immune responses. The MAP kinases cascade transduces signals from the cell membrane to the nucleus in response to a wide range of stimuli (Chang and Karin, 2001; Johnson et al, 2002).
There are three major groups of MAP kinases
ERK1 and ERK2 are activated in response to growth stimuli. Both JNKs and p38-MAPK are activated in response to a variety of cellular and environmental stresses. The MAP kinases are activated by dual phosphorylation of Thr and Tyr within the tripeptide motif Thr-Xaa-Tyr. The sequence of this tripeptide motif is different in each group of MAP kinases: ERK (Thr-Glu-Tyr); p38 (Thr-Gly-Tyr); and JNK (Thr-Pro-Tyr).
MAPK activation is mediated by signal transduction in the conserved three-tiered kinase cascade: MAPKKKK (MAP4K or MKKKK or MAPKKK Kinase) activates the MAPKKK. The MAPKKKs then phosphorylates a dual-specificity protein kinase MAPKK, which in turn phosphorylates the MAPK.
The dual specificity MAP kinase kinases (MAPKK or MKK) differ for each group of MAPK. The ERK MAP kinases are activated by the MKK1 and MKK2; the p38 MAP kinases are activated by MKK3, MKK4, and MKK6; and the JNK pathway is activated by MKK4 and MKK7. The ability of MAP kinase kinases (MKKs, or MEKs) to recognize their cognate MAPKs is facilitated by a short docking motif (the D-site) in the MKK N-terminus, which binds to a complementary region on the MAPK. MAPKs then recognize many of their targets using the same strategy, because many MAPK substrates also contain D-sites.
The upstream signaling events in the TLR cascade that initiate and mediate the ERK signaling pathway remain unclear. R-HSA-5674135 MAP2K and MAPK activation Activated RAF proteins are restricted substrate kinases whose primary downstream targets are the two MAP2K proteins, MAPK2K1 and MAP2K2 (also known as MEK1 and MEK2) (reviewed in Roskoski, 2010, Roskoski, 2012a). Phosphorylation of the MAPK2K activation loop primes them to phosphorylate the primary effector of the activated MAPK pathway, the two MAPK proteins MAPK3 and MAPK1 (also known as ERK1 and 2). Unlike their upstream counterparts, MAPK3 and MAPK1 catalyze the phosphorylation of hundreds of cytoplasmic and nuclear targets including transcription factors and regulatory molecules (reviewed in Roskoski, 2012b). Activation of MAP2K and MAPK proteins downstream of activated RAF generally occurs in the context of a higher order scaffolding complex that regulates the specificity and localization of the pathway (reviewed in Brown and Sacks, 2009; Matallanas et al, 2011). R-HSA-5684264 MAP3K8 (TPL2)-dependent MAPK1/3 activation Tumor progression locus-2 (TPL2, also known as COT and MAP3K8) functions as a mitogen-activated protein kinase (MAPK) kinase kinase (MAP3K) in various stress-responsive signaling cascades. MAP3K8 (TPL2) mediates phosphorylation of MAP2Ks (MEK1/2) which in turn phosphorylate MAPK (ERK1/2) (Gantke T et al., 2011).
In the absence of extra-cellular signals, cytosolic MAP3K8 (TPL2) is held inactive in the complex with ABIN2 (TNIP2) and NFkB p105 (NFKB1) (Beinke S et al., 2003; Waterfield MR et al., 2003; Lang V et al., 2004). This interaction stabilizes MAP3K8 (TPL2) but also prevents MAP3K8 and NFkB from activating their downstream signaling cascades by inhibiting the kinase activity of MAP3K8 and the proteolysis of NFkB precursor protein p105. Upon activation of MAP3K8 by various stimuli (such as LPS, TNF-alpha, and IL-1 beta), IKBKB phosphorylates NFkB p105 (NFKB1) at Ser927 and Ser932, which trigger p105 proteasomal degradation and releases MAP3K8 from the complex (Beinke S et al., 2003, 2004; Roget K et al., 2012). Simultaneously, MAP3K8 is activated by auto- and/or transphosphorylation (Gantke T et al. 2011; Yang HT et al. 2012). The released active MAP3K8 phosphorylates its substrates, MAP2Ks. The free MAP3K8, however, is also unstable and is targeted for proteasome-mediated degradation, thus restricting prolonged activation of MAP3K8 (TPL2) and its downstream signaling pathways (Waterfield MR et al. 2003; Cho J et al., 2005). Furthermore, partially degraded NFkB p105 (NFKB1) into p50 can dimerize with other NFkB family members to regulate the transcription of target genes.
MAP3K8 activity is thought to regulate the dynamics of transcription factors that control an expression of diverse genes involved in growth, differentiation, and inflammation. Suppressing the MAP3K8 kinase activity with selective inhibitors, such as C8-chloronaphthyridine-3-carbonitrile, caused a significant reduction in TNFalpha production in LPS- and IL-1beta-induced both primary human monocytes and human blood (Hall JP et al. 2007). Similar results have been reported for mouse LPS-stimulated RAW264.7 cells (Hirata K et al. 2010). Moreover, LPS-stimulated macrophages derived from Map3k8 knockout mice secreted lower levels of pro-inflammatory cytokines such as TNFalpha, Cox2, Pge2 and CXCL1 (Dumitru CD et al. 2000; Eliopoulos AG et al. 2002). Additionally, bone marrow-derived dendritic cells (BMDCs) and macrophages from Map3k8 knockout mice showed significantly lower expression of IL-1beta in response to LPS, poly IC and LPS/MDP (Mielke et al., 2009). However, several other studies seem to contradict these findings and Map3k8 deficiency in mice has been also reported to enhance pro-inflammatory profiles. Map3k8 deficiency in LPS-stimulated macrophages was associated with an increase in nitric oxide synthase 2 (NOS2) expression (López-Peláez et al., 2011). Similarly, expression of IRAK-M, whose function is to compete with IL-1R-associated kinase (IRAK) family of kinases, was decreased in Map3k8-/- macrophages while levels of TNF and IL6 were elevated (Zacharioudaki et al., 2009). Moreover, significantly higher inflammation level was observed in 12-O-tetradecanoylphorbol-13-acetate (TPA)-treated Map3k8-/- mouse skin compared to WT skin (DeCicco-Skinner K. et al., 2011). Additionally, MAP3K8 activity is associated with NFkB inflammatory pathway. High levels of active p65 NFkB were observed in the nucleus of Map3k8 -/- mouse keratinocytes that dramatically increased within 15-30 minutes of TPA treatment. Similarly, increased p65 NFkB was observed in Map3k8-deficient BMDC both basally and after stimulation with LPS when compared to wild type controls (Mielke et al., 2009). The data opposes the findings that Map3k8-deficient mouse embryo fibroblasts and human Jurkat T cells with kinase domain-deficient protein have a reduction in NFkB activation but only when certain stimuli are administered (Lin et al., 1999; Das S et al., 2005). Thus, it is possible that whether MAP3K8 serves more of a pro-inflammatory or anti-inflammatory role may depend on cell- or tissue type and on stimuli (LPS vs. TPA, etc.) (Mielke et al., 2009; DeCicco-Skinner K. et al., 2012).
MAP3K8 has been also studied in the context of carcinogenesis, however the physiological role of MAP3K8 in the etiology of human cancers is also convoluted (Vougioukalaki M et al., 2011; DeCicco-Skinner K. et al., 2012).
R-HSA-5683057 MAPK family signaling cascades The mitogen activated protein kinases (MAPKs) are a family of conserved protein serine threonine kinases that respond to varied extracellular stimuli to activate intracellular processes including gene expression, metabolism, proliferation, differentiation and apoptosis, among others.
The classic MAPK cascades, including the ERK1/2 pathway, the p38 MAPK pathway, the JNK pathway and the ERK5 pathway are characterized by three tiers of sequentially acting, activating kinases (reviewed in Kryiakis and Avruch, 2012; Cargnello and Roux, 2011). The MAPK kinase kinase kinase (MAPKKK), at the top of the cascade, is phosphorylated on serine and threonine residues in response to external stimuli; this phosphorylation often occurs in the context of an interaction between the MAPKKK protein and a member of the RAS/RHO family of small GTP-binding proteins. Activated MAPKKK proteins in turn phosphorylate the dual-specificity MAPK kinase proteins (MAPKK), which ultimately phosphorylate the MAPK proteins in a conserved Thr-X-Tyr motif in the activation loop.
Less is known about the activation of the atypical families of MAPKs, which include the ERK3/4 signaling cascade, the ERK7 cascade and the NLK cascade. Although the details are not fully worked out, these MAPK proteins don't appear to be phosphorylated downstream of a 3-tiered kinase system as described above (reviewed in Coulombe and Meloche, 2007; Cargnello and Roux, 2011) .
Both conventional and atypical MAPKs are proline-directed serine threonine kinases and, once activated, phosphorylate substrates in the consensus P-X-S/T-P site. Both cytosolic and nuclear targets of MAPK proteins have been identified and upon stimulation, a proportion of the phosphorylated MAPKs relocalize from the cytoplasm to the nucleus. In some cases, nuclear translocation may be accompanied by dimerization, although the relationship between these two events is not fully elaborated (reviewed in Kryiakis and Avruch, 2012; Cargnello and Roux, 2011; Plotnikov et al, 2010).
R-HSA-450282 MAPK targets/ Nuclear events mediated by MAP kinases MAPKs are protein kinases that, once activated, phosphorylate their specific cytosolic or nuclear substrates at serine and/or threonine residues. Such phosphorylation events can either positively or negatively regulate substrate, and thus entire signaling cascade activity.
The major cytosolic target of activated ERKs are RSKs (90 kDa Ribosomal protein S6 Kinase). Active RSKs translocates to the nucleus and phosphorylates such factors as c-Fos(on Ser362), SRF (Serum Response Factor) at Ser103, and CREB (Cyclic AMP Response Element-Binding protein) at Ser133. In the nucleus activated ERKs phosphorylate many other targets such as MSKs (Mitogen- and Stress-activated protein kinases), MNK (MAP interacting kinase) and Elk1 (on Serine383 and Serine389). ERK can directly phosphorylate CREB and also AP-1 components c-Jun and c-Fos. Another important target of ERK is NF-KappaB. Recent studies reveals that nuclear pore proteins are direct substrates for ERK (Kosako H et al, 2009). Other ERK nuclear targets include c-Myc, HSF1 (Heat-Shock Factor-1), STAT1/3 (Signal Transducer and Activator of Transcription-1/3), and many more transcription factors.
Activated p38 MAPK is able to phosphorylate a variety of substrates, including transcription factors STAT1, p53, ATF2 (Activating transcription factor 2), MEF2 (Myocyte enhancer factor-2), protein kinases MSK1, MNK, MAPKAPK2/3, death/survival molecules (Bcl2, caspases), and cell cycle control factors (cyclin D1).
JNK, once activated, phosphorylates a range of nuclear substrates, including transcription factors Jun, ATF, Elk1, p53, STAT1/3 and many other factors. JNK has also been shown to directly phosphorylate many nuclear hormone receptors. For example, peroxisome proliferator-activated receptor 1 (PPAR-1) and retinoic acid receptors RXR and RAR are substrates for JNK. Other JNK targets are heterogeneous nuclear ribonucleoprotein K (hnRNP-K) and the Pol I-specific transcription factor TIF-IA, which regulates ribosome synthesis. Other adaptor and scaffold proteins have also been characterized as nonnuclear substrates of JNK.
R-HSA-112411 MAPK1 (ERK2) activation Mitogen-activated protein kinase kinase MAP2K2 (also known as MEK2) is a dual threonine and tyrosine recognition kinase that phosphorylates and activates MAPK1 (ERK2) (Ohren et al. 2004; Roskoski 2012).
R-HSA-5684996 MAPK1/MAPK3 signaling The extracellular signal regulated kinases (ERKs) 1 and 2, also known as MAPK3 and MAPK1, are phosphorylated by the MAP2Ks 1 and 2 in response to a wide range of extracellular stimuli to promote differentiation, proliferation, cell motility, cell survivial, metabolism and transcription, among others (reviewed in Roskoski, 2012b; McKay and Morrison, 2007; Raman et al, 2007). In the classical pathway, MAPK1/3 activation is triggered by the GEF-mediated activation of RAS at the plasma membrane, leading to the activation of the RAF MAP3Ks (reviewed in McKay and Morrison, 2007; Matallanas et al, 2011; Wellbrock et al, 2004). However, many physiological and pathological stimuli have been found to activate MAPK1/3 independently of RAF and RAS, acting instead through MAP3Ks such as MOS, TPL2 and AMPK (Dawson et al, 2008; Wang et al, 2009; Kuriakose et al, 2014; Awane et al, 1999). Activated MAPK1/3 phosphorylate numerous targets in both the nucleus and cytoplasm (reviewed in Yoon and Seger, 2006; Roskoski 2012b).
R-HSA-110056 MAPK3 (ERK1) activation Mitogen-activated protein kinase kinase MAP2K1 (also known as MEK1) is a dual threonine and tyrosine recognition kinase that phosphorylates and activates MAPK3 (ERK1) (Ohren et al. 2004; Roskoski 2012a).
R-HSA-5687128 MAPK6/MAPK4 signaling MAPK6 and MAPK4 (also known as ERK3 and ERK4) are vertebrate-specific atypical MAP kinases. Atypical MAPK are less well characterized than their conventional counterparts, and are generally classified as such based on their lack of activation by MAPKK family members. Unlike the conventional MAPK proteins, which contain a Thr-X-Tyr motif in the activation loop, MAPK6 and 4 have a single Ser-Glu-Gly phospho-acceptor motif (reviewed in Coulombe and Meloche, 2007; Cargnello et al, 2011). MAPK6 is also distinct in being an unstable kinase, whose turnover is mediated by ubiquitin-dependent degradation (Coulombe et al, 2003; Coulombe et al, 2004). The biological functions and pathways governing MAPK6 and 4 are not well established. MAPK6 and 4 are phosphorylated downstream of class I p21 activated kinases (PAKs) in a RAC- or CDC42-dependent manner (Deleris et al, 2008; Perander et al, 2008; Deleris et al, 2011; De La Mota-Peynado et al, 2011). One of the only well established substrates of MAPK6 and 4 is MAPKAPK5, which contributes to cell motility by promoting the HSBP1-dependent rearrangement of F-actin (Gerits et al, 2007; Kostenko et al, 2009a; reviewed in Kostenko et al, 2011b). The atypical MAPKs also contribute to cell motility and invasiveness through the NCOA3:ETV4-dependent regulation of MMP gene expression (Long et al, 2012; Yan et al, 2008; Qin et al, 2008). Both of these pathways may be misregulated in human cancers (reviewed in Myant and Sansom, 2011; Kostenko et al, 2012)
R-HSA-2465910 MASTL Facilitates Mitotic Progression The activity of MASTL, also known as the Greatwall kinase (GWL), is necessary for the entry and progression of mitosis. MASTL is activated by phosphorylation of several key residues during mitotic entry. Phosphorylation on the serine residue S875 (S883 in Xenopus), likely through autophosphorylation (Blake-Hodek et al. 2012) appears to be critical (Vigneron et al. 2011). Several other sites, including putative CDK1 targets T194, T207 and T741, contribute to the full activation of MASTL (Yu et al. 2006, Blake-Hodek et al. 2012). Other kinases, such as PLK1 (Vigneron et al. 2011) and other MASTL phosphorylation sites may also be functionally important (Yu et al. 2006, Blake-Hodek et al. 2012).
Activated MASTL phosphorylates ARPP19 and ENSA on serines S62 and S67, respectively, enabling them to bind to and inhibit the phosphatase activity of PP2A complexed with the regulatory subunit PPP2R2D (B55-delta). Inhibition of PP2A-PPP2R2D activity by ARPP19 or ENSA prevents dephosphorylation of CDK1 targets, hence allowing entry and maintenance of mitosis (Mochida et al. 2010, Gharbi-Ayachi et al. 2010, Burgess et al. 2010).
R-HSA-9851151 MDK and PTN in ALK signaling The cytokines pleiotrophin (PTN) and midikine (MDK) were initially proposed to act as ligands for ALK (Stoica et al, 2001; Stoica et al, 2002; reviewed in Wellstein et al, 2012; Winkler et al, 2014; Herradon and Perez-Garcia, 2014). Binding of PTN or MDK to ALK either in cell-free assays or in intact cells was shown to stimulate signaling through IRS, SHC, PLC and PI3K and to support neurite outgrowth, growth and survival (Stoica et al, 2001; Stoica et al, 2002; reviewed in Wellstein et al, 2012; Winkler et al, 2014; Herradon and Perez-Garcia, 2014). The activating effects of PTN and MDK on the ALK receptor were not universally reproducible, however, despite eliciting similar downstream signaling to those with anti-ALK monoclonal antibodies (Mathivet et al, 2007; Moog-Lutz et al, 2005; Motegi et al, 2004; Dirks et al, 2002; Miyake et al, 2002). More recently, ALKAL1 and ALKAL2 have been identified as the physiologically relevant ALK ligands (Zhang et al, 2014; Guan et al, 2015; Reshetnyak et al, 2015; Reshetnyak et al, 2018).
R-HSA-9022699 MECP2 regulates neuronal receptors and channels Receptors directly transcriptionally regulated by MECP2 include glutamate receptor GRIA2 (Qiu et al. 2012), NMDA receptor subunits GRIN2A (Durand et al. 2012) and GRIN2B (Lee et al. 2008), opioid receptors OPRK1 (Chahrour et al. 2008) and OPRM1 (Hwang et al. 2009, Hwang et al. 2010, Samaco et al. 2012), GPRIN1 (Chahrour et al. 2008), MET (Plummer et al. 2013), and NOTCH1 (Li et al. 2014). Channels/transporters regulated by MECP2 include TRPC3 (Li et al. 2012) and SLC2A3 (Chen et al. 2013). MECP2 also regulates transcription of FKBP5, involved in trafficking of glucocorticoid receptors (Nuber et al. 2005, Urdinguio et al. 2008) and is implicated in regulation of expression of SEMA3F (semaphorin 3F) in mouse olfactory neurons (Degano et al. 2009). In zebrafish, Mecp2 is implicated in sensory axon guidance by direct stimulation of transcription of Sema5b and Robo2 (Leong et al. 2015). MECP2 may indirectly regulate signaling by neuronal receptor tyrosine kinases by regulating transcription of protein tyrosine phosphatases, PTPN1 (Krishnan et al. 2015) and PTPN4 (Williamson et al. 2015).
R-HSA-9022707 MECP2 regulates transcription factors MECP2 regulates transcription of several transcription factors involved in functioning of the nervous system, such as CREB1, MEF2C, RBFOX1 (Chahrour et al. 2008) and PPARG (Mann et al. 2010, Joss Moore et al. 2011).
R-HSA-9022927 MECP2 regulates transcription of genes involved in GABA signaling MECP2 regulates expression of several genes involved in GABA (gamma-aminobutyric acid) signaling. Transcription of GAD1 (GAD67) and GAD2 (GAD65) genes is directly positively regulated by MECP2. GAD1 and GAD2 are components of the glutamic acid decarboxylase complex involved in production of the neurotransmitter GABA. Mice lacking Mecp2 from GABA-releasing neurons have decreased GABA levels and exhibit multiple Rett syndrome features (Chao et al. 2010).
Mecp2 deletion in mouse GABAergic parvalbumin-expressing (PV) cells, cortical interneurons playing a key role in visual experience-induced ocular dominance plasticity, does not result in Rett-like phenotype, other than defects in motor coordination and motor learning. While functions of the visual cortex are preserved in mice lacking Mecp2 in GABAergic PV cells, the visual input-induced spiking responses are decreased. Mecp2 loss impairs maturation of membrane functions of cortical GABAergic PV cells. Mecp2 may be needed for PV cell-mediated cortical GABA inhibition. Mecp2-deficient cortical PV cells show reduced mRNA levels of several genes involved in GABA signaling, such as Parvalbumin, Gad2, Calretinin, Gabra1 and Gabra2, as well as reduced levels of Glu3, a glutamate receptor subunit, and Kv3.1, a potassium channel (He et al. 2014).
R-HSA-9022702 MECP2 regulates transcription of neuronal ligands Ligands regulated by MECP2 include BDNF (reviewed by Li and Pozzo Miller 2014, and KhorshidAhmad et al. 2016), CRH (McGill et al. 2006, Samaco et al. 2012), SST (Somatostatin) (Chahrour et al. 2008), and DLL1 (Li et al. 2014).
R-HSA-6806942 MET Receptor Activation Hepatocyte growth factor (HGF), the ligand for MET receptor tyrosine kinase (RTK), is secreted into the extracellular matrix (ECM) as an inactive single chain precursor (pro-HGF). The biologically active HGF is the heterodimer of alpha and beta chains that are produced via proteolytic cleavage of pro-HGF by the plasma membrane bound serine protease Hepsin (HPN) (Kirchhofer et al. 2005, Owen et al. 2010) or the ECM-associated serine protease Hepatocyte growth factor activator (HGFAC, commonly known as HGFA) (Shia et al. 2005). HGF binds to the extracellular SEMA and PSI domains of MET RTK, inducing a conformational change that enables MET dimerization or oligomerization (Kirchhofer et al. 2004, Stamos et al. 2004, Hays and Watowich 2004, Gherardi et al. 2006). MET dimers trans-autophosphorylate on tyrosine residues in the activation loop, leading to increased kinase activity, and on tyrosine residues at the cytoplasmic tail that serve as docking sites for adapter proteins involved in MET signal transduction (Ferracini et al. 1991, Longati et al. 1994, Rodrigues and Park 1994, Ponzetto et al. 1994).
CD44v6 was implicated as a MET co-receptor, but its role has been disputed (Orian-Rousseau et al. 2002, Dortet et al. 2010, Olaku et al. 2011, Hasenauer et al. 2013, Elliot et al. 2014).
R-HSA-8851907 MET activates PI3K/AKT signaling MET binds and phosphorylates the adapter protein GAB1, thus creating a docking site for the regulatory subunit PIK3R1 of the PI3K complex. Recruitment of PI3K to MET-bound phosphorylated GAB1 results in PI3K activation, production of PIP3, and stimulation of downstream AKT signaling (Rodrigues et al. 2000, Schaeper et al. 2000).
R-HSA-8874081 MET activates PTK2 signaling MET receptor activates the focal adhesion kinase PTK2 (FAK1) in a process that depends on the simultaneous interaction of PTK2 with integrins and with MET. SRC is needed for PTK2 to become fully active. Activation of PTK2 is needed for HGF-induced cell motility (Beviglia et al. 1999, Parr et al. 2001, Chen and Chen 2006, Lietha et al. 2007, Chen et al. 2011, Brami-Cherrier et al. 2014).
R-HSA-8865999 MET activates PTPN11 PTPN11 (SHP2), recruited to activated MET receptor through GAB1, is phosphorylated in response to HGF treatment, although phosphorylation sites and direct MET involvement have not been examined (Schaeper et al. 2000, Duan et al. 2006). Phosphorylation of PTPN11 in response to HGF treatment is required for the recruitment and activation of sphingosine kinase SPHK1, which may play a role in HGF-induced cell scattering (Duan et al. 2006). While PTPN11 promotes MAPK3/1 (ERK1/2) signaling downstream of MET, it can also dephosphorylate MET on unidentified tyrosine residues (Furcht et al. 2014).
R-HSA-8875555 MET activates RAP1 and RAC1 The adapter protein GAB1 is involved in recruitment, through CRK and related CRKL proteins, of guanyl nucleotide exchange factors (GEFs) to the activated MET receptor. MET-associated GEFs, such as RAPGEF1 (C3G) and DOCK7, activate RAP1 and RAC1, respectively, leading to morphological changes that contribute to cell motility (Schaeper et al. 2000, Sakkab et al. 2000, Lamorte et al. 2002, Watanabe et al. 2006, Murray et al. 2014).
R-HSA-8851805 MET activates RAS signaling Activated MET receptor recruits the RAS guanyl nucleotide exchange factor (GEF) SOS1 indirectly, either through the GRB2 adapter (Ponzetto et al. 1994, Fournier et al. 1996, Shen and Novak 1997, Besser et al. 1997), GAB1 (Weidner et al. 1996) or SHC1 and GRB2 (Pelicci et al. 1995), or RANBP9 (Wang et al. 2002, Wang et al. 2004). Association of SOS1 with the activated MET receptor complex leads to exchange of GDP to GTP on RAS and activation of RAS signaling (Pelicci et al. 1995, Besser et al. 1997, Shen and Novak 1997, Wang et al. 2004).
PTPN11 (SHP2) may contribute to activation of RAS signaling downstream of MET (Schaeper et al. 2000, Furcht et al. 2014).
Sustained activation of MAPK1 (ERK2) and MAPK3 (ERK1) downstream of MET-activated RAS may require MET endocytosis and signaling from endosomes (Peschard et al. 2001, Hammond et al. 2001, Petrelli et al. 2002, Kermorgant and Parker 2008).
Binding of MET to MUC20 or RANBP10 interferes with RAS activation (Higuchi et al. 2004, Wang et al. 2004).
R-HSA-8875791 MET activates STAT3 The STAT3 transcription factor binds to activated MET through phosphorylated tyrosine residue Y1356 of MET. STAT3 may also bind to activated MET indirectly through GAB1, but this interaction has not been studied in detail. Activated MET induces phosphorylation of STAT3 at Y705, triggering STAT3 dimerization and nuclear translocation (Schaper et al. 1997, Boccaccio et al. 1998, Zhang et al. 2002, Cramer et al. 2005). Endocytosis of MET and interaction with STAT3 at endosomes may be required for sustained STAT3 phosphorylation in response to HGF stimulation (Kermorgant and Parker 2008). Activated SRC may also contribute to phosphorylation of STAT3 at Y705. STAT3 may promote HGF transcription in a SRC-dependent way, but this autocrine HGF loop may be limited to breast cancer cells (Wojcik et al. 2006, Sam et al. 2007). MET-mediated activation of STAT3 is implicated in anchorage independent cell growth and invasiveness downstream of HGF (Zhang et al. 2002, Cramer et al. 2005). MET can also interact with STAT1A, STAT1B and STAT5, but the biological importance of these interactions is not known (Runge et al. 1999).
R-HSA-8875513 MET interacts with TNS proteins Interaction of MET with tensin protein TNS4 at focal adhesion sites promotes cell motility through and unknown mechanism. MET also interacts with TNS3, whose expression seems to be inversely correlated with TNS4 (Muharram et al. 2014).
R-HSA-8875878 MET promotes cell motility Direct and indirect interactions of MET with integrins, focal adhesion kinase PTK2 (FAK1), tensin-4 (TNS4) and GTPases RAP1 and RAC1, induce morphological changes that promote cell motility and play an important role in HGF-induced invasiveness of cancer cells (Weidner et al. 1993, Beviglia et al. 1999, Sakkab et al. 2000, Parr et al. 2001, Trusolino et al. 2001, Lamorte et al. 2002, Chen and Chen 2006, Watanabe et al. 2006, Muharram et al. 2014, Murray et al. 2014).
R-HSA-8875656 MET receptor recycling Activated MET receptor is subject to recycling from the plasma membrane through the endosomal compartment and back to the plasma membrane (Peschard et al. 2001, Hammond et al. 2001, Petrelli et al. 2002). In the recycling process, activated MET receptor is endocytosed, and the GGA3 protein directs it, via a largely unknown mechanism, through the RAB4 positive endosomal compartments back to the plasma membrane (Parachoniak et al. 2011). Endosomal signaling by MET during the recycling process appears to play an important role in sustained activation of ERK1/ERK2 (MAPK3/MAPK1) and STAT3 downstream of MET (Kermorgant and Parker 2008).
R-HSA-5657655 MGMT-mediated DNA damage reversal Reactive cellular catabolites can cause DNA damage by 6-O-methylation of guanine. 6-O-methylguanine can pair ambiguously with both C and T, and cause transition mutations. Active reversal of such damage can be facilitated by MGMT, a protein that has 6-O-methylguanine-DNA methyltransferase activity (Mitra and Kaina 1993).
R-HSA-2132295 MHC class II antigen presentation Antigen presenting cells (APCs) such as B cells, dendritic cells (DCs) and monocytes/macrophages express major histocompatibility complex class II molecules (MHC II) at their surface and present exogenous antigenic peptides to CD4+ T helper cells. CD4+ T cells play a central role in immune protection. On their activation they stimulate differentiation of B cells into antibody-producing B-cell blasts and initiate adaptive immune responses. MHC class II molecules are transmembrane glycoprotein heterodimers of alpha and beta subunits. Newly synthesized MHC II molecules present in the endoplasmic reticulum bind to a chaperone protein called invariant (Ii) chain. The binding of Ii prevents the premature binding of self antigens to the nascent MHC molecules in the ER and also guides MHC molecules to endocytic compartments. In the acidic endosomal environment, Ii is degraded in a stepwise manner, ultimately to free the class II peptide-binding groove for loading of antigenic peptides. Exogenous antigens are internalized by the APC by receptor mediated endocytosis, phagocytosis or pinocytosis into endocytic compartments of MHC class II positive cells, where engulfed antigens are degraded in a low pH environment by multiple acidic proteases, generating MHC class II epitopes. Antigenic peptides are then loaded into the class II ligand-binding groove. The resulting class II peptide complexes then move to the cell surface, where they are scanned by CD4+ T cells for specific recognition (Berger & Roche 2009, Zhou & Blum 2004, Watts 2004, Landsverk et al. 2009).
R-HSA-9856651 MITF-M-dependent gene expression MITF-M is a transcriptional regulator that is critical for the establishment of melanocyte fate during embryogenesis. Key targets include the enzymes responsible for the synthesis of the pigment compounds eumelanin and pheomelanin, as well as a number of structural components of the melanosome. In addition to regulating expression of genes involved in pigmentation, MITF has also been shown to play a role in the expression of genes involved in more diverse biological processes, including proliferation, survival, lysosome biogenesis, autophagy, metabolism, DNA damage, senescence and invasion (reviewed in Goding and Arnheiter, 2019; Mort et al, 2015; Zon and White, 2008, Cheli et al, 2010).
MITF is a basic helix loop helix leucine zipper (BHLH-ZIP)-containing protein and binds DNA as a dimer - either as a homodimer or as a heterodimer with the related transcription factors TFEB, TFE3, and TFEC. TFEB and TFE3 are both widely expressed, but TFEC displays more restricted expression. In this pathway, for simplicity, MITF is shown binding DNA exclusively as a homodimer (reviewed in Goding and Arnheiter, 2019).
MITF and related BHLH protein family members bind to an E-box-like element with sequence CANNTG. Specificity of binding is determined both by the flanking nucleotides and by the identity of the two internal nucleotides of the E-box element. MITF binds preferentially to sequences CATGTG or CACGTG, and binds with less affinity to the CAGCTG sequences preferred by other BHLH proteins such as AP4 (Lowing et al, 1992; Bentley et al, 1994; Yavuzer and Goding, 1994). High-affinity MITF-binding sites also show an enrichment for flanking 5'T and 3'A, further distinguishing these sites from those preferentially bound by transcription factors such as MYC and MAX (Aksan and Goding, 1998; Fisher et al, 1993; Solomon et al, 1993; Hejna et al, 2018). Variants of high-affinity MITF binding sites present in the promoters of pigmentation genes are called M-boxes, to distinguish them from related E-box sequences (reviewed in Goding and Arnheiter, 2019). High-throughput ChIP-seq in the human melanoma cell line 501Mel identified MITF-binding at 5578 potential target genes, with 2771 showing promoter-proximal binding; only a subset of these genes were shown to be directly regulated by MITF, however (465; 240 down-regulated and 225 upregulated) (Strub et al, 2001; reviewed in Goding and Arnheiter, 2019). MITF-bound genes included those involved in melanocyte biogenesis as well as DNA replication, repair and mitosis (Strub et al, 2011).
R-HSA-9730414 MITF-M-regulated melanocyte development Melanocyte Inducing Factor (MITF, also known as Microphthalmia-associated transcription factor) is a key regulator of melanocyte differentiation and development during embryogenesis, of differentiation of melanocyte stem cells post-natally, and of melanoma cells.
Melanocytes are cells that possess specialized organelles called melanosomes that synthesize eumelanin and pheomelanin from tyrosine in a series of reactions. Melanosomes are transferred from cutaneous melanocytes to adjacent keratinocytes to provide protection against UV as well as coloration of skin, eye, hair, feathers and scales. Besides being found in the basal layer of the skin, melanocytes are also present in hair follicles, the inner ear and in the iris eye, among other places. The eye also contains a layer of melanosome-containing cells behind the retina, called the retinal pigment epithelium (RPE) (reviewed in Mort et al, 2015; D'Mello et al, 2016; Goding and Arnheiter, 2019; Le et al, 2021; Cui and Man, 2023).
Cutaneous melanocytes and their precursors, melanoblasts, arise during embryogenesis from neural crest cells that migrate dorsolaterally through the developing embryo (reviewed in Mort et al, 2015). They also arise from glial/melanoblast precursors migrating on a ventromedial pathway and along nerves (Adameyko et al, 2009). Expression of MITF is a key determinant of melanocyte fate, and mutations in MITF are associated with a variety of defects in pigmentation as well as with deafness (due to absence of melanocytes in the inner ear) and microphthalmia (due to aberrant development of retina and RPE), among other conditions (reviewed in White and Zon, 2008; Mort et al, 2015; Goding and Arnheiter, 2019; Le et al, 2021).
The gene for MITF encodes several distinct isoforms based on alternative splicing. The gene has a 3' portion consisting of exons 2-9 that are generally shared by all transcripts. In mice and humans, the upstream region of the gene contains 9 exons, some of them coding, some not, and each regulated by its own promoter. Most of them are spliced to exon 2 via a common exon 1B. An exception is exon 1M which is directly spliced to exon 2, giving rise to the so-called M-isoform of MITF. This arrangement gives rise to a number of different mRNA and protein isoforms with preferential expression patterns. Exon 1A-containing transcripts, for instance, are ubiquitously expressed, exon 1H-containing transcripts are highly expressed in the heart, exon 1D-containing transcripts are expressed in the RPE, and exon 1M-containing transcripts are expressed in neural crest-derived melanocytes. Nevertheless, there is little information on whether the different isoforms have different functions except that exon 1B-containing transcripts (but not MITF-M) harbor a sequence subject to mTORC1 regulation (reviewed in Goding and Arnheiter, 2019; Vu et al, 2020). Most if not all transcripts come in two additional splice versions, one including and one excluding 18 bp of part of exon 6, called exon 6A, which encodes 6 amino acids lying upstream of the DNA-binding domain and which is regulated by MAPK signaling (Primot et al, 2010). They are usually referred to as the (+) and (-) versions of MITF. While the (-) version of a fragment of MITF-M has slightly reduced DNA-binding affinity compared to the (+) version, no specific role has so far been found for exon 6A (Pogenburg et al, 2012). Cell-based assays suggest that MITF (+) has a strong inhibitory effect on cellular proliferation relative to the (-) version, and MITF (-) is expressed at high levels in melanoma cells (Bismuth et al, 2005; Primot et al, 2010).
This pathway focuses on the activity of the melanocyte lineage-specific transcription factor MITF-M, although some of the biology described may also be relevant for other MITF isoforms.
R-HSA-9841922 MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis The ligand-activated complex of a master transcription regulator of adipogenesis, nuclear receptor PPARG, and its partner, nuclear receptor RXRA, recruits MLL3 and MLL4 complexes to target gene loci, leading to establishment of activating epigenetic chromatin marks. The existing experimental evidence implies that MLL3-ASCOM and MLL4-ASCOM complexes are recruited to PPARG:RXRA-target loci, as described below.
PPARG isoform PPARG2-positive adipocyte nuclei isolated from visceral adipose tissue show significantly higher expression level of KMT2C, the catalytic subunit of the MLL3 complex, and PAXIP1, a cofactor of MLL3 and KMT2D (MLL4) complexes, than PPARG2-negative nuclei (Yu et al. 2016). Based on mouse studies, PAXIP1 (PTIP), an accessory subunit of MLL3 and MLL4 complexes, is required for adipogenesis in mouse embryonic fibroblasts (MEFs) and primary preadipocytes. PAXIP1-deficient MEFs show significant defects in both PPARG- and CEBPA-stimulated adipogenesis (Cho et al. 2009). Knockout of Paxip1 gene in brown adipose tissue (BAT) leads to significant decrease of BAT in knockout mice, and a significant decrease of expression of markers shared between white adipose tissue and BAT, such as Pparg, Cebpa, and Fabp4, as well as BAT-specific/prevalent markers Prdm16, Cidea, Mpzl2 (Eva1), Ntrk3, Ucp1, Ppargc1a (Pgc1a), Cox5b and Cox8b (Cho et al. 2009). Paxip1 BAT knockout mice are cold intolerant, with impaired cold-mediated induction of genes involved in fatty acid catabolism, such as Cpt1a, Lpl, and Mlycd (Mcd) (Cho et al. 2009).
In prostate cancer, KMT2D and PPARG are overexpressed at the protein level relative to the normal tissue (Zhai et al. 2022). KMT2D knockdown significantly reduces the lipid droplet content in prostate cancer cell lines (Zhai et al. 2022). In prostate cancer tumors, KMT2D mRNA expression significantly correlates with mRNA expression of lipid metabolism genes FASN, ACC, SCD, and ACLY (Zhai et al. 2022). KMT2D knockdown in prostate cancer cell lines leads to significant decrease in the mRNA levels of ACC, ACLY, and FASN (Zhai et al. 2022). Stimulation of PPARG by the synthetic agonist rosiglitazone stimulates lipid synthesis in prostate cancer cell lines, but the effect of rosiglitazone is diminished upon KMT2D knockdown (Zhai et al. 2022).
In addition to regulating genes involved in lipid metabolism, the PPARG:RXRA complex (Nielsen et al. 2008) and MLL3/MLL4 complexes (Jang et al. 2019: supplementary information) may also regulate expression of some of the genes involved in glucose metabolism and the tricarboxylic acid (TCA) cycle.
Hepatic steatosis represents the synthesis and accumulation of triglycerides in hepatocytes which can, if prolonged, lead to the development of non-alcoholic fatty liver disease (NAFLD) that can progress to non-alcoholic steatohepatitis (NASH), ultimately resulting in liver cirrhosis (Hardy et al. 2016). Like Kmt2c (Mll3) delta/delta mice, which express catalytically inactive Kmt2c (Lee, Saha et al. 2008; Lee S., Lee J. et al. 2008), Kmt2d (Mll4)+/- mice, with deletion of one allele of Kmt2d, are resistant to high fat diet-induced hepatic steatosis, with Kmt2d+/- livers accumulating much less fat relative to wild type littermate controls in response to high fat diet feeding (Kim et al. 2016). Bulk transcriptomic analysis of Kmt2d+/- mouse livers shows that the expression of a large portion of high fat diet controlled genes requires Kmt2d (Kim et al. 2016). Among the defined hepatic steatotic transcription factors, which include MLXIPL (ChREBP), SREBF1 (SREBP1) isoform SREBP1c (SREBP 1C), the liver X receptors (LXRs) – NR1H3 (LXRA) and NR1H2 (LXRB), and PPARG, KMT2D has been reported to associate with LXRs (Lee S., Lee J. et al. 2008) and PPARG (Lee, Saha et al. 2008). No association between mouse orthologs of KMT2D and MLXIPL or SREBP1c could be detected (Kim et al. 2016).
R-HSA-2206302 MPS I - Hurler syndrome Mucopolysaccharidosis type I (MPS I, Hurler syndrome, Hurler's disease, gargoylism, Scheie, Hirler-Scheie syndrome; MIM:607014, 607015 and 607016) is an autosomal recessive genetic disorder where there is a deficiency of alpha-L iduronidase (IDUA, MIM:252800), a glycosidase that removes non-reducing terminal alpha-L-iduronide residues during the lysosomal degradation of the glycosaminoglycans heparan sulphate and dermatan sulphate (McKusick 1959). In 1992, Scott and colleagues were able to clone and purify the gene that encodes this enzyme, IDUA, demonstrating that it spans approximately 19 kb and contains 14 exons (Scott et al. 1992).
Hurler syndrome is named after a German paediatrician Gertrud Hurler (1919, no reference available). The result is build up of heparan sulfate and dermatan sulfate in the body and increased urinary excretion of these GAGs. Symptoms and signs include hepatosplenomegaly, dwarfism, unique facial features, corneal clouding, retinopathy, progressive mental retardation appears during childhood and early death can occur due to organ damage (Campos & Monaga 2012). MPS I is divided into three subtypes, ranging from severe to mild phenotypes; Mucopolysaccharidosis type IH (MPSIH, Hurler syndrome, MIM:607014), mucopolysaccharidosis type IH/S (MPSIH/S, HurlerScheie syndrome, MIM: 607015) and mucopolysaccharidosis type IS (MPSIS, Scheie syndrome, MIM: 607016) respectively (McKusick 1972).
R-HSA-2206296 MPS II - Hunter syndrome Mucopolysaccharidosis II (MPS II, Hunter syndrome, MIM:309900) is an X-linked, recessive genetic disorder which therefore primarily affects males. MPS II was first described in 1917, by Major Charles Hunter (Hunter 1917) and is caused by a deficiency (or absence) of iduronate-2-sulfatase (IDS, MIM:300823), which would normally hydrolyse the 2-sulfate groups of the L-iduronate 2-sulfate units of dermatan sulfate, heparan sulfate and heparin. Without IDS, these GAGs accumulate in the body and are excessively excreted in urine. Although the disease was known since the early 1970s, being the first MPS to be defined clinically in humans, it wasn't until the 1990s that IDS was cloned. It is now known to be localized to Xq28 (Wilson et al. 1991) and contain 9 exons (Flomen et al. 1993) spanning approximately 24 kb (Wilson et al. 1993).
Build up can occur in the liver and spleen as well as in the walls and valves of the heart (reduced hepatic and cardiac function, liver/spleen hepatosplenomegaly), airways (leading to obstructive airway disease), all major joints and bones (joint stiffness and skeletal deformities) and in brain (severe mental retardation). The rate of progression and degree of severity of the disorder can be different for each person with MPS II. Severe forms of the disorder can result in death in childhood whereas those with a "milder" form can expect to live to their 20's or 30's. Some patients even survive into their fifth and sixth decades of life (Wraith et al. 2008, Beck 2011).
R-HSA-2206307 MPS IIIA - Sanfilippo syndrome A Mucopolysaccharidosis III (MPS III, Sanfilippo syndrome) was described in 1963 by a pediatrician named Sylvester Sanfilippo (J. Pediat. 63: 837-838, 1963, no reference). Mucopolysaccharidosis IIIA (MPS IIIA, Sanfilippo syndrome A, MIM:252900) is a rare, autosomal recessive lysosomal storage disease characterised by severe CNS degeneration in early childhood leading to death between 10 and 20 years of age. A deficiency of the enzyme N-sulphoglucosamine sulphohydrolase (SGSH, MIM:605270), which normally hydrolyses the sulfate group from the terminal N-sulphoglucosamine residue of heparan sulfate (HS), leads to the build-up of HS in cells and tissues and its presence in urine (van de Kamp et al. 1981, Yogalingam & Hopwood 2001, de Ruijter et al. 2011). The gene encoding N-sulfoglucosamine sulfohydrolase, SGSH, was cloned in 1995 (Scott et al.1995) and, later, shown to contain 8 exons spanning approximately 11 kb (Karageorgos et al. 1996).
R-HSA-2206282 MPS IIIB - Sanfilippo syndrome B Mucopolysaccharidosis III (Sanfilippo syndrome) was described in 1963 by a pediatrician named Sylvester Sanfilippo (J. Pediat. 63: 837838, 1963, no reference). MPS IIIB (Mucopolysaccharidosis type IIIB, MPS IIIB, Sanfilippo syndrome type B; MIM:252920) is an autosomal recessive genetic disorder due to loss of function of alpha-N-acetylglucosaminidase (NAGLU; MIM:609701), involved in the hydrolysis of terminal non-reducing N-acetylglucosamine residues in heparan sulfate (HS) The gene encoding NAGLU was cloned in 1996 by Zhao and colleagues. It contains 6 exons and spans 8.3 kb on chromosome 17q21 (Zhao et al. 1996). MPSIIIB is characterized by severe CNS retardation but only mild somatic disease and death usually occurs in the second or third decade of life (Zhao et al. 1996, Yogalingam & Hopwood 2001, de Ruijter et al. 2011). MPS IIIB shows extensive molecular heterogeneity (Schmidtchen et al. 1998).
R-HSA-2206291 MPS IIIC - Sanfilippo syndrome C Mucopolysaccharidosis III (Sanfilippo syndrome) was described in 1963 by a pediatrician named Sylvester Sanfilippo (J. Pediat. 63: 837838, 1963, no reference). Mucopolysaccharidosis type IIIC (MPS IIIC, Sanfilippo syndrome C; MIM:252930) is an autosomal recessive genetic disorder due to the loss of heparan alpha-glucosaminide N-acetyltransferase (HGSNAT; MIM:610453) that normally acetylates the non-reducing terminal alpha-glucosamine residue of heparan sulfate. The molecular defects underlying MPS IIIC remained unknown for almost three decades due to the low tissue content and instability of HGSNAT. But, during the last decade, the gene was cloned in parallel by two different groups and shown to contain 18 exons and span approximately 62Kb (Fan et al. 2006, Hrebicek et al. 2006). Loss of HGSNAT results in build up of this glycosaminglycan (GAG) in cells and tissues and is characterized by severe central nervous system degeneration but only with mild somatic disease and death occurs typically during the second or third decade of life (Kresse et al. 1978, Klein et al. 1978, Feldhammer et al. 2009, de Ruijter et al. 2011).
R-HSA-2206305 MPS IIID - Sanfilippo syndrome D Mucopolysaccharidosis III (Sanfilippo syndrome) was described in 1963 by a pediatrician named Sylvester Sanfilippo (J. Pediat. 63: 837-838, 1963, no reference). Mucopolysaccharidosis type IIID (MPS IIID, Sanfilippo syndrome D, MIM:252940) is an autosomal recessive genetic disorder due to the loss of N-acetyl-D-glucosamine 6-sulfatase (GNS; MIM:607664), that hydrolyses the 6-sulfate groups of the N-acetyl-D-glucosamine 6-sulfate units of the glycosaminoglycans (GAGs) heparan sulfate and keratan sulfate. GNS is localized to chromosome 12q14 and has 14 exons spanning 46 kb (Robertson et al. 1988, Mok et al. 2003). Loss of enzyme activity leads to lysosomal accumulation and urinary excretion of heparan sulfate and N-acetylglucosamine 6-sulfate residues (Mok et al. 2003). Keratan sulphate does not accumulate in MPS IIID, as beta-linked N-acetyl-D-glucosamine 6-sulphate can be cleaved by beta-hexosaminidase A (Kresse et al. 1980). This disorder is characterized by progressive mental deterioration but only moderate physical abnormalities and death duing the second or third decade of life, presenting a phenotype similar to MPSIIIA (Jones et al. 1997, de Ruijter et al. 2011).
R-HSA-2206290 MPS IV - Morquio syndrome A Mucopolysaccharidosis IV A (MPS IVA, MPS4A, Morquio's syndrome, Morquio's; MIM:253000) is a rare, autosomal recessive mucopolysaccharide storage disease, first described simultaneously in 1929 by L Morquio (Morquio L, Sur une forme de distrophie familiale, Bull Soc Pediat, Paris, 27, 1929, 145-152) and JF Brailsford (Brailsford, JF, Chondro-osteo-dystrophy: roentgenographic and clinical features of child with dislocation of vertebrae, Am j Surg, 7, 1929, 404-410). MPSIVA is caused by a deficiency in N-acetylgalactosamine 6-sulfatase (GALNS; MIM:612222) which normally hydrolyses 6-sulfate groups of N-acetylgalactosamine 6-sulfate units of chondroitin sulfate (CS) and of galactose 6-sulfate units of keratan sulfate (KS) (Matalon et al. 1974). The result is accumulation of KS/DS in cells and overexcretion in urine. Severe osteochondrodysplasia is a commonly seen phenotype for this disease. The severity of the disease is variable but severe cases limits lifespan to their 20's or 30's (Prat et al. 2008, Tomatsu et al. 2011). The gene coding for human GALNS was mapped to chromosome 16q24.3 (Masuno et al. 1993) and its structure described at the same time by two independent groups as comprising 14 exons and spanning approximately 40-50 kb (Nakashima et al.1994, Morris et al.1994).
R-HSA-2206308 MPS IV - Morquio syndrome B Defects in beta-galactosidase (GLB1; MIM:611458) can result in GM1 gangliosidosis (GM1; MIM:230500) (Nishimoto et al. 1991) (not described here), with several phenotypes indicating mental deterioration, as well as in mucopolysaccharidosis IVB, a characteristic mucopolysaccharidosis with no neurological symptoms (Callahan 1999).
Mucopolysaccharidosis IVB (MPS IVB, Morquio's syndrome B; MIM:253010) is a rare, autosomal recessive mucopolysaccharide storage disease characterized by intracellular accumulation of keratan sulfate (KS), skeletal dysplasia and corneal clouding. There is no central nervous system involvement, intelligence is normal and there is increased KS excretion in urine (Suzuki et al. "Beta-galactosidase deficiency (beta-galactosidosis): GM1 gangliosidosis and Morquio B disease", p3775-3809 in Stryer et al. 2001). MPSIVB is caused by a defect in betagalactosidase (GLB1), which normally cleaves terminal galactosyl residues from glycosaminoglycans, gangliosides and glycoproteins. The GLB1 gene spans 62.5 kb and contains 16 exons (Oshima et al.1988, Santamaria et al. 2007) and maps to chromosome 3p21.33 (Takano & Yamanouchi 1993).
R-HSA-2206280 MPS IX - Natowicz syndrome Mucopolysaccharidosis type IX (MPS IX, Natowicz syndrome, Hyaluronidase deficiency, MIM:601492) is a rare lysosomal storage disease characterized by high hyaluronan (HA) concentration in the serum resulting from deficiency in hyaluronidase 1 (HYAL1, MIM:607071) which normally hydrolyses 1-4 linkages between N-acetylglucosamine (GlcNAc) and D-glucuronate (GlcA) residues. Symptoms of MPS IX are periodically painful soft tissue masses around the joints, acquired short stature and erosion of the hip joint, although joint movement and intelligence are normal (Natowicz et al. 1996, Triggs-Raine et al. 1999).
R-HSA-2206285 MPS VI - Maroteaux-Lamy syndrome Mucopolysaccharidosis type VI (MPS VI, Maroteaux-Lamy syndrome, polydystrophic dwarfism; MIM:253200) is an autosomal recessive lysosomal storage disorder caused by a deficiency in arylsulfatase B (ARSB, N-acetyl-galactosamine 4-sulfatase; MIM:611542). It is named after two French physicians, Pierre Maroteaux and Maurice Emil Joseph Lamy. Maroteaux first described this disorder as a novel dysostosis associated with increased urinary excretion of chondroitin sulfate (CS; Maroteaux et al. 1963). The gene encoding ARSB is mapped to chromosome 5q11-q13 (Fidzianska et al. 1984) and contains 8 exons spanning about 206 kb (Karangeorgos et al. 2007). Defective ARSB results in build up of dermatan sulfate (DS) and chondroitin sulfate (CS) in soft tissues causing compression and blockages in blood vessels, nerves, trachea, corneal clouding and disrupting normal bone development. Symptoms are similar to MPS I but with normal intelligence generally (Rapini et al. 2007, Valayannopoulos et al. 2010).
R-HSA-2206292 MPS VII - Sly syndrome Mucopolysaccharidosis type VII (MPS VII, Sly syndrome, beta-glucuronidase deficiency; MIM:253220) is an autosomal recessive lysosomal storage disease characterized by a deficiency of the enzyme beta-glucuronidase (GUSB; MIM:611499) which would normally cleave glucuronide residues from dematan sulphate, keratan sulphate and chondroitin sulphate, resulting in build up of these GAGs in cells and tissues (Sly et al. 1973). The gene encoding GUSB is 21 kb long, contains 12 exons and gives rise to two different types of cDNAs, through an alternate splicing mechanism (Miller et al. 1990). It maps to 7q11.21-q11.22 (Speleman et al. 1996). The phenotype is highly variable, ranging from severe causing death, non-immune hydrops fetalis (Vervoort et al. 1996) to mild forms with survival into adulthood (Storch et al. 2003). Most patients with the intermediate phenotype show hepatomegaly, skeletal anomalies, coarse facies, and variable degrees of mental impairment (Shipley et al. 1993, Tomatsu et al. 2009).
R-HSA-5660489 MTF1 activates gene expression The MTF1:zinc complex in the nucleus binds Metal Response Elements (MREs), DNA containing the core consensus sequence 5'-TGCRCNC-3', and activates or represses transcription depending on the context of the MRE (reviewed in Laity and Andrews 2007, Jackson et al. 2008, Gunther et al. 2012, Grzywacz et al. 2015). The 6 zinc fingers of each MTF1 monomer have different affinities for zinc and evidence from the mouse homolog indicates that different concentrations of zinc, and hence different metal loads in MTF1, activate different subsets of target genes (Wang et al. 2004, Dong et al. 2015). Genes activated by MTF1 include those encoding metallothioneins, zinc transporters, and stress-response proteins (Hardyman et al. 2016).
R-HSA-165159 MTOR signalling Target of rapamycin (mTOR) is a highly-conserved serine/threonine kinase that regulates cell growth and division in response to energy levels, growth signals, and nutrients (Zoncu et al. 2011). Control of mTOR activity is critical for the cell since its dysregulation leads to cancer, metabolic disease, and diabetes (Laplante & Sabatini 2012). In cells, mTOR exists as two structurally distinct complexes termed mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2), each one with specificity for different sets of effectors. mTORC1 couples energy and nutrient abundance to cell growth and proliferation by balancing anabolic (protein synthesis and nutrient storage) and catabolic (autophagy and utilization of energy stores) processes.
R-HSA-1632852 Macroautophagy Macroautophagy (hereafter referred to as autophagy) acts as a buffer against starvation by liberating building materials and energy sources from cellular components. It has additional roles in embryonic development, removal of apoptotic cells or organelles, antigen presentation, protection against toxins and as a degradation route for aggregate-prone proteins and infectious agents. The dysregulation of autophagy is involved in several human diseases, for example, Crohn's disease, cancer and neurodegeneration (Ravikumar et al. 2010).
Autophagy is highly conserved from yeast to humans; much of the machinery was first identified in yeast (see Klionsky et al. 2011). Initially, double-membraned cup-shaped structures called the isolation membrane or phagophore engulf portions of cytoplasm. The membranes fuse to form the autophagosome. In yeast cells, autophagosomes are formed at the phagophore assembly site (PAS) next to the vacuole. In mammals, autophagosomes appear throughout the cytoplasm then move along microtubules towards the microtubule-organising centre. This transport requires microtubules and the function of dynein motor proteins; depolymerization of microtubules or inhibition of dynein-dependent transport results in inhibition of autophagy (Kochl et al. 2006, Kimura et al. 2008). Autophagosomes fuse with lysosomes forming autolysosomes whose contents are degraded by lysosomal hydrolases (Mizushima et al. 2011).
The origins of the autophagosomal membrane and the incorporation of existing membrane material have been extensively debated. The endoplasmic reticulum (ER), mitochondria, mitochondria-associated ER membranes (MAMs), the Golgi, the plasma membrane and recycling endosomes have all been implicated in the nucleation of the isolation membrane and subsequent growth of the membrane (Lamb et al. 2013). Recently 3D tomographic imaging of isolation membranes has shown the cup-shaped isolation membrane tightly sandwiched between two sheets of ER and physically connected to the ER through a narrow membrane tube (Hayashi-Nishino et al. 2009, Yla-Anttila et al. 2009). This suggests that isolation membrane formation and elongation are guided by adjacent ER sheets, supporting the now prevalent 'ER cradle' model, which suggests that the isolation membrane arises from the ER (Hayashi-Nishino et al. 2009, Shibutani & Yoshimori 2014).
Autophagy is tightly regulated. The induction of autophagy in response to starvation is partly mediated by inactivation of the mammalian target of rapamycin (mTOR) (Noda & Ohsumi 1998) and activation of Jun N-terminal kinase (JNK), while energy loss induces autophagy by activation of AMP kinase (AMPK). Other pathways regulating autophagy are regulated by calcium, cyclic AMP, calpains and the inositol trisphosphate (IP3) receptor (Rubinsztein et al. 2012).
In mammals, two complexes cooperatively produce the isolation membrane. The ULK complex consists of ULK1/2, ATG13, (FIP200) and ATG101 (Alers et al. 2012). The PIK3C3-containing Beclin-1 complex consists of PIK3C3 (Vps34), BECN1 (Beclin-1, Atg6), PIK3R4 (p150, Vps15) and ATG14 (Barkor) (Matsunaga et al. 2009, Zhong et al. 2009). A similar complex where ATG14 is replaced by UVRAG functions later in autophagosome maturation and endocytic traffic (Itakura et al. 2008, Liang et al. 2008). Binding of KIAA0226 to this complex negatively regulates the maturation process (Matsunaga et al. 2009). The ULK and Beclin-1 complexes are recruited to specific autophagosome nucleation regions where they stimulate phosphatidylinositol-3-phosphate (PI3P) production and facilitate the elongation and initial membrane curvature of the phagophore membrane (Carlsson & Simonsen 2015).
The ULK complex is considered the most upstream component of the mammalian autophagy pathway (Itakura & Mizushima 2010), acting as an integrator of the autophagy signals downstream of mTORC1. It is not fully understood how ULK1 is modulated in response to environmental cues. Phosphorylation plays an essential role (Dunlop & Tee 2013) but it is not clear how phosphorylation regulates ULK1 activities (Ravikumar et al. 2010). ULK1 kinase activity is required for autophagy, but the substrate(s) of ULK1 that mediate its autophagic function are not certain. ULK1 may also have kinase-independent functions in autophagy (Wong et al. 2013).
PIK3C3 (Vps34) is a class III phosphatidylinositol 3-kinase that produces PI3P. It is essential for the early stages of autophagy and colocalizes strongly with early autophagosome markers (Axe et al. 2008). BECN1 binds several further proteins that affect autophagosome formation. Partners that induce autophagy include AMBRA1 (Fimia et al. 2007), UVRAG (Liang et al. 2006) and SH3GLB1 (Takahashi et al. 2007). Binding of BCL2 or BCL2L1 (Bcl-xL) inhibit autophagy (Pattingre et al. 2005, Ciechomska et al. 2009). The inositol 1,4,5-trisphosphate receptor complex that binds BCL2 also interacts with BECN1, inhibiting autophagy (Vincencio et al. 2009). CISD2 (Nutrient-deprivation autophagy factor-1, NAF1), a component in the IP3R complex, interacts with BCL2 at the ER and stabilizes the BCL2-BECN1 interaction (Chang et al. 2010). Starvation leads to activation of c-Jun NH2-terminal kinase-1 (JNK1), which results in the phosphorylation of BCL2 and BCL2L1, which release their binding to BECN1 and thus induces autophagosome formation (Wei et al. 2008).
AMBRA1 can simultaneously bind dynein and the Beclin-1 complex. During nutrient starvation, AMBRA1 is phosphorylated in a ULK1-dependent manner (Di Bartolomeo et al. 2010). This phosphorylation releases AMBRA1-associated Beclin-1 complexes from dynein and the microtubule network, freeing the complex to translocate to autophagy initiation sites (Di Bartolomeo et al. 2010).
A characteristic of this early phase of autophagosome formation is the formation of PI3P-enriched ER-associated structures called omegasomes (Axe et al. 2008) or cradles (Hayashi-Nishino et al. 2009). Omegasomes appear to concentrate at or near the connected mitochondria-associated ER membrane (Hamasaki et al. 2013). However, the phagophore also can incorporate existing material from other membrane sources such as ER exit sites (ERES), the ER-Golgi intermediate compartment (ERGIC), the Golgi, the plasma membrane and recycling endosomes (Carlsson & Simonsen 2015). Omegasomes lead to the formation of the isolation membrane or phagophore, which is thought to form de novo by an unknown mechanism (Simonsen & Stenmark 2008, Roberts & Ktistakis 2013). Phagophore expansion is probably mediated by membrane uptake from endomembranes and semi-autonomous organelles (Lamb et al. 2013, Shibutani & Yoshimori 2014).
ATG9 is a direct target of ULK1. In nutrient-rich conditions mammalian ATG9 is localized to the trans-Golgi network and endosomes (including early, late and recycling endosomes), whereas under starvation conditions it is localized to autophagosomes, in a process that is dependent on ULK1 (Young et al. 2006). ATG9 is believed to play a role in the delivery of vesicles derived from existing membranes to the expanding phagophore (Lamb et al. 2013). Yeast Atg9 forms a complex with Atg2 and Atg18 (Reggiori et al. 2004).
PI3P produced at the initiation site is sensed by WIPI2b, the mammalian homologue of Atg18 (Polson et al. 2010). WIPI2b then recruits Atg16L1 (Dooley et al. 2014). There are four WIPI proteins in mammalian cells (Proikas-Cezanne et al. 2015). They are all likely bind PI3P and be recruited to membranes but the function of WIPI1, 3 and 4 in autophagy is not yet clear. WIPI4 (WDR45) has been shown to bind Atg2 and to be involved in lipid droplet formation (Velikkakath et al. 2012); mutations in WIPI4 have been shown to cause a neurodegenerative disease (Saitsu et al. 2013).
The elongation of the membrane that will become the autophagosome is regulated by two ubiquitination-like reactions. First, the ubiquitin-like molecule ATG12 is conjugated to ATG5 by ATG7, which acts as an E1-like activating enzyme, and ATG10, which has a role similar to an E2 ubiquitin-conjugating enzyme. The ATG5:ATG12 complex then interacts non-covalently with ATG16L1. This complex associates with the forming autophagosome but dissociates from completed autophagosomes (Geng & Klionski 2008). The second ubiquitin-like reaction involves the conjugation of ubiquitin-like molecules of the LC3 family (Weidberg et al. 2010). LC3 proteins are conjugated through their C-terminal glycine residues with PE by the E1-like ATG7 and E2-like ATG3. This allows LC3 proteins to associate with the autophagosome membrane.
The ATG12:ATG5:ATG16L1 complex (Mizushima et al., 2011) acts as an E3 like enzyme for the conjugation of LC3 family proteins (mammalian homologues of yeast Atg8) to phosphatidylethanolamine (PE) (Hanada et al. 2007, Fujita et al. 2008). LC3 PE can be deconjugated by the protease ATG4 (Li et al. 2011, 2012). ATG4 is also responsible for priming LC3 proteins by cleaving the C terminus to expose a glycine residue (Kirisako et al, 2000, Scherz Shouval et al. 2007). LC3 proteins remain associated with autophagosomes until they fuse with lysosomes. The LC3-like proteins inside the resulting autolysosomes are degraded, while those on the cytoplasmic surface are delipidated and recycled. ATG5:ATG12:ATG16L1-positive LC3-negative vesicles represent pre-autophagosomal structures (pre-phagophores and possibly early phagophores), ATG5:ATG12:ATG16L1-positive LC3-positive structures can be considered to be phagophores, and ATG5:ATG12:ATG16L1-negative LC3-positive vesicles can be regarded as mature autophagosomes (Tandia et al. 2011).
Phagophore expansion is probably mediated by membrane uptake from endomembranes as well as from semiautonomous organelles (Lamb et al. 2013, Shibutani & Yoshimori 2014).
The mechanisms involved in the closure of the phagophore membrane are poorly understood. As the phagophore is a double-membraned structure, its closure involves the fusion of a narrow opening, a process that is distinct from other membrane fusion events (Carlsson & Simonsen 2015). The topology of the phagophore is similar to that of cytokinesis, viral budding or multivesicular body (MVB) formation. These processes rely on the Endosomal Sorting Complex Required for Transport (ESCRT) (Rusten et al. 2012). ESCRT and associated proteins facilitate membrane budding away from the cytosol and subsequent cleavage of the bud neck (Hurley & Hanson 2010). Several studies have shown that depletion of ESCRT subunits or the regulatory ATPase Vps4 causes an accumulation of autophagosomes (Filimonenko et al. 2007, Rusten et al. 2007) but it is not clear whether ESCRTs are required for autophagosome closure or for autophagosome to endosome fusion. UVRAG is also involved in the maturation step, recruiting proteins that bring about membrane fusion such as the class C Vps proteins, which activate Rab7 thereby promoting fusion with late endosomes and lysosomes (Liang et al. 2008).
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol In humans, a 47S precursor rRNA (pre-rRNA) is transcribed by RNA polymerase I from rRNA-encoding genes (rDNA) at the boundary of the fibrillar center and the dense fibrillar components of the nucleolus (Stanek et al. 2001). The 47S precursor is processed over the course of about 5-8 minutes (Popov et al. 2013) by endoribonucleases and exoribonucleases to yield the 28S rRNA and 5.8S rRNA of the 60S subunit and the 18S rRNA of the 40S subunit (reviewed in Mullineus and Lafontaine 2012, Henras et al. 2015). As the pre-rRNA is being transcribed, a large protein complex, the small subunit (SSU) processome, assembles in the region of the 18S rRNA sequence, forming terminal knobs on the pre-rRNA (reviewed in Phipps et al. 2011, inferred from yeast in Dragon et al. 2002). The SSU processome contains both ribosomal proteins of the small subunit and processing factors which process the pre-rRNA and modify nucleotides. Through addition of subunits the SSU processome appears to be converted into the larger 90S pre-ribosome (inferred from yeast in Grandi et al. 2002). An analogous large subunit processome (LSU) assembles in the region of the 28S rRNA, however the LSU is less well characterized (inferred from yeast in McCann et al. 2015).
Following cleavage of the pre-rRNA within internal transcribed spacer 1 (ITS1), the pre-ribosomal particle separates into a pre-60S subunit and a pre-40S subunit in the nucleolus (reviewed in Hernandez-Verdun et al. 2010, Phipps et al. 2011). The pre-60S and pre-40S ribosomal particles are then exported from the nucleus to the cytoplasm where the processing factors dissociate and recycle back to the nucleus
Nuclease digestions of the 47S pre-rRNA can follow several paths. In the major pathway, the ends of the 47S pre-rRNA are trimmed to yield the 45S pre-rRNA. Digestion at site 2 (also called site 2b in mouse, see Henras et al. 2015 for nomenclature) cleaves the 45S pre-rRNA to yield the 30S pre-rRNA containing the 18S rRNA of the small subunit and the 32S pre-rRNA containing the 5.8S rRNA and the 28S rRNA of the large subunit. The 32S pre-rRNA is digested in the nucleus to yield the 5.8S rRNA and the 28S rRNA while the 30S pre-rRNA is digested in the nucleus to yield the 18SE pre-rRNA which is then processed in the nucleus and cytosol to yield the 18S rRNA. At least 286 human proteins, 74 of which have no yeast homolog, are required for efficient processing of pre-rRNA in the nucleus (Tafforeau et al. 2013)
R-HSA-9856872 Malate-aspartate shuttle The malate-aspartate shuttle (MAS) is a redox process that supports oxidative pathways in the cytosol, and reductive potential in mitochondria. The mitochondrial succinate dehydrogenase (SDH) reaction provides reducing equivalents (electrons) for the respiratory electron transport, with the NADH needed to reduce malate coming from cytosolic processes. There is no NADH equilibrium between cytosol and mitochondria: cytosolic NADH/NAD+ ratio is 0.001, while in mitochondria, it is 0.1. The MAS creates this NADH gradient by reducing oxaloacetate (OA) to malate (MAL), catalyzed by cytosolic MDH1, and exchanging cytosolic MAL with mitochondrial 2-oxoglutarate (2OG, 2-KG), catalyzed by SLC25A11. At the same time, aspartate (L-Asp) gets exported and transaminated to glutamate (L-Glu), which subsequently gets coimported with a proton and transaminated back. In summary, mitochondria take up one proton and one reducing equivalent. The proton import by SLC25A12/13 is irreversible, so the MAS always runs in one direction. Hence, the mitochondrial outward proton-motive force drives the MAS toward cytosolic NADH oxidation. Defects in any of the reactions of this pathway lead to cytosolic NAD+ scarcity, affecting glycolysis, L-Glu, and L-Ser biosynthesis, as well as L-Asp availability. Neurotransmission in the CNS specifically needs L-Asp and L-Glu, and mutations in proteins catalyzing MAS reactions are commonly associated with early infantile epileptic encephalopathy (reviewed in Borst, 2020; Broeks et al., 2021).
R-HSA-9636667 Manipulation of host energy metabolism Mtb secretes proteins that enhance enzymatic activity of glucose metabolism in the phagocyte. The same proteins also appear to increase glucose uptake and to cause accumulation of DHAP, ultimately increasing the host cell's lipid production (Singh et al. 2015).
R-HSA-9865114 Maple Syrup Urine Disease The branched-chain alpha ketoacid dehydrogenase complex (BCKDH) catalyzes the oxidative decarboxylation of branched-chain keto acids in the mitochondrial matrix as the second step in the degradation of branched-chain amino acids (BCAAs) leucine, valine and isoleucine, providing acetyl CoA and succinyl CoA intermediates for the Krebs Cycle (reviewed in Strauss et al, 2020; Zhang et al, 2023).
BCKDH is a multi-enzyme complex consisting of three sub-complexes, the E2 transacylase, the E1 decarboxylase and the E3 dehydrogenase. The core of BCKDH is the E2 transacylase domain, made up of 24 copies of Dihydrolipoamide Branched-chain Transacylase (DBT) arranged in octahedral symmetry. Surrounding the E2 core are 12 copies of the E1 decarboxylase tetramer (each of which consists of a dimer of BCKDHA and a dimer of BCKDHB) and six copies of the E3 dehydrogenase (each consisting of a dimer of Dihydrolipoyl Dehydrogenase (DLD)). The E3 subcomplex is not specific to BCKDH but is also a component of the pyruvate dehydrogenase complex (PDC) and the alpha-ketoglutarate dehydrogenase complex (alpha-KGDC) (Chang et al, 2002; Brautigam et al, 2005; Aevarsson et al, 2000; reviewed in Biswas et al, 2019; Strauss et al, 2020).
In addition to the E1, E2 and E3 components, the BCKDH complex also depends on other cofactors- lipoamide for the function of the E2 transacylase, thiamine diphosphate and potassium for the function of the E1 decarboxylase and FAD and NAD+ for the function of the E3 dehydrogenase (Chang et al, 2002; Brautigam et al, 2005; Aevarsson et al, 2000; reviewed in Biswas et al, 2019; Strauss et al, 2020).
The activity of BCKDH is regulated by the association of BCKD kinase (BCKDK) and protein phosphatase 1K (PPM1K) with the macromolecular complex (Reed et al, 1985). Phosphorylation of BCKDHB S342 by BCKDK inhibits the catalytic activity of BCKDH, while PPM1K-mediated dephosphorylation activates it (Li et al, 2004; Wynn et al, 2004; Wynn et al, 2012). BCKDK is itself negatively regulated by thiamine (Chuang et al, 2006).
Structures for each of the subcomplexes of human BCKDH have been solved, and the complex has a total molecular mass on the order of 4 million Da (Chang et al, 2002; Brautigam et al, 2005; Aevarsson et al, 2000).
Loss-of-function mutations in the BCKDHA, BCKDHB and DBT genes disrupt the stability and the activity of the BCKDH complex, causing an accumulation of branched-chain keto-acids that causes the characteristic odor associated with Maple Syrup Urine disease (MSUD), an inborn error of metabolism with a prevalence of 1:185,000 live births (reviewed in Strauss et al, 2020; Biswas et al, 2019). MSUD is an autosomal recessive disorder and in its classic neonatal form is characterized by a maple syrup odor to the urine, poor feeding, mental and physical retardation, lethargy, seizures, coma and death. Classic MSUD, like the intermediate, intermittent and thiamine-responsive forms described below, may arise as a result of mutations in any of BCKDHA, BCKDHB or DBT. Classic MSUD is characterized by the lowest (~0-3%) residual enzymatic activity of all the forms, and presents clinically during the neonatal period. An intermediate form (residual activity ~3-30%) manifests clinically many months after birth with signs of mental retardation and developmental delay. Patients with the intermittent form of MSUD have normal levels of BCAA and BCKA and normal development and physiology while healthy, but are triggered into manifesting symptoms of MSUD when stressed by, for instance, infection. The existence of a thiamine-responsive form of MSUD, in which symptoms are alleviated by dietary thiamine, is somewhat controversial, but may reflect the inhibitory effect of thiamine on BCKDK, relieving inhibition of BCKDH activity (Chaung et al, 2006; reviewed in Strauss et al, 2020, Biswas et al, 2019). Mandatory newborn screening programs include testing for MSUD, allowing for early intervention that is especially critical in cases of classic MSUD (Strauss et al, 2020)
Mutations in DLD, the E3 subunit shared with PDH and alpha-KGDH, affect the enzymatic activity of all three complexes and are responsible for a more severe disorder called dihydrolipoamide dehydrogenase deficiency (DLDD). DLLD generally results in death in infancy due to lactic acidosis (Taylor et al, 1978; reviewed in Ambrus, 2019).
R-HSA-9669924 Masitinib-resistant KIT mutants Mastinib is a class II tyrosine kinase inhibitor that targets mutant and wild-type FGFR3, PDGFR and c-KIT (Dubreuil, 2009). Masitinib, like imatinib, is effective in inhibiting the activity of juxtamembrane mutant forms of KIT, but is ineffective against many of the mutations in the activation loop and ATP-binding cleft of the receptor (Dubreuil, 2009; Serrano et al, 2019; reviewed in Demetri, 2011).
R-HSA-9816359 Maternal to zygotic transition (MZT) Fertilization of the oocyte triggers the maternal-to-zygotic transition (MZT, reviewed in Vastenhous et al. 2019), a series of events that degrades maternal mRNAs (reviewed in Sha et al. 2019), alters chromatin to allow widespread transcription (reviewed in Eckersley-Maslin et al. 2018), and initiates transcription of the new zygotic genome (zygotic genome activation, ZGA, embryonic genome activation, EGA, reviewed in Wu and Vastenhouw 2020).
Immediately after fertilization, the oocyte completes the final stage of the second meiotic division and the resulting zygote contains separate female and male pronuclei. Within the male pronucleus, protamines are replaced by histones provided by the oocyte (reviewed in McLay and Clarke 2003, Yang et al. 2015). A specific set of maternal mRNAs is degraded by maternally provided factors in a process called M-decay (reviewed in Jiang and Fan 2022) and DNA methylation is lost in both the male pronucleus and the female pronucleus. In mouse zygotes, male DNA methylation is lost in an active process in which cytidine deamination by AICDA (AID) and excision repair initially remove 5-methylcytidine residues, then remaining 5-methylcytidine residues are oxidized by TET3 and removed by base excision repair so that male DNA methylation begins to decrease before fusion of the male and female pronuclei. Maternal DNA methylation is passively lost by dilution over subsequent cell generations, yielding a blastocyst that has low male and female DNA methylation (reviewed in Marcho et al. 2015, Eckersley-Maslin et al. 2018). In human embryos, DNA demethylation in male and female genomes is much faster and is complete by the 2-cell stage, suggesting that maternal DNA demethylation may occur at least partly actively (Guo et al. 2014, reviewed in Tesarik 2022).
In mouse embryos, methylation at histone H3 lysine-4 (H3K4me3), a mark of active chromatin, changes from broad regions that span genes in the maternal genome to peaks at the 5' and 3' ends of genes. Acetylation of H3K27, another mark of active chromatin, increases and methylation of H3K27 and H3K9, repressive marks, becomes reduced (reviewed in Marcho et al. 2015, Eckersley-Maslin et al. 2018). The result is a permissive state of chromatin that produces the first transcription of the zygotic genome and continues into the pluripotent cells of the blastocyst.
Activation of transcription of the zygotic genome, called zygotic genome activation (ZGA) or embryonic genome activation (EGA), occurs in two phases: an initial minor phase followed by a major phase (reviewed in Perry et al. 2022). In mouse zygotes and possibly in human zygotes, the minor phase starts at the 1-cell stage. In mice, the major phase occurs at the 2-cell stage; in humans the major phase occurs at the 8-cell stage. Surprisingly, many transcripts in the early embryo originate from the LTRs of endogenous retroviruses. The LTRs later become silenced after implantation of the embryo.
Developmental pluripotency-associated protein 2 (DPPA2), DPPA4, and Double homeobox protein 4 (DUX4, homolog of mouse Dux) are all key transcription factors that participate in initiating the first, minor wave of ZGA. DPPA2 and DPPA4 activate DUX4 and other genes. DUX4 is actually a small array of identical retroposed genes that were produced by reverse transcription in the germline. DUX4 acting with other factors then activates developmental regulators such as ZSCAN4, the double homeobox genes DUXA, DUXB, LEUTX, and the histone demethylase KDM4E. Significantly, DUX4 binds and activates bidirectional transcription from the LTRs of HERVL endogenous retroviruses and Mammalian Apparent LTRs (MaLRs). Interestingly, human DUX4 and its homolog mouse Dux bind species-specific LTRs, indicating that DUX4 and Dux are coevolving with the endogenous retroviruses in their respective genomes (Whiddon et al. 2017). DUX4 also binds and activates bidirectional transcription of species-specific pericentromeric repeats, the human HSATII repeats.
Activation of the zygotic genome produces factors that further degrade maternal mRNAs in a process called Z-decay (reviewed in Jiang and Fan 2022)
R-HSA-9854311 Maturation of TCA enzymes and regulation of TCA cycle (Citrate-synthase)-lysyl-methyltransferase (CSKMT, METTL12) transfers three methyl groups from S-adenosylmethionine (SAM) to lysine-395 of citrate synthase (CS). The expression of CSKMT is low or absent in many normal organ tissues, but the trimethylated form is predominant in most cell lines tested. The modification is evolutionarily conserved, with contradicting reports on the activity of modified CS, while the effect on the whole CS/ACO2 metabolon was not investigated. Oxalocetate inhibits methyltransferase activity (Malecki et al., 2017; Rhein et al., 2017; reviewed in Qi et al., 2023).
R-HSA-9828806 Maturation of hRSV A proteins Human respiratory syncytial virus contains 10 genes which are translated into 11 proteins, of which 2 have translation isoforms due to use of alternative translation initiation codons. These proteins function in viral replication and host interaction. Fusion protein F, glycoprotein G, and both variants of small hydrophobic protein, SH and SHt, get glycosylated and F, G, and SH later migrate to the plasma membrane where virion assembly takes place. Matrix protein M first translocates to the nucleus and back to cytosol before serving as a scaffold at the assembly site. M2-1 is also found in the nucleus. Phosphorylations, partially transient, appear to be necessary for oligomerization and function of the SH, N, P, M, and M2-1 proteins (Gan & Torres, 2011; McLellan et al, 2013; Muniyandi et al, 2018; Anderson et al, 2021).
R-HSA-9694631 Maturation of nucleoprotein This COVID-19 pathway has been created by a combination of computational inference from SARS-CoV-1 data (https://reactome.org/documentation/inferred-events) and manual curation, as described in the summation for the overall SARS-CoV-2 infection pathway.
Nucleoprotein, the most abundant viral protein expressed during infection, is found in the host cell cytosol, the nucleus and plasma membrane. After phosphorylation and sumoylation it di-/tetramerizes and is moved to the Golgi, the virion budding site (Li et al, 2005; Surjit et al, 2005).
R-HSA-9683610 Maturation of nucleoprotein Nucleoprotein, the most abundant viral protein expressed during infection, is found in the cytosol and plasma membrane. After phosphorylation and sumoylation it trimerizes and is moved to the Golgi, the virion budding site (Li et al, 2005; Surjit et al, 2005).
R-HSA-9694719 Maturation of protein 3a This COVID-19 pathway has been created by a combination of computational inference from SARS-CoV-1 data (https://reactome.org/documentation/inferred-events) and manual curation, as described in the summation for the overall SARS-CoV-2 infection pathway.
Protein 3a is associated with protein M and is found in the virion, although its function in the structure seems non-essential. 3a is O-glycosylated and forms a homotetramer with porin function (Oostra et al, 2006; Lu et al, 2006)
R-HSA-9683673 Maturation of protein 3a Protein 3a is associated with protein M and is found in the virion, although its function in the structure seems non-essential. 3a is O-glycosylated and forms a homotetramer with porin function (Oostra et al, 2006; Lu et al, 2006).
R-HSA-9683683 Maturation of protein E The envelope protein (E) gets palmitoylated and ubiquitinated after translation. It forms trimers that show porin activity but does not localize to the cell membrane (Tan et al, 2004; Liao et al, 2006; Alvarez et al, 2011).
R-HSA-9694493 Maturation of protein E This COVID-19 pathway has been created by a combination of computational inference from SARS-CoV-1 data (https://reactome.org/documentation/inferred-events) and manual curation, as described in the summation for the overall SARS-CoV-2 infection pathway.
The envelope protein (E) gets palmitoylated and ubiquitinated after translation. It forms trimers that show porin activity but does not localize to the cell membrane (Tan et al, 2004; Liao et al, 2006; Alvarez et al, 2011)
R-HSA-9694594 Maturation of protein M This COVID-19 pathway has been created by a combination of computational inference from SARS-CoV-1 data (https://reactome.org/documentation/inferred-events) and manual curation, as described in the summation for the overall SARS-CoV-2 infection pathway.
Protein M, part of which is N-glycosylated, accumulates in the Golgi complex and recruits Spike protein to the sites of virus assembly and budding in the ERGIC (Voss et al, 2006; Voss et al, 2009)
R-HSA-9683612 Maturation of protein M Protein M, part of which is N-glycosylated, accumulates in the Golgi complex and recruits Spike protein to the sites of virus assembly and budding in the ERGIC (Voss et al, 2006; Voss et al, 2009).
R-HSA-9684325 Maturation of replicase proteins Production of polyprotein fragments (so called replicase proteins) involves the repeated autocleavage of the polyprotein, liberating the two endopeptidases that finally cleave all fragments efficiently. Only nsp3 and nsp4 are post-translationally modified, they are glycosylated (Muramatsu et al, 2015; Harcourt et al, 2004; Oostra et al, 2007)
R-HSA-9694301 Maturation of replicase proteins This COVID-19 pathway has been created by a combination of computational inference from SARS-CoV-1 data (https://reactome.org/documentation/inferred-events) and manual curation, as described in the summation for the overall SARS-CoV-2 infection pathway.
Production of polyprotein fragments (so called replicase proteins) involves the repeated autocleavage of the polyprotein, liberating the two endopeptidases that finally cleave all fragments efficiently. Only nsp3 and nsp4 are post-translationally modified, they are glycosylated (Muramatsu et al, 2015; Harcourt et al, 2004; Oostra et al, 2007).
R-HSA-9683686 Maturation of spike protein Spike protein of SARS-Cov is subject to N-glycosylation and palmitoylation. The chaperone calnexin exclusively helps with protein folding. The end product is a homotrimer (Nal et al, 2005).
R-HSA-9694548 Maturation of spike protein This COVID-19 pathway has been created by a combination of computational inference from SARS-CoV-1 data (https://reactome.org/documentation/inferred-events) and manual curation, as described in the summation for the overall SARS-CoV-2 infection pathway.
The viral Spike protein of SARS-CoV-1 is subject to N-glycosylation and palmitoylation. The chaperone calnexin exclusively helps with protein folding. The end product is a homotrimer (Nal et al, 2005). In SARS-CoV-2 the Spike glycosylation patterns were extensively characterized, and consist of both N-glycans and O-glycans attached to about twenty amino acids (reviewed by Petrović et al, 2021; Gong et al, 2021; Shajahan et al, 2021). Although there is no reason for the host's glycosylation enzymes behaving differently than with other host or non-host proteins, direct involvement of host enzymes and chaperones with SARS-CoV-2 Spike glycosylation has not been shown. Indirect evidence from inhibition experiments (Reyes et al, 2021; Franco et al, 2022) is confounded by simultaneous inhibition of glycosylation of other proteins like the ACE2 receptor.
R-HSA-1500620 Meiosis During meiosis the replicated chromosomes of a single diploid cell are segregated into 4 haploid daughter cells by two successive divisions, meiosis I and meiosis II. In meiosis I, the distinguishing event of meiosis, pairs (bivalents) of homologous chromosomes in the form of sister chromatids are paired by synapsis along their regions of homologous DNA (Yang and Wang 2009), and then segregated, resulting in haploid daughters containing sister chromatids paired at their centromeres (Cohen et al. 2006, Handel and Schimenti 2010). The sister chromatids are then separated and segregated during meiosis II.
Recombination between chromosomal homologues but not between sister chromatids occurs during prophase of meiosis I (Inagaki et al. 2010). Though hundreds of recombination events are initiated, most are resolved without crossovers and only tens proceed to become crossovers. In mammals recombination events are required between homologues for normal pairing, synapsis, and segregation.
R-HSA-912446 Meiotic recombination Meiotic recombination exchanges segments of duplex DNA between chromosomal homologs, generating genetic diversity (reviewed in Handel and Schimenti 2010, Inagaki et al. 2010, Cohen et al. 2006). There are two forms of recombination: non-crossover (NCO) and crossover (CO). In mammals, the former is required for correct pairing and synapsis of homologous chromosomes, while CO intermediates called chiasmata are required for correct segregation of bivalents.
Meiotic recombination is initiated by double-strand breaks created by SPO11, which remains covalently attached to the 5' ends after cleavage. SPO11 is removed by cleavage of single DNA strands adjacent to the covalent linkage. The resulting 5' ends are further resected to produce protruding 3' ends. The single-stranded 3' ends are bound by RAD51 and DMC1, homologs of RecA that catalyze a search for homology between the bound single strand and duplex DNA of the chromosomal homolog. RAD51 and DMC1 then catalyze the invasion of the single strand into the homologous duplex and the formation of a D-loop heteroduplex. Approximately 90% of heteroduplexes are resolved without crossovers (NCO), probably by synthesis-dependent strand annealing.
The invasive strand is extended along the homolog and ligated back to its original duplex, creating a double Holliday junction. The mismatch repair proteins MSH4, MSH5 participate in this process, possibly by stabilizing the duplexes. The mismatch repair proteins MLH1 and MLH3 are then recruited to the double Holliday structure and an unidentified resolvase (Mus81? Gen1?) cleaves the junctions to yield a crossover.
Crossovers are not randomly distributed: The histone methyltransferase PRDM9 recruits the recombination machinery to genetically determined hotspots in the genome and each incipient crossover somehow inhibits formation of crossovers nearby, a phenomenon called crossover interference. Each chromosome bivalent, including the X-Y body in males, has at least one crossover and this is required for meiosis to proceed correctly.
For review, please refer to Cohen et al. 2006, Inagaki et al. 2010, Handel and Schimenti 2010.
The FIRRM:FIGNL1 complex has recently been reported to interact with both RAD51 and DMC1 recombinases and limit the formation of meiotic crossovers by regulating RAD51 and DMC1 dynamics during meiosis (Fernandes et al. 2018).
R-HSA-1221632 Meiotic synapsis Meiotic synapsis is the stable physical pairing of homologous chromosomes that begins in leptonema of prophase I and lasts until anaphase of prophase I. First, short segments of axial elements form along chromosomes. Telomeres then cluster at a region of the inner nuclear membrane and axial elements extend and fuse along the length of the chromosomes. Subsequent to the initiation of recombination transverse filaments of SYCP1 link axial/lateral elements to a central element containing SYCE1 and SYCE2, thus forming the synaptonemal complex (reviewed in Yang and Wang 2009).
Unsynapsed regions are silenced during pachynema by recruitment of BRCA1 and ATR, which phosphorylates histone H2AX (reviewed in Inagaki et al. 2010).
R-HSA-5662702 Melanin biosynthesis Melanin biosynthesis takes place in specialized cells called melanocytes, within membrane-bound organelles referred to as melanosomes. Melanosomes are transferred via dendrites to surrounding keratinocytes. Keratinocytes and melanocytes are collectively known as 'the epidermal melanin unit'. Each melanocyte is in contact with approximately 40 keratinocytes in the basal and suprabasal layers (Cichorek et al. 2013). Melanocytes are distributed in the epidermis, hair follicles, the inner ear and the eye (Yamaguchi et al. 2007, Tolleson 2005).
Melanocytes in mammals and birds produce two chemically distinct types of melanin, black to brown eumelanin and yellow to reddish-brown pheomelanin (Ito & Wakamatsu 2008, Simon et al. 2009, d'Ischia et al. 2013). These differ in their responses to UV radiation; eumelanin has the ability to convert absorbed light energy into heat energy (Meredith & Riesz 2004) and to detoxify reactive oxygen species (ROS) (Bustamante et al. 1993), while pheomelanin is a phototoxic pro-oxidant (Samokhvalov 2005). Most natural melanin pigments contain eumelanin and pheomelanin (Ito & Wakamatsu 2003) and are termed 'mixed' melanins. Neuromelanins are mixed melanin-like pigments which are mainly found in neurons of the substantia nigra and locus coeruleus (Fedorow et al. 2005). Synthesis of NM may prevent the accumulation of toxic catechol derivatives (Zecca et al. 2003). NM can sequester a variety of potentially damaging molecules such as beta-carbolines, heavy metal ions and 1-methyl-4-phenylpyridinium (MPP+) (D'Amato et al. 1986), a drug which causes Parkinson's Disease-like symptoms. Models suggest that mixed melanogenesis occurs in three stages (Ito et al. 2000). The initial stage of melanin biosynthesis is the production of cysteinyldopas, which continues while sufficient cysteine is available. The second stage is the oxidation of cysteinyldopas to produce pheomelanin, which continues while cysteinyldopa concentration is sufficiently high. The last stage is the production of eumelanin, which begins when cysteinyldopas and cysteine are depleted. The ratio of eumelanin to pheomelanin is determined by tyrosinase activity and the availability of tyrosine and cysteine (Land et al. 2003).
R-HSA-199991 Membrane Trafficking The secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is made up of distinct organelles, including the endoplasmic reticulum (ER), Golgi complex, plasma membrane, and tubulovesicular transport intermediates. These organelles mediate intracellular membrane transport between themselves and the cell surface. Membrane traffic within this system flows along highly organized directional routes. Secretory cargo is synthesized and assembled in the ER and then transported to the Golgi complex for further processing and maturation. Upon arrival at the trans Golgi network (TGN), the cargo is sorted and packaged into post-Golgi carriers that move through the cytoplasm to fuse with the cell surface. This directional membrane flow is balanced by retrieval pathways that bring membrane and selected proteins back to the compartment of origin.
R-HSA-174490 Membrane binding and targetting of GAG proteins One of the mysteries of Gag protein involvement in HIV virion assembly is how the proteins are targeted to the proper membrane for budding. Infectious retroviruses do not bud from all of the available membrane surfaces within an infected cell, but primarily from the plasma membrane, which constitutes a small proportion of the total membrane surface in most cells. In polarized cells, the sites of budding are further restricted to the basolateral membrane.
R-HSA-5579029 Metabolic disorders of biological oxidation enzymes The ability to process xenobiotica and many endogenous compounds is called biotransformation and is catalysed by enzymes mainly in the liver of higher organisms but also a number of other organs such as kidneys, gut and lungs. Metabolism occurs in two stages; phase 1 functionalisation and phase 2 conjugation. Defects in enzymes in these two phases can lead to disease (Nebert et al. 2013, Pikuleva & Waterman 2013, Zanger & Schwab 2013, Mudd 2013, Messenger et al. 2013, Aoyama & Nakaki 2013, Shih 2004, Millington 2013, Azimi et al. 2014, Sticova & Jirsa 2013).
R-HSA-1430728 Metabolism Metabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as the inactivation and elimination of toxic ones generated endogenously or present in the extracellular environment. The processes of energy metabolism can be classified into two groups according to whether they involve carbohydrate-derived or lipid-derived molecules, and within each group it is useful to distinguish processes that mediate the breakdown and oxidation of these molecules to yield energy from ones that mediate their synthesis and storage as internal energy reserves. Synthetic reactions are conveniently grouped by the chemical nature of the end products, such as nucleotides, amino acids and related molecules, and porphyrins. Detoxification reactions (biological oxidations) are likewise conveniently classified by the chemical nature of the toxin.
At the same time, all of these processes are tightly integrated. Intermediates in reactions of energy generation are starting materials for biosyntheses of amino acids and other compounds, broad-specificity oxidoreductase enzymes can be involved in both detoxification reactions and biosyntheses, and hormone-mediated signaling processes function to coordinate the operation of energy-generating and energy-storing reactions and to couple these to other biosynthetic processes.
R-HSA-2022377 Metabolism of Angiotensinogen to Angiotensins Angiotensinogen, a prohormone, is synthesized and secreted mainly by the liver but also from other tissues (reviewed in Fyhrquist and Saijonmaa 2008, Cat and Touyz 2011). Renin, an aspartyl protease specific for angiotensinogen, is secreted into the bloodstream by juxtaglomerular cells of the kidney in response to a drop in blood pressure. Renin cleaves angiotensinogen to yield a decapaptide, angiotensin I (angiotensin-1, angiotensin-(1-10)). Circulating renin can also bind the membrane-localized (pro)renin receptor (ATP6AP2) which increases its catalytic activity. After cleavage of angiotensinogen to angiotensin I by renin, two C-terminal amino acid residues of angiotensin I are removed by angiotensin-converting enzyme (ACE), located on the surface of endothelial cells, to yield angiotensin II (angiotensin-2, angiotensin-(1-8)), the active peptide that causes vasoconstriction, resorption of sodium and chloride, excretion of potassium, water retention, and aldosterone secretion.
More recently other, more tissue-localized pathways leading to angiotensin II and alternative derivatives of angiotensinogen have been identified (reviewed in Kramkowski et al. 2006, Kumar et al. 2007, Fyhrquist and Saijonmaa 2008, Becari et al. 2011). Chymase, cathepsin G, and cathepsin X (cathepsin Z) can each cleave angiotensin I to yield angiotensin II. Angiotensin-converting enzyme 2 (ACE2) cleaves 1 amino acid residue from angiotensin I (angiotensin-(1-10)) to yield angiotensin-(1-9), which can be cleaved by ACE to yield angiotensin-(1-7). ACE2 can also cleave angiotensin II to yield angiotensin-(1-7). Neprilysin can cleave either angiotensin-(1-9) or angiotensin I to yield angiotensin-(1-7). Angiotensin-(1-7) binds the MAS receptor (MAS1, MAS proto-oncogene) and, interestingly, produces effects opposite to those produced by angiotensin II.
Aminopeptidase A (APA, ENPEP) cleaves angiotensin II to yield angiotensin III (angiotensin-(2-8)), which is then cleaved by aminopeptidase N (APN, ANPEP) yielding angiotensin IV (angiotensin-(3-8)). Angiotensin IV binds the AT4 receptor (AT4R, IRAP, LNPEP, oxytocinase).
Inhibitors of renin (e.g. aliskiren) and ACE (e.g. lisinopril, ramipril) are currently used to treat hypertension (reviewed in Gerc et al. 2009, Verdecchia et al. 2010, Alreja and Joseph 2011).
R-HSA-8953854 Metabolism of RNA This superpathway encompasses the processes by which RNA transcription products are further modified covalently and non-covalently to yield their mature forms, and the regulation of these processes. Annotated pathways include ones for capping, splicing, and 3'-cleavage and polyadenylation to yield mature mRNA molecules that are exported from the nucleus (Hocine et al. 2010). mRNA editing and nonsense-mediated decay are also annotated. Processes leading to mRNA breakdown are described: deadenylation-dependent mRNA decay, microRNA-mediated RNA cleavage, and regulation of mRNA stability by proteins that bind AU-rich elements.psnRNP assembly is also annotated here.
The aminoacylation of mature tRNAs is annotated in the "Metabolism of proteins" superpathway, as a part of "Translation". R-HSA-209776 Metabolism of amine-derived hormones Catecholamines and thyroxine are synthesized from tyrosine, and serotonin and melatonin from tryptophan. R-HSA-71291 Metabolism of amino acids and derivatives Cellular metabolism of amino acids and related molecules includes the pathways for the catabolism of amino acids, the biosynthesis of the nonessential amino acids (alanine, arginine, aspartate, asparagine, cysteine, glutamate, glutamine, glycine, proline, and serine) and selenocysteine, the synthesis of urea, and the metabolism of carnitine, creatine, choline, polyamides, melanin, and amine-derived hormones. The metabolism of amino acids provides a balanced supply of amino acids for protein synthesis. In the fasting state, the catabolism of amino acids derived from breakdown of skeletal muscle protein and other sources is coupled to the processes of gluconeogenesis and ketogenesis to meet the body’s energy needs in the absence of dietary energy sources. These metabolic processes also provide the nitrogen atoms for the biosynthesis of nucleotides and heme, annotated as separate metabolic processes (Felig 1975; Häussinger 1990; Owen et al. 1979).
Transport of these molecuels across lipid bilayer membranes is annotated separately as part of the module on "transmembrane transport of small molecules". R-HSA-71387 Metabolism of carbohydrates Starches and sugars are major constituents of the human diet and the catabolism of monosaccharides, notably glucose, derived from them is an essential part of human energy metabolism (Dashty 2013). Glucose can be catabolized to pyruvate (glycolysis) and pyruvate synthesized from diverse sources can be metabolized to form glucose (gluconeogenesis). Glucose can be polymerized to form glycogen under conditions of glucose excess (glycogen synthesis), and glycogen can be broken down to glucose in response to stress or starvation (glycogenolysis). Other monosaccharides prominent in the diet, fructose and galactose, can be converted to glucose. The disaccharide lactose, the major carbohydrate in breast milk, is synthesized in the lactating mammary gland. The pentose phosphate pathway allows the synthesis of diverse monosaccharides from glucose including the pentose ribose-5-phosphate and the regulatory molecule xylulose-5-phosphate, as well as the generation of reducing equivalents for biosynthetic processes. Glycosaminoglycan metabolism and xylulose-5-phosphate synthesis from glucuronate are also annotated as parts of carbohydrate metabolism.
The digestion of dietary starch and sugars and the uptake of the resulting monosaccharides into the circulation from the small intestine are annotated as parts of the “Digestion and absorption” pathway. R-HSA-8978934 Metabolism of cofactors Many proteins depend for their activity on cofactors, associated ions and small molecules. This module contains annotations of processes involved in the synthesis of cofactors, either de novo or from essential molecules consumed in the diet (vitamins), as well as regeneration of active forms of cofactors (Lipmann 1984). R-HSA-6806667 Metabolism of fat-soluble vitamins Vitamins A, D, E, and K are classified as fat-soluble. Metabolic pathways by which dietary precursors of vitamins A (Harrison 2005) and K (Shearer et al. 2012) are converted to active forms are annotated here. The conversion of 7-dehydrocholesterol is converted to active vitamin D (Dusso et al. 2005) is annotated as part of metabolism of steroids. (Vitamin E (tocopherol) is available in active form from the diet.) R-HSA-196757 Metabolism of folate and pterines Folates are essential cofactors that provide one-carbon moieties in various states of reduction for biosynthetic reactions. Processes annotated here include transport reactions by which folates are taken up by cells and moved intracellularly, folate conjugation with glutamate (required for folate retention within a cell), and some of the key reactions in the generation of reduced folates and one-carbon derivatives of folate. R-HSA-2408550 Metabolism of ingested H2SeO4 and H2SeO3 into H2Se Ingested selenic acid (H2SeO4) and selenite (SeO3(2-)) are reduced to hydrogen selenide (H2Se) through a combination of actions involving bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 and 2 (PAPSS1/2), PAPSe reductase (PAPSeR), and thioredoxin reductase 1 (TXNRD1). R-HSA-5263617 Metabolism of ingested MeSeO2H into MeSeH Methylseleninic acid (MeSeO2H) is reduced to methylselenenic acid (MeSeOH) and then further reduced to methylselenol (MeSeH) by thioredoxin reductase (TXNRD1). R-HSA-2408508 Metabolism of ingested SeMet, Sec, MeSec into H2Se Inorganic (selenite, SeO3(2-); and selenate, SeO4(2-)) and organic (selenocysteine, Sec; and selenomethionine, SeMet) forms of selenium can introduced in the diet where they are transformed into the intermediate selenide (Se(2-)) through the trans-selenation pathway, selenocysteine lyase (SCLY), and cystathionine gamma-lyase (CTH). R-HSA-556833 Metabolism of lipids Lipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphingolipids, eicosanoids, cholesterol, bile salts, steroid hormones, and fat-soluble vitamins. They function as a major source of energy (fatty acids, triacylglycerols, and ketone bodies), are major constituents of cell membranes (cholesterol and phospholipids), play a major role in their own digestion and uptake (bile salts), and participate in numerous signaling and regulatory processes (steroid hormones, eicosanoids, phosphatidylinositols, and sphingolipids) (Vance & Vance 2008 - URL).
The central steroid in human biology is cholesterol, obtained from animal fats consumed in the diet or synthesized de novo from acetyl-coenzyme A. (Vegetable fats contain various sterols but no cholesterol.) Cholesterol is an essential constituent of lipid bilayer membranes and is the starting point for the biosyntheses of bile acids and salts, steroid hormones, and vitamin D. Bile acids and salts are mostly synthesized in the liver. They are released into the intestine and function as detergents to solubilize dietary fats. Steroid hormones are mostly synthesized in the adrenal gland and gonads. They regulate energy metabolism and stress responses (glucocorticoids), salt balance (mineralocorticoids), and sexual development and function (androgens and estrogens). At the same time, chronically elevated cholesterol levels in the body are associated with the formation of atherosclerotic lesions and hence increased risk of heart attacks and strokes. The human body lacks a mechanism for degrading excess cholesterol, although an appreciable amount is lost daily in the form of bile salts and acids that escape recycling.
Aspects of lipid metabolism currently annotated in Reactome include lipid digestion, mobilization, and transport; fatty acid, triacylglycerol, and ketone body metabolism; peroxisomal lipid metabolism; phospholipid and sphingolipid metabolism; cholesterol biosynthesis; bile acid and bile salt metabolism; and steroid hormone biosynthesis. R-HSA-202131 Metabolism of nitric oxide: NOS3 activation and regulation Nitric oxide (NO), a multifunctional second messenger, is implicated in physiological processes in mammals that range from immune response and potentiation of synaptic transmission to dilation of blood vessels and muscle relaxation. NO is a highly active molecule that diffuses across cell membranes and cannot be stored inside the producing cell. Its signaling capacity is controlled at the levels of biosynthesis and local availability. Its production by NO synthases is under complex and tight control, being regulated at transcriptional and translational levels, through co- and posttranslational modifications, and by subcellular localization. NO is synthesized from L-arginine by a family of nitric oxide synthases (NOS). Three NOS isoforms have been characterized: neuronal NOS (nNOS, NOS1) primarily found in neuronal tissue and skeletal muscle; inducible NOS (iNOS, NOS2) originally isolated from macrophages and later discovered in many other cell types; and endothelial NOS (eNOS, NOS3) present in vascular endothelial cells, cardiac myocytes, and in blood platelets. The enzymatic activity of all three isoforms is dependent on calmodulin, which binds to nNOS and eNOS at elevated intracellular calcium levels, while it is tightly associated with iNOS even at basal calcium levels. As a result, the enzymatic activity of nNOS and eNOS is modulated by changes in intracellular calcium levels, leading to transient NO production, while iNOS continuously releases NO independent of fluctuations in intracellular calcium levels and is mainly regulated at the gene expression level (Pacher et al. 2007).
The NOS enzymes share a common basic structural organization and requirement for substrate cofactors for enzymatic activity. A central calmodulin-binding motif separates an NH2-terminal oxygenase domain from a COOH-terminal reductase domain. Binding sites for cofactors NADPH, FAD, and FMN are located within the reductase domain, while binding sites for tetrahydrobiopterin (BH4) and heme are located within the oxygenase domain. Once calmodulin binds, it facilitates electron transfer from the cofactors in the reductase domain to heme enabling nitric oxide production. Both nNOS and eNOS contain an additional insert (40-50 amino acids) in the middle of the FMN-binding subdomain that serves as autoinhibitory loop, destabilizing calmodulin binding at low calcium levels and inhibiting electron transfer from FMN to the heme in the absence of calmodulin. iNOS does not contain this insert.
In this Reactome pathway module, details of eNOS activation and regulation are annotated. Originally identified as endothelium-derived relaxing factor, eNOS derived NO is a critical signaling molecule in vascular homeostasis. It regulates blood pressure and vascular tone, and is involved in vascular smooth muscle cell proliferation, platelet aggregation, and leukocyte adhesion. Loss of endothelium derived NO is a key feature of endothelial dysfunction, implicated in the pathogenesis of hypertension and atherosclerosis. The endothelial isoform eNOS is unique among the nitric oxide synthase (NOS) family in that it is co-translationally modified at its amino terminus by myristoylation and is further acylated by palmitoylation (two residues next to the myristoylation site). These modifications target eNOS to the plasma membrane caveolae and lipid rafts.
Factors that stimulate eNOS activation and nitric oxide (NO) production include fluid shear stress generated by blood flow, vascular endothelial growth factor (VEGF), bradykinin, estrogen, insulin, and angiopoietin. The activity of eNOS is further regulated by numerous post-translational modifications, including protein-protein interactions, phosphorylation, and subcellular localization.
Following activation, eNOS shuttles between caveolae and other subcellular compartments such as the noncaveolar plasma membrane portions, Golgi apparatus, and perinuclear structures. This subcellular distribution is variable depending upon cell type and mode of activation.
Subcellular localization of eNOS has a profound effect on its ability to produce NO as the availability of its substrates and cofactors will vary with location. eNOS is primarily particulate, and depending on the cell type, eNOS can be found in several membrane compartments: plasma membrane caveolae, lipid rafts, and intracellular membranes such as the Golgi complex. R-HSA-194441 Metabolism of non-coding RNA The term non-coding is commonly employed for RNA that does not encode a protein, but this does not mean that such RNAs do not contain information nor have function. There is considerable evidence that the majority of mammalian and other complex organism's genomes is transcribed into non-coding RNAs, many of which are alternatively spliced and/or processed into smaller products. Around 98% of all transcriptional output in humans is non-coding RNA. RNA-mediated gene regulation is widespread in higher eukaryotes and complex genetic phenomena like RNA interference are mediated by such RNAs. These non-coding RNAs are a growing list and include rRNAs, tRNAs, snRNAs, snoRNAs siRNAs, 7SL RNA, 7SK RNA, the RNA component of RNase P RNA, the RNA component of RNase MRP, and the RNA component of telomerase. R-HSA-15869 Metabolism of nucleotides Nucleotides and their derivatives are used for short-term energy storage (ATP, GTP), for intra- and extra-cellular signaling (cAMP; adenosine), as enzyme cofactors (NAD, FAD), and for the synthesis of DNA and RNA. Most dietary nucleotides are consumed by gut flora; the human body's own supply of these molecules is synthesized de novo. Additional metabolic pathways allow the interconversion of nucleotides, the salvage and reutilization of nucleotides released by degradation of DNA and RNA, the catabolism of excess nucleotides, and the transport of these molecules between the cytosol and the nucleus (Rudolph 1994). These pathways are regulated to control the total size of the intracellular nucleotide pool, to balance the relative amounts of individual nucleotides, and to couple the synthesis of deoxyribonucleotides to the onset of DNA replication (S phase of the cell cycle).
These pathways are also of major clinical interest as they are the means by which nucleotide analogues used as anti-viral and anti-tumor drugs are taken up by cells, activated, and catabolized (Weilin and Nordlund 2010). As well, differences in nucleotide metabolic pathways between humans and aplicomplexan parasites like Plasmodium have been exploited to design drugs to attack the latter (Hyde 2007).
The movement of nucleotides and purine and pyrimidine bases across lipid bilayer membranes, mediated by SLC transporters, is annotated as part of the module "transmembrane transport of small molecules".
R-HSA-351202 Metabolism of polyamines Polyamines is a family of molecules (i.e. putrescine, spermine, spermidine) derived from ornithine according to a decarboxylation/condensative process. More recently, it has been demonstrated that arginine can be metabolised according to the same pathway leading to agmatine formation. Polyamines are essential for the growth, the maintenance and the function of normal cells. The complexity of their metabolism and the fact that polyamines homeostasis is tightly regulated support the idea that polyamines are essential to cell survival. Multiple abnormalities in the control of polyamines metabolism might be implicated in several pathological processes (Moinard et al., 2005). Legend for the following figure:
R-HSA-189445 Metabolism of porphyrins Porphyrins are heterocyclic macrocycles, consisting of four pyrrole subunits (tetrapyrrole) linked by four methine (=CH-) bridges. The extensive conjugated porphyrin macrocycle is chromatic and the name itself, porphyrin, is derived from the Greek word for purple. The aromatic character of porphyrins can be seen by NMR spectroscopy.
Porphyrins readily combine with metals by coordinating them in the central cavity. Iron (heme) and magnesium (chlorophyll) are two well known examples although zinc, copper, nickel and cobalt form other known metal-containing phorphyrins. A porphyrin which has no metal in the cavity is called a free base.
Some iron-containing porphyrins are called hemes (heme-containing proteins or hemoproteins) and these are found extensively in nature ie. hemoglobin. Hemoglobin is quantitatively the most important hemoprotein. The hemoglobin iron is the transfer site of oxygen and carries it in the blood all round the body for cell respiration. Other examples are cytochromes present in mitochondria and endoplasmic reticulum which takes part in electron transfer events, catalase and peroxidase whic protect the body against the oxidant hydrogen peroxide and tryptophan oxygenase which is present in intermediary metabolism. Hemoproteins are synthesized in all mammalian cells and the major sites are erythropoietic tissue and the liver.
The processes by which heme is synthesized, transported, and metabolized are a critical part of human iron metabolism (Severance and Hamze 2009); here the core processes of heme biosynthesis and catabolism have been annotated. R-HSA-392499 Metabolism of proteins Metabolism of proteins, as annotated here, covers the full life cycle of a protein from its synthesis to its posttranslational modification and degradation, at various levels of specificity. Protein synthesis is accomplished through the process of Translation of an mRNA sequence into a polypeptide chain. Protein folding is achieved through the function of molecular chaperones which recognize and associate with proteins in their non-native state and facilitate their folding by stabilizing the conformation of productive folding intermediates (Young et al. 2004). Following translation, many newly formed proteins undergo Post-translational protein modification, essentially irreversible covalent modifications critical for their mature locations and functions (Knorre et al. 2009), including gamma carboxylation, synthesis of GPI-anchored proteins, asparagine N-linked glycosylation, O-glycosylation, SUMOylation, ubiquitination, deubiquitination, RAB geranylgeranylation, methylation, carboxyterminal post-translational modifications, neddylation, and phosphorylation. Peptide hormones are synthesized as parts of larger precursor proteins whose cleavage in the secretory system (endoplasmic reticulum, Golgi apparatus, secretory granules) is annotated in Peptide hormone metabolism. After secretion, peptide hormones are modified and degraded by extracellular proteases (Chertow, 1981 PMID:6117463). Protein repair enables the reversal of damage to some amino acid side chains caused by reactive oxygen species. Pulmonary surfactants are lipids and proteins that are secreted by the alveolar cells of the lung that decrease surface tension at the air/liquid interface within the alveoli to maintain the stability of pulmonary tissue (Agassandian and Mallampalli 2013). Nuclear regulation, transport, metabolism, reutilization, and degradation of surfactant are described in the Surfactant metabolism pathway. Amyloid fiber formation, the accumulation of mostly extracellular deposits of fibrillar proteins, is associated with tissue damage observed in numerous diseases including late phase heart failure (cardiomyopathy) and neurodegenerative diseases such as Alzheimer's, Parkinson's, and Huntington's. R-HSA-380612 Metabolism of serotonin Serotonin is first metabolized to 5-hydroxyindole acetaldehyde by monoamine oxidase. 5-hydroxyindole acetaldehyde is then catalyzed by aldehyde dehydrogenase to form 5-hydroxyindole acetic acid. R-HSA-196071 Metabolism of steroid hormones Steroid hormones are synthesized primarily in the adrenal gland and gonads. They regulate energy metabolism and stress responses (glucocorticoids), salt balance (mineralocorticoids), and sexual development and function (androgens and estrogens). All steroids are synthesized from cholesterol. Steroid hormone synthesis is largely regulated at the initial steps of cholesterol mobilization and transport into the mitochondrial matrix for conversion to pregnenolone. In the body, the fate of pregnenolone is tissue-specific: in the zona fasciculata of the adrenal cortex it is converted to cortisol, in the zona glomerulosa to aldosterone, and in the gonads to testosterone and then to estrone and estradiol. These pathways are outlined in the figure below, which also details the sites on the cholesterol molecule that undergo modification in the course of these reactions. R-HSA-8957322 Metabolism of steroids Steroids, defined by a four-ring cyclopenta[a]phenanthrene carbon skeleton, include cholesterol and bile acids and salts, steroid hormones, and vitamin D, three groups of molecules synthesized from it. In this module, pathways for the synthesis of cholesterol from HMG-CoA (hydroxymethylglutaryl-coenzyme A) (Russell 1992), and for its conversion to bile acids and salts (Russell 2003), steroid hormones (Payne & Hales 2004), and vitamin D (Dusso et al. 2005) are annotated, together with the SREBP-mediated regulatory process that normally links the rate of cholesterol synthesis to levels of cellular cholesterol (Brown & Goldstein 2009). R-HSA-6806664 Metabolism of vitamin K Vitamin K is a required co-factor in a single metabolic reaction, the gamma-carboxylation of glutamate residues of proteins catalyzed by GGCX (gamma-carboxyglutamyl carboxylase). Substrates of GGCX include blood clotting factors, osteocalcin (OCN), and growth arrest-specific protein 6 (GAS6) (Brenner et al. 1998). Vitamin K is derived from green leafy vegetables as phylloquinone and is synthesized by gut flora as menaquinone-7. These molecules are taken up by intestinal enterocytes with other lipids, packaged into chylomicrons, and delivered via the lymphatic and blood circulation to tissues of the body, notably hepatocytes and osteoblasts, via processes of lipoprotein trafficking (Shearer & Newman 2014; Shearer et al. 2012) described elsewhere in Reactome.
In these tissues, menadiol (reduced vitamin K3) reacts with geranylgeranyl pyrophosphate to form MK4 (vitamin K hydroquinone), the form of the vitamin required as cofactor for gamma-carboxylation of protein glutamate residues (Hirota et al. 2013). The gamma-carboxylation reactions, annotated elsewhere in Reactome as a part of protein metabolism, convert MK4 to its epoxide form, which is inactive as a cofactor. Two related enzymes, VKORC1 and VKORCL1, can each catalyze the reduction of MK4 epoxide to active MK4. VKORC1 activity is essential for normal operation of the blood clotting cascade and for osteocalcin function (Ferron et al. 2015). A physiological function for VKORCL1 has not yet been definitively established (Hammed et al. 2013; Tie et al. 2014). R-HSA-196854 Metabolism of vitamins and cofactors Vitamins are a diverse group of organic compounds, classified according to their solubility, either fat-soluble or water-soluble, that are either not synthesized or synthesized only in limited amounts by human cells. They are required in small amounts in the diet and have distinct biochemical roles, often as coenzymes (cofactors). The physiological processes dependent on vitamin-requiring reactions include many aspects of intermediary metabolism, vision, bone formation, and blood coagulation, and vitamin deficiencies are associated with a correspondingly diverse and severe group of diseases. Metabolic pathways for water-soluble B group and C vitamins, and for fat-soluble vitamins A, D and K are annotated in Reactome, covering processes that convert dietary forms of these molecules into active forms, and that regenerate active forms of vitamin cofactors consumed in other metabolic processes. R-HSA-196849 Metabolism of water-soluble vitamins and cofactors Vitamins are a diverse group of organic compounds, required in small amounts in the diet. They have distinct biochemical roles, often as coenzymes, and are either not synthesized or synthesized only in limited amounts by human cells. Vitamins are classified according to their solubility, either fat-soluble or water-soluble. The physiological processes dependent on vitamin-requiring reactions include many aspects of intermediary metabolism, vision, bone formation, and blood coagulation, and vitamin deficiencies are associated with a correspondingly diverse and severe group of diseases.
Water-soluble vitamins include ascorbate (vitamin C) and the members of the B group: thiamin (vitamin B1), riboflavin (B2), niacin (B3), pantothenate (B5), pyridoxine (B6), biotin (B7), folate (B9), and cobalamin (B12). Metabolic processes annotated here include the synthesis of thiamin pyrophosphate (TPP) from thiamin (B1), the synthesis of FMN and FAD from riboflavin (B2), the synthesis of nicotinic acid (niacin - B3) from tryptophan, the synthesis of Coenzyme A from pantothenate (B5), features of the metabolism of folate (B9), the uptake, transport, and metabolism of cobalamin (B12), and molybdenum cofactor biosynthesis.
R-HSA-425410 Metal ion SLC transporters Six SLC gene families encode proteins which mediate transport of metals. The families are SLC11, SLC30, SLC31, SLC39, SLC40 and SLC41 (He L et al, 2009; Bressler JP et al, 2007).
R-HSA-6799990 Metal sequestration by antimicrobial proteins Metals are necessary for all forms of life including microorganisms, evidenced by the fact that metal cations are constituents of approximately 40% of all proteins crystallized to date (Waldron KJ et al. 2009; Foster AW et al. 2014; Guengerich FP 2014, 2015). The ability of microorganisms to maintain the intracellular metal quota is essential and allows microorganisms to adapt to a variety of environments. Accordingly, the ability of the host to control metal quota at inflammation sites can influence host-pathogen interactions. The host may restrict microbial growth either by excluding essential metals from the microbes, by delivery of excess metals to cause toxicity, or by complexing metals in microorganisms (Becker KW & Skaar EP 2014).
R-HSA-5689901 Metalloprotease DUBs The JAB1/MPN +/MOV34 (JAMM) domain metalloproteases cleave the isopeptide bond at or near the the attachment point of polyubiquitin and substrate. PSMD14 (RPN11), STAMBP (AMSH), STAMBPL1 (AMSH-LP), and BRCC3 (BRCC36) are highly specific for the K63 poly-Ub linkage, which may be a general characteristic (Eletr & Wilkinson 2014). Two multisubunit complexes represented elsewhere in Reactome contain JAMM DUBs. The proteasome 19S lid complex includes PSMD14, an endopeptidase that cleaves poly-Ub chains from substrates as they are degraded by the proteasome (Verma et al. 2002). The COP9-Signalosome contains COPS5 (CSN5), which deconjugates the Ub-like modifier Nedd8, modulating the activity of the SCF E3 ligase (Cope et al. 2002).
JAMM DUB catalysis requires nucleophilic attack on the carbonyl carbon of the isopeptide bond by an activated water molecule bound to Zn2+ and a conserved glutamate. A negatively-charged tetrahedral transition state ensues, and a nearby conserved Ser/Thr in the JAMM domains stabilizes the oxyanion. The tetrahedral intermediate then collapses and the Glu serves as a general base donating a proton to the leaving Lys side chain (Ambroggio et al. 2004).
R-HSA-5661231 Metallothioneins bind metals Metallothioneins are highly conserved, cysteine-rich proteins that bind metals via thiolate bonds (recent general reviews in Capdevila et al. 2012, Blindauer et al. 2014, reviews of mammalian metallothioneins in Miles et al. 2000, Maret 2011, Vasak and Meloni 2011, Thirumoorthy et al. 2001, Babula et al. 2012). Mammals contain 4 general metallothionein isoforms (MT1,2,3,4). The MT1 isoform has radiated in primates to 8 or 9 functional proteins (depending on classification of MT1L). Each mammalian metallothionein binds a total of 7 divalent metal ions in two clusters, the alpha and beta clusters. Though the functions of metallothioneins have not been fully elucidated, they appear to participate in detoxifying heavy metals (reviewed in Sharma et al. 2013), storing and transporting zinc, and redox biochemistry. Metallothioneins interact with many other cellular proteins, with most interactions involving proteins of the central nervous system (reviewed in Atrian and Capdevila 2013).
R-HSA-1237112 Methionine salvage pathway Methionine salvage is a sequential pathway of six reactions that create methionine from 5'-methylthioadenosine (MTA) which is a byproduct of polyamine biosynthesis in nearly all organisms. The process happens completely in the cytosol. It is important in humans for recycling of sulphur that has to be assimilated using energy. (Pirkov et al, 2008; Albers, 2009)
R-HSA-156581 Methylation Methylation is a common but minor pathway of Phase II conjugation compared to glucuronidation or sulfonation. The cofactor used in methylation conjugation is S-adenosylmethionine (SAM). SAM is the second most widely used enzyme substrate after ATP and is involved in a wide range of important biological processes. SAM is sythesized from methionine's reaction with ATP, catalyzed by methionine adenosyltransferase (MAT). There are two genes, MAT1A and MAT2A, which encode for two homologous MAT catalytic subunits, 1 and 2.
During conjugation with nucleophilic substrates, the methyl group attached to the sulfonium ion of SAM is transferred to the substrate forming the conjugate. SAM, having lost the methyl moiety, is converted to S-adenosylhomocysteine (SAH). SAH can be hydrolyzed to form adenosine and homocysteine. Homocysteine can either be converted to glutathione or methylated to form methionine, thus forming the starting point for SAM synthesis and completing the cycle.
Fuctional groups attacked are phenols, catechols, aliphatic and aromatic amines and sulfhydryl-containing groups. The enzymes that catalyze the transfer of the methyl group to these functional groups are the methyltransferases (MT). MTs are small, cytosolic, monomeric enzymes that utilize SAM as a methyl donor. There are many MTs but the best studied ones are named on the basis of their prototypical substrates: COMT (catechol O-methyltransferase), TPMT (thiopurine methyltransferase), TMT (thiol methyltransferase), HNMT (histamine N-methyltransferase) and NNMT (nicotinamide N-methyltransferase). An example of each enzyme mentioned is given. In each case, a typical substrate for the enzyme is shown.
R-HSA-2408552 Methylation of MeSeH for excretion Methylselenol (MeSeH) is further methylated to dimethylselenide (Me2Se) and trimethylselenonium (Me3Se+) for excretion.
R-HSA-203927 MicroRNA (miRNA) biogenesis Biogenesis of microRNAs (miRNAs) can be summarized in five steps (reviewed in Ketting 2011, Nowotny and Yang 2009, Kim et al. 2009, Chua et al. 2009, Hannon and He 2004):
1. Transcription. miRNA transcripts may come from autonomously transcribed genes, they may be contained in cotranscripts with other genes, or they may be located in introns of host genes. Most miRNAs are transcribed by RNA polymerase II, however a few miRNAs originate as RNA polymerase III cotranscripts with neighboring repetitive elements. The initial transcript, termed a primary microRNA (pri-miRNA), contains an imperfectly double-stranded region within a hairpin loop. Longer sequences extend from the 5' and 3' ends of the hairpin and may also contain double-stranded regions.
2. Cleavage by DROSHA. The 5' and 3' ends of the pri-miRNA are removed during endoribonucleolytic cleavage by the DROSHA nuclease in a complex with the RNA-binding protein DGCR8 (the Microprocessor complex). The cleavage product is a short hairpin of about 60 to 70 nt called the pre-microRNA (pre-miRNA).
3. Nuclear export by Exportin-5. The resulting pre-miRNA is bound by Exportin-5 in a complex with Ran and GTP. The complex translocates the pre-miRNA through the nuclear pore into the cytoplasm.
4. Cleavage by DICER1. Once in the cytoplasm the pre-miRNA is bound by the RISC loading complex which contains DICER1, an Argonaute protein and either TARBP2 or PRKRA. DICER1 cleaves the pre-miRNA to yield an imperfectly double-stranded miRNA of about 21 to 23 nucleotides. At this stage the double-stranded miRNA has protruding single-stranded 3' ends of 2-3 nt.
5. Incorporation into RNA-Induced Silencing Complex (RISC) and strand selection. The double-stranded miRNA is passed to a Argonaute protein contained in the RISC loading complex. One strand, the passenger strand, will be removed and degraded; the other strand, the guide strand, will be retained and will guide the Argonaute:miRNA complex (RISC) to target mRNAs.
The human genome encodes 4 Argonaute proteins (AGO1 (EIF2C1), AGO2 (EIF2C2), AGO3 (EIF2C3), AGO4 (EIF2C4)), however only AGO2 (EIF2C2) can cleave target mRNAs with perfect or nearly perfect complementarity to the guide miRNA. For complexes that contain AGO2, cleavage of the passenger strand of the double-stranded miRNA accompanies removal of the passenger strand. Complexes containing other Argonautes may use a helicase to remove the passenger strand but this is not fully known. The resulting miRNA-loaded AGO2 is predominantly located in complexes with TARBP2 or PRKRA at the cytosolic face of the rough endoplasmic reticulum. AGO2, TARBP2, and DICER1 are also observed in the nucleus.
R-HSA-9686347 Microbial modulation of RIPK1-mediated regulated necrosis Activation of receptor-interacting serine/threonine protein (RIP) kinases RIPK1 and RIPK3 coordinate an immunogenic form of programmed cell death known as regulated necrosis or necroptosis (Upton JW et al. 2017). This form of necrosis leads to anti-viral inflammation in host through cell death-associated release of damage-associated molecular patterns (DAMPs) (Nailwal H & Ka-Ming Chan F 2019; Upton JW et al. 2017). Microbial pathogens are able to modulate host regulated necrosis through different triggers and pathways. The promotion and inhibition of host cell death vary and depend on the microbe types, virulence, and phenotypes (Upton JW et al. 2010, 2012, 2017; Jaclyn S Pearson JS et al. 2017; Petrie EJ et al. 2019; Fletcher-Etherington A et al. 2020; Nailwal H & Ka-Ming Chan F 2019; ).
R-HSA-190840 Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane Through videomicroscopy, a saltatory transport of connexon vesicles along curvilinear microtubules from the Golgi to the plasma membrane has been observed (Lauf et al., 2002). Such a transport system has been described for similar secretory vesicles (Toomre et al., 1999).
R-HSA-193993 Mineralocorticoid biosynthesis Aldosterone, the major human mineralocorticoid, is synthesized in the zona glomerulosa of the adrenal cortex from pregnenolone. Pregnenolone is converted to progesterone in two reactions, both catalyzed by 3-beta-hydroxysteroid dehydrogenase/isomerase. Progesterone is hydroxylated by CYP21A2 to form deoxycorticosterone, which in turn is converted to aldosterone in a three-reaction sequence catalyzed by CYP11B2 (Payne and Hales 2004).
R-HSA-164516 Minus-strand DNA synthesis In the first part of reverse transcription, minus-strand synthesis, a DNA strand complementary to the HIV genomic RNA is synthesized, using the viral RNA as a template and a host cell lysine tRNA molecule as primer. The synthesis proceeds in two discrete steps, separated by a strand transfer event. As minus strand DNA is synthesized, the viral genomic RNA is degraded, also in several discrete steps. Two specific polypurine tracts (PPT sequences) in the viral RNA, one within the pol gene (central or cPPT) and one immediately preceding the U3 sequence (3' PPT) are spared from degradation and serve to prime synthesis of DNA complementary to the minus strand (plus-strand synthesis). During plus-strand synthesis, Preston and colleagues observed secondary sites of plus-strand initiation at low frequency both in the cell-free system and in cultured virus (Klarman et al., 1997). Both DNA synthesis and RNA degradation activities are catalyzed by the HIV-1 reverse transcriptase (RT) heterodimer.
R-HSA-9715370 Miro GTPase Cycle Miro GTPases are a separate family of Ras-related GTPases that are sometimes included in the atypical RHO GTPases group, but are phylogenetically distinct from the Rho family (Jaffe and Hall 2005; Boureux et al. 2007; Devine et al. 2016; Liu et al. 2017). Miro GTPases possess an additional GTPase domain more closely related to Rheb (Klosowiak et al. 2013). Miro family of RAS-like GTPases includes two members, RHOT1 and RHOT2. RHOT1 and RHOT2 regulate the movement of mitochondria (Schwarz 2013; Devine et al. 2016) and peroxisomes (Castro et al. 2018, Okumoto et al. 2018, Covill-Cooke et al. 2020).
R-HSA-211958 Miscellaneous substrates Approximately a quarter of the 57 human CYPs still remain "orphans" in the sense that their function, expression sites, and regulation are largely not elucidated. While there is enough experimental evidence to know that all these proteins get made and can catalyze CYP-like reactions in vitro, evidence of in vivo function and substrate specificity is insufficient to allow them to be placed in any of the classes in the functional scheme.
R-HSA-5223345 Miscellaneous transport and binding events This section contains known transport and binding events that as of yet cannot be placed in exisiting pathways (Purves 2001, He et al. 2009, Rees et al. 2009).
R-HSA-5358508 Mismatch Repair The mismatch repair (MMR) system corrects single base mismatches and small insertion and deletion loops (IDLs) of unpaired bases. MMR is primarily associated with DNA replication and is highly conserved across prokaryotes and eukaryotes. MMR consists of the following basic steps: a sensor (MutS homologue) detects a mismatch or IDL, the sensor activates a set of proteins (a MutL homologue and an exonuclease) that select the nascent DNA strand to be repaired, nick the strand, exonucleolytically remove a region of nucleotides containing the mismatch, and finally a DNA polymerase resynthesizes the strand and a ligase seals the remaining nick (reviewed in Kolodner and Marsischkny 1999, Iyer et al. 2006, Li 2008, Fukui 2010, Jiricny 2013).
Humans have 2 different MutS complexes. The MSH2:MSH6 heterodimer (MutSalpha) recognizes single base mismatches and small loops of one or two unpaired bases. The MSH2:MSH3 heterodimer (MutSbeta) recognizes loops of two or more unpaired bases. Upon binding a mismatch, the MutS complex becomes activated in an ATP-dependent manner allowing for subsequent downstream interactions and movement on the DNA substrate. (There are two mechanisms proposed: a sliding clamp and a switch diffusion model.) Though the order of steps and structural details are not fully known, the activated MutS complex interacts with MLH1:PMS2 (MutLalpha) and PCNA, the sliding clamp present at replication foci. The role of PCNA is multifaceted as it may act as a processivity factor in recruiting MMR proteins to replicating DNA, interact with MLH1:PMS2 and Exonuclease 1 (EXO1) to initiate excision of the recently replicated strand and direct DNA polymerase delta to initiate replacement of bases. MLH1:PMS2 makes an incision in the strand to be repaired and EXO1 extends the incision to make a single-stranded gap of up to 1 kb that removes the mismatched base(s). (Based on assays of purified human proteins, there is also a variant of the mismatch repair pathway that does not require EXO1, however the mechanism is not clear. EXO1 is almost always required, it is possible that the exonuclease activity of DNA polymerase delta may compensate in some situations and it has been proposed that other endonucleases may perform redundant functions in the absence of EXO1.) RPA binds the single-stranded region and a new strand is synthesized across the gap by DNA polymerase delta. The remaining nick is sealed by DNA ligase I (LIG1).
Concentrations of MMR proteins MSH2:MSH6 and MLH1:PMS2 increase in human cells during S phase and are at their highest level and activity during this phase of the cell cycle (Edelbrock et al. 2009). Defects in MSH2, MSH6, MLH1, and PMS2 cause hereditary nonpolyposis colorectal cancer (HNPCC, also known as Lynch syndrome) (reviewed in Martin-Lopez and Fishel 2013).
R-HSA-5358606 Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) MSH2:MSH3 (MutSbeta) binds unpaired loops of 2 or more nucleotides (Palombo et al. 1996, Genschel et al. 1998). Human cells contain about 6-fold more MSH2:MSH6 than MSH2:MSH3 (MutSbeta) and an imbalance in the ratio can cause a mutator phenotype (Drummond et al. 1997, Marra et al. 1998). Binding of the mismatch activates MSH2:MSH3 to exchange ADP for ATP, adopt the conformation to allow movement along the DNA, and interact with downstream effectors PCNA, MLH1:PMS2 and EXO1. The interaction with PCNA initiates excision of the recently replicated strand. MLH1:PMS2 makes a nick that is enlarged to a gap of hundreds of nucleotides by EXO1. DNA is polymerized across the gap by DNA polymerase delta and the remaining nick is sealed by DNA ligase I.
R-HSA-5358565 Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) MSH2:MSH6 (MutSalpha) binds single base mismatches and unpaired loops of 1-2 nucleotides (reviewed in Edelbrock et al. 2013). Human cells contain about 6-fold more MSH2:MSH6 than MSH2:MSH3 (MutSbeta), which mediates repair of larger mismatches, and an imbalance in the ratio can cause a mutator phenotype (Drummond et al. 1997, Marra et al. 1998). The MSH6 subunit is responsible for binding the mismatch, which activates MSH2:MSH6 to exchange ADP for ATP, adopt the conformation to allow movement on the DNA, and interact with downstream effectors PCNA, MLH1:PMS2 and EXO1. The interaction with PCNA initiates excision of the recently replicated strand. MLH1:PMS2 has endonucleolytic activity and makes a nick that is enlarged to a gap of hundreds of nucleotides by EXO1. DNA is polymerized across the gap by DNA polymerase delta and the remaining nick is sealed by DNA ligase I.
R-HSA-1369007 Mitochondrial ABC transporters Mammalian ABC transporters are usually found on the plasma membrane and on organelles such as the ER and peroxisome but a small number are also located on the mitochondria. Here they are thought to play roles in heme biosynthesis and iron-sulphur cluster synthesis (Burke & Ardehali 2007).
R-HSA-77289 Mitochondrial Fatty Acid Beta-Oxidation Beta-oxidation begins once fatty acids have been imported into the mitochondrial matrix by carnitine acyltransferases. The beta-oxidation spiral of fatty acids metabolism involves the repetitive removal of two carbon units from the fatty acyl chain. There are four steps to this process: oxidation, hydration, a second oxidation, and finally thiolysis. The last step releases the two-carbon acetyl-CoA and a ready primed acyl-CoA that takes another turn down the spiral. In total each turn of the beta-oxidation spiral produces one NADH, one FADH2, and one acetyl-CoA.
Further oxidation of acetyl-CoA via the tricarboxylic acid cycle generates additional FADH2 and NADH. All reduced cofactors are used by the mitochondrial electron transport chain to form ATP. The complete oxidation of a fatty acid molecule produces numerous ATP molecules. Palmitate, used as the model here, produces 129 ATPs.
Beta-oxidation pathways differ for saturated and unsaturated fatty acids. The beta-oxidation of saturated fatty acids requires four different enzymatic steps. Beta-oxidation produces and consumes intermediates with a trans configuration; unsaturated fatty acids that have bonds in the cis configuration require three separate enzymatic steps to prepare these molecules for the beta-oxidation pathway.
R-HSA-9836573 Mitochondrial RNA degradation The human mitochondrial genome encodes two rRNAs, 22 tRNAs, and 13 proteins. The mitochondrial genome is transcribed from two divergent promoters into two large precursor RNAs, one from each strand, that are endonucleolytically processed into individual mRNAs, tRNAs, and rRNAs (Mercer et al. 2011, reviewed in Barchiesi and Vascotto 2019, Jedynak-Slyvka et al. 2021, Rackham and Filipovska 2022). Heavy strand (H-strand) DNA is significantly more G-rich than light strand (L-strand) DNA. Transcripts from the H-strand encode eight monocistronic mRNAs, two bicistronic mRNAs (MT-ATP8/6 and MT-ND4L/4), 14 tRNAs, and two rRNAs. Transcripts from the L‑strand encode only one mRNA (MT‑ND6), one long non-coding RNA (lncRNA), lncND6, which is antisense to MT-ND6, and eight tRNAs, and two long non-coding RNAs designated as lncND5, and lncCyt b RNA that are antisense to the coding mRNAs MT-ND5 and MT-CYB (CYTB, MT-Cytb) (Rackham et al. 2011). The L-strand and H-strand transcripts are complementary and, therefore, have the potential to form large double-stranded RNAs (dsRNAs), yet very little dsRNA is observed in wild-type mitochondria.
Both dsRNAs and normal mRNAs, tRNAs, and rRNAs are hydrolyzed by the SUPV3L1:PNPT1 complex, called the degradosome, which is located mostly in mitochondrial RNA granules (MRGs) adjacent to the DNA-containing nucleoid (reviewed in Borowski et al. 2010, Rorbach and Minczuk 2012, Kotrys and Szczesny 2019, Rackham and Filipovska 2022). Degradation appears to occur in subregions of MRGs called D-foci (Borowski et al. 2013, Van Haute et al. 2015). SUPV3L1 is a helicase that unwinds double-stranded RNA (Shu et al. 2004, Wang et al. 2009, Dhir et al. 2018, Jain et al. 2022) to provide single-stranded substrate to the PNPT1 exonuclease (Wang et al. 2009, Lin et al. 2012). Additionally, G quadruplex structures in a subset of RNAs are unwound by GRSF1 to provide substrates to the SUPV3L1:PNPT1 complex (Antonicka et al. 2013, Pietras et al. 2018). However, other RNAs are stabilized by GRSF1 (Antonicka et al. 2013). The PNPT1 3'-5' exonuclease hydrolyzes RNAs to yield 4-5 nucleotide "nanoRNAs" which are further hydrolyzed to mononucleotides by the REXO2 dimer (Bruni et al. 2013, Szewczyk et al. 2020).
Degradation of mitochondrial RNAs is regulated by RNA-binding proteins: FASTK, FASTKD1-5, and the SLIRP:LRPPRC complex (Sasarman et al. 2010, Chujo et al. 2021, Ruzzenente et al. 2012, Jourdain et al. 2017, Siira et al. 2017, reviewed in Rackham and Filipovska 2022). SLIRP:LRPPRC binds throughout the mitochondrial transcriptome, including 12S rRNA, 16S rRNA, and 13 mRNAs, and acts to stabilize RNA structures, inhibit hybridization of complementary RNAs, and extend the half-lives of RNAs (Sasarman et al. 2010, Chujo et al. 2012, Siira et al. 2017). Fas-activated serine/threonine kinase (FASTK) and its homologs FASTKD1-5 bind particular mitochondrial RNAs and affect their stability and processing (reviewed in Jourdain et al. 2017, Rackham and Filipovska 2022).
R-HSA-166187 Mitochondrial Uncoupling The protonmotive force across the inner mitochondrial membrane built up by respiratory electron transport does not go entirely into ATP production. Transport proteins of the SLC25 type utilize the gradient to symport small molecules with protons into the matrix, simultaneously generating heat ("thermogenesis"). UCP1 and AAC1 have been shown to import protons exclusively and are responsible for most heat generated in brown fat and other tissue, respectively (reviewed in Bertholet & Kirichok, 2022).
Uncoupling proteins (UCPs) are members of the mitochondrial transport carrier family. The crystal structure of one member of the family, the adenine nucleotide translocase, is known, and UCPs can be successfully folded into this structure to indicate their probable 3D arrangement (Pebay-Peyroula et al. 2003, Kunji 2004, Esteves & Brand 2005).
The most studied member of the family, UCP1, catalyzes adaptive thermogenesis (i.e., heat generation) in mammalian brown adipose tissue. It does so by promoting a leak of protons through the mitochondrial inner membrane, which uncouples ATP production from substrate oxidation, leading to fast oxygen consumption and ultimately to heat production. The thermogenic activity of UCP1 in brown adipose tissue plays an important role when the organism needs extra heat, e.g., during cold weather conditions (for small rodents), the cold stress of birth, or arousal from hibernation. UCP1 homologs have been found in lower vertebrates such as fish, where their role is unclear (Cannon & Nedergaard 2004, Jastroch et al. 2005).
The proton conductance of UCP1 in brown adipose tissue is tightly controlled. It is strongly inhibited by physiological concentrations of purine nucleotides. This inhibition is overcome by fatty acids released from intracellular triacylglycerol stores following adrenergic activation in response to cold or overfeeding. Other activators include superoxide, retinoic acid, the retinoid 4-[(E)-2-(5,6,7,8-tetrahydro-5,5,8,8-tetra-methyl-2-naphtalenyl)-1-propenyl]benzoic acid (TTNPB) and reactive alkenals, such as hydroxynonenal.
There is strong evidence that the regulated uncoupling caused by these proteins attenuates mitochondrial reactive oxygen species production, protects against cellular damage, and (in beta-cells) diminishes insulin secretion. There are also untested suggestions that their transport of fatty acids may be physiologically important (Brand & Esteves 2005, Esteves & Brand 2005, Krauss et al. 2005).
Several models have been proposed for the molecular mechanism by which fatty acids lead to increased proton conductance by UCP1 in brown adipose tissue mitochondria and presumably by the other UCPs. We have depicted the most likely model, the "fatty acid cycling" model, in this pathway .
Studies of mouse models and cultured human cells have suggested that oleoyl-phenylalanine, synthesized by extracellular PM20D1, may play a role in uncoupling independent of the action of UCPs (Long et al., 2016). Its synthesis and hydrolysis are annotated here.
R-HSA-1592230 Mitochondrial biogenesis Mitochondrial biogenesis and remodeling occur in response to exercise and redox state (reviewed in Scarpulla et al. 2012, Handy and Loscalzo 2012, Piantadosi and Suliman 2012, Scarpulla 2011, Wenz et al. 2011, Bo et al. 2010, Jornayvaz and Shulman 2010, Ljubicic et al. 2010, Hock and Kralli 2009, Canto and Auwerx 2009, Lin 2009, Scarpulla 2008, Ventura-Clapier et al. 2008). It is hypothesized that calcium influx and energy depletion are the signals that initiate changes in gene expression leading to new mitochondrial proteins. Energy depletion causes a reduction in ATP and an increase in AMP which activates AMPK. AMPK in turn phosphorylates the coactivator PGC-1alpha (PPARGC1A), one of the master regulators of mitochondrial biosynthesis. Likewise, p38 MAPK is activated by muscle contraction (possibly via calcium and CaMKII) and phosphorylates PGC-1alpha. CaMKIV responds to intracellular calcium by phosphorylating CREB, which activates expression of PGC-1alpha.
Deacetylation of PGC-1alpha by SIRT1 may also play a role in activation (Canto et al. 2009, Gurd et al. 2011), however Sirt11 deacetylation of Ppargc1a in mouse impacted genes related to glucose metabolism rather than mitochondrial biogenesis (Rodgers et al. 2005) and mice lacking SIRT1 in muscle had normal levels of mitochondrial biogenesis in response to exercise (Philp et al. 2011) so the role of deacetylation is not fully defined. PGC-1beta and PPRC appear to act similarly to PGC-1alpha but they have not been as well studied.
Phosphorylated PGC-1alpha does not bind DNA directly but instead interacts with other transcription factors, notably NRF1 and NRF2 (via HCF1). NRF1 and NRF2 together with PGC-1alpha activate the transcription of nuclear-encoded, mitochondrially targeted proteins such as TFB2M, TFB1M, and TFAM.
R-HSA-8949215 Mitochondrial calcium ion transport Divalent calcium ions (Ca2+) are transported from the cytosol into the mitochondrial matrix and back out of the matrix into the cytosol (reviewed in Santo-Domingo et al. 2010, De Stefani et al. 2016). In the matrix, Ca2+ binds and allosterically regulates pyruvate dehydrogenase, isocitrate dehydrogenase, 2-oxoglutarate dehydrogenase, and possibly other enzymes (Rizzuto et al. 2012). Matrix calcium is also observed to regulate release of caspase cofactors and calcium flux through channels on neighboring membranes, The pathway into the mitochondrion involves VDAC1, VDAC2, and VDAC3 in the outer membrane and the mitochondrial calcium uniporter (MCU) complex in the inner membrane. VDACs in the open conformation are anion channels. However in the closed conformation they transport Ca2+ from the cytosol to the intermembrane space. When calcium concentrations in the cytosol and intermembrane space are high, the MCU complex opens and transports Ca2+ from the intermembrane space to the mitochondrial matrix using the driving force of the membrane potential (reviewed in Drago et al. 2011, Marchi et al. 2014, De Stefani et al. 2015).
Efflux of Ca2+ from the matrix to the intermembrane space is catalyzed by the Na+/Ca2+ antiporter SLC8B1 (NCLX) located in the inner membrane. LETM1 is also observed to export calcium from the matrix to the intermembrane space by acting as an H+/Ca2+ antiporter, although somewhat contradictory results have been found in knockdowns of LETM1. Calcium in the intermembrane space may be transported to the cytosol by the Na+/Ca2+ antiporter SLC8A3 (NCX3), however the mitochondrial localization of SLC8A3 is controversial and SLC8A3 has a limited distribution among tissues.
R-HSA-1362409 Mitochondrial iron-sulfur cluster biogenesis Iron-sulfur (Fe-S) proteins are localized in the cytosol, nucleus, and mitochondria of mammalian cells (reviewed in Stemmler et al. 2010, Rouault 2012, Bandyopadhyay et al. 2008, Lill 2009, Lill et al. 2012). Fe-S protein biogenesis in the mitochondrial matrix involves the iron-sulfur cluster (ISC) assembly machinery. Ferrous iron is transported across the inner mitochondrial membrane into the mitochondrial matrix by Mitoferrin-1 (SLC25A37) and Mitoferrin-2 (SLC25A28). (Mitoferrin-1 is enriched in erythroid cells while Mitoferrin-2 is ubiquitous.) Frataxin binds ferrous iron in the mitochondrial matrix. The cysteine desulfurase NFS1 in a subcomplex with ISD11 provides the sulfur by converting cyteine into alanine and forming a persulfide which is used for cluster formation on ISCU, the scaffold protein. Interaction between NFS1 and ISD11 is necessary for desulfurase activity. Frataxin binds to a complex containing NFS1, ISD11, and ISCU and is proposed to function as an iron donor to ISCU or as an allosteric switch that activates sulfur transfer and Fe-S cluster assembly (Tsai and Barondeau 2010). Cluster formation also involves the electron transfer chain ferredoxin reductase and ferredoxin. ISCU initially forms clusters containing 2 iron atoms and 2 sulfur atoms ([2Fe-2S] clusters). They are released by the function of HSP70-HSC20 chaperones and the monothiol glutaredoxin GLRX5 and used for assembly of [2Fe-2S] proteins. Assembly of larger clusters such as [4Fe-4S] clusters may involve the function of ISCA1, ISCA2, and IBA57. The clusters are transferred to apo-enzymes such as the respiratory complexes, aconitase, and lipoate synthase through dedicated targeting factors such as IND1, NFU1, and BOLA3.
R-HSA-9837999 Mitochondrial protein degradation Mitochondrial proteases participate in proteostasis, the regulation of proteins to maintain a functional proteome, by degrading unfolded, unassembled, and oxidatively damaged proteins (reviewed in Ng et al. 2021, Song et al. 2021). Degradation of mitochondrial proteins by proteases also serves to regulate transcription by TFAM, oxidative phosphorylation by electron carriers, lipid translocation by PRELID1 and STARD7, and mitochondrial fission and fusion by OPA1 and OMA1 (reviewed in Ahola et al. 2019). Because of the bacterial origin of mitochondria, they contain a number of bacterial type proteases, including LONP1 in the matrix, CLPP:CLPX (CLPXP) in the matrix, HTRA2 (OMI) in the intermembrane space, AFG3L2 in the mitochondrial inner membrane and protruding into the matrix, and YME1L1 in the mitochondrial inner membrane and protruding into the intermembrane space (reviewed in Deshwal et al. 2020, Szczepanowska and Trifunovic 2022).
The hexameric LONP1 complex, which is homologous to Lon proteases of eubacteria such as E. coli, binds substrate proteins in the matrix and inner membrane, unfolds them in an ATP-dependent mechanism, and degrades them (reviewed in Gibellini et al. 2020). LONP1 also acts as an ATP-dependent chaperone that is independent of its protease function (reviewed in Gibellini et al. 2020).
Like LONP1, the CLPXP complex unfolds matrix proteins in an ATP-dependent reaction and degrades them, however, the ATPase/unfolding function and the protease function are performed by separate subunits, with CLPX hexamers unfolding substrate proteins and translocating them to CLPP tetradecamers for processive degradation (reviewed in Mabanglo et al. 2021, Mabanglo and Houry 2022).
AFG3L2 (m-AAA+) forms either homohexamers or heterohexamers with its paralog SPG7 (Paraplegin) that are anchored in the mitochondrial inner membrane and protrude into the matrix (reviewed in Patron et al. 2018, Steele and Glynn 2019, Zhang and Mao 2020). The substrate protein enters the central channel formed by the ATPase domains of AFG3L2 and is unfolded and translocated to the pore formed by the protease domains, where it is degraded (reviewed inZhang and Mao 2020).
Like AFG3L2, YME1L1 (YME1L, i-AAA+) is a homohexameric complex that is anchored in the mitochondrial inner membrane, however, YME1L1 protrudes into the intermembrane space where it unfolds substrate proteins of the intermembrane space and inner membrane in an ATP-dependent reaction and then degrades them (reviewed in Steele and Glynn 2019, Ohba et al. 2020, Zhang and Mao 2020).
HTRA2 (OMI) forms soluble trimeric complexes in the intermembrane space that degrade substrate proteins, notably amyloid precursor proteins that are translocated to the intermembrane space and inner membrane. HTRA2 released from mitochondria into the cytosol also participates in regulating apoptosis (reviewed in Vande Walle et al. 2008).
Mutations in mitochondrial proteases cause diseases, such as spastic paraplegia (SPG7), ataxia (AFG3L2), and Parkinson's Disease (HTRA2), that typically have neurological symptoms among others (reviewed in Su et al. 2019, Gomez-Fabra Gala and Vogtle 2021).
R-HSA-1268020 Mitochondrial protein import A human mitochondrion contains about 1500 proteins, more than 99% of which are encoded in the nucleus, synthesized in the cytosol and imported into the mitochondrion. Proteins are targeted to four locations (outer membrane, intermembrane space, inner membrane, and matrix) and must be sorted accordingly (reviewed in Kutik et al. 2007, Milenkovic et al. 2007, Bolender et al. 2008, Endo and Yamano 2009, Wiedemann and Pfanner 2017, Kang et al. 2018). Newly synthesized proteins are transported from the cytosol across the outer membrane by the TOMM40:TOMM70 complex. Proteins that contain presequences first interact with the TOMM20 subunit of the complex while proteins that contain internal targeting elements first interact with the TOMM70 subunit. After initial interaction the protein is conducted across the outer membrane by TOMM40 subunits. In yeast some proteins such as Aco1, Atp1, Cit1, Idh1, and Atp2 have both presequences that interact with TOM20 and mature regions that interact with TOM70 (Yamamoto et al. 2009).
After passage across the outer membrane, proteins may be targeted to the outer membrane via the SAMM50 complex, to the inner membrane via the TIMM22 or TIMM23 complexes (reviewed in van der Laan et al. 2010), to the matrix via the TIMM23 complex (reviewed in van der Laan et al. 2010), or proteins may fold and remain in the intermembrane space (reviewed in Stojanovski et al. 2008, Deponte and Hell 2009, Sideris and Tokatlidis 2010). Presequences on matrix and inner membrane proteins cause interaction with TIMM23 complexes; internal targeting sequences cause outer membrane proteins to interact with the SAMM50 complex and inner membrane proteins to interact with the TIMM22 complex. While in the intermembrane space hydrophobic proteins are chaperoned by the TIMM8:TIMM13 complex and/or the TIMM9:TIMM10:FXC1 complex.
R-HSA-9916720 Mitochondrial short-chain enoyl-CoA hydratase deficiency 1 ECHS1 (short-chain enoyl-CoA hydratase, also known as SCEH) is a mitochondrial enzyme that plays roles in fatty acid oxidation and valine metabolism (Yamada et al, 2015). In the branched-chain amino acid catabolism pathway, ECHS1 has specificity for the valine derivative methylacrylyl-CoA, but can also act on the leucine derivative 3-methylcrotonyl-CoA. ECHS1 binds to the isoleucine derivative tiglyl-CoA, but does not appreciably catalyze its hydration (Yamada et al, 2015; Ferdinandusse et al, 2015). Homozygous mutations in ECHS1 are associated with a severe Leigh-like disorder, characterized by cardiac aberrations, encephalopathy and epilepsy and severe developmental and neurological delays, likely arising at least in large measure from the accumulation of toxic levels of methylacrylyl-CoA (Peters et al, 2014; Haack et al, 2015; Yamada et al, 2015; Ferinandusse et al, 2015; Sakai et al, 2015; Tetreault et al, 2015; Kohda et al, 2016; Fitzsimmons et al, 2018).
R-HSA-379726 Mitochondrial tRNA aminoacylation Mitochondrial tRNA synthetases act in the mitochondrial matrix to catalyze the reactions of tRNAs encoded in the mitochondrial genome, their cognate amino acids, and ATP to form aminoacyl-tRNAs, AMP, and pyrophosphate (Schneider et al. 2000). The synthetase enzymes that catalyze these reactions are all encoded in the nuclear genome. In three cases, glycine, lysine, and glutamine, a single gene encodes two enzyme isoforms, one cytosolic and one mitochondrial. All other mitochondrial tRNA synthetases are encoded by genes different from the ones encoding the corresponding cytosolic enzymes.
R-HSA-163282 Mitochondrial transcription initiation Human mtDNA is transcribed by a dedicated mitochondrial RNA polymerase (POLRMT), which displays significant sequence similarity to the monomeric RNA polymerases found in bacteriophages. In contrast to the phage T7 RNA polymerase, POLRMT cannot interact with promoter DNA and initiate transcription on its own, but requires the presence of the mitochondrial transcription factor A (TFAM), and either transcription factor B1 (TFB1M) or B2 (TFB2M). The 4 proteins of the basal mitochondrial transcription machinery have been purified in recombinant form and used to reconstitute transcription in vitro with a promoter containing DNA fragment (Falkenberg et al., 2002). Although both TFB1M and TFB2M can support in vitro transcription with POLRMT, TFB2M is at least two orders of magnitude more active than TFB1M and the physiological role of TFB1M in mitochondrial transcription has not yet been completely defined. The TFB1M and TFB2M display primary sequence similarity to a family of rRNA methyltransferases, which dimethylates two adjacent adenosine bases near the 3' end of the small subunit rRNA during ribosome biogenesis (Falkenberg et al., 2002; McCulloch et al., 2002). Human TFB1M is, in fact, a dual function protein, which not only support mitochondrial transcription in vitro, but also acts as a rRNA methyltransferase (Seidel-Rogol et al., 2003). The methyltransferase activity is not required for transcription, since point mutations in conserved methyltransferase motifs of TFB1M revealed that it stimulates transcription in vitro independently of S-adenosylmethionine binding and rRNA methyltransferase activity.
R-HSA-163316 Mitochondrial transcription termination Transcription of the heavy (H)-strand of mitochondrial DNA (mtDNA) involves two overlapping transcription units (Montoyaet al.,1982; Montoya et al., 1983). The first unit starts right upstream of the tRNAPhe gene and spans the tRNAPhe, rRNA 12S, rRNA 16S and tRNAVal genes (initiation site IH1). The other starts about 100 bp further downstream (initiation site IH2), at the boundary between tRNAPhe and rRNA12S genes, and produces a single polycistronic RNA that encompasses almost the entire length of the H-strand. The ribosomal transcription unit is transcribed at a much higher rate compared to the other transcription unit and control of its expression is exerted both at the level of initiation and termination (Gelfand and Attardi, 1981; Attardi et al., 1990). A central role in the control of termination has been attributed to the mitochondrial transcription termination factor (mTERF), a 39-kDa protein that binds to a 28-base pair region of mtDNA located within the tRNALeu(UUR) gene, at a position immediately downstream of the rRNA 16S gene (Fernandez-Silva et al.,1997; Kruse et al., 1989).
R-HSA-5368287 Mitochondrial translation Of the roughly 1000 human mitochondrial proteins only 13 proteins, all of them hydrophobic inner membrane proteins that are components of the oxidative phosphorylation apparatus, are encoded in the mitochondrial genome and translated by mitoribosomes at the matrix face of the inner membrane (reviewed in Herrmann et al. 2012, Hallberg and Larsson 2014, Lightowlers et al. 2014). The remainder, including all proteins of the mitochondrial translation system, are encoded in the nucleus and imported from the cytosol into the mitochondrion. Translation in the mitochondrion reflects both the bacterial origin of the organelle and subsequent divergent evolution during symbiosis (reviewed in Huot et al. 2014, Richman et al. 2014). Human mitochondrial ribosomes have a low sedimentation coefficient of only 55S, but at 2.71 MDa they retain a similar mass to E. coli 70S particles. The 55S particles are protein-rich compared to both cytosolic ribosomes and eubacterial ribosomes. This is due to shorter mt-rRNAs, mitochondria-specific proteins, and numerous rearrangements in individual protein positions within the two ribosome subunits (inferred from bovine ribosomes in Sharma et al. 2003, Greber et al. 2014, Kaushal et al. 2014, reviewed in Agrawal and Sharma 2012).
Mitochondrial mRNAs have either no untranslated leader or short leaders of 1-3 nucleotides, with the exception of the 2 bicistronic transcripts, RNA7 and RNA14, which have overlapping orfs that encode ND4L/ND4 and ATP8/ATP6 respectively. Translation is believed to initiate with the mRNA binding the 28S subunit:MTIF3 (28S subunit:IF-3Mt, 28S subunit:IF2mt) complex together with MTIF2:GTP (IF-2Mt:GTP, IF2mt:GTP) at the matrix face of the inner membrane (reviewed in Christian and Spremulli 2012). MTIF3 can dissociate 55S particles in preparation for initiation, enhances formation of initiation complexes, and inhibits N-formylmethionine-tRNA (fMet-tRNA) binding to 28S subunits in the absence of mRNA. Binding of fMet-tRNA to the start codon of the mRNA results in a stable complex while absence of a start codon at the 5' end of the mRNA causes eventual dissociation of the mRNA from the 28S subunit. After recognition of a start codon, the 39S subunit then binds the stable complex, GTP is hydrolyzed, and the initiation factors MTIF3 and MTIF2:GDP dissociate.
Translation elongation then proceeds by cycles of aminoacyl-tRNAs binding, peptide bond formation, and displacement of deacylated tRNAs. In each cycle an aminoacyl-tRNA in a complex with TUFM:GTP (EF-Tu:GTP) binds at the A-site of the ribosome, GTP is hydrolyzed, and TUFM:GDP dissociates. The elongating polypeptide bonded to the tRNA at the P-site is transferred to the aminoacyl group at the A-site by peptide bond formation at the peptidyl transferase center, leaving a deacylated tRNA at the P-site and the elongating polypeptide attached to the tRNA at the A-site. The polypeptide is co-translationally inserted into the inner mitochondrial membrane via an interaction with OXA1L (Haque et al. 2010, reviewed in Ott and Hermann 2010). After peptide bond formation, GFM1:GTP (EF-Gmt:GTP) then binds the ribosome complex, GTP is hydrolyzed, GFM1:GDP dissociates, and the ribosome translocates 3 nucleotides in the 3' direction along the mRNA, relocating the polypeptide-tRNA to the P-site and allowing another cycle to begin. TUFM:GDP is regenerated to TUFM:GTP by the guanine nucleotide exchange factor TSFM (EF-Ts, EF-TsMt).
Translation is terminated when MTRF1L:GTP (MTRF1a:GTP) recognizes an UAA or UAG termination codon at the A-site of the ribosome (Tsuboi et al. 2009). GTP hydrolysis does not appear to be required. The tRNA-aminoacyl bond between the translated polypeptide and the final tRNA at the P-site is hydrolyzed by the 39S subunit, facilitating release of the polypeptide. MRRF (RRF) and GFM2:GTP (EF-G2mt:GTP) then act to release the remaining tRNA and mRNA from the ribosome and dissociate the 55S ribosome into 28S and 39S subunits.
Mutations have been identified in genes encoding mitochondrial ribosomal proteins and translation factors. These have been shown to be pathogenic, causing neurological and other diseases (reviewed in Koopman et al. 2013, Pearce et al. 2013).
R-HSA-5389840 Mitochondrial translation elongation Translation elongation proceeds by cycles of aminoacyl-tRNAs binding, peptide bond formation, and displacement of deacylated tRNAs (reviewed in Christian and Spremulli 2012). In each cycle an aminoacyl-tRNA in a complex with TUFM:GTP (EF-Tu:GTP) binds a cognate codon at the A-site of the ribosome, GTP is hydrolyzed, and TUFM:GDP dissociates. The elongating polypeptide bonded to the tRNA at the P-site is transferred to the aminoacyl group at the A-site by peptide bond formation, leaving a deacylated tRNA at the P-site and the elongating polypeptide attached to the tRNA at the A-site. GFM1:GTP (EF-Gmt:GTP) binds, GTP is hydrolyzed, GFM1:GDP dissociates, and the ribosome translocates 3 nucleotides in the 3' direction, relocating the peptidyl-tRNA to the P-site and allowing another cycle to begin. Mitochondrial ribosomes associate with the inner membrane and polypeptides are co-translationally inserted into the membrane (reviewed in Ott and Herrmann 2010, Agrawal and Sharma 2012). TUFM:GDP is regenerated to TUFM:GTP by the guanine nucleotide exchange factor TSFM (EF-Ts, EF-TsMt).
R-HSA-5368286 Mitochondrial translation initiation Translation initiates with the mitochondrial mRNA binding the 28S subunit:MTIF3 (28S subunit:IF-3Mt, 28S subunit:IF3mt) complex together with MTIF2:GTP (IF-2Mt:GTP, IF2mt:GTP) (reviewed in Christian and Spremulli 2012, Kuzmenko et al. 2014). As inferred from bovine homologs, the 28S subunit, 39S subunit, and 55S holoribosome associate with the matrix-side face of the inner membrane and the translation products are inserted into the inner membrane as translation occurs (Liu and Spremulli 2000). Mitochondrial mRNAs have either no untranslated leader or short leaders of 1-3 nucleotides, with the exception of the 2 bicistronic transcripts, RNA7 and RNA14, which have overlapping orfs that encode ND4L/ND4 and ATP8/ATP6 respectively.. Binding of N-formylmethionine-tRNA to the start codon results in a stable complex between the mRNA and the 28S subunit while absence of a start codon at the 5' end of the mRNA causes the mRNA to slide though the 28S subunit and eventually dissociate. The 39S subunit then binds the 28S subunit:mRNA complex, GTP is hydrolyzed, and the initiation factors MTIF3 and MTIF2:GDP dissociate.
R-HSA-5419276 Mitochondrial translation termination Translation is terminated when MTRF1L:GTP (MTRF1a:GTP) recognizes a UAA or UAG termination codon in the mRNA at the A site of the ribosome (Soleimanpour-Lichaei et al. 2007, reviewed in Richter et al. 2010, Chrzanowska-Lightowlers et al. 2011. Christian and Spremulli 2012). GTP is hydrolyzed, and the aminoacyl bond between the translated polypeptide and the final tRNA at the P site is hydrolyzed by the 39S ribosomal subunit, releasing the translated polypeptide. MRRF (RRF) and GFM2:GTP (EF-G2mt:GTP) then act to release the remaining tRNA and mRNA from the ribosome and dissociate the 55S ribosome into 28S and 39S subunits.
R-HSA-9841251 Mitochondrial unfolded protein response (UPRmt) Misfolded proteins in mitochondria activate the mitochondrial unfolded protein response (mtUPR), a program of gene expression that increases capacities for protein folding and protein degradation within the mitochondria (Zhao et al. 2002, Aldridge et al. 2007, reviewed in Cilleros-Holgado et al. 2023). Four interrelated pathways that regulate the mtUPR have been delineated: activation of Heat Shock Factor 1 (HSF1) by dissociation from HSPA1A,B (HSP70) (Sutandy et al. 2023), enhanced translocation of ATF5 to the nucleus (Fiorese et al. 2016), activation of the estrogen receptor alpha (ESR1) by phosphorylation, and activation of FOXO3 by deacetylation (reviewed in Kenny and Germain 2017, Munch 2018, Shpilka and Haynes 2018, Zhou et al. 2022).
The mtUPR appears to be initiated by the accumulation of reactive oxygen species (ROS) and mitochondrial precursor proteins in the cytosol (Sutandy et al. 2023). The ROS oxidize cysteine residues on DNAJA1, causing DNAJA1 to displace HSF1 from the chaperone HSPA1A,B (HSP70). HSF1 then transits to the nucleus, trimerizes, and activates expression of genes encoding chaperones (Sutandy et al. 2023).
The transcription factor ATF5, which is normally imported into mitochondria, instead accumulates in the cytosol and transits to the nucleus (Fiorese et al. 2016), where it acts with HSF1 to increase expression of chaperone genes (Fiorese et al. 2016, Sutandy et al. 2023). ATF5 may act downstream of HSF1, as ATF5 is not required to initiate the mtUPR (Sutandy et al. 2023).
ROS also activate the protein kinase AKT1 (PKB) (Papa and Germain 2011), which phosphorylates the estrogen receptor ESR1 (Campbell et al. 2001, Papa and Germain 2011). Phosphorylated ESR1 transits to the nucleus and, independently of estrogen, activates the expression of HTRA2 (OMI), NRF1, and other genes involved in mitochondrial homeostasis as part of the mitochondrial unfolded response (Papa and Germain 2011).
Through an uncharacterized mechanism, ROS cause increased expression of the deacetylase SIRT3, which directly or indirectly causes the deacetylation of the transcription factor FOXO3. Deacetylated FOXO3 in the nucleus increases expression of the antioxidant enzymes mitochondrial superoxide dismutase (SOD2, MnSOD) and peroxisomal catalase (CAT) in the mitochondrial unfolded response (Papa and Germain 2014).
Though ATF4 and CHOP are also key regulators of the mtUPR (Zhao et al. 2002, Quiros et al. 2017), the mechanisms that activate them in response to unfolded protein are not well characterized and may involve the phosphorylation of the EIF2S1 subunit of the translation factor eIF2alpha; however, none of the four known EIF2S1 kinases (GCN2, HRI, PERK, and PKR) are required for activation of CHOP (Munch and Harper 2016).
R-HSA-5205647 Mitophagy Mitophagy is a specific form of autophagy where mitochondria are specifically targeted for degradation by autophagolysosomes. In mammals there are a number of known mechanisms of mitophagy. One ensures maternal inheritance of mitochondrial DNA through the elimination of sperm derived mitochondria. A second is elimination of functional mitochondria during erythrocyte maturation and eye lens maturation. It is established that the outer mitochondrial membrane receptor Nix (or Bnip3l) and autophagosome associated protein LC3 are important for mitochondrial degradation in erythrocytes. A third mechanism is driven by the PINK1 and Parkin (PRKN) proteins. PRKN is recruited to the mitochondria when the mitochondrial membrane potential is reduced due to uncoupling, thereby initiating mitophagy.
R-HSA-68882 Mitotic Anaphase In anaphase, the paired chromosomes separate at the centromeres, and move to the opposite sides of the cell. The movement of the chromosomes is facilitated by a combination of kinetochore movement along the spindle microtubules and through the physical interaction of polar microtubules.
R-HSA-453279 Mitotic G1 phase and G1/S transition Mitotic G1-G1/S phase involves G1 phase of the mitotic interphase and G1/S transition, when a cell commits to DNA replication and divison genetic and cellular material to two daughter cells.
During early G1, cells can enter a quiescent G0 state. In quiescent cells, the evolutionarily conserved DREAM complex, consisting of the pocket protein family member p130 (RBL2), bound to E2F4 or E2F5, and the MuvB complex, represses transcription of cell cycle genes (reviewed by Sadasivam and DeCaprio 2013).
During early G1 phase in actively cycling cells, transcription of cell cycle genes is repressed by another pocket protein family member, p107 (RBL1), which forms a complex with E2F4 (Ferreira et al. 1998, Cobrinik 2005). RB1 tumor suppressor, the product of the retinoblastoma susceptibility gene, is the third member of the pocket protein family. RB1 binds to E2F transcription factors E2F1, E2F2 and E2F3 and inhibits their transcriptional activity, resulting in prevention of G1/S transition (Chellappan et al. 1991, Bagchi et al. 1991, Chittenden et al. 1991, Lees et al. 1993, Hiebert 1993, Wu et al. 2001). Once RB1 is phosphorylated on serine residue S795 by Cyclin D:CDK4/6 complexes, it can no longer associate with and inhibit E2F1-3. Thus, CDK4/6-mediated phosphorylation of RB1 leads to transcriptional activation of E2F1-3 target genes needed for the S phase of the cell cycle (Connell-Crowley et al. 1997). CDK2, in complex with cyclin E, contributes to RB1 inactivation and also activates proteins needed for the initiation of DNA replication (Zhang 2007). Expression of D type cyclins is regulated by extracellular mitogens (Cheng et al. 1998, Depoortere et al. 1998). Catalytic activities of CDK4/6 and CDK2 are controlled by CDK inhibitors of the INK4 family (Serrano et al. 1993, Hannon and Beach 1994, Guan et al. 1994, Guan et al. 1996, Parry et al. 1995) and the Cip/Kip family, respectively.
R-HSA-453274 Mitotic G2-G2/M phases Mitotic G2 (gap 2) phase is the second growth phase during eukaryotic mitotic cell cycle. G2 encompasses the interval between the completion of DNA synthesis and the beginning of mitosis. During G2, the cytoplasmic content of the cell increases. At G2/M transition, duplicated centrosomes mature and separate and CDK1:cyclin B complexes become active, setting the stage for spindle assembly and chromosome condensation that occur in the prophase of mitosis (O'Farrell 2001, Bruinsma et al. 2012, Jiang et al. 2014).
R-HSA-2555396 Mitotic Metaphase and Anaphase Metaphase is marked by the formation of the metaphase plate. The metaphase plate is formed when the spindle fibers align the chromosomes along the middle of the cell. Such an organization helps to ensure that later, when the chromosomes are separated, each new nucleus that is formed receives one copy of each chromosome. This pathway has not yet been annotated in Reactome.
The metaphase to anaphase transition during mitosis is triggered by the destruction of mitotic cyclins.
In anaphase, the paired chromosomes separate at the centromeres, and move to the opposite sides of the cell. The movement of the chromosomes is facilitated by a combination of kinetochore movement along the spindle microtubules and through the physical interaction of polar microtubules.
R-HSA-68881 Mitotic Metaphase/Anaphase Transition The metaphase to anaphase transition during mitosis is triggered by the destruction of mitotic cyclins.
R-HSA-68877 Mitotic Prometaphase The dissolution of the nuclear membrane marks the beginning of the prometaphase. Kinetochores are created when proteins attach to the centromeres. Microtubules then attach at the kinetochores, and the chromosomes begin to move to the metaphase plate.
R-HSA-68875 Mitotic Prophase During prophase, the chromatin in the nucleus condenses, and the nucleolus disappears. Centrioles begin moving to the opposite poles or sides of the cell. Some of the fibers that extend from the centromeres cross the cell to form the mitotic spindle.
R-HSA-69618 Mitotic Spindle Checkpoint The mitotic checkpoint or spindle assembly checkpoint is an evolutionarily conserved mechanism that ensures that cells with misaligned chromosomes do not exit mitosis and divide to form aneuploid cells. As chromosome attachment to the spindle microtubules is a stochastic process, not all chromosomes achieve alignment at the spindle equator at the same time. It is therefore essential that even a single unaligned chromosome can prevent the onset of anaphase. The ability of the checkpoint to monitor the status of chromosome alignment is achieved by assigning checkpoint proteins to the kinetochore, a macromolecular complex that resides at centromeres of chromosomes that establishes connections with spindle microtubules.
The checkpoint proteins monitor, in an unknown way, the mechanical activities between kinetochore-associated proteins and microtubules. Defects in mechanical activities at kinetochores activate the resident checkpoint proteins to initiate a signal that is amplified throughout the cell that ultimately prevents the activation of the proteolytic process that is required for sister chromatid separation and the onset of anaphase. Kinetochores of unaligned chromosomes differ from those of aligned chromosomes in two ways. Kinetochores of aligned chromosomes are saturated with between 20 to 30 microtubules. In addition, poleward directed forces exerted at each sister kinetochore generates tension between them. Unaligned kinetochores on the other hand, are not saturated with microtubules and are not under tension. The mitotic checkpoint detects the presence of unattached kinetochores rather than monitoring for the presence of attached kinetochores. Consequently, unattached kinetochores emit an inhibitory signal that inhibits the biochemical events that are required to initiate the onset of anaphase. The mechanism by which this inhibitory signal is generated at unattached kinetochores has not precisely been determined but the signal is generated as a result of the lack of microtubule occupancy and kinetochore tension. A single unattached kinetochore is capable of preventing cells from exiting mitosis. The mitotic checkpoint provides a way for a localized defect to affect the global biochemical status of the cell. In principle, the signal that is generated at an unattached kinetochore diffuses throughout the cell to affect its target. There are currently two models for how this is achieved. One model is based on the observation that the Mad2 checkpoint protein binds and is rapidly released from unattached kinetochores. The kinetochore is believed to act as a catalyst that converts Mad2 into an inhibitory state that diffuses throughout the cell upon its release from the kinetochore. A second model proposes that the signal is amplified by a kinase cascade much like a conventional signal transduction pathway. This kinase cascade is believed to be comprised of the checkpoint kinases, hBUBR1, hBUB1, hMPS1.
R-HSA-68884 Mitotic Telophase/Cytokinesis In this final phase of mitosis, new membranes are formed around two sets of chromatids and two daughter cells are formed. The chromosomes and the spindle fibers disperse, and the fiber ring around the center of the cell, composed of actin, contracts, pinching the cell into two daughter cells.
R-HSA-9637628 Modulation by Mtb of host immune system Mtb enhances its chances for being taken up by a phagocyte by blocking adaptive immune responses, as well as other innate immune system responses. Components of the bacterial cell wall also specifically promote phagocytosis via both the opsonic pathway and the presentation of adhesins (Esparza et al. 2015).
R-HSA-2129379 Molecules associated with elastic fibres Proteins found associated with microfibrils include vitronectin (Dahlback et al. 1990), latent transforming growth factor beta-binding proteins (Kielty et al. 2002, Munger & Sheppard 2011), emilin (Bressan et al. 1993, Mongiat et al. 2000), members of the microfibrillar-associated proteins (MFAPs, Gibson et al.1996), and fibulins (Roark et al. 1995, Yanagisawa et al. 2002). The significance of these interactions is not well understood but may help mediate elastin-fibrillin interactions during elastic fibre assembly.
Proteoglycans such as versican (Isogai et al. 2002), biglycan, and decorin (Reinboth et al. 2002) can interact with the microfibrils. They confer specific properties including hydration, impact absorption, molecular sieving, regulation of cellular activities, mediation of growth factor association, and release and transport within the extracellular matrix (Buczek-Thomas et al. 2002). In addition, glycosaminoglycans have been shown to interact with tropoelastin through its lysine side chains (Wu et al. 1999) regulating tropoelastin assembly (Tu and Weiss, 2008).
R-HSA-947581 Molybdenum cofactor biosynthesis Molybdenum cofactor (MoCo) is needed by three enzymes in humans: sulfite oxidase, xanthine oxidase and aldehyde oxidase. The pathway of its synthesis is so conserved that plants and bacteria can readily use human enzymes. Bacteria, however, diverge after the first three steps from this path and their final MoCo differs from that of the eukaryotes. Plants and animals have also developed a refinement of their MoCo which is needed for the function of their xanthine and aldehyde oxidases. This means, in humans we find sulfurated instead of desulfurated molybdenum cofactor on these two enzymes (Schwarz 2005; Schwarz, Mendel, Ribbe 2009).
R-HSA-1222449 Mtb iron assimilation by chelation Uptake of iron in Mtb, especially when the bacterium is in the host, strongly depends on siderophores. Humans, through secretion of lactoferrin, maintain an iron concentration of 10^(-18) M within macrophages, and the bacterium has evolved the siderophores mycobactin T and exomycobactin T (formerly exochelin) to cope with this shortage. While nonpolar mycobactin T stays in the cell wall and only moves around in liquid droplets, polar exochelin is abundantly secreted. As it can bind iron with higher affinity than lactoferrin, it frequently scavenges iron ions from this molecule (Miethke & Marahiel 2007).
R-HSA-2206281 Mucopolysaccharidoses The mucopolysaccharidoses (MPS) are a group of rare, inherited lysosomal storage disorders caused by deficiencies of enzymes catalyzing the stepwise degradation of glycosaminoglycans (GAGs, originally called mucopolysaccharides) (Neufeld & Muenzer in Scriver et al. 2001). Catabolism of the GAGs dermatan sulfate, heparan sulfate, heparin, keratan sulfate, chondroitin sulfate or hyaluronan may be blocked at one or more steps, resulting in lysosomal accumulation of GAG fragments of varying size. Over time these collect in the cells, blood and connective tissues ultimately resulting in progressive irreversible cellular damage which affects appearance, physical abilities, organ and system function, vision, and usually mental development (Lehman et al. 2011, Ashworth et al. 2006). Life expectancy is also reduced. There are 11 known enzyme deficiencies that give rise to 7 distinct MPS. These disorders are biochemically characterized by elevated levels of partially or undegraded GAGs in lysosomes, blood, urine and cerebro-spinal fluid (Muenzer 2011, Coutinho et al. 2012). The MPS are part of the lysosomal storage disease family, a group of about 50 genetic disorders caused by deficient lysosomal proteins (Ballabio & Gieselmann 2009).
R-HSA-427601 Multifunctional anion exchangers The human SLC26 gene family consists of eleven members which encode multifunctional anion exchangers.These exchangers are capable of transporting a variety of anions such as sulphate, bicarbonate, oxalate, hydroxyl, formate, iodide and chloride. SLC26 members can be grouped according to functional similiarities and three groups can be classified this way. Group 1 are selective sulphate transporters and include SLC26A1 and 2. Group 2 are Cl-/HCO3- exchangers and include SLC26A3, 4 and 6. Group 3 function as ion channels and include SLC26A7 and 9.
R-HSA-390648 Muscarinic acetylcholine receptors Muscarinic acetylcholine (mAChRs) receptors were so named because they are more sensitive to muscarine than to nicotine (Ishii M and Kurachi Y, 2006). Their counterparts are nicotinic acetylcholine receptors (nAChRs), ion channels receptors that are also important in the autonomic nervous system. Many drugs can manipulate these two distinct receptors by acting as selective agonists or antagonists. mAChRs bind to the bioamine acetylcholine, have a widespread tissue distribution and are involved in the control of numerous central and peripheral physiological responses, particularly voluntary muscle contraction. They are also major targets for drugs in human diseases such as Alzheimer's, Parkinson's and schizophrenia. This family of G-protein coupled receptors consists of five members designated M1-M5 and are sub-divided into two groups based on their primary coupling to G proteins. M2 and M4 receptors couple to Gi/o proteins and M1, M3 and M5 receptors couple to Gq/11 proteins (Caulfield MP and Birdsall NJ, 1998).
R-HSA-397014 Muscle contraction In this module, the processes by which calcium binding triggers actin - myosin interactions and force generation in smooth and striated muscle tissues are annotated.
R-HSA-975871 MyD88 cascade initiated on plasma membrane Mammalian myeloid differentiation factor 88 (MyD88) is Toll/interleukin (IL)-1 (TIR)-domain containing adapter protein which plays crucial role in TLR signaling. All TLRs, with only one exception of TLR3, can initiate downstream signaling trough MyD88. In the MyD88 - dependent pathway, once the adaptor is bound to TLR it leads to recruitment of IL1 receptor associated kinase family IRAK which is followed by activation of tumour necrosis factor receptor-associated factor 6 (TRAF6) . TRAF6 is an ubiquitin E3 ligase which in turn induces TGF-beta activating kinase 1 (TAK1) auto phosphorylation. Once activated TAK1 can ultimately mediate the induction of the transcription factor NF-kB or the mitogen-activated protein kinases (MAPK), such as JNK, p38 and ERK. This results in the translocation of the activated NF-kB and MAPKs to the nucleus and the initiation of appropriate gene transcription leading to the production of many proinflammatory cytokines and antimicrobial peptides.
R-HSA-5602498 MyD88 deficiency (TLR2/4) Myeloid differentiation primary response (MyD88) is an adaptor protein that mediates intracellular signaling pathways evoked by all Toll-like receptors (TLRs) except for TLR3 and by several interleukin-1 receptors (IL-1Rs) (Medzhitov R et al. 1998). Upon ligand binding, TLRs hetero- or homodimerize and recruit MyD88 through their respective TIR domains. Then, MyD88 oligomerizes via its death domain (DD) and TIR domain and interacts with the interleukin-1 receptor-associated kinases (IRAKs) to form the Myddosome complex (MyD88:IRAK4:IRAK1/2) (Motshwene PG et al. 2009; Lin SC et al. 2010). The Myddosome complex transmits the signal leading to activation of transcription factors such as nuclear factor-kappaB (NFkB) and activator protein 1 (AP1).
Studies have identified patients with autosomal recessive (AR) form of MyD88 deficiency caused by homozygous or compound heterozygous mutations in MYD88 gene leading to abolished protein production (von Bernuth et al. 2008). AR MyD88 deficiency is a type of a primary immunodeficiency characterized by greater susceptibility to pyogenic bacteria (such as Streptococcus pneumoniae, Staphylococcus aureus or Pseudomonas aeruginosa) manifested in infancy and early childhood. Patients with MyD88 deficiency show delayed or weak signs of inflammation (Picard C et al. 2010; Picard C et al. 2011).
Functional assessment of MyD88 deficiency revealed that cytokine responses were impaired in patient-derived blood cells upon stimulation with the agonists of TLR2 and TLR4 (PAM2CSK4 and LPS respectively), although some were produced in response to LPS. (von Bernuth et al. 2008). NFkB luciferase reporter gene assays using human embryonic kidney 293 (HEK293T) cells showed that MyD88 variants, S34Y, E52del, E53X, L93P, R98C, and R196C, were compromised in their ability to enhance NFkB activation (Yamamoto T et al. 2014). The molecular basis for the observed functional effects (reported for selected mutations) probably faulty Myddosome formation due to impaired MyD88 oligomerization and/or interaction with IRAK4 (George J et al. 2011; Nagpal K et al. 2011; Yamamoto T et al. 2014).
While MyD88-deficiency might be expected to perturb MyD88?IRAK4 dependent TLR7 and TLR8 signaling events associated with the sensing viral infections, patients with MyD88 and IRAK4 deficiencies have so far not been reported to be susceptible to viral infection. R-HSA-5602680 MyD88 deficiency (TLR5) Myeloid differentiation primary response (MyD88) is an adaptor protein that mediates intracellular signaling pathways evoked by all Toll-like receptors (TLRs) (except for TLR3) and several interleukin-1 receptors (IL-1Rs) (Medzhitov R et al. 1998). Upon ligand binding, TLRs hetero- or homodimerize and recruit MyD88 through their respective TIR domains. Then, MyD88 oligomerizes via its death domain (DD) and TIR domain and interacts with the interleukin-1 receptor-associated kinases (IRAKs) to form the Myddosome complex (MyD88:IRAK4:IRAK1/2) (Motshwene PG et al. 2009; Lin SC et al. 2010). The Myddosome complex transmits the signal leading to activation of transcription factors such as nuclear factor-kappaB (NFkB) and activator protein 1 (AP1).
Studies have identified patients with autosomal recessive (AR) form of MyD88 deficiency caused by homozygous or compound heterozygous mutations in MYD88 gene leading to abolished protein production (von Bernuth et al. 2008). AR MyD88 deficiency is a type of a primary immunodeficiency characterized by greater susceptibility to pyogenic bacteria such as invasive pneumococcal disease manifested in infancy and early childhood. Patients with MyD88-deficiency show delayed or weak signs of inflammatory responses (Picard C et al. 2010; Picard C et al. 2011).
Functional assessment of MyD88 deficiency revealed that cytokine responses were abolished in patient-derived blood cells upon stimulation with bacterial flagellin, which is recognized by TLR5 (von Bernuth et al. 2008). An NFkB luciferase reporter gene assay using human embryonic kidney 293 (HEK293T) cells showed that MyD88 variants, S34Y, E52del, E53X, L93P, R98C, and R196C, were compromised in the ability to enhance NFkB activation (Yamamoto T et al. 2014). The molecular basis for the observed functional effects (reported for selected mutations) probably faulty Myddosome formation due to impaired MyD88 oligomerization and/or interaction with IRAK4 (George J et al. 2011; Nagpal K et al. 2011; Yamamoto T et al. 2014).
While MyD88 deficiency might be expected to perturb MyD88?IRAK4 dependent TLR7 and TLR8 signaling events associated with the sensing viral infections in the endosome, patients with MyD88 and IRAK4 deficiencies have so far not been reported to be susceptible to viral infection. R-HSA-975155 MyD88 dependent cascade initiated on endosome Upon binding of their ligands, TLR7/8 and TLR9 recruit a cytoplasmic adaptor MyD88 and IRAKs, downstream of which the signaling pathways are divided to induce either inflammatory cytokines or type I IFNs. R-HSA-166166 MyD88-independent TLR4 cascade The MyD88-independent signaling pathway is shared by TLR3 and TLR4 cascades. TIR-domain-containing adapter-inducing interferon-beta (TRIF or TICAM1) is a key adapter molecule in transducing signals from TLR3 and TLR4 in a MyD88-independent manner (Yamamoto M et al. 2003a). TRIF is recruited to the ligand-stimulated TLR3 or 4 complex via its TIR domain. TLR3 directly binds TRIF (Oshiumi H et al 2003). In contrast, the TLR4-mediated signaling pathway requires two adapter molecules, TRAM (TRIF-related adapter molecule or TICAM2) and TRIF. TRAM(TICAM2) is thought to bridge the activated TLR4 complex and TRIF (Yamamoto M et al. 2003b, Tanimura N et al. 2008, Kagan LC et al. 2008).
TRIF recruitment to the TLR complex stimulates distinct pathways leading to the production of type I interferons (IFNs) and pro-inflammatory cytokines and to the induction of programmed cell death. R-HSA-166058 MyD88:MAL(TIRAP) cascade initiated on plasma membrane The first known downstream component of TLR4 and TLR2 signaling is the adaptor MyD88. Another adapter MyD88-adaptor-like (Mal; also known as TIR-domain-containing adaptor protein or TIRAP) has also been described for TLR4 and TLR2 signaling. MyD88 comprises an N-terminal Death Domain (DD) and a C-terminal TIR, whereas Mal lacks the DD. The TIR homotypic interactions bring adapters into contact with the activated TLRs, whereas the DD modules recruit serine/threonine kinases such as interleukin-1-receptor-associated kinase (IRAK). Recruitment of these protein kinases is accompanied by phosphorylation, which in turn results in the interaction of IRAKs with TNF-receptor-associated factor 6 (TRAF6). The oligomerization of TRAF6 activates TAK1, a member of the MAP3-kinase family, and this leads to the activation of the IkB kinases. These kinases, in turn, phosphorylate IkB, leading to its proteolytic degradation and the translocation of NF-kB to the nucleus. Concomitantly, members of the activator protein-1 (AP-1) transcription factor family, Jun and Fos, are activated, and both AP-1 transcription factors and NF-kB are required for cytokine production, which in turn produces downstream inflammatory effects. R-HSA-3785653 Myoclonic epilepsy of Lafora Lafora disease is a progressive neurodegenerative disorder with onset typically late in childhood, characterized by seizures and progressive neurological deterioration and death within ten years of onset. Recessive mutations in EPM2A (laforin) and NHLRC1 (malin) have been identified as causes of the disease. The disease is classified here as one of glycogen storage as EPM2A (laforin) and NHLRC1 (malin) regulate normal glycogen turnover and defects in either protein are associated with the formation of Lafora bodies, accumulations of abnormal, insoluble glycogen molecules in tissues including brain, muscle, liver, and heart (Ramachandran et al. 2009; Roach et al. 2012). Consistent with a central role for glycogen accumulation in the disease, reduced (Turnbull et al. 2011) or absent (Pederson et al. 2013) glycogen synthase activity prevents Lafora Disease in mouse models.
Type 2A disease. EPM2A (laforin) associated with cytosolic glycogen granules, normally catalyzes the removal of the phosphate groups added rarely but consistently to growing glycogen molecules (Tagliabracci et al. 2011). Defects in this catalytic activity lead to the formation of phosphorylated glycogen molecules that are insoluble and that show abnormal branching patterns (Minassian et al. 1998, Serratosa et al. 1999, Tagliabracci et al. 2011).
Type 2B disease. NHLRC1 (malin) normally mediates polyubiquitination of EPM2A (laforin) and PPP1R3C (PTG). The two polyubiquitinated proteins are targeted for proteasome-mediated degradation, leaving a glycogen-glycogenin particle associated with glycogen synthase. In the absence of NHLRC1 activity, EPM2A and PPP1R3C proteins appear to persist, associated with the formation of abnormal, stable glycogen granules (Lafora bodies) (Chan et al. 2003; Gentry et al. 2005). In NHLRC1 knockout mice PPP1R3C levels are unchanged rather than increased, suggesting that NHLRC1 does not target PPP1R3C for degradation. However, EPM2A protein levels are increased in this knockout consistent with NHLRC1's proposed role (DePaoli-Roach et al. 2010). R-HSA-525793 Myogenesis Myogenesis, the formation of muscle tissue, is a complex process involving steps of cell proliferation mediated by growth factor signaling, cell differentiation, reorganization of cells to form myotubes, and cell fusion. Here, one regulatory feature of this process has been annotated, the signaling cascade initiated by CDO (cell-adhesion-molecule-related/downregulated by oncogenes) and associated co-receptors.
CDO/Cdon is a type I transmembrane multifunctional co-receptor consisting of five immunoglobulin and three fibronectin type III (FNIII) repeats in the extracellular domain, and an intracellular domain with no identifiable motifs. It has been implicated in enhancing muscle differentiation in promyogenic cells. CDO exert its promyogenic effects as a component of multiprotein complexes that include the closely related factor Boc, the Ig superfamily receptor neogenin and its ligand netrin-3, and the adhesion molecules N- and M-cadherin. CDO modulates the Cdc42 and p38 mitogen-activated protein kinase (MAPK) pathways via a direct association with two scaffold-type proteins, JLP and Bnip-2, to regulate activities of myogenic bHLH factors and myogenic differentiation. CDO activates myogenic bHLH factors via enhanced heterodimer formation, most likely by inducing hyper-phosphorylation of E proteins.
Myogenic basic helix-loop-helix (bHLH) proteins are master regulatory proteins that activate the transcription of many muscle-specific genes during myogenesis. These myogenic bHLH proteins also referred to as MyoD family includes four members, MyoD, myogenin, myf5 and MRF4. These myogenic factors dimerize with E-proteins such as E12/E47, ITF-2 and HEB to form heterodimeric complexes that bind to a conserved DNA sequence known as the E box, which is present in the promoters and enhancers of most muscle-specific genes. Myocyte enhancer binding factor 2 (MEF2), which is a member of the MADS box family, also plays an important role in muscle differentiation. MEF2 activates transcription by binding to the consensus sequence, called the MEF2-binding site, which is also found in the control regions of numerous muscle-specific genes. MEF2 and myogenic bHLH proteins synergistically activate expression of muscle-specific genes via protein-protein interactions between DNA-binding domains of these heterologous classes of transcription factors. Members of the MyoD and MEF2 family of transcription factors associate combinatorially to control myoblast specification, differentiation and proliferation.
R-HSA-975577 N-Glycan antennae elongation N-glycans are further modified after the commitment to Complex or Hybrid N-glycans. The exact structure of the network of metabolic reactions involved is complex and not yet validated experimentally. Here we will show a generic reaction for each of the genes known to be involved in N-Glycosylation.
For a better annotation of the reactions and genes involved in the synthesis of Complex and Hybrid N-glycans we recommend the GlycoGene Database (Ito H. et al, 2010) (http://riodb.ibase.aist.go.jp/rcmg/ggdb/textsearch.jsp) for annotations of genes, and the Consortium for Functional Genomics (http://riodb.ibase.aist.go.jp/rcmg/ggdb/textsearch.jsp) for annotation of Glycan structures and reactions. Moreover, a computationally inferred prediction for the structure of this network is available through the software GlycoVis (Hossler P. et. al. 2006).
R-HSA-975576 N-glycan antennae elongation in the medial/trans-Golgi In the latter compartments of the distal Golgi the N-Glycan is further modified, leading to the wide range of N-Glycans observed in multicellular organisms. The first step of N-Glycan elongation in the Golgi is the addition of a GlcNAc residue on the alpha 1,3 branch by the enzyme MGAT1 (GlcNAc-TI), which commits the elongation pathway to Complex or Hybrid N-Glycans from Oligomannose N-Glycans. At this point, the pathway bifurcates again to generate Complex or Hybrid N-Glycans. The addition of a GlcNAc in the middle of the two arms of the N-Glycan, catalyzed by MGAT3 (GNT-III), inhibits the removal of the mannoses on the alpha1,3 branches by MAN2 and the addition of a GlcNAc by MGAT2 (GlcNAc-TII), and commits the pathway toward the synthesis of hybrid N-Glycans. Alternatively, the removal of these mannoses and the action of MGAT2 leads to the synthesis of complex N-Glycans (Kornfeld and Kornfeld 1985).
The exact structure of the network of reactions leading to Complex or Hybrid N-Glycans is still not completely described and validated experimentally. Here we will annotate only one generic reaction for each of the enzymes known to participate in this process. For a better annotation on the reactions and genes involved in the synthesis of Complex and Hybrid N-Glycans we recommend the GlycoGene Database (Ito H. et al, 2010) (http://riodb.ibase.aist.go.jp/rcmg/ggdb/textsearch.jsp) for annotations on genes, and the Consortium for Functional Genomics (http://riodb.ibase.aist.go.jp/rcmg/ggdb/textsearch.jsp) for annotation of Glycan structures and reactions. Moreover, a computationally inferred prediction on the structure of this network is available through the software GlycoVis (Hossler P. et. al. 2006).
R-HSA-964739 N-glycan trimming and elongation in the cis-Golgi After the transport of the glycoprotein to the cis-Golgi, the pathway of N-glycosylation bifurcates. Some N-glycans can be moved to subsequent steps of the secretory pathway without further modifications, or alternatively, with the removal of a few mannoses (Oligo Mannoses pathway). In yeast and other unicellular species, a series of mannose residues are added (High Mannoses pathway). The presence of this modification is a major obstacle to the production of pharmaceutical drugs in yeast, where the HighMannose pathway must be inhibited or modified in order to avoid the presence of high mannose xenoglycans.
The first N-glycan modification step is the trimming of up to four mannoses by one of three mannosidase enzymes. Moreover, Glycoproteins that have not entered in the Calnexin/Calreticulin cycle or that have not had their glucose residues trimmed earlier in the ER, can enter the main pathway here due to the existence to an alternative route catalyzed by the enzyme Endomannosidase I (Schachter, 2000; Stanley et al, 2009)
R-HSA-532668 N-glycan trimming in the ER and Calnexin/Calreticulin cycle After being synthesized in the ER membrane the 14-sugars lipid-linked oligosaccharide is co-translationally transferred to an unfolded protein, as described in the previous steps. After this point the N-glycan is progressively trimmed of the three glucoses and some of the mannoses before the protein is transported to the cis-Golgi. The role of these trimming reactions is that the N-glycan attached to an unfolded glycoprotein in the ER assume the role of 'tags' that direct the interactions of the glycoprotein with different elements that mediate its folding. The removal of the two outer glucoses leads to an N-glycan with only one glucose, which is a signal for the binding of either one of two chaperone proteins, calnexin (CNX) and calreticulin (CRT). These chaperones provide an environment where the protein can fold more easily. The interaction with these proteins is not transient and is terminated by the trimming of the last remaining glucose, after which the glycoprotein is released from CNX or CRT and directed to the ER Quality Control compartment (ERQC) if it still has folding defects, or transported to the Golgi if the folding is correct. The involvement of N-glycans in the folding quality control of proteins in the ER explains why this form of glycosylation is so important, and why defects in the enzymes involved in these reactions are frequently associated with congenital diseases. However, there are many unknown points in this process, as it is known that even proteins without N-glycosylation sites can be folded properly (Caramelo JJ and Parodi AJ, 2008).
R-HSA-205025 NADE modulates death signalling NADE protein (p75NTR-associated cell death executor) may induce cell death upon NGF binding, but not BDNF, NT3, or NT4/5 binding, to p75NTR. The NADE-dependent apoptosis is modulated by the 14-3-3-epsilon protein (Kimura MT et al, 2001).
R-HSA-389542 NADPH regeneration The conversion of isocitrate to 2-oxoglutarate (alpha-ketoglutarate) with the concomitant synthesis of NADPH from NADP+ is thought to play a significant role in supplying NADPH for other reactions in both the cytosol and the peroxisome (Geisbrecht and Gould 1999). The activity of H6PD (Hexose-6-phosphate dehydrogenase) is thought to play a role in maintaining NADP+ : NADPH balance within the endoplasmic reticulum (Zielinska et al. 2011).
R-HSA-375165 NCAM signaling for neurite out-growth The neural cell adhesion molecule, NCAM, is a member of the immunoglobulin (Ig) superfamily and is involved in a variety of cellular processes of importance for the formation and maintenance of the nervous system. The role of NCAM in neural differentiation and synaptic plasticity is presumed to depend on the modulation of intracellular signal transduction cascades. NCAM based signaling complexes can initiate downstream intracellular signals by at least two mechanisms: (1) activation of FGFR and (2) formation of intracellular signaling complexes by direct interaction with cytoplasmic interaction partners such as Fyn and FAK. Tyrosine kinases Fyn and FAK interact with NCAM and undergo phosphorylation and this transiently activates the MAPK, ERK 1 and 2, cAMP response element binding protein (CREB) and transcription factors ELK and NFkB. CREB activates transcription of genes which are important for axonal growth, survival, and synaptic plasticity in neurons.
NCAM1 mediated intracellular signal transduction is represented in the figure below. The Ig domains in NCAM1 are represented in orange ovals and Fn domains in green squares. The tyrosine residues susceptible to phosphorylation are represented in red circles and their positions are numbered. Phosphorylation is represented by red arrows and dephosphorylation by yellow. Ig, Immunoglobulin domain; Fn, Fibronectin domain; Fyn, Proto-oncogene tyrosine-protein kinase Fyn; FAK, focal adhesion kinase; RPTPalpha, Receptor-type tyrosine-protein phosphatase; Grb2, Growth factor receptor-bound protein 2; SOS, Son of sevenless homolog; Raf, RAF proto-oncogene serine/threonine-protein kinase; MEK, MAPK and ERK kinase; ERK, Extracellular signal-regulated kinase; MSK1, Mitogen and stress activated protein kinase 1; CREB, Cyclic AMP-responsive element-binding protein; CRE, cAMP response elements.
R-HSA-419037 NCAM1 interactions The neural cell adhesion molecule, NCAM1 is generally considered as a cell adhesion mediator, but it is also considered to be a signal transducing receptor molecule. NCAM1 is involved in multiple cis- and trans-homophilic interactions. It is also involved in several heterophilic interactions with a broad range of other molecules, thereby modulating diverse biological phenomena including cellular adhesion, migration, proliferation, differentiation, survival and synaptic plasticity.
R-HSA-9636003 NEIL3-mediated resolution of ICLs DNA glycosylase activity of NEIL3 is involved in resolution (unhooking) of psolaren-induced interstrand crosslinks (ICLs), as well as abasic site-induced ICLs (AP-ICLs) in a Fanconia anemia (FA) pathway-independent fashion (Semlow et al. 2016, Martin et al. 2017).
R-HSA-168333 NEP/NS2 Interacts with the Cellular Export Machinery The viral RNP complex is exported from the nucleus via the host cell CRM1 export pathway (Fukuda, 1997; Neumann, 2000; reviewed in Buolo, 2006). The vRNP complex does not interact directly with CRM1 to form an export complex. Rather, an additional viral protein, nuclear export protein (NEP/NS2), acts as an adaptor, binding the viral matrix M1 protein and CRM1, thus linking the viral RNP with CRM1 (Martin, 1991; O'Neill, 1998; Neumann, 2000; Akarsu, 2003). The CRM1/exportin-1 complex recruits additional host cell proteins, and traverses the nuclear pore into the cytosol.
R-HSA-933543 NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 Fas-AssociatedDeathDomain (FADD) and receptor interacting protein 1 (RIP1) are death domain containing molecules that interact with the C-terminal portion of IPS-1 and induce NF-kB through interaction and activation of initiator caspases (caspase-8 and -10). Caspases are usually involved in apoptosis and inflammation but they also exhibit nonapoptotic functions. These nonapoptotic caspase functions involve prodomain-mediated activation of NF-kB. Processed caspases (caspase-8/10) encoding the DED (death effector domain) strongly activate NF-kB. The exact mechanism by which caspases mediate NF-kB activation is unclear, but the prodomains of caspase-8/10 may act as a scaffolding and allow the recruitment of the IKK complex in association with other signaling molecules.
R-HSA-209560 NF-kB is activated and signals survival Upon activation in response to NGF, NF-kB moves to the nucleus, where it turns on genes that promote survival, and triggers the expression of HES1/5 to modulate dendritic growth.
R-HSA-9818028 NFE2L2 regulates pentose phosphate pathway genes Sub-pathway for representing the pentose phosphate pathway gene regulated by NFE2L2 (NRF2). NFE2L2 directs the transcription of genes related to the Pentose Phosphate pathway which helps in programming the metabolic pathway to cope with oxidative stress and also has a significant role in cancer progression (Chartoumpekis et al, 2015; DeBlasi et al, 2020)
R-HSA-9818035 NFE2L2 regulating ER-stress associated genes Subpathway representing ER-stress-associated genes regulated by NFE2L2 (NRF2). Activating transcription factor 4 (ATF4) is a stress-induced transcription factor that is frequently upregulated in cancer cells. ATF4 controls the expression of a wide range of adaptive genes that allow cells to endure periods of stress, such as hypoxia or amino acid limitation. However, under persistent stress conditions, ATF4 promotes the induction of apoptosis (Wortel et al, 2017). ATF4 is also known to regulate serine and glycine biosynthesis in NSCLC (Denicola et al, 2016)
R-HSA-9818032 NFE2L2 regulating MDR associated enzymes Subpathway representing multi-drug resistance (MDR) gene regulated by NFE2L2 (NRF2). These MDR-related genes are known to play a role in Drug resistance. For example, ABCF2 have a role in Cisplatin resistance in ovarian cancer (Bao et al, 2017). Similarly ABCC1 (MRP1), ABCC3 and ABCG2 also have a role in multiple drug resistance (Cole et al,2014; Zeng et al,1999; Mo et al, 2012).
R-HSA-9818025 NFE2L2 regulating TCA cycle genes Sub-pathway representing TCA cycle genes regulated by NFE2L2. NFE2L2 has a role in directing cellular metabolic processes in normal and cancer cells. By regulating the TCA-specific genes, it controls the progression of the TCA cycle in stress and disease conditions (DeBlasi et al, 2020; Okazaki et al, 2020)
R-HSA-9818027 NFE2L2 regulating anti-oxidant/detoxification enzymes Subpathway representing cytoprotective genes regulated by NFE2L2 (NRF2). NFE2L2 is well-studied for its role in oxidative stress where it gets activated by ROS and then induces a plethora of gene expression regulation the oxidative damage. It induces genes/enzymes that regulate the phase 2 detoxification system (eg. GSTs and Glutathione system), ROS scavenging (SODs,PRDX1 ) and cytoprotection (HO1) by regulating inflammation and tissue damage (Tonelli et al, 2018; Shaw et al, 2020)
R-HSA-9818026 NFE2L2 regulating inflammation associated genes Subpathway representing inflammatory genes regulated by NFE2L2. NFE2L2 plays a pivotal role in regulating inflammation directly (by regulating inflammation-related genes like CCL2, IL8) and indirectly (through the HO-1-NFKB axis). This role of NFE2L2 plays a role in inflammatory diseases and expands NFE2L2 role beyond the antioxidant system. (Ahmed et al, 2017; Saha et al, 2020)
R-HSA-9818030 NFE2L2 regulating tumorigenic genes Sub-pathway representing tumor-inducing genes regulated by NFE2L2 (NRF2). NFE2L2 plays a key role in cancer progression by inducing cytoprotection, regulating cancer metabolism and also directly regulating the expression of pro-tumorogenic genes(Deblasi et al, 2020; Wu et al, 2019)
R-HSA-205017 NFG and proNGF binds to p75NTR When the co-receptor sortilin is present at the cell surface, proNGF preferentially interacts with a p75NTR:sortilin complex. Thus, proNGF, which does not bind TRKA, discriminates between TRKA and p75NTR, in cells that express both receptors. The same is true for proBDNF. Pro-neurotrophin binding to p75NTR:sortilin activates an apoptotic cascade, which may be involved in cell death after injury, and in neurodegenerative diseases such as Alzheimer's dementia.
R-HSA-167060 NGF processing All neurotrophins (NTs) are generated as pre-pro-neurotrophin precursors. The signal peptide is cleaved off as NT is associated with the endoplasmic reticulum (ER). The resulting pro-NT can form a homodimer spontaneously which then transits to the Golgi apparatus and then onto the trans-Golgi network (TGN). Resident protein convertases (PCs) can cleave off the pro-sequence and mature NT is is targeted to constitutively released vesicles. The pro-NT form can also be released to the extracellular region.
R-HSA-187024 NGF-independant TRKA activation TRK receptors can also be activated by at least two G-protein-coupled receptors (GPCR), the adenosine A2a receptor and the PACAP type I receptor, without involvement of neurotrophins. Activity of both receptors is mediated by G proteins that activate adenyl cyclase. How this leads to TRKA activation has not been fully elucidated, although a SRC-family tyrosine kinase and intracellular Ca2+ appear to play a role. TRKA activation through GPCRs occurs with slow kinetics (over 1 hr adenosine or PACAP treatment is required) in an intracellular location (probably the Golgi apparatus), and requires transcriptional and protein synthesis events that may influence the processing and activation of the receptors. GPCR-mediated transactivation of TRK receptors causes the preferential activation of AKT versus ERKs. This leads to a cell survival response.
R-HSA-9031628 NGF-stimulated transcription NGF stimulation induces expression of a wide array of transcriptional targets. In rat PC12 cells, a common model for NGF signaling, stimulation with NGF causes cells to exit the cell cycle and undergo a differentiation program leading to neurite outgrowth. This program is driven by the expression of immediate early genes (IEGs), which frequently encode transcription factors regulating the activity of NGF-specific delayed response genes (reviewed in Sheng and Greenberg, 1990; Flavell and Grennberg, 2008; Santiago and Bashaw, 2014).
R-HSA-5676590 NIK-->noncanonical NF-kB signaling In addition to the activation of canonical NF-kB subunits, activation of SYK pathway by Dectin-1 leads to the induction of the non-canonical NF-kB pathway, which mediates the nuclear translocation of RELB-p52 dimers through the successive activation of NF-kB-inducing kinase (NIK) and IkB kinase-alpha (IKKa) (Geijtenbeek & Gringhuis 2009, Gringhuis et al. 2009). Noncanonical activity tends to build more slowly and remain sustained several hours longer than does the activation of canonical NF-kB. The noncanonical NF-kB pathway is characterized by the post-translational processing of NFKB2 (Nuclear factor NF-kappa-B) p100 subunit to the mature p52 subunit. This subsequently leads to nuclear translocation of p52:RELB (Transcription factor RelB) complexes to induce cytokine expression of some genes (C-C motif chemokine 17 (CCL17) and CCL22) and transcriptional repression of others (IL12B) (Gringhuis et al. 2009, Geijtenbeek & Gringhuis 2009, Plato et al. 2013).
R-HSA-168638 NOD1/2 Signaling Pathway NOD1 is ubiquitously expressed, while NOD2 expression is restricted to monocytes, macrophages, dendritic cells, and intestinal Paneth cells (Inohara et al. 2005). NOD1 and NOD2 activation induces transcription of immune response genes, predominantly mediated by the proinflammatory transcriptional factor NFkappaB but also by AP-1 and Elk-1 (Inohara et al. 2005). NFkappaB translocates to the nucleus following release from IkappaB proteins. NOD1 and NOD2 signaling involves an interaction between their caspase-recruitment domain (CARD) and the CARD of the kinase RIPK2 (RIP2/RICK). This leads to the activation of the NFkappaB pathway and MAPK pathways (Windheim et al. 2007).
Activated NODs oligomerize via their NACHT domains, inducing physical proximity of RIP2 proteins that is believed to trigger their K63-linked polyubiquitination, facilitating recruitment of the TAK1 complex. RIP2 also recruits NEMO, bringing the TAK1 and IKK complexes into proximity, leading to NF-kappaB activation and activation of MAPK signaling. Recent studies have demonstrated that K63-linked regulatory ubiquitination of RIP2 is essential for the recruitment of TAK1 (Hasegawa et al. 2008, Hitosumatsu et al. 2008). As observed for toll-like receptor (TLR) signaling, ubiquitination can be removed by the deubiquitinating enzyme A20, thereby dampening NOD1/NOD2-induced NF-kappaB activation. NOD1 and NOD2 both induce K63-linked ubiquitination of RIP2, but NOD2-signaling appears to preferentially utilize the E3 ligase TRAF6, while TRAF2 and TRAF5 were shown to be important for NOD1-mediated signaling. In both cases, activation of NF-kappaB results in the upregulated transcription and production of inflammatory mediators.
R-HSA-203754 NOSIP mediated eNOS trafficking eNOS-interacting protein (NOSIP) is a 34-kDa nucleocytoplasmic shuttling protein that binds to the COOH-terminal region (amino acids 366-486) of the eNOS oxygenase domain. This protein association promotes translocation of eNOS from the plasma membrane caveolae to the cytoskeleton and inhibits eNOS activity. Studies have found that NOSIP accumulates in the cytoplasm specifically during the G2 phase of the cell cycle.
R-HSA-203641 NOSTRIN mediated eNOS trafficking eNOS traffic inducer (NOSTRIN) is a novel 506-amino acid eNOS-interacting protein. Along with a decrease in eNOS activity, NOSTRIN causes translocation of eNOS from the plasma membrane to intracellular vesicular structures. NOSTRIN functions as an adaptor protein through homotrimerization and recruitment of eNOS, dynamin-2, and N-WASP to its SH3 domain. Studies indicated that NOSTRIN may facilitate vesicle fission and endocytosis of eNOS by coordinating the function of dynamin and N-WASP, which in turn, recruits the Arp2/3 complex, initiating actin filament polymerization. Overall, this process is thought to occur via caveolar endocytosis.
R-HSA-2122947 NOTCH1 Intracellular Domain Regulates Transcription NICD1 produced by activation of NOTCH1 in response to Delta and Jagged ligands (DLL/JAG) presented in trans, traffics to the nucleus where it acts as a transcription regulator. In the nucleus, NICD1 displaces the NCOR corepressor complex from RBPJ (CSL). When bound to the co-repressor complex that includes NCOR proteins (NCOR1 and NCOR2) and HDAC histone deacetylases, RBPJ (CSL) represses transcription of NOTCH target genes (Kao et al. 1998, Zhou et al. 2000, Perissi et al. 2004, Perissi et al. 2008). Once the co-repressor complex is displaced, NICD1 recruits MAML (mastermind-like) to RBPJ, while MAML recruits histone acetyltransferases EP300 (p300) and PCAF, resulting in formation of the NOTCH coactivator complex that activates transcription from NOTCH regulatory elements. The minimal functional NOTCH coactivator complex that activates transcription from NOTCH regulatory elements is a heterotrimer composed of NICD, MAML and RBPJ (Fryer et al. 2002, Wallberg et al. 2002, Nam et al. 2006).
NOTCH1 coactivator complex is known to activate transcription of HES1 (Jarriault et al. 1995), HES5 (Arnett et al. 2010), HEY genes (Fischer et al. 2004, Leimeister et al. 2000, Maier et al. 2000, Arnett et al. 2010) and MYC (Palomero et al. 2006) and likely regulates transcription of many other genes (Wang et al. 2011). NOTCH1 coactivator complex on any specific regulatory element may involve additional transcriptional regulatory proteins. HES1 binds TLE proteins, forming an evolutionarily conserved transcriptional corepressor involved in regulation of neurogenesis, segmentation and sex determination (Grbavec et al. 1996, Fisher et al. 1996, Paroush et al. 1994).
After NOTCH1 coactivator complex is assembled on a NOTCH-responsive promoter, MAML (mastermind-like) recruits CDK8 in complex with cyclin C, triggering phosphorylation of conserved serine residues in TAD and PEST domains of NICD1 by CDK8. Phosphorylated NICD1 is recognized by the E3 ubiquitin ligase FBXW7 which ubiquitinates NICD1, leading to degradation of NICD1 and downregulation of NOTCH1 signaling. FBXW7-mediated ubiquitination and degradation of NOTCH1 depend on C-terminally located PEST domain sequences in NOTCH1 (Fryer et al. 2004, Oberg et al. 2001, Wu et al. 2001). The PEST domain of NOTCH1 and the substrate binding WD40 domain of FBXW7 are frequent targets of mutations in T-cell acute lymphoblastic leukemia - T-ALL (Welcker and Clurman 2008).
NICD1, which normally has a short half-life, can be stabilized by binding to the hypoxia-inducable factor 1-alpha (HIF1A) which accumulates in the nucleus when oxygen levels are low. This results in HIF1A-induced inhibition of cellular differentiation that is NOTCH-dependent (Gustafsson et al. 2005).
R-HSA-2979096 NOTCH2 Activation and Transmission of Signal to the Nucleus Similar to NOTCH1, NOTCH2 is activated by Delta-like and Jagged ligands (DLL/JAG) expressed in trans on a neighboring cell (Shimizu et al. 1999, Shimizu et al. 2000, Hicks et al. 2000, Ji et al. 2004). The activation triggers cleavage of NOTCH2, first by ADAM10 at the S2 cleavage site (Gibb et al. 2010, Shimizu et al. 2000), then by gamma-secretase at the S3 cleavage site (Saxena et al. 2001, De Strooper et al. 1999), resulting in the release of the intracellular domain of NOTCH2, NICD2, into the cytosol. NICD2 subsequently traffics to the nucleus where it acts as a transcription regulator.
While DLL and JAG ligands are well established, canonical NOTCH2 ligands, there is limited evidence that NOTCH2, similar to NOTCH1, can be activated by CNTN1 (contactin 1), a protein involved in oligodendrocyte maturation (Hu et al. 2003). MDK (midkine), which plays an important role in epithelial to mesenchymal transition, can also activate NOTCH2 signaling and is able to bind to the extracellular domain of NOTCH2, but the exact mechanism of MDK-induced NOTCH2 activation has not been elucidated (Huang et al. 2008, Gungor et al. 2011).
R-HSA-2197563 NOTCH2 intracellular domain regulates transcription In the nucleus, NICD2 forms a complex with RBPJ (CBF1, CSL) and MAML (mastermind). NICD2:RBPJ:MAML complex activates transcription from RBPJ-binding promoter elements (RBEs) (Wu et al. 2000). Besides NICD2, RBPJ and MAML, NOTCH2 coactivator complex likely includes other proteins, shown as components of the NOTCH1 coactivator complex.
NOTCH2 coactivator complex directly stimulates transcription of HES1 and HES5 genes (Shimizu et al. 2002), both of which are known NOTCH1 targets.
The promoter of FCER2 (CD23A) contains several RBEs that are occupied by NOTCH2 but not NOTCH1 coactivator complexes, and NOTCH2 activation stimulates FCER2 transcription. Overexpression of FCER2 (CD23A) is a hallmark of B-cell chronic lymphocytic leukemia (B-CLL) and correlates with the malfunction of apoptosis, which is thought be an underlying mechanism of B-CLL development. The Epstein-Barr virus protein EBNA2 can also activate FCER2 transcription through RBEs, possibly by mimicking NOTCH2 signaling (Hubmann et al. 2002).
NOTCH2 coactivator complex occupies the proximal RBE of the GZMB (granzyme B) promoter and at the same time interacts with phosphorylated CREB1, bound to an adjacent CRE site. EP300 transcriptional coactivator is also recruited to this complex through association with CREB1 (Maekawa et al. 2008). NOTCH2 coactivator complex together with CREBP1 and EP300 stimulates transcription of GZMB (granzyme B), which is important for the cytotoxic function of CD8+ T-cells (Maekawa et al. 2008).
There are indications that NOTCH2 genetically interacts with hepatocyte nuclear factor 1-beta (HNF1B) in kidney development (Massa et al. 2013, Heliot et al. 2013) and with hepatocyte nuclear factor 6 (HNF6) in bile duct formation (Vanderpool et al. 2012), but the exact nature of these genetic interactions has not been defined.
R-HSA-9013507 NOTCH3 Activation and Transmission of Signal to the Nucleus NOTCH3 receptor can be activated by DLL/JAG ligands DLL1, JAG1, and JAG2 (Shimizu et al. 2000), as well as DLL4 (Claxton and Fruttiger 2004, Indraccolo et al. 2009). Ligand binding induces a conformational change in NOTCH3, which exposes the S2 site in the extracellular region of NOTCH3. The S2 site is cleaved by ADAM10 metalloprotease, generating the membrane anchored NOTCH3 fragment NEXT3. The NEXT3 fragment of NOTCH3 is further cleaved at the S3 site by the gamma secretase complex, releasing the intracellular domain NICD3 into the cytosol (Groot et al. 2014). Besides DLL/JAG ligands, NOTCH3 signaling can also be activated by binding of NOTCH3 to YBX1 (YB 1) (Rauen et al. 2009). NICD3 traffics to the nucleus where it acts as a transcription factor. WWP2, an E3 ubiquitin ligase, negatively regulates NOTCH3 signaling by ubiquitinating NEXT3 and NICD3 in the cytosol and targeting them for lysosome-mediated degradation (Jung et al. 2014). NOTCH3 signaling is also negatively regulated by binding to TACC3 (Bargo et al. 2010) and by EGFR-mediated phosphorylation (Arasada et al. 2014).
R-HSA-9013508 NOTCH3 Intracellular Domain Regulates Transcription In the nucleus, NICD3 forms a complex with RBPJ (CBF1, CSL) and MAML (mastermind) proteins MAML1, MAML2 or MAML3 (possibly also MAMLD1). NICD3:RBPJ:MAML complex, also known as the NOTCH3 coactivator complex, activates transcription from RBPJ-binding promoter elements (Lin et al. 2002). While NOTCH1 prefers paired RBPJ binding sites, NOTCH3 preferentially binds to single RBPJ binding sites (Ong et al. 2006).
NOTCH3 coactivator complex induces transcription of the well established NOTCH target genes HES1 (Lin et al. 2002, Boelens et al. 2014), HEYL (Maier and Gessler 2000, Geimer Le Lay et al. 2014), HES5 (Lin te al. 2002, Shimizu et al. 2002), and HEY2 (Wang et al. 2002).
NOTCH3 positively regulates transcription of the pre-T-cell receptor alpha chain (PTCRA, commonly known as pT-alpha or pre-TCRalpha) (Talora et al. 2003, Bellavia et al. 2007). IK1, splicing isoform of the transcription factor Ikaros (IKZF1), competes with RBPJ for binding to the PTCRA promoter and inhibits PTCRA transcription. NOTCH3, through pre-TCR signaling, stimulates expression of the RNA binding protein HuD, which promotes splicing of IKZF1 into dominant negative isoforms. These dominant negative isoforms of IKZF1 heterodimerize with IK1, preventing its binding to target DNA sequences and thus contributing to sustained transcription of PTCRA (Bellavia et al. 2007, reviewed by Bellavia, Mecarrozzi, Campese, Grazioli, Gulino and Screpanti 2007).
NOTCH3-triggered pre-TCR-signaling downregulates the activity of the transcription factor TCF3 (E2A), through ERK-dependent induction of ID1. Inhibition of TCF3-mediated transcription downstream of NOTCH3 contributes to development of T-cell lymphomas in transgenic mice expressing NICD3 (Talora et al. 2003). Activation of ERKs downstream of NOTCH3-stimulated pre-TCR signaling leads to phosphorylation of the transcription factor TAL1, formation of the TAL1:SP1 complex, and activation of cyclin D1 (CCND1) transcription, which stimulates cell division (Talora et al. 2006).
NOTCH3 signaling can activate NF-kappaB (NFKB)-mediate transcription either indirectly, through activation of pre-TCR signaling, or directly, through association of NOTCH3 with IKKA. NFKB is constitutively active in T lymphoma cells derived from NOTCH3 transgenic mice (Vacca et al. 2006).
Transcription of the PLXND1 gene, encoding the semaphorin receptor Plexin D1, is directly stimulated by NOTCH1 and NOTCH3 coactivator complexes. PLXND1 is involved in neuronal migration and cancer cell invasiveness (Rehman et al. 2016). Expression of FABP7 (BLBP) in radial glia is positively regulated by NOTCH1 and NOTCH3 during neuronal migration (Anthony et al. 2005, Keilani and Sugaya 2008).
NOTCH3 gene is frequently amplified in ovarian cancer (Park et al. 2006). NOTCH3 coactivator complex directly stimulates DLGAP5 transcription. DLGAP5 is involved in G2/M transition and is overexpressed in ovarian cancer cells. (Chen et al. 2012). Another gene overexpressed in ovarian cancer whose transcription is directly stimulated by NOTCH3 is PBX1 (Park et al. 2008). The NOTCH3 coactivator complex directly stimulates WWC1 gene transcription. WWC1 gene encodes protein Kibra, involved in Hippo signaling. NOTCH3-mediated induction of WWC1 positively regulates Hippo signaling and inhibits epithelial-to-mesenchymal transition (EMT) in triple negative breast cancer cells (Zhang et al. 2016).
R-HSA-9013700 NOTCH4 Activation and Transmission of Signal to the Nucleus NOTCH4 is co-expressed with DLL4 (Delta-4) and JAG1 (Jagged-1) in the vascular system (Shutter et al. 2000, Uyttendaele et al. 2000). NOTCH4 can be activated by DLL4 and JAG1 when HMVECd cells (human primary endothelial cell line derived from neonatal dermal microvasculature) or HUVEC cells (human umbilical venous endothelial cell line) expressing recombinant mouse Notch4 are co-cultured with HMVECd or HUVEC cells expressing recombinant human or mouse DLL4 (Shawber et al. 2003, Shawber et al. 2007) or mouse Jag1 (Shawber et al. 2007). Activation of NOTCH4 by DLL4 and JAG1 could not be reproduced when the mouse fibroblast cell line NIH 3T3 or human embryonic kidney cell line HEK293 was transduced with Notch4- or either Dll4- or Jag1-expressing vectors and used in co-culture experiments (Aste-Amezaga et al. 2010, James et al. 2014).
Signaling by NOTCH4, similar to other NOTCH family proteins, involves proteolytic cleavage of the membrane-bound NOTCH4 receptor and release of the NOTCH4 intracellular domain fragment (NICD4) into the cytosol (Saxena et al. 2001, Das et al. 2004). NICD4 traffics from the cytosol to the nucleus, where it acts as a transcription factor (Lin et al. 2002).
R-HSA-9013695 NOTCH4 Intracellular Domain Regulates Transcription In the nucleus, NOTCH4 intracellular domain fragment (NICD4) binds transcription factors RBPJ (CSL) and mastermind family members (MAML1, MAML2 or MAML3) to form the NOTCH4 co-activator complex (Lin et al. 2002). The NOTCH4 coactivator complex stimulates transcription of well-established NOTCH targets HES1, HES5, HEY1 and HEY2 in a cellular context-dependent manner (Lin et al. 2002, Raafat et al.2004, Tsunematsu et al. 2004, Bargo et al. 2010). NOTCH4 also stimulates transcription of the FLT4 (VEGFR3) gene, encoding vascular endothelial growth factor receptor-3 (Shawber et al. 2007) and ACTA2 gene, encoding smooth muscle alpha actin (Tang et al. 2008).
NICD4 inhibits TGF-beta-induced SMAD-mediated transcription via binding of NICD4 to TGF-beta activated SMAD3 (Sun et al. 2005, Grabias and Konstantopoulos 2013).
R-HSA-9768919 NPAS4 regulates expression of target genes NPAS4 is a basic helix loop helix (bHLH) transcription factor that needs to dimerize with another bHLH protein, either ARNT, ARNT2 or ARNTL, in order to be able to bind to target DNA (Ooe et al. 2004; Ooe et al. 2009; Brigidi et al. 2019).
NPAS4 is implicated as a transcriptional regulator of genes involved in neuronal development such as CDK5 (Yun et al. 2013), CDK5R1 (Yun et al. 2013), RBFOX3 (NeuN) (Yun et al. 2013), BDNF (Pruunsild et al. 2011) and RET (Sribudiani et al. 2011), genes involved in synaptogenesis and synaptic transmission such as NPTX2 (Lin et al. 2008), MDM2 (Yoshihara et al. 2014; Lv et al. 2021), FOS (Ramamoorthi et al. 2011), IQSEC3 (Kim et al. 2021), PLK2 (Weng et al. 2018) and possibly other genes (Lin et al. 2008; Shan et al. 2018), circadian rhythm-related genes such as NAMPT (West et al. 2013), and genes involved in neuroprotection upon injury such as GEM (Takahashi et al. 2021), SYT10 (Woitecki et al. 2016) and possibly other genes (Qiu et al. 2013). In pancreatic beta-cell, NPAS4 is implicated as a regulator of insulin synthesis under stress conditions (Sabatini et al. 2013).
The circadian clock regulated gene CRY1 was identified as NPAS4 target gene in sheep brain (West et al. 2013), but this finding was not reproduced in the high throughput identification of NPAS4 targets in rat primary neurons (Brigidi et al. 2019). The DBNL gene, encoding Drebrin, a dendrytic cytoskeleton modulator, was initially identified as a gene directly upregulated by Npas4 (Ooe et al. 2004), but a high throughput study of NPAS4 targets showed DBNL gene expression to be repressed by NPAS4, although not significantly (Brigidi et al. 2019).
NPAS4 is expressed in endothelial cells and may play a role in angiogenesis (Esser et al. 2017).
R-HSA-1368071 NR1D1 (REV-ERBA) represses gene expression REV-ERBA binds DNA elements very similar to those bound by the transcription activator RORA. RORAREV-ERBA bound to DNA and heme recruits the corepressors NCoR and HDAC3 to repress transcription. Thus REV-ERBA and RORA appear to compete to repress or activate genes, repectively.
R-HSA-9632974 NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis Activation of liver X receptor α (LXRα, NR1H3) alters the expression of genes in liver and adipose tissue that collectively may limit hepatic glucose output and improve peripheral glucose uptake (Laffitte BA et al. 2003). In the liver, activation of NR1H3 led to the suppression of the expression of genes involved in gluconeogenesis including glucose-6-phosphatase (G6Pase) and phosphoenolpyruvate carboxykinase (PCK1 or PEPCK) (Laffitte BA et al. 2003; Dalen KT et al. 2003; Herzog B et al. 2007; Commerford et al. 2007). In adipose tissue, activation of NR1H3 led to the transcriptional induction of the insulin-sensitive glucose transporter, GLUT4 (Laffitte BA et al. 2003; Dalen KT et al. 2003). In contrast, basal expression of LXRβ (NR1H2) has been shown to be essential for the regulation of PCK1 by another nuclear receptor, the glucocorticoid receptor GR (NR3C1) (Patel et al. 2011; Patel et. al. 2017). The LXRs appear to have somewhat opposing roles in the regulation of PCK1 in the liver since NR1H3 (LXRα) activation represses PCK1 mRNA expression induced by glucocorticoids (Nader et al. 2012) and NR1H2 (LXRβ) antagonism reduces glucocorticoid-induced PCK1 mRNA expression (Patel et al. 2017).
R-HSA-9029558 NR1H2 & NR1H3 regulate gene expression linked to lipogenesis The liver X receptor α (LXRα or NR1H3) and LXRβ (NR1H2) are nuclear receptors that are activated by endogenous oxidized derivatives of cholesterol known as oxysterols (Janowski BA et al. 1999; Jakobsson T et al. 2012). NR1H2 and NR1H3 act as whole-body cholesterol sensors and their activation results in a net elimination of cholesterol from the body and amelioration of the plasma lipoprotein profile by mobilizing cholesterol from the periphery (Venkateswaran A et al. 2000; Repa JJ et al. 2000a; Ishibashi M et al. 2013). NR1H3 (LXRα) and NR1H2 (LXRβ) also contribute to lowering of whole-body cholesterol levels by shifting acetyl-CoA units from cholesterol de novo biosynthesis to fatty acid synthesis. NR1H2 or 3-induced hepatic lipogenesis in rodents and humans is mediated by direct upregulation of sterol regulatory element-binding protein 1 (SREBF1), the main regulator of hepatic lipogenesis that controls the transcription of genes involved in fatty acid biosynthesis (Schultz JR et al. 2000). NR1H2 & NR1H3 may activate lipogenic gene transcription directly by biding LXR responsive element (LXRE) found in the promoter regions of several genes, such as fatty acid synthase (FAS or FASN) and stearoyl-CoA desaturase 1 (SCD1) (Repa JJ et al. 2000b; Yoshikawa T et al. 2001; Joseph SB et al. 2002; Chu K et al. 2006). Mice carrying a targeted disruption in the NR1H3 (LXRα) gene were deficient in expression of FAS, SCD1, ACC, and SREBF1 (Peet DJ et al. 1998). Mice ablated of both NR1H3 and NR1H2 showed defective hepatic lipid metabolism decreasing lipogenesis by 80% and were resistant to obesity (Repa JJ et al. 2000; Kalaany NY et al. 2005; Beaven SW et al. 2013). Further, the administration of the synthetic NR1H2 or NR1H3 ligands to mice triggered induction of the lipogenic pathway and raised plasma triglyceride levels (Schultz JR et al. 2000). These studies demonstrate the role of NR1H3 (LXRα) and NR1H2 (LXRβ) in the control of lipogenesis.
R-HSA-9031528 NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose Adipose tissue triglycerides (TGs) represent the major energy store of the body. During adipocyte lipolysis triglycerides (TGs) are hydrolyzed into free fatty acids (FFAs) and glycerol by the action of adipose triglyceride lipase (ATGL, encoded by PNPLA2), then hormone-sensitive lipase (HSL), which is activated by glucagon and adrenaline (epinephrine) and inhibited by insulin. Both isoforms of liver X receptor, LXRα (NR1H3) and LXRβ (NR1H2), are expressed in mature mouse and human adipocytes (Juvet LK et al. 2003). Expression of NR1H3 is up-regulated during adipocyte differentiation (Juvet LK et al. 2003; Darimont C et al. 2006). Ligand activation of LXRs (NR1H2 or NR1H3) can induce adipocyte lipolysis and FFA oxidation (Stenson BM et al. 2011; Ross SE et al. 2002). For instance, in mouse 3T3L1 adipocytes and human primary adipocytes, LXR activation led to an increase in basal, but not hormone-stimulated, lipolysis as measured by glycerol release (Ross SE et al. 2002; Stenson BM et al. 2011). Another study showed that administration of synthetic ligands of NR1H2/ NR1H3, T0901317 or GW3965, to mice resulted in smaller adipocytes and increased serum free fatty acid and glycerol concentrations, suggesting increased adipocyte lipolysis (Commerford SR et al. 2007). Further, microarray analysis of human adipocytes following NR1H3 or NR1H2 activation revealed altered gene expression of several lipolysis-regulating proteins such as perilipin1 (PLIN1), which was also confirmed by quantitative real-time PCR (Stenson BM et al. 2011). Selective knockdown of either NR1H2 or NR1H3 showed that NR1H3 (LXRα) was the major isoform mediating the lipolysis-related effects of LXR agonists (Stenson BM et al. 2011). In addition, the absence of NR1H3 (LXRα) in mouse adipose tissue resulted in elevated adiposity through a decrease of both lipolytic and oxidative capacities in white adipose tissue (Dib L et al. 2014).
R-HSA-9623433 NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis Liver X receptors NR1H3 (LXR alpha) and NR1H2 (LXR beta) are sterol-responsive transcription factors that become activated upon the engagement with their cognate oxysterol ligands. Besides inducing a genetic program aimed to reduce the cellular sterol load, ligand-activated NR1H2 & NR1H3 also modulate the expression and activity of genes controlling bile acid synthesis, transport and metabolism such as bile acid-glucuronidating enzyme UGT1A3 which converts hydrophobic bile acids into polar metabolites that can be excreted in the urine (Verreault M et al. 2006).
R-HSA-9031525 NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake Liver X receptors NR1H3 (LXR alpha) and NR1H2 (LXR beta) are sterol-responsive transcription factors that become activated upon the engagement with their cognate oxysterol ligands. Ligand-activated NR1H2 & NR1H3 induce a genetic program aimed at reducing the cellular sterol load by limiting cholesterol uptake, attenuating cholesterol biosynthesis and promoting cholesterol efflux. This Reactome module describes the NR1H2 & NR1H3-regulated expression of MYLIP (IDOL) gene, an E3 ubiquitin ligase, that triggers ubiquitination of the low-density lipoprotein receptor (LDLR) on its cytoplasmic domain, targeting it for degradation and thereby limiting cholesterol uptake (Zelcer N et al. 2009; Zhang L et al. 2012).
R-HSA-9024446 NR1H2 and NR1H3-mediated signaling The liver X receptors LXRα (NR1H3) and LXRβ (NR1H2) are members of the nuclear receptor superfamily and function as ligand-activated transcription factors. The natural ligands of NR1H2 and NR1H3 are oxysterols (e.g., 24(S),25-epoxycholesterol, 24(S)-hydroxycholesterol (OH), 25-OH, and 27-OH) that are produced endogenously by enzymatic reactions, by reactive oxygen species (ROS)-dependent oxidation of cholesterol and by the alimentary processes (reviewed in:Jakobsson T et al. 2012; Huang C 2014; Komati R et al. 2017). It has been shown that these oxysterols bind directly to the ligand-binding domain of LXRs with Kd values ranging from 0.1 to 0.4 microM. 24(S), 25-epoxycholesterol was found to be the most potent endogenous agonist (Janowski BA et al. 1999). NR1H3 (LXRα) and NR1H2 (LXRβ) showed similar affinities for these compounds (Janowski BA et al. 1999). In physiological conditions, oxysterols are formed in amounts proportional to cholesterol content in the cell and therefore the LXRs operate as cholesterol sensors to alter gene expression and protect the cells from cholesterol overload via: (1) inhibiting intestinal cholesterol absorption; (2) stimulating cholesterol efflux from cells to high-density lipoproteins through the ATP-binding cassette transporters ABCA1 and ABCG1: (3) activating the conversion of cholesterol to bile acids in the liver; and (4) activating biliary cholesterol and bile acid excretion (reviewed in: Wójcicka G et al. 2007; Baranowski M 2008; Laurencikiene J & Rydén M 2012; Edwards PA et al. 2002; Zelcer N & Tontonoz P 2006; Zhao C & Dahlman-Wright K 2010). In addition, LXR agonists enhance de novo fatty acid synthesis by stimulating the expression of a lipogenic transcription factor, sterol regulatory element-binding protein-1c (SREBP-1c), leading to the elevation of plasma triglycerides and hepatic steatosis (Wójcicka G et al. 2007; Baranowski M 2008; Laurencikiene J & Rydén M 2012). In addition to their function in lipid metabolism, NR1H2,3 have also been found to modulate immune and inflammatory responses in macrophages (Zelcer N & Tontonoz P 2006). The NR1H2 and NR1H3 molecules can be viewed as having four functional domains: (1) an amino-terminal ligand-independent activation function domain (AF-1), which may stimulate transcription in the absence of ligand; (2) a DNA-binding domain (DBD) containing two zinc fingers; (3) a hydrophobic ligand-binding domain (LBD) required for ligand binding and receptor dimerization; and, (4) a carboxy-terminal ligand-dependent transactivation sequence (also referred to as the activation function-2 (AF-2) domain) that stimulates transcription in response to ligand binding (Robinson-Rechavi M et al. 2003; Jakobsson T et al. 2012; Färnegardh M et al. 2003; Lin CY & Gustafsson JA 2015). Although both NR1H3 and NR1H2 are activated by the same ligands and are structurally similar, their tissue expression profiles are very different. NR1H3 is selectively expressed in specific tissues and cell types, such as the liver, intestine, adrenal gland, adipose tissue and macrophages, whereas NR1H2 is ubiquitously expressed (Nishimura M et al. 2004; Bookout AL et al. 2006). Upon activation NR1H2 or NR1H3 heterodimerizes with retinoid X receptors (RXR) and binds to LXR-response elements (LXREs) consisting of a direct repeat of the core sequence 5'-AGGTCA-3' separated by 4 nucleotides (DR4) in the DNA of target genes (Wiebel FF & Gustafsson JA 1997). An inverted repeat of the same consensus sequence with no spacer region(IR-0) and an inverted repeat of the same consensus sequence separated by a 1 bp spacer (IR-1) have also been shown to mediate LXR transactivation (Mak PA et al. 2002, Landrier JF et al. 2003). NR1H3 and NR1H2 have been shown to regulate gene expression via LXREs in the promoter regions of their target genes such as UDP glucuronosyltransferase 1 family, polypeptide A3 (UGT1A3) (Verreault M et al. 2006), fatty acid synthase (FAS) (Joseph SB et al. 2002a), carbohydrate response element binding protein (ChREBP, also known as MLX-interacting protein-like or MLXIPL) (Cha JY & Repa JJ 2007) and phospholipid transfer protein (PLTP) (Mak PA et al. 2002). LXREs have also been reported to be present in introns of target genes such as the ATP-binding cassette transporter G1 (ABCG1) (Sabol SL et al. 2005). NR1H3 has been shown to activate gene expression via the FXR-responsive element found in the proximal promoter of the human ileal bile acid-binding protein (FABP6) (Landrier JF et al. 2003). The NR1H2,3:RXR heterodimers are permissive, in that they can be activated by ligands for either NR1H2,3 (LXR) or RXR (Willy PJ et al. 1995).
R-HSA-9029569 NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux The liver X receptors (LXRs), LXRα (NR1H3) and LXRβ (NR1H2), are nuclear receptors that are activated by endogenous oxysterols, oxidized derivatives of cholesterol (Janowski BA et al. 1996). When cellular oxysterols accumulate as a result of increasing concentrations of cholesterol, NR1H2,3 induce the transcription of genes that protect cells from cholesterol overload (Zhao C & Dahlman‑Wright K 2010; Ma Z et al. 2017). In peripheral cells such as macrophages, NR1H2 and NR1H3 increase cholesterol efflux by inducing expression of ATP-binding cassette subfamily A type 1 (ABCA1), ABCG1, and apolipoprotein APOE (Jakobsson T et al. 2009; Laffitte BA et al. 2001; Mak PA et al. 2002). In the intestine, LXR agonists decrease cholesterol absorption through induction of ABCA1, ABCG5, and ABCG8 (Repa JJ et al. 2000; Back SS et al. 2013). Cholesterol removal from non-hepatic peripheral cells, such as lipid-laden macrophages, and its delivery back to the liver for catabolism and excretion are processes collectively known as reverse cholesterol transport (RCT) (Francis GA 2010; Rosenson RS et al. 2012). This Reactome module describes the activation of several direct NR1H2,3 target genes that are closely associated with the RCT pathway, including genes encoding membrane lipid transporters, such ABCA1, ABCG1, ABCG5, ABCG8 and a cluster of apolipoprotein genes APOE, APOC1, APOC2 and APOC4 (Jakobsson T et al. 2009; Back SS et al. 2013; Mak PA et al. 2002).
R-HSA-193648 NRAGE signals death through JNK Once bound by either NGF or proNGF, p75NTR interacts with NRAGE, thus leading to phosphorylation and activation of JUN Kinase (JNK). JNK controls apoptosis in two ways: it induces transcription of pro-apoptotic genes, and directly activates the cell death machinery. Only NGF-bound p75NTR is shown here.
R-HSA-205043 NRIF signals cell death from the nucleus NRIF (nuclear receptor-interacting factor) is a DNA binding protein that is essential for p75-mediated apoptosis in retina and sympathetic neurons. Neurotrophin or proneurotrophin binding to p75TR induces nuclear translocation of NRIF, which involves gamma-secretase cleavage of p75NTR ICD (Intra Cellular Domain). Once in the nucleus, NRIF mediates apoptosis, probably by acting as transcription factor.
R-HSA-168276 NS1 Mediated Effects on Host Pathways Viral NS1 protein is a nuclear, dimeric protein that is highly expressed in infected cells and has dsRNA-binding activity. The RNA-binding domain lies within the N-terminal portion of the protein. The NS1 RNA-binding domain forms a symmetric homodimer with a six-helical fold. Mutational analysis has demonstrated that dimer formation is crucial for RNA-binding. The basic residues are believed to make contact with the phosphate backbone of the RNA which is consistent with an observed lack of sequence specificity. Neither NS1 nor its bound RNA undergo any significant structural changes upon binding. The NS1 dimer spans the minor groove of canonical A-form dsRNA. The non-RNA binding portion of NS1 has been termed the effector domain and includes binding sites for host cell poly (A)-binding protein II (PABII) and the 30kDa subunit of cleavage and polyadenylation specificity factor (CPSF).
R-HSA-9025046 NTF3 activates NTRK2 (TRKB) signaling Neurotrophin receptor tyrosine kinase NTRK2 (TRKB) is a low affinity receptor for neurotrophin-3 (NTF3, also known as NT-3) (Soppet et al. 1991). NTF3 predominantly functions as the ligand for the NTRK3 (TRKC) receptor (Marsh and Palfrey 1996). Binding to NTF3 can trigger NTRK2 dimerization (Ohira et al. 2001) and trans-autophosphorylation of NTRK2 dimers on conserved tyrosine residues in the cytoplasmic tail of the receptor (Middlemas et al. 1994). The efficacy of this process, however, is low in comparison to NTRK2 activation by BDNF and NTF3, and downstream signaling has not been studied.
R-HSA-9034013 NTF3 activates NTRK3 signaling NTRK3 (TRKC) is activated by binding to its ligand neurotrophin-3 (NTF3, also known as NT-3). Ligand binding induces dimerization of NTRK3 and trans-autophosphorylation of dimerized receptors on conserved tyrosine residues in the cytoplasmic tail. Autophosphorylated tyrosines serve as docking sites for binding of adaptor proteins that mediate downstream signaling (Lamballe et al. 1991, Philo et al. 1994, Tsoulfas et al. 1996, Huang and Reichardt 2001, Werner et al. 2014).
R-HSA-9026357 NTF4 activates NTRK2 (TRKB) signaling Signaling by the neurotrophin receptor tyrosine kinase NTRK2 (TRKB) can be activated by binding to neurotrophin-4 (NTF4, also known as NT-4), which functions as a ligand for NTRK2 (Klein et al. 1992, Ip et al. 1993, Ohira et al. 2001). Binding to NTF4 triggers NTRK2 dimerization (Ohira et al. 2001) and trans-autophosphorylation of NTRK2 dimers on conserved tyrosine residues in the cytoplasmic tail of the receptor (Minichiello et al. 1998). Phosphorylated tyrosine residues subsequently serve as docking sites for recruitment of effector proteins that trigger downstream signaling cascades.
R-HSA-9032759 NTRK2 activates RAC1 DOCK3-mediated activation of RAC1 downstream of BDNF-induced signaling by NTRK2 (TRKB) plays a role in axonal growth and regeneration. DOCK3 can be recruited to the plasma membrane to activate RAC1 by binding to NTRK-associated FYN (Namekata et al. 2010). Alternatively, DOCK3 can, upon poorly elucidated RHOG activation by the BDNF:NTRK2 complex, bind to the RHOG:GTP complex and activate RAC1 in an ELMO1-dependent manner (Namekata et al. 2012).
R-HSA-9603505 NTRK3 as a dependence receptor When neuronal cells are deprived of the NTRK3 (TRKC) ligand NTF3 (NT-3), NTRK3 functions as a dependence receptor, promoting apoptosis. The pro-apoptotic activity of NTRK3 is implicated in proper nervous system development, by dictating the number of surviving sensory neurons (Tauszig-Delamasure et al. 2007). In the absence of its ligand, NTRK3 undergoes caspase-dependent cleavage (Tauszig-Delamasure et al. 2007), resulting in release of the NTRK3 killer fragment (KF). The NTRK3 KF, in complex with NELFB (COBRA1), inserts into the mitochondrial membrane, promoting cytochrome c release and apoptosome-mediated apoptosis (Ichim et al. 2013).
R-HSA-9717301 NVP-TAE684-resistant ALK mutants NVP TAE684 is a second generation tyrosine kinase inhibitor with activity against some ALK mutants, including some that show resistance to crizotinib (George et al, 2008; Sasaki et al, 2011; Heuckmann et al, 2011; Ceccon et al, 2013). This pathway describes ALK mutants that show resistance to inhibition by NVP TAE684.
R-HSA-442660 Na+/Cl- dependent neurotransmitter transporters The SLC6 gene family encodes proteins that mediate neurotransmitter uptake thus terminating a synaptic signal. The proteins mediate transport of GABA (gamma-aminobutyric acid), norepinephrine, dopamine, serotonin, glycine, taurine, L-proline, creatine and betaine. These transporters are mainly present in the CNS and PNS (Chen NH et al, 2004).
R-HSA-420597 Nectin/Necl trans heterodimerization Nectins and Nectin-like molecules (Necls) also undergo trans-heterophilic interactions to interact with other nectin or Necl family members. Besides these trans interactions among nectins and nectin-like family members, trans-homophilic interactions have also been described between nectins or Necls with other immunoglobulin-superfamily members like CD96, CD226 and CRTAM (Sakisaka et al., 2007; Takai et al., 2008). It should be noted that some of these interactions might not exist in epithelial cell-cell contacts but may occur in other cell-cell adhesion systems.
R-HSA-8951664 Neddylation NEDD8 is a small ubiquitin-like molecule that is conjugated to substrate proteins through an E1 to E3 enzyme cascade similar to that for ubiquitin. The best characterized target of neddylation is the cullin scaffold subunit of cullin-RING E3 ubiquitin ligases (CRLs), which themselves target numerous cellular proteins for degradation by the proteasome (Hori et al, 1999; reviewed in Soucy et al, 2010; Lyedeard et al, 2013). The multisubunit CRL complexes are compositionally diverse, but each contains a scaffolding cullin protein (CUL1, 2, 3, 4A, 4B, 5, 7 or 9) and a RING box-containing E3 ligase subunit RBX, along with other adaptor and substrate-interacting subunits. RBX2 (also known as RNF7) interacts preferentially with CUL5, while RBX1 is the primary E3 for most other cullin family members (reviewed in Mahon et al, 2014). Neddylation of the cullin subunit increases the ubiquitination activity of the CRL complex (Podust et al, 2000; Read et al, 2000; Wu et al, 2000; Kawakami et al, 2001; Ohh et al, 2002; Yu et al, 2015). In addition to CRL complexes, a number of other less-well characterized NEDD8 targets have been identified. These include other E3 ubiquitin ligases such as SMURF1 and MDM2, receptor tyrosine kinases such as EGFR and TGF beta RII, and proteins that contribute to transcriptional regulation, among others (Xie et al, 2014; Watson et al, 2010; Oved et al, 2006; Zuo et al, 2013; Xirodimas et al, 2004; Singh et al, 2007; Abida et al, 2007; Liu et al 2010; Watson et al, 2006; Loftus et al, 2012; Aoki et al, 2013; reviewed in Enchev et al, 2015).
Like ubiquitin, NEDD8 undergoes post-translational processing to generate the mature form. UCHL3- or SENP8-mediated proteolysis removes the C-terminal 5 amino acids of NEDD8, generating a novel C-terminal glycine residue for conjugation to the cysteine residues in the E1, E2 enzymes or lysine residues in the substrate protein, usually the E3 NEDD8 ligase itself (Wada et al, 1998; reviewed in Enchev et al, 2015). Most substrates in vivo appear to be singly neddylated on one or more lysine residues, but NEDD8 chains have been formed on cullin substrates in vitro and on histone H4 in cultured human cells after DNA damage (Jones et al, 2008; Ohki et al, 2009; Xirodimas et al, 2008; Jeram et al, 2010; Ma et al, 2013; reviewed in Enchev et al, 2015). The significance of NEDD8 chains is still not clear.
NEDD8 has a single heterodimeric E1 enzyme, consisting of NAE1 (also known as APPBP1) and UBA3, and two E2 enzymes, UBE2M and UBE2F, which are N-terminally acetylated (Walden et al, 2003; Bohnsack et al, 2003; Huang et al, 2004; Huang et al, 2005; Huang et al, 2009; Scott et al, 2011a; Monda et al, 2013; reviewed in Enchev et al, 2015). All NEDD8 E3 enzymes reported to date also function as E3 ubiquitin ligases, and most belong to the RING domain class. The best characterized NEDD8 E3 enzymes are the CRL complexes described above. RBX1-containing complexes interact preferentially with UBE2M, while UBE2F is the E2 for RBX2-containing complexes (Huang et al, 2009; Monda et al, 2013).
Neddylation is regulated in vivo by interaction with DCUN1D proteins (also called DCNLs). The 5 human DCUN1D proteins interact both with cullins and with the NEDD8 E2 proteins and thereby increase the kinetic efficiency of neddylation (Kurz et al, 2005; Kurz et al, 2008; Scott et al, 2010; Scott et al, 2011a; Scott et al, 2014; Monda et al, 2013). Glomulin (GLMN) is another regulator of CRL function that binds to the neddylated cullin and competitively inhibits interaction with the ubiquitin E2 enzyme (Arai et al, 2003; Tron et al, 2012; Duda et al, 2012; reviewed in Mahon et al, 2014).
The multisubunit COP9 signalosome is the only cullin deneddylase, while SENP8 (also known as DEN1) contributes to deneddylation of other non-cullin NEDD8 targets (Cope et al, 2002; Emberley et al, 2012; Chan et al, 2008; Wu et al, 2003; reviewed in Wei et al, 2008; Enchev et al, 2015). In the deneddylated state, cullins bind to CAND1 (cullin associated NEDD8-dissociated protein1), which displaces the COP9 signalosome and promotes the exchange of the ubiquitin substrate-specific adaptor. This allows CRL complexes to be reconfigured to target other subtrates for ubiquitination (Liu et al, 2002; Schmidt et al, 2009; Pierce et al, 2013; reviewed in Mahon et al, 2014).
R-HSA-167590 Nef Mediated CD4 Down-regulation The presence of Nef accelerates endocytosis and lysosomal degradation of the transmembrane glycoprotein CD4. CD4 has its own internalization motif, though this motif is normally concealed by CD4 interaction with Lck, a tyrosine kinase. Nef is known to disrupt this interaction and then facilitate a cascade of protein interactions that ultimately result in the degradation of internalized CD4 protein. The final set of protein interactions that direct Nef to the beta-subunit of the COPI coatomers are at this time unclear.
A benefit for the virus from CD4 down-modulation is abolition of interaction between the receptor and the Env protein of the budding virus, which likely increases HIV release from infected cell as well as infectivity of viral particles.
R-HSA-182218 Nef Mediated CD8 Down-regulation Human immunodeficiency virus (HIV) Nef is a membrane-associated protein decreasing surface expression of CD4, CD28, and major histocompatibility complex class I on infected cells. Nef also strongly down-modulates surface expression of the beta-chain of the CD8alphabeta receptor by accelerated endocytosis, while CD8 alpha-chain expression is less affected. Mutational analysis of the cytoplasmic tail of the CD8 beta-chain indicates that an FMK amino acid motif is critical for the Nef-induced endocytosis. Although independent of CD4, endocytosis of the CD8 beta-chain is abrogated by the same mutations in Nef that affect CD4 down-regulation, suggesting common molecular interactions. The ability to down-regulate the human CD8 beta-chain was conserved in HIV-1, HIV-2, and simian immunodeficiency virus SIVmac239 Nef and required an intact AP-2 complex.
R-HSA-164944 Nef and signal transduction Nef interferes with cellular signal transduction pathways in a number of ways. Nef is associated with lipid rafts through its amino-terminal myristoylation and a proline-rich SH3-binding domain. These cholesterol-rich membrane microdomains appear to concentrate potent signaling mediators. Nef was found to complex with and activate serine/threonine protein kinase PAK-2, which may contribute to activation of infected cells. In vitro, HIV-infected T cells produce enhanced levels of interleukin-2 during activation. When expressed in macrophages, Nef intersects the CD40L signaling pathway inducing secretion of chemokines and other factors that attract resting T cells and promote their infection by HIV.
R-HSA-164939 Nef mediated downregulation of CD28 cell surface expression Down-regulation of CD28 receptors involves a dileucine-based motif in the second disordered loop of Nef, which connects Nef to adaptor protein (AP) complex, which is a part of cellular endocytosis machinery. Nef induces accelerated endocytosis of CD28 via clathrin-coated pits followed by lysosomal degradation.
R-HSA-164940 Nef mediated downregulation of MHC class I complex cell surface expression Down-regulation of MHC class I involves Nef-mediated connection in the endosomes between MHC-I's cytoplasmic tail and the phosphofurin acidic cluster sorting protein-1 (PACS-1)-dependent protein-sorting pathway. Down-regulation of MHC I protects HIV-infected cells from host CTL response.
R-HSA-164938 Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters The maximal virulence of HIV-1 requires Nef, a virally encoded peripheral membrane protein. Nef binds to the adaptor protein (AP) complexes of coated vesicles, inducing an expansion of the endosomal compartment and altering the surface expression of cellular proteins including CD4 and class I major histocompatibility complex.
Nef affects the cell surface expression of several cellular proteins. It down-regulates CD4, CD8, CD28, and major histocompatibility complex class I and class II proteins, but upregulates the invariant chain of MHC II (CD74). To modulate cell surface receptor expression, Nef utilizes several strategies, linked to distinct regions within the Nef protein.
Since all these receptors are essential for proper functions of the immune system, modulation of their surface expression by Nef has profound effects on anti-HIV immune responses. Down-regulation of MHC I protects HIV-infected cells from host CTL response, whereas down-modulation of CD28 and CD4 probably limits the adhesion of a Nef-expressing T cell to the antigen-presenting cell, thus promoting the movement of HIV-infected cells into circulation and the spread of the virus.
R-HSA-5250941 Negative epigenetic regulation of rRNA expression Transcription of rRNA genes is controlled by epigenetic activation and repression (reviewed in McStay and Grummt 2008, Goodfellow and Zomerdijk 2012, Grummt and Langst 2013). About half of the roughly 400 rRNA genes are expressed and these have the modifications of active chromatin: unmethylated DNA and acetylated histones. Repressed genes generally have methylated DNA and histone H3 methylated at lysine-9. Regulators of repression include the eNoSC complex, SIRT1, and the NoRC complex.
SIRT1 negatively regulates rRNA expression as a subunit of the eNoSC complex, which deacetylates histone H3 and dimethylates lysine-9 of histone H3 (H3K9me2).
NoRC negatively regulates rRNA expression by shifting a nucleosome near the start of rRNA transcription into a more repressive location and recruiting Histone Deacetylase 1 and 2 (HDAC1, HDAC2) and DNA Methyltransferase 1 and 3b (DNMT1, DNMT3b).
R-HSA-5674499 Negative feedback regulation of MAPK pathway MAPK pathway activation is limited by a number of negative feedback loops established by MAPK-dependent phosphorylations. Known substrates of activated MAPK proteins that lie upstream in the RAF/MAPK pathway include SOS, RAF1, BRAF, and MAP2K1 (Buday et al, 1995; Dong et al, 1996; Dougherty et al, 2005; Sturm et al, 2010; Fritsche-Guenther et al, 2011; Rushworth et al, 2006; Brummer et al, 2003; Ritt et al, 2010; Catalanotti et al, 2009)
R-HSA-5654726 Negative regulation of FGFR1 signaling Once activated, the FGFR signaling pathway is regulated by numerous negative feedback mechanisms. These include downregulation of receptors through CBL-mediated ubiquitination and endocytosis, ERK-mediated inhibition of FRS2-tyrosine phosphorylation and the attenuation of ERK signaling through the action of dual-specificity phosphatases, IL17RD/SEF, Sprouty and Spred proteins. A number of these inhibitors are themselves transcriptional targets of the activated FGFR pathway.
R-HSA-5654727 Negative regulation of FGFR2 signaling Once activated, the FGFR signaling pathway is regulated by numerous negative feedback mechanisms. These include downregulation of receptors through CBL-mediated ubiquitination and endocytosis, ERK-mediated inhibition of FRS2-tyrosine phosphorylation and the attenuation of ERK signaling through the action of dual-specificity phosphatases, IL17RD/SEF, Sprouty and Spred proteins. A number of these inhibitors are themselves transcriptional targets of the activated FGFR pathway.
R-HSA-5654732 Negative regulation of FGFR3 signaling Once activated, the FGFR signaling pathway is regulated by numerous negative feedback mechanisms. These include downregulation of receptors through CBL-mediated ubiquitination and endocytosis, ERK-mediated inhibition of FRS2-tyrosine phosphorylation and the attenuation of ERK signaling through the action of dual-specificity phosphatases, IL17RD/SEF, Sprouty and Spred proteins. A number of these inhibitors are themselves transcriptional targets of the activated FGFR pathway.
R-HSA-5654733 Negative regulation of FGFR4 signaling Once activated, the FGFR signaling pathway is regulated by numerous negative feedback mechanisms. These include downregulation of receptors through CBL-mediated ubiquitination and endocytosis, ERK-mediated inhibition of FRS2-tyrosine phosphorylation and the attenuation of ERK signaling through the action of dual-specificity phosphatases, IL17RD/SEF, Sprouty and Spred proteins. A number of these inhibitors are themselves transcriptional targets of the activated FGFR pathway.
R-HSA-9706369 Negative regulation of FLT3 FLT3 activity is negatively regulated through several mechanisms including dephosphorylation, interaction with protein partners that limit downstream signaling pathways, and by ubiquitin-mediated internalization and degradation (reviewed in Kazi and Roonstrand, 2019).
R-HSA-5675221 Negative regulation of MAPK pathway The duration and extent of activated MAPK signaling is regulated at many levels through mechanisms that include phosphorylation and dephosphorylation, changes to protein interacting partners and subcellular localization (reviewed in Matallanas et al, 2011).
Activated RAF proteins are subject to MAPK-dependent phosphorylation that promotes the subsequent dephosphorylation of the activation loop and NtA region, terminating RAF kinase activity. This dephosphorylation, catalyzed by PP2A and PP5, primes the RAF proteins for PKA or AKT-mediated phosphorylation of residues S259 and S621, restoring the 14-3-3 binding sites and returning the RAF proteins to the inactive state (von Kriegsheim et al, 2006; Dougherty et al, 2005; reviewed in Matallanas et al, 2011). The phosphorylated RAF1 NtA is also subject to additional regulation through binding to the PEBP1 protein, which promotes its dissociation from MAP2K substrates (Shin et al, 2009).
Activated MAPK proteins also phosphorylate T292 of MAP2K1; this phosphorylation limits the activity of MAP2K1, and indirectly affects MAP2K2 activity through by modulating the activity of the MAP2K heterodimer (Catalanotti et al, 2009; reviewed in Matallanas et al, 2011).
Dephosphorylation of MAPKs by the dual specificity MAPK phosphatases (DUSPs) plays a key role in limiting the extent of pathway activation (Owens et al, 2007; reviewed in Roskoski, 2012b). Class I DUSPs are localized in the nucleus and are induced by activation of the MAPK pathway, establishing a negative feedback loop, while class II DUSPs dephosphorylate cytoplasmic MAPKs (reviewed in Rososki, 2012b).
MAPK signaling is also regulated by the RAS GAP-mediated stimulation of intrinsic RAS GTPase activity which returns RAS to the inactive, GDP bound state (reviewed in King et al, 2013).
R-HSA-6807004 Negative regulation of MET activity Signaling by MET receptor is negatively regulated mainly by MET receptor dephosphorylation or MET receptor degradation. Protein tyrosine phosphatase PTPRJ dephosphorylates MET tyrosine residue Y1349, thus removing the docking site for the GAB1 adapter (Palka et al. 2003). Protein tyrosine phosphatases PTPN1 and PTPN2 dephosphorylate MET tyrosines Y1234 and Y1235 in the kinase activation loop, thus attenuating catalytic activity of MET (Sangwan et al. 2008). The E3 ubiquitin ligase CBL promotes ubiquitination of the activated MET receptor and subsequent MET degradation. CBL contains a RING finger domain that engages E2 protein ubiquitin ligases to mediate ubiquitination of MET, which may occur at the cell membrane or in the early endocytic compartment. Ubiquitinated MET is degraded in a late endosomal or lysosomal compartment in a proteasome-dependent manner. The involvement of proteasome in MET degradation seems to be indirect, through an effect on MET endocytic trafficking (Jeffers et al. 1997, Peschard et al. 2001, Hammond et al. 2001, Petrelli et al. 2002). LRIG1 promotes lysosome-dependent degradation of MET in the absence of HGF-mediated activation (Lee et al. 2014, Oh et al. 2014).
MET-mediated activation of RAS signaling is inhibited by MET receptor binding to MUC20 (Higuchi et al. 2004) or RANBP10 (Wang et al. 2004).
R-HSA-9617324 Negative regulation of NMDA receptor-mediated neuronal transmission The duration of NMDA receptor-mediated neuronal transmission can be limited by binding of the activated calmodulin to the activated NMDA receptor. In addition to shortening the NMDA channel pore open state, calmodulin interferes with ACTN2-mediated anchoring of NMDA receptors to the postsynaptic density (Ehlers et al. 1996, Wyszynski et al. 1997). Protein phosphatases PPM1E and PPM1F dephosphorylate activated calcium/calmodulin-dependent kinases (CaMKs), thus halting CaMK-mediated signaling (Ishida, Okuno et al. 1998, Ishida et al. 1998, Kitani et al. 2003).
R-HSA-9604323 Negative regulation of NOTCH4 signaling NOTCH4 signaling can be negatively regulated at the level of nuclear translocation of the NOTCH4 intracellular domain fragment (NICD4). AKT-mediated phosphorylation of NICD4 promotes binding of NICD4 with 14-3-3-zeta (YWHAZ), leading to retention of NICD4 in the cytosol (Ramakrishnan et al. 2015).
The E3 ubiquitin ligase FBXW7, a component of the SCF ubiquitin ligase complex, binds to and ubiquitinates phosphorylated NICD4, targeting it for proteasome-mediated degradation (Wu et al. 2001). The level of NICD4 is significantly increased in Fbxw7 knockout mouse embryos, which die in utero and have impaired development of the vascular system (Tsunematsu et al. 2004).
Binding of NOTCH4 to ELOC (elongin C) is involved in proteasome-mediated degradation of NOTCH4, but the exact mechanism has not been elucidated (Cummins et al. 2011). MDM2, a TP53-induced ubiquitin ligase, was reported to ubiquitinate NICD4 and target it for degradation in response to TP53 activation (Sun et al. 2011).
NOTCH4 signaling is inhibited by binding of NICD4 to the transforming acidic coiled-coil protein-3, but he mechanism is not known (Bargo et al. 2010).
R-HSA-5368598 Negative regulation of TCF-dependent signaling by DVL-interacting proteins DVL is a central component of WNT signaling that plays roles in both canonical and non-canonical pathways (reviewed in Gao and Chen, 2010). In the canonical pathway, DVL recruits AXIN from the destruction complex upon WNT stimulation, allowing cytosolic beta-catenin to accumulate (reviewed in MacDonald et al, 2009). DVL activity is regulated by phosphorylation as well as by regulated proteasomal or lysosomal degradation (reviewed in Gao and Chen, 2010). In addition, DVL activity can be regulated by interaction with other proteins; both CXXC4 and CCDC88C were identified as negative regulators of WNT signaling that interact directly with DVL, although the role of these proteins in limiting WNT signaling remain to be fully worked out (Hino et al, 2001; Oshita et al, 2003; Ekici et al, 2010; Ishida-Takagishi et al, 2012).
R-HSA-3772470 Negative regulation of TCF-dependent signaling by WNT ligand antagonists Several unrelated families of secreted proteins antagonize WNT signaling. Secreted frizzled-related proteins (sFRPs) have a cysteine rich domain (CRD) that is also found in FZD and ROR receptors, while WNT inhibitory factor (WIF) proteins contain a WIF domain also present in the WNT-receptor RYK. Both these classes of secreted WNT antagonists inhibit signaling by binding to WNTs and preventing their interaction with the FZD receptors. sFRPs may also able to bind the receptors, blocking ligand binding (Bafico et al, 1999; reviewed in Kawano and Kypta, 2003). The interaction of WIF and sFRPs with WNT ligand may also play a role in regulating WNT diffusion and gradient formation (reviewed in Boloventa et al, 2008).
Dickkopf (DKK) and Sclerostin (SOST) family members, in contrast, antagonize WNT signaling by binding to LRP5/6. There are four DKK family members in vertebrates; the closely related DKK1, 2 and 4 proteins have been shown to have roles in WNT signaling, while the more divergent DKK3 appears not to (Glinka et al, 1998; Fedi et al, 1999; Mao et al, 2001; Semenov et al, 2001; reviewed in Niehrs, 2006). Secreted DKK proteins bind to LRP6 in conjunction with the single-pass transmembrane proteins Kremen 1 and 2, and this interaction is thought to disrupt the WNT-induced FZD-LRP5/6 complex. In some cases, DKK2 has also been shown to function as a WNT agonist (reviewed in N (reviewed in Niehrs, 2006).
Like DKK proteins, SOST binds LRP5/6 and disrupts WNT-dependent receptor activation (Semenov et al, 2005).
R-HSA-8866904 Negative regulation of activity of TFAP2 (AP-2) family transcription factors Transcriptional activity of TFAP2 (AP-2) transcription factor family homo- and heterodimers in inhibited by binding of KCTD1 or KCTD15 to the AP-2 transactivation domain (Ding et al. 2009, Zarelli and Dawid 2013). Transcriptional activity of TFAP2A, TFAP2B and TFAP2C is also negatively regulated by SUMOylation mediated by UBE2I (UBC9) (Eloranta and Hurst 2002, Berlato et al. 2011, Impens et al. 2014, Bogachek et al. 2014). Binding of the tumor suppressor WWOX to TFAP2C inhibits TFAP2C translocation to the nucleus (Aqeilan et al. 2004). Transcription of the TFAP2A gene may be inhibited by CREB and E2F1 (Melnikova et al. 2010).
R-HSA-199418 Negative regulation of the PI3K/AKT network The PI3K/AKT network is negatively regulated by phosphatases that dephosphorylate PIP3, thus hampering AKT activation.
R-HSA-936440 Negative regulators of DDX58/IFIH1 signaling As with other cytokine systems, production of type I IFN is a transient process, and can be hazardous to the host if unregulated, resulting in chronic cellular toxicity or inflammatory and autoimmune diseases. RIG-I-mediated production of IFN can, in turn, increase the transcription of RIG-I itself, thus setting into motion an IFN amplification loop, which if left unchecked, could become deleterious to the host. This module mainly focuses on the endogenous negative regulation of the RIG-I-like receptor (RLR) family proteins RIG-I and MDA5.
R-HSA-373753 Nephrin family interactions Nephrin (NPHS1) is a member of the Super-IgG-Molecule family and is most prominently expressed in kidney podocytes. It is a major if not the most important structural component of the slit diaphragm, a modified adherens junction in between these cells. NPHS1 has an extracellular domain that contains eight distal IgG like domains and one proximal fibronectin type III domain, a transmembrane domain and a short intracellular domain. NPHS1 molecules show both homophilic and heterophilic interactions. Among heterophilic interaction partners, slit diaphragm proteins such as Kin of IRRE-like protein 1 (KIRREL, Nephrin-like protein 1, NEPH1), KIRREL3 (NEPH2) and KIRREL2 (NEPH3) were shown to stabilize the slit diaphragm structure. Intracellularly Podocin (NPHS2), CD2 associated protein (CD2AP) and adherins junction associated proteins like IQGAP, MAGI, CASK and spectrins all interact with NPHS1. Hence it seems to play a major role in organizing the molecular structure of the slit diaphragm itself and via its binding partners links it to the actin cytoskeleton. NPHS1 tyrosine phosphorylation by the Src kinase FYN initiates the PI3K-AKT signaling cascade, which seems to promote antiapoptotic signals.
R-HSA-9831926 Nephron development A nephron of an amniote such as mouse or human comprises the glomerulus where small molecules are filtered out of the blood, the proximal tubule and the loop of Henle where small molecules are selectively reabsorbed, the thick ascending limb, the macula densa, the distal convoluted tubule, the connecting tubule, and the collecting duct which drains into the ureter.
Initiation of nephron development occurs at the termini of the branches of the ureteric bud where cells of the ureteric bud interact with cells of the metanephric mesenchyme. Rather than differentiating in place, analysis of cellular migration indicates that progenitors are recruited from the mesenchyme to the developing epithelial elements of the nephron (Lindstrom et al. 2018). The transcriptional program that operates during human nephrogenesis has been mapped in extraordinary detail (Lindstrom et al. 2021). WNT9B secreted by the ureteric bud induces a subset of renal progenitor cells to aggregate and express WNT4, which causes the pre-tubular aggregates to further undergo a mesenchymal to epithelial transition to form renal vesicles (inferred from mouse embryos in Park et al. 2007, reviewed in El-Dahr et al. 2008, Costantini and Kopan 2010, Desgrange and Cereghini 2015). A subset of renal progenitor cells express SIX2 and respond to WNT9B by proliferating to maintain a renewing population of renal progenitors. The reason for the difference in responses may be the local concentration of WNT9B (inferred from mouse embryos in Ramalingam et al. 2018) or the presence of the transcription factor SIX2 (inferred from mouse embryos in Karner et al. 2011).
The renal vesicle becomes polarized early. The distal region contains a gene regulatory network containing LHX1, POU3F3 (BRN1), DLL1, and JAG1. LHX1 is required for proximo-distal differentiation (inferred from mouse embryos in Kobayashi et al. 2005) and POU3F3 participates in elongation of the loop of Henle and formation of the distal convoluted tubule (inferred from mouse embryos in Nakai et al. 2003). The proximal region of the renal vesicle expresses WT1, which directly represses PAX2 to enable formation of podocytes (inferred from mouse homologs in Ryan et al. 1995). The renal vesicle develops into the comma-shaped body in which HNF1B in the distal region activates NOTCH pathway components DLL1, JAG1, and LFNG (inferred from mouse embryos in Heliot et al. 2013). The comma-shaped body in turn develops into the S-shaped body in which HNF1B activates IRX1 and IRX2 in the intermediate region (inferred from mouse embryos in Heliot et al. 2013). Podocytes, the proximal tubule, the intermediate tubule, and the distal tubule then differentiate.
R-HSA-9675108 Nervous system development Neurogenesis is the process by which neural stem cells give rise to neurons, and occurs both during embryonic and perinatal development as well as in specific brain lineages during adult life (reviewed in Gotz and Huttner, 2005; Yao et al, 2016; Kriegstein and Alvarez-Buylla, 2009).
R-HSA-418886 Netrin mediated repulsion signals Unc5 netrin receptors mediate repellent responses to netrin. Four Unc5 members have been found in humans: Unc5A, B, C and D. Different studies have suggested that long-range repulsion to netrin requires the cooperation of Unc5 and DCC, but that Unc5 without DCC is sufficient for short-range repulsion. The binding of netrin to Unc5 triggers the phosphorylation of Unc5 in its ZU-5 domain. Several proteins have been proposed to interact with Unc5 family members in mediating a repellent response, including tyrosine phosphatase Shp2, the F-actin anti-capping protein Mena, and ankyrin.
R-HSA-373752 Netrin-1 signaling Netrins are secreted proteins that play a crucial role in neuronal migration and in axon guidance during the development of the nervous system. To date, several Netrins have been described in mouse and humans: Netrin-1, -3/NTL2, -4/h and G-Netrins. Netrin-1 is the most studied member of the family and has been shown to play a crucial role in neuronal navigation during nervous system development mainly through its interaction with its receptors DCC and UNC5. Members of the Deleted in colorectal cancer (DCC) family- which includes DCC and Neogenin in vertebrates- mediate netrin-induced axon attraction, whereas the C. elegans UNC5 receptor and its four vertebrate homologs Unc5a-Unc5d mediate repulsion.
R-HSA-6794361 Neurexins and neuroligins Neurexins (NRXNs) and neuroligins (NLGNs) are best characterized synaptic cell-adhesion molecules. They are part of excitatory glutamatergic and inhibitory GABAergic synapses in mammalian brain, mediate trans-synaptic signaling, and shape neural network properties by specifying synaptic functions. As cell-adhesion molecules, NRXNs and NLGNs probably function by binding to each other and by interacting with intracellular PDZ-domain proteins, but the precise mechanisms involved and their relation to synaptic transmission remain unclear. The binding of NRXNs and NLGNs to their partners, helps to align the pre-synaptic release machinery and post-synaptic receptors. The importance of neurexins and neuroligins for synaptic function is evident from the dramatic deficits in synaptic transmission in mice lacking Nrxns or Nlgns. In humans, alterations in NRXNs or NLGNs genes are implicated in autism and other cognitive diseases, connecting synaptic cell adhesion to cognition and its disorders (Sudhof 2008, Craig et al. 2006, Craig & Kang 2007).
R-HSA-8863678 Neurodegenerative Diseases Neurodegenerative diseases manifest as the progressive dysfunction and loss of neurons, which is frequently accompanied by formation of misfolded protein deposits in the brain. Classification of neurodegenerative diseases is based on clinical symptoms, which depend on the anatomical region affected by neuronal dysfunction, the identity of misfolded proteins and cellular and subcellular pathology.
In Alzheimer’s disease (AD), beta-amyloid protein (APP) deposits form in the extracellular space, where they can make plaques, while abnormally phosphorylated tau protein (MAPT) accumulates in neuronal cells.
Beside AD, neuronal and/or glial inclusions of hyperphosphorylated tau are also found in Pick disease (PiD), neurofibrillary tangle-dementia (NFT), primary age-related tauopathy (PART), progressive supranuclear palsy (PSP), corticobasal degeneration (CBD), argyrophilic grain disease (AGD) and globular glial tauopathies (GGT).
In prion disease, such as Creutzfeldt-Jakob disease, deposits of PrP protein are formed mostly in the extracellular and presynaptic space. PrP deposits in neuronal cell bodies are mainly confined to endosomes and lysosomes, which is attributed to neuronal uptake of pathological proteins and intercellular prion spreading.
In Parkinson disease (PD) and dementia with Lewy bodies (DLB), deposits of alpha-synuclein (SNCA) are formed in the cytoplasm of neuronal cell bodies and neurites. In multiple system atrophy (MSA), deposits of alpha-synuclein form in the cytoplasm of glial cells (Papp-Lantos bodies).
Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are characterized by ubiquitin-positive cytoplasmic inclusions of TAR DNA-binding protein 43 (TARDBP, commonly known as TDP-43), a protein that normally localizes to the nucleus. Pathological TDP-43 inclusions have been associated with the TDP-43 gene mutations, as well as mutations in several other genes, including C9orf72, GRN, VCP, SQSTM1, DCTN1 and OPTN. TDP-43 inclusions have also been reported in AD, DLB, hippocampal sclerosis (HS) and chronic traumatic encephalopathy.
FUS protein-positive inclusion bodies are found in familial ALS, caused by mutations in the FUS gene, as well as in a small subgroup of FTLD-related diseases. FUS-positive inclusions may be accompanied by FET protein-positive inclusions.
For a detailed review of molecular pathology of neurodegenerative diseases, please refer to Kovacs 2016.
Within this broad domain, the process by which APP-triggered deregulation of CDK5 (cyclin-dependent kinase 5) triggers multiple neurodegenerative pathways associated with Alzheimer's disease has been annotated.
R-HSA-447043 Neurofascin interactions Neurofascin is an L1 family immunoglobulin cell adhesion molecule involved in axon subcellular targeting and synapse formation during neural development. There are a range of different isoforms identified in Neurofascin of which two of them are well studied the 186kDa commonly referred to as neuronal form and is present in node of Ranvier neurons and the 155kDa form known as a glial form present in schwann cells.
Neurofascin colocalizes with NrCAM and ankyrinG at the nodes of Ranvier. Neurofascin participates in transheterophilic adhesion with NrCAM and stimulates neurite outgrowth in chicken tectal neurons. The last few amino acids of neurofascin form the PDZ class I binding motif (SLA) and through these last few amino acids it associates with syntenin-1.
R-HSA-112316 Neuronal System The human brain contains at least 100 billion neurons, each with the ability to influence many other cells. Clearly, highly sophisticated and efficient mechanisms are needed to enable communication among this astronomical number of elements. This communication occurs across synapses, the functional connection between neurons. Synapses can be divided into two general classes: electrical synapses and chemical synapses. Electrical synapses permit direct, passive flow of electrical current from one neuron to another. The current flows through gap junctions, specialized membrane channels that connect the two cells. Chemical synapses enable cell-to-cell communication using neurotransmitter release. Neurotransmitters are chemical agents released by presynaptic neurons that trigger a secondary current flow in postsynaptic neurons by activating specific receptor molecules. Neurotransmitter secretion is triggered by the influx of Ca2+ through voltage-gated channels, which gives rise to a transient increase in Ca2+ concentration within the presynaptic terminal. The rise in Ca2+ concentration causes synaptic vesicles (the presynaptic organelles that store neurotransmitters) to fuse with the presynaptic plasma membrane and release their contents into the space between the pre- and postsynaptic cells.
R-HSA-194306 Neurophilin interactions with VEGF and VEGFR The plasma membrane-associated Neuropilin receptors NRP-1 and -2 bind some of the VEGF proteins and associate with VEGF receptor proteins. NRP-1 binds VEGF-A165, -B, and PLGF-2; NRP-2 also binds VEGF-A165 and PLGF-2, as well as VEGF-A145 and -C. The Neurolipin receptors appear to act as cofactors for the VEGF receptors, increasing their affinities for specific VEGF ligands, although the importance of this function in vivo remains unclear (Neufeld et al. 2002).
R-HSA-168799 Neurotoxicity of clostridium toxins Clostridial neurotoxins, when taken up by human neurons, block synaptic transmission by cleaving proteins required for the fusion of synaptic vesicles with the plasma membrane. They are remarkably efficient so that very small doses cause paralysis of an affected person (Lalli et al. 2003; Turton et al. 2002). All characterized clostridial neurotoxins are synthesized as products of chromosomal, plasmid or prophage-borne bacterial genes. The nascent toxin may be cleaved into light (LC) and heavy (HC) chain moieties that remain attached by noncovalent interactions and a disulfide bond (Turton et al. 2002).
Strains of Clostridium botulinum produce seven serologically distinct toxins, BoNT/A, B, C, D, E, F, and G. An eighth toxin, BoNT/H has recently been identified (Barash & Arnon 2014) but its molecular properties have not yet been described. Human poisoning most commonly result from ingestion of toxin contaminated food. More rarely, it is due to wound infection or clostridial colonization of the gut of an infant whose own gut flora have not yet developed or of an older individual whose flora have been suppressed. While all seven characterized toxins can cleave human target proteins, three, BoNT/A, B, and E, are most commonly associated with human disease (Hatheway 1995; Sakaguchi 1982). BoNT/F is also able to cause human botulism.
Once ingested, the botulinum toxin must be taken up from the gut lumen into the circulation, a process mediated by four accessory proteins. These proteins form a complex that mediates transcytosis of the toxin molecule across the gut epithelium, allowing its entry into the circulation. The accessory proteins produced by different C. botulinum strains differ in their affinities for polarized epithelia of different species (e.g., human versus canine), and may thus be a key factor in human susceptibility to the toxins of strains A, B, and E and resistance to the others (Simpson 2004).
Clostridium tetani produces TeNT toxin. Human poisoning is the result of toxin secretion by bacteria growing in an infected wound and the toxin is released directly into the circulation.
Circulating clostridial toxins are taken up by neurons at neuromuscular junctions. They bind to specific gangliosides (BoNT/C, TeNT) or to both gangliosides and synaptic vesicle proteins (BoNT/A, B, D G) exposed on the neuronal plasma membrane during vesicle exocytosis (Montal 2010). All seven characterized forms of BoNT are thought to be taken up into synaptic vesicles as these re-form at the neuromuscular junction. These vesicles remain close to the site of uptake and are rapidly re-loaded with neurotransmitter and acidified (Sudhoff 2004). TeNT, in contrast, is taken up into clathrin coated vesicles that reach the neuron cell body by retrograde transport and then possibly other neurons before undergoing acidification. Vesicle acidification causes a conformational change in the toxin, allowing its HC part to function as a channel through which its LC part is extruded into the neuronal cytosol. The HC - LC disulfide bond is cleaved and the cytosolic LC functions as a zinc metalloprotease to cleave specific bonds in proteins on the cytosolic faces of synaptic vesicles and plasma membranes that normally mediate exocytosis (Lalli et al. 2003; Montal 2010).
R-HSA-112311 Neurotransmitter clearance Neurotransmitter released in the synaptic cleft binds to specific receptors on the post-synaptic cell and the excess of the neurotransmitter is cleared to prevent over activation of the post-synaptic cell. The neurotransmitter is cleared by either re-uptake by the pre-synaptic neuron, diffusion in the perisynaptic area, uptake by astrocytes surrounding the synaptic cleft or enzymatic degradation of the neurotransmitter.
R-HSA-112314 Neurotransmitter receptors and postsynaptic signal transmission The neurotransmitter in the synaptic cleft released by the pre-synaptic neuron binds specific receptors located on the post-synaptic terminal. These receptors are either ion channels or G protein coupled receptors that function to transmit the signals from the post-synaptic membrane to the cell body.
R-HSA-112310 Neurotransmitter release cycle Neurotransmitter is stored in the synaptic vesicle in the pre-synaptic terminal prior to its release in the synaptic cleft upon depolarization of the pre-synaptic membrane. The release of the neurotransmitter is a multi-step process that is controlled by electrical signals passing through the axons in form of action potential. Neurotransmitters include glutamate, acetylcholine, nor-epinephrine, dopamine and seratonin. Each of the neurotransmitter cycle is independently described.
R-HSA-112313 Neurotransmitter uptake and metabolism In glial cells Neuotransmitter uptake by astrocytes is mediated by a specific transporter located on the astrocytic membrane. The imported neurotransmitter is metabolized and transported back to the neuron.
R-HSA-6798695 Neutrophil degranulation Neutrophils are the most abundant leukocytes (white blood cells), indispensable in defending the body against invading microorganisms. In response to infection, neutrophils leave the circulation and migrate towards the inflammatory focus. They contain several subsets of granules that are mobilized to fuse with the cell membrane or phagosomal membrane, resulting in the exocytosis or exposure of membrane proteins. Traditionally, neutrophil granule constituents are described as antimicrobial or proteolytic, but granules also introduce membrane proteins to the cell surface, changing how the neutrophil responds to its environment (Borregaard et al. 2007). Primed neutrophils actively secrete cytokines and other inflammatory mediators and can present antigens via MHC II, stimulating T-cells (Wright et al. 2010).
Granules form during neutrophil differentiation. Granule subtypes can be distinguished by their content but overlap in structure and composition. The differences are believed to be a consequence of changing protein expression and differential timing of granule formation during the terminal processes of neutrophil differentiation, rather than sorting (Le Cabec et al. 1996).
The classical granule subsets are Azurophil or primary granules (AG), secondary granules (SG) and gelatinase granules (GG). Neutrophils also contain exocytosable storage cell organelles, storage vesicles (SV), formed by endocytosis they contain many cell-surface markers and extracellular, plasma proteins (Borregaard et al. 1992). Ficolin-1-rich granules (FG) are like GGs highly exocytosable but gelatinase-poor (Rorvig et al. 2009).
R-HSA-197264 Nicotinamide salvaging Nicotinamide (NAM) levels are modulated by the action of three enzymes involved in nicotinamide salvaging. They are nicotinamide deaminase, nicotinamide phosphoribosyltransferase and nicotinate phosphoribosyltransferase. These enzymes are poorly characterized in humans, depsite their importance in NAM utilization (Magni et al. 2004). Although not a salvage reaction, NAM levels can also be regulated by nicotinamide N-methyltransferase (NNMT), a potential regulator of diet-induced obesity (Kraus et al. 2014).
R-HSA-196807 Nicotinate metabolism Nicotinate (niacin) and nicotinamide are precursors of the coenzymes nicotinamide-adenine dinucleotide (NAD+) and nicotinamide-adenine dinucleotide phosphate (NADP+). When NAD+ and NADP+ are interchanged in a reaction with their reduced forms, NADH and NADPH respectively, they are important cofactors in several hundred redox reactions. Nicotinate is synthesized from 2-amino-3-carboxymuconate semialdehyde, an intermediate in the catabolism of the essential amino acid tryptophan (Magni et al. 2004).
R-HSA-9669926 Nilotinib-resistant KIT mutants Nilotinib is a type II tyrosine kinase inhibitor currently in clinical trials for treatment of KIT-mutant cancers, and shows variable effectiveness against mutations in exon 11, 13, 17 and 18. Nilotinib is ineffective against the gatekeeper mutation T670I (Kissova et al, 2016; Guo et al, 2007; Roberts et al, 2007; Serrano et al, 2019).
R-HSA-392154 Nitric oxide stimulates guanylate cyclase Nitric Oxide (NO) inhibits smooth muscle cell proliferation and migration, oxidation of low-density lipoproteins, and platelet aggregation and adhesion. It can stimulate vasodilatation of the endothelium, disaggregation of preformed platelet aggregates and inhibits activated platelet recruitment to the aggregate. NO is synthesized from L-arginine by a family of isoformic enzymes known as nitric oxide synthase (NOS). Three isoforms, namely endothelial, neuronal, and inducible NOS (eNOS, nNOS, and iNOS, respectively), have been identified. The eNOS isoform is found in the endothelium and platelets. NO regulation of cyclic guanosine-3,5-monophosphate (cGMP), via activation of soluble guanylate cyclase, is the principal mechanism of negative control over platelet activity. Defects in this control mechanism have been associated with platelet hyperaggregability and associated thrombosis.
R-HSA-427413 NoRC negatively regulates rRNA expression The Nucleolar Remodeling Complex (NoRC) comprising TIP5 (BAZ2A) and the chromatin remodeller SNF2H (SMARCA5) silences rRNA gene (reviewed in Santoro and Grummt 2001, Grummt 2007, Preuss and Pikaard 2007, Birch and Zommerdijk 2008, McStay and Grummt 2008, Grummt and Langst 2013). The TAM domain of TIP5 (BAZ2A) binds promoter-associated RNA (pRNA) transcribed from the intergenic spacer region of rDNA. The pRNA bound by TIP5 is required to direct the complex to the main promoter of the rRNA gene possibly by triple helix formation between pRNA and the rDNA. The PHD domain of TIP5 binds histone H4 acetylated at lysine-16. Transcription Termination Factor-I (TTF-I) binds to a promoter-proximal terminator (T0 site) in the rDNA and interacts with the TIP5 subunit of NoRC. NoRC also interacts with the SIN3-HDAC complex, HDAC1, HDAC2, DNMT1, and DNMT3B. DNMT3B interacts with a triple helix formed by pRNA and the rDNA. HDAC1, DNMT1, and DNMT3B have been shown to be required for proper DNA methylation of silenced rRNA gene copies, although the catalytic activity of DNMT3B was not required.
R-HSA-3000171 Non-integrin membrane-ECM interactions Several non-integrin membrane proteins interact with extracellular matrix proteins. Transmembrane proteoglycans may associate with integrins and growth factor receptors to influence their function, or they can signal independently, often influencing the actin cytoskeleton.
R-HSA-9017802 Noncanonical activation of NOTCH3 Besides DLL/JAG ligands, NOTCH3 signaling can also be activated by binding of NOTCH3 to YBX1 (YB 1) (Rauen et al. 2009). YBX1, a protein involved in mRNA processing, is secreted by mesangial cells and monocytes during inflammation and acts as an extracellular mitogen (Frye et al. 2009). YBX1 triggers the gamma secretase complex mediated cleavage of NOTCH3, resulting in release of NOTCH3 intracellular domain (NICD3) and activation of NOTCH3 target genes (Rauen et al. 2009).
R-HSA-5693571 Nonhomologous End-Joining (NHEJ) The nonhomologous end joining (NHEJ) pathway is initiated in response to the formation of DNA double-strand breaks (DSBs) induced by DNA-damaging agents, such as ionizing radiation. DNA DSBs are recognized by the MRN complex (MRE11A:RAD50:NBN), leading to ATM activation and ATM-dependent recruitment of a number of DNA damage checkpoint and repair proteins to DNA DSB sites (Lee and Paull 2005). The ATM phosphorylated MRN complex, MDC1 and H2AFX-containing nucleosomes (gamma-H2AX) serve as scaffolds for the formation of nuclear foci known as ionizing radiation induced foci (IRIF) (Gatei et al. 2000, Paull et al. 2000, Stewart et al. 2003, Stucki et al. 2005). Ultimately, both BRCA1:BARD1 heterodimers and TP53BP1 (53BP1) are recruited to IRIF (Wang et al. 2007, Pei et al. 2011, Mallette et al. 2012), which is necessary for ATM-mediated CHEK2 activation (Wang et al. 2002, Wilson et al. 2008). In G1 cells, TP53BP1 promotes NHEJ by recruiting RIF1 and PAX1IP, which displaces BRCA1:BARD1 and associated proteins from the DNA DSB site and prevents resection of DNA DSBs needed for homologous recombination repair (HRR) (Escribano-Diaz et al. 2013, Zimmermann et al. 2013, Callen et al. 2013). TP53BP1 also plays an important role in ATM-mediated phosphorylation of DCLRE1C (ARTEMIS) (Riballo et al. 2004, Wang et al. 2014). Ku70:Ku80 heterodimer (also known as the Ku complex or XRCC5:XRCC6) binds DNA DSB ends, competing away the MRN complex and preventing MRN-mediated resection of DNA DSB ends (Walker et al. 2001, Sun et al. 2012). The catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs, PRKDC) is then recruited to DNA-bound Ku to form the DNA-PK holoenzyme. Two DNA-PK complexes, one at each side of the break, bring DNA DSB ends together, joining them in a synaptic complex (Gottlieb 1993, Yoo and Dynan 2000). DNA-PK complex recruits DCLRE1C (ARTEMIS) to DNA DSB ends (Ma et al. 2002). PRKDC-mediated phosphorylation of DCLRE1C, as well as PRKDC autophosphorylation, enables DCLRE1C to trim 3'- and 5'-overhangs at DNA DSBs, preparing them for ligation (Ma et al. 2002, Ma et al. 2005, Niewolik et al. 2006). The binding of inositol phosphate may additionally stimulate the catalytic activity of PRKDC (Hanakahi et al. 2000). Other factors, such as polynucleotide kinase (PNK), TDP1 or TDP2 may remove unligatable damaged nucleotides from 5'- and 3'-ends of the DSB, converting them to ligatable substrates (Inamdar et al. 2002, Gomez-Herreros et al. 2013). DNA ligase 4 (LIG4) in complex with XRCC4 (XRCC4:LIG4) is recruited to ligatable DNA DSB ends together with the XLF (NHEJ1) homodimer and DNA polymerases mu (POLM) and/or lambda (POLL) (McElhinny et al. 2000, Hsu et al. 2002, Malu et al. 2002, Ahnesorg et al. 2006, Mahajan et al. 2002, Lee et al. 2004, Fan and Wu 2004). After POLL and/or POLM fill 1- or 2-nucleotide long single strand gaps at aligned DNA DSB ends, XRCC4:LIG4 performs the ligation of broken DNA strands, thus completing NHEJ. The presence of NHEJ1 homodimer facilitates the ligation step, especially at mismatched DSB ends (Tsai et al. 2007). Depending on other types of DNA damage present at DNA DSBs, NHEJ can result in error-free products, produce dsDNA with microdeletions and/or mismatched bases, or result in translocations (reviewed by Povrik et al. 2012).
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) During normal translation termination eRF3 associates with the ribosome and then interacts with PABP bound to the polyadenylate tail of the mRNA to release the ribosome and allow a new round of translation to commence. Nonsense-mediated decay (NMD) is triggered if eRF3 at the ribosome interacts with UPF1, which may compete with PABP (reviewed in Isken and Maquat 2007, Chang et al. 2007, Behm-Ansmant et al. 2007, Rebbapragada and Lykke-Andersen 2009, Bhuvanagiri et al. 2010, Nicholson et al. 2010, Durand and Lykke-Andersen 2011). An exon junction located 50-55 nt downstream of a termination codon is observed to enhance NMD.
Exon-junction complexes (EJCs) are deposited on the mRNA during splicing in the nucleus, remain on mRNAs after transport to the cytosol, and are dislodged by the ribosome as it progresses along the mRNA during the pioneer round of translation (Gehring et al. 2009). EJCs contain the core factors eIF4A-III, Magoh-Y14, and CASC3 as well as the peripheral factors RNPS1, UPF2, and UPF3. UPF2 and UPF3 recruit UPF1 to eRF3 at the terminating ribosome. Thus an EJC downstream of a termination codon will not have been dislodged during translation and will recruit UPF1, triggering NMD.
UPF1 is believed to form a complex containing SMG1, SMG8, and SMG9. In the key regulatory step of NMD SMG1 phosphorylates UPF1. The phosphorylated UPF1 then recruits either SMG6 or SMG5 and SMG7. SMG6 is itself an endoribonuclease that cleaves the mRNA. SMG5 and SMG7 do not have endoribonuclease activty, but are thought to recruit ribonucleases. Nonsense-mediated decay has been observed to involve deadenlyation, decapping, and both 5' to 3' and 3' to 5' exonuclease activities, but the exact degradative pathways taken by a given mRNA are not yet known.
UPF1 also plays roles in Staufen-mediated decay, histone mRNA decay, telomere maintenance, genome integrity, and may play a role in normal termination of translation.
R-HSA-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) Nonsense-mediated decay has been observed with mRNAs that do not have an exon junction complex (EJC) downstream of the termination codon (reviewed in Isken and Maquat 2007, Chang et al. 2007, Behm-Ansmant et al. 2007, Rebbapragada and Lykke-Andersen 2009, Nicholson et al. 2010). In these cases the trigger is unknown but a correlation with the length of the 3' UTR has sometimes been seen. The current model posits a competition between PABP and UPF1 for access to eRF3 at the terminating ribosome (Ivanov et al. 2008, Singh et al. 2008, reviewed in Bhuvanagiri et al. 2010). Abnormally long 3' UTRs may prevent PABP from efficiently interacting with eRF3 and allow UPF1 to bind eRF3 instead. Long UTRs with hairpin loops may bring PABP closer to eRF3 and help evade NMD (Eberle et al. 2008).
The pathway of degradation taken during EJC-independent NMD has not been elucidated. It is thought that phosphorylation of UPF1 by SMG1 and recruitment of SMG6 or SMG5 and SMG7 are involved, as with EJC-enhanced NMD, but this has not yet been shown.
R-HSA-927802 Nonsense-Mediated Decay (NMD) The Nonsense-Mediated Decay (NMD) pathway activates the destruction of mRNAs containing premature termination codons (PTCs) (reviewed in Isken and Maquat 2007, Chang et al. 2007, Behm-Ansmant et al. 2007, Neu-Yilik and Kulozik 2008, Rebbapragada and Lykke-Andersen 2009, Bhuvanagiri et al. 2010, Nicholson et al. 2010, Durand and Lykke-Andersen 2011). In mammalian cells a termination codon can be recognized as premature if it precedes an exon-exon junction by at least 50-55 nucleotides or if it is followed by an abnormal 3' untranslated region (UTR). While length of the UTR may play a part, the qualifications for being "abnormal" have not been fully elucidated. Also, some termination codons preceding exon junctions are not degraded by NMD so the criteria for triggering NMD are not yet fully known (reviewed in Rebbapragada and Lykke-Andersen 2009). While about 30% of disease-associated mutations in humans activate NMD, about 10% of normal human transcripts are also degraded by NMD (reviewed in Stalder and Muhlemann 2008, Neu-Yilik and Kulozik 2008, Bhuvanagiri et al. 2010, Nicholson et al. 2010). Thus NMD is a normal physiological process controlling mRNA stability in unmutated cells.
Exon junction complexes (EJCs) are deposited on an mRNA during splicing in the nucleus and are displaced by ribosomes during the first round of translation. When a ribosome terminates translation the A site encounters the termination codon and the eRF1 factor enters the empty A site and recruits eRF3. Normally, eRF1 cleaves the translated polypeptide from the tRNA in the P site and eRF3 interacts with Polyadenylate-binding protein (PABP) bound to the polyadenylated tail of the mRNA.
During activation of NMD eRF3 interacts with UPF1 which is contained in a complex with SMG1, SMG8, and SMG9. NMD can arbitrarily be divided into EJC-enhanced and EJC-independent pathways. In EJC-enhanced NMD, an exon junction is located downstream of the PTC and the EJC remains on the mRNA after termination of the pioneer round of translation. The core EJC is associated with UPF2 and UPF3, which interact with UPF1 and stimulate NMD. Once bound near the PTC, UPF1 is phosphorylated by SMG1. The phosphorylation is the rate-limiting step in NMD and causes UPF1 to recruit either SMG6, which is an endoribonuclease, or SMG5 and SMG7, which recruit ribonucleases. SMG6 and SMG5:SMG7 recruit phosphatase PP2A to dephosphorylate UPF1 and allow further rounds of degradation. How EJC-independent NMD is activated remains enigmatic but may involve competition between PABP and UPF1 for eRF3.
R-HSA-181430 Norepinephrine Neurotransmitter Release Cycle Noradrenalin release cycle consists of reacidification of the empty clathrin sculpted monoamine transport vesicle, loading of dopamine into reacidified clathrin coated monamine transport vesicle, conversion of dopamine into Noradrenalin, docking and priming of the noradrenalin synaptic veiscle and then release of noradrenalin synaptic vesicle. In the peripheral nervous system in the peripheral nervous system noradrenalin is stored in large and small dense vesicles and is realesed from large vesicles.
R-HSA-350054 Notch-HLH transcription pathway THE NOTCH-HLH TRANSCRIPTION PATHWAY:
Notch signaling was first identified in Drosophila, where it has been studied in detail at the genetic, molecular, biochemical and cellular levels (reviewed in Justice, 2002; Bray, 2006; Schweisguth, 2004; Louvri, 2006). In Drosophila, Notch signaling to the nucleus is thought always to be mediated by one specific DNA binding transcription factor, Suppressor of Hairless. In mammals, the homologous genes are called CBF1 (or RBPJkappa), while in worms they are called Lag-1, so that the acronym "CSL" has been given to this conserved transcription factor family. There are at least two human CSL homologues, which are now named RBPJ and RBPJL.
CSL is an example of a bifunctional DNA-binding transcription factor that mediates repression of specific target genes in one context, but activation of the same targets in another context. This bifunctionality is mediated by the association of specific Co-Repressor complexes vs. specific Co-Activator complexes in different contexts, namely in the absence or presence of Notch signaling.
In Drosophila, Su(H) represses target gene transcription in the absence of Notch signaling, but activates target genes during Notch signaling. At least some of the mammalian CSL homologues are believed also to be bifunctional, and to mediate target gene repression in the absence of Notch signaling, and activation in the presence of Notch signaling.
Notch Co-Activator and Co-Repressor complexes: This repression is mediated by at least one specific co-repressor complexes (Co-R) bound to CSL in the absence of Notch signaling. In Drosophila, this co-repressor complex consists of at least three distinct co-repressor proteins: Hairless, Groucho, and dCtBP (Drosophila C-terminal Binding Protein). Hairless has been show to bind directly to Su(H), and Groucho and dCtBP have been shown to bind directly to Hairless (Barolo, 2002). All three of the co-repressor proteins have been shown to be necessary for proper gene regulation during Notch signaling in vivo (Nagel, 2005).
In mammals, the same general pathway and mechanisms are observed, where CSL proteins are bifunctional DNA binding transcription factors (TFs), that bind to Co-Repressor complexes to mediate repression in the absence of Notch signaling, and bind to Co-Activator complexes to mediate activation in the presence of Notch signaling. However, in mammals, there may be multiple co-repressor complexes, rather than the single Hairless co-repressor complex that has been observed in Drosophila.
During Notch signaling in all systems, the Notch transmembrane receptor is cleaved and the Notch intracellular domain (NICD) translocates to the nucleus, where it there functions as a specific transcription co-activator for CSL proteins. In the nucleus, NICD replaces the Co-R complex bound to CSL, thus resulting in de-repression of Notch target genes in the nucleus. Once bound to CSL, NICD and CSL proteins recruit an additional co-activator protein, Mastermind, to form a CSL-NICD-Mam ternary co-activator (Co-A) complex. This Co-A complex was initially thought to be sufficient to mediate activation of at least some Notch target genes. However, there now is evidence that still other co-activators and additional DNA-binding transcription factors are required in at least some contexts (reviewed in Barolo, 2002).
Mammalian CSL Corepressor Complexes: In the absence of activated Notch signaling, DNA-bound CSL proteins recruit a corepressor complex to maintain target genes in the repressed state until Notch is specifically activated. The mammalian corepressor complexes include NCOR complexes, but may also include additional corepressor proteins, such as SHARP (reviewed in Mumm, 2000 and Kovall, 2007). The exact composition of the CSL NCOR complex is not known, but in other pathways the "core" NCOR corepressor complex includes at least one NCOR protein (NCOR1, NCOR2, CIR), one Histone Deacetylase protein (HDAC1, HDAC2, HDAC3, etc), and one TBL1 protein (TBL1X, TBL1XR1) (reviewed in Rosenfeld, 2006). In some contexts, the core NCOR corepressor complex may also recruit additional corepressor proteins or complexes, such as the SIN3 complex, which consists of SIN3 (SIN3A, SIN3B), and SAP30, or other SIN3-associated proteins. An additional CSL - NCOR binding corepressor, SHARP, may also contribute to the CSL corepressor complex in some contexts (Oswald, 2002). The CSL corepressor complex also includes a bifunctional cofactor, SKIP, that is present in both CSL corepressor complexes and CSL coactivator complexes, and may function in the binding of NICD and displacement of the corepressor complex during activated Notch signaling (Zhou, 2000).
Mammalian CSL Coactivator Complexes: Upon activation of Notch signaling, cleavage of the transmembrane Notch receptor releases the Notch Intracellular Domain (NICD), which translocates to the nucleus, where it binds to CSL and displaces the corepressor complex from CSL (reviewed in Mumm, 2000 and Kovall, 2007). The resulting CSL-NICD "binary complex" then recruits an additional coactivator, Mastermind (Mam), to form a ternary complex. The ternary complex then recruits additional, more general coactivators, such as CREB Binding Protein (CBP), or the related p300 coactivator, and a number of Histone Acetytransferase (HAT) proteins, including GCN5 and PCAF (Fryer, 2002). There is evidence that Mam also can subsequently recruit specific kinases that phosphorylate NICD, to downregulate its function and turn off Notch signaling (Fryer, 2004).
Combinatorial Complexity in Transcription Cofactor Complexes: HDAC9 has at least 7 splice isoforms, with some having distinct interaction and functional properties. Isoforms 6 and 7 interact with NCOR1. Isoforms 1 and 4 interact with MEF2 (Sparrow, 1999), which is a specific DNA-binding cofactor for a subset of HLH proteins. Isoform 3 interacts with both NCOR1 and MEF2. Although many HDACs only have one or two isoforms, this complexity for HDAC9 illustrates the level of transcript complexity and functional specificity that such "general" transcriptional cofactors can have.
R-HSA-447038 NrCAM interactions The NgCAM-related cell adhesion molecule (NrCAM) is member of the L1 family involved in the eye development and node of Ranvier. Like all the other members of L1 family NrCAM also has the ability to bind to ankyrins. The last C-terminal amino acids of NrCAM form a PDZ-binding motif and can interact with SAP (synapse-associated protein) 102 and SAP97. Member of the GPI-anchored TAG-1/axonin-1 have been shown to interact with NrCAM. NrCAM also binds the Sema3B receptor NP-2 to mediate repulsive axon guidance.
R-HSA-2995410 Nuclear Envelope (NE) Reassembly Reassembly of the nuclear envelope (NE) around separated sister chromatids begins in late anaphase and is completed in telophase (reviewed by Wandke and Kutay 2013). Characteristic proteins of the inner nuclear membrane and nuclear lamina accumulate at the reforming NE (reviewed by Wandke and Kutay 2013). Concurrently, nuclear pore complexes (NPCs) assemble and insert into the reforming NE, and the NE becomes sealed to reestablish the nucleocytoplasmic diffusion barrier (reviewed by Otsuka and Ellenberg 2018).
R-HSA-2980766 Nuclear Envelope Breakdown The nuclear envelope breakdown (NEBD) happens in late prophase of mitosis and involves disassembly of the nuclear pore complex, depolymerization of the nuclear lamina, and clearance of nuclear envelope from chromatin. NEBD allows mitotic spindle microtubules to access condensed chromosomes at kinetochores and enables nuclear division and segregation of genetic material to two daughter cells. For a recent review, please refer to Guttinger et al. 2009.
In mitotic prophase, chromatin detaches from the nuclear envelope, and this contributes to the nuclear envelope breakdown. VRK1 (and possibly VRK2) mediated phosphorylation of BANF1 (BAF), a protein that simultaneously interacts with DNA, LEM-domain inner nuclear membrane proteins, and lamins (Zheng et al. 2000, Shumaker et al. 2001, Haraguchi et al. 2001, Mansharamani and Wilson 2005, Brachner et al. 2005) is considered to be one of the key steps in the detachment of the nuclear envelope from chromatin (Bengtsson and Wilson 2006, Nichols et al. 2006, Gorjanacz et al. 2007).
R-HSA-198725 Nuclear Events (kinase and transcription factor activation) An important function of the kinase cascade triggered by neurotrophins is to induce the phosphorylation and activation of transcription factors in the nucleus to initiate new programs of gene expression. Transcription factors directly activated by neurotrophin signalling are responsible for induction of immediate-early genes, many of which are transcription factors. These in turn are involved in the induction of delayed-early genes.
R-HSA-3301854 Nuclear Pore Complex (NPC) Disassembly Nuclear envelope breakdown in mitosis involves permeabilization of the nuclear envelope through disassembly of the nuclear pore complex (NPC) (reviewed by Guttinger et al. 2009). Nucleoporin NUP98, located at both the cytoplasmic and the nucleoplasmic side of the NPC (Griffis et al. 2003), and involved in the formation of the transport barrier through its FG (phenylalanine glycine) repeats that protrude into the central cavity of the NPC (Hulsmann et al. 2012), is probably the first nucleoporin that dissociates from the NPC at the start of mitotic NPC disassembly (Dultz et al. 2008). NUP98 dissociation is triggered by phosphorylation. Phosphorylation of NUP98 by CDK1 and NIMA family kinases NEK6 and/or NEK7 is needed for NUP98 dissociation from the NPC (Laurell et al. 2011). While the phosphorylation of NUP98 by CDK1 and NEK6/7 is likely to occur simultaneously, CDK1 and NEK6/7-mediated phosphorylations are shown as separate events, for clarity purposes.
R-HSA-383280 Nuclear Receptor transcription pathway A classic example of bifunctional transcription factors is the family of Nuclear Receptor (NR) proteins. These are DNA-binding transcription factors that bind certain hormones, vitamins, and other small, diffusible signaling molecules. The non-liganded NRs recruit specific corepressor complexes of the NCOR/SMRT type, to mediate transcriptional repression of the target genes to which they are bound. During signaling, ligand binding to a specific domain the NR proteins induces a conformational change that results in the exchange of the associated CoR complex, and its replacement by a specific coactivator complex of the TRAP / DRIP / Mediator type. These coactivator complexes typically nucleate around a MED1 coactivator protein that is directly bound to the NR transcription factor.
A general feature of the 49 human NR proteins is that in the unliganded state, they each bind directly to an NCOR corepressor protein, either NCOR1 or NCOR2 (NCOR2 was previously named "SMRT"). This NCOR protein nucleates the assembly of additional, specific corepressor proteins, depending on the cell and DNA context. The NR-NCOR interaction is mediated by a specific protein interaction domain (PID) present in the NRs that binds to specific cognate PID(s) present in the NCOR proteins. Thus, the human NRs each take part in an NR-NCOR binding reaction in the absence of binding by their ligand.
A second general feature of the NR proteins is that they each contain an additional, but different PID that mediates specific binding interactions with MED1 proteins. In the ligand-bound state, NRs each take part in an NR-MED1 binding reaction to form an NR-MED1 complex. The bound MED1 then functions to nucleate the assembly of additional specific coactivator proteins, depending on the cell and DNA context, such as what specific target gene promoter they are bound to, and in what cell type.
The formation of specific MED1-containing coactivator complexes on specific NR proteins has been well-characterized for a number of the human NR proteins (see Table 1 in (Bourbon, 2004)). For example, binding of thyroid hormone (TH) to the human TH Receptor (THRA or THRB) was found to result in the recruitment of a specific complex of Thyroid Receptor Associated Proteins - the TRAP coactivator complex - of which the TRAP220 subunit was later identified to be the Mediator 1 (MED1) homologue.
Similarly, binding of Vitamin D to the human Vitamin D3 Receptor was found to result in the recruitment of a specific complex of D Receptor Interacting Proteins - the DRIP coactivator complex, of which the DRIP205 subunit was later identified to be human MED1.
R-HSA-9759194 Nuclear events mediated by NFE2L2 In response to chemical and other stressors, the constitutive degradation of NFE2L2 by the KEAP1:CUL3:26S proteasome system is disrupted, allowing NFE2L2 to accumulate. Stabilized NFE2L2 translocates to the nucleus where it binds to antioxidant response elements (AREs) in the promoters and enhancers of target genes to upregulate their expression (reviewed in Baird and Yamamoto, 2020).
R-HSA-9725371 Nuclear events stimulated by ALK signaling in cancer Signaling through oncogenic forms of ALK activate nuclear events that drive cellular survival, escape from apoptosis and transformation (reviewed in Della Corte et al, 2018; Roskoski, 2013; Chiarle et al, 2008). Changes to gene expression are effected both by epigenetic mechanisms and by inducing expression of key transcription factors and cell cycle regulators, among other critical targets. Many of these gene expression events are dependent on activation of STAT3 and to a lesser extent, MAP kinase signaling downstream of ALK (reviewed in Hallberg and Palmer, 2013; Hallberg and Palmer, 2016; Ducray et al, 2019). Unique among fusion proteins identified to date, the well-studied NPM-ALK fusion appears to be partially localized to the nucleus by virtue of oligomerization with endogenous full-length NPM.
R-HSA-180746 Nuclear import of Rev protein Nuclear import of Rev involves the cellular proteins including importin-beta and B23 and is mediated by an arginine-rich nuclear localization signal (NLS) within the RNA binding domain of the Rev protein. The NLS of Rev associates with importin- beta as well as B23 which has been shown to function in the nuclear import of ribosomal proteins. The Rev-importin beta-B23 complex associates with the nuclear pore through interactions between importin beta and nucleoporin. Upon entry into the nucleus, Ran-GTP associates with importin beta resulting in in the disassembly of the importin beta-Rev-B23 complex and the release of Rev cargo.
R-HSA-1251985 Nuclear signaling by ERBB4 Besides signaling as a transmembrane receptor, ligand activated homodimers of ERBB4 JM-A isoforms (ERBB4 JM-A CYT1 and ERBB4 JM-A CYT2) undergo proteolytic cleavage by ADAM17 (TACE) in the juxtamembrane region, resulting in shedding of the extracellular domain and formation of an 80 kDa membrane bound ERBB4 fragment known as ERBB4 m80 (Rio et al. 2000, Cheng et al. 2003). ERBB4 m80 undergoes further proteolytic cleavage, mediated by the gamma-secretase complex, which releases the soluble 80 kDa ERBB4 intracellular domain, known as ERBB4 s80 or E4ICD, into the cytosol (Ni et al. 2001). ERBB4 s80 is able to translocate to the nucleus, promote nuclear translocation of various transcription factors, and act as a transcription co-factor. In neuronal precursors, ERBB4 s80 binds the complex of TAB and NCOR1, helps to move the complex into the nucleus, and is a co-factor of TAB:NCOR1-mediated inhibition of expression of astrocyte differentiation genes GFAP and S100B (Sardi et al. 2006). In mammary cells, ERBB4 s80 recruits STAT5A transcription factor in the cytosol, shuttles it to the nucleus, and acts as the STAT5A co-factor in binding to and promoting transcription from the beta-casein (CSN2) promoter, and may be involved in the regulation of other lactation-related genes (Williams et al. 2004, Muraoka-Cook et al. 2008). ERBB4 s80 was also shown to bind activated estrogen receptor in the nucleus and act as its transcriptional co-factor in promoting transcription of some estrogen-regulated genes, such as progesterone receptor gene NR3C3 and CXCL12 i.e. SDF1 (Zhu et al. 2006). ERBB4s80 may inhibit transcription of telomerase reverse transcriptase (TERT) by increasing methylation of the TERT gene promoter through an unknown mechanism (Ishibashi et al. 2012).
The C-tail of ERBB4 possesses several WW-domain binding motifs (three in CYT1 isoform and two in CYT2 isoform), which enable interaction of ERBB4 with WW-domain containing proteins. ERBB4 s80, through WW-domain binding motifs, interacts with YAP1 transcription factor, a known proto-oncogene, and may be a co-regulator of YAP1-mediated transcription (Komuro et al. 2003, Omerovic et al. 2004). The tumor suppressor WWOX, another WW-domain containing protein, competes with YAP1 in binding to ERBB4 s80 and prevents translocation of ERBB4 s80 to the nucleus (Aqeilan et al. 2005). ERBB4 s80 is also able to translocate to the mitochondrial matrix, presumably when its nuclear translocation is inhibited. Once in the mitochondrion, the BH3 domain of ERBB4, characteristic of BCL2 family members, may enable it to act as a pro-apoptotic factor (Naresh et al. 2006).
R-HSA-774815 Nucleosome assembly The formation of centromeric chromatin assembly outside the context of DNA replication involves the assembly of nucleosomes containing the histone H3 variant CenH3 (also called CENP-A).
R-HSA-5696398 Nucleotide Excision Repair Nucleotide excision repair (NER) was first described in the model organism E. coli in the early 1960s as a process whereby bulky base damage is enzymatically removed from DNA, facilitating the recovery of DNA synthesis and cell survival. Deficient NER processes have been identified from the cells of cancer-prone patients with different variants of xeroderma pigmentosum (XP), trichothiodystrophy (TTD), and Cockayne's syndrome. The XP cells exhibit an ultraviolet radiation hypersensitivity that leads to a hypermutability response to UV, offering a direct connection between deficient NER, increased mutation rate, and cancer. While the NER pathway in prokaryotes is unique, the pathway utilized in yeast and higher eukaryotes is highly conserved.
NER is involved in the repair of bulky adducts in DNA, such as UV-induced photo lesions (both 6-4 photoproducts (6-4 PPDs) and cyclobutane pyrimidine dimers (CPDs)), as well as chemical adducts formed from exposure to aflatoxin, benzopyrene and other genotoxic agents. Specific proteins have been identified that participate in base damage recognition, cleavage of the damaged strand on both sides of the lesion, and excision of the oligonucleotide bearing the lesion. Reparative DNA synthesis and ligation restore the strand to its original state.
NER consists of two related pathways called global genome nucleotide excision repair (GG-NER) and transcription-coupled nucleotide excision repair (TC-NER). The pathways differ in the way in which DNA damage is initially recognized, but the majority of the participating molecules are shared between these two branches of NER. GG-NER is transcription-independent, removing lesions from non-coding DNA strands, as well as coding DNA strands that are not being actively transcribed. TC-NER repairs damage in transcribed strands of active genes.
Several of the proteins involved in NER are key components of the basal transcription complex TFIIH. An ubiquitin ligase complex composed of DDB1, CUL4A or CUL4B and RBX1 participates in both GG-NER and TC-NER, implying an important role of ubiquitination in NER regulation. The establishment of mutant mouse models for NER genes and other DNA repair-related genes has been useful in demonstrating the associations between NER defects and cancer.
For past and recent reviews of nucleotide excision repair, please refer to Lindahl and Wood 1998, Friedberg et al. 2002, Christmann et al. 2003, Hanawalt and Spivak 2008, Marteijn et al. 2014).
R-HSA-8956320 Nucleotide biosynthesis The purine ribonucleotide inosine 5'-monophosphate (IMP) is assembled on 5-phospho-alpha-D-ribose 1-diphosphate (PRPP), with atoms derived from aspartate, glutamine, glycine, N10-formyl-tetrahydrofolate, and carbon dioxide. Although several of the individual reactions in this sequence are reversible, as indicated by the double-headed arrows in the diagram, other irreversible steps drive the pathway in the direction of IMP synthesis in the normal cell. All of these reactions are thus annotated here only in the direction of IMP synthesis. Guanosine 5'-monophosphate (GMP) and adenosine 5'-monophosphate (AMP) are synthesized from IMP (Zalkin & Dixon 1992).
The pyrimidine orotate (orotic acid) is synthesized in a sequence of four reactions, deriving its atoms from glutamine, bicarbonate, and aspartate. A single multifunctional cytosolic enzyme catalyzes the first three of these reactions, while the last one is catalyzed by an enzyme associated with the inner mitochondrial membrane. In two further reactions, catalyzed by a bifunctional cytosolic enzyme, orotate reacts with 1-phosphoribosyl 5-pyrophosphate (PRPP) to yield orotidine 5'-monophosphate, which is decarboxylated to yield uridine 5'-monophosphate (UMP). While several individual reactions in this pathway are reversible, other irreversible reactions drive the pathway in the direction of UMP biosynthesis in the normal cell. All reactions are thus annotated here only in the forward direction.
This pathway has been most extensively analyzed at the genetic and biochemical level in hamster cell lines. All three enzymes have also been purified from human sources, however, and the key features of these reactions have been confirmed from studies of this human material (Jones 1980).
All other pyrimidines are synthesized from UMP. The reactions annotated here, catalyzed by dCMP deaminase and dUTP diphosphatase yield dUMP, which in turn is converted to TMP by thymidylate synthase. R-HSA-8956319 Nucleotide catabolism The purine bases guanine and hypoxanthine (derived from adenine by events in the purine salvage pathways) are converted to xanthine and then to uric acid, which is excreted from the body (Watts 1974). The end-point of this pathway in humans and hominoid primates is unusual. Most other mammals metabolize uric acid further to yield more soluble end products, and much speculation has centered on possible roles for high uric acid levels in normal human physiology.
In parallel sequences of three reactions each, the pyrimidines thymine and uracil are converted to beta-aminoisobutyrate and beta-alanine respectively. Both of these molecules are excreted in human urine and appear to be normal end products of pyrimidine catabolism (Griffith 1986). Mitochondrial AGXT2, however, can also catalyze the transamination of both molecules with pyruvate, yielding 2-oxoacids that can be metabolized further by reactions of branched-chain amino acid and short-chain fatty acid catabolism (Tamaki et al. 2000).
Hydrolysis of phosphate bonds in nucleotides catalyzed by members of the NUDT and NTPD families of enzymes have been grouped here as well, although the physiological roles of these groups of catabolic reactions are diverse.
R-HSA-9735786 Nucleotide catabolism defects Purine nucleotide phosphorylase defects (Aust et al. 1992, Williams et al. 1987) are annotated here.
R-HSA-8956321 Nucleotide salvage Nucleosides and free bases generated by RNA and DNA breakdown are converted back to nucleotide monophosphates, allowing them to re-enter the pathways of nucleotide biosynthesis and interconversion. Under normal conditions, DNA turnover is limited and deoxyribonucleotide salvage operates at a correspondingly low level (Watts 1974).
R-HSA-9734207 Nucleotide salvage defects Defects in APRT and HGPRT lead to synthesis of 2,8-dioxo-adenine and overproduction of uric acid, respectively, associated with kidney damage and other symptoms (Bollée et al. 2012; Fu & Jinnah 2012). Defects in ADA lead to accumulation of (deoxy)adenosine and consequent severe combined immunodeficiency (Akeson et al. 1988).
R-HSA-168643 Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways The innate immune system is the first line of defense against invading microorganisms, a broad specificity response characterized by the recruitment and activation of phagocytes and the release of anti-bacterial peptides. The receptors involved recognize conserved molecules present in microbes called pathogen-associated molecular patterns (PAMPs), and/or molecules that are produced as a result of tissue injury, the damage associated molecular pattern molecules (DAMPs). PAMPs are essential to the pathogen and therefore unlikely to vary. Examples are lipopolysaccharide (LPS), peptidoglycans (PGNs) and viral RNA. DAMPs include intracellular proteins, such as heat-shock proteins and extracellular matrix proteins released by tissue injury, such as hyaluronan fragments. Non-protein DAMPs include ATP, uric acid, heparin sulfate and dsDNA. The receptors for these factors are referred to collectively as pathogen- or pattern-recognition receptors (PRRs). The best studied of these are the membrane-associated Toll-like receptor family. Less well studied but more numerous are the intracellular nucleotide-binding domain, leucine rich repeat containing receptors (NLRs) also called nucleotide binding oligomerization domain (NOD)-like receptors, a family with over 20 members in humans and over 30 in mice. These recognise PAMPs/DAMPs from phagocytosed microorganisms or from intracellular infections (Kobayashi et al. 2003, Proell et al. 2008, Wilmanski et al. 2008). Some NLRs are involved in process unrelated to pathogen detection such as tissue homeostasis, apoptosis, graft-versus-host disease and early development (Kufer & Sansonetti 2011).
Structurally NLRs can be subdivided into the caspase-recruitment domain (CARD)-containing NLRCs (NODs) and the pyrin domain (PYD)-containing NLRPs (NALPs), plus outliers including ice protease (caspase-1) activating factor (IPAF) (Martinon & Tschopp, 2005). In practical terms, NLRs can be divided into the relatively well characterized NOD1/2 which signal via RIP2 primarily to NFkappaB, and the remainder, some of which participate in macromolecular structures called Inflammasomes that activate caspases. Mutations in several members of the NLR protein family have been linked to inflammatory diseases, suggesting these molecules play important roles in maintaining host-pathogen interactions and inflammatory responses.
Most NLRs have a tripartite structure consisting of a variable amino-terminal domain, a central nucleotide-binding oligomerization domain (NOD or NACHT) that is believed to mediate the formation of self oligomers, and a carboxy-terminal leucine-rich repeat (LRR) that detects PAMPs/DAMPs. In most cases the amino-terminal domain includes protein-interaction modules, such as CARD or PYD, some harbour baculovirus inhibitor repeat (BIR) or other domains. For most characterised NLRs these domains have been attributed to downstream signaling
Under resting conditions, NLRs are thought to be present in an autorepressed form, with the LRR folded back onto the NACHT domain preventing oligomerization. Accessory proteins may help maintain the inactive state. PAMP/DAMP exposure is thought to triggers conformational changes that expose the NACHT domain enabling oligomerization and recruitment of effectors, though it should be noted that due to the lack of availability of structural data, the mechanistic details of NLR activation remain largely elusive.
New terminology for NOD-like receptors was adopted by the Human Genome Organization (HUGO) in 2008 to standardize the nomenclature of NLRs. The acronym NLR, once standing for NOD-like receptor, now is an abbreviation of 'nucleotide-binding domain, leucine-rich repeat containing' protein. The term NOD-like receptor is officially outdated and replaced by NLRC where the C refers to the CARD domain. However the official gene symbols for NOD1 and NOD2 still contain NOD and this general term is still widely used.
R-HSA-418038 Nucleotide-like (purinergic) receptors Purinergic receptors (Burnstock G, 2006; Abbracchio MP et al, 2009) are a family of newly characterized plasma membrane molecules involved in several cellular functions such as vascular reactivity, apoptosis and cytokine secretion. The functions of these receptors are as yet only partially characterized. The family includes the GPCR P2Y purinergic receptors and adenosine P1 receptors. A third family member, the P2X receptor, is a ligand-gated ion channel.
R-HSA-5173214 O-glycosylation of TSR domain-containing proteins The O-fucosylation of proteins containing thrombospondin type 1 repeat (TSR) domains is an important PTM, regulating many biological processes such as Notch signalling, inflammation, wound healing, angiogenesis amd neoplasia (Adams & Tucker 2000, Moremen et al. 2012). Fucose addition is carried out by two protein fucosyltransferases, POFUT1 and 2. Only POFUT2 recognises the consensus sequence CSXS/TCG found in TSR1 domains and the fucosyl residue is attached to the hydroxyl group of conserved serine (S) or threonine (T) residues within the consensus sequence. The modification was first demonstrated on thrombospondin 1, found in platelets and the ECM (Hofsteenge et al. 2001, Luo et al. 2006). The resulting O-fucosyl-protein is subsequently a substrate for beta-1,3-glucosyltransferase-like protein (B3GALTL), which adds a glucosyl moiety to form the rare disaccharide modification Glc-beta-1,3-Fuc. More than 60 human proteins contain TSR1 domains, The disaccharide modification has been demonstrated on a small number of these TSR1 domain-containing proteins such as thrombospondin 1 (Hofsteenge et al. 2001, Luo et al. 2006), properdin (Gonzalez de Peredo et al. 2002) and F-spondin (Gonzalez de Peredo et al. 2002). The ADAMTS (a disintegrin-like and metalloprotease domain with thrombospondin type-1 repeats) superfamily consists of 19 secreted metalloproteases (ADAMTS proteases) and at lease five ADAMTS-like proteins in humans. Five members of the ADAMTS superfamily have also had experimental confirmation of the disaccharide modification. Examples are ADAMTS13 (Ricketts et al. 2007) and ADAMTSL1 (Wang et al. 2007). In the two reactions described here, the TSR1 domain-containing proteins with similarity to the experimentally confirmed ones are included as putative substrates.
R-HSA-5173105 O-linked glycosylation O-glycosylation is an important post-translational modification (PTM) required for correct functioning of many proteins (Van den Steen et al. 1998, Moremen et al. 2012). The O-glycosylation of proteins containing thrombospondin type 1 repeat (TSR) domains and O-glycosylation of mucins are currently described here.
R-HSA-913709 O-linked glycosylation of mucins Mucins are a family of high molecular weight, heavily glycosylated proteins (glycoconjugates) produced by epithelial tissues in most metazoa. Mucins' key characteristic is their ability to form gels; therefore they are a key component in most gel-like secretions, serving functions from lubrication to cell signalling to forming chemical barriers. To date, there are approximately 20 genes that express mucins. Mature mucins are composed of two distinct regions:
(1) The amino- and carboxy-terminal regions are very lightly glycosylated, but rich in cysteines. The cysteine residues participate in establishing disulfide linkages within and among mucin monomers.
(2) A large central region rich in serine, threonine and proline residues called the variable number of tandem repeat (VNTR) region which can become heavily O-glycosylated with hundreds of O-GalNAc glycans.
N-acetyl-galactosamine (GalNAc) is the first glycan to be attached, forming the simplest mucin O-glycan. After this, several different pathways are possible generating "core" structures. Four core structures are commonly formed, several others are possible but infrequent. O-linked glycans are often capped by the addition of a sialic acid residue, terminating the addition of any more O-glycans (Brockhausen et al, 2009; Tarp and Clausen, 2008).
R-HSA-1480926 O2/CO2 exchange in erythrocytes In capillaries of the lungs Erythrocytes take up oxygen and release carbon dioxide. In other tissues of the body the reverse reaction occurs: Erythrocytes take up carbon dioxide and release oxygen (reviewed in Nikinmaa 1997, Jensen 2004).
In the lungs, carbon dioxide (CO2) bound as carbamate to the N-terminus of hemoglobin (HbA) and protons bound to histidine residues in HbA are released as HbA binds oxygen (O2). Bicarbonate (HCO3-) present in plasma is taken up by erythrocytes via the band3 anion exchanger (AE1, SLC4A1) and combined with protons by carbonic anhydrases I and II (CA1, CA2) to yield water and CO2 (reviewed by Esbaugh & Tufts 2006, De Rosa et al. 2007). The CO2 is passively transported out of the erythrocyte by AQP1 and RhAG. HCO3- in plasma is also directly dehydrated by extracellular carbonic anhydrase IV (CA4) present on endothelial cells lining the capillaries in the lung.
In non-pulmonary tissues CO2 in plasma is hydrated to yield protons and HCO3- by CA4 located on the apical plasma membranes of endothelial cells. Plasma CO2 is also taken up by erythrocytes via AQP1 and RhAG. Within erythrocytes CA1 and, predominantly, CA2 hydrate CO2 to yield HCO3- and protons (reviewed in Geers & Gros 2000, Jensen 2004, Boron 2010). HCO3- is transferred out of the erythrocyte by the band 3 anion exchange protein (AE1, SLC4A1) which cotransports a chloride ion into the erythrocyte.
Also within the erythrocyte, CO2 combines with the N-terminal alpha amino groups of HbA to form carbamates while protons bind histidine residues in HbA. The net result is the Bohr effect, a conformational change in HbA that reduces its affinity for O2 and hence assists the delivery of O2 to tissues.
R-HSA-9858328 OADH complex synthesizes glutaryl-CoA from 2-OA The mitochondrial alpha-oxoadipate dehydrogenase complex (OADH, OADHC) catalyzes the overall reaction of 2-oxoadipate (OA), CoASH, and NAD+ to form glutaryl-CoA, CO2, and NADH. The complex contains multiple copies of three different enzymes, E1 (DHTKD1), E2 (DLST), and E3 (DLD), each with distinct catalytic activities. As in other dehydrogenase complexes, the lipoyl scaffold bound to DLST accepts the glutaryl moiety after the decarboxylation of OA by DHTKD1. Secondly, glutaryl is transferred to CoA by DLST, and finally, the dihydrolipoyl moiety is dehydrogenated by DLD using NAD+ (Nemeria et al., 2018; Zhang et al., 2020; Nemeria et al., 2021). Crystallographic studies show that in the OADH complex, DHTKD1 dimers bind to a 24-mer DLST core (Bezerra et al., 2020).
R-HSA-8983711 OAS antiviral response The human oligoadenylate synthetase (OAS) family consists of four proteins whose production is stimulated by interferon, OAS1, OAS2, OAS3, and OASL. The first three members have the 2'-5'-oligoadenylate synthetase activity for which the family is named (Sadler AJ & Williams BR 2008), whereas OASL is devoid of this activity despite sharing significant sequence similarity with the other OAS proteins (Zhu J et al. 2015). OAS1, 2, and 3 are activated by double-stranded RNA to synthesize 5'-triphosphorylated 2'-5'-oligoadenylates (2-5A) from ATP (Kerr IM & Brown RE 1978). The 2-5A serve as chemically unique second messengers that induce regulated RNA decay by activating ribonuclease L (RNase L), thus mediating antiviral innate immunity (Zhou A et al. 1993; Lin RJ et al. 2009; Huang H et al. 2014; Han Y et al. 2014). RNase L has also been implicated in antibacterial innate immunity (Li XL et al. 2008). RNase L cleaves single-stranded RNA (ssRNA) in U-rich sequences, typically after UU or UA dinucleotides leaving a 5'-OH and 2',3'-cyclic phosphate (Floyd-Smith G et al. 1981; Wreschner DH et al.1981; Cooper DA et al. 2014).
Some OAS proteins have additional or alternative antiviral functions that are independent of RNase L activity (Perelygin AA et al., 2002; Kristiansen H et al. 2011). The precise mechanisms of RNase L-independent OAS antiviral activities remain to be fully elucidated.
R-HSA-9853506 OGDH complex synthesizes succinyl-CoA from 2-OG The mitochondrial alpha-oxoglutarate dehydrogenase complex (αOGDH, αKGDH, OGDHC) catalyzes the reaction of 2-oxoglutarate (2OG), CoASH, and NAD+ to form succinyl-CoA, CO2, and NADH. The enzyme complex ("metabolon") contains multiple copies of three different proteins, E1 (OGDH), E2 (DLST), and E3 (DLD), each with distinct catalytic activities (Reed and Hackert 1990; Zhou et al 2001). Specifically, it is composed of a core of 24 E2 subunits exhibiting octahedral symmetry. To these subunits are bound up to six E1 dimers and to each of these is bound an E3 dimer (Nagy et al., 2021; Skalidis et al., 2023) and to an adaptive MRPS36 unit (Hevler et al., 2023). The reaction starts with the oxidative decarboxylation of 2OG catalyzed by E1alpha and beta (alpha ketoglutarate dehydrogenase). Lipoamide cofactor associated with E2 is reduced at the same time. Next, the succinyl group derived from alpha ketoglutarate is transferred to coenzyme A in two steps catalyzed by E2 (dihydrolipolyl transacetylase). Finally, the oxidized form of lipoamide is regenerated and electrons are transferred to NAD+ in two steps catalyzed by E3 (dihydrolipoyl dehydrogenase). The biochemical details of this reaction have been worked out first with alpha ketoglutarate dehydrogenase complex and subunits purified from bovine tissue (McCartney et al. 1998).
Generation of reactive oxygen species by OGDHC is a major source of mitochondrial oxidative stress under certain pathological conditions.
R-HSA-9673163 Oleoyl-phe metabolism Extracellular PM20D1 (N-fatty-acyl-amino acid synthase/hydrolase PM20D1) catalyzes the reversible condensation of L-phenylalanine (L-phe) and oleate ((9Z)-octadecenoate) to form oleoyl-phe (N-(9Z-octadecenoyl)-L-phenylalanine) and water. In addition to the condensation of phe with oleate ((9Z)-octadecenoate) annotated here, purified human PM20D1 protein in vitro can catalyze the condensation of leucine and isoleucine with oleate and with other long-chain unsaturated fatty acids including arachidonate, with lower efficiencies. Although the reverse (hydrolysis) direction of this reaction is thermodynamically favored, expression of PM20D1 protein in mice or in cultured cells was associated with elevated levels of oleoyl-phe in serum and culture media, respectively. Treatment of cultured mouse brown adipose tissue adipocytes and of isolated mitochondria with oleoyl-phe induced uncoupled respiration independently of UCP1 (uncoupling protein 1). Photolabeling studies of isolated mitochondria identified the ADP/ATP symporters SLC25A4 and SLC25A5 as possible targets of oleoyl-phe. Consistent with these observations, expression of PM20D1 and elevated blood levels of oleoyl-phe in mice were associated with increased energy expenditure and improved glucose homeostasis. These results suggest a physiological role for PM20D1 and its condensation reaction product in thermogenesis and raise the possibility that oleoyl-phe and related molecules might have a clinical role in treatment of obesity (Long et al. 2016).
R-HSA-381753 Olfactory Signaling Pathway Mammalian Olfactory Receptor (OR, also called odorant receptor) genes were discovered in rats by Linda Buck and Richard Axel, who predicted that odorants would be detected by a large family of G protein-coupled receptors (GPCRs) that are selectively expressed in the olfactory epithelium. This prediction was based on previous biochemical evidence that cAMP levels increased in olfactory neurons upon odor stimulation. These predictions proved to be accurate, and Buck and Axel received a Nobel Prize for this and subsequent work (reviewed in Keller & Vosshall 2008).
Subsequent work in mice and other vertebrates has confirmed that OR genes are comprised of a very large family of G Protein-Coupled Receptors (GPCRs) that are selectively-expressed in olfactory epithelium. Although some OR are also expressed selectively in one or a few other tissues, their expression in olfactory-epithelium generally indicates a functional role in mediating olfaction, where they couple binding by odorant ligands with intracellular olfactory signaling. (Note: the other subclasses of GPCR signaling pathways are described under "GPCR Signaling".)
The ligands for ORs are diverse, ranging from chemical compounds to peptides. Intracellular signaling by OR proteins in mice and other mammalian systems is known to be mediated via direct interactions of OR proteins with an olfactory-specific heterotrimeric G Protein, that contains an olfactory-specific G alpha protein: G alpha S OLPH (also named "GNAL").
In model genetic systems such as mice, many candidate OR genes have been shown experimentally to function in olfactory signaling (reviewed in (Keller & Vosshall 2008). For the human OR genes, experimental analysis has been more limited, although some specific OR genes, such as OR7D4 and OR11H7P have been confirmed to mediate olfactory response and signaling in humans for specific chemical odorants (Keller et al. 2007, Abbafy 2007). Mice and other rodents are believed to have about 1000 functional OR genes, as well as many additional pseudogenes. Based on sequence similarities, there are 960 human OR genes, but approximately half of these are pseudogenes (Keller 2008). In mice, essentially all olfactory signaling requires G-alpha-S (OLF); mouse G-OLF knockouts have been shown to lack olfactory responses (Belluscio 1998). Bona fide human OR genes identified by sequence similarity (not pseudogenes with function-blocking mutations) that are expressed in olfactory epithelium are expected to interact with G alpha S OLF containing G Protein trimers.
Of the 960 human OR genes and pseudogenes, there is experimental evidence that indicates over 430 are expressed in human olfactory epithelium, including 80 expressed OR pseudogenes (Zhang 2007).
When expressed in model cell systems mammalian olfactory receptors (ORs) are typically retained in the ER and degraded by the proteasome (McClintock et al. 1997). A study using Caenorhabditis elegans showed that the transport of ORs to the cilia of olfactory neurons required the expression and association of ORs with a transmembrane protein, ODR4 (Dwyer et al. 1998). Co-transfection of rat ORs with ODR4 enhanced the transport and expression of ORs at the cell-surface (Gimelbrant et al. 2001). These studies suggested that olfactory neurons might have a selective molecular machinery that promotes expression of ORs at the cells surface. Two human protein families have been identified as potential accessory proteins involved in the trafficking of ORs to the plasma membrane (Saito et al. 2004). Receptor transporting proteins 1 and 2 (RTP1, RTP2) both strongly induced expression of several ORs at the cell-surface. To a lesser extent, the receptor expression enhancing protein 1 (REEP1) also promoted cell-surface expression. These proteins are specifically expressed in olfactory neurons with no expression in testis, where a subset of ORs are expressed (Parmentier et al. 1992, Spehr et al. 2003). Other members of the RTP and REEP families have a widespread distribution. RTP3 and RTP4 have been shown to promote cell-surface expression of the bitter taste receptors, TAS2Rs (Behrens et al. 2006). REEP1 and REEP5 (also known as DP1) are involved in shaping the ER by linking microtubule fibers to the ER (Park et al. 2010, Voeltz et al. 2006). A recent study looking at the role of REEP in the trafficking of Alpha2A- and Alpha2C-adrenergic receptors showed that REEP1-2 and 6 enhance the cell-surface expression of Alpha2C, but not Alpha2A, by increasing the capacity of ER cargo, thereby allowing more receptors to reach the cell-surface (Bjork et al. 2013). Unlike RTP1, REEP1-2 and 6 are only present in the ER, do not traffic to the plasma membrane and specifically interact with the minimal/non-glycosylated forms of Alpha2C via an interaction with its C-terminus (Saito et al. 2004, Bjork et al. 2013). REEPs may function as general modulators of the ER, rather than specifically interacting with GPCRs. Loss of association of REEP2 with membranes leads to hereditary spastic paraplegia (Esteves et al. 2014).
Olfactory receptors (ORs, also called odorant receptors) are present on the plasma membrane of cilia of olfactory sensory neurons located in the olfactory epithelium of the nasal sinus. Each mature neuron expresses only one OR gene (reviewed in Nagai et al. 2016) and each OR binds one particular volatile chemical or set of volatile chemicals, known as odorants. The binding of an odorant to an OR (Mainland et al. 2015) causes a conformational change in the receptor that activates the G alpha subunit (Golf, GNAL) of an associated heterotrimeric G protein complex to exchange GDP for GTP (inferred from mouse homologs in Jones et al. 1990). GNAL:GTP and the Gbeta:Ggamma subcomplex (GNB1:GNG13) dissociate from the olfactory receptor and GNAL:GTP then binds and activates adenylate cyclase 3 (ADCY3) (inferred from rat homologs in Bakalyar and Reed 1990, reviewed in Boccaccio et al. 2021). Cyclic AMP produced by ADCY3 binds and opens the olfactory cyclic nucleotide-gated channel (CNG channel) composed of CNGA2, CNGA4, and CNGB isoform 1b (inferred from rat homologs in Liman and Buck 1994). The CNG channel translocates sodium and calcium cations from the extracellular region into the cytosol. The resulting cytosolic calcium ions bind ANO2 and increase the transport of chloride ions by ANO2 from the cytosol to the extracellular region (inferred from mouse homologs in Pifferi et al. 2009, Stephan et al. 2009). The translocations of ions across the plasma membrane causes depolarization of the neuron yielding a receptor potential and action potential that is transmitted to the olfactory bulb of the brain.
R-HSA-190704 Oligomerization of connexins into connexons The mechanism of connexin assembly into connexons has been well characterized. Two different types of connexons can be formed. A connexon containing six identical connexin molecules is referred to as an homomeric connexon, while a connexon containing at least two different connexin molecules is referred to as an heteromeric connexon. The connexin molecules making up an heteromeric connexon appear to belong to only one subgroup (alpha or beta); heteromeric connexons containing both alpha and beta subunits have not yet been observed. Indeed, an intrinsic signal in four amino acid positions appears to confer different physicochemical characteristics to certain connexins in the alpha and beta groups (Lagr et al., 2003). These intrinsic signals are Cx specific, however (see Gemel et al., 2006). Therefore, additional yet unknown signals are required to regulate connexin compatibility and hetero-oligomerization.
The identification of the subcellular location at which gap junction assembly occurs has proven difficult. One explanation for this difficulty may be that the location of oligomerization for each connexon varies depending upon Cx type or cell type. Oligomerization has been observed after ER membrane insertion (Cx43, Cx32, Cx26) (Falk et al., 1997; Ahmad et al., 1999; Ahmad and Evans, 2002), in the ER-Golgi-intermediate compartment (ERGIC) (Cx32) (Diez et al. 1999) and inside the trans-Goligi network (Cx43) (Musil and Goodenough, 1993).
R-HSA-2559585 Oncogene Induced Senescence Oncogene-induced senescence (OIS) is triggered by high level of RAS/RAF/MAPK signaling that can be caused, for example, by oncogenic mutations in RAS or RAF proteins, or by oncogenic mutations in growth factor receptors, such as EGFR, that act upstream of RAS/RAF/MAPK cascade. Oncogene-induced senescence can also be triggered by high transcriptional activity of E2F1, E2F2 or E2F3 which can be caused, for example, by the loss-of-function of RB1 tumor suppressor.
Oncogenic signals trigger transcription of CDKN2A locus tumor suppressor genes: p16INK4A and p14ARF. p16INK4A and p14ARF share exons 2 and 3, but are expressed from different promoters and use different reading frames (Quelle et al. 1995). Therefore, while their mRNAs are homologous and are both translationally inhibited by miR-24 microRNA (Lal et al. 2008, To et al. 2012), they share no similarity at the amino acid sequence level and perform distinct functions in the cell. p16INK4A acts as the inhibitor of cyclin-dependent kinases CDK4 and CDK6 which phosphorylate and inhibit RB1 protein thereby promoting G1 to S transition and cell cycle progression (Serrano et al. 1993). Increased p16INK4A level leads to hypophosphorylation of RB1, allowing RB1 to inhibit transcription of E2F1, E2F2 and E2F3-target genes that are needed for cell cycle progression, which results in cell cycle arrest in G1 phase. p14-ARF binds and destabilizes MDM2 ubiquitin ligase (Zhang et al. 1998), responsible for ubiquitination and degradation of TP53 (p53) tumor suppressor protein (Wu et al. 1993, Fuchs et al. 1998, Fang et al. 2000). Therefore, increased p14-ARF level leads to increased level of TP53 and increased expression of TP53 target genes, such as p21, which triggers p53-mediated cell cycle arrest and, depending on other factors, may also lead to p53-mediated apoptosis. CDKN2B locus, which encodes an inhibitor of CDK4 and CDK6, p15INK4B, is located in the vicinity of CDKN2A locus, at the chromosome band 9p21. p15INK4B, together with p16INK4A, contributes to senescence of human T-lymphocytes (Erickson et al. 1998) and mouse fibroblasts (Malumbres et al. 2000). SMAD3, activated by TGF-beta-1 signaling, controls senescence in the mouse multistage carcinogenesis model through regulation of MYC and p15INK4B gene expression (Vijayachandra et al. 2003). TGF-beta-induced p15INK4B expression is also important for the senescence of hepatocellular carcinoma cell lines (Senturk et al. 2010).
MAP kinases MAPK1 (ERK2) and MAPK3 (ERK1), which are activated by RAS signaling, phosphorylate ETS1 and ETS2 transcription factors in the nucleus (Yang et al. 1996, Seidel et al. 2002, Foulds et al. 2004, Nelson et al. 2010). Phosphorylated ETS1 and ETS2 are able to bind RAS response elements (RREs) in the CDKN2A locus and stimulate p16INK4A transcription (Ohtani et al. 2004). At the same time, activated ERKs (MAPK1 i.e. ERK2 and MAPK3 i.e. ERK1) phosphorylate ERF, the repressor of ETS2 transcription, which leads to translocation of ERF to the cytosol and increased transcription of ETS2 (Sgouras et al. 1995, Le Gallic et al. 2004). ETS2 can be sequestered and inhibited by binding to ID1, resulting in inhibition of p16INK4A transcription (Ohtani et al. 2004).
Transcription of p14ARF is stimulated by binding of E2F transcription factors (E2F1, E2F2 or E2F3) in complex with SP1 to p14ARF promoter (Parisi et al. 2002).
Oncogenic RAS signaling affects mitochondrial metabolism through an unknown mechanism, leading to increased generation of reactive oxygen species (ROS), which triggers oxidative stress induced senescence pathway. In addition, increased rate of cell division that is one of the consequences of oncogenic signaling, leads to telomere shortening which acts as another senescence trigger.
While OIS has been studied to considerable detail in cultured cells, establishment of in vivo role of OIS has been difficult due to lack of specific biomarkers and its interconnectedness with other senescence pathways (Baek and Ryeom 2017, reviewed in Sharpless and Sherr 2015).
R-HSA-6802957 Oncogenic MAPK signaling The importance of the RAS/RAF/MAPK cascade in regulating cellular proliferation, differentiation and survival is highlighted by the fact that components of the pathway are mutated with high frequency in a large number of human cancers. Activating mutations in RAS are found in approximately one third of human cancers, while ~8% of tumors express an activated form of BRAF. RAS pathway activation is also achieved in a smaller subset of cancers by loss-of-function mutations in negative regulators of RAS signaling, such as the RAS GAP NF1(reviewed in Prior et al, 2012; Pylayeva-Gupta et al, 2011; Stephen et al, 2014; Lavoie and Therrien, 2015; Lito et al, 2013; Samatar and Poulikakos, 2014; Maertens and Cichowski, 2014).
R-HSA-111885 Opioid Signalling Opioids are chemical substances similar to opiates, the active substances found in opium (morphine, codeine etc.). Opioid action is mediated by the receptors for endogenous opioids; peptides such as the enkephalins, the endorphins or the dynorphins. Opioids possess powerful analgesic and sedative effects, and are widely used as pain-killers. Their main side-effect is the rapid establishment of a strong addiction. Opioids receptors are G-protein coupled receptors (GPCR). There are four classes of receptors: mu (MOR), kappa (KOR) and delta (DOR), and the nociceptin receptor (NOP).
R-HSA-419771 Opsins Opsins are light-sensitive, 35-55 kDa membrane-bound G protein-coupled receptors of the retinylidene protein family found in photoreceptor cells of the retina. Five classical groups of opsins are involved in vision, mediating the conversion of a photon of light into an electrochemical signal, the first step in the visual transduction cascade (Terakita A, 2005; Nickle B and Robinson PR, 2007). Another opsin found in the mammalian retina, melanopsin, is involved in circadian rhythms and pupillary reflex but not in image-forming (Hankins MW et al, 2008; Kumbalasiri T and Provencio I, 2005). Guanine nucleotide-binding proteins (G proteins) are involved as modulators or transducers in various transmembrane signaling systems. The G protein transducin, encoded by GNAT genes, is one of the transducers of a visual impulse that performs the coupling between rhodopsin and cGMP-phosphodiesterase. Defects in GNAT1 are the cause of congenital stationary night blindness autosomal dominant type 3, also known as congenital stationary night blindness Nougaret type. Congenital stationary night blindness is a non-progressive retinal disorder characterized by impaired night vision (Dryja TP et al, 1996). Defects in GNAT2 are the cause of achromatopsia type 4 (ACHM4). Achromatopsia is an autosomal recessively inherited visual disorder that is present from birth and that features the absence of color discrimination (Kohl S et al, 2002).
R-HSA-68949 Orc1 removal from chromatin Mammalian Orc1 protein is phosphorylated and selectively released from chromatin and ubiquitinated during the S-to-M transition in the cell division cycle.
R-HSA-389397 Orexin and neuropeptides FF and QRFP bind to their respective receptors The orphan G protein-coupled receptors mentioned here regulate sleep and appetite.
R-HSA-1852241 Organelle biogenesis and maintenance This module describes the biogenesis of organelles. Organelles are subcellular structures of distinctive morphology and function. The organelles of human cells include: mitochondria, endoplasmic reticulum, Golgi apparatus, vacuoles, nucleus, (auto)phagosome, centriole, lysosome, melanosome, myofibril, nucleolus, peroxisome, cilia (in some cell types), proteasome, ribsome, and transport vesicles.
R-HSA-561048 Organic anion transport Organic anion transporters (OATs) mediate the renal absorption and excretion of a broad range of endogenous substrates and anionic drugs such as diuretics and NSAIDs. Five members belong to these polyspecific transporters (OAT1-4 and URAT1) and are predominantly expressed in the kidney (Koepsell H and Endou H, 2004; Rizwan AN and Burckhardt G, 2007; Ahn SY and Bhatnagar V, 2008).
R-HSA-428643 Organic anion transporters The SLC17 gene family encode proteins which are organic anion transporters. There are three distinct subfamilies within SLC17; vesicular glutamate transporters (VGLUT1-3 encoded by SLC17A7,6 and 8), type I Na+-coupled phosphate co-transporters (encoded by SLC17A1-4) and a proton-coupled sialic acid co-transporter (encoded by SLC17A5) (Reimer RJ and Edwards RH, 2004).
Two members of the SLC5 gene family encode carboxylate transporters, SMCT1 and SMCT2 (Ganapathy V et al, 2008).
R-HSA-549127 Organic cation transport The organic cation transporters comprise three SLC22 members, OCT1-3. They can transport a wide range of organic cations including weak bases. All transport by OCTs is electrogenic, sodium-independent and bidirectional. Two further organic cation transporters mediate transport of ergothioneine and carnitine (Koepsell H and Endou H, 2004).
R-HSA-549132 Organic cation/anion/zwitterion transport The SLC22 gene family of solute carriers function as organic cation transporters (OCTs), cation/zwitterion transporters (OCTNs) and organic anion transporters (OATs). The SLC22 family belongs to the major facilitator superfamily and comprises uniporters, symporters and antiporters.Most of this family are polyspecific transporters. Since many of these transporters are expressed in the liver, kidney and intestine, they play an important role in drug absorption and excretion. Substrates include xenobiotics, drugs, and endogenous amine compounds (Koepsell H and Endou H, 2004).
R-HSA-449836 Other interleukin signaling Interleukins are low molecular weight proteins that bind to cell surface receptors and act in an autocrine and/or paracrine fashion. They were first identified as factors produced by leukocytes but are now known to be produced by many other cells throughout the body. They have pleiotropic effects on cells which bind them, impacting processes such as tissue growth and repair, hematopoietic homeostasis, and multiple levels of the host defense against pathogens where they are an essential part of the immune system.
R-HSA-416700 Other semaphorin interactions There are eight classes of semaphorins and four types of plexins. Semaphorin (SEMA) classes 1 and 2 are found in invertebrates and classes 3-7 are vertebrate sempahorines. Sempahorin class 3 is secreted, whereas the other classes are synthesised as transmembrane proteins. Vertebrate plexins (PLXNs) are classified into four subfamilies plexin-A to -D. There are four A-type plexins, three B-type, one C-type and D-type. Interactions between different subfamilies of plexins and semaphorins show differential specificity, which trigger different sets of biological functions. Another level of functional specificity specificity is attained by plexins by coupling with various coreceptors expressed in a cell- or tissue-specific manner, such as neuropilins (NRP), L1CAM, c-MET proto-oncogene, ERB2, CD72 and CD45 (Kruger et al. 2005, Law & Lee 2012).
R-HSA-5689896 Ovarian tumor domain proteases Humans have 16 Ovarian tumour domain (OTU) family DUBs that can be evolutionally divided into three classes, the OTUs, the Otubains (OTUBs), and the A20-like OTUs (Komander et al. 2009).
OTU family DUBs can be highly selective in the type of ubiquitin crosslinks they cleave. OTUB1 is specific for K48-linked chains, whereas OTUB2 can cleave K11, K63 and K48-linked poly-Ub (Wang et al. 2009, Edelmann et al. 2009, Mevissen et al. 2013). A20 prefers K48-linked chains, Cezanne is specific for K11-linked chains, and TRABID acts on both K29, K33 and K63-linked poly-Ub (Licchesi et al. 2011, Komander & Barford 2008, Bremm et al. 2010, Mevissen et al. 2013). The active site of the OTU domain contains an unusual loop not seen in other thiol-DUBs and can lack an obvious catalytic Asp/Asn (Komander & Barford 2009, Messick et al. 2008, Lin et al. 2008). A20 and OTUB1 have an unusual mode of activity, binding directly to E2 enzymes (Nakada et al. 2010, Wertz et al. 2004).
R-HSA-2559580 Oxidative Stress Induced Senescence Oxidative stress, caused by increased concentration of reactive oxygen species (ROS) in the cell, can happen as a consequence of mitochondrial dysfunction induced by the oncogenic RAS (Moiseeva et al. 2009) or independent of oncogenic signaling. Prolonged exposure to interferon-beta (IFNB, IFN-beta) also results in ROS increase (Moiseeva et al. 2006). ROS oxidize thioredoxin (TXN), which causes TXN to dissociate from the N-terminus of MAP3K5 (ASK1), enabling MAP3K5 to become catalytically active (Saitoh et al. 1998). ROS also stimulate expression of Ste20 family kinases MINK1 (MINK) and TNIK through an unknown mechanism, and MINK1 and TNIK positively regulate MAP3K5 activation (Nicke et al. 2005).
MAP3K5 phosphorylates and activates MAP2K3 (MKK3) and MAP2K6 (MKK6) (Ichijo et al. 1997, Takekawa et al. 2005), which act as p38 MAPK kinases, as well as MAP2K4 (SEK1) (Ichijo et al. 1997, Matsuura et al. 2002), which, together with MAP2K7 (MKK7), acts as a JNK kinase.
MKK3 and MKK6 phosphorylate and activate p38 MAPK alpha (MAPK14) and beta (MAPK11) (Raingeaud et al. 1996), enabling p38 MAPKs to phosphorylate and activate MAPKAPK2 (MK2) and MAPKAPK3 (MK3) (Ben-Levy et al. 1995, Clifton et al. 1996, McLaughlin et al. 1996, Sithanandam et al. 1996, Meng et al. 2002, Lukas et al. 2004, White et al. 2007), as well as MAPKAPK5 (PRAK) (New et al. 1998 and 2003, Sun et al. 2007).
Phosphorylation of JNKs (MAPK8, MAPK9 and MAPK10) by MAP3K5-activated MAP2K4 (Deacon and Blank 1997, Fleming et al. 2000) allows JNKs to migrate to the nucleus (Mizukami et al. 1997) where they phosphorylate JUN. Phosphorylated JUN binds FOS phosphorylated by ERK1 or ERK2, downstream of activated RAS (Okazaki and Sagata 1995, Murphy et al. 2002), forming the activated protein 1 (AP-1) complex (FOS:JUN heterodimer) (Glover and Harrison 1995, Ainbinder et al. 1997).
Activation of p38 MAPKs and JNKs downstream of MAP3K5 (ASK1) ultimately converges on transcriptional regulation of CDKN2A locus. In dividing cells, nucleosomes bound to the CDKN2A locus are trimethylated on lysine residue 28 of histone H3 (HIST1H3A) by the Polycomb repressor complex 2 (PRC2), creating the H3K27Me3 (Me3K-28-HIST1H3A) mark (Bracken et al. 2007, Kotake et al. 2007). The expression of Polycomb constituents of PRC2 (Kuzmichev et al. 2002) - EZH2, EED and SUZ12 - and thereby formation of the PRC2, is positively regulated in growing cells by E2F1, E2F2 and E2F3 (Weinmann et al. 2001, Bracken et al. 2003). H3K27Me3 mark serves as a docking site for the Polycomb repressor complex 1 (PRC1) that contains BMI1 (PCGF4) and is therefore named PRC1.4, leading to the repression of transcription of p16INK4A and p14ARF from the CDKN2A locus, where PCR1.4 mediated repression of p14ARF transcription in humans may be context dependent (Voncken et al. 2005, Dietrich et al. 2007, Agherbi et al. 2009, Gao et al. 2012). MAPKAPK2 and MAPKAPK3, activated downstream of the MAP3K5-p38 MAPK cascade, phosphorylate BMI1 of the PRC1.4 complex, leading to dissociation of PRC1.4 complex from the CDKN2A locus and upregulation of p14ARF transcription (Voncken et al. 2005). AP-1 transcription factor, formed as a result of MAP3K5-JNK signaling, as well as RAS signaling, binds the promoter of KDM6B (JMJD3) gene and stimulates KDM6B expression. KDM6B is a histone demethylase that removes H3K27Me3 mark i.e. demethylates lysine K28 of HIST1H3A, thereby preventing PRC1.4 binding to the CDKN2A locus and allowing transcription of p16INK4A (Agger et al. 2009, Barradas et al. 2009, Lin et al. 2012).
p16INK4A inhibits phosphorylation-mediated inactivation of RB family members by CDK4 and CDK6, leading to cell cycle arrest (Serrano et al. 1993). p14ARF inhibits MDM2-mediated degradation of TP53 (p53) (Zhang et al. 1998), which also contributes to cell cycle arrest in cells undergoing oxidative stress. In addition, phosphorylation of TP53 by MAPKAPK5 (PRAK) activated downstream of MAP3K5-p38 MAPK signaling, activates TP53 and contributes to cellular senescence (Sun et al. 2007).
R-HSA-1234176 Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha HIF-alpha subunits, comprising HIF1A (Bruick and McKnight 2001, Ivan et al. 2001, Jaakkola et al. 2001), HIF2A (Percy et al. 2008, Furlow et al. 2009), and HIF3A (Maynard et al. 2003), are hydroxylated at proline residues by the prolyl hydroxylases PHD1 (EGLN2), PHD2 (EGLN1), and PHD3 (EGLN3) (Bruick and McKnight 2001, Berra et al. 2003, Hirsila et al. 2003, Metzen et al. 2003, Tuckerman et al. 2004, Appelhoff et al. 2004, Fedulova et al. 2007, Tian et al. 2011). The reaction requires molecular oxygen as a substrate and so it is inhibited by hypoxia. PHD2 (EGLN1) is predominantly cytosolic (Metzen et al. 2003) and is the key determinant in the regulation of HIF-alpha subunits by oxygen (Berra et al. 2003).
HIF-alpha subunits hydroxylated at proline residues are bound by VHL, an E3 ubiquitin ligase in a complex containing ElonginB, Elongin C, CUL2, and RBX1. VHL ubiquitinates HIF-alpha, resulting in destruction of HIF-alpha by proteolysis. Hypoxia inhibits proline hydroxylation and interaction with VHL, stabilizing HIF-alpha, which transits to the nucleus and activates gene expression.
R-HSA-417957 P2Y receptors P2Y receptors are a family of purinergic receptors, G protein-coupled receptors stimulated by nucleotides such as ATP, ADP, UTP, UDP and UDP-glucose. To date, 12 P2Y receptors have been cloned in humans (Abbracchio MP et al, 2006; Fischer W and Krugel U, 2007). P2Y receptors are present in almost all human tissues where they exert various biological functions based on their G-protein coupling. Purine nucleotides are involved in a large number of intermediate metabolic pathways, taking part as substrates, products or allosteric factors.
R-HSA-141334 PAOs oxidise polyamines to amines Polyamine oxidases (PAOs), like MAOs, are also FAD-dependant and form aldehydes and hydrogen peroxide. PAOs are approximately 60KDa in size, are monomers and are located in peroxisomes. They act on endogenous polyamines as well as some xenobiotics. The polyamines of the spermine and spermidine families are important physiologically as they mediate cell function and growth and also play a role in programmed cell death. The balance between biosynthesis, degradation and uptake of these polyamines is strictly controlled in cells and the PAO system is one of a set of enzymes that maintains this regulation (Tabor & Tabor 1984, Benedetti 2001).
R-HSA-5651801 PCNA-Dependent Long Patch Base Excision Repair Long-patch base excision repair (BER) can proceed through PCNA-dependent DNA strand displacement synthesis by replicative DNA polymerases - DNA polymerase delta complex (POLD) or DNA polymerase epsilon (POLE) complex. The PCNA-dependent branch of long-patch BER may occur in cells in the S phase of the cell cycle, when the replication complexes that contain PCNA, POLD or POLE, RPA and RFC are available. POLB incorporates the first nucleotide at the 3'-end of APEX1-generated single strand break (SSB), thus displacing the damaged AP (abasic) dideoxyribose phosphate residue at the 5'-end of SSB (5'ddRP). PCNA is recruited to BER sites by APEX1 and flap endonuclease FEN1, and loaded onto damaged DNA by RFC. POLD and POLE in complex with PCNA continue the displacement DNA strand synthesis. FEN1 cleaves the displaced DNA strand with the AP residue (5'ddRP), and DNA ligase I (LIG1) ligates the multiple nucleotide patch at the 3' end of the SSB with the FEN1-processed 5'-end of the SSB (Klungland and Lindahl 1997, Stucki et al. 1998, Dianov et al. 1999, Matsumoto et al. 1999, Podlutsky et al. 2001, Dianova et al. 2001, Ranalli et al. 2002).
R-HSA-4086400 PCP/CE pathway The planar cell polarity (PCP) pathway controls the establishment of polarity within the plane of a sheet of cells. PCP was initially characterized in Drosophila, where it controls the arrangement of hair bristles and photoreceptors in the eye (reviewed in Maung and Jenny, 2011). In vertebrates, PCP regulates convergent extension (CE, a process by which a tissue narrows along one axis and lengthens along a perpendicular one), closure of the neural tube, hair orientation and inner ear development, among others (reviewed in Seifert and Mlodzik, 2007). Studies in Drosophila identified a core group of PCP genes including Frizzled (Fz), Flamingo (Fmi), Van Gogh (Vang), Dishevelled (Dsh), Prickle (Pk) and Diego (Dgo), whose products become asymmetrically localized in the cell upon initiation of PCP (reviewed Maung and Jenny, 2011). Subsequent studies in vertebrates have shown that many of these PCP genes are conserved.
Unlike in Drosophila, where the upstream signal for the PCP pathway has not been defined, in vertebrates, a number of so-called 'non-canonical' WNTs have been shown to have roles in PCP processes. WNT5B and WNT11 are both required for CE during gastrulation, and WNT5A physically and genetically interacts with VANGL2 in the inner ear and the developing limb bud (Heisenberg et al, 2000; Rauch et al, 1997; Qian et al, 2007; Gao et al, 2011). WNT ligand can be bound by one of a number of FZD receptors or the single pass transmembrane proteins RYK or ROR, depending on context (reviewed in Green et al, 2008; Fradkin et al, 2010). Although the downstream pathway is not well established, vertebrate PCP signaling appears to work at least in part through DVL, DAAM1 and small GTPases to remodel the actin cytoskeleton (reviewed in Lai et al, 2009; Gao et al, 2012).
R-HSA-389948 PD-1 signaling The Programmed cell death protein 1 (PD-1) is one of the negative regulators of TCR signaling. PD-1 may exert its effects on cell differentiation and survival directly by inhibiting early activation events that are positively regulated by CD28 or indirectly through IL-2. PD-1 ligation inhibits the induction of the cell survival factor Bcl-xL and the expression of transcription factors associated with effector cell function, including GATA-3, Tbet, and Eomes. PD-1 exerts its inhibitory effects by bringing phosphatases SHP-1 and SHP-2 into the immune synapse, leading to dephosphorylation of CD3-zeta chain, PI3K and AKT.
R-HSA-165160 PDE3B signalling AKT (PKB) is recruited to the plasma membrane by binding phosphatidylinositol (3,4,5)-trisphosphate (PIP3). AKT is then activated by phosphorylation. Activated AKT in turn phosphorylates Phosphodiesterase 3B (PDE3B) which hydrolyzes 3',5'-cyclic AMP (cAMP) (reviewed in Manning and Toker 2017).
R-HSA-9674428 PDGFR mutants bind TKIs Aberrant signaling by activated forms of PDGFR can be inhibited by tyrosine kinase inhibitors (TKIs). PDGF receptors are class III receptor tyrosine kinase receptors, also known as dual-switch. Dual-switch receptors are activated through a series of phosphorylation and conformational changes that move the receptor from the inactive form to the fully activated form. Type II TKIs bind to the inactive form of the receptor at a site adjacent to the ATP-binding cleft, while type I TKIs bind to the active form (reviewed in Roskoski, 2018; Klug et al, 2018).
Primary mutations in PDGRFA occur in the activation loop, with a minor fraction found in the juxtamembrane domain (reviewed in Roskoski, 2018; Klug et al, 2018). Juxtamembrane domain mutations affect an autoinhibitory loop, shifting the equilibrium of the receptor towards the activated state; despite this, however, juxtamembrane domain mutants remain predominantly in the inactive state and as such are susceptible to inhibition by type II TKIs. Activation loop mutations more strongly favor the active conformation of the receptor and are susceptible to inhibition by both type II and type I TKI. The most prevalent PDGFRA mutation, D842V, promotes the active conformation strongly enough to be resistant to type II TKIs (reviewed in Roskoski, 2018; Klug et al, 2018).
R-HSA-9861559 PDH complex synthesizes acetyl-CoA from PYR The mitochondrial pyruvate dehydrogenase complex catalyzes the reaction of pyruvate, CoASH, and NAD+ to form acetylCoA, CO2, and NADH. The enzyme complex contains multiple copies of E1 alpha, E1 beta, E2, and E3, each with distinct catalytic activities (Reed and Hackert 1990; Zhou et al 2001), and the X-component (PDHX) which is required for anchoring E3 to E2 (Hiromasa et al., 2004; Vijayakrishnan et al., 2010). The reaction starts with the oxidative decarboxylation of pyruvate catalyzed by E1 alpha and beta (pyruvate dehydrogenase). Lipoamide cofactor associated with E2 is reduced at the same time. Next, the acetyl group derived from pyruvate is transferred to coenzyme A in two steps catalyzed by E2 (DLAT, dihydrolipolyl transacetylase). Finally, the oxidized form of lipoamide is regenerated and electrons are transferred to NAD+ in two steps catalyzed by E3 (DLD, dihydrolipoyl dehydrogenase). The biochemical details of this reaction have been worked out with pyruvate dehydrogenase complex and subunits purified from bovine tissue and other non-human sources. Direct evidence for the roles of the corresponding human proteins comes from studies of patients expressing mutant forms of E1 alpha (Lissens et al. 2000), E1 beta (Brown et al. 2004), E2 (Head et al. 2005), and E3 (Brautigam et al. 2005). The most common PDH complex deficiencies are caused by defects in PDHA and PDHX but can be caused by defects in any component of the complex (e.g. Pavlu-Pereira et al., 2020; reviewed in Prasad et al., 2011).
R-HSA-210990 PECAM1 interactions PECAM-1/CD31 is a member of the immunoglobulin superfamily (IgSF) and has been implicated to mediate the adhesion and trans-endothelial migration of T-lymphocytes into the vascular wall, T cell activation and angiogenesis. It has six Ig homology domains within its extracellularly and an ITIM motif within its cytoplasmic region. PECAM-1 mediates cellular interactions by both homophilic and heterophilic interactions. The cytoplasmic domain of PECAM-1 contains tyrosine residues which serves as docking sites for recruitment of cytosolic signaling molecules. Under conditions of platelet activation, PECAM-1 is phosphorylated by Src kinase members. The tyrosine residues 663 and 686 are required for recruitment of the SH2 domain containing PTPs.
R-HSA-381042 PERK regulates gene expression PERK (EIF2AK3) is a single-pass transmembrane protein located in the endoplasmic reticulum (ER) membrane such that the N-terminus of PERK is luminal and the C-terminus is cytosolic. PERK is maintained in an inactive form by interaction of its luminal domain with BiP, an ER chaperone. BiP also binds unfolded proteins and so BiP dissociates from PERK when unfolded proteins accumulate in the ER. Dissociated PERK monomers spontaneously form homodimers and the homodimeric form of PERK possesses kinase activity in its cytosolic C-terminal domain. The kinase specifically phosphorylates the translation factor eIF2alpha at Ser52, resulting in an arrest of translation. Thus translation of proteins targeted to the ER is downregulated. The translation arrest also causes depletion of Cyclin D1, a rapidly turned over protein. The depletion of Cyclin D1 in turn causes arrest of the cell cycle in G1 phase.
R-HSA-1483255 PI Metabolism Phosphatidylinositol (PI), a membrane phospholipid, can be reversibly phosphorylated at the 3, 4, and 5 positions of the inositol ring to generate seven phosphoinositides: phosphatidylinositol 3-phosphate (PI3P), phosphatidylinositol 4-phosphate (PI4P), phosphatidylinositol 5-phosphate (PI5P), phosphatidylinositol 3,4-bisphosphate PI(3,4)P2, phosphatidylinositol 4,5-bisphosphate PI(4,5)P2, phosphatidylinositol 3,5-bisphosphate PI(3,5)P2, and phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3). These seven phosphoinositides, which are heterogeneously distributed within cells, can serve as signature components of different intracellular compartment membranes and so help to mediate specificity of membrane interactions. Phosphoinositide levels are tightly regulated spatially and temporally by the action of various kinases and phosphatases whilst PI(4,5)P2 is also a substrate for phospholipase C. The differential localisation of each of these enzymes on specific compartment membranes ensures maintenance of the heterogeneous distribution of phosphoinositides despite the continuous membrane flow from one compartment to another.
PI is primarily synthesised in the endoplasmic reticulum from where the phospholipid is exported to other compartments via membrane traffic or via cytosolic phospholipid transfer proteins. Phosphorylation of PI to PI4P primarily occurs in the Golgi, where PI4P plays an important role in the biogenesis of transport vesicles such as the secretory vesicle involved in its transport to the plasma membrane. At this place, PI4P has a major function acting as a precursor of PI(4,5)P2, which is located predominantly at this membrane. PI(4,5)P2 binds and regulates a wide range of proteins that function on the cell surface and serves as a precursor for second messengers. Additionally, it helps define this membrane as a target for secretory vesicles, functions as a coreceptor in endocytic processes, and functions as a cofactor for actin nucleation.
At the plasma membrane, PI(4,5)P2 is further phosphorylated to PI(3,4,5)P3, another phosphoinositide with important signalling functions including stimulating cell survival and proliferation. The inositol 3-phosphatase, phosphatase and tensin homolog (PTEN) regenerates PI(4,5)P2, while the 5-phosphatases convert PI(3,4,5)P3 into the phosphoinositide, PI(3,4)P2, propagating the signal initiated by PI(3,4,5)P3. PI(3,4)P2 is further dephosphorylated in the endocytic pathway by inositol 4-phosphatases to PI3P, the signature phosphoinositide of the early endosomal compartment and a ligand for numerous endosomal proteins. However, the bulk of PI3P is generated directly in the endosomes by phosphorylation of PI. The subsequent endosomal phosphorylation of PI3P to PI(3,5)P2 is believed to generate docking sites for recruitment of cytosolic factors responsible for the control of outgoing traffic from the endosomes. The main localisation and function of the low abundance phosphoinositide PI5P, that can be generated by several pathways, remains to be determined (Krauss & Haucke 2007, Leventis & Grinstein 2010, Roth 2004, Gees et al. 2010, De Matteis & Godi 2004, van Meer et al. 2008, Vicinanza et al. 2008, Lemmon 2008, Kutaleladze 2010, Robinson & Dixon 2006, Blero et al. 2007, Liu & Bankaitis 2010, McCrea & De Camilli 2009, Vicinanza et al. 2008, Di Paolo & De Camilli, 2006).
R-HSA-1483196 PI and PC transport between ER and Golgi membranes The phosphatidylinositol transfer protein beta isoform (PITPNB) bound to phosphatidylinositol (PI) complex transports from the endoplasmic reticulum (ER) membrane to the Golgi membrane, where phosphatidylcholine (PC) is exchanged for PI. PITPNB now in complex with PC transports back to the ER membrane where PI is now exchanged for PC, and the cycle repeats. This process has been characterized in detail in bovine and rodent model systems (e.g., Wirtz et al. 2006; Ghosh and Bankaitis 2011), which provide a framework for organizing the more limited data available for the very well conserved human proteins and processes( Carvou et al. 2010, Shadan et al. 2008).
R-HSA-5654689 PI-3K cascade:FGFR1 The ability of growth factors to protect from apoptosis is primarily due to the activation of the AKT survival pathway. P-I-3-kinase dependent activation of PDK leads to the activation of AKT which in turn affects the activity or expression of pro-apoptotic factors, which contribute to protection from apoptosis. AKT activation also blocks the activity of GSK-3b which could lead to additional antiapoptotic signals.
R-HSA-5654695 PI-3K cascade:FGFR2 The ability of growth factors to protect from apoptosis is primarily due to the activation of the AKT survival pathway. P-I-3-kinase dependent activation of PDK leads to the activation of AKT which in turn affects the activity or expression of pro-apoptotic factors, which contribute to protection from apoptosis. AKT activation also blocks the activity of GSK-3b which could lead to additional antiapoptotic signals.
R-HSA-5654710 PI-3K cascade:FGFR3 The ability of growth factors to protect from apoptosis is primarily due to the activation of the AKT survival pathway. P-I-3-kinase dependent activation of PDK leads to the activation of AKT which in turn affects the activity or expression of pro-apoptotic factors, which contribute to protection from apoptosis. AKT activation also blocks the activity of GSK-3b which could lead to additional antiapoptotic signals.
R-HSA-5654720 PI-3K cascade:FGFR4 The ability of growth factors to protect from apoptosis is primarily due to the activation of the AKT survival pathway. P-I-3-kinase dependent activation of PDK leads to the activation of AKT which in turn affects the activity or expression of pro-apoptotic factors, which contribute to protection from apoptosis. AKT activation also blocks the activity of GSK-3b which could lead to additional antiapoptotic signals.
R-HSA-109704 PI3K Cascade The PI3K (Phosphatidlyinositol-3-kinase) - AKT signaling pathway stimulates cell growth and survival.
R-HSA-1963642 PI3K events in ERBB2 signaling ERBB2:ERBB3 and ERBB2:ERBB4cyt1 heterodimers activate PI3K signaling by direct binding of PI3K regulatory subunit p85 (Yang et al. 2007, Cohen et al. 1996, Kaushansky et al. 2008) to phosphorylated tyrosine residues in the C-tail of ERBB3 (Y1054, Y1197, Y1222, Y1224, Y1276 and Y1289) and ERBB4 CYT1 isoforms (Y1056 in JM-A CYT1 isoform and Y1046 in JM-B CYT1 isoform). Regulatory subunit p85 subsequently recruits catalytic subunit p110 of PI3K, resulting in the formation of active PI3K, conversion of PIP2 to PIP3, and PIP3-mediated activation of AKT signaling (Junttila et al. 2009, Kainulainen et al. 2000). Heterodimers of ERBB2 and EGFR recruit PI3K indirectly, through GRB2:GAB1 complex (Jackson et al. 2004), which again leads to PIP3-mediated activation of AKT signaling.
R-HSA-1250342 PI3K events in ERBB4 signaling The CYT1 isoforms of ERBB4 possess a C-tail tyrosine residue that, upon trans-autophosphorylation, serves as a docking site for the p85 alpha subunit of PI3K - PIK3R1 (Kaushansky et al. 2008, Cohen et al. 1996). Binding of PIK3R1 to CYT1 isoforms of ERBB4 is followed by recruitment of the p110 catalytic subunit of PI3K (PIK3CA), leading to assembly of an active PI3K complex that converts PIP2 to PIP3 and activates AKT signaling (Kainulainen et al. 2000).
R-HSA-2219528 PI3K/AKT Signaling in Cancer Class IA PI3K is a heterodimer of a p85 regulatory subunit (encoded by PIK3R1, PIK3R2 or PIK3R3) and a p110 catalytic subunit (encoded by PIK3CA, PIK3CB or PIK3CD). In the absence of activating signals, the regulatory subunit stabilizes the catalytic subunit while inhibiting its activity. The complex becomes activated when extracellular signals stimulate the phosphorylation of the cytoplasmic domains of transmembrane receptors or receptor-associated proteins. The p85 regulatory subunit binds phosphorylated motifs of activator proteins, which induces a conformational change that relieves p85-mediated inhibition of the p110 catalytic subunit and enables PI3K to phosphorylate PIP2 to form PIP3. The phosphoinositide kinase activity of PI3K is opposed by the phosphoinositide phosphatase activity of PTEN.
PIP3 acts as a messenger that recruits PDPK1 (PDK1) and AKT (AKT1, AKT2 or AKT3) to the plasma membrane. PDPK1 also possesses a low affinity for PIP2, so small amounts of PDPK1 are always present at the membrane. Binding of AKT to PIP3 induces a conformational change that enables TORC2 complex to phosphorylate AKT at a conserved serine residue (S473 in AKT1). Phosphorylation at the serine residue enables AKT to bind to PDPK1 and exposes a conserved threonine residue (T308) that is phosphorylated by PDPK1. AKT phosphorylated at both serine and threonine residues dissociates from the plasma membrane and acts as a serine/threonine kinase that phosphorylates a number of cytosolic and nuclear targets involved in regulation of cell metabolism, survival and gene expression. For a recent review, please refer to Manning and Cantley, 2007.
Signaling by PI3K/AKT is frequently constitutively activated in cancer. This activation can be via gain-of-function mutations in PI3KCA (encoding catalytic subunit p110alpha), PIK3R1 (encoding regulatory subunit p85alpha) and AKT1. The PI3K/AKT pathway can also be constitutively activated by loss-of-function mutations in tumor suppressor genes such as PTEN.
Gain-of-function mutations activate PI3K signaling by diverse mechanisms. Mutations affecting the helical domain of PIK3CA and mutations affecting nSH2 and iSH2 domains of PIK3R1 impair inhibitory interactions between these two subunits while preserving their association. Mutations in the catalytic domain of PIK3CA enable the kinase to achieve an active conformation. PI3K complexes with gain-of-function mutations therefore produce PIP3 and activate downstream AKT in the absence of growth factors (Huang et al. 2007, Zhao et al. 2005, Miled et al. 2007, Horn et al. 2008, Sun et al. 2010, Jaiswal et al. 2009, Zhao and Vogt 2010, Urick et al. 2011). While AKT1 gene copy number, expression level and phosphorylation are often increased in cancer, only one low frequency point mutation has been repeatedly reported in cancer and functionally studied. This mutation represents a substitution of a glutamic acid residue with lysine at position 17 of AKT1, and acts by enabling AKT1 to bind PIP2. PIP2-bound AKT1 is phosphorylated by TORC2 complex and by PDPK1 that is always present at the plasma membrane, due to low affinity for PIP2. Therefore, E17K substitution abrogates the need for PI3K in AKT1 activation (Carpten et al. 2007, Landgraf et al. 2008).
Loss-of-function mutations affecting the phosphatase domain of PTEN are frequently found in sporadic cancers (Kong et al. 1997, Lee et al. 1999, Han et al. 2000), as well as in PTEN hamartoma tumor syndromes (PHTS) (Marsh et al. 1998). PTEN can also be inactivated by gene deletion or epigenetic silencing, or indirectly by overexpression of microRNAs that target PTEN mRNA (Huse et al. 2009). Cells with deficient PTEN function have increased levels of PIP3, and therefore increased AKT activity. For a recent review, please refer to Hollander et al. 2011.
Because of their clear involvement in human cancers, PI3K and AKT are targets of considerable interest in the development of small molecule inhibitors. Although none of the currently available inhibitors display preference for mutant variants of PIK3CA or AKT, several inhibitors targeting the wild-type kinases are undergoing clinical trials. These include dual PI3K/mTOR inhibitors, class I PI3K inhibitors, pan-PI3K inhibitors, and pan-AKT inhibitors. While none have yet been approved for clinical use, these agents show promise for future therapeutics. In addition, isoform-specific PI3K and AKT inhibitors are currently being developed, and may provide more specific treatments along with reduced side-effects. For a recent review, please refer to Liu et al. 2009.
R-HSA-198203 PI3K/AKT activation PI3K/AKT signalling is a major regulator of neuron survival. It blocks cell death by both impinging on the cytoplasmic cell death machinery and by regulating the expression of genes involved in cell death and survival. In addition, it may also use metabolic pathways to regulate cell survival.The PI3K/AKT pathway also affects axon diameter and branching (Marcus et al, 2002) and regulates small G proteins like RhoA (Vanhaesebroeck, B and Waterman, MD, 1999), which control the behaviour of the F-actin cytoskeleton. Moreover, through its connection with the TOR pathway, it promotes translation of a subset of mRNAs.
R-HSA-6811555 PI5P Regulates TP53 Acetylation Under conditions of cellular stress, nuclear levels of phosphatidylinositol-5-phosphate (PI5P) increase and, through interaction with ING2, result in nuclear retention/accumulation of ING2. ING2 binds TP53 (p53) and recruits histone acetyltransferase EP300 (p300) to TP53, leading to TP53 acetylation. Increased nuclear PI5P levels positively regulate TP53 acetylation (Ciruela et al. 2000, Gozani et al. 2003, Jones et al. 2006, Zou et al. 2007, Bultsma et al. 2010).
R-HSA-6811558 PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling Phosphatidylinositol-5-phosphate (PI5P) may modulate PI3K/AKT signaling in several ways. PI5P is used as a substrate for production of phosphatidylinositol-4,5-bisphosphate, PI(4,5)P2 (Rameh et al. 1997, Clarke et al. 2008, Clarke et al. 2010, Clarke and Irvine 2013, Clarke et al. 2015), which serves as a substrate for activated PI3K, resulting in the production of PIP3 (Mandelker et al. 2009, Burke et al. 2011). The majority of PI(4,5)P2 in the cell, however, is produced from the phosphatidylinositol-4-phosphate (PI4P) substrate (Zhang et al. 1997, Di Paolo et al. 2002, Oude Weernink et al. 2004, Halstead et al. 2006, Oude Weernink et al. 2007). PIP3 is necessary for the activating phosphorylation of AKT. AKT1 can be deactivated by the protein phosphatase 2A (PP2A) complex that contains a regulatory subunit B56-beta (PPP2R5B) or B56-gamma (PPP2R5C). PI5P inhibits AKT1 dephosphorylation by PP2A through an unknown mechanism (Ramel et al. 2009). Increased PI5P levels correlate with inhibitory phosphorylation(s) of the PP2A complex. MAPK1 (ERK2) and MAPK3 (ERK1) are involved in inhibitory phosphorylation of PP2A, in a process that involves IER3 (IEX-1) (Letourneux et al. 2006, Rocher et al. 2007). It is uncertain, however, whether PI5P is in any way involved in ERK-mediated phosphorylation of PP2A or if it regulates another PP2A kinase.
R-HSA-5205685 PINK1-PRKN Mediated Mitophagy This is the process of selective removal of damaged mitochondria by autophagosomes and subsequent catabolism by lysosomes. In healthy mitochondria, PTEN-induced putative kinase 1 (PINK1) is imported to the inner mitochondrial membrane, presumably through the TOM/TIM complex. The TIM complex associated protease, mitochondrial MPP, cleaves PINK1 mitochondrial targeting sequence (MTS). PINK1 may be cleaved by the inner membrane presenilin-associated rhomboid-like protease (PARL) and ultimately proteolytically degraded. Loss of membrane potential in damaged mitochondria prevents the import of PINK1 which accumulates on the mitochondrial outer membrane (MOM) of the defective mitochondria. Activation of PINK1 at MOM is achieved via dimerization-mediated trans-autophosphorylation of PINK1 at multiple sites including S228 and S402 (Okatsu K et al., 2012, 2013; Aerts L et al., 2015; Rasool S et al., 2018, 2022; Gan ZY et al., 2022). Activated PINK1 phosphorylates S65 of ubiquitin (Ub) on MOM proteins which leads to increased recruitment of the E3 ubiquitin ligase Parkin (PRKN) to damaged mitochondria (Koyano F et al., 2014; Shiba-Fukushima K et al., 2014; Ordureau A et al., 2015). Activated PINK1 also phosphorylates PRKN at S65 in the N-terminal Ub-like domain inducing the E3 ligase activity of PRKN (Kondapalli et al., 2012; Kazlauskaite A et al., 2015; Ordureau A et al., 2015). Activated PRKN promotes the ubiquitination of mitochondrial substrates including mitofusin 1 and 2 (MFN1, 2) and the voltage-dependent anion channel 1 and 3 (VDAC1, 3). The E3 ligase activity of PRKN generates Ub moieties for PINK1-mediated phosphorylation of Ub thus leading to a feedforward loop in the PINK1:PRKN pathway (Ordureau A et al., 2015; Sauve V et al., 2022). Ubiquitin chains on PRKN-ubiquitinated substrates recruit cargo receptors such as SQSTM1 (p62) and OPTN linking the ubiquitinated substrates to the microtubule-associated proteins 1A/1B light chain 3 (LC3, MAP1LC3) (Heo LM et al., 2015; Lazarou M et al., 2015). The recruitment of both MAP1LC3 (LC3) complexes and the autophagy proteins 5 and 12 (Atg5: Atg12) complex to the autophagosome membrane promotes autophagosome formation. The mitochondrion is engulfed after the isolation membrane grows to a sufficient size to engulf the mitochondrion. Once autophagic vesicle formation is complete, vesicle fusion with lysosomes occurs to form autophagolysosomes in which the lysosomal hydrolases (cathepsins and lipases) degrade the intra autophagosomal content. Cathepsin also degrades LC3 on the intra autophagosomal surface of the autophagic vesicle.
R-HSA-1257604 PIP3 activates AKT signaling Signaling by AKT is one of the key outcomes of receptor tyrosine kinase (RTK) activation. AKT is activated by the cellular second messenger PIP3, a phospholipid that is generated by PI3K. In ustimulated cells, PI3K class IA enzymes reside in the cytosol as inactive heterodimers composed of p85 regulatory subunit and p110 catalytic subunit. In this complex, p85 stabilizes p110 while inhibiting its catalytic activity. Upon binding of extracellular ligands to RTKs, receptors dimerize and undergo autophosphorylation. The regulatory subunit of PI3K, p85, is recruited to phosphorylated cytosolic RTK domains either directly or indirectly, through adaptor proteins, leading to a conformational change in the PI3K IA heterodimer that relieves inhibition of the p110 catalytic subunit. Activated PI3K IA phosphorylates PIP2, converting it to PIP3; this reaction is negatively regulated by PTEN phosphatase. PIP3 recruits AKT to the plasma membrane, allowing TORC2 to phosphorylate a conserved serine residue of AKT. Phosphorylation of this serine induces a conformation change in AKT, exposing a conserved threonine residue that is then phosphorylated by PDPK1 (PDK1). Phosphorylation of both the threonine and the serine residue is required to fully activate AKT. The active AKT then dissociates from PIP3 and phosphorylates a number of cytosolic and nuclear proteins that play important roles in cell survival and metabolism. For a recent review of AKT signaling, please refer to Manning and Cantley, 2007.
R-HSA-1660510 PIPs transport between Golgi and plasma membranes A secretory vesicle containing primarily containing the phospholipid phosphatidylinositol 4-phosphate (PI4P) is exported from the Golgi membrane to the plasma membrane (Szentpetery et al. 2010, Godi et al. 2004, Hammond et al. 2009).
R-HSA-1660502 PIPs transport between early and late endosome membranes The maturation of the early endosome compartment into a late endosome is triggered by the presence of phosphoinositide phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) (Cabezas et al. 2006, Ikonomov et al. 2006, Ikonomov et al. 2001).
R-HSA-1660537 PIPs transport between early endosome and Golgi membranes The phosphoinositide phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) is exported from the early endosome membrane to the Golgi membrane (Rutherford et al. 2006).
R-HSA-1660508 PIPs transport between late endosome and Golgi membranes The phosphoinositide phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) is exported from the late endosome membrane to the Golgi membrane (Rutherford et al. 2006).
R-HSA-1660524 PIPs transport between plasma and early endosome membranes The phosphoinositide phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2) translocates from the plasma membrane to the early endosome membrane (Watt et al. 2004, Ivetac et al. 2005).
R-HSA-5601884 PIWI-interacting RNA (piRNA) biogenesis In germ cells of humans and mice, precursors of PIWI-interacting RNAs (piRNAs) are transcribed from a few hundred sequence clusters, as well as individual transposons, intergenic regions, and genes in the genome. These longer transcripts are processed to yield piRNAs of 26-30 nucleotides independently of DICER, the enzyme responsible for microRNAs (miRNAs) and small interfering RNAs (siRNAs) (reviewed in Girard and Hannon 2008, Siomi et al. 2011, Ishizu et al. 2012, Pillai and Chuma 2012, Bortvin 2013, Chuma and Nakano 2013, Sato and Siomi 2013). The initial step in processing long transcripts to piRNAs is cleavage by PLD6 (MitoPLD), which generates the mature 5' end. The cleavage products of PLD6 are bound by either PIWIL1 (HIWI, MIWI) or PIWIL2 (HILI, MILI) in complexes with several other proteins. The 3' end is trimmed by an unknown exonuclease to generate the mature piRNA. PIWIL1:piRNA complexes appear to be involved in post-transcriptional silencing in the cytosol while PIWIL2:piRNA complexes generate further piRNAs from transposon transcripts and other transcripts in the cytosol. Cleavage products from PIWIL2:piRNA may be loaded into either PIWIL2 or PIWIL4 (HIWI2, MIWI2). Loading into PIWIL2 forms a step in a cytosolic amplification loop called the "ping-pong cycle" which yields further PIWIL2:piRNA complexes from cleaved precursor RNAs. Loading into PIWIL4 yields a complex also containing TDRD9 that translocates to the nucleus and directs DNA methylation of cognate loci, causing transcriptional silencing during spermatogenesis. Transcriptional silencing by piRNAs is necessary to limit transposition of endogenous transposons such as L1 elements in the genome.
R-HSA-163615 PKA activation A number of inactive tetrameric PKA holoenzymes are produced by the combination of homo- or heterodimers of the different regulatory subunits associated with two catalytic subunits. When cAMP binds to two specific binding sites on the regulatory subunits, these undergo a conformational change that causes the dissociation of a dimer of regulatory subunits bound to four cAMP from two monomeric, catalytically active PKA subunits.
R-HSA-164378 PKA activation in glucagon signalling Adenylate cyclase catalyses the synthesis of cyclic AMP (cAMP) from ATP. In the absence of cAMP, protein kinase A (PKA) exists as inactive tetramers of two catalytic subunits and two regulatory subunits. cAMP binding to PKA tetramers causes them to dissociate and release their catalytic subunits as active monomers. Four isoforms of the regulatory subunit are known, that differ in their tissue specificity and functional characteristics, but the specific isoform activated in response to glucagon signaling has not yet been identified.
R-HSA-111931 PKA-mediated phosphorylation of CREB Cyclic adenosine 3',5'-monophosphate (cAMP) induces gene transcription through activation of cAMP-dependent protein kinase (PKA), and subsequent phosphorylation of the transcription factor cAMP response element-binding protein, CREB, at serine-133.
R-HSA-163358 PKA-mediated phosphorylation of key metabolic factors Upon dissociation of protein kinase A (PKA) tetramers in the presence of cAMP, the released PKA catalytic monomers phosphorylate specific serine and threonine residues of several metabolic enzymes. These target enzymes include glycogen phosphorylase kinase, glycogen synthase and PF2K-Pase. PKA also phosphorylates ChREBP (Carbohydrate Response Element Binding Protein), preventing its movement into the nucleus and thus its function as a positive transcription factor for genes involved in glycolytic and lipogenic reactions.
R-HSA-109703 PKB-mediated events PKB and PDK1 are activated via membrane-bound PIP3. Activated PDK1 phosphorylates PKB, which in turn phosphorylates PDE3B. The latter hydrolyses cAMP to 5'AMP, depleting cAMP pools.
R-HSA-3214841 PKMTs methylate histone lysines Lysine methyltransferases (KMTs) and arginine methyltransferases (RMTs) have a common mechanism of catalysis. Both families transfer a methyl group from a common donor, S-adenosyl-L-methionine (SAM), to the nitrogen atom on the epsilon-amino group of lysine or arginine (Smith & Denu 2009) using a bimolecular nucleophillic substitution (SN2) methyl transfer mechanism (Smith & Denu 2009, Zhang & Bruice 2008). All human KMTs except DOT1L (KMT4) (Feng et al. 2002, van Leeuwen et al. 2002, Lacoste et al. 2002) have a ~130 amino acid catalytic domain referred to as the SET domain (Del Rizzo & Trievel 2011, Dillon et al. 2005, Herz et al. 2013).
Some KMTs selectively methylate a particular lysine residue on a specific histone type. The extent of this methylation (mono-, di- or tri-methylation) also can be stringent (Herz et al. 2013, Copeland et al. 2009). Many KMTs also have non-histone substrates (Herz et al 2013), which are not discussed in this module.
The coordinates of post-translational modifications represented and described here follow UniProt standard practice whereby coordinates refer to the translated protein before any processing. Histone literature typically refers to specific residues by numbers which are determined after the initiating methionine has been removed. Therefore the coordinates of post-translated residues in the Reactome database and described here are frequently +1 when compared to the histone literature.
SET domain-containing proteins are classified in one of 7 families (Dillon et al. 2005). First to be discovered were the SUV39 family named after founding member SUV39H1 (KMT1A), which selectively methylates lysine-10 of histone H3 (H3K9) (Rea et al. 2000). Family member EHMT2 (KMT1C, G9A) is the predominant H3K9 methyltransferase in mammals (Tachibana et al. 2002). SETDB1 (KMT1E, ESET) also predominantly methylates H3K9, most effectively when complexed with ATF7IP (MCAF, hAM) (Wang et al. 2003).
SETD2 (KMT3A, HYPB), a member of the SET2 family, specifically methylates histone H3 lysine-37 (H3K36) (Sun et al. 2005). WHSC1 (KMT3G, NSD2, MMSET) a member of the same family, targets H3K36 when provided with nucleosome substrates but also can methylate histone H4 lysine-45 when octameric native or recombinant nucleosome substrates are provided (Li et al. 2009); dimethylation of histone H3 at lysine-37 (H3K36me2) is thought to be the principal chromatin-regulatory activity of WHSC1 (Kuo et al. 2011). Relatives NSD1 (KMT3B) and WHSC1L1 (KMT3F, NSD3) also methylate nucleosomal H3K36. NSD1 is active on unmethylated or a mimetic monomethylated H3K36, but not di- or trimethylated H3K36 mimetics (Li et al. 2009). Human SETD7 (KMT7, SET7/9), not classified within the 7 SET-domain containing families, mono-methylates lysine-5 of histone H3 (H3K4) (Xiao et al. 2003).
R-HSA-9833482 PKR-mediated signaling Interferon-induced, double-stranded RNA-activated protein kinase PKR (EIF2AK2) mainly halts cellular protein translation by phosphorylating eIF2α, which blocks the recycling of GDP-eIF2 to GTP-eIF2 required for cap-dependent translation initiation. PKR is constitutively expressed at low level, and its expression is up-regulated by interferon alpha/beta signaling. PKR is mainly localized in the cytoplasm with a small fraction in the nucleus (Tian & Mathews 2001).
PKR was identified in the 1970s (Friedman et al, 1972; Kerr et al., 1977). Its activation is characterized by the shifting of its monomer/dimer equilibrium towards the dimer, with subsequent autophosphorylation (reviewed by Sadler & Williams, 2007; Bou-Nader et al, 2019). Possible activating factors include binding of viral dsRNA to the PKR dsRNA binding domain (reviewed by Nallagatla et al, 2011), as well as cellular proteins (ISG15, PACT, DCP1A) and heparin (Patel & Sen, 1998; Dougherty et al., 2014; George et al., 1996; Fasciano et al., 2005; reviewed by Zhang et al, 2021). General translation shutdown by PKR can therefore be promoted by both viral infection and the integrated response of the cell to stress stimuli (reviewed by Pizzinga et al, 2019; Costa-Mattioli & Walter, 2020). Several cellular inhibitors of PKR activation and eIF2α phosphorylation by PKR have been identified and binding of PKR to viral proteins from RNA viruses (e.g. HIV, influenza A, RSV) has also been shown to contribute to inhibition (reviewed by Cesaro & Michiels, 2021). In addition to its role in translation shutdown via eIF2α, PKR affects translation through NFAR protein phosphorylation; it can also phosphorylate RNA helicase A, CDC2, and MKK6, thus modulating RNA metabolism, G2 arrest, and p38 MAPK activation. Finally, PKR can bind to TRAF proteins, the IkappaB kinase complex, GSK-3beta, and several inflammasome components leading to NF-kappa B activation, tau phosphorylation, apoptosis, and inflammasome activation (reviewed by Gil & Esteban, 2000; Garcia et al, 2007; Pindel & Sadler, 2011; Marchal et al, 2014; Yim & Williams, 2014; McKey et al, 2021).
R-HSA-112043 PLC beta mediated events The phospholipase C (PLC) family of enzymes is both diverse and complex. The isoforms beta, gamma and delta (each have subtypes) make up the members of this family. PLC hydrolyzes phosphatidylinositol bisphosphate (PIP2) into two second messengers, inositol 1,4,5-trisphosphate (IP3) and diacylglycerol (DAG). IP3 mobilizes intracellular calcium stores while DAG activates protein kinase C isoforms which are involved in regulatory functions.
R-HSA-167021 PLC-gamma1 signalling The activation of phosphlipase C-gamma (PLC-gamma) and subsequent mobilization of calcium from intracellular stores are essential for neurotrophin secretion. PLC-gamma is activated through the phosphorylation by TrkA receptor kinase and this form hydrolyses PIP2 to generate inositol tris-phosphate (IP3) and diacylglycerol (DAG). IP3 promotes the release of Ca2+ from internal stores and this results in activation of enzymes such as protein kinase C and Ca2+ calmodulin-regulated protein kinases.
R-HSA-1251932 PLCG1 events in ERBB2 signaling Activation of PLCG1 signaling is observed only in the presence of ERBB2:EGFR heterodimers, with PLCG1 binding to phosphorylated tyrosine Y992 and Y1173 in the C-tail of EGFR (Chattopadhyay et al. 1999), and potentially Y1023 in the C-tail of ERBB2 (Fazioli et al. 1991, Cohen et al. 1996).
R-HSA-110362 POLB-Dependent Long Patch Base Excision Repair During POLB-dependent long patch base excision repair (BER), PARP1 and/or PARP2 is recruited to the BER site along with flap endonuclease FEN1. PARP1 and/or PARP2 and FEN1 facilitate POLB-mediated strand displacement synthesis which involves incorporation of 2-10 nucleotides at the 3' end of the APEX1-created single strand break (SSB). After the DNA strand displacement synthesis is completed and the displaced strand is cleaved, POLB recruits DNA ligase I (LIG1) to ligate the SSB (Klungland and Lindahl 1997, Dimitriadis et al. 1998, Prasad et al. 2001, Lavrik et al. 2001, Tomkinson et al. 2001, Ranalli et al. 2002, Cistulli et al. 2004, Liu et al. 2005).
R-HSA-2892247 POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation POU5F1 (OCT4), SOX2, and NANOG bind elements in the promoters of target genes. The target genes of each transcription factor overlap extensively: POU5F1, SOX2, and NANOG co-occupy at least 353 genes (Boyer et al. 2005). About half of POU5F1 targets also bind SOX2 and about 90% of these also bind NANOG (Boyer et al. 2005). Upon binding the transcription factors activate expression of one subset of target genes and repress another subset (Kim et al. 2006, Matoba et al. 2006, Player et al. 2006, Babaie et al. 2007). The targets listed in this module are those that have been described as composing activated genes in the core transcriptional network of pluripotent stem cells (Assou et al. 2007, Chavez et al. 2009, Jung et al. 2010). Inferences from mouse to human have been made with caution because of significant differences between the two species (Ginis et al. 2004).
R-HSA-2892245 POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation POU5F1 (OCT4), SOX2, and NANOG bind elements in the promoters of target genes. The target genes of each transcription factor overlap extensively: POU5F1, SOX2, and NANOG co-occupy at least 353 genes (Boyer et al. 2005). About half of POU5F1 targets also bind SOX2 and about 90% of these also bind NANOG (Boyer et al. 2005). Upon binding the transcription factors activate expression of one subset of target genes in the core transcriptional network of pluripotent stem cells and repress another subset (Kim et al. 2006, Matoba et al. 2006, Player et al. 2006, Assou et al. 2007, Babaie et al. 2007, Chavez et al. 2009, Jung et al. 2010). The target genes listed in this module are the repressed genes. Caution must be used when making inferences about human stem cells from mouse stem cells because of significant differences between the two species (Ginis et al. 2004).
R-HSA-163767 PP2A-mediated dephosphorylation of key metabolic factors A member of the PP2A family of phosphatases dephosphorylates both cytosolic and nuclear forms of ChREBP (Carbohydrate Response Element Binding Protein). In the nucleus, dephosphorylated ChREBP complexes with MLX protein and binds to ChRE sequence elements in chromosomal DNA, activating transcription of genes involved in glycolysis and lipogenesis. The phosphatase is activated by Xylulose-5-phosphate, an intermediate of the pentose phosphate pathway (Kabashima et al. 2003). The rat enzyme has been purified to homogeneity and shown by partial amino acid sequence analysis to differ from previously described PP2A phosphatases (Nishimura and Uyeda 1995) - the human enzyme has not been characterized.
R-HSA-1989781 PPARA activates gene expression The set of genes regulated by PPAR-alpha is not fully known in humans, however many examples have been found in mice. Genes directly activated by PPAR-alpha contain peroxisome proliferator receptor elements (PPREs) in their promoters and include:
1) genes involved in fatty acid oxidation and ketogenesis (Acox1, Cyp4a, Acadm, Hmgcs2);
2) genes involved in fatty acid transport (Cd36, , Slc27a1, Fabp1, Cpt1a, Cpt2);
3) genes involved in producing fatty acids and very low density lipoproteins (Me1, Scd1);
4) genes encoding apolipoproteins (Apoa1, Apoa2, Apoa5);
5) genes involved in triglyceride clearance ( Angptl4);
6) genes involved in glycerol metabolism (Gpd1 in mouse);
7) genes involved in glucose metabolism (Pdk4);
8) genes involved in peroxisome proliferation (Pex11a);
9) genes involved in lipid storage (Plin, Adfp).
Many other genes are known to be regulated by PPAR-alpha but whether their regulation is direct or indirect remains to be found. These genes include: ACACA, FAS, SREBP1, FADS1, DGAT1, ABCA1, PLTP, ABCB4, UGT2B4, SULT2A1, Pnpla2, Acsl1, Slc27a4, many Acot genes, and others (reviewed in Rakhshandehroo et al. 2010).
R-HSA-212300 PRC2 methylates histones and DNA Polycomb group proteins are responsible for the heritable repression of genes during development (Lee et al. 2006, Ku et al. 2008, reviewed in Simon and Kingston 2009, Margueron and Reinberg 2011, Di Croce and Helin 2013). Two major families of Polycomb complexes exist: Polycomb Repressive Complex 1 (PRC1) and Polycomb Repressive Complex 2 (PRC2). PRC1 and PRC2 each appear to comprise sets of distinct complexes that contain common core subunits and distinct accessory subunits (reviewed in Nayak et al. 2011). PRC2, through its component EZH2 or, in some complexes, EZH1 produces the initial molecular mark of repression, the trimethylation of lysine-27 of histone H3 (H3K27me3). How PRC2 is initially recruited to a locus remains unknown, however cytosine-guanine (CpG) motifs and transcripts have been suggested. Different mechanisms may be used at different loci. The trimethylated H3K27 produced by PRC2 is bound by the Polycomb subunit of PRC1. PRC1 ubiquitinates histone H2A and maintains repression.
R-HSA-5674404 PTEN Loss of Function in Cancer Loss-of-function mutations affecting the phosphatase domain of PTEN are frequently found in sporadic cancers (Kong et al. 1997, Lee et al. 1999, Han et al. 2000), as well as in PTEN hamartoma tumor syndromes (PHTS) (Marsh et al. 1998). PTEN can also be inactivated by gene deletion or epigenetic silencing, or indirectly by overexpression of microRNAs that target PTEN mRNA (Huse et al. 2009). Cells with deficient PTEN function have increased levels of PIP3, and therefore increased AKT activity. For a recent review, please refer to Hollander et al. 2011.
R-HSA-6807070 PTEN Regulation PTEN is regulated at the level of gene transcription, mRNA translation, localization and protein stability.
Transcription of the PTEN gene is regulated at multiple levels. Epigenetic repression involves the recruitment of Mi-2/NuRD upon SALL4 binding to the PTEN promoter (Yang et al. 2008, Lu et al. 2009) or EVI1-mediated recruitment of the polycomb repressor complex (PRC) to the PTEN promoter (Song et al. 2009, Yoshimi et al. 2011). Transcriptional regulation is also elicited by negative regulators, including NR2E1:ATN1 (atrophin-1) complex, JUN (c-Jun), SNAIL and SLUG (Zhang et al. 2006, Vasudevan et al. 2007, Escriva et al. 2008, Uygur et al. 2015) and positive regulators such as TP53 (p53), MAF1, ATF2, EGR1 or PPARG (Stambolic et al. 2001, Virolle et al. 2001, Patel et al. 2001, Shen et al. 2006, Li et al. 2016).
MicroRNAs miR-26A1, miR-26A2, miR-22, miR-25, miR-302, miR-214, miR-17-5p, miR-19 and miR-205 bind PTEN mRNA and inhibit its translation into protein. These microRNAs are altered in cancer and can account for changes in PTEN levels (Meng et al. 2007, Xiao et al. 2008, Yang et al. 2008, Huse et al. 2009, Kim et al. 2010, Poliseno, Salmena, Riccardi et al. 2010, Cai et al. 2013). In addition, coding and non-coding RNAs can prevent microRNAs from binding to PTEN mRNA. These RNAs are termed competing endogenous RNAs or ceRNAs. Transcripts of the pseudogene PTENP1 and mRNAs transcribed from SERINC1, VAPA and CNOT6L genes exhibit this activity (Poliseno, Salmena, Zhang et al. 2010, Tay et al. 2011, Tay et al. 2014).
PTEN can translocate from the cytosol to the nucleus after undergoing monoubiquitination. PTEN's ability to localize to the nucleus contributes to its tumor suppressive role (Trotman et al. 2007). The ubiquitin protease USP7 (HAUSP) targets monoubiquitinated PTEN in the nucleus, resulting in PTEN deubiquitination and nuclear exclusion. PML, via an unknown mechanism that involves USP7- and PML-interacting protein DAXX, inhibits USP7-mediated deubiquitination of PTEN, thus promoting PTEN nuclear localization. Disruption of PML function in acute promyelocytic leukemia, through a chromosomal translocation that results in expression of a fusion protein PML-RARA, leads to aberrant PTEN localization (Song et al. 2008).
Several ubiquitin ligases, including NEDD4, WWP2, STUB1 (CHIP), RNF146, XIAP and MKRN1, polyubiquitinate PTEN and target it for proteasome-mediated degradation (Wang et al. 2007, Van Themsche et al. 2009, Ahmed et al. 2011, Maddika et al. 2011, Lee et al. 2015, Li et al. 2015). The ubiquitin proteases USP13 and OTUD3, frequently down-regulated in breast cancer, remove polyubiquitin chains from PTEN, thus preventing its degradation and increasing its half-life (Zhang et al. 2013, Yuan et al. 2015). The catalytic activity of PTEN is negatively regulated by PREX2 binding (Fine et al. 2009, Hodakoski et al. 2014) and TRIM27-mediated ubiquitination (Lee et al. 2013), most likely through altered PTEN conformation.
In addition to ubiquitination, PTEN also undergoes SUMOylation (Gonzalez-Santamaria et al. 2012, Da Silva Ferrada et al. 2013, Lang et al. 2015, Leslie et al. 2016). SUMOylation of the C2 domain of PTEN may regulate PTEN association with the plasma membrane (Shenoy et al. 2012) as well as nuclear localization of PTEN (Bassi et al. 2013, Collaud et al. 2016). PIASx-alpha, a splicing isorom of E3 SUMO-protein ligase PIAS2 has been implicated in PTEN SUMOylation (Wang et al. 2014). SUMOylation of PTEN may be regulated by activated AKT (Lin et al. 2016). Reactions describing PTEN SUMOylation will be annotated when mechanistic details become available.
Phosphorylation affects the stability and activity of PTEN. FRK tyrosine kinase (RAK) phosphorylates PTEN on tyrosine residue Y336, which increases PTEN half-life by inhibiting NEDD4-mediated polyubiquitination and subsequent degradation of PTEN. FRK-mediated phosphorylation also increases PTEN enzymatic activity (Yim et al. 2009). Casein kinase II (CK2) constitutively phosphorylates the C-terminal tail of PTEN on serine and threonine residues S370, S380, T382, T383 and S385. CK2-mediated phosphorylation increases PTEN protein stability (Torres and Pulido 2001) but results in ~30% reduction in PTEN lipid phosphatase activity (Miller et al. 2002).
PTEN localization and activity are affected by acetylation of its lysine residues (Okumura et al. 2006, Ikenoue et al. 2008, Meng et al. 2016). PTEN can undergo oxidation, which affects its function, but the mechanism is poorly understood (Tan et al. 2015, Shen et al. 2015, Verrastro et al. 2016). R-HSA-8849474 PTK6 Activates STAT3 PTK6-mediated phosphorylation activates STAT3 transcription factor via STAP2 adapter protein. STAT3 transcriptional target SOCS3 is a negative regulator of PTK6 and inhibits PTK6-mediated phosphorylation of STAT3, thus creating a negative feedback loop (Liu et al. 2006, Ikeda et al. 2009, Ikeda et al. 2010). PTK6 may also activate STAT5-mediated transcription (Ikeda et al. 2011). R-HSA-8849472 PTK6 Down-Regulation The kinase activity of PTK6 is negatively regulated by both PTPN1 phosphatase (Fan et al. 2013), which dephosphorylates tyrosine Y342 of PTK6, and SRMS kinase (Fan et al. 2015), which phosphorylates PTK6 on tyrosine residue Y447. R-HSA-8849473 PTK6 Expression Levels of PTK6 increase under hypoxic conditions due to direct transcriptional regulation of PTK6 gene by hypoxia inducible transcription factors (HIFs) (Regan Anderson et al. 2013). PTK6 protein levels are also rapidly stabilized in hypoxic conditions in a HIF-independent manner (Pires et al. 2014). It has also been shown that PTK6 is ubiquitinated in normoxic conditions by a so far unknown E3 ligase (Pires et al. 2014). R-HSA-8849470 PTK6 Regulates Cell Cycle PTK6 promotes cell cycle progression by phosphorylating and inactivating CDK inhibitor CDKN1B (p27) (Patel et al. 2015). PTK6 also negatively modulates CDKN1B expression via regulation of the activity of the FOXO3 (FOXO3A) transcription factor (Chan and Nimnual 2010). R-HSA-8849468 PTK6 Regulates Proteins Involved in RNA Processing PTK6 binds and phosphorylates several nuclear RNA-binding proteins, including SAM68 family members (KHDRSB1, KHDRSB2 and KHDRSB3) (Derry et al. 2000, Haegebarth et al. 2004, Lukong et al. 2005) and SFPQ (PSF) (Lukong et al. 2009). The biological role of PTK6 in RNA processing is not known. R-HSA-8849471 PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases PTK6 promotes cell motility and migration by regulating the activity of RHO GTPases RAC1 (Chen et al. 2004) and RHOA (Shen et al. 2008). PTK6 inhibits RAS GTPase activating protein RASA1 (Shen et al. 2008) and may be involved in MAPK7 (ERK5) activation (Ostrander et al. 2007, Zheng et al. 2012) R-HSA-8849469 PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 PTK6 enhances EGFR signaling by inhibiting EGFR down-regulation (Kang et al. 2010, Li et al. 2012, Kang and Lee 2013). PTK6 may also enhance signaling by other receptor tyrosine kinases (RTKs), such as IGF1R (Fan et al. 2013) and ERBB3 (Kamalati et al. 2000).
PTK6 affects AKT1 activation (Zhang et al. 2005, Zheng et al. 2010) and targets negative regulator of RTKs, DOK1, for degradation (Miah et al. 2014).
R-HSA-8857538 PTK6 promotes HIF1A stabilization HBEGF-stimulated formation of EGFR heterodimers with GPNMB triggers PTK6-mediated phosphorylation and stabilization of the hypoxia inducible factor 1 alpha (HIF1A) under normoxic conditions. This process depends on the presence of a long non-coding RNA LINC01139 (LINK-A) (Lin et al. 2016).
R-HSA-171306 Packaging Of Telomere Ends Multiple steps, including C-strand resection, telomerase-mediated elongation, and C-strand synthesis are involved in processing and maintaining the telomere. Though this module posits a linear transit for the steps, in humans it is not well understood how these steps are coordinated and what other events may be involved.
Telomeric DNA can form higher order structures. Electron microscopy of telomeric DNA isolated from human cells provided evidence for lariat-type structures termed telomeric loops, or t-loops (Griffith et al., 1999). t-loops are proposed to result from the invasion of the 3' G-rich single strand overhang into the double stranded telomeric TTAGGG repeat tract. The function of the t-loop is presumed to be the masking of the 3' telomeric overhang. Multiple protein factors can bind telomeric DNA and likely contribute to dynamic, higher order structures.
R-HSA-168303 Packaging of Eight RNA Segments For a budding influenza virus to be fully infectious is it essential that it contains a full complement of the eight vRNA segments. Two different models have been proposed for packaging of the vRNPs into newly assembling virus particles; the random incorporation model and the selective incorporation model.
The random incorporation model as its name suggests proposes that there is no selection at all on which vRNPs are packaged. It is assumed that each vRNP has equal probability of being packaged, and that if enough vRNPS are packaged a particular percentage of budding virions will receive at least one copy of each genome segment. This model is supported by evidence that infectious virions may possess more than eight vRNPs assuring the presence of a full complement of eight vRNPs in a significant percentage of virus particles. Mathematical analysis of packaging suggested that twelve RNA segments would need to be packaged in order to obtain approximately 10% of virus particles that are fully infectious (Enami, 1991), a number that is compatible with experimental data (Donald, 1954). Due to the low amount of RNA per virion (estimated at 1-2% w/w), enumeration of the precise number of RNAs packaged in a virion is difficult.
The selective incorporation model, suggests that each vRNA segment contains a unique "packaging signal" allowing it to act independently, with each vRNA segment being packaged selectively. There is increasing evidence to support the theory of a packaging signal within the coding regions at both the 5' and 3' end of the genomic RNA, with signals being reported for all segments except segment 7 (Ozawa 2007, Muramoto 2006, Fujii 2005, Fujii 2003, Watanabe 2003, Liang 2005). The exact method by which individual vRNP segments are packaged is not known but it has been hypothesized to occur via specific RNA-RNA or protein-RNA interactions. This model is also supported by thin section electron microscopy images of influenza particles that show eight distinct "dots", presumably vRNPs within virus particles (Noda 2006).
R-HSA-9753281 Paracetamol ADME Paracetamol (APAP, aka acetaminophen or N-acetyl-p-aminophenol) is an analgesic drug used for to treat mild to moderate pain and as an antipyretic agent. It is one of the most widely used drugs in the world and is available alone or in combination with other drugs for pain relief, fever and allergy. It is thought to act through the inhibition of cyclooxygenases 1 and 2 (Graham et al. 2013, Esh et al. 2021). Paracetamol is generally safe at therapeutic doses but in overdose cases, it causes mitochondrial dysfunction and centrilobular necrosis in the liver which can lead to death.
APAP has a high oral bioavailability (~88%), is well absorbed and reaches peak blood concentrations after 90 minutes after ingestion. APAP binds plasma proteins to a small extent and has a plasma half-life of 1.5-3 hours. Most of the drug is eliminated by glucuronidate and sulfate conjugation (~55% and ~30% respectively) in the liver or as unchanged drug (~5%) (Forrest et al. 1982). A small amount (5-15%) is oxidised to the reactive metabolite N-acetyl-para-benzoquinone imine (NAPQI). NAPQI is usually detoxified by binding to liver glutathione but in overdose cases, glutathione is depleted and NAPQI instead, binds to sulfhydryl groups on proteins, leading to liver damage. ABCC2, ABCC3, ABCC4 and ABCG2 transporters mediate the efflux of APAP metabolites out of cells (McGill & Jaeschke 2013).
R-HSA-6802955 Paradoxical activation of RAF signaling by kinase inactive BRAF While BRAF-specific inhibitors inhibit MAPK/ERK activation in the presence of the BRAF V600E mutant, paradoxical activation of ERK signaling has been observed after treatment of cells with inhibitor in the presence of WT BRAF (Wan et al, 2004; Garnett et al, 2005; Heidorn et al, 2010; Hazivassiliou et al, 2010; Poulikakos et al, 2010). This paradoxical ERK activation is also seen in cells expressing kinase-dead or impaired versions of BRAF such as D594V, which occur with low frequency in some cancers (Wan et al, 2004; Heidorn et al, 2010). Unlike BRAF V600E, which occurs exclusively of activating RAS mutations, kinase-impaired versions of BRAF are coincident with RAS mutations in human cancers, and indeed, paradoxical activation of ERK signaling in the presence of inactive BRAF is enhanced in the presence of oncogenic RAS (Heidorn et al, 2010; reviewed in Holderfield et al, 2014). Although the details remain to be worked out, paradoxical ERK activation in the presence of inactive BRAF appears to rely on enhanced dimerization with and transactivation of CRAF (Heidorn et al, 2010; Hazivassiliou et al, 2010; Poulikakos et al, 2010; Roring et al, 2012; Rajakulendran et al, 2009; Holderfield et al, 2013; Freeman et al, 2013; reviewed in Roskoski, 2010; Samatar and Poulikakos, 2014; Lavoie and Therrien, 2015). RAF inhibitors can promote association of RAF-RAS interaction and enhanced RAF dimerization through disruption of intramolecular interactions between the kinase domain and its N-terminal regulatory region. Moreover, specific BRAF inhibitors can only occupy one protomer within the transcactivated BRAF dimer due to negative co-operativity leading to paradoxical ERK activation. (Karoulia et al, 2016; Jin et al, 2017, reviewed in Karoulia et al, 2017).
R-HSA-9664407 Parasite infection Leishmania parasites are dimorphic protozoa, being extracellular and flagellated (promastigotes) in the vector insect, and intracellular and aflagellated (amastigotes) in the host. While the vector fly feeds on the blood of the host, it transmits the promastigotes which are subsequently phagocytosed. The transition to the non motile form occurs within the phagosomal pathway; this process requires the delay of the maturation of the phagosome in such a way that the pH conditions are not harmful to the promastigote. Once it is in the amastigote form, maturation of the parasitophorous vacuole continues (Martínez López et al. 2018).
R-HSA-9824443 Parasitic Infection Pathways Parasitic infection pathways aim to capture molecular mechanisms of human parasitic diseases related to parasite adhesion to and invasion of human host cells and tissues, toxigenicity (interaction of parasite-produced toxins with the human host), and evasion of the host's immune defense.
Parasitic infection pathways currently include Leishmania infection-related pathways.
The parasites of the genus Leishmania are blood flagellates transmitted to humans by sandflies. Leishmania causes infections of the skin and mucous membranes that can spread to internal organs (viscera), such as liver, spleen and bone marrow. Visceral leishmaniasis is often fatal.
R-HSA-432047 Passive transport by Aquaporins Aquaporins (AQP's) are six-pass transmembrane proteins that form channels in membranes. Each monomer contains a central channel formed in part by two asparagine-proline-alanine motifs (NPA boxes) that confer selectivity for water and/or solutes. The monomers assemble into tetramers. During passive transport by Aquaporins most aquaporins (i.e. AQP0/MIP, AQP1, AQP2, AQP3, AQP4, AQP5, AQP7, AQP8, AQP9, AQP10) transport water into and out of cells according to the osmotic gradient across the membrane. Four aquaporins (the aquaglyceroporins AQP3, AQP7, AQP9, AQP10) conduct glycerol, three aquaporins (AQP7, AQP9, AQP10) conduct urea, and one aquaporin (AQP6) conducts anions, especially nitrate. AQP8 also conducts ammonia in addition to water.
AQP11 and AQP12, classified as group III aquaporins, were identified as a result of the genome sequencing project and are characterized by having variations in the first NPA box when compared to more traditional aquaporins. Additionally, a conserved cysteine residue is present about 9 amino acids downstream from the second NPA box and this cysteine is considered indicative of group III aquaporins. Purified AQP11 incorporated into liposomes showed water transport. Knockout mice lacking AQP11 had fatal cyst formation in the proximal tubule of the kidney. Exogenously expressed AQP12 showed intracellular localization. AQP12 is expressed exclusively in pancreatic acinar cells.
Aquaporins are important in fluid and solute transport in various tissues. During Transport of glycerol from adipocytes to the liver by Aquaporins, glycerol generated by triglyceride hydrolysis is exported from adipocytes by AQP7 and is imported into liver cells via AQP9. AQP1 plays a role in forming cerebrospinal fluid and AQP1, AQP4, and AQP9 appear to be important in maintaining fluid balance in the brain. AQP0, AQP1, AQP3, AQP4, AQP8, AQP9, and AQP11 play roles in the physiology of the hepatobiliary tract.
In the kidney, water and solutes are passed out of the bloodstream and into the proximal tubule via the slit-like structure formed by nephrin in the glomerulus. Water is reabsorbed from the filtrate during its transit through the proximal tubule, the descending loop of Henle, the distal convoluted tubule, and the collecting duct. Aquaporin-1 (AQP1) in the proximal tubule and the descending thin limb of Henle is responsible for about 90% of reabsorption (as estimated from mouse knockouts of AQP1). AQP1 is located on both the apical and basolateral surface of epithelial cells and thus transports water through the epithelium and back into the bloodstream. In the collecting duct epithelial cells have AQP2 on their apical surfaces and AQP3 and AQP4 on their basolateral surfaces to transport water across the epithelium. Vasopressin regulates renal water homeostasis via Aquaporins by regulating the permeability of the epithelium through activation of a signaling cascade leading to the phosphorylation of AQP2 and its translocation from intracellular vesicles to the apical membrane of collecting duct cells.
Here, three views of aquaporin-mediated transport have been annotated: a generic view of transport mediated by the various families of aquaporins independent of tissue type (Passive transport by Aquaporins), a view of the role of specific aquaporins in maintenance of renal water balance (Vasopressin regulates renal water homeostasis via Aquaporins), and a view of the role of specific aquaporins in glycerol transport from adipocytes to the liver (Transport of glycerol from adipocytes to the liver by Aquaporins).
R-HSA-167290 Pausing and recovery of HIV elongation After Pol II pauses by back tracking 2 -4 nuleotides on the HIV-1 template, elongation of the HIV-1 transcript resumes.
R-HSA-167238 Pausing and recovery of Tat-mediated HIV elongation After Pol II pauses by back tracking 2 -4 nuleotides on the HIV-1 template, elongation of the HIV-1 transcript resumes.
R-HSA-71336 Pentose phosphate pathway The pentose phosphate pathway is responsible for the generation of a substantial fraction of the cytoplasmic NADPH required for biosynthetic reactions, and for the generation of ribose 5-phosphate for nucleotide synthesis. Although the pentose phosphate pathway and glycolysis are distinct, they involve three common intermediates, glucose 6-phosphate, glyceraldehyde 3-phosphate, and fructose 6-phosphate, so the two pathways are interconnected. The pentose phosphate pathway consists of eight reactions:1. Conversion glucose 6-phosphate to D-glucono-1,5-lactone 6-phosphate, with the formation of NADPH; 2. Conversion of D-glucono-1,5-lactone 6-phosphate to 6-phospho-D-gluconate; 3. Conversion of 6-phospho-D-gluconate to ribulose 5-phosphate, with the formation of NADPH; 4. Conversion of ribulose 5-phosphate to xylulose 5-phosphate; 5. Conversion of ribulose 5-phosphate to ribose 5-phosphate; 6. Rearrangement of ribose 5-phosphate and xylulose 5-phosphate to form sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate; 7. Rearrangement of sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate to form erythrose 4-phosphate and fructose 6-phosphate; and 8. Rearrangement of xylulose 5-phosphate and erythrose 4-phosphate to form glyceraldehyde 3-phosphate and fructose-6-phosphate.
The oxidative branch of the pentose phosphate pathway, reactions 1-3, generates NADPH and pentose 5-phosphate. The non-oxidative branch of the pathway, reactions 4-8, converts pentose 5-phosphate to other sugars.
The overall pathway can operate to generate only NADPH (glucose 6-phosphate is converted to pentose 5-phosphates, which are directed to the synthesis of fructose 6-phosphate and glyceraldehyde 3-phosphate, which in turn are converted back to glucose 6-phosphate). The reactions of the non-oxidative branch can operate to generate net amounts of ribose 5-phosphate with no production of NADPH. Net flux through this network of reactions appears to depend on the metabolic state of the cell and the nature of the biosynthetic reactions underway (Casazza and Veech 1987).
G6PD, the enzyme that catalyzes the first reaction of the pathway, is more extensively mutated in human populations than any other enzyme, pehaps because these mutant alleles confer malaria resistance (Luzzatto and Afolayan 1968). Mutations affecting other parts of the pathway are rare, though several have been described and studies of their effects have contributed to our understanding of the normal flux of metabolites through this network of reactions (Wamelink et al. 2008).
R-HSA-6791465 Pentose phosphate pathway disease Mutant forms of two enzymes of the pentose phosphate pathway have been associated with disease in humans. A mutation in ribose-5-phosphate isomerase (RPIA), which normally mediates the reversible interconversion of D-ribulose-5-phosphate and ribose-5-phosphate, has been associated with a slowly progressive leukoencephalopathy, and mutations in transaldolase 1 (TALDO1), which normally mediates the reversible interconversion of D-fructose 6-phosphate and D-erythrose-4-phosphate to form sedoheptulose-7-phosphate and D-glyceraldehyde-3-phosphate, have been associated with congenital liver disease (Wamelink et al. 2008).
R-HSA-156902 Peptide chain elongation The mechanism of a peptide bond requires the movement of three protons. First the deprotonation of the ammonium ion generates a reactive amine, allowing a nucleophilic attack on the carbonyl group. This is followed by the loss of a proton from the reaction intermediate, only to be taken up by the oxygen on the leaving group (from the end of the amino acid chain bound to the tRNA in the P-site). The peptide bond formation results in the net loss of one water molecule, leaving a deacylated-tRNA in the P-site, and a nascent polypeptide chain one amino acid larger in the A-site.
For the purpose of illustration, the figures used in the section show one amino acid being added to a peptidyl-tRNA with a growing peptide chain.
R-HSA-209952 Peptide hormone biosynthesis Peptide hormones are peptides that are secreted directly into the blood stream (endocrine hormones). They are synthesized as precursors that require proteolytic processing (not discussed here) to generate the biologically active peptides that mediate neurotransmission and hormonal action. Glycoprotein hormones (those which include carbohydrate side-chains) and the processing of corticotropin are annotated here.
R-HSA-2980736 Peptide hormone metabolism Peptide hormones are cleaved from larger precursors in the secretory system (endoplasmic reticulum, Golgi apparatus, secretory granules) of the cell. After secretion peptide hormones are modified and degraded by extracellular proteases.
Insulin processing occurs in 4 steps: formation of intramolecular disulfide bonds, formation of proinsulin-zinc-calcium complexes, proteolytic cleavage of proinsulin by PCSK1 (PC1/3) and PCSK2 to yield insulin, translocation of the granules across the cytosol to the plasma membrane.
During Synthesis, secretion, and deacetylation of Ghrelin, proghrelin is acylated by ghrelin O-acyltransferase and cleaved by PCSK1 to yield the mature acyl ghrelin and C-ghrelin. In the bloodstream acyl ghrelin is deacylated by butyrylcholinesterase and platelet-activating factor acetylhydrolase.
During Metabolism of Angiotensinogen to Angiotensin, Renin cleaves angiotensinogen to yield a decapaptide, angiotensin I (angiotensin-1, angiotensin-(1-10)). Two C-terminal amino acid residues of angiotensin I are then removed by angiotensin-converting enzyme (ACE), located on the surface of endothelial cells, to yield angiotensin II (angiotensin-2, angiotensin-(1-8)), the active peptide that causes vasoconstriction, resorption of sodium and chloride, excretion of potassium, water retention, and aldosterone secretion. More recently other, more tissue-localized pathways leading to angiotensin II and alternative derivatives of angiotensinogen have been identified and described.
Incretin synthesis, secretion, and inactivation occurs through processing of incretin precursors (preproGLP-1 and preproGIP) by PCSK1. After secretion both incretins (GLP-1 and GIP) can be inactivated by cleavage by DPP4.
Peptide hormone biosynthesis describes processing of glycoprotein hormones (those which include carbohydrate side-chains) and corticotropin.
R-HSA-375276 Peptide ligand-binding receptors These receptors, a subset of the Class A/1 (Rhodopsin-like) family, all bind peptide ligands which include the chemokines, opioids and somatostatins.
R-HSA-390918 Peroxisomal lipid metabolism In humans, the catabolism of phytanate, pristanate, and very long chain fatty acids as well as the first four steps of the biosynthesis of plasmalogens are catalyzed by peroxisomal enzymes. Defects in any of these enzymes or in the assembly of peroxisomes are associated with severe developmental disorders (Wanders and Watherham 2006).
R-HSA-9033241 Peroxisomal protein import Peroxisomes are small cellular organelles that are bounded by a single membrane and contain variable compositions of proteins depending on cell type. Peroxisomes function in oxidation of fatty acids, detoxification of glyoxylate, and synthesis of plasmalogens, glycerophospholipids containing an alcohol with a vinyl-ether bond (reviewed in Lohdi and Semenkovich 2014). All of the approximately 46 proteins contained in peroxisomal matrix are imported from the cytosol by a unique mechanism that does not require the imported proteins to be unfolded as they cross the membrane (Walton et al. 1995, reviewed in Ma et al. 2011, Fujiki et al. 2014, Baker et al. 2016, Dias et al 2016, Emmanoulidis et al. 2016, Erdmann 2016, Francisco et al. 2017). The incompletely characterized process appears to involve the transport of the proteins through a variably sized pore in the membrane comprising at least PEX5 and PEX14 (inferred from the yeast homologs in Meinecke et al. 2010, the yeast pore is reviewed in Meinecke et al. 2016). Oligomeric proteins are also observed to cross the peroxisomal membrane (Otera and Fujiki 2012) but their transport appears to be less efficient than monomeric proteins (Freitas et al. 2011, inferred from mouse homologs in Freitas et al. 2015, reviewed in Dias et al. 2016).
In the cytosol, receptor proteins, PEX5 and PEX7, bind to specific sequence motifs in cargo proteins (Dodt et al. 1995, Wiemer et al. 1995, Braverman et al. 1997). The long and short isoforms of PEX5 (PEX5L and PEX5S) bind peroxisome targeting sequence 1 (PTS1, originally identified in firefly luciferase by Gould et al. 1989) found on most peroxisomal matrix proteins; PEX7 binds PTS2 (originally identified in rat 3-ketoacyl-CoA thiolase by Swinkels et al. 1991) found on 3 imported proteins thus far in humans. The long isoform of PEX5, PEX5L, then binds the PEX7:cargo protein complex (Braverman et al. 1998, Otera et al. 2000). PEX5S,L bound to a cargo protein or PEX5L bound to PEX7:cargo protein then interacts with a complex comprising PEX13, PEX14, PEX2, PEX10, and PEX12 at the peroxisomal membrane (Gould et al. 1996, Fransen et al. 1998, inferred from rat homologs in Reguenga et al. 2001).
The ensuing step in which the cargo protein is translocated across the membrane is not completely understood. During translocation, PEX5 and PEX7 become inserted into the membrane (Wiemer et al. 1995, Dodt et al. 1995, Oliveira et al. 2003) and expose a portion of their polypeptide chains to the organellar matrix (Rodrigues et al. 2015). One current model envisages PEX5 as a plunger that inserts into a transmembrane barrel formed by PEX14, PEX13, PEX2, PEX10, and PEX12 (the Docking-Translocation Module) (Francisco et al. 2017).
After delivering cargo to the matrix, PEX5 and PEX7 are recycled back to the cytosol by a process requiring mono-ubiquitination of PEX5 and ATP hydrolysis (Imanaka et al. 1987, Thoms and Erdmann 2006, Carvalho et al. 2007). PEX7 is not ubiquitinated but its recycling requires PEX5 mono-ubiquitination. A subcomplex of the Docking-Translocation Module comprising the RING-finger proteins PEX2, PEX10, and PEX12 conjugates a single ubiquitin to a cysteine residue of PEX5 (Carvalho et al. 2007, reviewed in Platta et al. 2016). The mono-ubiquitinated PEX5 and associated PEX7 are then extracted by the exportomer complex consisting of PEX1, PEX6, PEX26, and ZFAND6 (inferred from rat homologs in Miyata et al. 2012). PEX1 and PEX6 are members of the ATPases Associated with diverse cellular Activities (AAA) family, a group of proteins that use the energy of ATP hydrolysis to remodel molecular complexes. PEX1 and PEX6 form a hetero-hexameric ring, best described as a trimer of PEX1/PEX6 dimers (inferred from yeast in Platta et al. 2005, yeast homologs reviewed in Schwerter et al. 2017). Data on the yeast PEX1:PEX6 complex suggest that these ATPases use a substrate-threading mechanism to disrupt protein-protein interactions (Gardner et al. 2018). PEX7 is also then returned to the cytosol (Rodrigues et al. 2014). Once in the cytosol, ubiquitinated PEX5 is enzymatically deubiquitinated by USP9X and may also be non-enzymatically deubiquitinated by nucleophilic attack of the thioester bond between ubiquitin and the cysteine residue of PEX5 by small metabolites such as glutathione (Grou et al. 2012).
Defects in peroxisomal import cause human diseases: Zellweger syndrome, neonatal adrenoleukodystrophy, infantile Refsum disease and rhizomelic chondrodysplasia punctata types 1 and 5 (Barøy et al. 2015, reviewed in Nagotu et al. 2012, Braverman et al. 2013, Wanders 2014, Fujiki 2016, Waterham et al. 2016).
R-HSA-9005895 Pervasive developmental disorders Pervasive developmental disorders (PDDs) largely overlap with the autism spectrum disorders (ASDs). PDDs manifest in childhood and mainly affect social interaction, including communication and behavior. PDDs can be caused by mutations in genes involved in brain development and function, environmental insults, or the combination of environmental factors and genetic susceptibility. The pervasive developmental disorder pathway that Reactome has annotated is the "Loss of function of MECP2 in Rett syndrome". For review of this topic, please refer to Picket and London 2005, Currenti 2010, Elsabbagh et al. 2012, Ferreri 2014.
R-HSA-9664873 Pexophagy Peroxisomes are cytosolic organelles involved in the catabolism of branched and long-chain fatty acids and in the reduction of reactive oxygen species (ROS). Peroxisomes homeostasis is critical to maintain ROS levels. Consequently, it is important to eliminate dysfunctional peroxisomes. The degradation of peroxisomes by autophagy is known as pexophagy (Katarzyna ZR et al. 2016). Pexophagy can be triggered by a shift in nutrient conditions.
R-HSA-9637698 Phagocyte cell death caused by cytosolic Mtb Mycobacterium tuberculosis (Mtb), when located in the cytosol of phagocytes, induce cell death similar to necrosis as a means to exit the host cell, ultimately spreading the infection (Moraco & Kornfeld 2014).
R-HSA-5576892 Phase 0 - rapid depolarisation Phase 0 is the rapid depolarisation phase in which electrical stimulation of a cell initiates events involving the influx and efflux of ions resulting in the production of a cell's action potential. The cell's excitation opens the closed, fast Na+ channel proteins, causing a large influx of Na+ creating a Na+ current (INa+). This causes depolarisation of the cell then voltage-dependent L-type calcium channels (LTCCs) transport Ca2+ into excitable cells. The slope of phase 0 represents the maximum rate of potential change and differs in contractile and pacemaker cells. The potential in this phase changes from around -90mV to around +50mV (Park & Fishman 2011, Grant 2009).
R-HSA-5576894 Phase 1 - inactivation of fast Na+ channels Phase 1 of the cardiac action potential is the inactivation of the fast Na+ channels. The transient net outward current causing the small downward deflection (the "notch" of the action potetial) is due to the movement of K+ and Cl- ions. In pacemaker cells, this phase is due to rapid K+ efflux and closure of L-type Ca2+ channels (Park & Fishman 2011, Grant 2009).
R-HSA-5576893 Phase 2 - plateau phase Phase 2 of the cardiac action potential is the plateau phase which is sustained by a balance of Ca2+ influx through L-type Ca2+ channels (LTCCs) and K+ efflux through the slow delayed rectifier K+ channel 1 (KCNQ1). This phase sustains muscle contraction (Park & Fishman 2011, Grant 2009).
R-HSA-5576890 Phase 3 - rapid repolarisation In phase 3 (the "rapid repolarisation" phase), the L-type Ca2+ channels close, while the slow delayed rectifier (IKs) K+ channels remain open as more K+ leak channels open. This ensures a net outward positive current, corresponding to negative change in membrane potential, thus allowing more types of K+ channels to open. These are primarily the rapid delayed rectifier K+ channels (IKr) and the inwardly rectifying K+ current, IK1 (Kir). This net outward, positive current (equal to loss of positive charge from the cell) causes the cell to repolarize. The primary delayed rectifier K+ currents (IKs and IKr) are generated by K+ efflux mediated by potassium voltage-gated channel subfamily KQT member 1 (KCNQ1 aka Kv7.1) and potassium voltage-gated channel subfamily H member 2 (KCNH2 aka HERG) channels respectively (Park & Fishman 2011, Grant 2009). Specific to the atria, an ultra-rapidly activating delayed rectifier outward K+ current (IKur) generated primarily by potassium voltage-gated channel subfamily A member 5 (KCNA5) helps to repolarize atrial cells (Wang et al. 1993, Feng et al. 1997).
R-HSA-5576886 Phase 4 - resting membrane potential Phase 4 describes the membrane potential when a cell is not being stimulated. The normal resting potential in the ventricular myocardium is between -85 to -95 mV. The membrane is most permeable to K+ and relatively impermeable to other ions therefore the K+ gradient across the cell membrane is the key determinant in the normal resting potential (Park & Fishman 2011, Grant 2009). In this phase, K+ currents are generated by inward rectifier potassium channels (KCNJs) and tandem pore domain K+ channels (KCNKs). Some Na+/K+-ATPases and Na+/Ca2+-exchangers can also play roles during this phase.
R-HSA-211945 Phase I - Functionalization of compounds Phase 1 of metabolism is concerned with functionalization, that is the introduction or exposure of functional groups on the chemical structure of a compound. This provides a 'handle' for phase 2 conjugating species with which to react with. Many xenobiotics are lipophilic and almost chemically inert (e.g. PAHs) so would not necessarily undergo a phase 2 reaction. Making them more chemically reactive would facilitate their excretion but also increases their chance of reacting with cellular macromolecules (e.g. proteins, DNA). There is a fine balance between producing a more reactive metabolite and conjugation reactions.
There are two groups of enzymes in phase 1 - oxidoreductases and hydrolases. Oxidoreductases introduce an oxygen atom into or remove electrons from their substrates. The major oxidoreductase enzyme system is called the P450 monooxygenases. Other systems include flavin-containing monooxygenases (FMO), cyclooxygenases (COX) and monoamine oxidases (MAO). Hydrolases hydrolyse esters, amides, epoxides and glucuronides.
R-HSA-156580 Phase II - Conjugation of compounds Phase II of biotransformation is concerned with conjugation, that is using groups from cofactors to react with functional groups present or introduced from phase I on the compound. The enzymes involved are a set of transferases which perform the transfer of the cofactor group to the substrate. The resultant conjugation results in greatly increasing the excretory potential of compounds. Although most conjugations result in pharmacological inactivation or detoxification, some can result in bioactivation. Most of the phase II enzymes are located in the cytosol except UDP-glucuronosyltransferases (UGT), which are microsomal. Phase II reactions are typically much faster than phase I reactions therefore the rate-limiting step for biotransformation of a compound is usually the phase I reaction.
Phase II metabolism can deal with all the products of phase I metabolism, be they reactive (Type I substrate) or unreactive/poorly active (Type II substrate) compounds. With the exception of glutathione, the conjugating species needs to be made chemically reactive after synthesis. The availability of the cofactor in the synthesis may be a rate-limiting factor in some phase II pathways as it may prevent the formation of enough conjugating species to deal with the substrate or it's metabolite. As many substrates and/or their metabolites are chemically reactive, their continued presence may lead to toxicity.
R-HSA-8963691 Phenylalanine and tyrosine metabolism The hydroxylation of phenylalanine, an essential amino acid, to form tyrosine is a major source of the latter amino acid in the body under normal conditions and is also the first step in phenylalanine catabolism. To continue the catabolic process, tyrosine is transaminated to 3-(4-hydroxyphenyl)pyruvate which is broken down to fumarate and acetoacetate (Blau et al. 2001; Mitchell et al. 2001).
R-HSA-8964208 Phenylalanine metabolism The first reaction in this pathway converts phenylalanine to tyrosine, coupled to the conversion of tetrahydrobiopterin to 4a-hydroxytetrahydrobiopterin, catalyzed by phenylalanine hydroxylase. Deficiencies in this enzyme are responsible for the commonest form of phenylketonuria (PKU) in humans. This reaction functions both as the first step in the pathway by which the body disposes of excess phenylalanine, and as a source of the amino acid tyrosine. The next two reactions are responsible for the regeneration of tetrahydrobiopterin from 4a-hydroxytetrahydrobiopterin (Blau et al. 2001).
R-HSA-2160456 Phenylketonuria Phenylalanine hydroxylase (PAH) normally catalyzes the conversion of phenylalanine to tyrosine. In the absence of functional PAH, phenylalanine accumulates to high levels in the blood and is converted to phenylpyruvate and phenyllactate (Clemens et al. 1990; Langenbeck et al. 1992; Mitchell et al. 2011). The extent of these conversions is modulated by genetic factors distinct from PAH, as siblings with the identical PAH defect can produce different amounts of them (Treacy et al. 1996).
Both L-amino acid oxidase (Boulland et al. 2004) and Kynurenine--oxoglutarate transaminase 3 (Han et al. 2004) can catalyze the conversion of phenylalanine to phenylpyruvate and lactate dehydrogenase can catalyze the conversion of the latter molecule to phenyllactate (Meister 1950), in reactions not annotated here.
R-HSA-8850843 Phosphate bond hydrolysis by NTPDase proteins The ectonucleoside triphosphate diphosphatase (E-NTPDase family) of ectonucleotidases includes 8 enzymes: NTPDase1 (encoded by the ENTPD1 gene), NTPDase2 (encoded by the ENTPD2 gene), NTPDase3 (encoded by the ENTPD3 gene), NTPDase4 (encoded by the ENTPD4 gene), NTPDase5 (encoded by the ENTPD5 gene), NTPDase6 (encoded by the ENTPD6 gene), NTPDase7 (encoded by the ENTPD7 gene) and NTPDase8 (encoded by the ENTPD8 gene). NTPDases hydrolyze nucleoside triphosphates and nucleoside diphosphates, producing the corresponding nucleoside monophosphates as final products. Different family members show different specificity for particular nucleotides. NTPDases are involved in various biological processes, such as hemostasis, immune response and development of the nervous system.
The catalytic domain of NTPDases is contained within the loop formed by a cluster of apyrase conserved regions (ACRs). All family members require divalent cations, such as calcium (Ca2+) or magnesium (Mg2+) ions, for catalytic activity. The hydrolysis involves a nucleophilic attack of a water molecule on the terminal phosphate of a nucleotide substrate.
All E-NTPDase family members are transmembrane proteins, associated with either plasma membrane (NTPDase1, NTPDase2, NTPDase3 and NTPDase8) or organelle membranes (NTPDase4 and NTPDase7). Two family members, NTPDase5 and NTPDase6, can be secreted into extracellular space following a proteolytic cleavage from the plasma membrane. NTPDases hydrolyze exocytoplasmic nucleotides, thus regulating the availability of ligands for purinergic receptors. Glycosylation and oligomerization are involved in the regulation of NTPDases, but have not been thoroughly studied.
For reviews of the NTPDase family, please refer to Robson et al. 2006 and Zimmermann et al. 2012. R-HSA-2393930 Phosphate bond hydrolysis by NUDT proteins Enzymes that belong to the NUDT (Nudix) superfamily catalyze the hydrolysis of phosphodiester bonds in molecules including nucleoside triphosphates and diphosphates and nucleotide sugars. Family members are defined by the presence of an amino acid sequence motif shared with the E. coli MutT gene product, and are involved in diverse physiological processes (Mildvan et al. 2005; McLennan 2006).
The hydrolysis of nucleoside di and triphosphates whose purine bases have been oxidized, deaminated, or methylated may protect the cell from the mutational damage that would occur if modified deoxyribonucleotides were incorporated into DNA and from the aberrant protein synthesis that would occur if modified ribonucleotides were incorporated into mRNA (Iyama et al. 2010; Takagi et al. 2012). The hydrolysis of ADP ribose may prevent the aberrant spontaneous ADP ribosylation of cellular proteins that could occur were this molecule to accumulate to high levels in the cell (Perraud et al. 2003; Shen et al. 2003).
R-HSA-5654219 Phospholipase C-mediated cascade: FGFR1 Phospholipase C-gamma (PLC-gamma) is a substrate of the fibroblast growth factor receptor (FGFR) and other receptors with tyrosine kinase activity. It is known that the src homology region 2 (SH2 domain) of PLC-gamma and of other signaling molecules (such as GTPase-activating protein and phosphatidylinositol 3-kinase-associated p85) direct their binding toward autophosphorylated tyrosine residues of the FGFR. Recruitment of PLC-gamma results in its phosphorylation and activation by the receptor. Activated PLC-gamma hydrolyzes phosphatidyl inositol[4,5] P2 to form the second messengers diacylglycerol (DAG) and Ins [1,4,5]P3, which stimulate calcium release and activation of calcium/calmodulin dependent kinases.
R-HSA-5654221 Phospholipase C-mediated cascade; FGFR2 Phospholipase C-gamma (PLC-gamma) is a substrate of the fibroblast growth factor receptor (FGFR) and other receptors with tyrosine kinase activity. It is known that the src homology region 2 (SH2 domain) of PLC-gamma and of other signaling molecules (such as GTPase-activating protein and phosphatidylinositol 3-kinase-associated p85) direct their binding toward autophosphorylated tyrosine residues of the FGFR. Recruitment of PLC-gamma results in its phosphorylation and activation by the receptor. Activated PLC-gamma hydrolyzes phosphatidyl inositol[4,5] P2 to form the second messengers diacylglycerol (DAG) and Ins [1,4,5]P3, which stimulate calcium release and activation of calcium/calmodulin dependent kinases.
R-HSA-5654227 Phospholipase C-mediated cascade; FGFR3 Phospholipase C-gamma (PLC-gamma) is a substrate of the fibroblast growth factor receptor (FGFR) and other receptors with tyrosine kinase activity. It is known that the src homology region 2 (SH2 domain) of PLC-gamma and of other signaling molecules (such as GTPase-activating protein and phosphatidylinositol 3-kinase-associated p85) direct their binding toward autophosphorylated tyrosine residues of the FGFR. Recruitment of PLC-gamma results in its phosphorylation and activation by the receptor. Activated PLC-gamma hydrolyzes phosphatidyl inositol[4,5] P2 to form the second messengers diacylglycerol (DAG) and Ins [1,4,5]P3, which stimulate calcium release and activation of calcium/calmodulin dependent kinases.
R-HSA-5654228 Phospholipase C-mediated cascade; FGFR4 Phospholipase C-gamma (PLC-gamma) is a substrate of the fibroblast growth factor receptor (FGFR) and other receptors with tyrosine kinase activity. It is known that the src homology region 2 (SH2 domain) of PLC-gamma and of other signaling molecules (such as GTPase-activating protein and phosphatidylinositol 3-kinase-associated p85) direct their binding toward autophosphorylated tyrosine residues of the FGFR. Recruitment of PLC-gamma results in its phosphorylation and activation by the receptor. Activated PLC-gamma hydrolyzes phosphatidyl inositol[4,5] P2 to form the second messengers diacylglycerol (DAG) and Ins [1,4,5]P3, which stimulate calcium release and activation of calcium/calmodulin dependent kinases.
R-HSA-1483257 Phospholipid metabolism Phospholipids contain a polar head group and two long-chain fatty acyl moieties, one of which is generally unsaturated. The head group is a glycerol or serine phosphate attached to a polar group such as choline. These molecules are a major constituent of cellular membranes, where their diverse structures and asymmetric distributions play major roles in determining membrane properties (Dowhan 1997). The four major classes of phospholipids in human plasma membranes are phosphatidylethanolamine, phosphatidylserine, phosphatidylcholine, and sphingomyelin. The first three are derivatives of glycerol while sphingomyelin is a derivative of serine.
Here, pathways for the metabolism of glycerophospholipids, phosphphatidylinositol (PI), and sphingolipids are annotated. R-HSA-202427 Phosphorylation of CD3 and TCR zeta chains Prior to T cell receptor (TCR) stimulation, CD4/CD8 associated LCK remains seperated from the TCR and is maintained in an inactive state by the action of CSK. PAG bound CSK phosphorylates the negative regulatory tyrosine of LCK and inactivates the LCK kinase domain (step 1). CSK also inhibits PTPN22 by sequestering it via binding (step 2). Upon TCR stimulation, CSK dissociates from PAG1 (step 3) and PTPN22 (step4) and is unable to inhibit LCK. Furthermore, LCK becomes activated via PTPRC-mediated dephosphorylation of negative regulatory tyrosine residues (step 5). CD4/CD8 binds MHCII receptor in APC and the associated LCK co-localizes with the TCR. LCK is further activated by trans-autophosphorylation on the tyrosine residue on its activation loop (step 6). Active LCK further phosphorylates the tyrosine residues on CD3 chains. The signal-transducing CD3 delta/epsilon/gamma and TCR zeta chains contain a critical signaling motif known as the immunoreceptor tyrosine-based activation motif (ITAM). The two critical tyrosines of each ITAM motif are phosphorylated by LCK (step 7). R-HSA-176417 Phosphorylation of Emi1 The phosphorylation of Emi1, which is required for its degradation in mitosis, appears to involve both Plk1 and Cdk1. R-HSA-69200 Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes The G1/S transition is facilitated by Cyclin E:Cdk2-mediated phoshorylation of proteins including Rb and Cyclin Kinase Inhibitors (CKIs). R-HSA-170145 Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes Cyclin A:Cdc2 complexes are detected in the nucleus earlier that cyclin B1:Cdc2 complexes and may play a role in the initial events in prophase. Inactivation of Cdc25B by proteasome-mediated degradation is dependent upon cyclin A:Cdc2-mediated phosphorylation (Cans et al, 1999) R-HSA-176412 Phosphorylation of the APC/C Phosphorylation of APC subunits is required for Cdc20 mediated activation by of the APC/C at the metaphase anaphase transition (Kramer et al., 2000). While the kinases responsible for phosphorylation in vivo have not been determined with certainty, both Plk1 and Cyclin B:Cdc2 have been implicated in this process. R-HSA-5578768 Physiological factors Cardiovascular homeostasis can be regulated by natriuretic peptides (Pandey 2014). R-HSA-8963898 Plasma lipoprotein assembly Because of their hydrophobicity, lipids are found in the extracellular spaces of the human body primarily in the form of lipoprotein complexes. Chylomicrons form in the small intestine and transport dietary lipids to other tissues in the body. Very low density lipoproteins (VLDL) form in the liver and transport triacylglycerol synthesized there to other tissues of the body. High density lipoprotein (HDL) particles are formed primarily by the liver and shuttle several kinds of lipids between tissues and other lipoproteins (Vance & Vance 1990). The assembly of these three classses of lipoproteins is annotated here. R-HSA-174824 Plasma lipoprotein assembly, remodeling, and clearance Because of their hydrophobicity, lipids are found in the extracellular spaces of the human body primarily in the form of lipoprotein complexes. Chylomicrons form in the small intestine and transport dietary lipids to other tissues in the body. Very low density lipoproteins (VLDL) form in the liver and transport triacylglycerol synthesized there to other tissues of the body. As they circulate, VLDL are acted on by lipoprotein lipases on the endothelial surfaces of blood vessels, liberating fatty acids and glycerol to be taken up by tissues and converting the VLDL first to intermediate density lipoproteins (IDL) and then to low density lipoproteins (LDL). IDL and LDL are cleared from the circulation via a specific cell surface receptor, found in the body primarily on the surfaces of liver cells. High density lipoprotein (HDL) particles, initially formed primarily by the liver, shuttle several kinds of lipids between tissues and other lipoproteins. Notably, they are responsible for the so-called reverse transport of cholesterol from peripheral tissues to LDL for return to the liver.
Three aspects of lipoprotein function are currently annotated in Reactome: chylomicron-mediated lipid transport, LDL endocytosis and degradation, and HDL-mediated lipid transport, each divided into assembly, remodeling, and clearance subpathways.
R-HSA-8964043 Plasma lipoprotein clearance Circulating chylomicrons acquire molecules of apolipoproteins C and E and through interaction with endothelial lipases lose a large fraction of their triacylglycerol. These changes convert them to chylomicron remnants which bind to LDL receptors, primarily on the surfaces of liver cells, clearing them from the circulation (Redgrave 2004).
Most very-low-density lipoproteins (VLDL) are converted to low-density lipoproteins (LDL) (VLDL remodeling pathway). A small fraction are taken up by VLDL receptors on extrahepatic cells, as annotated here. Clearance of LDL from the blood involves binding to LDL receptors associated with coated pits at the cell surface, forming complexes that are internalized and passed via clathrin-coated vesicles to endosomes, where they dissociate. The LDL particles move into lysosomes and are degraded while the LDL receptors are returned to the cell surface. This process occurs in most cell types but is especially prominent in hepatocytes. It plays a major role in returning cholesterol from peripheral tissues to the liver (Hobbs et al. 1990).
Clearance of circulating HDL particles involves particle binding to cell-surface SR-BI receptors, particle disassembly with rlease of pre-beta HDL (Silver & Tall 2001), and uptake of the latter mediated by cell-surface CUBN:AMN complex (Kozyraki et al. 1999).
VLDLR internalization plays a clinically significant role in determining the efficiency of lipoprotein clearance from the blood (Poirier et al. 2008).
R-HSA-8963899 Plasma lipoprotein remodeling As chylomicrons circulate in the body, they acquire molecules of apolipoproteins C and E, and through interaction with endothelial lipases can lose a large fraction of their triacylglycerol. These changes convert them to chylomicron remnants which bind to LDL receptors, primarily on the surfaces of liver cells, clearing them from the circulation. This whole sequence of events is rapid: the normal lifespan of a chylomicron is 30 - 60 minutes (Redgrave 2004).
As they circulate, VLDL are acted on by lipoprotein lipases on the endothelial surfaces of blood vessels, liberating fatty acids and glycerol to be taken up by tissues and converting the VLDL first to intermediate density lipoproteins (IDL) and then to low density lipoproteins (LDL) (Gibbons et al. 2004).
HDL remodeling includes the conversion of HDL-associated cholesterol to cholesterol esters (remodeling of spherical HDL), the transfer of HDL lipids to target cells with the regeneration of pre-beta HDL (lipid-poor apoA-I), and the conversion of pre-beta HDL to discoidal HDL (Rye et al. 1999).
R-HSA-75896 Plasmalogen biosynthesis 1-Acylglycerol-3-phosphate is synthesized from dihydroxyacetone phosphate, an acyl CoA molecule and NADPH + H+ in four reactions catalyzed by peroxisomal enzymes, either in the matrix of the organelle or associated with its membrane. These reactions are annotated here for palmityl (C16:0) CoA. In a series of less well-characterized reactions in the cytosol and endoplasmic reticulum, these molecules are converted to ether lipids (plasmalogens). The functions of plasmalogens are not well understood. They are an abundant subclass of phospholipids, however, and defects in their metabolism are associated with serious human disease (de Vet et al. 1999; Nagan and Zoeller 2001).
R-HSA-75892 Platelet Adhesion to exposed collagen Initiation of platelet adhesion is the first step in the formation of the platelet plug. Circulating platelets are arrested and subsequently activated by exposed collagen and von Willebrand factor (VWF). It is not entirely clear which type of collagen is responsible for adhesion and activation; collagen types I and III are abundant in vascular epithelia but several other types including IV are present (Farndale RW 2006). Several collagen binding proteins are expressed on platelets, including integrin alpha2 beta1 (α2β1 or ITGA2:ITGB1), GPVI, and GPIV. ITGA2:ITGB1, known on leukocytes as VLA-2, is the major platelet collagen receptor (Kunicki TJ et al., 1988). ITGA2:ITGB1 (α2β1) requires Mg2+ to interact with collagen. The activation of ITGA2:ITGB1 (α2β1) is modulated by the activation of integrin alphaIIb beta3 (αIIbβ3 or ITGA2B:ITGB3), which functions as a platelet receptor for fibrinogen and VWF (van de Walle GR et al., 2007). The I domain of α2 (ITGA2) subunit binds a collagen motif with the sequence Gly-Phe-Hyp-Gly-Glu-Arg (Emsley J et al., 2000). Binding of collagen to ITGA2:ITGB1 (α2β1) generates intracellular signals that contribute to platelet activation. These interactions facilitate the engagement of the lower-affinity collagen receptor, GPVI (Tsuji M et al., 1997), the key receptor involved in collagen-induced platelet activation. The GPVI receptor is a complex of the GPVI protein with a dimer of Fc epsilon R1 gamma (FceRI gamma). The Src family kinases Fyn and Lyn constitutively associate with the GPVI:FceRIgamma complex in platelets and initiate platelet activation through phosphorylation of the immunoreceptor tyrosine-based activation motif (ITAM) in FceRI gamma, leading to binding and activation of the tyrosine kinase Syk. Downstream of Syk, a series of adapter molecules and effectors lead to platelet activation. VWF circulates in plasma as a multimeric molecule that senses hydrodynamic shear forces in the bloodstream (Reininger AJ 2008; Mojzisch A & Brehm MA 2021). Upon vascular injury, circulating VWF binds to subendothelial collagen, which becomes exposed to the flowing blood (Bergmeier W & Hynes RO 2012; Colace TV & Diamond SL 2013). Upon binding to collagen, VWF becomes anchored to the damaged surface. Shear forces then induce conformational changes to mechanosensitive VWF causing the bound VWF to stretch and unfold (Li F et al., 2004; Schneider SW et al., 2007; Fu H et al., 2017). VWF unfolding leads to exposure of the A1 domain to allow binding to glycoprotein Ib α (GPIbα, encoded by GP1BA), a subunit of the platelet surface GPIb:IX:V complex (Dumas JJ et al., 2004; Ju L et al., 2013). Shear-induced aggregation is achieved when VWF interacts both with exposed collagen and platelets to initiate platelet adhesion to vascular injury sites. The interaction between VWF and GPIb is regulated by shear force; an increase in the shear stress results in a corresponding increase in the affinity of VWF for GPIb.
R-HSA-76009 Platelet Aggregation (Plug Formation) The tethering of platelets to the site of vascular injury is the first step in the formation of a platelet thrombus. Firm adhesion of these tethered platelets, as well as the additional recruitment of others onto their surface leads to the formation of large platelet aggregates. The formation of a thrombus is strictly dependent on the formation of interplatelet bonds.
R-HSA-76002 Platelet activation, signaling and aggregation Platelet activation begins with the initial binding of adhesive ligands and of the excitatory platelet agonists (released or generated at the sites of vascular trauma) to cognate receptors on the platelet membrane (Ruggeri 2002). Intracellular signaling reactions then enhance the adhesive and procoagulant properties of tethered platelets or of platelets circulating in the proximity. Once platelets have adhered they degranulate, releasing stored secondary agents such as ADP, ATP, and synthesize thromboxane A2. These amplify the response, activating and recruiting further platelets to the area and promoting platelet aggregation. These amplify the response, activating and recruiting further platelets to the area and promoting platelet aggregation. Adenosine nucleotides signal through P2 purinergic receptors on the platelet membrane. ADP activates P2Y1 and P2Y12, which signal via both the alpha and gamma:beta components of the heterotrimeric G-protein (Hirsch et al. 2001, 2006), while ATP activates the ionotropic P2X1 receptor (Kunapuli et al. 2003). Activation of these receptors initiates a complex signaling cascade that ultimately results in platelet activation, aggregation and thrombus formation (Kahner et al. 2006). Integrin AlphaIIbBeta3 is the most abundant platelet receptor, with 40 000 to 80 000 copies per resting platelet, acting as a major receptor for fibrinogen and other adhesive molecules (Wagner et al. 1996). Activation of AlphaIIbBeta3 enhances adhesion and leads to platelet-platelet interactions, and thus aggregation (Philips et al. 1991). GP VI is the most potent collagen receptor initiating signal generation, an ability derived from its interaction with the FcRI gamma chain. This results in the phosphorylation of the gamma-chain by non-receptor tyrosine kinases of the Src family (1). The phosphotyrosine motif is recognized by the SH2 domains of Syk, a tyrosine kinase. This association activates the Syk enzyme, leading to activation (by tyrosine phosphorylation) of PLC gamma2 (2). Thrombin is an important platelet agonist generated on the membrane of stimulated platelets. Thrombin acts via cell surface Protease Activated Receptors (PARs). PARs are G-protein coupled receptors activated by a proteolytic cleavage in an extracellular loop (Vu, 1991) (3). Activated PARs signal via G alpha q (4) and via the beta:gamma component of the G-protein (5). Both stimulate PLC giving rise to PIP2 hydrolysis and consequent activation of PI3K (6). PLCgamma2 activation also gives rise to IP3 (7) which stimulates the IP3 receptor (8) leading to increased intracellular calcium. Platelet activation further results in the scramblase-mediated transport of negatively-charged phospholipids to the platelet surface. These phospholipids provide a catalytic surface (with the charge provided by phosphatidylserine and phosphatidylethanolamine) for the tenase complex (formed by the activated forms of the blood coagulation factors factor VIII and factor I).
R-HSA-418360 Platelet calcium homeostasis Ca2+ homeostasis is controlled by processes that elevate or counter the elevation of cytosolic Ca2+. During steady state conditions, cytoplasmic Ca2+ is reduced by the accumulation of Ca2+ in intracellular stores and by Ca2+ extrusion. The primary intracellular calcium store in platelets is the dense tubular system, the equivalent of the ER system in other cell types. Ca2+ is extruded by Ca2+-ATPases including plasma membrane Ca2+ ATPases (PMCAs) and sarco/endoplasmic reticulum Ca2+ -ATPase isoforms (SERCAs).
Activation of non- excitable cells involves the agonist-induced elevation of cytosolic Ca2+, an essential process for platelet activation. It occurs through Ca2+ release from intracellular stores and Ca2+ entry through the plasma membrane. Ca2+ store release involves phospholipase C (PLC)-mediated production of inositol-1,4,5-trisphosphate (IP3), which in turn stimulates IP3 receptor channels to release Ca2+ from intracellular stores. This is followed by Ca2+ entry into the cell through plasma membrane calcium channels, a process referred to as store-operated calcium entry (SOCE). Stromal interaction molecule 1 (STIM1), a Ca2+ sensor molecule in intracellular stores, and the four transmembrane channel protein Orai1 are the key players in platelet SOCE. Other major Ca2+ entry mechanisms are mediated by the direct receptor-operated calcium (ROC) channel, P2X1 and transient receptor potential channels (TRPCs).
R-HSA-114608 Platelet degranulation Platelets function as exocytotic cells, secreting a plethora of effector molecules at sites of vascular injury. Platelets contain a number of distinguishable storage granules including alpha granules, dense granules and lysosomes. On activation platelets release a variety of proteins, largely from storage granules but also as the result of apparent cell lysis. These act in an autocrine or paracrine fashion to modulate cell signaling.
Alpha granules contain mainly polypeptides such as fibrinogen, von Willebrand factor, growth factors and protease inhibitors that that supplement thrombin generation at the site of injury. Dense granules contain small molecules, particularly adenosine diphosphate (ADP), adenosine triphosphate (ATP), serotonin and calcium, all recruit platelets to the site of injury. The molecular mechanism which facilitates granule release involves soluble NSF attachment protein receptors (SNAREs), which assemble into complexes to form a universal membrane fusion apparatus. Although all cells use SNAREs for membrane fusion, different cells possess different SNARE isoforms. Platelets and chromaffin cells use many of the same chaperone proteins to regulate SNARE-mediated secretion (Fitch-Tewfik & Flaumenhaft 2013).
R-HSA-418346 Platelet homeostasis Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhesion and activation, suppresses coagulation, enhances fibrin cleavage and is anti-inflammatory in character. Under acute vascular trauma, vasoconstrictor mechanisms predominate and the endothelium becomes prothrombotic, procoagulatory and proinflammatory in nature. This is achieved by a reduction of endothelial dilating agents: adenosine, NO and prostacyclin; and by the direct action of ADP, serotonin and thromboxane on vascular smooth muscle cells to elicit their contraction (Becker et al. 2000). Cyclooxygenase-2 (COX-2) and endothelial nitric oxide synthase (eNOS) are primarily expressed in endothelial cells. Both are important regulators of vascular function. Under normal conditions, laminar flow induces vascular endothelial COX-2 expression and synthesis of Prostacyclin (PGI2) which in turn stimulates endothelial Nitric Oxide Synthase (eNOS) activity. PGI2 and NO both oppose platelet activation and aggregation, as does the CD39 ecto-ADPase, which decreases platelet activation and recruitment by metabolizing platelet-released ADP.
R-HSA-432142 Platelet sensitization by LDL Physiological concentrations (1g/L) of Low density lipoprotein (LDL) enhance platelet aggregation responses initiated by thrombin, collagen, and ADP. This enhancement involves the rapid phosphorylation of p38 mitogen-activated protein kinase (p38MAPK) at Thr180 and Tyr182. The receptor for LDL is ApoER2, a splice variant of the classical ApoE receptor. ApoER2 stimulation leads to association of the Src family kinase Fgr which is probably responsible for subsequent phosphorylation of p38MAPK. This stimulation is transient because LDL also increases the activity of PECAM-1, which stimulates phosphatases that dephosphorylate p38MAPK.
R-HSA-164525 Plus-strand DNA synthesis Two specific polypurine tracts (PPT sequences) in the viral RNA, one within the pol gene (central or cPPT) and one immediately preceding the U3 sequence (3' PPT), are spared from degradation during minus strand DNA synthesis and prime plus-strand synthesis. At least two discrete steps of DNA replication, removal of the PPT RNAs and the tRNA primer that initiated minus-strand synthesis, and a strand transfer lead to the synthesis of a linear duplex DNA corresponding to the full length of the HIV genomic RNA with long terminal repeat (LTR) sequences at both ends. Both DNA synthesis and RNA degradation are catalyzed by domains of the HIV-1 reverse transcriptase (RT) heterodimer. During plus-strand synthesis, Preston and colleagues observed secondary sites of plus-strand initiation at low frequency both in the cell-free system and in cultured virus-infected cells (Klarman et al., 1997).
R-HSA-156711 Polo-like kinase mediated events At mitotic entry, Plk1 phosphorylates and activates Cdc25C phosphatase, whereas it phosphorylates and down-regulates Wee1A (Watanabe et al. 2004). Plk1 also phosphorylates and inhibits Myt1 activity (Sagata 2005). Cyclin B1-bound Cdc2, which is the target of Cdc25C, Wee1A, and Myt1, functions in a feedback loop and phosphorylates the latter components (Cdc25C, Wee1A, Myt1). The Cdc2- dependent phosphorylation provides docking sites for the polo-box domain of Plk1, thus promoting the Plk1-dependent regulation of these components and, as a result, activation of Cdc2-Cyclin B1.
PLK1 phosphorylates and activates the transcription factor FOXM1 which stimulates the expression of a number of genes needed for G2/M transition, including PLK1, thereby creating a positive feedback loop (Laoukili et al. 2005, Fu et al. 2008, Sadasivam et al. 2012, Chen et al. 2013).
R-HSA-69091 Polymerase switching After the primers are synthesized, Replication Factor C binds to the 3'-end of the initiator DNA to trigger polymerase switching. The non-processive nature of pol alpha catalytic activity and the tight binding of Replication Factor C to the primer-template junction presumably lead to the turnover of the pol alpha:primase complex. After the Pol alpha-primase primase complex is displaced from the primer, the proliferating cell nuclear antigen (PCNA) binds to form a "sliding clamp" structure. Replication Factor C then dissociates, and DNA polymerase delta binds and catalyzes the processive synthesis of DNA.
R-HSA-174411 Polymerase switching on the C-strand of the telomere After the primers are synthesized on the G-Rich strand, Replication Factor C binds to the 3'-end of the initiator DNA to trigger polymerase switching. The non-processive nature of pol alpha catalytic activity and the tight binding of Replication Factor C to the primer-template junction presumably lead to the turnover of the pol alpha:primase complex. After the Pol alpha-primase primase complex is displaced from the primer, the proliferating cell nuclear antigen (PCNA) binds to form a "sliding clamp" structure. Replication Factor C then dissociates, and DNA polymerase delta binds and catalyzes the processive synthesis of DNA.
R-HSA-5250913 Positive epigenetic regulation of rRNA expression Transcription of rRNA genes is controlled by epigenetic activation and repression according to the metabolic requirements of the cell (reviewed in Percipalle and Farrants 2006, McStay and Grummt 2008, Goodfellow and Zomerdijk 2012, Grummt and Langst 2013). Depending on the growth state of the cell, about half of the approximately 400 rRNA genes are expressed and these have the modifications characteristic of active chromatin: unmethylated DNA and acetylated histones. Repressed genes generally have methylated DNA and histone H3 methylated at lysine-9. Regulators of activation include ERCC6 (CSB), histone acetylases such as KAT2B (PCAF), and the B-WICH complex. Dysregulation of RNA polymerase I transcription plays a role in disease (reviewed in Hannan et al. 2013).
The B-WICH complex positively regulates rRNA expression by remodeling chromatin and recruiting histone acetyltransferases that modify histones to transcriptionally active states
ERCC6 (CSB) and EHMT2(G9a) positively regulate rRNA expression by ERCC6 recruiting the histone methyltransferase EHMT2 (also known as G9a) which dimethylates histone H3 at lysine-9 within the transcribed regions of rRNA genes.
ERCC6 (CSB) and KAT2B (PCAF) positively regulate rRNA expression by ERCC6 recruiting the histone acetyltransferase KAT2B to the promoter where KAT2B acetylates histone H4 at several lysine residues and histone H3 at lysine-9. The acetylated chromatin facilitates the assembly of RNA polymerase I initiation complex.
R-HSA-438064 Post NMDA receptor activation events Ca2+ influx through the NMDA receptor initiates subsequent molecular pathways that have a defined role in establishing long-lasting synaptic changes. The molecular signaling initiated by a rise in Ca2+ within the spine leads to phosphorylation of Cyclic AMP Response Element binding protein (CREB1) at serine S133, leading to transcription of genes involved in long lasting changes at the synapse. The phosphorylation of CREB1 triggered by increased Ca2+ can be brought about by distinct molecular pathways that may involve MAP kinase, activation of adenylate cyclase and activation of CaMKIV (reviewed by Cohen and Greenberg 2008 and Hunt and Castillo 2012).
R-HSA-389977 Post-chaperonin tubulin folding pathway Alpha and beta tubulin folding intermediates are formed through ATP-dependent interaction with TriC/CCT. In order to form a functional heterodimer, these folding intermediates undergo a series of interactions with five proteins: (cofactors A-E) following release from TriC/CCT (reviewed in Cowan and Lewis et al., 2001). These interactions are described in the reactions below. Ultimately, alpha tubulin, when associated with cofactor E, interacts with cofactor D-bound beta-tubulin. The entry of cofactor C into this complex results in the discharge of native heterodimer triggered by GTP hydrolysis in beta tubulin (Tian et al., 1997).
R-HSA-426496 Post-transcriptional silencing by small RNAs Small RNAs act with components of the RNA-induced silencing complex (RISC) to post-transcriptionally repress expression of mRNAs (reviewed in Nowotny and Yang 2009, Chua et al. 2009). Two mechanisms exist: 1) cleavage of target RNAs by complexes containing Argonaute2 (AGO2, EIF2C2) and a guide RNA that exactly matches the target mRNA and 2) inhibition of translation of target RNAs by complexes containing AGO2 and an inexactly matching guide RNA or by complexes containing a nonendonucleolytic Argonaute (AGO1 (EIF2C1), AGO3 (EIF2C3), or AGO4 (EIF2C4)) and a guide RNA of exact or inexact match. Small interfering RNAs (siRNAs) and microRNAs (miRNAs) can serve as guide RNAs in both types of mechanism.
RNAi also appears to direct chromatin modifications that cause transcriptional gene silencing (reviewed in Verdel et al. 2009).
R-HSA-163125 Post-translational modification: synthesis of GPI-anchored proteins Glycosylphosphatidyl inositol (GPI) acts as a membrane anchor for many cell surface proteins. GPI is synthesized in the endoplasmic reticulum. In humans, a single pathway consisting of eleven reactions appears to be responsible for the synthesis of the major GPI species involved in membrane protein anchoring.
As a nascent protein fated to become GPI-anchored moves into the lumen of the endoplasmic reticulum, it is attacked by a transamidase complex that cleaves it near its carboxy terminus and attaches an acylated GPI moiety. The GPI moiety is deacylated, yielding a protein-GPI conjugate that can be efficiently transported to the Golgi apparatus. R-HSA-597592 Post-translational protein modification After translation, many newly formed proteins undergo further covalent modifications that alter their functional properties. Modifications associated with protein localization include the attachment of oligosaccharide moieties to membrane-bound and secreted proteins (N-linked and O-linked glycosylation), the attachment of lipid (RAB geranylgeranylation) or glycolipid moieties (GPI-anchored proteins) that anchor proteins to cellular membranes, and the vitamin K-dependent attachment of carboxyl groups to glutamate residues. Modifications associated with functions of specific proteins include gamma carboxylation of clotting factors, hypusine formation on eukaryotic translation initiation factor 5A, conversion of a cysteine residue to formylglycine (arylsulfatase activation), methylation of lysine and arginine residues on non-histone proteins (protein methylation), protein phosphorylation by secretory pathway kinases, and carboxyterminal modifications of tubulin involving the addition of polyglutamate chains.
Protein ubiquitination and deubiquitination play a major role in regulating protein stability and, together with SUMOylation and neddylation, can modulate protein function as well.
R-HSA-8957275 Post-translational protein phosphorylation Secretory pathway kinases phosphorylate a diverse array of substrates involved in many physiological processes.
R-HSA-9615933 Postmitotic nuclear pore complex (NPC) reformation The NPC is reassembled during late anaphase/telophase when nascent nuclear membranes associate with the chromatin surfaces (reviewed by Wandke and Kutay 2013). Assembly of specific NPC proteins (nucleoporins) into the reforming NPC occurs in a temporally ordered fashion (reviewed by Otsuka and Ellenberg 2018). The GTPase RAN plays a central role in regulating NPC assembly during telophase, as well as earlier events in mitosis, such as mitotic spindle assembly (reviewed by Zierhut and Funabiki 2015). The active form of RAN (RAN:GTP), which is generated by the chromatin-associated RAN guanine nucleotide exchange factor RCC1, is converted to the inactive form (RAN:GDP) by the cytoplasmically localized RAN GTPase activating protein RANGAP1. During telophase, the elevated RAN:GTP near chromatin releases nucleoporins from complexes with nuclear transport receptors, including KPNB1/KPNA (importin alpha/beta) and TPNO1 (transportin), thereby liberating the nucleoporins for NPC assembly (reviewed by Forbes et al. 2015).
R-HSA-622327 Postsynaptic nicotinic acetylcholine receptors Nicotinic acetylcholine receptors are found in the postsynaptic terminals and these receptors are responsible in mediating postsynaptic currents. Most common types of neuronal postsynaptic nicotinic acetylcholine receptors are homomeric alpha 7 containing acetylcholine receptors. The densities of acetylcholine receptors are found to be similar to NMDA and AMPA receptors at these sites. Nicotinic acetylcholine receptors may permit both sodium and calcium ions, however, the ratio of sodium and calcium influx makes the receptors either highly sodium permeable or highly calcium permeable.
R-HSA-1296071 Potassium Channels Potassium channels are tetrameric ion channels that are widely distributed and are found in all cell types. Potassium channels control resting membrane potential in neurons, contribute to regulation of action potentials in cardiac muscle and help release of insulin form pancreatic beta cells.
Broadly K+ channels are classified into voltage gated K+ channels, Hyperpolarization activated cyclic nucleotide gated K+ channels (HCN), Tandem pore domain K+ channels, Ca2+ activated K+ channels and inwardly rectifying K+ channels.
R-HSA-1296067 Potassium transport channels Inwardly rectifying potassium transport are tetrameric channels that are found in kidney in the nephron. Kir 1.1 works as a homotetramer, however, Kir 4.1 and 5.1 work as heterotetramers. These channels transport K+ from cytosol to the lumen of the tubules.
R-HSA-9679191 Potential therapeutics for SARS The search for drugs to prevent or reduce the severity of human infection with SARS-CoV-1 or SARS-CoV-2 has centered on ones that are effective in treatment of human infections with other RNA viruses or in diminishing cytokine storms and other pathologies due to destructive host reactions. The interactions of a large number of these candidate drugs with their known viral and human protein targets are annotated, as are some drugs that inhibit Cytochrome P450 (CYP) oxidoreductases to prolong the plasma half-lives of antiviral drugs. In addition, effects of these drugs on unrelated essential human proteins, that might limit their use in vivo, are annotated.
A notable success of this search is a combination treatment, Paxlovid (NCT04960202), involving ritonavir, an inhibitor of CYP3A4 and CYP2B6 oxidoreductases, and nirmatrelvir, an inhibitor of SARS-CoV-2 3CLp protease, to block steps in maturation of viral replicase proteins (Hashemian et al. 2023).
R-HSA-1912422 Pre-NOTCH Expression and Processing In humans and other mammals the NOTCH gene family has four members, NOTCH1, NOTCH2, NOTCH3 and NOTCH4, encoded on four different chromosomes. Their transcription is developmentally regulated and tissue specific, but very little information exists on molecular mechanisms of transcriptional regulation. Translation of NOTCH mRNAs is negatively regulated by a number of recently discovered microRNAs (Li et al. 2009, Pang et al.2010, Ji et al. 2009, Kong et al. 2010, Marcet et al. 2011, Ghisi et al. 2011, Song et al. 2009, Hashimoto et al. 2010, Costa et al. 2009).
The nascent forms of NOTCH precursors, Pre-NOTCH1, Pre-NOTCH2, Pre-NOTCH3 and Pre-NOTCH4, undergo extensive posttranslational modifications in the endoplasmic reticulum and Golgi apparatus to become functional. In the endoplasmic reticulum, conserved serine and threonine residues in the EGF repeats of NOTCH extracellular domain are fucosylated and glucosylated by POFUT1 and POGLUT1, respectively (Yao et al. 2011, Stahl et al. 2008, Wang et al. 2001, Shao et al. 2003, Acar et al. 2008, Fernandez Valdivia et al. 2011).
In the Golgi apparatus, fucose groups attached to NOTCH EGF repeats can be elongated by additional glycosylation steps initiated by fringe enzymes (Bruckner et al. 2000, Moloney et al. 2000, Cohen et al. 1997, Johnston et al. 1997, Chen et al. 2001). Fringe-mediated modification modulates NOTCH signaling but is not an obligatory step in Pre-NOTCH processing. Typically, processing of Pre-NOTCH in the Golgi involves cleavage by FURIN convertase (Blaumueller et al. 1997, Logeat et al. 1998, Gordon et al. 2009, Rand et al. 2000, Chan et al. 1998). The cleavage of NOTCH results in formation of mature NOTCH heterodimers that consist of NOTCH extracellular domain (NEC i.e. NECD) and NOTCH transmembrane and intracellular domain (NTM i.e. NTMICD). NOTCH heterodimers translocate to the cell surface where they function in cell to cell signaling.
R-HSA-1912420 Pre-NOTCH Processing in Golgi NOTCH undergoes final posttranslational processing in the Golgi apparatus (Lardelli et al. 1994, Blaumueller et al. 1997, Weinmaster et al. 1991, Weinmaster et al. 1992, Uyttendaele et al. 1996). Movement of NOTCH precursors from the endoplasmic reticulum to Golgi is controlled by SEL1L protein, a homolog of C. elegans sel-1. SEL1L localizes to the endoplasmic reticulum membrane and prevents translocation of misfolded proteins, therefore serving as a quality control check (Li et al. 2010, Sundaram et al. 1993, Francisco et al. 2010). Similarly, C. elegans sel-9 and its mammalian homolog TMED2 are Golgi membrane proteins that participate in quality control of proteins transported from Golgi to the plasma membrane. Translocation of a mutant C. elegans NOTCH homolog lin-12 from the Golgi to the plasma membrane is negatively regulated by sel-9 (Wen et al. 1999). A GTPase RAB6 positively controls NOTCH trafficking through Golgi (Purcell et al. 1999).
Processing of mammalian NOTCH precursors in the Golgi typically involves the cleavage by FURIN convertase. Pre-NOTCH is a ~300 kDa protein, and cleavage by FURIN produces two fragments with approximate sizes of 110 kDa and 180 kDa. The 110 kDa fragment contains the transmembrane and intracellular domains of NOTCH and is known as NTM or NTMICD. The 189 kDa fragment contains NOTCH extracellular sequence and is known as NEC or NECD. The NTM and NEC fragments heterodimerize (Blaumueller et al. 1997, Logeat et al. 1998, Chan et al. 1998) and are held together by disulfide bonds and calcium ions (Rand et al. 2000, Gordon et al. 2009).
An optional step in Pre-NOTCH processing in the Golgi is modification by fringe enzymes. Fringe enzymes are glycosyl transferases that initiate elongation of O-linked fucose on fucosylated peptides by addition of a beta 1,3 N-acetylglucosaminyl group, resulting in formation of disaccharide chains on NOTCH EGF repeats (GlcNAc-bet1,3-fucitol). Three fringe enzymes are known in mammals: LFNG (lunatic fringe), MFNG (manic fringe) and RFNG (radical fringe). LFNG shows the highest catalytic activity in modifying NOTCH (Bruckner et al. 2000, Moloney et al. 2000). Fringe-created disaccharide chains on NOTCH EGF repeats are further extended by B4GALT1 (beta-1,4-galactosyltransferase 1), which adds galactose to the N-acetylglucosaminyl group, resulting in formation of trisaccharide Gal-beta1,4-GlcNAc-beta1,3-fucitol chains (Moloney et al. 2000, Chen et al. 2001). Formation of trisaccharide chains is the minimum requirement for fringe-mediated modulation of NOTCH signaling, although fringe-modified NOTCH expressed on the cell surface predominantly contains tetrasaccharide chains on EGF repeats. The tetrasaccharide chains are formed by sialyltransferase(s) that add sialic acid to galactose, resulting in formation of Sia-alpha2,3-Gal-beta1,4-GlcNAc-beta1,3-fucitol (Moloney et al. 2000). Three known Golgi membrane sialyltransferases could be performing this function: ST3GAL3, ST3GAL4 and ST3GAL6 (Harduin-Lepers et al. 2001). The modification of NOTCH by fringe enzymes modulates NOTCH-signaling by increasing the affinity of NOTCH receptors for delta-like ligands, DLL1 and DLL4, while decreasing affinity for jagged ligands, JAG1 and JAG2.
R-HSA-1912399 Pre-NOTCH Processing in the Endoplasmic Reticulum In the endoplasmic reticulum, glycosyl transferases modify NOTCH precursors by glycosylating conserved serine and threonine residues in EGF repeats of NOTCH.
O-fucosyl transferase POFUT1 fucosylates NOTCH serine and threonine residues that conform to the consensus sequence C2-X(4-5)-S/T-C3, where C2 and C3 are the second and third cysteine residue within the EGF repeat, and X(4-5) is four to five amino acid residues of any type (Yao et al. 2011, Stahl et al. 2008, Wang et al. 2001, Shao et al. 2003).
O-glucosyl transferase POGLUT1, mammalian homolog of the Drosophila enzyme Rumi, adds a glucosyl group to conserved serine residues within the EGF repeats of NOTCH. The consensus sequence for POGLUT1-mediated glucosylation is C1-X-S-X-P-C2, where C1 and C2 are the first and second cysteine residue in the EGF repeat, respectively, while X represents any amino acid (Acar et al. 2008, Fernandez-Valdivia et al. 2011). Both fucosylation and glucosylation of NOTCH receptor precursors are essential for functionality.
R-HSA-1912408 Pre-NOTCH Transcription and Translation In humans, the NOTCH protein family has four members: NOTCH1, NOTCH2, NOTCH3 and NOTCH4. NOTCH1 protein was identified first, as the product of a chromosome 9 gene translocated in T-cell acute lymphoblastic leukemia that was homologous to Drosophila Notch (Ellisen et al. 1991). At the same time, rat Notch1 was cloned (Weinmaster et al. 1991), followed by cloning of mouse Notch1, named Motch (Del Amo et al. 1992). NOTCH2 protein is the product of a gene on chromosome 1 (Larsson et al. 1994). NOTCH2 expression is differentially regulated during B-cell development (Bertrand et al. 2000). NOTCH2 mutations are a rare cause of Alagille syndrome (McDaniell et al. 2006). NOTCH3 is the product of a gene on chromosome 19. NOTCH3 mutations are the underlying cause of CADASIL, cerebral arteriopathy with subcortical infarcts and leukoencephalopathy (Joutel et al. 1996). NOTCH4, the last NOTCH protein discovered, is the product of a gene on chromosome 6 (Li et al. 1998).
MicroRNAs play an important negative role in translation and/or stability of NOTCH mRNAs. MicroRNAs miR-34 (miR-34A, miR-34B and mi-R34C), whose transcription is directly induced by the tumor suppressor protein p53 (Chang et al. 2007, Raver-Shapira et al. 2007, He et al. 2007, Corney et al. 2007) bind and negatively regulate translation of NOTCH1 mRNA (Li et al. 2009, Pang et al. 2010, Ji et al. 2009) and NOTCH2 mRNA (Li et al. 2009). NOTCH1 mRNA translation is also negatively regulated by microRNAs miR-200B and miR-200C (Kong et al. 2010), as well as miR-449A, miR-449B and miR-449C (Marcet et al. 2011). Translation of NOTCH3 mRNA is negatively regulated by microRNAs miR-150 (Ghisi et al. 2011) and miR-206 (Song et al. 2009). Translation of NOTCH4 mRNA is negatively regulated by microRNAs miR-181C (Hashimoto et al. 2010) and miR-302A (Costa et al. 2009).
Nascent NOTCH peptides are co-translationally targeted to the endoplasmic reticulum for further processing, followed by modification in the Golgi apparatus, before trafficking to the plasma membrane. Endoplasmic reticulum calcium ATPases, positively regulate NOTCH trafficking, possibly by contributing to accurate folding of NOTCH precursors (Periz et al. 1999).
R-HSA-9757110 Prednisone ADME Prednisone (PREDN) is a prodrug of prednisolone (PREDL), and is rapidly absorbed. To achieve high uptake of the near water-insoluble molecule the highest dose 50 mg has to be dissolved in 250 ml water. Its conversion to the highly active prednisolone (PREDL) in liver cells is reversible but represents the favored reaction direction (Pickup, 1979).
Prednisone and prednisolone are considered to be fully therapeutically equivalent. The theoretical advantage of avoiding high GI concentrations of prednisone by administering prednisolone directly has never been shown to be clinically relevant (Vogt et al, 2007).
Only 2–5% of a given dose of prednisone is excreted unchanged in urine. After hydrogenation to prednisolone at least 20 metabolites and their conjugates are formed and excreted. The main metabolites both after systemic and topical use are 20alpha- and 20beta-dihydro-prednisone, as well as 20alpha- and 20beta-dihydro-prednisolone (20AH-PREDN, 20BH-PREDN, 20AH-PREDL, 20BH-PREDL), in addition to the 6beta-hydroxy compounds 6B-OH-PREDN and 6B-OH-PREDL (Matabosch et al, 2015; Mazzarino et al, 2019). Hydrogenation of PREDN and dehydrogenation of PREDL are complementary reactions that are dominant in different cell types. While liver and fat cells convert PREDN to PREDL, colon and kidney cells partly convert PREDL back to PREDN (Jamieson et al, 1995; Ricketts et al, 1998; Diederichs et al, 2002). We have depicted this equilibrium by showing example reactions in hepatocytes and kidney cells in the diagram.
R-HSA-389957 Prefoldin mediated transfer of substrate to CCT/TriC Unfolded actins and tubulins bound to prefoldin are transferred to CCT via a docking mechanism (McCormack and Willison, 2001).
R-HSA-196108 Pregnenolone biosynthesis The first process in the synthesis of all steroid hormones is the synthesis of pregnenolone from cholesterol. In this process, cholesterol mobilized from cytosolic lipid droplets or from lysosomes is transported to mitochondria and becomes localized to the inner mitochondrial membrane. Cholesterol transport appears to be rate-limiting for steroid hormone synthesis and its regulation, at the step of StAR-mediated traversal of the mitochondrial membrane, plays a central role in determining the amounts and identities of steroid hormones made in the body. In the inner mitochondrial membrane, cholesterol is converted to pregnenolone in a sequence of three reactions, all catalyzed by CYP11A (side chain cleavage enzyme). Finally, pregnenolone re-enters the cytosol (Payne and Hales 2004; Stocco 2001).
R-HSA-112308 Presynaptic depolarization and calcium channel opening Action potentials occur in electrically excitable cells such as neurons, muscles, and endocrine cells. They are initiated by transient opening of voltage dependent sodium channels, causing a rapid, large depolarization of membrane potentials that spread along the axon membrane.
The action potential travels down the axon and reaches the presynaptic terminal depolarizing the membrane in the pre synaptic terminal. The depolarization causes the voltage gated Ca2+ channels to open allowing the influx of Ca2+ that signals the release of neurotransmitter into the synaptic cleft.
R-HSA-500657 Presynaptic function of Kainate receptors Kainate receptors in the presynaptic neuron are involved in modulating the release of neurotransmitters like glutamate and gamma amino butyric acid (GABA). This activity of Kainate receptors is independent of ionic fluxes through the channel. Homomeric kainate receptors containing GRIK3 are shown to be involved in this process. Kainate receptors in these neurons bind G-protein coupled receptors that activate phospholipase C which eventually triggers the release of Ca2+ from the intracellular stores. The released Ca2+ further initiates the fusion and release of vesicles containing the neurotransmitter.
R-HSA-622323 Presynaptic nicotinic acetylcholine receptors Presynaptic acetylcholine receptors are located at or near nerve terminal and modulate the release of neurotransmitter such as glutamate, noradrenaline and dopamine. Activation of presynaptic acetylcholine receptors leads to influx of Ca2+ and sufficient increase in local Ca2+ concentrations which could be due to either direct or indirect Ca2+ entry. Direct Ca2+ entry through acetylcholine receptors containing alpha3 beta4 receptors is sufficient for the release of noradrenaline in hippocampus. Indirect Ca2+ increase could be due to Na+ dependent depolarization and activation of voltage dependent calcium channels (VDCC) as in the case of dopamine release. Local Ca2+ increase could also be due to an initial Ca2+ influx through acetlycholine homomeric receptors containing alpha7 subunits and further increase in Ca2+ is elicited due to Ca2+ induced Ca2+ release (CICR) that involves the ryanodine receptors in the ER and the IP3 receptors. This mechanism is used in hippocampal mossy fibre pathway. Nicotinic acetylcholine receptors may permit both sodium and calcium ions, however, the ratio of sodium and calcium influx makes these receptors either highly sodium permeable or highly calcium permeable.
R-HSA-5693616 Presynaptic phase of homologous DNA pairing and strand exchange The presynaptic phase of homologous DNA pairing and strand exchange during homologous recombination repair (HRR) begins with the displacement of RPA from ssDNA (Thompson and Limoli 2003) by the joint action of RAD51 and BRCA2. CHEK1-mediated phosphorylation of RAD51 and BRCA2 (Sorensen et al. 2005, Bahassi et al. 2008) is needed for BRCA2-mediated nucleation of RAD51 on 3'-ssDNA overhangs, RPA displacement and formation of RAD51 nucleofilaments (Yang et al. 2005, Jensen et al. 2010, Liu et al. 2010, Thorslund et al. 2010). Invasive RAD51 nucleofilaments are stabilized by the BCDX2 complex composed of RAD51B, RAD51C, RAD51D and XRCC2 (Masson et al. 2001, Chun et al. 2013, Amunugama et al. 2013).
R-HSA-9636383 Prevention of phagosomal-lysosomal fusion Lipoarabinomannan (LAM) is transported to Mtb's outer cell wall. When Mtb is interned by the phagocyte, LAM is shedded into the phagocyte's membrane, gets incorporated into lipid rafts of the phagosomal membrane, where it acts to prevent phagosomal-lysosomal fusion (Welin et al. 2008, Gaur et al. 2014). Other processes that get inhibited include the cytoskeletal protein coronin-1A and the fusion mediator vacuolar protein sorting-associated protein 33B (VPS33B) (Deghmane et al. 2007, Bach et al. 2008). Also the Ras-related protein (Rab5) effector phosphatidylinositol 3-phosphate (PI3P) gets enzymatically depleted (Vergne et al. 2005).
R-HSA-3215018 Processing and activation of SUMO The initial translation products of SUMO1, SUMO2, and SUMO3 are precursors that have extra amino acid residues at the C-terminus (reviewed in Wang and Dasso 2009, Wilkinson and Henley 2010, Hannoun et al. 2010, Gareau and Lima 2010, Hay 2007). SUMO1 has 4 extra residues, SUMO2 has 2 extra residues, and SUMO3 has 11 extra residues. Proteolytic cleavage by SUMO peptidases (SENPs) removes the propeptide and leaves diglycine residues at the C-terminus. Each SENP has distinct preferences for certain SUMOs. SENP1 has highest activity on SUMO1; SENP2 and SENP5 have highest activity on SUMO2 (Shen et al. 2006, Reverter and Lima 2006, Mikolajczyk et al. 2007). SENP1 and SENP2 are predominantly nucleoplasmic (Bailey and O'Hare 2004, Kim et al. 2005, Zhang et al. 2002, Hang and Dasso 2002, Itahana et al. 2006) and SENP5 is predominantly nucleolar (Di Bacco et al. 2006, Gong and Yeh 2006), therefore the processing reactions are believed to occur in the nucleus. The processed SUMO is then activated by formation of a thioester bond with a cysteine residue of an E1 enzyme, UBA2 (SAE2) in a complex with SAE1. SUMO is then transferred from the E1 enzyme to an E2 enzyme, UBC9 (UBE2I).
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA Co-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per gene, which cannot serve as splicing substrates until both 5' and 3' ends of each intron are synthesized. Thus the time that it takes for pol II to synthesize each intron defines a minimal time and distance along the gene in which splicing factors can be recruited. The time that it takes for pol II to reach the end of the gene defines the maximal time in which splicing could occur co-transcriptionally. Thus, the kinetics of transcription can affect the kinetics of splicing.Any covalent change in a primary (nascent) mRNA transcript is mRNA Processing. For successful gene expression, the primary mRNA transcript needs to be converted to a mature mRNA prior to its translation into polypeptide. Eucaryotic mRNAs undergo a series of complex processing reactions; these begin on nascent transcripts as soon as a few ribonucleotides have been synthesized during transcription by RNA Polymerase II, through the export of the mature mRNA to the cytoplasm, and culminate with mRNA turnover in the cytoplasm.
R-HSA-75067 Processing of Capped Intronless Pre-mRNA Co-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per gene, which cannot serve as splicing substrates until both 5' and 3' ends of each intron are synthesized. Thus the time that it takes for pol II to synthesize each intron defines a minimal time and distance along the gene in which splicing factors can be recruited. The time that it takes for pol II to reach the end of the gene defines the maximal time in which splicing could occur co-transcriptionally. Thus, the kinetics of transcription can affect the kinetics of splicing.
There are two classes of intronless pre-mRNAs (mRNAs expressed from genes that lack introns). The first class encodes the replication dependent histone mRNAs. These mRNAs have unique 3' ends that do not have a polyA tail. The replication dependent histone mRNAs in all metazoans, as well as Chlamydomonas and Volvox fall into this class.
The second class of mRNAs end in polyA tails, which are formed by a mechanism similar to that which poly-adenylate pre-mRNAs containing introns. In the intronless genes there is a different method of replacing the 3' splice site that activates polyadenylation.
R-HSA-5693607 Processing of DNA double-strand break ends Homology directed repair (HDR) through homologous recombination (HRR) or single strand annealing (SSA) requires extensive resection of DNA double-strand break (DSB) ends (Thompson and Limoli 2003, Ciccia and Elledge 2010). The resection is performed in a two-step process, where the MRN complex (MRE11A:RAD50:NBN) and RBBP8 (CtIP) bound to BRCA1 initiate the resection. This step is regulated by the complex of CDK2 and CCNA (cyclin A), ensuring the initiation of HRR during S and G2 phases of the cell cycle, when sister chromatids are available. The initial resection is also regulated by ATM-mediated phosphorylation of RBBP8 and CHEK2-mediated phosphorylation of BRCA1 (Chen et al. 2008, Yun and Hiom 2009, Buis et al. 2012, Wang et al. 2013, Davies et al. 2015, Parameswaran et al. 2015). After the initial resection, DNA nucleases EXO1 and/or DNA2 perform long-range resection, which is facilitated by DNA helicases BLM or WRN, as well as BRIP1 (BACH1) (Chen et al. 2008, Nimonkar et al. 2011, Sturzenegger et al. 2014, Suhasini et al. 2011). The resulting long 3'-ssDNA overhangs are coated by the RPA heterotrimers (RPA1:RPA2:RPA3), which recruit ATR:ATRIP complexes to DNA DSBs and, in collaboration with RAD17:RFC and RAD9:HUS1:RAD1 complexes, and TOPBP1 and RHNO1, activate ATR signaling. Activated ATR phosphorylates RPA2 and activates CHEK1 (Cotta-Ramusino et al. 2011), both of which are necessary prerequisites for the subsequent steps in HRR and SSA.
R-HSA-77595 Processing of Intronless Pre-mRNAs The 3' ends of eukaryotic mRNAs are generated by posttranscriptional processing of an extended primary transcript. For almost all RNAs, 3' processing consists of two steps: The mRNA is first cleaved at a particular phosphodiester bond downstream of the coding sequence. The upstream fragment then receives a poly(A) tail of approximately 250 adenylate residues whereas the downstream fragment is degraded. The two partial reactions are coupled so that reaction intermediates are usually undetectable. While 3' processing can be studied as an isolated event in vitro, it appears to be connected to transcription, splicing and transcription termination in vivo.
R-HSA-8949664 Processing of SMDT1 Proteolytic processing of proSMDT1 (proEMRE) regulates assembly of properly regulated mitochondrial calcium uniporter (MCU) complex (Konig et al. 2016). C2orf47 (MAIP) in a complex with AFG3L2 (m-AAA protease) binds the transit peptide of proSMDT1, promotes cleavage of the transit peptide by mitochondrial processing endopeptidase, and prevents proteolytic destruction of proSMDT1. SMDT1 that is not then incorporated with the regulatory subunits MICU1 and MICU2 (or MICU1 and MICU3 in neurons) into the MCU complex is degraded by AFG3L2, preventing assembly of unregulated MCU. Unprocessed proSMDT1 is proteolyzed by YME1L1.
R-HSA-174414 Processive synthesis on the C-strand of the telomere Once polymerase switching from pol alpha to pol delta is complete the processive synthesis of a short run of DNA called an Okazaki fragment begins. DNA synthesis is discontinuous and as the extending Okazaki fragment reaches the RNA primer, this primer is folded into a single-stranded flap, which is removed by endonucleases. The process of extension is completed by the ligation of adjacent Okazaki fragments.
R-HSA-69183 Processive synthesis on the lagging strand The key event that allows the processive synthesis on the lagging strand, is polymerase switching from pol alpha to pol delta, as on the leading strand. However, the processive synthesis on the lagging strand proceeds very differently. DNA synthesis is discontinuous, and involves the formation of short fragments called the Okazaki fragments. During the synthesis of Okazaki fragments, the RNA primer is folded into a single-stranded flap, which is removed by endonucleases. This is followed by the ligation of adjacent Okazaki fragments.
R-HSA-5357801 Programmed Cell Death Cell death is a fundamental cellular response that has a crucial role in shaping our bodies during development and in regulating tissue homeostasis by eliminating unwanted cells. There are a number of different forms of cell death, each with a corresponding number of complex subprocesses. The first form of regulated or programmed cell death to be characterized was apoptosis. Evidence has emerged for a number of regulated non-apoptotic cell death pathways, including some with morphological features that were previously attributed to necrosis. More recently necrosis has been subdivided into parts including programmed necrotic cell death processes, such as RIP1-mediated regulated necrosis or pyroptosis.
Reactome currently represents programmed cell death using the model of extrinsic signalling that leads to a molecular decision point pivoting on caspase-8 activation or inhibition. Caspase-8 activation tilts the cell towards apoptosis, while caspase-8 inhibition tilts the cell towards Regulated Necrosis.
The terminology and molecular definitions of cell death-related events annotated here are consistent with the 2015 recommendations of the Nomenclature Committee on Cell Death (NCCD) (Galluzzi L et al. 2015).
R-HSA-964827 Progressive trimming of alpha-1,2-linked mannose residues from Man9/8/7GlcNAc2 to produce Man5GlcNAc2 In the cis-Golgi, Man7, Man8 or Man9 N-glycans are progressively trimmed to Man5 N-glycans. The reaction can be catalyzed by one of three known mannosidases, expressed in different tissues and with slightly different affinity. These enzymes trim the mannoses in a different order (Tremblay and Herscovics, 2000), but produce the same output with 5 mannoses.
A small confusion on the nomenclature of these genes coding for these enzymes is present in the literature: the standard HGNC symbols are MAN1A1, MAN1A2, MAN1C1, but MAN1A2 is also referred to as MAN1B in certain publications, while MAN1B1 is the enzyme acting in the ERQC compartment on unfolded glycoproteins. Moreover, the names do not correspond to a preference of these enzymes for which of the three mannose branches these trim first.
R-HSA-1170546 Prolactin receptor signaling Prolactin (PRL) is a hormone secreted mainly by the anterior pituitary gland. It was originally identified by its ability to stimulate the development of the mammary gland and lactation, but is now known to have numerous and varied functions (Bole-Feysot et al. 1998). Despite this, few pathologies have been associated with abnormalities in prolactin receptor (PRLR) signaling, though roles in various forms of cancer and certain autoimmune disorders have been suggested (Goffin et al. 2002). A vast body of literature suggests effects of PRL in immune cells (Matera 1996) but PRLR KO mice have unaltered immune system development and function (Bouchard et al. 1999). In addition to the pituitary, numerous other tissues produce PRL, including the decidua and myometrium, certain cells of the immune system, brain, skin and exocrine glands such as the mammary, sweat and lacrimal glands (Ben-Jonathan et al. 1996). Pituitary PRL secretion is negatively regulated by inhibitory factors originating from the hypothalamus, the most important of which is dopamine, acting through the D2 subclass of dopamine receptors present in lactotrophs (Freeman et al. 2000). PRL-binding sites or receptors have been identified in numerous cells and tissues of adult mammals. Various forms of PRLR, generated by alternative splicing, have been reported in several species including humans (Kelly et al. 1991, Clevenger et al. 2003).
PRLR is a member of the cytokine receptor superfamily. Like many other members of this family, the first step in receptor activation was generally believed to be ligand-induced dimerization whereby one molecule of PRL bound to two molecules of receptor (Elkins et al. 2000). Recent reports suggest that PRLR pre-assembles at the plasma membrane in the absence of ligand (Gadd & Clevenger 2006, Tallet et al. 2011), suggesting that ligand-induced activation involves conformational changes in preformed PRLR dimers (Broutin et al. 2010).
PRLR has no intrinsic kinase activity but associates (Lebrun et al. 1994, 1995) with Janus kinase 2 (JAK2) which is activated following receptor activation (Campbell et al. 1994, Rui et al. 1994, Carter-Su et al. 2000, Barua et al. 2009). JAK2-dependent activation of JAK1 has also been reported (Neilson et al. 2007). It is generally accepted that activation of JAK2 occurs by transphosphorylation upon ligand-induced receptor activation, based on JAK activation by chimeric receptors in which various extracellular domains of cytokine or tyrosine kinase receptors were fused to the IL-2 receptor beta chain (see Ihle et al. 1994). This activation step involves the tyrosine phosphorylation of JAK2, which in turn phosphorylates PRLR on specific intracellular tyrosine residues leading to STAT5 recruitment and signaling, considered to be the most important signaling cascade for PRLR. STAT1 and STAT3 activation have also been reported (DaSilva et al. 1996) as have many other signaling pathways; signaling through MAP kinases (Shc/SOS/Grb2/Ras/Raf/MAPK) has been reported as a consequence of PRL stimuilation in many different cellular systems (see Bole-Feysot et al. 1998) though it is not clear how this signal is propagated. Other cascades non exhaustively include Src kinases, Focal adhesion kinase, phospholipase C gamma, PI3 kinase/Akt and Nek3 (Clevenger et al. 2003, Miller et al. 2007). The protein tyrosine phosphatase SHP2 is recruited to the C terminal tyrosine of PRLR and may have a regulatory role (Ali & Ali 2000). PRLR phosphotyrosines can recruit insulin receptor substrates (IRS) and other adaptor proteins to the receptor complex (Bole-Feysot et al. 1998).
Female homozygous PRLR knockout mice are completely infertile and show a lack of mammary development (Ormandy et al. 1997). Hemizogotes are unable to lactate following their first pregnancy and depending on the genetic background, this phenotype can persist through subsequent pregnancies (Kelly et al. 2001).
R-HSA-70688 Proline catabolism Proline is catabolized in two steps to yield L-glutamate gamma-semialdehyde, which can react further with glutamate to yield ornithine and alpha-ketoglutarate (annotated as a reaction of amino acid synthesis and interconversion) or with NAD+ to yield glutamate and NADH + H+ (Phang et al. 2001).
R-HSA-169893 Prolonged ERK activation events After NGF binding, activated Trk receptors provide multiple docking sites for adaptor proteins and enzymes. Two docking proteins, the Ankyrin-Rich Membrane Spanning protein (ARMS/Kidins220) and Fibroblast growth factor receptor substrate 2 (Frs2), target signaling molecules in response to NGF stimulation and link receptor activation with the MAP kinase (also called the Extracellular signal-Regulated Kinase cascade, ERK) cascade, an essential process for growth factor-induced cell proliferation and differentiation.
A feature of NGF signaling is the sustained activation of the MAPK cascade. This is achieved by the small G protein, Rap1 which binds to and activates B-Raf, an activator of the MAPK cascade. Rap1 is a member of the Ras family of G proteins and like all G proteins, Rap1 is in an inactive state when bound to GDP and is active when bound to GTP. A specific GEF (guanine nucleotide exchange factor) called C3G can activate Rap1 by exchanging GDP for GTP.
R-HSA-71032 Propionyl-CoA catabolism Propionyl-CoA is a product of the catabolism of the amino acids, leucine, methionine, and threonine, and of the beta-oxidation of fatty acids with odd numbers of carbon atoms. The three reactions of this pathway convert propionyl-CoA to succinyl-CoA, an intermediate of the citric acid cycle. Through these reactions, carbon atoms from these sources can be fully oxidized to produce energy, or can be directed to gluconeogenesis. The three reactions of propionyl-CoA catabolism take place in the mitochondrial matrix.
R-HSA-392851 Prostacyclin signalling through prostacyclin receptor Prostacyclin (PGI2) is continuously produced by healthy vascular endothelial cells. It inhibits platelet activation through interaction with the Gs-coupled receptor PTGIR, leading to increased cAMP, a consequent increase in cAMP-dependent protein kinase activity which prevents increases of cytoplasmic [Ca2+] necessary for activation (Woulfe et al. 2001). PGI2 is also an effective vasodilator. These effects oppose the effects of thromboxane (TXA2), another eicosanoid, creating a balance of blood circulation and platelet activation.
R-HSA-391908 Prostanoid ligand receptors Fatty acid cyclo-oxygenase (COX) converts arachidonic acid to prostaglandin H2 (PGH2) from which the prostanoids PGD2, PGE2, PGF2alpha, PGI2 (prostacyclin) and thromboxane A2 (TXA2) are derived. Based on the agonist potencies, five prostanoid receptors are recognized and correspondingly named DP, EP, FP, IP and TP receptors (Coleman RA et al, 1994). Additionally, EP receptors contains four subtypes, termed EP1, EP2, EP3 and EP4; the DP receptor also has two subtypes, DP1 and DP2 (CRTH2).
R-HSA-9907900 Proteasome assembly Proteasome comes in several varieties. From the most ubiquitous 26S proteasome, through P28 proteasomes, to the tissue-specific proteasomes such as immunoproteasome, thymoproteasome, and spermatoproteasome.
26S proteasome, responsible for most aspects of ubiquitin-dependent regulatory and quality-control protein degradation in cells, is a 2.6-MDa protein complex that consists of a barrel-shaped proteolytic 20S core particle (20S CP) of 28 subunits capped on one or both ends by a 19S regulatory particle (19S RP) comprised of at least 19 subunits (reviewed in Tomko and Hochstrasser 2013). The 19S RP, which consists of a base and a lid, coordinates substrate recognition, removal of substrate polyubiquitin chains, and substrate unfolding and translocation into the 20S CP for degradation (reviewed in Tomko and Hochstrasser 2013).
The 20S CP consists of four axially stacked heteroheptameric rings - two inner and two outer rings (reviewed in Tomko and Hochstrasser 2013). Inner rings contain seven distinct beta-subunits (beta-1-7, officially PSMB1-7 in humans, where beta-1 corresponds to PSMB6, beta-2 to PSMB7, beta-3 to PSMB3, beta-4 to PSMB2, beta-5 to PSMB5, beta-6 to PSMB1, and beta-7 to PSMB4), while the outer rings contain seven distinct alpha-subunits (alpha1-7, officially PSMA1-7 in humans, where alpha-1 corresponds to PSMA6, alpha-2 to PSMA2, alpha-3 to PSMA4, alpha-4 to PSMA7, alpha-5 to PSMA5, alpha-6 to PSMA1, and alpha-7 to PSMA3).
P28 proteasomes consist of the 20S CP and a P28 regulatory particle that does not have a ubiquitin receptor and comes in at least two different types of heptamers: P28-alpha-beta, composed of PSME1 (P28alpha) and PSME2 (P28beta), and P28-gamma, composed of PSME3 (P28gamma). P28 proteasomes are thought to be important for rapid degradation of misfolded proteins under conditions of oxidative stress (reviewed in Thomas et al. 2023).
In the immunoproteasome, the 20S CP inner ring subunits with proteolytic activity, PSMB6 (beta-1), PSMB7 (beta-2), and PSMB5 (beta-5), are substituted with PSMB9 (beta-1i), PSMB10 (beta-2i), and PSMB8 (beta-5i), respectively, and this variation of the core particle is known as 20S iCP. The immunoproteasome generates substrate cleavage patterns that enhance loading of peptides onto the class I major histocompatibility complex (MHC I) for immune presentation to killer T cells (reviewed in Tomko and Hochstrasser 2013). Immunoproteasomes utilize the P28 regulatory particle (Chen et al. 2021).
In the thymoproteasome, expressed in the thymus, the 20S CP inner ring proteolytic subunits PSMB6 (beta-1), PSBM7 (beta-2), and PSMB5 (beta-5), are replaced with PSMB9 (beta-1i), PSMB10 (beta-2i) and PSMB11 (beta-5t), respectively, and this variation of the core particle is known as 20S tCP. Thymoproteasomes appear to increase the repertoire of self peptides for positive selection during T cell development in the thymus (reviewed in Tomko and Hochstrasser 2013). The regulatory particle used by thymoproteasomes is not known.
In the spermatoproteasome, specifically expressed in differentiating spermatocytes, the outer ring subunit PSMA7 (alpha-4) is replaced with PSMA8 (alpha-4s). Spermatoproteasomes use the 19S RP and include an additional component, PSME4 (PA200) (Kniepert and Groettrup 2014).
An important endogenous inhibitor of the catalytic activity of 20S CP is the protein PSMF1 (PI31) (Hsu et al. 2023).
For a high-throughput study of subunit-subunit interactions in the human 26S proteasome, please refer to Chen et al. 2008, and for the cryogenic electron microscope (cryo-EM) studies of the human 26S proteasome please refer to Lu et al. 2017 and Adolf et al. 2024.
R-HSA-391251 Protein folding Due to the crowded envirnoment within the cell, many proteins must interact with molecular chaperones to attain their native conformation (reviewed in Young et al., 2004). Chaperones recognize and associate with proteins in their non-native state and facilitate their folding by stabilizing the conformation of productive folding intermediates. Chaperones that take part broadly in de novo protein folding, such as the Hsp70s and the chaperonins, facilitate the folding process through cycles of substrate binding and release regulated by their ATPase activity (see Young et al., 2004; Spiess et al., 2004; Bigotti and Clarke, 2008).
R-HSA-9629569 Protein hydroxylation This pathway groups reactions mediated by 2-OG (2-oxoglutarate)-dependent oxygenases that target proline, lysine, asparagine, arginine, aspartate, and histidine residues of diverse proteins, with effects that potentially modulate transcription and translation (Herr & Hausinger 2018; Markolovic et al. 2015; Stoehr et al. 2016; Zurlo et al. 2016).
The roles of members of this enzyme family in collagen assembly are annotated separately in pathway R-HSA-1650814, "Collagen biosynthesis and modifying enzymes".
R-HSA-9857492 Protein lipoylation Lipoate is an essential cofactor for five redox reactions: four in oxoacid dehydrogenases (active in energy and amino acid metabolism) and one in the glycine cleavage system (GCS). Lipoate synthesis and transfer to target proteins in mitochondria requires three steps. Octanoyl carried by ACP from mitochondrial fatty acid synthesis is first transferred to GCSH. In the second step, two sulfur atoms of an iron-sulfur cluster are inserted on the side chain, synthesizing the lipoyl group in a highly complicated reaction. Finally, lipoyl is transferred onto the lipoyl domains of the E2 subunits (DLST, DLAT, DBT) of the target enzyme complexes (OGDH, OADH, PDH, BCKDH) (Schonauer et al., 2009; Cao et al., 2018; reviewed in Cronan, 2020). Defects in the enzymes catalyzing the three steps cause severe lactic acidosis and metabolic imbalances due to dehydrogenase deficiency. Mutations in the lipoyl carrier GCSH additionally cause hyperglycinemia, leading to epileptic encephalopathy, since GCSH moonlights in glycine catabolism (Arribas-Carreira et al., 2023).
R-HSA-9609507 Protein localization Protein localization encompasses the processes that establish and maintain proteins at specific locations. Mechanisms that target proteins to particular locations in the cell typically involve a motif in the targeted protein that interacts with proteins located at the destination (reviewed in Bauer et al. 2015).
Mitochondrial proteins encoded in the nucleus may be targeted to the outer membrane, intermembrane space, inner membrane, or the matrix (reviewed in Kutik et al. 2007, Milenkovic et al. 2007, Bolender et al. 2008, Ender and Yamano 2009, Wiedemann and Pfanner 2017, Kang et al. 2018). A presequence or an internal targeting sequence causes a protein in the cytosol to interact with the TOMM40:TOMM70 complex in the outer mitochondrial membrane. After passage across the outer membrane, sequence motifs cause proteins to be targeted to the outer membrane via the SAMM50 complex, to the inner membrane via the TIMM22 or TIMM23 complexes, to the matrix via the TIMM23 complex, or proteins may fold and remain in the intermembrane space.
All of the proteins contained in the peroxisomal matrix are imported from the cytosol by a unique mechanism that does not require the imported proteins to be unfolded as they cross the membrane (reviewed in Ma et al. 2011, Fujiki et al. 2014, Francisco et al. 2017). In the cytosol, receptor proteins, PEX5 and PEX7, bind to specific sequence motifs in cargo proteins and then interact with a protein complex containing PEX13, PEX14, PEX2, PEX10, and PEX12 in the peroxisome membrane. The cargo proteins then pass through a proteinaceous channel in the membrane and PEX5 is recycled by a mechanism involving ubiquitination and deubiquitination.
Most peroxisomal membrane proteins (PMPs) are inserted into the peroxisomal membrane by the receptor-chaperone PEX19 and the docking receptor PEX3 (reviewed in Ma et al. 2011, Fujiki et al. 2014). PEX19 binds the PMP as it is translated in the cytosol. The PEX19:PMP complex then interacts with PEX3 located in the peroxisomal membrane. Through a mechanism that is not yet clear, the PMP is inserted into the peroxisomal membrane and PEX19 dissociates from PEX3.
R-HSA-8876725 Protein methylation Methylation of lysine (Lys) and arginine (Arg) residues on non-histone proteins is a prevalent post-translational modification and important regulator of cellular signal transduction pathways including MAPK, WNT, BMP, Hippo and JAK–STAT. Crosstalk between methylation and other types of post-translational modifications and between histone and non-histone protein methylation is frequent, affecting cellular functions such as chromatin remodelling, gene transcription, protein synthesis, signal transduction and DNA repair (Biggar & Li 2015).
R-HSA-5676934 Protein repair Reactive oxygen species (ROS) such as H2O2, superoxide anions and hydroxyl radicals interact with molecules in the cell causing damage that impairs cellular functions. Although cells have mechanisms to destroy ROS and repair the damage caused by ROS, it is considered to be a major factor in age-related diseases and the ageing process (Zhang & Weissbach 2008, Kim et al. 2014). ROS-scavenging systems include enzymes such as peroxiredoxins, superoxide dismutases, catalases and glutathione peroxidases exist to minimise the potential damage.
ROS reactions can also cause specific modifications to amino acid side chains that result in structural changes to proteins/enzymes. Methionine (Met) and cysteine (Cys) can be oxidised by ROS to sulfoxide and further oxidised to sulfone derivatives. Both free Met and protein-based Met are readily oxidized to form methionine sulphoxide (MetO) (Brot & Weissbach 1991). Many proteins have been demonstrated to undergo such oxidation and as a consequence have altered function (Levine et al. 2000). Sulphoxide formation can be reversed by the action of the methionine sulphoxide reductase system (MSR) which catalyses the reduction of MetO to Met (Brot et al. 1981). This repair uses one ROS equivalent, so MSR proteins can act as catalytic antioxidants, removing ROS (Levine et al. 1996). Methionine oxidation results in a mixture of methionine (S)-S- and (R)-S-oxides of methionine, diastereomers which are reduced by MSRA and MSRB, respectively. MSRA can reduce both free and protein-based methionine-(S)-S-oxide, whereas MSRB is specific for protein-based methionine-(R)-S-oxide. Mammals typically have only one gene encoding MSRA, but at least three genes encoding MSRBs (Hansel et al. 2005). Although structurally distinct, MRSA and MRSB share a common three-step catalytic mechanism. In the first step, the MSR catalytic cysteine residue interacts with the MetO substrate, which leads to product release and formation of the sulfenic acid. In the second step, an intramolecular disulfide bridge is formed between the catalytic cysteine and the regenerating cysteine. In the final step, the disulfide bridge is reduced by an electron donor, the NADPH-dependent thioredoxin/TR system, leading to the regeneration of the MSR active site (Boschi-Muller et al. 2008).
Beta-linked isoaspartyl (isoAsp) peptide bonds can arise spontaneously via succinimide-linked deamidation of asparagine (Asn) or dehydration of aspartate (Asp). Protein-L-isoaspartate (D-aspartate) O-methyltransferase (PCMT1, PIMT EC 2.1.1.77) transfers the methyl group from S-adenosyl-L-methionine (AdoMet) to the alpha side-chain carboxyl group of L-isoaspartyl and D-aspartatyl amino acids. The resulting methyl ester undergoes spontaneous transformation to L-succinimide, which spontaneously hydrolyses to generates L-aspartyl residues or L-isoaspartyl residues (Knorre et al. 2009). This repair process helps to maintain overall protein integrity.
R-HSA-8852135 Protein ubiquitination Ubiquitin is a small, 76 amino acid residue protein that is conjugated by E3 ubiquitin ligases to other proteins in order to regulate their function or degradation (enzymatic cascade reviewed in Neutzner and Neutzner 2012, Kleiger and Mayor 2014, structures and mechanisms of conjugating enzymes reviewed in Lorenz et al. 2013). Ubiquitination of target proteins usually occurs between the C-terminal glycine residue of ubiquitin and a lysine residue of the target, although linkages with cysteine, serine, and threonine residues are also observed (reviewed in Wang et al. 2012, McDowell and Philpott 2013).
Ubiquitin must first be processed from larger precursors and then activated by formation of a thiol ester bond between ubiquitin and an E1 activating enzyme (UBA1 or UBA6) and transfer to an E2 conjugating enzyme before being transferred by an E3 ligase to a target protein. Precursor proteins containing multiple ubiquitin monomers (polyubiquitins) are produced from the UBB and UBC genes; precursors containing a single ubiquitin monomer and a ribosomal protein are produced from the UBA52 and RPS27A genes. Many proteases (deubiquitinases) may potentially process these precursors yielding monomeric ubiquitin. The proteases OTULIN and USP5 are particularly active in cleaving the polyubiquitin precursors, whereas the proteases UCHL3, USP7, and USP9X cleave the ubiquitin-ribosomal protein precursors yielding ubiquitin monomers (Grou et al. 2015). A resultant ubiquitin monomer is activated by adenylation of the C-terminal glycine followed by conjugation of the C-terminus to a cysteine residue of the E1 enzymes UBA1 or UBA6 via a thiol ester bond. The ubiquitin is then transferred from the E1 enzyme to a cysteine residue of one of several E2 enzymes (reviewed in van Wijk and Timmers 2010, Stewart et al. 2016). Through a less well characterized mechanism, E3 ubiquitin ligases then bring a target protein and the E2-ubiquitin conjugate into proximity so that the ubiquitin is transferred via formation of an amide bond to a particular lysine residue (or, in rarer cases, a thiol ester bond to a cysteine residue or an ester bond to a serine or threonine residue) of the target protein (reviewed in Berndsen and Wolberger 2014). Based on protein homologies, families of E3 ubiquitin ligases have been identified that include RING-type ligases (reviewed in Deshaies et al. 2009, Metzger et al. 2012, Metzger et al. 2014), HECT-type ligases (reviewed in Rotin et al. 2009, Metzger et al. 2012), and RBR-type ligases (reviewed in Dove et al. 2016). A subset of the RING-type ligases participate in CULLIN-RING ligase complexes (CRLs which include SCF complexes, reviewed in Lee and Zhou 2007, Genschik et al. 2013, Skaar et al. 2013, Lee et al. 2014).
Some E3-E2 combinations catalyze mono-ubiquitination of the target protein (reviewed in Nakagawa and Nakayama 2015). Other E3-E2 combinations catalyze conjugation of further ubiquitin monomers to the initial ubiquitin, forming polyubiquitin chains. (It may also be possible for some E3-E2 combinations to preassemble polyubiquitin and transfer it as a unit to the target protein.) Ubiquitin contains several lysine (K) residues and a free alpha amino group to which further ubiquitin can be conjugated. Thus different types of polyubiquitin are possible: K11 linked polyubiquitin is observed in endoplasmic reticulum-associated degradation (ERAD), K29 linked polyubiquitin is observed in lysosomal degradation, K48 linked polyubiquitin directs target proteins to the proteasome for degradation, whereas K63 linked polyubiquitin generally acts as a scaffold to recruit other proteins in several cellular processes, notably DNA repair (reviewed in Komander et al. 2009). Ubiquitination is highly regulated (reviewed in Vittal et al. 2015) and affects all cellular processes including DNA damage response (reviewed in Brown and Jackson 2015), immune signaling (reviewed in Park et al. 2014, Lutz-Nicoladoni et al. 2015), and regulation of normal and cancerous cell growth (reviewed in Skaar and Pagano 2009, Yerlikaya and Yontem 2013, Strikoudis et al. 2014).
R-HSA-6794362 Protein-protein interactions at synapses Synapses constitute highly specialized sites of asymmetric cell-cell adhesion and intercellular communication. Its formation involves the recruitment of presynaptic and postsynaptic molecules at newly formed contacts. Synapse assembly and maintenance invokes heterophilic presynaptic and postsynaptic transmembrane proteins that bind each other in the extracellular space and recruit additional proteins via their intracellular domains. Members of the cadherin and immunoglobulin (Ig) superfamilies are thought to mediate this function. Several molecules, including synaptic cell-adhesion molecule (SynCAM), N-cadherin, neural cell-adhesion molecule (NCAM), Eph receptor tyrosine kinases, and neuroligins and neurexins, have been implicated in synapse formation and maintenance (Dean & Dresbach 2006, Craig et al. 2006, Craig & Kang 2007, Sudhof 2008).
R-HSA-433692 Proton-coupled monocarboxylate transport The SLC16A gene family encode proton-linked monocarboxylate transporters (MCT) which mediate the transport of monocarboxylates such as lactate and pyruvate. Monocarboxylates are a major energy source for all cells in the body so their transport in and out of cells is crucial for cellular function. To date, 14 SLC16A members have been identified through sequence homology. Of these 14 members, only seven isoforms have been functionally characterized and not all of these function as proton-coupled transporters. A number can transport diuretics, thyroid hormones and aromatic amino acids. The seven remaining SLC16A members are classed as orphan MCTs (Morris & Felmlee 2008, Merezhinskaya & Fishbein 2009).
In mammalian cells, MCTs (monocarboxylate transporters) require association with an ancillary protein to enable plasma membrane expression of the active transporter. Basigin (BSG, CD147) is the preferred binding partner for MCT1, MCT3 and MCT4, while MCT2 requires Embigin (EMB) (Wilson et al. 2005).
R-HSA-428559 Proton-coupled neutral amino acid transporters The human SLC36A gene family encodes four proton-coupled neutral amino acid transporters, PAT1-4. PAT1 and 2 mediate electroneutral symport of protons and small neutral amino acids like glycine, alanine and proline. PAT3 and 4 are orphans with unknown function (Boll M et al, 2004).
R-HSA-427975 Proton/oligopeptide cotransporters The human SLC15 gene family encode four proton-coupled oligopeptide transporters; PEPT1 (SLC15A1), PEPT2 (SLC15A2), PHT2 (SLC15A3) and PHT1 (SLC15A4). These cotransporters are part of the Proton-coupled Oligopeptide Transporter (POT) superfamily (also called Peptide Transporter (PTR) family) (Daniel H and Kottra G, 2004).
R-HSA-74259 Purine catabolism The purine bases guanine and hypoxanthine (derived from adenine by events in the purine salvage pathways) are converted to xanthine and then to urate uric acid, which is excreted from the body (Watts 1974). The end-point of this pathway in humans and hominoid primates is unusual. Most other mammals metabolize uric acid further to yield more soluble end products, and much speculation has centered on possible roles for high uric acid levels in normal human physiology.
R-HSA-73817 Purine ribonucleoside monophosphate biosynthesis The purine ribonucleotide inosine 5'-monophosphate (IMP) is assembled on 5-phospho-alpha-D-ribose 1-diphosphate (PRPP), with atoms derived from aspartate, glutamine, glycine, N10-formyl-tetrahydrofolate, and carbon dioxide. Although several of the individual reactions in this sequence are reversible, as indicated by the double-headed arrows in the diagram, other irreversible steps drive the pathway in the direction of IMP synthesis in the normal cell. All of these reactions are thus annotated here only in the direction of IMP synthesis. Guanosine 5'-monophosphate (GMP) and adenosine 5'-monophosphate (AMP) are synthesized from IMP.
R-HSA-74217 Purine salvage Nucleosides and free bases generated by DNA and RNA breakdown are converted back to nucleotide monophosphates, allowing them to re-enter the pathway of purine biosynthesis and interconversion. Under normal conditions, DNA turnover is limited and deoxyribonucleotide salvage operates at a correspondingly low level (Watts 1974).
R-HSA-9660826 Purinergic signaling in leishmaniasis infection The purinoreceptors are divided into inotropic (P2XR) and metabotropic (P2YR) subtypes whose ligands are the nucleotides ATP and UDP respectively (Cekic et al. 2016). The binding of these nucleotides to their receptors on macrophages have been associated with the activation of the inflammasome leading to the subsequent activation of interleukin 1 beta (IL1β) and TNF-α (Cekic et al. 2016 & Figueiredo et al. 2016). The liberation of ATP comes from tissues facing stressful stimuli such as a tissue injury or microorganism infection, amongst others. As a regulatory mechanism, certain enzymes can reduce ATP to Adenosine and a nucleoside can stimulate signalling pathways leading to the synthesis of anti-inflammatory cytokines (Cekic et al. 2016).
The activation of the receptor P2RX7 was shown to lead to the activation of killing mechanisms or cell death programs, ending up in the elimination of microbes such as Leishmania amazonensis, Mycobacterium tuberculosis, Chlamydia psittaci, and Toxoplasma gondii (Coutinho-Silva et al. 2012 & Idzko, 2014).
R-HSA-500753 Pyrimidine biosynthesis The pyrimidine orotate (orotic acid) is synthesized in a sequence of four reactions, deriving its atoms from glutamine, bicarbonate, and aspartate. A single multifunctional cytosolic enzyme catalyzes the first three of these reactions, while the last one is catalyzed by an enzyme associated with the inner mitochondrial membrane. In two further reactions, catalyzed by a bifunctional cytosolic enzyme, orotate reacts with 1-phosphoribosyl 5-pyrophosphate (PRPP) to yield orotidine 5'-monophosphate, which is decarboxylated to yield uridine 5'-monophosphate (UMP). While several individual reactions in this pathway are reversible, other irreversible reactions drive the pathway in the direction of UMP biosynthesis in the normal cell. All reactions are thus annotated here only in the forward direction.
This pathway has been most extensively analyzed at the genetic and biochemical level in hamster cell lines. All three enzymes have also been purified from human sources, however, and the key features of these reactions have been confirmed from studies of this human material (Jones 1980; Webster et al. 2001).
All other pyrimidines are synthesized from UMP. The reactions annotaed here, catalyzed by dCMP deaminase and dUTP diphosphatase yield dUMP, which in turn is converted to TMP by thymidylate synthase.
R-HSA-73621 Pyrimidine catabolism In parallel sequences of three reactions each, thymine is converted to beta-aminoisobutyrate and uracil is converted to beta-alanine. Both of these molecules are excreted in human urine and appear to be normal end products of pyrimidine catabolism (Griffith 1986; Webster et al. 2001). Mitochondrial AGXT2, however, can also catalyze the transamination of both molecules with pyruvate, yielding 2-oxoacids that can be metabolized further by reactions of branched-chain amino acid and short-chain fatty acid catabolism (Tamaki et al. 2000). The importance of these reactions in normal human pyrimidine catabolism has not been well worked out.
R-HSA-73614 Pyrimidine salvage In pyrimidine salvage reactions, nucleosides and free bases generated by DNA and RNA breakdown are converted back to nucleotide monophosphates, allowing them to re-enter the pathways of pyrimidine biosynthesis and interconversion.
R-HSA-71737 Pyrophosphate hydrolysis Many biosynthetic reactions are coupled to the cleavage of ATP to yield AMP and pyrophosphate. These reactions are typically freely reversible when carried out with purified substrates and enzymes in vitro. In vivo, however, the pyrophosphate is rapdily and essentially irreversibly hydrolyzed by a ubiquitous inorganic pyrophosphatase. This hydrolysis has the effect of pulling the first reaction strongly in the direction of biosynthesis, at the expense of two high-energy phosphate bonds. Studies of human cells have identified two forms of the enzyme, one localized to the cytosol and the other to the mitochondrial matrix (Raja et al. 1981).
Pyrophosphatase activity has likewise been shown for LHPP (Phospholysine phosphohistidine inorganic pyrophosphate phosphatase). Recent work indicates that LHPP acts as well to dephosphorylate phosphohistidine residues, that variants of it may be associated with suceptibilty to depression, and that it may be a tumor suppressor (reviewed in Gohla 2019), although without the molecular detail needed for a Reactome annotation.
R-HSA-5620971 Pyroptosis Pyroptosis is a form of lytic inflammatory programmed cell death that is triggered by microbial infection or pathological stimuli, such as stroke or cancer (reviewed in Shi J et al. 2017; Man SM et al. 2017; Tang D et al. 2019; Zheng Z & Li G 2020). The process of pyroptosis protects the host from microbial infection but can also lead to pathological inflammation if overactivated. The morphologic characteristics of pyroptosis include cell swelling, rupture of the cell membrane and release of intracellular contents into the extracellular environment. Pyroptosis is also characterized by chromatin condensation, however this is not the key or universal feature of pyroptosis (reviewed in Man SM et al. 2017; Tang D et al. 2019). Pyroptosis is executed by proteins of the gasdermin family, which mediate formation of membrane pores (Liu X et al. 2016; Ding J et al. 2016; Mulvihill E et al. 2018; Broz P et al. 2020). Pyroptosis can be defined as gasdermin-mediated programmed necrotic cell death (Shi J et al. 2017; Galluzzi L et al. 2018). The gasdermin (GSDM) superfamily includes GSDMA, GSDMB, GSDMC, GSDMD, GSDME (or DFNA5) and PJVK (DFNB59) (Kovacs SB & Miao EA 2018). Each protein contains an N-terminal domain with intrinsic necrotic pore-forming activity and a C‑terminal domain reported to inhibit cell death through intramolecular domain association (Liu X et al. 2016; Ding J et al. 2016; Liu Z et al. 2018, 2019; Kuang S et al. 2017). Proteolytic cleavage in the linker connecting the N‑ and C‑terminal domains of gasdermins releases the C‑terminus, allowing the gasdermin N‑terminus to translocate to the cell membrane and oligomerize to form pores (Shi J et al. 2015; Ding J et al. 2016; Sborgi L et al. 2016; Feng S et al. 2018; Yang J et al. 2018; Mulvihill E et al. 2018). Although PJVK (DFNB59) is included to the gasdermin family, it is not known whether PJVK is cleaved and whether the full length or the N-terminal portion of PJVK is responsible for forming membrane pores. The N‑terminal fragments of GSDMs strongly bind to phosphatidylinositol phosphates and weakly to phosphatidylserine, found on the inner leaflet of the plasma membrane (Liu X et al. 2016; Ding J et al. 2016; Mulvihill E et al. 2018). Gasdermins are also able to target cardiolipin, which is often found in mitochondrial membranes and membranes of bacteria (Liu X et al. 2016; Rogers C et al. 2019). The size of the GSDMD pore is estimated to be 10–20 nm (Ding J et al. 2016; Sborgi L et al. 2016). The pore‑forming activity of GSDMs in the cell membrane facilitates the release of inflammatory molecules such as interleukin (IL)‑1β and IL‑18 (mainly in GSDMD-mediated pyroptosis), and eventually leads to cytolysis in mammalian cells, releasing additional proinflammatory cellular contents including danger signals such as high mobility group box‑1 (HMGB1) (Shi J et al. 2015; He W et al. 2015; Evavold CL et al. 2017; Semino C et al. 2018; Volchuk A et al. 2020). Pyroptosis can occur in immune cells such as macrophages, monocytes and dendritic cells and non‑immune cell types such as intestinal epithelial cells, trophoblasts and hepatocytes (Taabazuing CY et al. 2017; Li H et al. 2019; Jia C et al. 2019). GSDME can be cleaved by caspase‑3 (CASP3) to induce pyroptosis downstream of the “apoptotic” machinery (Wang Y et al. 2017; Rogers C et al. 2017), whereas GSDMD is cleaved by inflammatory CASP1, CASP4 and CASP5 in humans, and CASP1, CASP11 in mice to induce pyroptosis associated with inflammasome activation (Shi J et al. 2015; Kayagaki N et al. 2015). CASP3 cleavage of GSDMD results in its inactivation (Taabazuing et al. 2017). In mouse macrophages, CASP8 can also cleave GSDMD and cause pyroptosis when TAK1 is inhibited (Malireddi R et al. 2018; Orning P et al. 2018; Sarhan J et al. 2018), and TAK1 inhibition also leads to GSDME cleavage (Sarhan J et al. 2018). Furthermore, activated CASP8 can drive inflammasome-independent cleavage of both pro-IL-1β and GSDMD downstream of the extrinsic cell death receptor signaling pathway switching apoptotic signaling to GSDMD-dependent pyroptotic-like cell death (Donado CA et al. 2020). The cleavage and activation of GSDMD in neutrophils is mediated by neutrophil elastase (NE or ELANE), which is released from azurophil granules into the cytosol during neutrophil extracellular trap (NET) formation (Kambara H et al. 2018). Further, granzyme A (GZMA) released from cytotoxic T lymphocytes and natural killer (NK) cells specifically target GSDMB for interdomain cleavage to activate GSDMB-dependent pyroptosis in target tumor cells (Zhou Z et al. 2020). Similarly, granzyme B (GZMB) released from cytotoxic T lymphocytes and natural killer (NK) cells, can induce GSDME‑dependent lytic cell death in tumor targets via the CASP3‑mediated cleavage of GSDME (Zhang Z et al. 2020).
This Reactome module describes pyroptotic activities of GSDMD and GSDME. While the N‑terminal domains of mammalian GSDMA, GSDMB, and GSDMC also have the ability to form pores (Feng S et al. 2018; Ruan J et al. 2018), their functions in the induction of pyroptosis, secretion of proinflammatory cytokines or in bactericidal activity in host remain to be studied and are not covered by this Reactome module.
R-HSA-70268 Pyruvate metabolism Pyruvate sits at an intersection of key pathways of energy metabolism. It is the end product of glycolysis and the starting point for gluconeogenesis and can be generated by the transamination of alanine. The pyruvate dehydrogenase complex can convert it to acetyl CoA (Reed and Hackert 1990), which can enter the TCA cycle or serve as the starting point for the syntheses of long-chain fatty acids, steroids, and ketone bodies depending on the tissue and metabolic state in which it is formed. It also plays a central role in balancing the energy needs of various tissues in the body. Under conditions in which oxygen supply is limiting, e.g., in exercising muscle, or in the absence of mitochondria, e.g., in red blood cells, re-oxidation of NADH produced by glycolysis cannot be coupled to the generation of ATP. Instead, re-oxidation is coupled to the reduction of pyruvate to lactate. This lactate is released into the blood and taken up primarily by the liver, where it is oxidized to pyruvate and can be used for gluconeogenesis (Cori 1981). For a recent review, see Prochownik & Wang, 2021.
R-HSA-5365859 RA biosynthesis pathway The major activated retinoid, all-trans-retinoic acid (atRA) is produced by the dehydrogenation of all-trans-retinol (atROL) by members of the short chain dehydrogenase/reductase (SDR) and aldehyde dehydrogenase (RALDH) gene families (Das et al. 2014, Napoli 2012).
R-HSA-8876198 RAB GEFs exchange GTP for GDP on RABs Human cells have more than 60 RAB proteins that are key regulators of intracellular membrane trafficking. These small GTPases contribute to trafficking specificity by localizing to the membranes of different organelles and interacting with effectors such as sorting adaptors, tethering factors, kinases, phosphatases and tubular-vesicular cargo (reviewed in Stenmark et al, 2009; Wandinger-Ness and Zerial, 2014; Zhen and Stenmark, 2015).
RAB localization depends on a number of factors including C-terminal prenylation, the sequence of upstream hypervariable regions and what nucleotide is bound, as well as interaction with RAB-interacting proteins (Chavrier et al, 1991; Ullrich et al, 1993; Soldati et al, 1994; Farnsworth et al, 1994; Seabra, 1996; Wu et al, 2010; reviewed in Stenmark, 2009; Wandinger-Ness and Zerial, 2014). More recently, the activity of RAB GEFs has also been implicated in regulating the localization of RAB proteins (Blumer et al, 2103; Schoebel et al, 2009; Cabrera and Ungermann, 2013; reviewed in Barr, 2013; Zhen and Stenmark, 2015)
In the active, GTP-bound form, RAB proteins are membrane-associated, while in the inactive GDP-bound form, RABs are extracted from the target membrane and exist in a soluble form in complex with GDP dissociation inhibitors (GDIs) (Ullrich et al, 1993; Soldati et al, 1994; Gavriljuk et al, 2013). Conversion between the inactive and active form relies on the activities of RAB guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs) (Yoshimura et al, 2010; Wu et al, 2011; Pan et al, 2006; Frasa et al, 2012; reviewed in Stenmark, 2009; Wandinger-Ness and Zerial, 2014; Ishida et al, 2016).
Newly synthesized RABs are bound to a RAB escort protein, CHM (also known as REP1) or CHML (REP2) (Alexandrov et al, 1994; Shen and Seabra, 1996). CHM/REP proteins are the substrate-binding component of the trimeric RAB geranylgeranyltransferase enzyme (GGTaseII) along with the two catalytic subunits RABGGTA and RABGGTB (reviewed in Gutkowska and Swiezewska, 2012; Palsuledesai and Distefano, 2015). REP proteins recruit the unmodified RAB in its GDP-bound state to the GGTase for sequential geranylgeranylation at one or two C-terminal cysteine residues (Alexandrov et al, 1994; Seabra et al 1996; Shen and Seabra, 1996; Baron and Seabra, 2008). After geranylation, CHM/REP proteins remain in complex with the geranylated RAB and escort it to its target membrane, where RAB activity is regulated by GAPs, GEFs, GDIs and membrane-bound GDI displacement factors (GDFs) (Sivars et al, 2003; reviewed in Stenmark, 2009; Wandinger-Ness and Zerial, 2014).
Unlike the RAB GAPS, which (to date) all contain a shared TBC domain, RAB GEFs are structurally diverse and range from monomeric to multisubunit complexes (reviewed in Fukuda et al, 2011; Frasa et al, 2012; Cherfils and Zeghouf, 2013; Ishida et al, 2016). While many GEFs contain one of three conserved GEF domains identified to date - the DENN (differentially expressed in normal and neoplastic cell) domain, the VPS9 domain and the SEC2 domain- other GEFs lack a conserved domain (reviewed in Ishida et al, 2016). Based on sequence conservation and subunit organization, GEFs can be grouped into 6 general classes: the DENND-containing GEFs, the VPS9-containing GEFs (both monomeric), the SEC2-containing GEFs (homodimeric), heterodimeric GEF complexes such as RIC1:RGP1, the multisubunit TRAPPC GEF, and others (reviewed in Barr and Lambright, 2010; Marat et al, 2011; Ishida et al, 2016). GEFs for many RABs have still not been identified, however.
R-HSA-8873719 RAB geranylgeranylation Human cells have more than 60 RAB proteins that are involved in trafficking of proteins in the endolysosomal system. These small GTPases contribute to trafficking specificity by localizing to the membranes of different endocytic compartments and interacting with effectors such as sorting adaptors, tethering factors, kinases, phosphatases and tubular-vesicular cargo (reviewed in Stenmark et al, 2009; Wandinger-Ness and Zerial, 2014). RAB localization depends on a number of factors including C-terminal prenylation, the sequence of an upstream hypervariable regions and what nucleotide is bound (Chavrier et al, 1991; Ullrich et al, 1993; Soldati et al, 1994; Farnsworth et al, 1994; Seabra, 1996; Wu et al, 2010; reviewed in Stenmark, 2009; Wandinger-Ness and Zerial, 2014). In the active, GTP-bound form, prenylated RAB proteins are membrane associated, while in the inactive GDP-bound form, RABs are extracted from the target membrane and exist in a soluble form in complex with GDP dissociation inhibitors (GDIs) (Ullrich et al, 1993; Soldati et al, 1994; Gavriljuk et al, 2103). Conversion between the inactive and active form relies on the activities of RAB guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs) (Yoshimura et al, 2010; Wu et al, 2011; Pan et al, 2006; Frasa et al, 2012; reviewed in Stenmark, 2009; Wandinger-Ness and Zerial, 2014).
Newly synthesized RABs are bound by a RAB escort protein, CHM (also known as REP1) or CHML (REP2) (Alexandrov et al, 1994; Shen and Seabra, 1996). CHM/REP proteins are the substrate-binding component of the trimeric RAB geranylgeranyltransferase enzyme (GGTaseII) along with the two catalytic subunits RABGGTA and RABGGTB (reviewed in Gutkowska and Swiezewska, 2012; Palsuledesai and Distefano, 2015). REP proteins recruit the unmodified RAB in its GDP-bound state to the GGTase for sequential geranylgeranylation at one or two C-terminal cysteine residues (Alexandrov et al, 1994; Seabra et al 1996; Shen and Seabra, 1996; Baron and Seabra, 2008). After geranylgeranylation, CHM/REP proteins remain in complex with the geranylgeranylated RAB and escort it to its target membrane, where its activity is regulated by GAPs, GEFs, GDIs and membrane-bound GDI displacement factors (GDFs) (Sivars et al, 2003; reviewed in Stenmark, 2009; Wandinger-Ness and Zerial, 2014).
R-HSA-9013149 RAC1 GTPase cycle This pathway catalogues RAC1 guanine nucleotide exchange factors (GEFs), GTPase activator proteins (GAPs), GDP dissociation inhibitors (GDIs) and RAC1 effectors (reviewed by Payapilli and Malliri 2018). RAC1 is one of the three best characterized RHO GTPases, the other two being RHOA and CDC42. RAC1 regulates the cytoskeleton and the production of reactive oxygen species (ROS) (Acevedo and Gonzalez-Billault 2018) and is involved in cell adhesion and cell migration (Marei and Malliri 2017). RAC1 is involved in neuronal development (de Curtis et al. 2014). In neurons, RAC1 activity is regulated by synaptic activation and RAC1-mediated changes in actin cytoskeleton are implicated in dendritic spine morphogenesis, which plays a role in memory formation and learning (Tajeda-Simon 2015; Costa et al. 2020). RAC1 is involved in metabolic regulation of pancreatic islet β-cells and in diabetes pathophysiology (Kowluru 2017; Kowluru et al. 2020). RAC1-mediated activation of NOX2 contributes to mitochondrial damage and the development of retinopathy in patients with diabetes (Sahajpal et al. 2019). RAC1 is important for exercise and contraction-stimulated glucose uptake in skeletal muscles (Sylow et al. 2014). RAC1 plays an important role in the maintenance of intestinal barrier integrity under physiological conditions and during tissue repair after resolution of colitis. Toxins of many diarrhea-causing bacteria target RAC1 (Kotelevets and Chastre 2020). RAC1 is important for skin homeostasis and wound healing and is involved in the pathogenesis of psoriasis (Winge and Marinkovich 2019). RAC1 is essential to vascular homeostasis and chronically elevated RAC1 signaling contributes to vascular pathology (Marinkovic et al. 2015). RAC1 hyperactivation, mutation and copy-number gain are frequently observed in solid tumors (Zou et al. 2017; De et al. 2019; De et al. 2020; Cannon et al. 2020; Kotelevets and Chastre 2020).
R-HSA-9013404 RAC2 GTPase cycle This pathway catalogues RAC2 guanine nucleotide exchange factors (GEFs), GTPase activator proteins (GAPs), GDP dissociation inhibitors (GDIs) and RAC2 effectors. RAC2 is exclusively expressed in hematopoietic cells (Troeger and Williams 2013). RAC2 is a component of the phagocytic oxidase complex in neutrophils (Troeger and Williams 2013). RAC2 is required for adhesion and mobilization of hematopoietic stem cells and progenitor cells (Troeger and Williams 2013). RAC2 is also needed for adhesion, migration and degranulation of mast cells (Troeger and Williams 2013). Mutations in RAC2 have been found in a small number of patients with primary immunodeficiencies (Gu and Williams 2002; Troeger and Williams 2013; Lougaris et al. 2020).
R-HSA-9013423 RAC3 GTPase cycle This pathway catalogues RAC3 guanine nucleotide exchange factors (GEFs), GTPase activator proteins (GAPs), GDP dissociation inhibitors (GDIs) and RAC3 effectors. RAC3 is highly similar to RAC1 (92% amino acid sequence identity), but it is expressed in fewer tissues than RAC1. RAC3 orthologues only exist in vertebrates (de Curtis 2019). RAC3 is highly expressed in neurons and plays an important role in neuronal and brain development (de Curtis 2014, de Curtis 2019). RAC3 mutations have been reported in patients with intellectual disability and brain malformations (de Curtis 2019). RAC3 is frequently overexpressed in cancer and contributes to proliferation, migration and invasiveness of cancer cells (de Curtis 2019).
R-HSA-5673000 RAF activation Mammals have three RAF isoforms, A, B and C, that are activated downstream of RAS and stimulate the MAPK pathway. Although CRAF (also known as RAF-1) was the first identified and remains perhaps the best studied, BRAF is most similar to the RAF expressed in other organisms. Notably, MAPK (ERK) activation is more compromised in BRAF-deficient cells than in CRAF or ARAF deficient cells (Bonner et al, 1985; Mikula et al, 2001, Huser et al, 2001, Mercer et al, 2002; reviewed in Leicht et al, 2007; Matallanas et al, 2011; Cseh et al, 2014). Consistent with its important role in MAPK pathway activation, mutations in the BRAF gene, but not in those for A- or CRAF, are associated with cancer development (Davies et al, 2002; reviewed in Leicht et al, 2007). ARAF and CRAF may have arisen through gene duplication events, and may play additional roles in MAPK-independent signaling (Hindley and Kolch, 2002; Murakami and Morrison, 2001).
Despite divergences in function, all mammalian RAF proteins share three conserved regions (CRs) and each interacts with RAS and MEK proteins, although with different affinities. The N-terminal CR1 contains a RAS-binding domain (RBD) and a cysteine-rich domain (CRD) that mediate interactions with RAS and the phospholipid membrane. CR2 contains inhibitory phosphorylation sites that impact RAS binding and RAF activation, while the C-terminal CR3 contains the bi-lobed kinase domain with its activation loop, and an adjacent upstream "N-terminal acidic motif" -S(S/G)YY in C- and A-RAF,respectively, and SSDD in B-RAF - that is required for RAF activation (Tran et al, 2005; Dhillon et al, 2002; Chong et al, 2001; Cutler et al, 1998; Chong et al, 2003; reviewed in Matallanas et al, 2011).
Regulation of RAF activity involves multiple phosphorylation and dephosphorylation events, intramolecular conformational changes, homo- and heterodimerization between RAF monomers and changes to protein binding partners, including scaffolding proteins which bring pathway members together (reviewed in Matallanas et al, 2011; Cseh et al, 2014). The details of this regulation are not completely known and differ slightly from one RAF isoform to another. Briefly, in the inactive state, RAF phosphorylation on conserved serine residues in CR2 promote an interaction with 14-3-3 dimers, maintaining the kinase in a closed conformation. Upon RAS activation, these sites are dephosphorylated, allowing the RAF CRD and RBD to bind RAS and phospholipids, facilitating membrane recruitment. RAF activation requires homo- or heterodimerization, which promotes autophosphorylation in the activation loop of the receiving monomer. Of the three isoforms, only BRAF is able to initiate this allosteric activation of other RAF monomers (Hu et al, 2013; Heidorn et al, 2010; Garnett et al, 2005). This activity depends on negative charge in the N-terminal acidic region (NtA; S(S/G)YY or SSDD) adjacent to the kinase domain. In BRAF, this region carries permanent negative charge due to the presence of the two aspartate residues in place of the tyrosine residues of A- and CRAF. In addition, unique to BRAF, one of the serine residues of the NtA is constitutively phosphorylated. In A- and CRAF, residues in this region are subject to phosphorylation by activated MEK downstream of RAF activation, establishing a positive feedback loop and allowing activated A- and CRAF monomers to act as transactivators in turn (Hu et al, 2013; reviewed in Cseh et al, 2014). RAF signaling is terminated through dephosphorylation of the NtA region and phosphorylation of the residues that mediate the inhibitory interaction with 14-3-3, promoting a return to the inactive state (reviewed in Matallanas et al, 2011; Cseh et al, 2014).
R-HSA-112409 RAF-independent MAPK1/3 activation Depending upon the stimulus and cell type mitogen-activated protein kinases (MAPK) signaling pathway can transmit signals to regulate many different biological processes by virtue of their ability to target multiple effector proteins (Kyriakis JM & Avruch J 2012; Yoon and Seger 2006; Shaul YD & Seger R 2007; Arthur JS & Ley SC 2013). In particular, the extracellular signal-regulated kinases MAPK3(ERK1) and MAPK1 (ERK2) are involved in diverse cellular processes such as proliferation, differentiation, regulation of inflammatory responses, cytoskeletal remodeling, cell motility and invasion through the increase of matrix metalloproteinase production (Viala E & Pouyssegur J 2004; Hsu MC et al. 2006; Dawson CW et al.2008; Kuriakose T et al. 2014).The canonical RAF:MAP2K:MAPK1/3 cascade is stimulated by various extracellular stimuli including hormones, cytokines, growth factors, heat shock and UV irradiation triggering the GEF-mediated activation of RAS at the plasma membrane and leading to the activation of the RAF MAP3 kinases. However, many physiological and pathological stimuli have been found to activate MAPK1/3 independently of RAF and RAS (Dawson CW et al. 2008; Wang J et al. 2009; Kuriakose T et al. 2014). For example, AMP-activated protein kinase (AMPK), but not RAF1, was reported to regulate MAP2K1/2 and MAPK1/3 (MEK and ERK) activation in rat hepatoma H4IIE and human erythroleukemia K562 cells in response to autophagy stimuli (Wang J et al. 2009). Tumor progression locus 2 (TPL2, also known as MAP3K8 and COT) is another MAP3 kinase which promotes MAPK1/3 (ERK)-regulated immune responses downstream of toll-like receptors (TLR), TNF receptor and IL1beta signaling pathways (Gantke T et al. 2011).
In response to stimuli the cell surface receptors transmit signals inducing MAP3 kinases, e.g., TPL2, MEKK1, which in turn phosphorylate MAP2Ks (MEK1/2). MAP2K then phosphorylate and activate the MAPK1/3 (ERK1 and ERK2 MAPKs). Activated MAPK1/3 phosphorylate and regulate the activities of an ever growing pool of substrates that are estimated to comprise over 160 proteins (Yoon and Seger 2006). The majority of ERK substrates are nuclear proteins, but others are found in the cytoplasm and other organelles. Activated MAPK1/3 can translocate to the nucleus, where they phosphorylate and regulate various transcription factors, such as Ets family transcription factors (e.g., ELK1), ultimately leading to changes in gene expression (Zuber J et al. 2000).
R-HSA-5673001 RAF/MAP kinase cascade The RAS-RAF-MEK-ERK pathway regulates processes such as proliferation, differentiation, survival, senescence and cell motility in response to growth factors, hormones and cytokines, among others. Binding of these stimuli to receptors in the plasma membrane promotes the GEF-mediated activation of RAS at the plasma membrane and initiates the three-tiered kinase cascade of the conventional MAPK cascades. GTP-bound RAS recruits RAF (the MAPK kinase kinase), and promotes its dimerization and activation (reviewed in Cseh et al, 2014; Roskoski, 2010; McKay and Morrison, 2007; Wellbrock et al, 2004). Activated RAF phosphorylates the MAPK kinase proteins MEK1 and MEK2 (also known as MAP2K1 and MAP2K2), which in turn phophorylate the proline-directed kinases ERK1 and 2 (also known as MAPK3 and MAPK1) (reviewed in Roskoski, 2012a, b; Kryiakis and Avruch, 2012). Activated ERK proteins may undergo dimerization and have identified targets in both the nucleus and the cytosol; consistent with this, a proportion of activated ERK protein relocalizes to the nucleus in response to stimuli (reviewed in Roskoski 2012b; Turjanski et al, 2007; Plotnikov et al, 2010; Cargnello et al, 2011). Although initially seen as a linear cascade originating at the plasma membrane and culminating in the nucleus, the RAS/RAF MAPK cascade is now also known to be activated from various intracellular location. Temporal and spatial specificity of the cascade is achieved in part through the interaction of pathway components with numerous scaffolding proteins (reviewed in McKay and Morrison, 2007; Brown and Sacks, 2009).
The importance of the RAS/RAF MAPK cascade is highlighted by the fact that components of this pathway are mutated with high frequency in a large number of human cancers. Activating mutations in RAS are found in approximately one third of human cancers, while ~8% of tumors express an activated form of BRAF (Roberts and Der, 2007; Davies et al, 2002; Cantwell-Dorris et al, 2011).
R-HSA-9649913 RAS GTPase cycle mutants RAS proteins cycle between an active GTP-bound state and an inactive GDP-bound state. GTPase activating proteins (GAPs) stimulate the low intrinsic GTPase activity of RAS proteins, converting the active to the inactive form, while guanine nucleotide exchange factors (GEFs) stimulate the intrinsic dissociation of GDP, allowing its replacement with GTP and consequent activation of RAS. Disease-causing mutations in RAS promote constitutive signaling by favouring the accumulation of RAS:GTP. The vast majority of these mutations are loss of function mutations at G12, G13 and Q61. These mutations disrupt the GTPase activity of RAS proteins by interfering with nucleophilic attack on the gamma phosphate of GTP. A smaller proportion of RAS mutations increase the intrinsic GDP dissociation rate, while other mutations interfere with RAS interactions with GAPs (reviewed in Prior et al, 2012; Pylayeva-Gupta et al, 2011; Stephen et al, 2014; Samatar and Poulikakos, 2014).
R-HSA-9648002 RAS processing RAS proteins undergo several processing steps during maturation including farnesylation, carboxy-terminal cleavage and carboxymethylation, among others. These steps are required for their membrane localization and function and ultimately for their ability to activate RAF (reviewed in Gysin et al, 2011; Ahearn et al, 2018).
R-HSA-6802953 RAS signaling downstream of NF1 loss-of-function variants NF1 is a RAS GAP that stimulates the intrinsic RAS GTPase activity, thereby shifting the RAS pathway towards the inactive state (reviewed in King et al, 2013). Loss-of-function mutations in NF1 have been identified both in germline diseases like neurofibromatosis 1 and in a range of sporadically occurring cancers. These mutations, which range from complete gene deletions to missense or frameshift mutations, generally decrease NF1 protein levels and abrogate RAS GAP activity in the cells, resulting in constitutive RAS pathway activation (reviewed in Maertens and Cichowski, 2014; Tidyman and Rauen, 2009; Ratner and Miller, 2015).
R-HSA-8853659 RET signaling The RET proto-oncogene encodes a receptor tyrosine kinase expressed primarily in urogenital precursor cells, spermatogonocytes, dopaminergic neurons, motor neurons and neural crest progenitors and derived cells. . It is essential for kidney genesis, spermatogonial self-renewal and survivial, specification, migration, axonal growth and axon guidance of developing enteric neurons, motor neurons, parasympathetic neurons and somatosensory neurons (Schuchardt et al. 1994, Enomoto et al. 2001, Naughton et al. 2006, Kramer et al. 2006, Luo et al. 2006, 2009). RET was identified as the causative gene for human papillary thyroid carcinoma (Grieco et al. 1990), multiple endocrine neoplasia (MEN) type 2A (Mulligan et al. 1993), type 2B (Hofstra et al. 1994, Carlson et al. 1994), and Hirschsprung's disease (Romeo et al. 1994, Edery et al. 1994).
RET contains a cadherin-related motif and a cysteine-rich domain in the extracellular domain (Takahashi et al. 1988). It is the receptor for members of the glial cell-derived neurotrophic factor (GDNF) family of ligands, GDNF (Lin et al. 1993), neurturin (NRTN) (Kotzbauer et al. 1996), artemin (ARTN) (Baloh et al. 1998), and persephin (PSPN) (Milbrandt et al. 1998), which form a family of neurotrophic factors. To stimulate RET, these ligands need a glycosylphosphatidylinositol (GPI)-anchored co-receptor, collectively termed GDNF family receptor-alpha (GFRA) (Treanor et al. 1996, Jing et al. 1996). The four members of this family have different, overlapping ligand preferences. GFRA1, GFRA2, GFRA3, and GFRA4 preferentially bind GDNF, NRTN, ARTN and PSPN, respectively (Jing et al. 1996, 1997, Creedon et al. 1997, Baloh et al. 1997, 1998, Masure et al. 2000). The GFRA co-receptor can come from the same cell as RET, or from a different cell. When the co-receptor is produced by the same cell as RET, it is termed cis signaling. When the co-receptor is produced by another cell, it is termed trans signaling. Cis and trans activation has been proposed to diversify RET signaling, either by recruiting different downstream effectors or by changing the kinetics or efficacy of kinase activation (Tansey et al. 2000, Paratcha et al. 2001). Whether cis and trans signaling has significant differences in vivo is unresolved (Fleming et al. 2015). Different GDNF family members could activate similar downstream signaling pathways since all GFRAs bind to and activate the same tyrosine kinase and induce coordinated phosphorylation of the same four RET tyrosines (Tyr905, Tyr1015, Tyr1062, and Tyr1096) with similar kinetics (Coulpier et al. 2002). However the exact RET signaling pathways in different types of cells and neurons remain to be determined.
R-HSA-195258 RHO GTPase Effectors RHO GTPases regulate cell behaviour by activating a number of downstream effectors that regulate cytoskeletal organization, intracellular trafficking and transcription (reviewed by Sahai and Marshall 2002).
One of the best studied RHO GTPase effectors are protein kinases ROCK1 and ROCK2, which are activated by binding RHOA, RHOB or RHOC. ROCK1 and ROCK2 phosphorylate many proteins involved in the stabilization of actin filaments and generation of actin-myosin contractile force, such as LIM kinases and myosin regulatory light chains (MRLC) (Amano et al. 1996, Ishizaki et al. 1996, Leung et al. 1996, Ohashi et al. 2000, Sumi et al. 2001, Riento and Ridley 2003, Watanabe et al. 2007).
PAK1, PAK2 and PAK3, members of the p21-activated kinase family, are activated by binding to RHO GTPases RAC1 and CDC42 and subsequent autophosphorylation and are involved in cytoskeleton regulation (Manser et al. 1994, Manser et al. 1995, Zhang et al. 1998, Edwards et al. 1999, Lei et al. 2000, Parrini et al. 2002; reviewed by Daniels and Bokoch 1999, Szczepanowska 2009).
RHOA, RHOB, RHOC and RAC1 activate protein kinase C related kinases (PKNs) PKN1, PKN2 and PKN3 (Maesaki et al. 1999, Zong et al. 1999, Owen et al. 2003, Modha et al. 2008, Hutchinson et al. 2011, Hutchinson et al. 2013), bringing them in proximity to the PIP3-activated PDPK1 (PDK1) and thus enabling PDPK1-mediated phosphorylation of PKN1, PKN2 and PKN3 (Flynn et al. 2000, Torbett et al. 2003). PKNs play important roles in cytoskeleton organization (Hamaguchi et al. 2000), regulation of cell cycle (Misaki et al. 2001), receptor trafficking (Metzger et al. 2003) and apoptosis (Takahashi et al. 1998). PKN1 is also involved in the ligand-dependent transcriptional activation by the androgen receptor (Metzger et al. 2003, Metzger et al. 2005, Metzger et al. 2008).
Citron kinase (CIT) binds RHO GTPases RHOA, RHOB, RHOC and RAC1 (Madaule et al. 1995), but the mechanism of CIT activation by GTP-bound RHO GTPases has not been elucidated. CIT and RHOA are implicated to act together in Golgi apparatus organization through regulation of the actin cytoskeleton (Camera et al. 2003). CIT is also involved in the regulation of cytokinesis through its interaction with KIF14 (Gruneberg et al. 2006, Bassi et al. 2013, Watanabe et al. 2013).
RHOA, RHOG, RAC1 and CDC42 bind kinectin (KTN1), a kinesin anchor protein involved in kinesin-mediated vesicle motility (Vignal et al. 2001, Hotta et al. 1996). The effect of RHOG activity on cellular morphology, exhibited in the formation of microtubule-dependent cellular protrusions, depends both on RHOG interaction with KTN1, as well as on the kinesin activity (Vignal et al. 2001). RHOG and KTN1 also cooperate in microtubule-dependent lysosomal transport (Vignal et al. 2001).
IQGAP proteins IQGAP1, IQGAP2 and IQGAP3, bind RAC1 and CDC42 and stabilize them in their GTP-bound state (Kuroda et al. 1996, Swart-Mataraza et al. 2002, Wang et al. 2007). IQGAPs bind F-actin filaments and modulate cell shape and motility through regulation of G-actin/F-actin equilibrium (Brill et al. 1996, Fukata et al. 1997, Bashour et al. 1997, Wang et al. 2007, Pelikan-Conchaudron et al. 2011). Binding of IQGAPs to F-actin is inhibited by calmodulin (Bashour et al. 1997, Pelikan-Conchaudron et al. 2011). IQGAP1 is involved in the regulation of adherens junctions through its interaction with E-cadherin (CDH1) and catenins (CTTNB1 and CTTNA1) (Kuroda et al. 1998, Hage et al. 2009). IQGAP1 contributes to cell polarity and lamellipodia formation through its interaction with microtubules (Fukata et al. 2002, Suzuki and Takahashi 2008).
RHOQ (TC10) regulates the trafficking of CFTR (cystic fibrosis transmembrane conductance regulator) by binding to the Golgi-associated protein GOPC (also known as PIST, FIG and CAL). In the absence of RHOQ, GOPC bound to CFTR directs CFTR for lysosomal degradation, while GTP-bound RHOQ directs GOPC:CFTR complex to the plasma membrane, thereby rescuing CFTR (Neudauer et al. 2001, Cheng et al. 2005).
RAC1 and CDC42 activate WASP and WAVE proteins, members of the Wiskott-Aldrich Syndrome protein family. WASPs and WAVEs simultaneously interact with G-actin and the actin-related ARP2/3 complex, acting as nucleation promoting factors in actin polymerization (reviewed by Lane et al. 2014).
RHOA, RHOB, RHOC, RAC1 and CDC42 activate a subset of formin family members. Once activated, formins bind G-actin and the actin-bound profilins and accelerate actin polymerization, while some formins also interact with microtubules. Formin-mediated cytoskeletal reorganization plays important roles in cell motility, organelle trafficking and mitosis (reviewed by Kuhn and Geyer 2014).
Rhotekin (RTKN) and rhophilins (RHPN1 and RHPN2) are effectors of RHOA, RHOB and RHOC and have not been studied in detail. They regulate the organization of the actin cytoskeleton and are implicated in the establishment of cell polarity, cell motility and possibly endosome trafficking (Sudo et al. 2006, Watanabe et al. 1996, Fujita et al. 2000, Peck et al. 2002, Mircescu et al. 2002). Similar to formins (Miralles et al. 2003), cytoskeletal changes triggered by RTKN activation may lead to stimulation of SRF-mediated transcription (Reynaud et al. 2000).
RHO GTPases RAC1 and RAC2 are needed for activation of NADPH oxidase complexes 1, 2 and 3 (NOX1, NOX2 and NOX3), membrane associated enzymatic complexes that use NADPH as an electron donor to reduce oxygen and produce superoxide (O2-). Superoxide serves as a secondary messenger and also directly contributes to the microbicidal activity of neutrophils (Knaus et al. 1991, Roberts et al. 1999, Kim and Dinauer 2001, Jyoti et al. 2014, Cheng et al. 2006, Miyano et al. 2006, Ueyama et al. 2006).
R-HSA-9012999 RHO GTPase cycle RHO family of GTPases is large and diverse, with many of its members considered to be master regulators of actin cytoskeleton. RHO GTPases are involved in the regulation of many cellular processes that depend on dynamic reorganization of the cytoskeleton, including cell migration, cell adhesion, cell division, establishment of cellular polarity and intracellular transport. As a consequence, RHO GTPases play important roles in neuronal development, immunity and cardio-vascular homeostasis. RHO GTPases are involved in the etiology of infectious diseases, congenital immunodeficiencies, neurodegenerative diseases and cancer. For review, please refer to Jaffe and Hall 2005, Lemichez and Aktories 2013, Ridley 2015, Hodge and Ridley 2016, Haga and Ridley 2016, Olson 2018, and Kalpachidou et al. 2019.
Phylogenetically, RHO GTPases can be grouped into four clusters. The first cluster consists of three subfamilies: Rho, RhoD/RhoF and Rnd. The second cluster consists of three subfamilies: Rac, Cdc42 and RhoU/RhoV. The third cluster consists of the RhoH subfamily. The fourth cluster consists of the RhoBTB subfamily. Miro GTPases and RHOBTB3 ATPase are sometimes described as Rho family members, but they are phylogenetically distant from the Rho family and constitute two separate families of Ras-like GTPases, which, besides Rho, Miro and RHOBTB3 also includes Ran, Arf, Rab and Ras families (Boureux et al. 2007). Based on their activation type, RHO GTPases can be divided into classical (typical) and atypical (reviewed by Haga and Ridley 2016, and Kalpachidou et al. 2019). Classical RHO GTPases cycle between active GTP-bound states and inactive GDP-bound states through steps that are tightly controlled by members of three classes of proteins: (1) guanine nucleotide dissociation inhibitors or GDIs, which maintain Rho proteins in an inactive state in the cytoplasm, (2) guanine nucleotide exchange factors or GEFs, which destabilize the interaction between Rho proteins and their bound nucleotide, the net result of which is the exchange of bound GDP for the more abundant GTP, and (3) GTPase activating proteins or GAPs, which stimulate the low intrinsic GTP hydrolysis activity of Rho family members, thus promoting their inactivation. GDIs, GEFs, and GAPs are themselves subject to tight regulation, and the overall level of Rho activity reflects the balance of their activities. Many of the Rho-specific GEFs, GAPs, and GDIs act on multiple Rho GTPases, so that regulation of these control proteins can have complex effects on the functions of multiple Rho GTPases (reviewed by Van Aelst and D'Souza-Schorey 1997, and Hodge and Ridley 2016). The classical Rho GTPase cycle is diagrammed in the figure below. External or internal cues promote the release of Rho GTPases from the GDI inhibitory complexes, which allows them to associate with the plasma membrane, where they are activated by GEFs (1), and can signal to effector proteins (4). Then, GAPs inactivate the GTPases by accelerating the intrinsic GTPase activity, leading to the GDP bound form (2). Once again, the GDI molecules stabilize the inactive GDP bound form in the cytoplasm, waiting for further instructions (3) (Tcherkezian and Lamarche-Vane, 2007). Classical RHO GTPases include four subfamilies: Rho (includes RHOA, RHOB and RHOC), Rac (includes RAC1, RAC2, RAC3 and RHOG), Cdc42 (includes CDC42, RHOJ and RHOQ) and RhoD/RhoF (includes RHOD and RHOF) (reviewed in Haga and Ridley 2016). RHOA, the founding member of the RHO GTPase family, regulates the actin cytoskeleton, formation of stress fibers and cell contractility, which is implicated in cell adhesion and migration (Lessey et al. 2012). RHOB and RHOC functions resemble RHOA (Vega and Ridley 2018; Guan et al. 2018). RHOB is also involved in membrane trafficking and DNA repair (Vega and Ridley 2018). RAC1 regulates the cytoskeleton and the production of reactive oxygen species (ROS) (Acevedo and Gonzalez-Billault 2018), and is involved in cell adhesion and cell migration (Marei and Malliri 2017). RAC2 expression is restricted to hematopoietic cells and RAC2 is a component of the phagocytic oxidase complex in neutrophils (Troeger and Williams 2013). RAC3 shares 92% sequence identity with RAC1 and is highly expressed in neurons (de Curtis 2019). CDC42 regulate the cytoskeleton and cell polarity, and is involved in cell adhesion and migration as well as in intracellular membrane trafficking (Egorov and Polishchuk 2017; Xiao et al. 2018; Pichaud et al. 2019; Woods and Lew 2019). RHOJ is highly expressed in endothelial cells, regulating their motility and vascular morphogenesis (Leszczynska et al. 2011; Shi et al. 2016). RHOQ (also known as TC10) is highly activated on exocytosing vesicles and recycling endosomes (Donnelly et al. 2014) and is involved in trafficking of CFTR (cystic fibrosis transmembrane conductance regulator) (Cheng et al. 2005). RHOD regulates cytoskeletal dynamics and intracellular transport of vesicles (Randazzo 2003; Gad and Aspenstrom 2010; Aspenstrom et al. 2014, Aspenstrom et al. 2020). RHOF regulates cytoskeletal dynamics (Gad and Aspenstrom 2010; Aspenstrom et al. 2014, Aspenstrom et al. 2020) and promotes the formation of filopodia and stress fibers (Fan and Mellor 2012). RHOD and RHOF do possess GTPase activity and are therefore grouped with classical RHO GTPases, but they are atypical in the sense that they possess high intrinsic guanine nucleotide exchange activity and do not require GEFs for activation (Aspenstrom et al. 2020).
Atypical RHO GTPases do not possess GTPase activity. They therefore constitutively exist in the active GTP-bound state. Atypical RHO GTPases include three subfamilies: Rnd (includes RND1, RND2 and RND3), RhoBTB (includes RHOBTB1 and RHOBTB2), RhoH (RHOH is the only member) and RhoU/RhoV (includes RHOU and RHOV). RND1 and RND3 can antagonize RHOA activity, leading to loss of stress fibers and cell rounding (Haga and Ridley 2016). RND1, RND2 and RND3 regulate cell migration (Ridley 2015; Mouly et al. 2019). RHOBTB1 is a component of a signaling cascade that regulates vascular function and blood pressure (Ji and Rivero 2016). RHOBTB2 is involved in COP9 signalosome-regulated and CUL3-dependent protein ubiquitination (Berthold et al. 2008; Ji and Rivero 2016). RHOH expression is restricted to hematopoietic cells, and it is known to be involved in T cell receptor (TCR) signaling and T cell development (Suzuki and Oda 2008; Troeger and Williams 2013). RHOU and RHOV expression is induced by WNT signaling and they are involved in regulation of cell shape and cell adhesion (Faure and Fort 2015; and Hodge and Ridley 2016).
Almost every classical RHO GTPase interacts with multiple GEFs, GAPs and GDIs, and every RHO GTPase activates multiple downstream effectors. There are 82 Rho GEFs (71 Dbl, reviewed in Fort and Blangy 2017, and 11 DOCK, reviewed in Meller et al. 2005), 66 Rho GAPs (Amin et al. 2016) and 3 Rho GDIs (Dransart et al. 2005) encoded by the human genome. To keep our reaction annotations compact, we have grouped the GEF, GAP, GDI and effector proteins associated with each RHO GTPase into sets. Within a set, we have distinguished full set members from candidate members on the basis of the amount of experimental evidence supporting the member’s molecular function. Note that members of a set can otherwise be functionally quite diverse. Annotation of upstream activators of GEFs, GAPs and GDIs was outside the scope of this catalogue pathway and is or will be shown elsewhere in Reactome. Signaling through downstream effectors is shown in more detail in the Reactome pathway “RHO GTPase Effectors”.
R-HSA-5663220 RHO GTPases Activate Formins Formins are a family of proteins with 15 members in mammals, organized into 8 subfamilies. Formins are involved in the regulation of actin cytoskeleton. Many but not all formin family members are activated by RHO GTPases. Formins that serve as effectors of RHO GTPases belong to different formin subfamilies but they all share a structural similarity to Drosophila protein diaphanous and are hence named diaphanous-related formins (DRFs).
DRFs activated by RHO GTPases contain a GTPase binding domain (GBD) at their N-terminus, followed by formin homology domains 3, 1, and 2 (FH3, FH1, FH2) and a diaphanous autoregulatory domain (DAD) at the C-terminus. Most DRFs contain a dimerization domain (DD) and a coiled-coil region (CC) in between FH3 and FH1 domains (reviewed by Kuhn and Geyer 2014). RHO GTPase-activated DRFs are autoinhibited through the interaction between FH3 and DAD which is disrupted upon binding to an active RHO GTPase (Li and Higgs 2003, Lammers et al. 2005, Nezami et al. 2006). Since formins dimerize, it is not clear whether the FH3-DAD interaction is intra- or intermolecular. FH2 domain is responsible for binding to the F-actin and contributes to the formation of head-to-tail formin dimers (Xu et al. 2004). The proline-rich FH1 domain interacts with the actin-binding proteins profilins, thereby facilitating actin recruitment to formins and accelerating actin polymerization (Romero et al. 2004, Kovar et al. 2006).
Different formins are activated by different RHO GTPases in different cell contexts. FMNL1 (formin-like protein 1) is activated by binding to the RAC1:GTP and is involved in the formation of lamellipodia in macrophages (Yayoshi-Yamamoto et al. 2000) and is involved in the regulation of the Golgi complex structure (Colon-Franco et al. 2011). Activation of FMNL1 by CDC42:GTP contributes to the formation of the phagocytic cup (Seth et al. 2006). Activation of FMNL2 (formin-like protein 2) and FMNL3 (formin-like protein 3) by RHOC:GTP is involved in cancer cell motility and invasiveness (Kitzing et al. 2010, Vega et al. 2011). DIAPH1, activated by RHOA:GTP, promotes elongation of actin filaments and activation of SRF-mediated transcription which is inhibited by unpolymerized actin (Miralles et al. 2003). RHOF-mediated activation of DIAPH1 is implicated in formation of stress fibers (Fan et al. 2010). Activation of DIAPH1 and DIAPH3 by RHOB:GTP leads to actin coat formation around endosomes and regulates endosome motility and trafficking (Fernandez-Borja et al. 2005, Wallar et al. 2007). Endosome trafficking is also regulated by DIAPH2 transcription isoform 3 (DIAPH2-3) which, upon activation by RHOD:GTP, recruits SRC kinase to endosomes (Tominaga et al. 2000, Gasman et al. 2003). DIAPH2 transcription isoform 2 (DIAPH2-2) is involved in mitosis where, upon being activated by CDC42:GTP, it facilitates the capture of astral microtubules by kinetochores (Yasuda et al. 2004, Cheng et al. 2011). DIAPH2 is implicated in ovarian maintenance and premature ovarian failure (Bione et al. 1998). DAAM1, activated by RHOA:GTP, is involved in linking WNT signaling to cytoskeleton reorganization (Habas et al. 2001). R-HSA-5668599 RHO GTPases Activate NADPH Oxidases NADPH oxidases (NOX) are membrane-associated enzymatic complexes that use NADPH as an electon donor to reduce oxygen and produce superoxide (O2-) that serves as a secondary messenger (Brown and Griendling 2009).
NOX2 complex consists of CYBB (NOX2), CYBA (p22phox), NCF1 (p47phox), NCF2 (p67phox) and NCF4 (p40ohox). RAC1:GTP binds NOX2 complex in response to VEGF signaling by directly interracting with CYBB and NCF2, leading to enhancement of VEGF-signaling through VEGF receptor VEGFR2, which plays a role in angiogenesis (Price et al. 2002, Bedard and Krause 2007). RAC2:GTP can also activate the NOX2 complex by binding to CYBB and NCF2, leading to production of superoxide in phagosomes of neutrophils which is necessary fo the microbicidal activity of neutrophils (Knaus et al. 1991, Roberts et al. 1999, Kim and Dinauer 2001, Jyoti et al. 2014).
NOX1 complex (composed of NOX1, NOXA1, NOXO1 and CYBA) and NOX3 complex (composed of NOX3, CYBA, NCF1 amd NCF2 or NOXA1) can also be activated by binding to RAC1:GTP to produce superoxide (Cheng et al. 2006, Miyano et al. 2006, Ueyama et al. 2006). R-HSA-5627117 RHO GTPases Activate ROCKs RHO associated, coiled-coil containing protein kinases ROCK1 and ROCK2 consist of a serine/threonine kinase domain, a coiled-coil region, a RHO-binding domain and a plekstrin homology (PH) domain interspersed with a cysteine-rich region. The PH domain inhibits the kinase activity of ROCKs by an intramolecular fold. ROCKs are activated by binding of the GTP-bound RHO GTPases RHOA, RHOB and RHOC to the RHO binding domain of ROCKs (Ishizaki et al. 1996, Leung et al. 1996), which disrupts the autoinhibitory fold. Once activated, ROCK1 and ROCK2 phosphorylate target proteins, many of which are involved in the stabilization of actin filaments and generation of actin-myosin contractile force. ROCKs phosphorylate LIM kinases LIMK1 and LIMK2, enabling LIMKs to phosphorylate cofilin, an actin depolymerizing factor, and thereby regulate the reorganization of the actin cytoskeleton (Ohashi et al. 2000, Sumi et al. 2001). ROCKs phosphorylate MRLC (myosin regulatory light chain), which stimulates the activity of non-muscle myosin II (NMM2), an actin-based motor protein involved in cell migration, polarity formation and cytokinesis (Amano et al. 1996, Riento and Ridley 2003, Watanabe et al. 2007, Amano et al. 2010). ROCKs also phosphorylate the myosin phosphatase targeting subunit (MYPT1) of MLC phosphatase, inhibiting the phosphatase activity and preventing dephosphorylation of MRLC. This pathway acts synergistically with phosphorylation of MRLC by ROCKs towards stimulation of non-muscle myosin II activity (Kimura et al. 1996, Amano et al. 2010). R-HSA-5666185 RHO GTPases Activate Rhotekin and Rhophilins Rhotekin (RTKN) is a protein with an N-terminally located RHO GTPase binding domain, that shares a limited sequence homology with PKNs and rhophilins. RTKN binds to GTP-bound RHOA, RHOB and RHOC and can inhibit their GTPase activity (Reid et al. 1996, Fu et al. 2000), which can be corroborated by protein kinase D-mediated phosphorylation of RTKN (Pusapati et al. 2012). RTKN is implicated in the establishment of cell polarity (Sudo et al. 2006), septin organization (Ito et al. 2005, Sudo et al. 2007) and stimulation of SRF-mediated transcription (Reynaud et al. 2000). RTKN can have an anti-apoptotic effect that depends on the activation of NFKB (NF-kappaB) (Liu et al. 2004). RTKN2 (rhotekin-2) is another rhotekin exclusively expressed in lymphocytes (Collier et al. 2004). The function and the mechanism of action of RTKN2 are unknown.
Rhophillins include two family members - rhophilin-1 (RHNP1) and rhophilin-2 (RHPN2) with ~75% sequence identity. A RHO GTPase binding domain is located at the N-terminus of rhophilins, followed by a BRO1 domain (characteristic of proteins involved in protein kinase C signaling) and a C-terminal PDZ domain. RHOA:GTP binds both RHPN1 and RHPN2 and these interactions may be involved in organization of the actin cytoskeleton and/or cell motility (Watanabe et al. 1996, Fujita et al. 2000, Peck et al. 2002). RHOB:GTP recruits RHPN2 to endosomes which may be involved in the function of thyroid cells (Mircescu et al. 2002). R-HSA-5663213 RHO GTPases Activate WASPs and WAVEs WASP and WAVE proteins belong to the Wiskott-Aldrich Syndrome protein family, with recessive mutations in the founding member WASP being responsible for the X-linked recessive immunodeficieny known as the Wiskott-Aldrich Syndrome. WASP proteins include WASP and WASL (N-WASP). WAVE proteins include WASF1 (WAVE1), WASF2 (WAVE2) and WASF3 (WAVE3). WASPs and WAVEs contain a VCA domain (consisting of WH2 and CA subdomains) at the C-terminus, responsible for binding to G-actin (WH2 subdomain) and the actin-associated ARP2/3 complex (CA subdomain). WASPs contain a WH1 (WASP homology 1) domain at the N-terminus, responsible for binding to WIPs (WASP-interacting proteins). A RHO GTPase binding domain (GBD) is located in the N-terminal half of WASPs and C-terminally located in WAVEs. RHO GTPases activate WASPs by disrupting the autoinhibitory interaction between the GBD and VCA domains, which allows WASPs to bind actin and the ARP2/3 complex and act as nucleation promoting factors in actin polymerization. WAVEs have the WAVE/SCAR homology domain (WHD/SHD) at the N-terminus, which binds ABI, NCKAP1, CYFIP2 and BRK1 to form the WAVE regulatory complex (WRC). Binding of the RAC1:GTP to the GBD of WAVEs most likely induces a conformational change in the WRC that allows activating phosphorylation of WAVEs by ABL1, thus enabling them to function as nucleation promoting factors in actin polymerization through binding G-actin and the ARP2/3 complex (Reviewed by Lane et al. 2014). R-HSA-5625900 RHO GTPases activate CIT Citron kinase (CIT) or citron RHO-interacting kinase (CRIK) shares similarities with ROCK kinases. Like ROCK, it consists of a serine/threonine kinase domain, a coiled-coil region, a RHO-binding domain, a cysteine rich region and a plekstrin homology (PH) domain, but additionally features a proline-rich region and a PDZ-binding domain. A shorter splicing isoform of CIT, citron-N, is specifically expressed in the nervous system and lacks the kinase domain. Citron-N is a component of the post-synaptic density, where it binds to the PDZ domains of the scaffolding protein PDS-95/SAP90 (Zhang et al. 2006).
While the binding of CIT to RHO GTPases RHOA, RHOB, RHOC and RAC1 is well established (Madaule et al. 1995), the mechanism of CIT activation by GTP-bound RHO GTPases has not been elucidated. There are indications that CIT may be activated through autophosphorylation in the presence of active forms of RHO GTPases (Di Cunto et al. 1998). CIT appears to phosphorylate the myosin regulatory light chain (MRLC), the only substrate identified to date, on the same residues that are phosphorylated by ROCKs, but it has not been established yet how this relates to activation by RHO GTPases (Yamashiro et al. 2003). CIT and RHOA are implicated to act together in Golgi apparatus organization through regulation of the actin cytoskeleton (Camera et al. 2003). CIT is also involved in the regulation of cytokinesis through its interaction with KIF14 (Gruneberg et al. 2006, Bassi et al. 2013, Watanabe et al. 2013) and p27(Kip1) (Serres et al. 2012). R-HSA-5626467 RHO GTPases activate IQGAPs IQGAPs constitute a family of scaffolding proteins characterized by a calponin homology (CH) domain, a polyproline binding region (WW domain), a tandem of four IQ (isoleucine and glutamine-rich) repeats and a RAS GTPase-activating protein-related domain (GRD). Three IQGAPs have been identified in human, IQGAP1, IQGAP2 and IQGAP3. The best characterized is IQGAP1 and over 90 proteins have been reported to bind to it. IQGAPs integrate multiple signaling pathways and coordinate a large variety of cellular activities (White et al. 2012). IQGAP proteins IQGAP1, IQGAP2 and IQGAP3, bind activated RHO GTPases RAC1 and CDC42 via their GRD and stabilize them in their GTP-bound state (Kuroda et al. 1996, Swart-Mataraza et al. 2002, Wang et al. 2007). IQGAPs bind F-actin filaments via the CH domain and modulate cell shape and motility through regulation of G-actin/F-actin equilibrium (Brill et al. 1996, Fukata et al. 1997, Bashour et al. 1997, Wang et al. 2007, Pelikan-Conchaudron et al. 2011). Binding of IQGAPs to F-actin is inhibited by calmodulin binding to the IQ repeats (Bashour et al. 1997, Pelikan-Conchaudron et al. 2011). Based on IQGAP1 studies, IQGAPs presumably function as homodimers (Bashour et al. 1997).
IQGAP1 is involved in the regulation of adherens junctions through its interaction with E-cadherin (CDH1) and catenins (CTTNB1 and CTTNA1) (Kuroda et al. 1998, Hage et al. 2009). IQGAP1 contributes to cell polarity and lamellipodia formation through its interaction with microtubules (Fukata et al. 2002, Suzuki and Takahashi 2008). R-HSA-5625970 RHO GTPases activate KTN1 GTP-bound active forms of RHO GTPases RHOA, RHOG, RAC1 and CDC42 bind kinectin (KTN1), a protein inserted in endoplasmic reticulum membranes that interacts with the cargo-binding site of kinesin and activates its microtubule-stimulated ATPase activity required for vesicle motility (Vignal et al. 2001, Hotta et al. 1996). The effect of RHOG activity on cellular morphology, exhibited in the formation of microtubule-dependent cellular protrusions, depends both on RHOG interaction with KTN1, as well as on the kinesin activity (Vignal et al. 2001). RHOG and KTN1 also cooperate in microtubule-dependent lysosomal transport (Vignal et al. 2001). The precise mechanism of kinectin-mediated Rho GTPase signaling cascade needs further elucidation, and only the first two steps, KTN1-activated RHO GTPase binding, and KTN1-kinesin-1 binding are annotated here. R-HSA-5627123 RHO GTPases activate PAKs The PAKs (p21-activated kinases) are a family of serine/threonine kinases mainly implicated in cytoskeletal rearrangements. All PAKs share a conserved catalytic domain located at the carboxyl terminus and a highly conserved motif in the amino terminus known as p21-binding domain (PBD) or Cdc42/Rac interactive binding (CRIB) domain. There are six mammalian PAKs that can be divided into two classes: class I (or conventional) PAKs (PAK1-3) and class II PAKs (PAK4-6). Conventional PAKs are important regulators of cytoskeletal dynamics and cell motility and are additionally implicated in transcription through MAPK (mitogen-activated protein kinase) cascades, death and survival signaling and cell cycle progression (Chan and Manser 2012).
PAK1, PAK2 and PAK3 are direct effectors of RAC1 and CDC42 GTPases. RAC1 and CDC42 bind to the CRIB domain. This binding induces a conformational change that disrupts inactive PAK homodimers and relieves autoinhibition of the catalytic carboxyl terminal domain (Manser et al. 1994, Manser et al. 1995, Zhang et al. 1998, Lei et al. 2000, Parrini et al. 2002; reviewed by Daniels and Bokoch 1999, Szczepanowska 2009). Autophosphorylation of a conserved threonine residue in the catalytic domain of PAKs (T423 in PAK1, T402 in PAK2 and T436 in PAK3) is necessary for the kinase activity of PAK1, PAK2 and PAK3. Autophosphorylation of PAK1 serine residue S144, PAK2 serine residue S141, and PAK3 serine residue S154 disrupts association of PAKs with RAC1 or CDC42 and enhances kinase activity (Lei et al. 2000, Chong et al. 2001, Parrini et al. 2002, Jung and Traugh 2005, Wang et al. 2011). LIMK1 is one of the downstream targets of PAK1 and is activated through PAK1-mediated phosphorylation of the threonine residue T508 within its activation loop (Edwards et al. 1999). Further targets are the myosin regulatory light chain (MRLC), myosin light chain kinase (MLCK), filamin, cortactin, p41Arc (a subunit of the Arp2/3 complex), caldesmon, paxillin and RhoGDI, to mention a few (Szczepanowska 2009).
Class II PAKs also have a CRIB domain, but lack a defined autoinhibitory domain and proline-rich regions. They do not require GTPases for their kinase activity, but their interaction with RAC or CDC42 affects their subcellular localization. Only conventional PAKs will be annotated here. R-HSA-5625740 RHO GTPases activate PKNs Protein kinases N (PKN), also known as protein kinase C-related kinases (PKR) feature a C-terminal serine/threonine kinase domain and three RHO-binding motifs at the N-terminus. RHO GTPases RHOA, RHOB, RHOC and RAC1 bind PKN1, PKN2 and PKN3 (Maesaki et al. 1999, Zhong et al. 1999, Owen et al. 2003, Modha et al. 2008, Hutchinson et al. 2011, Hutchinson et al. 2013), bringing them in proximity to the PIP3-activated co-activator PDPK1 (PDK1) (Flynn et al. 2000, Torbett et al. 2003). PDPK1 phosphorylates PKNs on a highly conserved threonine residue in the kinase activation loop, which is a prerequisite for PKN activation. Phosphorylation of other residues might also be involved in activation (Flynn et al. 2000, Torbett et al. 2003, Dettori et al. 2009). PKNs are activated by fatty acids like arachidonic acid and phospholipids in vitro, but the in vivo significance of this activation remains unclear (Palmer et al. 1995, Yoshinaga et al. 1999).
PKNs play important roles in diverse functions, including regulation of cell cycle, receptor trafficking, vesicle transport and apoptosis. PKN is also involved in the ligand-dependent transcriptional activation by the androgen receptor. More than 20 proteins and several peptides have been shown to be phosphorylated by PKN1 and PKN2, including CPI-17 (Hamaguchi et al. 2000), alpha-actinin (Mukai et al. 1997), adducin (Collazos et al. 2011), CDC25C (Misaki et al. 2001), vimentin (Matsuzawa et al. 1997), TRAF1 (Kato et al. 2008), CLIP170 (Collazos et al. 2011) and EGFR (Collazos et al. 2011). There are no known substrates for PKN3 (Collazos et al. 2011).
R-HSA-5627083 RHO GTPases regulate CFTR trafficking Activated RHO GTPase RHOQ (TC10) regulates the trafficking of CFTR (cystic fibrosis transmembrane conductance regulator) by binding to GOPC (Golgi-associated and PDZ and coiled-coil motif-containing protein) also known as PIST, FIG or CAL. GOPC is a Golgi resident protein that binds several membrane proteins, thereby modulating their expression. In the absence of RHOQ, GOPC bound to CFTR directs CFTR for lysosomal degradation, while GTP-bound RHOQ directs GOPC:CFTR complex to the plasma membrane, thereby rescuing CFTR (Neudauer et al. 2001, Cheng et al. 2005).
R-HSA-8980692 RHOA GTPase cycle This pathway catalogues RHOA guanine nucleotide exchange factors (GEFs), GTPase activator proteins (GAPs), GDP dissociation inhibitors (GDIs) and RHOA effectors. RHOA is one of the three best characterized RHO GTPases, the other two being RAC1 and CDC42, and is the founding member of the RHO GTPase family (Zhou and Zheng 2013). RHOA regulates the cytoskeleton and cell contractility (Lessey et al. 2012), thus playing a role in a number of cellular functions, such as adhesion, migration, survival, division, vesicle trafficking and gene expression (Zhou and Zheng 2013). RHOA-regulated processes are involved in mechanotransduction (Lessey et al. 2012; Marjoram et al. 2014), neuronal development (Zhou and Zheng 2013; Fujita and Yamashita 2014; Hu and Selzer 2017), immune system development (Zhou and Zheng 2013; Ricker et al. 2016; Bros et al. 2019), and cardiovascular regulation (Zhou and Zheng 2013; Cai et al. 2016; Shimokawa et al. 2016). RHOA mutations are frequently found in cancer (Kataoka and Ogawa 2016). Toxins of numerous pathogens target RHOA to hijack the host cytoskeleton (Jamilloux et al. 2018).
R-HSA-9013026 RHOB GTPase cycle This pathway catalogues RHOB guanine nucleotide exchange factors (GEFs), GTPase activator proteins (GAPs), GDP dissociation inhibitors (GDIs) and RHOB effectors. RHOB belongs to the RHOA subfamily of RHO GTPases and shares 85% sequence identity with RHOA and RHOC. Posttranslational modifications of the unique C-terminus of RHOB regulate its subcellular localization. Similar to RHOA and RHOC, RHOB regulates the cytoskeleton and plays a role in cell migration. RHOB plays a role in regulation of membrane trafficking (Vega and Ridley 2018), cell proliferation (Vega and Ridley 2018), cell adhesion (Vega and Ridley 2018), DNA repair (Vega and Ridley 2018), and apoptosis (Prendergast 2001; Vega and Ridley 2018). RHOB-regulated cellular processes are important for the immune system function (Vega and Ridley 2018), pulmonary gas exchange (Wojciak-Stothard et al. 2012; Vega and Ridley 2018), and angiogenesis and vascular function (Vega and Ridley 2018). RHOB has been implicated both as a tumor suppressor and as an oncogene in cancer (Prendergast 2001; Huang and Prendergast 2006; Ju and Gilkes 2018; Calvayrac et al. 2018).
R-HSA-9706574 RHOBTB GTPase Cycle RHO BTB family belongs to atypical RHO GTPases, which are characterized by the absence of GTPase activity. RhoBTB family includes RHOBTB1 and RHOBTB2. RHOBTB3 is sometimes classified as the third RhoBTB family member, but it is divergent from the other two RHOBTBs and from Rho GTPases in general. RHOBTB1 is a component of a signaling cascade that regulates vascular function and blood pressure (Ji and Rivero 2016). RHOBTB2 is involved in COP9 signalosome-regulated and CUL3-dependent protein ubiquitination (Berthold et al. 2008; Ji and Rivero 2016).
R-HSA-9013422 RHOBTB1 GTPase cycle RHOBTB1 is an atypical member of the RHO GTPase family that is predicted not to cycle between a GTP-bound form and a GDP-bound form (Berthold et al. 2008). RHOBTB family proteins, in contrast to other RHO GTPases, possess other conserved domains in addition to the GTPase domain. The GTPase domain at the N-terminus is followed by a proline-rich region, a tandem of two BTB (broad-complex, tramtrack, bric à brac) domains, and a conserved C-terminal BACK (BTB and C-terminal Kelch) domain (Berthold et al. 2008, Ji and Rivero 2016). RHOBTB proteins can form homo- and heterodimers, but the role of dimerization in RHOBTB function is not known (Berthold et al. 2008, Ji and Rivero 2016). RHOBTB1 is highly expressed in skeletal muscle, placenta, stomach, kidney, testis, ovary, uterus and adrenal gland (Berthold et al. 2008). RHOBTB1 is a component of a signaling cascade that regulates vascular function and blood pressure (Ji and Rivero 2016). RHOBTB1 level is decreased in many cancer types and it is proposed to function as a tumor suppressor, but no mutations in RHOBTB1 have been detected in cancer (Berthold et al. 2008; Ji and Rivero 2016). RHOBTB1 localizes at early endosomes and participates in the architecture of the endosomal-lysosomal system (Long et al. 2020).
R-HSA-9013418 RHOBTB2 GTPase cycle RHOBTB2 is an atypical member of the RHO GTPase family that is predicted not to cycle between a GTP-bound form and a GDP-bound form (Berthold et al. 2008). RHOBTB family proteins, in contrast to other RHO GTPases, possess other conserved domains in addition to the GTPase domain. The GTPase domain at the N terminus is followed by a proline rich region, a tandem of two BTB (broad complex, tramtrack, bric à brac) domains, and a conserved C terminal BACK (BTB and C terminal Kelch) domain (Berthold et al. 2008, Ji and Rivero 2016). RHOBTB proteins can form homo- and heterodimers, but the role of dimerization in RHOBTB function is not known (Berthold et al. 2008, Ji and Rivero 2016). RHOBTB2 is usually expressed weakly (Berthold et al. 2008), at a lower level than RHOBTB1 (Ji and Rivero 2016). Relatively high levels of RHOBTB2 can be detected in neural and cardiac tissues (Berthold et al. 2016). RHOBTB2 is involved in COP9 signalosome-regulated and CUL3-dependent protein ubiquitination (Berthold et al. 2008; Ji and Rivero 2016). RHOBTB2 suppresses cellular proliferation and promotes apoptosis (Ji and Rivero 2016). RHOBTB2 takes part in vesicle transport (Ji and Rivero 2016). RHOBTB2 was initially discovered as the gene homozygously deleted in breast cancer and was named DBC2 (deleted in breast cancer 2) (Berthold et al. 2008). RHOBTB2 level is decreased in many tumor types and it is proposed to act as a tumor suppressor. Genomic deletions and a small number of pathogenic mutations in RHOBTB2 have been reported in cancer (Berthold et al. 2008; Ji and Rivero 2016). Mutations of RHOBTB2 that result in impaired interaction with CUL3 have been found to cause epileptic encephalopathy (Belal et al. 2018).
R-HSA-9706019 RHOBTB3 ATPase cycle RHOBTB3 is a member of the Ras-like superfamily of proteins that is phylogenetically distinct from other related Ras-like families, which include, besides RHOBTB3, Rho, Miro, Ras, Ran, Arf and Rab (Boureux et al. 2007). Due to its similarity with RHOBTB1 and RHOBTB2 Rho GTPases, RHOBTB3 is sometimes classified as an atypical member of the RHO GTPase family. However, the GTPase domain of RHOBTB3 is divergent from other Ras-like superfamily members and actually displays ATPase activity (Espinosa et al. 2009). All three RHOBTBs possess other conserved domains in addition to the GTPase domain. The GTPase domain at the N terminus is followed by a proline rich region, a tandem of two BTB (broad complex, tramtrack, bric à brac) domains, and a conserved C terminal BACK (BTB and C terminal Kelch). Unlike RHOBTB1 and RHOBTB2, RHOBTB3 has a CAAX box (prenylation motif) domain (Berthold et al. 2008, Ji and Rivero 2016). RHOBTB proteins can form homo and heterodimers, but the role of dimerization in RHOBTB function is not known (Berthold et al. 2008, Ji and Rivero 2016). RHOBTB3 is ubiquitously expressed, with high levels in placenta, testis, pancreas, adrenal and salivary glands and neural and cardiac tissues (Berthold et al. 2016). RHOBTB3 is involved in CUL3-dependent protein ubiquitination (Berthold et al. 2008; Ji and Rivero 2016). RHOBTB3 is involved in retrograde transport from endosomes to the Golgi apparatus (Espinosa et al. 2009). RHOBTB3 participates in regulation of the cell cycle and in modulating the adaptive response to hypoxia (Ji and Rivero 2016). RHOBTB3 level is decreased in many tumor types and it is proposed to act as a tumor suppressor, although no pathogenic mutations have been reported (Berthold et al. 2008; Ji and Rivero 2016).
R-HSA-9013106 RHOC GTPase cycle This pathway catalogues RHOC guanine nucleotide exchange factors (GEFs), GTPase activator proteins (GAPs), GDP dissociation inhibitors (GDIs) and RHOC effectors. RHOC belongs to the RHOA subfamily of RHO GTPases and shares 85% sequence identity with RHOA and RHOB (Wheeler and Ridley 2004). Like RHOA and RHOB, RHOC regulates the cytoskeleton and is involved in cell adhesion and migration (Guan et al. 2018). RHOC contributes to invasiveness and metastatic potential of cancer cells (Bravo-Cordero et al. 2014; Guan et al. 2018; Thomas et al. 2019).
R-HSA-9013405 RHOD GTPase cycle This pathway catalogues RHOD GTPase activator proteins (GAPs) and RHOD effectors. RHOD possesses GTPase activity and is therefore grouped with classical RHO GTPases but it is atypical in the sense that no known guanine nucleotide exchange factors (GEFs) and no GDP dissociation inhibitors (GDIs) (Blom et al. 2017) are involved in the regulation of RHOD activity. RHOD possesses an elevated intrinsic guanine nucleotide exchange activity and auto-activates (Jaiswal, Fansa et al. 2013). RHOD regulates cytoskeletal dynamics and intracellular transport of vesicles (Gad and Aspenstrom 2010; Aspenstrom et al. 2014), especially actin-dependent movement of endosomes (Gasman et al. 2003, reviewed in Randazzo 2003).
R-HSA-9035034 RHOF GTPase cycle This pathway catalogues RHOF (RIF) GTPase activator proteins (GAPs) and RHOF effectors. RHOF GTPase is thought to exist in the active GTP-bound state in the absence of any GEF activity (Tian et al. 2017). No GDP dissociation inhibitors (GDIs) have been shown to interact with RHOF. RHOF is only found in vertebrates (Gad and Aspenstrom 2010; Fan and Mellor 2012). RHOF regulates cytoskeletal dynamics (Gad and Aspenstrom 2010; Aspenstrom et al. 2014) and promotes the formation of filopodia and stress fibers (Fan and Mellor 2012). RHOF may be involved in actin remodelling in lymphocyte microvilli (Fan and Mellor 2012). In neurons, RHOF contributes to the formation of dendritic spines (Fan and Mellor 2012).
R-HSA-9013408 RHOG GTPase cycle This pathway catalogues RHOG guanine nucleotide exchange factors (GEFs), GTPase activator proteins (GAPs), GDP dissociation inhibitors (GDIs) and RHOG effectors. RHOG is a RAC-related RHO GTPase, ~70% identical to RAC1 (Vincent et al. 1992, de Curtis 2008). RHOG is broadly expressed in different tissue types. It regulates the cytoskeleton, acting either upstream of or in parallel to RAC1. RHOG regulates cell polarity, adhesion, migration and invasion, contributing to the formation of lamellipodia and invadopodia (Gauthier-Rouvière et al. 1998, Al-Koussa et al. 2020). The ortholog of RHOG is required for neuronal development in C. elegans (de Curtis 2008). RHOG is involved in VEGF signaling and angiogenesis (El Baba et al. 2020). RHOG cooperates with RAC1 and CDC42 in malignant cell transformation (Roux et al. 1997) and may contribute to invasiveness of cancer cells (Al-Koussa et al. 2020).
R-HSA-9013407 RHOH GTPase cycle RHOH is constitutively bound to GTP and does not require a guanine nucleotide exchange factor (GEF) for activation (Li et al. 2002). RHOH does not possess a GTPase activity (Li et al. 2002), but has been reported to bind to a small number of GTPase activator proteins (GAPs) (Bagci et al. 2020), which possibly function as RHOH effectors. While RHOH is not found in the GDP bound state, GDP dissociation inhibitors (GDIs), still interact with RHOH, presumably affecting its translocation to the site of activity by sequestering it in the cytosol (Li et al. 2002). Similar to RAC2, RHOH expression is also restricted to hematopoietic cells. RHOH function is required for T cell development and RHOH activity is regulated by posttranslational modifications downstream of activated T cell receptor (TCR). Following TCR activation, RhoH is degraded in lysosomes (Schmidt-Mende et al. 2010). In blood neutrophils from patients suffering from cystic fibrosis or eosinophils from patients with hypereosinophilic syndromes, an upregulation of RhoH expression has been found (Daryadel et al., 2009; Stoeckle et al., 2016). RHOH is subject to mutations and translocations in lymphoma (Suzuki and Oda 2008; Troeger and Williams 2013). Mutations in RHOH are associated with abnormal susceptibility to human beta-papillomavirus (beta-HPV) skin infections, which leads to epidermodysplasia verruciformis, a condition characterized by persistent flat warts or beta-HPV associated skin lesions (Przybyszewska et al. 2017).
R-HSA-9013409 RHOJ GTPase cycle This pathway catalogues RHOJ (also known as TCL or RHOI) guanine nucleotide exchange factors (GEFs), GTPase activator proteins (GAPs), and RHOJ effectors. No GDP dissociation inhibitors (GDIs) have been shown to interact with RHOJ. RHOJ, together with RHOQ (TC10), belongs to the CDC42 subfamily of RHO GTPases and shares 85% and 78% amino acid similarity with RHOQ and CDC42, respectively (Vignal et al. 2000). RHOJ regulates the cytoskeleton, including formation of lamellipodia and actin filaments (Vignal et al. 2000, Abe et al. 2003, Aspenstrom et al. 2004, Shi et al. 2016). RHOJ is highly expressed in endothelial cells, regulating their motility and, consequently, vascular morphogenesis (Leszczynska et al. 2011; Shi et al. 2016). As a part of the VEGF signaling cascade, RHOJ promotes retinal angiogenesis (Fukushima et al. 2013). RHOJ plays a role in cancer cell migration and cancer-related angiogenesis (Shi et al. 2016). RHOJ is involved in adipocyte differentiation (Nishizuka 2003; Shi et al. 2016).
R-HSA-9013406 RHOQ GTPase cycle This pathway catalogues RHOQ (also known as TC10) guanine nucleotide exchange factors (GEFs), GTPase activator proteins (GAPs), and RHOQ effectors. No GDP dissociation inhibitors (GDIs) have been shown to interact with RHOQ. Two GDIs, ARHGDIA (also known as Rho-GDI alpha) (Michaelson et al. 2001; Murphy et al. 2001) and ARHGDIB (also known as D4-GDI) (Zhang et al. 2009), were specifically shown not to interact with RHOQ. RHOQ, together with RHOJ (TCL), belongs to the CDC42 subfamily of RHO GTPases, with the three family members sharing 65-85% of homology (Murphy et al. 1999, Vignal et al. 2000, Donnelly et al. 2014; Shi et al. 2016). RHOQ is highly activated on exocytosing vesicles and recycling endosomes. RHOQ GTPase activity is necessary for fusion of vesicles with the plasma membrane (Kawase et al. 2006, Donnelly et al. 2014). RHOQ is required for insulin-stimulated glucose uptake (Kanzaki and Pessin 2003; Saltiel and Pessin 2003) and is involved in insulin signaling in adipocytes (Satoh 2014). While some studies reported RHOQ involvement in neurite outgrowth (Abe et al. 2003, Gonzalez‐Billault et al. 2012) and regulation of membrane addition during axon formation (Dupraz et al. 2009, Gonzalez‐Billault et al. 2012), other studies failed to identify RHOQ as a regulator of neurite outgrowth (Murphy et al. 1999, Murphy et al. 2001).
R-HSA-9013425 RHOT1 GTPase cycle This pathway catalogues guanine nucleotide exchange factors (GEFs) and effectors of RHOT1 (also known as MIRO-1). RHOT1 possesses a high intrinsic GTP-ase activity and does not require a GTPase activator protein (GAP) (Peters et al. 2018). No GDP dissociation inhibitors (GDIs) have been reported to interact with RHOT1. RHOT1 is a mitochondrial RHO GTPase. Like related RHOT2 (MIRO-2), RHOT1 localizes to the outer mitochondrial membrane. RHOT1 is implicated in mitochondrial movement inside the cells (Schwarz 2013), including the axonal transport of mitochondria in neurons (Saxton and Hollenbeck 2012; Birsa et al. 2013; Devine et al. 2016), as well as mitochondrial fission and fusion (Saxton and Hollenbeck 2012). RHOT1/RHOT2-mediated mitochondrial turnover is affected in neurodegenerative diseases (Birsa et al. 2013; Devine et al. 2016). RHOT1 can localize to peroxisomes and regulate peroxisome motility and fission (Castro et al. 2018, Okumoto et al. 2018, Covill-Cooke et al. 2020). RHOT1 is also involved in the regulation of ER-mitochondria membrane contact sites (Grossmann et al. 2019, Modi et al. 2019).
Upregulation of RHOT1 has a neuroprotective effect in ischemic stroke (Wei et al. 2019).
R-HSA-9013419 RHOT2 GTPase cycle This pathway catalogues guanine nucleotide exchange factors (GEFs) and effectors of RHOT2 (also known as MIRO-2). RHOT2 possesses a high intrinsic GTP-ase activity and does not require a GTPase activator protein (GAP) (Peters et al. 2018). No GDP dissociation inhibitors (GDIs) have been reported to interact with RHOT2. RHOT2 is a mitochondrial RHO GTPase. Like related RHOT1 (MIRO-1), RHOT2 localizes to the outer mitochondrial membrane. Similar to RHOT1, RHOT2 regulates mitochondrial movement by coupling mitochondria to kinesin and dynein motors that transport them along microtubules (Devine et al. 2016). RHOT2 is also localized to peroxisomes and it is involved in peroxisomal dynamics (Covill-Cooke et al. 2020).
R-HSA-9013420 RHOU GTPase cycle RHO GTPase RHOU (Wrch-1) possesses a high intrinsic guanine nucleotide exchange activity and is constitutively present in the active GTP-bound state in the absence of guanine nucleotide exchange factors (GEFs) (Shutes et al. 2004, Saras et al. 2004). RHOU does not possess a GTPase activity (Saras et al. 2004). RHOU has been reported to interact with some GTPase activator proteins (GAPs) (Bagci et al. 2020), which may serve as effectors that enable cross-talk with other RHO GTPases. RHOU was shown to regulate cytoskeletal dynamics, cell migration and adhesion. RHOU is expressed during embryonic development and regulates cardiac (Dickover et al. 2014) and intestinal (Slaymi et al. 2019) development. RHOU activates JNK and AKT signaling during cell migration (Chuang et al. 2007).
For review, please refer to Faure and Fort 2015, and Hodge and Ridley 2020.
R-HSA-9013424 RHOV GTPase cycle RHOV (also known as Chp) is an atypical RHO GTPase that is thought to be constitutively active due to its high intrinsic guanine nucleotide exchange activity. No guanine nucleotide exchange factors (GEFs) nor GTPase activator proteins (GAPs) that act on RHOV have been identified. RHOV is expressed at very low levels. The expression of RHOV is detected during embryonic development in fish (Tay et al. 2010), frog (Guémar et al. 2007) and chicken (Notarnicola et al. 2008). RHOV is involved in neural crest formation, where its expression is induced downstream of WNT signaling. RHOV is thought to regulate cell adhesion, as its zebrafish orthologue is required for proper localization of E-cadherin and beta-catenin at adherens junctions. RHOV activates JNK and induces apoptosis in rat pheochromocytoma cell line PC12 (Shepelev et al 2011) and in macrophages (Song et al. 2015).
RHOV gene overexpression is a molecular marker of human lung adenocarcinoma (Shepelev and Korobko 2013, Shukla et al. 2017, Ma et al. 2020, Zhang et al. 2020), where RHOV is likely to act as an oncogene (Chen et al. 2021).
For review, please refer to Faure and Fort 2015, and Hodge and Ridley 2020.
R-HSA-1810476 RIP-mediated NFkB activation via ZBP1 Overexpression of human or murine ZBP1 (DAI) in human embryonic kidney 293T cells (HEK293T) activated NF-kB-dependent promoter in a dose-dependent manner. Two RHIM-contaning kinases RIP1 and RIP3 are implicated in ZBP1-induced NFkB activation (Rebsamen M et al 2009; Kaiser WJ et al 2008).
R-HSA-5213460 RIPK1-mediated regulated necrosis Receptor-interacting serine/threonine-kinase protein 1 (RIPK1) and RIPK3-dependent necrosis is called necroptosis or programmed necrosis. The kinase activities of RIPK1 and RIPK3 are essential for the necroptotic cell death in human, mouse cell lines and genetic mice models (Cho YS et al. 2009; He S et al. 2009, 2011; Zhang DW et al. 2009; McQuade T et al. 2013; Newton et al. 2014). The initiation of necroptosis can be stimulated by the same death ligands that activate extrinsic apoptotic signaling pathway, such as tumor necrosis factor (TNF) alpha, Fas ligand (FasL), and TRAIL (TNF-related apoptosis-inducing ligand) or toll like receptors 3 and 4 ligands (Holler N et al. 2000; He S et al. 2009; Feoktistova M et al. 2011; Voigt S et al. 2014). In contrast to apoptosis, necroptosis represents a form of cell death that is optimally induced when caspases are inhibited (Holler N et al. 2000; Hopkins-Donaldson S et al. 2000; Sawai H 2014). Specific inhibitors of caspase-independent necrosis, necrostatins, have recently been identified (Degterev A et al. 2005, 2008). Necrostatins have been shown to inhibit the kinase activity of RIPK1 (Degterev A et al. 2008). Importantly, cell death of apoptotic morphology can be shifted to a necrotic phenotype when caspase 8 activity is compromised, otherwise active caspase 8 blocks necroptosis by the proteolytic cleavage of RIPK1 and RIPK3 (Kalai M et al. 2002; Degterev A et al. 2008; Lin Y et al. 1999; Feng S et al. 2007). When caspase activity is inhibited under certain pathophysiological conditions or by pharmacological agents, deubiquitinated RIPK1 is engaged in physical and functional interactions with the cognate kinase RIPK3 leading to formation of necrosome, a necroptosis-inducing complex consisting of RIPK1 and RIPK3 (Sawai H 2013; Moquin DM et al. 2013; Kalai M et al. 2002; Cho YS et al. 2009, He S et al. 2009, Zhang DW et al. 2009). Within the necrosome RIPK1 and RIPK3 bind to each other through their RIP homotypic interaction motif (RHIM) domains. The RHIMs can facilitate RIPK1:RIPK3 oligomerization, allowing them to form amyloid-like fibrillar structures (Li J et al. 2012; Mompean M et al. 2018). RIPK3 in turn interacts with mixed lineage kinase domain-like protein (MLKL) (Sun L et al. 2012; Zhao J et al. 2012; Murphy JM et al. 2013; Chen W et al. 2013). The precise mechanism of MLKL activation by RIPK3 is incompletely understood and may vary across species (Davies KA et al. 2020). Mouse MLKL activation relies on transient engagement of RIPK3 to facilitate phosphorylation of the pseudokinase domain (Murphy JM et al. 2013; Petrie EJ et al. 2019a), while it appears that stable recruitment of human MLKL by necrosomal RIPK3 is an additional crucial step in human MLKL activation (Davies KA et al. 2018; Petrie EJ et al. 2018, 2019b). RIPK3-mediated phosphorylation is thought to initiate MLKL oligomerization, membrane translocation and membrane disruption (Sun L et al. 2012; Wang H et al. 2014; Petrie EJ et al. 2020; Samson AL et al. 2020). Studies in human cell lines suggest that upon induction of necroptosis MLKL shifts to the plasma membrane and membranous organelles such as mitochondria, lysosome, endosome and ER (Wang H et al. 2014), but it is trafficking via a Golgi-microtubule-actin-dependent mechanism that facilitates plasma membrane translocation, where membrane disruption causes death (Samson AL et al. 2020). The mechanisms of necroptosis regulation and execution downstream of MLKL remain elusive. The precise oligomeric form of MLKL that mediates plasma membrane disruption has been highly debated (Cai Z et al. 2014; Chen X et al. 2014; Dondelinger Y et al. 2014; Wang H et al. 2014; Petrie EJ et al. 2017, 2018; Samson AL et al. 2020 ). However, microscopy data revealed that MLKL assembles into higher molecular weight species upon cytoplasmic necrosomes within human cells, and upon phosphorylation by RIPK3, MLKL is trafficked to the plasma membrane (Samson AL et al. 2020). At the plasma membrane, phospho-MLKL forms heterogeneous higher order assemblies, which are thought to permeabilize cells, leading to release of DAMPs to invoke inflammatory responses. MLKL also exerts non-necroptotic functions such as regulation of endosomal trafficking or MLKL-induced activation of the NLRP3 inflammasome (Yoon S et al. 2017; Shlomovitz I et al. 2020; Yoon S et al. 2022). While RIPK1, RIPK3 and MLKL are the core signaling components in the necroptosis pathway, many additional molecules have been proposed to positively and negatively tune the signaling pathway. Currently, this picture is evolving rapidly as new modulators continue to be discovered.
The Reactome module describes MLKL-mediated necroptotic events on the plasma membrane.
R-HSA-3214858 RMTs methylate histone arginines Arginine methylation is a common post-translational modification; around 2% of arginine residues are methylated in rat liver nuclei (Boffa et al. 1977). Arginine can be methylated in 3 different ways: monomethylarginine (MMA); NG,NG-asymmetric dimethylarginine (ADMA) and NG,N'G-symmetric dimethylarginine (SDMA). The formation of MMA, ADMA and SDMA in mammalian cells is carried out by members of a family of nine protein arginine methyltransferases (PRMTs) (Bedford & Clarke 2009).
Type I, II and III PRMTs generate MMA on one of the two terminal guanidino nitrogen atoms. Subsequent generation of asymmetric dimethylarginine (ADMA) is catalysed by the type I enzymes PRMT1, PRMT2, PRMT3, co-activator-associated arginine methyltransferase 1 (CARM1), PRMT6 and PRMT8. Production of symmetric dimethylarginine (SDMA) is catalysed by the type II enzymes PRMT5 and PRMT7. On certain substrates, PRMT7 also functions as a type III enzyme, generating MMA only. PRMT9 activity has not been characterized. No known enzyme is capable of both ADMA and SDMA modifications. Arginine methylation is regarded as highly stable; no arginine demethylases are known (Yang & Bedford 2013).
Most PRMTs methylate glycine- and arginine-rich (GAR) motifs in their substrates (Boffa et al. 1977). CARM1 methylates a proline-, glycine- and methionine-rich (PGM) motif (Cheng et al. 2007). PRMT5 can dimethylate arginine residues in GAR and PGM motifs (Cheng et al. 2007, Branscombe et al. 2001).
PRMTs are widely expressed and are constitutively active as purified recombinant proteins. However, PRMT activity can be regulated through PTMs, association with regulatory proteins, subcellular compartmentalization and factors that affect enzyme-substrate interactions. The target sites of PRMTs are influenced by the presence of other PTMs on their substrates. The best characterized examples of this are for histones. Histone H3 lysine-19 acetylation (H3K18ac) primes the histone tail for asymmetric dimethylation at arginine-18 (H3R17me2a) by CARM1 (An et al. 2003, Daujat et al. 2002, Yue et al. 2007). H3 lysine-10 acetylation (H3K9ac) blocks arginine-9 symmetric dimethylation (H3R8me2s) by PRMT5 (Pal et al. 2004). H4R3me2a catalyzed by PRMT1 favours subsequent acetylation of the histone H4 tail (Huang et al. 2005). At the same time histone H4 lysine-5 acetylation (H4K5ac) makes the H4R3 motif a better substrate for PRMT5 compared with PRMT1, thereby moving the balance from an activating ADMA mark to a suppressive SDMA mark at the H4R3 motif (Feng et al. 2011). Finally methylation of Histone H3 on arginine-3 (H3R2me2a) by PRMT6 blocks methylation of H3 lysine-5 by the MLL complex (H3K4me3), and vice versa, methylation of H3K4me3 prevents H3R2me2a methylation (Guccione et al. 2007, Kirmizis et al. 2007, Hyllus et al. 2007). N.B. The coordinates of post-translational modifications represented and described here follow UniProt standard practice whereby coordinates refer to the translated protein before any further processing. Histone literature typically refers to coordinates of the protein after the initiating methionine has been removed. Therefore the coordinates of post-translated residues in the Reactome database and described here are frequently +1 when compared with the literature.
R-HSA-77075 RNA Pol II CTD phosphorylation and interaction with CE To facilitate co-transcriptional capping, and thereby restrict the cap structure to RNAs made by RNA polymerase II, the capping enzymes bind directly to the RNA polymerase II. The C-terminal domain of the largest Pol II subunit contains several phosphorylation sites on its heptapeptide repeats. The capping enzyme guanylyltransferase and the methyltransferase bind specifically to CTD phosphorylated at Serine 5 within the CTD. Kinase subunit of TFIIH, Cdk7, catalyzes this phosphorylation event that occurs near the promoter. In addition, it has been shown that binding of capping enzyme to the Serine-5 phosphorylated CTD stimulates guanylyltransferase activity in vitro.
R-HSA-167160 RNA Pol II CTD phosphorylation and interaction with CE during HIV infection To facilitate co-transcriptional capping, and thereby restrict the cap structure to RNAs made by RNA polymerase II, the capping enzymes bind directly to the RNA polymerase II. The C-terminal domain of the largest Pol II subunit contains several phosphorylation sites on its heptapeptide repeats. The capping enzyme guanylyltransferase and the methyltransferase bind specifically to CTD phosphorylated at Serine 5 within the CTD. Kinase subunit of TFIIH, Cdk7, catalyzes this phosphorylation event that occurs near the promoter. In addition, it has been shown that binding of capping enzyme to the Serine-5 phosphorylated CTD stimulates guanylyltransferase activity in vitro.
R-HSA-73854 RNA Polymerase I Promoter Clearance Promoter clearance is one of the rate-limiting steps in Polymerase I transcription. This step is composed of three phases, promoter opening, transcription initiation and promoter escape.
R-HSA-73772 RNA Polymerase I Promoter Escape As the active RNA Polymerase I complex leaves the promoter Rrn3 dissociates from the complex. RNA polymerase I Promoter Clearance is complete and Chain Elongation begins (Milkereit and Tschochner, 1998). The assembly of the initiation complex on the promoter and the transition from a closed to an open complex is then followed by promoter clearance and transcription elongation by RNA Pol I. Unlike the RNA polymerase II system, RNA polymerase I transcription does not require a form of energy such as ATP for initiation and elongation. Regulatory mechanisms operating at both the level of transcription initiation and elongation probably concurrently to adjust the level of rRNA synthesis to the need of the cell.
R-HSA-73728 RNA Polymerase I Promoter Opening The activity of the upstream binding factor (UBF-1) plays an important role in the regulation of rRNA synthesis. Studies reveal that phosphorylation of UBF-1 is required for its interaction with the RNA polymerase I complex, suggesting that phosphorylation of UBF-1 bound to the rDNA promoter during promoter opening modulates the assembly of the transcription initiation complex.
R-HSA-73864 RNA Polymerase I Transcription RNA polymerase (Pol) I (one of three eukaryotic nuclear RNA polymerases) is devoted to the transcription of the ribosomal DNA genes, which are found in multiple arrayed copies in every eukaryotic cell. These genes encode for the large ribosomal RNA precursor, which is then processed into the three largest subunits of the ribosomal RNA, the 18S, 28S, and 5.8S RNAs. In human cells the rDNA gene clusters are localized on the short arm of the five pairs of the acrocentric chromosomes. The rRNA promoter has two essential and specially spaced sequences: a CORE element and an upstream control element (UCE, also called UPE). The CORE element of the human promoter overlaps with the transcription start site, extending from 20 to 45, and is required for specific initiation of transcription.
The polymerase is a multisubunit complex, composed of two large subunits (the most conserved portions include the catalytic site that shares similarity with other eukaryotic and bacterial multisubunit RNA polymerases) and a number of smaller subunits. Under a number of experimental conditions the core is competent to mediate ribonucleic acid synthesis, in vivo however, it requires additional factors to select the appropriate template. In humans the RNA transcript (45S) is approximately 13,000 nucleotides long. Before leaving the nucleus as assembled ribosomal particles, the 45S rRNA is cleaved to give one copy each of the 28S rRNA, the 18S rRNA, and the 5.8S rRNA. Equal quantities of the three rRNAs are produced by initially transcribing them as one transcript.
R-HSA-73762 RNA Polymerase I Transcription Initiation During initiation the double-stranded DNA must be melted and transcription begins. SL1 forms and interacts with UBF-1 and the rDNA promoter. It is this platform that will recruit active RNA polymerase I to the SL1:phosphorlated UBF-1:rDNA promoter complex.
Mammalian rRNA genes are preceded by a terminator element that is recognized by the SL1 complex. This SL1 modulated acetylation of the basal Pol I transcription machinery has functional consequences suggesting that the reversible acetylation may be one way to regulate rDNA transcription.
R-HSA-73863 RNA Polymerase I Transcription Termination Termination of transcription by RNA polymerase I is a 4 step process. Initially TTF-1 binds the template rDNA. This complex pauses polymerase I allowing PTRF to interact with the quaternary complex releasing both pre-rRNA and Pol I from the template and TTF-1.
R-HSA-167162 RNA Polymerase II HIV Promoter Escape RNA Polymerase II promoter escape occurs after the first phosphodiester bond has been created.
R-HSA-674695 RNA Polymerase II Pre-transcription Events For initiation, Pol II assembles with the general transcription factors TFIIB, TFIID, TFIIE, TFIIF and TFIIH, which are collectively known as the general transcription factors, at promoter DNA to form the pre-initiation complex (PIC). Until the nascent transcript is about 15 nucleotides long, the early transcribing complex is functionally unstable. In the beginning, short RNAs are frequently released and Pol II has to restart transcription (abortive cycling). There is a decline in the level of abortive transcription when the RNA reaches a length of about four nucleotides, and this transition is termed escape commitment
R-HSA-73776 RNA Polymerase II Promoter Escape RNA Polymerase II promoter escape occurs after the first phosphodiester bond has been created.
R-HSA-73857 RNA Polymerase II Transcription RNA polymerase II (Pol II) is the central enzyme that catalyses DNA- directed mRNA synthesis during the transcription of protein-coding genes. Pol II consists of a 10-subunit catalytic core, which alone is capable of elongating the RNA transcript, and a complex of two subunits, Rpb4/7, that is required for transcription initiation.
The transcription cycle is divided in three major phases: initiation, elongation, and termination. Transcription initiation include promoter DNA binding, DNA melting, and initial synthesis of short RNA transcripts. The transition from initiation to elongation, is referred to as promoter escape and leads to a stable elongation complex that is characterized by an open DNA region or transcription bubble. The bubble contains the DNA-RNA hybrid, a heteroduplex of eight to nine base pairs. The growing 3-end of the RNA is engaged with the polymerase complex active site. Ultimately transcription terminates and Pol II dissocitates from the template.
R-HSA-75955 RNA Polymerase II Transcription Elongation The mechanisms governing the process of elongation during eukaryotic mRNA synthesis are being unraveled by recent studies. These studies have led to the expected discovery of a diverse collection of transcription factors that directly regulate the activities of RNA Polymerase II and unexpected discovery of roles for many elongation factors in other basic processes like DNA repair, recombination, etc. The transcription machinery and structural features of the major RNA polymerases are conserved across species. The genes active during elongation fall under different classes like, housekeeping, cell-cycle regulated, development and differentiation specific genes etc. The list of genes involved in elongation has been growing in recent times, and include: -TFIIS,DSIF, NELF, P-Tefb etc. that are involved in drug induced or sequence-dependent arrest - TFIIF, ELL, elongin, elongator etc. that are involved in increasing the catalytic rate of elongation by altering the Km and/or the Vmax of Pol II -FACT, Paf1 and other factors that are involved chromatin modification - DNA repair proteins, RNA processing and export factors, the 19S proteasome and a host of other factors like Spt5-Spt5, Paf1, and NELF complexes, FCP1P etc. (Arndt and Kane, 2003). Elongation also represents processive phase of transcription in which the activities of several mRNA processing factors are coupled to transcription through their binding to RNA polymerase (Pol II). One of the key events that enables this interaction is the differential phosphorylation of Pol II CTD. Phosphorylation pattern of CTD changes during transcription, most significantly at the beginning and during elongation process. TFIIH-dependent Ser5 phosphorylation is observed primarily at promoter regions while P-Tefb mediated Ser2 phosphorylation is seen mainly in the coding regions, during elongation. Experimental evidence suggests a dynamic association of RNA processing factors with differently modified forms of the polymerase during the transcription cycle. (Komarnitsky et al., 2000). [Komarnitsky et al 2000, Arndt & Kane 2003, Shilatifard et al 2003]
R-HSA-75953 RNA Polymerase II Transcription Initiation Formation of the open complex exposes the template strand to the catalytic center of the RNA polymerase II enzyme. This facilitates formation of the first phosphodiester bond, which marks transcription initiation. As a result of this, the TFIIB basal transcription factor dissociates from the initiation complex.
The open transcription initiation complex is unstable and can revert to the closed state. Initiation at this stage requires continued (d)ATP-hydrolysis by TFIIH. Dinucleotide transcripts are not stably associated with the transcription complex. Upon dissociation they form abortive products. The transcription complex is also sensitive to inhibition by small oligo-nucleotides.
Dinucleotides complementary to position -1 and +1 in the template can also direct first phosphodiester bond formation. This reaction is independent on the basal transcription factors TFIIE and TFIIH and does not involve open complex formation. This reaction is sensitive to inhibition by single-stranded oligonucleotides. R-HSA-76042 RNA Polymerase II Transcription Initiation And Promoter Clearance The transcription cycle is divided in three major phases: initiation, elongation, and termination. Transcription initiation include promoter DNA binding, DNA melting, and initial synthesis of short RNA transcripts. Many changes must occur to the RNA polymerase II (pol II) transcription complex as it makes the transition from initiation into transcript elongation. During this intermediate phase of transcription, contact with initiation factors is lost and stable association with the nascent transcript is established. These changes collectively comprise promoter clearance. R-HSA-73779 RNA Polymerase II Transcription Pre-Initiation And Promoter Opening Formation of the pre-initiation complex proceeds in five steps, recognition and binding of core promoter elements by TFIID, binding of TFIIA and TFIIB to the pol II promoter:TFIID complex, recruitment of RNA Polymerase II Holoenzyme by TFIIF to the pol II promoter:TFIID:TFIIA:TFIIB complex, binding of TFIIE to the growing preinitiation complex, and formation of the closed pre-initiation complex (Orphanides et al. 1997). R-HSA-73856 RNA Polymerase II Transcription Termination This section includes the cleavage of both polyadenylated and non-polyadenylated transcripts.
In the former case polyadenylation has to precede transcript cleavage, while in the latter case there is no polyadenylation. R-HSA-749476 RNA Polymerase III Abortive And Retractive Initiation Abortive initiation, the repetitive formation of short oligonucleotides, is a ubiquitous feature of transcriptional initiation. This Pathway contains events inferred from events in Saccharomyces cerevisiae. R-HSA-73780 RNA Polymerase III Chain Elongation Pol III initiation complexes open the promoter spontaneously similar to the mechanism employed in archaeal and bacterial transcription. R-HSA-74158 RNA Polymerase III Transcription RNA polymerase III is one of three types of nuclear RNA polymerases present in eucaryotic cells. About 10% of the total transcription in dividing cells can be attributed to its activity. It synthesizes an eclectic collection of catalytic or structural RNA molecules, some of which are involved in protein synthesis, pre-mRNA splicing, tRNA processing, and the control of RNA polymerase II elongation, whereas some others have still unknown functions. Like other RNA polymerases, RNA polymerase III cannot recognize its target promoters directly. Instead it is recruited to specific promoter sequences through the help of transcription factors. There are three basic types of RNA polymerase III promoters, called types 1, 2, and 3(Geiduschek and Kassavetis, 1992). Although in vivo, RNA polymerase III may be recruited to these promoters as part of a large complex (holo RNA polymerase III) containing the polymerase and its initiation factors (Wang et al., 1997), in vitro the reaction can be divided into several steps. First, the promoter elements are recognized by DNA binding factors, which then recruit a factor known as TFIIIB. TFIIIB itself then directly contacts RNA polymerase III. In human cells but not in S. cerevisiae, there are at least two versions of TFIIIB. One contains TBP, Bdp1, and Brf1 (Brf1-TFIIIB), and the other TBP, Bdp1, and Brf2 (Brf2-TFIIIB) (Schramm et al., 2000; Teichmann et al., 2000). R-HSA-76046 RNA Polymerase III Transcription Initiation There are three basic types of RNA polymerase III promoters. The three types of RNA polymerase III promoters are known as type 1, type 2, and type 3 promoters. Type 1 promoters are found in the 5S genes and consist of a gene-internal element called the internal control region (ICR), that is subdivided into A block, intermediate element, and C block (Bogenhagen, 1985; Sakonju et al., 1980). Type 2 promoters are found in tRNA genes, Adenovirus 2 VAI gene, and other genes (Galli et al., 1981; Sharp et al., 1981). These promoters consists of two gene-internal elements called the A and the B boxes. Type 3 promoters consist of a distal sequence element (DSE) that serves as an enhancer, a proximal sequence element (PSE), and a TATA box (Baer et al., 1989; Lobo and Hernandez, 1989).
Some promoters combine elements from type 2 and 3 promoters. For example, the S. cerevisiae U6 promoter, also shown in the figure, contains the TATA box typical of type 3 promoters and the A and B boxes typical of type 2 promoters. Moreover, in S. pombe, nearly all tRNA and 5S genes contain a TATA box in addition to gene-internal elements, and the TATA box is required for transcription. R-HSA-76061 RNA Polymerase III Transcription Initiation From Type 1 Promoter The type 1 promoters recruit TFIIIA, the founding member of the C2H2 zinc finger family of DNA-binding proteins (Engelke et al., 1980; Sakonju et al., 1981). The binding of TFIIIA then allows the binding of TFIIC (Lassar et al., 1983), a complex consisting of five subunits (which differs from the six subunits in S. cerevisiae) in human cells and S. pombe. Once the DNA/TFIIIA/TFIIIC complex is formed, Brf1-TFIIIB joins the complex and this in turn allows the recruitment of RNA polymerase III (Bieker et al., 1985; Setzer and Brown, 1985). R-HSA-76066 RNA Polymerase III Transcription Initiation From Type 2 Promoter The type 2 promoters can recruit TFIIIC without the help of TFIIIA because TFIIIC binds directly to the A and B boxes. As for the type 1 promoters, this then allows the binding of Brf1-TFIIIB and RNA polymerase III. Importantly, in the yeast system, once Brf1-TFIIIB has been recruited to type 1 or 2 promoters, TFIIIA and/or TFIIIC can be stripped from the DNA with high salt or heparin treatment. Brf1-TFIIIB remains bound to the DNA and is sufficient to direct multiple rounds of transcription . R-HSA-76071 RNA Polymerase III Transcription Initiation From Type 3 Promoter The metazoan-specific type 3 promoters, which are exemplified by the human U6 promoter, recruit a complex variously called the snRNA activating protein complex (SNAPc) (Sadowski et al., 1993), the PSE binding protein (PBP) (Waldschmidt et al., 1991), or the PSE transcription factor (PTF) (Murphy et al., 1992). The complex contains five types of subunits and binds to the PSE. Type 3 promoters also recruit Brf2-TFIIIB through a combination of protein-protein contacts with SNAPc and a direct association of the TBP component of Brf2-TFIIIB with the TATA box. This then allows RNA polymerase III to join the complex.
The down stream element (DSE) of type 3 promoters, which enhances transcription from the core promoter, almost invariably contains an octamer sequence and an SPH element (also called NONOCT element)(Cheung et al., 1993; Danzeiser et al., 1993; Kunkel et al., 1996; Myslinski et al., 1992). The octamer sequence recruits the POU domain protein Oct-1 (Herr et al., 1988; Sturm et al., 1988), and the SPH element recruits a zinc finger protein known as Staf or SPH binding factor (SBF), which has been cloned from humans (Myslinski et al., 1998; Rincon et al., 1998).
R-HSA-73980 RNA Polymerase III Transcription Termination At the end of the cycle, the elongation complex (EC) must be destabilized to release its transcript and DNA. Analogous to initiation, cis-signals and protein factors are required to mediate EC destabilization and release of the transcript from the grip of the RNA polymerase (RNAP). RNAP III achieves efficient termination despite the apparent simplicity of its cis-acting DNA terminator element, a stretch of five or more T residues on the non-template (NT) strand, which directs termination within this site without need for additional cis-elements or trans-acting factors.
R-HSA-6807505 RNA polymerase II transcribes snRNA genes Small nuclear RNAs (snRNAs) play key roles in splicing and some of them, specifically the U1 and U2 snRNAs, are encoded by multicopy snRNA gene clusters containing tandem arrays of genes, about 30 in the RNU1 cluster (Bernstein et al. 1985) and about 10-20 in the RNU2 cluster (Van Ardsell and Weiner 1984). Whereas U6 snRNA genes are transcribed by RNA polymerase III, U1,U2, U4, U4atac, U5, U11, and U12 genes are transcribed by RNA polymerase II. Transcription of the U1 and U2 genes has been most extensively studied and the other snRNA genes as well as other genes with similar promoter structures, for example the SNORD13 gene, are inferred to be transcribed by similar reactions. The snRNA genes transcribed by RNA polymerase II are distinguished from mRNA-encoding genes by the presence of a proximal sequence element (PSE) rather than a TATA box and the presence of the Integrator complex rather than the Mediator complex (reviewed in Egloff et al. 2008, Jawdeker and Henry 2008).
The snRNA genes are among the most rapidly transcribed genes in the genome. The 5' transcribed region of the U2 snRNA gene is largely single-stranded during interphase and metaphase (Pavelitz et al. 2008) and chromatin within the transcribed region is cleared of nucleosomes (O'Reilly et al. 2014). Transcriptional activation of the RNA polymerase II transcribed snRNA genes begins with binding of transcription factors to the distal sequence element (DSE) of the promoter (reviewed in Hernandez 2001, Egloff et al. 2008, Jawdeker and Henry 2008). The factors, which include POU2F1 (Oct-1), POU2F2 (Oct-2), ZNF143 (Staf) and Sp1, promote binding of the SNAPc complex (also known as PTF and PBP) to the PSE. SNAPc helps clear the gene of nucleosomes (O'Reilly et al. 2014) and recruits initiation factors (TFIIA, TFIIB, TFIIE, TFIIF, and snTAFc:TBP) which recruit RNA polymerase II. Phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (reviewed in Egloff and Murphy 2008) by CDK7 recruits RPAP2 and the Integrator complex, which is required for later processing of the 3' end of the pre-snRNA transcript (reviewed in Chen and Wagner 2010, Baillat and Wagner 2015). The Little Elongation Complex (LEC) also appears to bind around the time of transcription initiation (Hu et al. 2013). As transcription proceeds, RPAP2 dephosphorylates serine-5 and P-TEFb phosphorylates serine-2 of the CTD. As transcription reaches the end of the snRNA gene serine-7 of the CTD is phosphorylated. These marks serve to bind protein complexes and are required for 3' processing of the pre-snRNA (reviewed in Egloff and Murphy 2008). After transcription proceeds through the conserved 3' processing sequence of the pre-snRNA the Integrator complex cleaves the pre-snRNA. Transcription then terminates downstream in a less well characterized reaction that requires elements of the polyadenylation system.
R-HSA-9696273 RND1 GTPase cycle RND1 is an atypical RHO GTPase from the RND subfamily. RND1 is constitutively bound to GTP and lacks GTPase activity. No guanine nucleotide exchange factors (GEFs), GTPase activator proteins (GAPs) or guanine nucleotide dissociation inhibitors (GDIs) act on RND1. RND1 localizes to the plasma membrane, but can be extracted from the plasma membrane and sequestered to the cytosol upon phosphorylation-induced binding to 14-3-3 protein. RND1 antagonizes RHOA, leading to reduced actomyosin contractility and loss of stress fibers and focal adhesions, which results in a rounded cell phenotype. RND1 plays a role in embryogenesis, neuronal development, myometrium changes during pregnancy, and angiogenesis. RND1 is frequently downregulated in cancer and is implicated as a tumor suppressor, but may play an oncogenic role in some cancer types. RND1 expression increases in response to anti-cancer agents and in may be involved in resistance to treatment. For review, please refer to Mouly et al. 2019.
R-HSA-9696270 RND2 GTPase cycle RND2 (RHON) is an atypical RHO GTPase and the least studied member of the RND subfamily. RND2 is constitutively bound to GTP and lacks GTPase activity. No guanine nucleotide exchange factors (GEFs), GTPase activator proteins (GAPs) or guanine nucleotide dissociation inhibitors (GDIs) act on RND2. RND2 is predominantly expressed in brain, testis and liver (Nobes et al. 1998; Nishi et al. 1999). RND2 regulates neurite outgrowth and branching (Fujita et al. 2002; Kakimoto et al. 2004; Tanaka et al. 2006; Wakita et al. 2011) and migration of newborn neurons within the embryonic cerebral cortex (Nakamura et al. 2006; Heng et al. 2008; Alfano et al. 2011; Pacary et al. 2011; Gladwyn-Ng et al. 2015; Heng et al. 2015).
R-HSA-9696264 RND3 GTPase cycle RND3 (RHOE) is an atypical RHO GTPase from the RND subfamily. RND3 is constitutively bound to GTP and lacks GTPase activity. No guanine nucleotide exchange factors (GEFs), GTPase activator proteins (GAPs) or guanine nucleotide dissociation inhibitors (GDIs) act on RND3. RND3 is a direct antagonist of ROCK1 kinase activity. RND3 prevents phosphorylation of ROCK1 targets and, similar to RND1, induces stress fiber disassembly. RND3 regulates cell migration, establishment of neuronal polarity, heart development, and myometrium changes during pregnancy. Defective RND3 function is related to cardiomyopathy, hydrocephalus and cancer. Like RND1, RND3 is implicated both as a tumor suppressor and an oncogene in cancer, and can both increase and decrease sensitivity to chemotherapeutic agents, which depends on cancer type and stage. For review, please refer to Jie et al. 2015 and Paysan et al. 2016.
R-HSA-9010642 ROBO receptors bind AKAP5 AKAP5 (also known as AKAP79 in humans and Akap150 in mice) is an A-kinase anchoring protein which is able to bind to ROBO receptors ROBO2 and ROBO3.1, an isoform of ROBO3, by interacting with their cytoplasmic tails. The interaction was originally detected between endogenous proteins from the mouse brain lysates. AKAP5 can recruit protein kinase A (PKA), protein kinase C (PKC) and protein phosphatase PP2B to ROBO2. AKAP5-mediated recruitment of PKC to ROBO3.1 leads to phosphorylation of ROBO3.1 by PKC. Functional implications of AKAP5 interaction with ROBO receptors are not known (Samelson et al. 2015).
R-HSA-1368082 RORA activates gene expression As inferred from mouse, RORA binds ROR elements (ROREs) in DNA and recruits the coactivators PPARGC1A (PGC-1alpha) and p300 (EP300, a histone acetylase) to activate transcription.
R-HSA-1222556 ROS and RNS production in phagocytes The first line of defense against infectious agents involves an active recruitment of phagocytes to the site of infection. Recruited cells include polymorhonuclear (PMN) leukocytes (i.e., neutrophils) and monocytes/macrophages, which function together as innate immunity sentinels (Underhill DM & Ozinsky A 2002; Stuart LM & Ezekowitz RA 2005; Flannagan RS et al. 2012). Dendritic cells are also present, serving as important players in antigen presentation for ensuing adaptive responses (Savina A & Amigorena S 2007). These cell types are able to bind and engulf invading microbes into a membrane-enclosed vacuole - the phagosome, in a process termed phagocytosis. Phagocytosis can be defined as the receptor-mediated engulfment of particles greater than 0.5 micron in diameter. It is initiated by the cross-linking of host cell membrane receptors following engagement with their cognate ligands on the target surface (Underhill DM & Ozinsky A 2002; Stuart LM & Ezekowitz RA 2005; Flannagan RS et al. 2012). When engulfed by phagocytes, microorganisms are exposed to a number of host defense microbicidal events within the resulting phagosome. These include the production of reactive oxygen and nitrogen species (ROS and RNS, RONS) by specialized enzymes (Fang FC et al. 2004; Kohchi C et al. 2009; Gostner JM et al. 2013; Vatansever F et al. 2013). NADPH oxidase (NOX) complex consume oxygen to produce superoxide radical anion (O2.-) and hydrogen peroxide (H2O2) (Robinson et al. 2004). Induced NO synthase (iNOS) is involved in the production of NO, which is the primary source of all RNS in biological systems (Evans TG et al. 1996). The phagocyte NADPH oxidase and iNOS are expressed in both PMN and mononuclear phagocytes and both cell types have the capacity for phagosomal burst activity. However, the magnitude of ROS generation in neutrophils far exceeds that observed in macrophages (VanderVen BC et al. 2009). Macrophages are thought to produce considerably more RNS than neutrophils (Fang FC et al. 2004; Nathan & Shiloh 2000).
The presence of RONS characterized by a relatively low reactivity, such as H2O2, O2˙− or NO, has no deleterious effect on biological environment (Attia SM 2010; Weidinger A & and Kozlov AV 2015). Their activity is controlled by endogenous antioxidants (both enzymatic and non-enzymatic) that are induced by oxidative stress. However the relatively low reactive species can initiate a cascade of reactions to generate more damaging “secondary” species such as hydroxyl radical (•OH), singlet oxygen or peroxinitrite (Robinson JM 2008; Fang FC et al. 2004). These "secondary" RONS are extremely toxic causing irreversible damage to all classes of biomolecules (Weidinger A & and Kozlov AV 2015; Fang FC et al. 2004; Kohchi C et al. 2009; Gostner JM et al. 2013; Vatansever F et al. 2013).
Although macrophages and neutrophils use similar mechanisms for the internalization of targets, there are differences in how they perform phagocytosis and in the final outcome of the process (Tapper H & Grinstein S 1997; Vierira OV et al. 2002). Once formed, the phagosome undergoes an extensive maturation process whereby it develops into a microbicidal organelle able to eliminate the invading pathogen. Maturation involves re-modeling both the membrane of the phagosome and its luminal contents (Vierira OV et al. 2002). In macrophages, phagosome formation and maturation follows a series of strictly coordinated membrane fission/fusion events between the phagosome and compartments of the endo/lysosomal network gradually transforming the nascent phagosome into a phagolysosome, a degradative organelle endowed with potent microbicidal properties (Zimmerli S et al. 1996; Vierira OV et al. 2002). Neutrophils instead contain a large number of preformed granules such as azurophilic and specific granules that can rapidly fuse with phagosomes delivering antimicrobial substances (Karlsson A & Dahlgren C 2002; Naucler C et al. 2002; Nordenfelt P and Tapper H 2011). Phagosomal pH dynamics may also contribute to the maturation process by regulating membrane traffic events. The microbicidal activity of macrophages is characterized by progressive acidification of the lumen (down to pH 4–5) by the proton pumping vATPase. A low pH is a prerequisite for optimal enzymatic activity of most late endosomal/lysosomal hydrolases reported in macrophages. Neutrophil phagosome pH regulation differs significantly from what is observed in macrophages (Nordenfelt P and Tapper H 2011; Winterbourn CC et al. 2016). The massive activation of the oxidative burst is thought to result in early alkalization of neutrophil phagosomes which is linked to proton consumption during the generation of hydrogen peroxide (Segal AW et al. 1981; Levine AP et al. 2015). Other studies showed that neutrophil phagosome maintained neutral pH values before the pH gradually decreased (Jankowski A et al. 2002). Neutrophil phagosomes also exhibited a high proton leak, which was initiated upon activation of the NADPH oxidase, and this activation counteracted phagosomal acidification (Jankowski A et al. 2002).
The Reactome module describes ROS and RNS production by phagocytic cells. The module includes cell-type specific events, for example, myeloperoxidase (MPO)-mediated production of hypochlorous acid in neutrophils. It also highlights differences between phagosomal pH dynamics in neutrophils and macrophages. The module describes microbicidal activity of selective RONS such as hydroxyl radical or peroxynitrite. However, detection of any of these species in the phagosomal environment is subject to many uncertainties (Nüsse O 2011; Erard M et al. 2018). The mechanisms by which reactive oxygen/nitrogen species kill pathogens in phagocytic immune cells are still not fully understood.
R-HSA-5659996 RPIA deficiency: failed conversion of R5P to RU5P A mutation in ribose-5-phosphate isomerase (RPIA), an enzyme of the pentose phosphate pathway that normally mediates the reversible interconversion of ribose 5-phosphate and D-ribulose 5-phosphate, has been associated with a slowly progressive leukoencephalopathy (Wamelink et al. 2008).
R-HSA-6791461 RPIA deficiency: failed conversion of RU5P to R5P A mutation in ribose-5-phosphate isomerase (RPIA), an enzyme of the pentose phosphate pathway that normally mediates the reversible interconversion of D-ribulose 5-phosphate and ribose 5-phosphate, has been associated with a slowly progressive leukoencephalopathy (Wamelink et al. 2008).
R-HSA-444257 RSK activation Ribosomal S6 kinase (RSK) has four isoforms in humans, RPS6KA1 (RSK1), RPS6KA2 (RSK3), RPS6KA3 (RSK2) and RPS6KA6 (RSK4), and each of the isoforms have six conserved phosphorylation sites (in RPS6KA1, these are serine residues S221, S363 and S380 and threonine residues T359, T573 and T732). Phosphorylation at four of these residues appears to be critically important for the catalytic activity of RSKs: S221, S363, S380 and T573 (in RPS6KA1).
Phosphorylation and activation of RSKs primarily occurs at the plasma membrane, but can occur in the cytoplasm and in the nucleus. ERKs (MAPK1 and MAPK3), activated downstream of RAS signaling, phosphorylate RSKs on threonine and serine residues T359, S363 and T573 (in RPS6KA1). Phosphorylation by ERKs enables autophosphorylation of RSKs on serine residue S380 and threonine residue T732 (in RPS6KA1). Phosphorylation of RSKs by PDPK1 (PDK1) at serine residue S221 (in RPS6KA1) is necessary for the full activation of RSKs and phosphorylation of RSK substrates (reviewed by Anjum and Blenis 2012). RSK4 differs from other RSKs because it shows high level of constitutive phosphorylation and activity in the absence of growth factors, although it is still responsive to growth factors and ERK activity (Dummler et al. 2005).
RSKs, especially RSK2, are highly expressed in brain regions with high synaptic activity. RSK2 mutations are the underlying cause of Coffin-Lowry syndrome (CLS), which is characterized by cognitive impairment and skeletal anomalies (Zeniou et al. 2002).
R-HSA-9833110 RSV-host interactions Airway epithelial cells are the primary target for human respiratory syncytial virus (hRSV) and other inhaled pathogens (Zhang et al., 2002). In response to RSV infection, airway epithelial cells initiate both inflammatory responses and antiviral immune responses to effectively eliminate the virus (reviewed by Espinoza, Bueno et al., 2014; Lay et al., 2016; Hu et al., 2020; Ouyang et al., 2022). Pattern recognition receptors (PRRs), including Toll-like receptors (TLRs) and retinoic acid-inducible gene-I-like receptors (RLRs), detect viral components such as RSV genomic RNA and trigger the production of pro-inflammatory cytokines, chemokines, and type I interferons (Liu et al. 2007; reviewed by Espinoza et al., 2014; Hu et al., 2020; Ouyang et al., 2022). Additionally, airway epithelial cells recruit other innate immune cells including polymorphonuclear leukocytes (PMNs), macrophages, and natural killer cells to establish an antiviral environment and facilitate the resolution of inflammation within the lungs (Miura 2019). The impact of RSV infection on the host cell transcriptome and proteome is reviewed by Hu et al., 2020. The adaptive immune response controls RSV infection by secreting antibodies (Jones et al., 2018; Fong et al., 2023) or by cytotoxic T lymphocytes (CTLs) that recognize and eliminate RSV-infected cells (Lukens et al., 2010; De et al., 2023). RSV evolved strategies to evade or subvert these host responses, allowing an infection to be established and persist within the host (reviewed by Espinoza, Bohmwald et al., 2014; Lay et al., 2016; Hu et al., 2020; Brasier 2020; Stephens & Varga 2020; Ouyang et al., 2022; van Royen et al., 2022). For example, the NS1 and NS2 proteins target the signaling molecules involved in the innate immune response suppressing PRR-induced IFN production and IFN-mediated signaling pathways (reviewed by Sedeyn et al., 2019; Thornhill & Verhoeven, 2020). Viral SH has been implicated in inhibiting apoptotic pathway, a type of non-inflammatory cell death that limits viral propagation (Li et al., 2015). At the same time, Triantafilou et al. (2013) have reported that viral SH promotes an inflammatory necrotic cell death to release the cell content. Further, the binding of RSV G protein to leukocytes involves the host CX3C chemokine receptor 1 (CX3CR1) and results in blocking signaling and trafficking of CX3CR1-expressing Th1 immune cells to the lungs, facilitating RSV infection (Harcourt et al., 2006). The hRSV NS2 protein induces cell shedding into large airways causing an acute airway obstruction in an animal model of RSV infection through an unknown mechanism (Liesman et al., 2014).
Several host factors contribute to the pathogenesis of RSV infection and its long-term effects, including age, prematurity, underlying respiratory conditions such as chronic lung disease including cystic fibrosis, deficiencies in specific immune components or dysregulated immune responses (reviewed by Carvajal et al., 2019). In some cases, an exaggerated immune response to RSV infection can affect the host's ability to control viral infection leading to immunopathology. For example, elevated production of Th2-type cytokines (IL-4, IL-5 and IL-13) in response to RSV infection leads to airway hyperreactivity and increased risk of developing asthma after hRSV infection (Vu et al., 2019; Dong et al., 2023; reviewed by Norlander & Peebles 2020; Manti & Piedimonte 2022). The outcome of RSV infection depends on a complex interplay between the immune responses induced by the host and the strategies developed by RSV to subvert these responses.
This Reactome module describes molecular mechanisms by which specific RSV components modulate innate and adaptive immune responses, programmed cell death, and host gene expression.
R-HSA-8877330 RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) The complex of CBFB and RUNX1 (AML1) controls transcription of the FOXP3 gene. FOXP3 is a transcription factor that acts as a key regulator of development and function of regulatory T lymphocytes (Tregs). Tregs are CD25+CD4+ T lymphocytes involved in suppression of aberrant immune responses seen in autoimmune diseases and allergies. FOXP3 can bind to RUNX1 and control transcriptional activity of the RUNX1:CBFB complex. RUNX1 stimulates transcription of IL2 and IFNG1 (IFN-gamma), and the expression of these two genes is repressed upon binding of FOXP3 to RUNX1. The complex of FOXP3 and RUNX1, on the other hand, stimulates transcription of cell surface markers of Tregs, such as CD25, CTLA-4 and GITR. In the absence of FOXP3, RUNX1 represses transcription of these genes (Shevach 2000, Maloy and Powrie 2001, Sakaguchi 2004, Ono et al. 2007, Kitoh et al. 2009).
The RUNX1:CBFB complex directly stimulates transcription of the CR1 gene, encoding Complement receptor type 1 (CD35) (Kim et al. 1999, Rho et al. 2002). Expression of CR1 on the surface of activated T cells contributes to generation of Tregs (Torok et al. 2015).
R-HSA-8939243 RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known The transcriptional activity of the RUNX1:CBFB complex is regulated by interaction with co-factors and posttranslational modifications of RUNX1. Protein serine/threonine kinase HIPK2 can phosphorylate RUNX1 and affect transcriptional activity of the RUNX1:CBFB complex during hematopoiesis. Some CBFB mutations found in leukemia interfere with HIPK2-mediated phosphorylation of RUNX1. HIPK2 can simultaneously phosphorylate RUNX1 and EP300 (p300) bound to the RUNX1:CBFB1 complex (Aikawa et al. 2006, Wee et al. 2008).
The RUNX1:CBFB complex can associate with the polycomb repressor complex 1 (PRC1). PRC1 complexes are found at many RUNX1 target promoters and can act either as co-activators or co-repressors in the transactivation of RUNX1 targets (Yu et al. 2011).
RUNX1 recruits the SWI/SNF chromatin remodeling complex to many RUNX1 target promoters by directly interacting with several SWI/SNF subunits (Bakshi et al. 2010).
Other co-factors of the RUNX1:CBFB complex are annotated in the context of transcriptional regulation of specific genes.
R-HSA-8931987 RUNX1 regulates estrogen receptor mediated transcription The RUNX1:CBFB complex can associate with the activated estrogen receptor alpha (ESR1) through direct interaction between RUNX1 and ESR1. The RUNX1:CBFB complex is thus involved in transcriptional regulation of estrogen responsive genes, including GPAM, KCTD6 and AXIN1 (Stender et al. 2010). High GPAM expression correlates with better overall survival in breast cancer (Brockmoller et al. 2012).
R-HSA-8935964 RUNX1 regulates expression of components of tight junctions The RUNX1 transcription factor, which functions as part of the RUNX1:CBFB complex, was shown to directly transcriptionally regulate expression of several genes that encode components of tight junctions. Namely, RUNX1 binds to promoters of TJP1 (encoding ZO-1), OCLDN (encoding Occludin) and CLDN5 (encoding Claudin-5) and stimulates their transcription. Downregulation of RUNX1 by microRNA miR-18a negatively regulates expression of these three tight junction genes, which may affect the permeability of blood-tumor barrier in glioma (Miao et al. 2015).
R-HSA-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function In human hematopoietic progenitors, RUNX1 and its partner CBFB are up-regulated at the onset of megakaryocytic differentiation and down-regulated at the onset of erythroid differentiation. The complex of RUNX1 and CBFB cooperates with the transcription factor GATA1 in the transactivation of megakaryocyte-specific genes. In addition, RUNX1 and GATA1 physically interact (Elagib et al. 2003), and this interaction involves the zinc finger domain of GATA1 (Xu et al. 2006). Other components of the RUNX1:CBFB activating complex at megakaryocytic promoters are GATA1 heterodimerization partner, ZFPM1 (FOG1), histone acetyltransferases EP300 (p300) and KAT2B (PCAF), the WDR5-containing histone methyltransferase MLL complex and the arginine methyltransferase PRMT1 (Herglotz et al. 2013). In the absence of PRMT1, the transcriptional repressor complex can form at megakaryocytic promoters, as RUNX1 that is not arginine methylated can bind to SIN3A/SIN3B co-repressors (Zhao et al. 2008). Besides SIN3A/SIN3B, the RUNX1:CBFB repressor complex at megakaryocytic promoters also includes histone deacetylase HDAC1 and histone arginine methyltransferase PRMT6 (Herglotz et al. 2013).
Megakaryocytic promoters regulated by the described RUNX1:CBFB activating and repressing complexes include ITGA2B, GP1BA, THBS1 and MIR27A (Herglotz et al. 2013). ITGA2B is only expressed in maturing megakaryocytes and platelets and is involved in platelet aggregation (Block and Poncz 1995). GP1BA is expressed at the cell surface membrane of maturing megakaryocytes and platelets and participates in formation of platelet plugs (Cauwenberghs et al. 2000, Jilma-Stohlawetz et al. 2003, Debili et al. 1990). THBS1 homotrimers contribute to stabilization of the platelet aggregate (Bonnefoy and Hoylaerts 2008). MIR27A is a negative regulator of RUNX1 mRNA translation and may be involved in erythroid/megakaryocytic lineage determination (Ben-Ami et al. 2009).
The RUNX1:CBFB complex stimulates transcription of the PF4 gene, encoding a component of platelet alpha granules (Aneja et al. 2011), the NR4A3 gene, associated with the familial platelet disorder (FPD) (Bluteau et al. 2011), the PRKCQ gene, associated with inherited thrombocytopenia (Jalagadugula et al. 2011), the MYL9 gene, involved in thrombopoiesis (Jalagadugula et al. 2010), and the NFE2 gene, a regulator of erythroid and megakaryocytic maturation and differentiation (Wang et al. 2010).
R-HSA-8939245 RUNX1 regulates transcription of genes involved in BCR signaling The RUNX1:CBFB complex, in association with transcription co-factors ELF1 (MEF), ELF2 (NERF2) or PAX5 (BSAP) stimulates transcription of the BLK gene, encoding a B-cell specific tyrosine kinase involved in B cell receptor (BCR) signaling, B cell development and differentiation (Libermann et al. 1999, Cho et al. 2004).
R-HSA-8939256 RUNX1 regulates transcription of genes involved in WNT signaling The RUNX1:CBFB complex directly regulates transcription of at least two components of WNT signaling. In association with its co-factor FOXP3, the RUNX1:CBFB complex stimulates transcription of the RSPO3 gene, encoding a WNT ligand that is implicated as a breast cancer oncogene (Recouvreux et al. 2016). In association with the activated estrogen receptor alpha (ESR1), the RUNX1:CBFB complex stimulates the expression of AXIN1, which functions as a regulator of WNT signaling (Stender et al. 2010).
R-HSA-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs The RUNX1:CBFB complex regulates transcription of the SPI1 (PU.1) gene, involved in differentiation of hematopoietic stem cells (HSCs). RUNX1 recruits histone methyltransferase KMT2A (MLL) to the SPI1 gene locus, leading to generation of the activating H3K4Me3 mark on nucleosomes associated with the SPI1 promoter and the upstream regulatory element (Huang et al. 2011). SPI1 transactivation represses self-renewal and proliferation of HSCs (Fukuchi et al. 2008) and is needed for commitment of HSCs to specific hematopoietic lineages (Imperato et al. 2015).
As a component of the TAL1 transcription factor complex, involved in acute T cell lymphoblastic leukemia (T-ALL), RUNX1 can promote growth and inhibit apoptosis of hematopoietic stem cells by stimulating transcription of the MYB gene and possibly the TRIB2 gene (Sanda et al. 2012, Mansour et al. 2014).
R-HSA-8939242 RUNX1 regulates transcription of genes involved in differentiation of keratinocytes The RUNX1:CBFB complex directly inhibits transcription of the SERPINB13 gene (Nomura et al. 2005), a gene involved in keratinocyte differentiation that is frequently down-regulated in head and neck cancers (Boyapati et al. 2011). RUNX1 also inhibits transcription of STAT3 inhibitors SOCS3 and SOCS4, resulting in elevated STAT3 activity. RUNX1-mediated increase in STAT3 activity, first discovered in keratinocytes, is thought to be involved in the maintenance of epithelial stem cells and contributes to development of epithelial cancers, including squamous cell carcinoma (SCC) of the skin (Scheitz et al. 2012).
R-HSA-8939246 RUNX1 regulates transcription of genes involved in differentiation of myeloid cells The RUNX1:CBFB complex regulates expression of genes involved in differentiation of myeloid progenitors which can commit to hematopoietic lineages that lead to generation of platelets, erythrocytes, leukocytes or monocytes.
The RUNX1:CBFB complex recruits histone acetyltransferase CREBBP (CBP) to the promoter of the CSF2 gene, encoding Granulocyte-macrophage colony stimulating factor (GM-CSF), thus inducing GM-CSF expression (Oakford et al. 2010). GM-CSF induces growth, differentiation and survival of macrophages, granulocytes, erythrocytes and megakaryocytes from myeloid progenitors (Barreda et al. 2004).
The RUNX1:CBFB complex directly stimulates transcription of the LGALS3 gene, encoding galectin-3 (Zhang et al. 2009). Galectin-3 is expressed in myeloid progenitors and its levels increase during the maturation process (Le Marer 2000).
The PRKCB gene, encoding protein kinase C-beta, which regulates apoptosis of myeloid cells, is directly transactivated by the RUNX1:CBFB complex (Hu et al. 2004).
R-HSA-8939247 RUNX1 regulates transcription of genes involved in interleukin signaling The RUNX1:CBFB complex regulates transcription of at least a couple of genes involved in interleukin signaling. The LIFR gene, a direct transcriptional target of the RUNX1:CBFB complex (Qadi et al. 2016), encodes the receptor for the leukemia inhibitory factor (LIF), a member of the interleukin-6 family. LIFR is implicated in hematopoiesis, embryo implantation, placental formation and nervous system development (Nicola et al. 2015). In association with its co-activator ELF1, the RUNX1:CBFB complex stimulates transcription of the IL3 gene, encoding interleukin-3 (Mao et al. 1999).
R-HSA-8941326 RUNX2 regulates bone development RUNX2 is required for the development of both intramembraneous and endochondral bones through regulation of osteoblast differentiation and chondrocyte maturation, respectively. In its absence, intramembraneous ossification is blocked while endochondral ossification is arrested at the cartilaginous stage (Otto et al. 1997, Komori et al. 1997). In mice and humans, RUNX2 haploinsufficiency causes Cleidocranial dysplasia, a generalized bone disorder (Otto et al. 1997, Lee et al. 1997).
RUNX2 stimulates transcription of most of the genes constituting the bone extracellular matrix and of BGLAP gene, which encodes Osteocalcin, a bone-derived hormone controlling glucose metabolism, male fertility and cognition (Ducy et al. 1997).
RUNX2 promotes chondrocyte maturation by stimulating transcription of the IHH gene, encoding Indian hedgehog (Takeda et al. 2001, Yoshida et al. 2004).
In response to BMP2 signaling, RUNX2 forms a complex with SMAD1:SMAD4 heterotrimer in the nucleus and stimulates transcription of SMAD6 (Wang et al. 2007).
RBM14, a negative regulator of RUNX2 transcriptional activity, is frequently overexpressed in osteosarcoma (Li et al. 2009).
R-HSA-8941284 RUNX2 regulates chondrocyte maturation In addition to regulating osteoblast differentiation, RUNX2 regulates skeletal development by regulating maturation of chondrocytes (Takeda et al. 2001). Chondrocyte maturation happens during the process of endochondral ossification. Expression of the parathyroid hormone receptor (PTHR1) and Indian hedgehog (IHH) are hallmarks of chondrocyte maturation. Mice that are double knockouts for Runx2 and Runx3 show a complete absence of chondrocyte maturation and, hence, aberrant limb growth. Based on mouse studies, RUNX2 directly regulates transcription of the IHH gene. RUNX2 binding sites in the IHH gene promoter are conserved in humans (Yoshida et al. 2004). Also based on mouse studies, RUNX2 positively regulates transcription of NELL1 (neural EGFL-like 1), a key functional mediator of chondrogenesis, but direct binding of RUNX2 to the NELL1 gene locus has not been demonstrated (Li et al. 2017). Runx2 binding sites exist in the enhancer of the mouse Col10a1 gene, encoding type X collagen, a marker of hypertrophic chondrocytes, which is critical for endochondral bone formation. While Runx2 binding is required, it is not sufficient to trigger Col10a1 transcription (Gu et al. 2014).
R-HSA-8941332 RUNX2 regulates genes involved in cell migration RUNX2 regulates expression of several genes implicated in cell migration during normal development and bone metastasis of breast cancer cells.
RUNX2 stimulates transcription of the ITGA5 gene, encoding Integrin alpha 5. Integrin alpha-5 promotes adhesion of breast cancer cells to the bone, thus facilitating formation of bone metastases (Li et al. 2016). ITGA5 is implicated in migration of human dental pulp stem cells (Xu et al. 2015). In zebrafish, Integrin alpha-5 coordinates cell migration during development of sensory organs (Bhat et al. 2011). During mouse retinal angiogenesis, Integrin alpha-5 regulates migration of endothelial cells (Stenzel et al. 2011).
The ITGBL1 gene encodes Integrin beta like protein 1, which is implicated in regulation of TGF-beta signaling and RUNX2-induced bone metastasis of breast cancer (Li et al. 2015).
RUNX2 mediated transcription of the MMP13 gene, encoding Colagenase 3 (Matrix metalloproteinase 13), is stimulated by AKT mediated phosphorylation of RUNX2 and is implicated in invasiveness of breast cancer cells (Pande et al. 2013). MMP13 is involved in migration of innate immune system cells in response to injury (Zhang et al. 2008) and in remodelling of skeletal tissues (Ortega et al. 2003).
R-HSA-8941333 RUNX2 regulates genes involved in differentiation of myeloid cells Both RUNX2 and RUNX1 can stimulate transcription of the LGALS3 gene, encoding Galectin-3 (Vladimirova et al. 2008, Zhang et al. 2009). Galectin 3 is expressed in myeloid progenitors and its levels increase during the maturation process (Le Marer 2000). Galectin 3 is highly expressed in pituitary tumors and glioma (Vladimirova et al. 2008, Zhang et al. 2009).
R-HSA-8940973 RUNX2 regulates osteoblast differentiation The complex of RUNX2 and CBFB regulates transcription of genes involved in differentiation of osteoblasts.
RUNX2 stimulates transcription of the BGLAP gene, encoding osteocalcin (Ducy and Karsenty 1995, Ducy et al. 1997). Binding of the RUNX2:CBFB complex to the BGLAP gene promoter is increased when RUNX2 is phosphorylated on serine residue S451 (Wee et al. 2002). Osteocalcin, a bone-derived hormone, is one of the most abundant non-collagenous proteins of the bone extracellular matrix (reviewed in Karsenty and Olson 2016). Association of the activated androgen receptor (AR) with RUNX2 prevents binding of RUNX2 to the BGLAP promoter (Baniwal et al. 2009). When YAP1, tyrosine phosphorylated by SRC and/or YES1, binds to RUNX2 at the BGLAP gene promoter, transcription of the BGLAP gene is inhibited (Zaidi et al. 2004). Signaling by SRC is known to inhibit osteoblast differentiation (Marzia et al. 2000).
Simultaneous binding of RUNX2 and SP7 (Osterix, also known as OSX) to adjacent RUNX2 and SP7 binding sites, respectively, in the UCMA promoter, synergistically activates UCMA transcription. UCMA stimulates osteoblast differentiation and formation of mineralized nodules (Lee et al. 2015).
The SCF(SKP2) E3 ubiquitin ligase complex inhibits differentiation of osteoblasts by polyubiquitinating RUNX2 and targeting it for proteasome-mediated degradation (Thacker et al. 2016). This process is inhibited by glucose uptake in osteoblasts (Wei et al. 2015).
R-HSA-8949275 RUNX3 Regulates Immune Response and Cell Migration RUNX3-mediated transcription regulates development of immune system cells. RUNX3 is necessary for the development of innate lymphoid cells (ILCs) of ILC1 and ILC3 lineages, which reside in the mucosa and are involved in response to external pathogens. RUNX3 exerts its role in the development of ILC1 and ILC3 lineages by stimulating expression of the RORC (RORgamma) gene, encoding nuclear retinoid-related orphan receptor-gamma (Ebihara et al. 2015).
RUNX3 regulates transcription of integrin genes ITGAL (CD11a) and ITGA4 (CD49d), involved in transendothelial migration of leukocytes during immune and inflammatory responses as well as co-stimulation of T cells (Domniguez-Soto et al. 2005). The RUNX3 splicing isoform p33 lacks the Runt domain and is unable to transactivate integrin genes. The p33 isoform is induced during maturation of monocyte-derived dendritic cells (MDDC), leading to reduced expression of genes involved in inflammatory responses, such as IL8 (interleukin-8) (Puig-Kroger et al. 2010).
RUNX3 positively regulates transcription of the SPP1 (osteopontin) gene, which contributes to invasiveness of pancreatic cancer cells (Whittle et al. 2015).
R-HSA-8952158 RUNX3 regulates BCL2L11 (BIM) transcription In response to TGF-beta signaling, RUNX3, in cooperation with activated SMADs and FOXO3A, induces transcription of the pro-apoptotic gene BCL2L11 (BIM) (Wildey et al. 2003, Yano et al. 2006, Yamamura et al. 2006).
R-HSA-8941855 RUNX3 regulates CDKN1A transcription RUNX3 contributes to the upregulation of the CDKN1A (p21) gene transcription in response to TGF-beta (TGFB1) signaling. RUNX3 binds to SMAD3 and SMAD4, and cooperates with the activated SMAD3:SMAD4 complex in transactivation of CDKN1A. Runx3 knockout mice exhibit decreased sensitivity to TGF-beta and develop gastric epithelial hyperplasia (Chi et al. 2005). In response to TGF-beta signaling, the CBFB:RUNX3 complex binds to the tumor suppressor ZFHX3 (ATBF1) and, through an unknown mechanism, this complex positively regulates the CDKN1A transcription (Mabuchi et al. 2010).
In addition, RUNX3 may act as a TP53 co-factor, stimulating TP53-mediated transcription of target genes, including CDKN1A (p21) (Yamada et al. 2010).
R-HSA-8941856 RUNX3 regulates NOTCH signaling RUNX3 negatively regulates NOTCH signaling, which contributes to the tumor suppressor role of RUNX3 in hepatocellular carcinoma. RUNX3 binds the promoter of the JAG1 gene, encoding NOTCH ligand JAG1 and inhibits its transcription (Nishina et al. 2011). In addition, RUNX3 also binds to the NOTCH1 coactivator complex at the promoter of HES1, a NOTCH target gene, and inhibits HES1 transcription (Gao et al. 2010).
R-HSA-8951911 RUNX3 regulates RUNX1-mediated transcription RUNX3 binds to Runx response elements in the distal (P1) promoter of the RUNX1 gene, repressing RUNX1 transcription (Spender et al. 2005).
R-HSA-8951430 RUNX3 regulates WNT signaling RUNX3 binds to complexes of beta-catenin (CTNNB1) and TCF/LEF family members. Binding of RUNX3 to CTNNB1:TCF/LEF complexes prevents their loading onto cyclin D1 (CCND1) and MYC gene promoters and interferes with WNT signaling-mediated activation of CCND1 and MYC1 transcription. RUNX3 therefore inhibits WNT-induced cellular proliferation (Ito et al. 2008).
R-HSA-8951671 RUNX3 regulates YAP1-mediated transcription Association of RUNX3 with the TEADs:YAP1 complex inhibits loading of the TEADs:YAP1 to the CTGF promoter, thus negatively regulating transcription of the CTGF gene which encodes the Connective tissue growth factor (Yagi et al. 1999, Zhao et al. 2008, Qiao et al. 2016).
R-HSA-8951936 RUNX3 regulates p14-ARF Acetylation of RUNX3 by the histone acetyl transferase p300 (EP300) and the subsequent association of acetylated RUNX3 with BRD2 correlates with upregulation of p14-ARF transcription from the CDKN2A locus. Cyclin D1 (CCND1) negatively regulates RUNX3-facilitated induction of p14-ARF by recruiting histone deacetylase HDAC4 to RUNX3, leading to RUNX3 deacetylation (Lee et al. 2013).
R-HSA-9007101 Rab regulation of trafficking Human cells have more than 60 RAB proteins that are key regulators of intracellular membrane trafficking. These small GTPases contribute to trafficking specificity by localizing to the membranes of different organelles and interacting with effectors such as sorting adaptors, tethering factors, kinases, phosphatases and tubular-vesicular cargo (reviewed in Stenmark et al, 2009; Wandinger-Ness and Zerial, 2014; Zhen and Stenmark, 2015).
RAB localization depends on a number of factors including C-terminal prenylation, the sequence of upstream hypervariable regions and what nucleotide is bound, as well as interaction with RAB-interacting proteins (Chavrier et al, 1991; Ullrich et al, 1993; Soldati et al, 1994; Farnsworth et al, 1994; Seabra, 1996; Wu et al, 2010; reviewed in Stenmark, 2009; Wandinger-Ness and Zerial, 2014). More recently, the activity of RAB GEFs has also been implicated in regulating the localization of RAB proteins (Blumer et al, 2103; Schoebel et al, 2009; Cabrera and Ungermann, 2013; reviewed in Barr, 2013; Zhen and Stenmark, 2015).
R-HSA-392517 Rap1 signalling Rap1 (Ras-proximate-1) is a small G protein in the Ras superfamily. Like all G proteins, Rap1 is activated when bound GDP is exchanged for GTP. Rap1 is targeted to lipid membranes by the covalent attachment of lipid moieties to its carboxyl terminus. Movement of Rap1 from endosomal membranes to the plasma membrane upon activation has been reported in several cell types including Jurkat T cells and megakaryocytes. On activation, Rap1 undergoes conformational changes that facilitate recruitment of a variety of effectors, triggering it's participation in integrin signaling, ERK activation, and others.
R-HSA-442982 Ras activation upon Ca2+ influx through NMDA receptor Ca2+ influx through the NMDA receptor triggers RAS signaling through the activation of RAS guanyl nucleotide exchange factor RasGRF (Krapivinsky et al. 2003).
R-HSA-975578 Reactions specific to the complex N-glycan synthesis pathway If MAN2 acts before MGAT3, the pathway progresses to complex N-glycans, because MAN2 is not able to operate on bisected oligosaccharides (11421343, page 5). The expression of MAN2 over MGAT3 in a tissue can regulate the synthesis of hybrid or complex N-glycans.
R-HSA-975574 Reactions specific to the hybrid N-glycan synthesis pathway The transfer of a bisecting GlcNAc by MGAT3 commits the pathway toward the synthesis of hybrid glycans, because MAN2 is not able to operate on bisected oligosaccharides (Schachter et al 2000, Priatel JJ et al, 1997). The expression of MGAT3 over MGAT2 in a tissue can regulate the synthesis of hybrid toward complex N-glycans. The addition of a GlcNAc between the two arms also prevents the action of MGAT4, MGAT5 and FUT8.
R-HSA-8934903 Receptor Mediated Mitophagy Mitochondrial autophagy in mammalian cells was first observed in glucagon-stimulated hepatocytes. The mechanisms of mitophagy in mammalian cells remain unclear. Oxidative stress and mPTP are involved in the initiation of mitophagy. Receptor mediated mitophagy links both cellular differentiation signals and markers of mitochondrial function to LC3 and Atg32, scaffold proteins important for cargo selection and autophagosome formation. These scaffold proteins recruit other autophagy proteins to form the autophagosomes; destroying and recycling mitochondria.
Mitophagy receptors have to meet at least three criteria: 1) it must be mitochondrially localized, 2) it must interact with LC3/ ATG8 in response to a certain stimulus, and 3) it must have a consensus sequence of W/F/YxxL/I known as the LIR motif. This tetrapeptide sequence is present in several Atg8 or LC3-binding partners that are important for selective autophagy.
FUNDC1-mediated mitophagy is inhibited by its phosphorylation at the Tyr 18 position in the LIR motif by Src kinase under normoxia conditions. Upon hypoxia stimulation, Src is inactivated and FUNDC1 at the Tyr 18 position is dephosphorylated by an unknown phosphatase, resulting in an increase of the interaction between FUNDC1 and LC3-II, leading to the selective incorporation and autophagic removal of the mitochondrion.
The outer mitochondrial membrane protein NIX/BNIP3L is involved in autophagic turnover of mitochondria in reticulocytes, a process essential for red blood cell maturation [43]. The mechanism through which NIX senses signals from red blood cell differentiation is unclear. Phosphorylation of serine residues 17 and 24 flanking the BNIP3 LIR promotes binding to specific LC3 family members LC3B and GATE-16 and increases lysosomal destruction of mitochondria.
R-HSA-388844 Receptor-type tyrosine-protein phosphatases Like neurexins, Receptor-like protein tyrosine phosphatases (RPTPs) make trans-synaptic adhesion complexes with multiple postsynaptic binding partners to regulate synapse organization. The type IIa RPTPs include three members, Receptor-type tyrosine-protein phosphatase F (PTPRF) sometimes referred to as leukocyte common antigen-related (LAR), Receptor-type tyrosine-protein phosphatase sigma (PTPRS) and Receptor-type tyrosine-protein phosphatase delta (PTPRD). These proteins contain typical cell adhesion immunoglobulin-like (Ig) and fibronectin III (FNIII) domains, suggesting the involvement of RPTPs in cell-cell and cell-matrix interactions. To date, six different types of postsynaptic organizers for type-IIa RPTPs have been reported: interleukin-1 receptor accessory protein (IL1RAP, IL-1RAcP) (Yoshida et al. 2012), IL-1RAcP-like-1 (IL1RAPL1) (Yoshida et al. 2011), Neurotrophin receptor tyrosine kinase 3 (NTRK3, TrkC) (Takahashi et al. 2011), Leucine-rich repeat-containing protein 4B (LRRC4B, Netrin-G ligand-3, NGL-3) (Woo et al. 2009, Kwon et al. 2010), the Slit- and Trk-like (Slitrk) family proteins (Takahashi et al. 2012, Yim et al. 2013, Yamagata et al. 2015) and the liprins (Serra-Pagès et al. 1998, Dunah et al. 2005).
R-HSA-110330 Recognition and association of DNA glycosylase with site containing an affected purine The recognition and removal of an altered base by a DNA glycosylase is thought to involve the diffusion of the enzyme along the minor grove of the DNA molecule. The enzyme presumably compresses the backbone of the affected DNA strand at the site of damage. This compression is thought to result in an outward rotation of the damaged residue into a "pocket" of the enzyme that recognizes and cleaves the altered base from the backbone (Slupphaug et al. 1996, Parikh et al. 1998).
R-HSA-110328 Recognition and association of DNA glycosylase with site containing an affected pyrimidine Base excision repair is initiated by a DNA glycosylase which first recognizes and removes a damaged or incorrect (e.g. mismatched) base (Sokhansanj et al. 2002).
R-HSA-110314 Recognition of DNA damage by PCNA-containing replication complex Damaged double strand DNA (dsDNA) cannot be successfully used as a template by replicative DNA polymerase delta (POLD) and epsilon (POLE) complexes (Hoege et al. 2002). When the replication complex composed of PCNA, RPA, RFC and POLD or POLE stalls at a DNA damage site, PCNA becomes monoubiquitinated by RAD18 bound to UBE2B (RAD6). POLD or POLE dissociate from monoubiquitinated PCNA, while Y family DNA polymerases - REV1, POLH (DNA polymerase eta), POLK (DNA polymerase kappa) and POLI (DNA polymerase iota) - bind monoubiquitinated PCNA through their ubiquitin binding and PCNA binding motifs, resulting in a polymerase switch and initiation of translesion synthesis (TLS) (Hoege et al. 2002, Friedberg et al. 2005).
R-HSA-5693565 Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks Activated ATM phosphorylates a number of proteins involved in the DNA damage checkpoint and DNA repair (Thompson and Schild 2002, Ciccia and Elledge 2010), thereby triggering and coordinating accumulation of DNA DSB repair proteins in nuclear foci known as ionizing radiation-induced foci (IRIF). While IRIFs include chromatin regions kilobases away from the actual DSB site, this Reactome pathway represents simplified foci and events that happen proximal to the DNA DSB ends. In general, proteins localizing to the nuclear foci in response to ATM signaling are cooperatively retained at the DNA DSB site, forming a positive feedback loop and amplifying DNA damage response (Soutoglou and Misteli 2008).
Activated ATM phosphorylates the NBN (NBS1) subunit of the MRN complex (MRE11A:RAD50:NBN) (Gatei et al. 2000), as well as the nucleosome histone H2AFX (H2AX) on serine residue S139, producing gamma-H2AFX (gamma-H2AX) containing nucleosomes (Rogakou et al. 1998, Burma et al. 2001). H2AFX is phosphorylated on tyrosine 142 (Y142) under basal conditions (Xiao et al. 2009). After ATM-mediated phosphorylation of H2AFX on S139, tyrosine Y142 has to be dephosphorylated by EYA family phosphatases in order for the DNA repair to proceed and to avoid apoptosis induced by DNA DSBs (Cook et al. 2009). Gamma-H2AFX recruits MDC1 to DNA DSBs (Stucki et al. 2005). After ATM phosphorylates MDC1 (Liu et al. 2012), the MRN complex, gamma-H2AFX nucleosomes, and MDC1 serve as a core of the nuclear focus and a platform for the recruitment of other proteins involved in DNA damage signaling and repair (Lukas et al. 2004, Soutoglou and Misteli 2008).
RNF8 ubiquitin ligase binds phosphorylated MDC1 (Kolas et al. 2007) and, in cooperation with HERC2 and RNF168 (Bekker-Jensen et al. 2010, Campbell et al. 2012), ubiquitinates H2AFX (Mailand et al. 2007, Huen et al. 2007, Stewart et al. 2009, Doil et al. 2009) and histone demethylases KDM4A and KDM4B (Mallette et al. 2012).
Ubiquitinated gamma-H2AFX recruits UIMC1 (RAP80), promoting the assembly of the BRCA1-A complex at DNA DSBs. The BRCA1-A complex consists of RAP80, FAM175A (Abraxas), BRCA1:BARD1 heterodimer, BRCC3 (BRCC36), BRE (BRCC45) and BABAM1 (MERIT40, NBA1) (Wang et al. 2007, Wang and Elledge 2007)
Ubiquitin mediated degradation of KDM4A and KDM4B allows TP53BP1 (53BP1) to associate with histone H4 dimethylated on lysine K21 (H4K20Me2 mark) by WHSC1 at DNA DSB sites (Pei et al. 2011).
Once recruited to DNA DSBs, both BRCA1:BARD1 heterodimers and TP53BP1 are phosphorylated by ATM (Cortez et al. 1999, Gatei et al. 2000, Kim et al. 2006, Jowsey et al. 2007), which triggers recruitment and activation of CHEK2 (Chk2, Cds1) (Wang et al. 2002, Wilson and Stern 2008, Melchionna et al. 2000).
Depending on the cell cycle stage, BRCA1 and TP53BP1 competitively promote either homology directed repair (HDR) or nonhomologous end joining (NHEJ) of DNA DSBs. HDR through homologous recombination repair (HRR) or single strand annealing (SSA) is promoted by BRCA1 in association with RBBP8 (CtIP), while NHEJ is promoted by TP53BP1 in association with RIF1 (Escribano-Diaz et al. 2013).
R-HSA-380320 Recruitment of NuMA to mitotic centrosomes The NuMA protein, which functions as a nuclear matrix protein in interphase (Merdes and Cleveland 1998), redistributes to the cytoplasm following nuclear envelope breakdown where it plays an essential role in formation and maintenance of the spindle poles (Gaglio, et al., 1995; Gaglio, et al., 1996; Merdes et al, 1996). The mitotic activation of NuMA involves Ran-GTP-dependent dissociation from importin (Nachury et al, 2001, Wiese et al, 2001). NuMA is transported to the mitotic poles where it forms an insoluble crescent around centrosomes tethering microtubules into the bipolar configuration of the mitotic apparatus (Merdes et al., 2000; Kisurina-Evgenieva et al, 2004). Although NuMA is not a bona fide constituent of the mitotic centrosome but rather a protein associated with microtubules at the spindle pole, specific splice variants of NuMA have been identified that associate with the centrosome during interphase (Tang et al, 1994).
R-HSA-380270 Recruitment of mitotic centrosome proteins and complexes The mitotic spindle becomes established once centrosomes have migrated to opposite poles and the nuclear envelope has broken down. During this stage, interphase centrosomes mature into mitotic centrosomes recruiting additional gamma TuRC complexes and acquiring mitosis-associated centrosomal proteins including NuMA, Plk1 and CDK11p58 (reviewed in Schatten 2008; Raynaud-Messina and Merdes 2007).
R-HSA-159418 Recycling of bile acids and salts Of the 20-40 grams of bile salts released daily by the liver, all but approximately 0.5 grams are reabsorbed from the intestine, returned to the liver, and re-used. This recycling involves a series of transport processes: uptake by enterocytes mediated by ASBT (SLC10A2), traversal of the enterocyte cytosol mediated by ileal bile acid binding protein (I-BABP - FABP6), efflux from enterocytes mediated by MRP3 (ABCC3), travel through the portal blood as a complex with albumin, and uptake by hepatocytes mediated by Na+-taurocholate transporting protein (NTPC - SLC10A1) and, to a lesser extent by organic anion transporting proteins A, C, and 8 (OATPA - SLCO1A2, OATPC - SLCO1B1, and OATP-8 - SLCO1B3). Once returned to the hepatocyte cytosol, bile acids (generated in the intestine by the action of bacteria on secreted bile salts) are activated by conjugation with coenzyme A, then coupled to glycine or taurine, regenerating bile salts for re-export into the bile, mediated by the bile salt export pump, ABCB11 (Kullak-Ublick et al. 2004; Mihalik et al. 2002; Trauner and Boyer 2003). Unmodified bile salts returned to the hepatocyte cytosol can be re-exported by ABCB11 without further modification.
R-HSA-72731 Recycling of eIF2:GDP The active eIF2:GTP complex may be formed by direct binding of GTP to free eIF2 or by GDP-GTP exchange on the eIF2:GDP:eIF2B complex. The eIF2:GDP complex binds eIF2B forming an eIF2:GDP:eIF2B intermediate complex. eIF2B is a guanine nucleotide releasing factor required to cause GDP release so that a new GTP molecule can bind and activate eIF2. Phosphorylated eIF2:GDP sequesters all eIF2B as an inactive complex, and thus, reuse of eIF2 is inhibited as a consequence of the tight bond it forms with eIF2B, which prevents nucleotide exchange. Therefore, in the absence of free eIF2B, excess eIF2 remains in its inactive GDP-bound form and protein synthesis slows dramatically.
R-HSA-437239 Recycling pathway of L1 L1 functions in many aspects of neuronal development including axon outgrowth and neuronal migration. These functions require coordination between L1 and the actin cytoskeleton. F-actin continuously moves in a retrograde direction from the P-(peripheral) domain of the growth cone towards the growth cone's C-(central) domain. L1, attached to the actin cytoskeleton via membrane cytoskeletal linkers (MCKs) such as ankyrins (Ankyrin-G, -B and -R) and members of the ERMs (ezrin, radixin, and moesin) family, link this retrograde F-actin flow with extracellular immobile ligands.
Forward translocation of growth cone requires not only the CAM-actin linkage but also a gradient of cell substrate adhesion (strong adhesion at the front and weak adhesion at the rear) so that the cytoskeletal machinery is able to pull the cell forward as attachments at the rear are released. This asymmetry is achieved in part by internalizing L1 molecules as they are moved to the rear of the growth cone coupled to retrograde F-actin flow and recycling them to the leading edge plasma membrane.
L1 internalization is mediated by phosphorylation and dephosphorylation. The L1 cytoplasmic domain (L1CD) carries an endocytic or sorting motif, YRSLE, that is recognized by the clathrin associated adaptor protein-2 (AP-2). AP-2 binds the YRSLE motif only when its tyrosine is not phosphorylated and triggers L1 endocytosis. SRC kinase associated with lipid rafts in the P-domain membrane phosphorylates L1 molecules on tyrosine-1176, stabilizing them in the plasma membrane. L1 endocytosis is triggered by the dephosphorylation of Y1176 within the C domain. Some of these internalized L1 molecules are transported in an anterograde direction along microtubules for reuse in the leading edge.
R-HSA-418359 Reduction of cytosolic Ca++ levels During steady state conditions, cytoplasmic [Ca2+] is reduced by the accumulation of Ca2+ in intracellular stores and Ca2+ extrusion.
R-HSA-8866376 Reelin signalling pathway Reelin (RELN) is an extracellular, multifunctional signal glycoprotein that controls not only the positioning of neurons in the developing brain, but also their growth, maturation, and synaptic activity in the adult brain (Stranahan et al. 2013). Abnormal Reelin expression in the brain is implicated in a number of neuropsychiatric disorders including autism, schizophrenia, bipolar disorder and Alzheimer's disease (Folsom & Fatemi 2013).
R-HSA-9669929 Regorafenib-resistant KIT mutants Regorafenib is a type II tyrosine kinase inhibitor that is approved for treatment of advanced gastrointestinal stromal tumors with KIT mutations. Regorafenib is effective in imatinib-resistant tumors carrying secondary mutations in exon 14 (gatekeeper mutation), and most KIT secondary mutations encoded by exons 17 and 18 (the activation loop) (Demetri et al, 2013; Serrano et al, 2017, Serrano et al, 2019; reviewed in Roskoski, 2018; Klug et al, 2018; ).
R-HSA-9674403 Regorafenib-resistant PDGFR mutants Regorafenib is a type II TKI that is approved for the treatment of advanced gastrointestinal stromal tumors. Although regorafenib is effective against a number of KIT and PDGFR mutations, it only weakly inhibits the activity of the most prevalent PDGFRA allele, D842V (Evans et al, 2017).
R-HSA-5218859 Regulated Necrosis Necrosis has traditionally been considered as a passive, unregulated cell death. However, accumulating evidence suggests that necrosis, like apoptosis, can be executed by genetically controlled and highly regulated cellular process that is morphologically characterized by a loss of cell membrane integrity, intracellular organelles and/or the entire cell swelling (oncosis) (Rello S et al. 2005; Galluzzi L et al. 2007; Berghe TV et al. 2014; Ros U et al. 2020). The morphological hallmarks of the nectotic death have been associated with different forms of programmed cell death including (but not limited to) parthanatos, necroptosis, glutamate-induced oxytosis, ferroptosis, inflammasome-mediated necrosis etc. Each of them can be triggered under certain pathophysiological conditions. For example UV, ROS or alkylating agents may induce poly(ADP-ribose) polymerase 1 (PARP1) hyperactivation (parthanatos), while tumor necrosis factor (TNF) or toll like receptor ligands (LPS and dsRNA) can trigger necrosome-mediated necroptosis. The initiation events, e.g., PARP1 hyperactivation, necrosome formation, activation of NADPH oxidases, in turn trigger one or several common intracellular signals such as NAD+ and ATP-depletion, enhanced Ca2+ influx, dysregulation of the redox status, increased production of reactive oxygen species (ROS) and the activity of phospholipases. These signals affect cellular organelles and membranes leading to osmotic swelling, massive energy depletion, lipid peroxidation and the loss of lysosomal membrane integrity. Different mechanisms of permeabilization have emerged depending on the cell death form. Pore formation by gasdermins (GSDMs) is a hallmark of pyroptosis, while mixed lineage kinase domain-like (MLKL) protein facilitates membrane permeabilization in necroptosis, and phospholipid peroxidation leads to membrane damage in ferroptosis. This diverse repertoire of mechanisms leading to membrane permeabilization contributes to define the specific inflammatory and immunological outcome of each type of regulated necrosis. Regulated or programmed necrosis eventually leads to cell lysis and release of cytoplasmic content into the extracellular region that is often associated with a tissue damage resulting in an intense inflammatory response.
The Reactome module describes necroptosis and pyroptosis. R-HSA-193692 Regulated proteolysis of p75NTR p75NTR undergoes a process of regulated intramembrane proteolysis (RIP) similar to other transmembrane proteins such as NOTCH, beta-amyloid precursor protein (APP), and ERBB4. Each of these proteins is subjected to two sequential cleavages. The first one occurs in the extracellular part of the protein and is mediated by the metalloproteinase alpha-secretase which causes shedding of the extracellular domain. The second cleavage occurs in the intramembrane region and is mediated by gamma-secretase and causes release of the intracellular domain, ICD, and of a small peptide. The ICD often traffics to the nucleus and, in some instances (e.g. NOTCH), was found to act as transcriptional regulator. Whether the p75NTR ICD does translocate to the nucleus to regulate gene expression in a way similar to the NOTCH receptor remains to be seen. The alpha- and gamma-secretase mediated cleavage of p75 appears to be regulated by neurotrophin (NGF, BDNF) binding to TRKA or TRKB. p75NTR processing also occurs in response to MAG in cerebellar granule neurons. R-HSA-3248023 Regulation by TREX1 Three prime repair exonuclease 1 (TREX1) is a DNase type III enzyme, which targets and digests unpaired nucleotides on ssDNA and dsDNA ends through a 3'to 5' exonuclease activity (Perrino FW et al. 1994; de Silva U et al. 2007; Lehtinen DA et al. 2008; Fye JM et al 2011). TREX1 is an endoplasmic reticulum (ER)-associated protein, which is anchored to ER membrane via the C-terminal transmembrane domain (Chowdhury D et al. 2006; Richards A et al. 2007; Stetson DB et al. 2009). TREX1 has been implicated in innate immune responses against self (damaged or retrotransposons-derived DNA) and retroviral-derived DNA (Stetson DB et al. 2009; Yan N et al. 2010; Hasan M et al. 2012). TREX1 deficiency in human and mouse cells led to accumulation of cytosolic DNA which resulted in a continual activation of cytosolic DNA-sensors. In addition, cells lacking TREX1 function were less susceptible to infection with different types of RNA viruses (Yan N et al. 2010; Hasan M et al. 2012).Thus, the physiological role of the exonuclease TREX1 is to digest cytosolic host DNA to avoid autoimmunity. Loss-of-function mutations in the gene encoding human TREX1 are associated with several autoimmune diseases (Aicardi-Goutieres syndrome (AGS), familial chilblain lupus (FCL), systemic lupus erythematosus (SLE)) that result in increased levels of interferon and circulating antibodies to DNA (Crow YJ et al. 2006; Rice G et al. 2007; Lee-Kirsch MA et al. 2007). During infection with human immunodeficiency virus (HIV) or other RNA viruses, TREX1 activity may inhibit the innate immune responses by processing viral DNA generated during reverse transcription (Yan N et al. 2010; Hasan M et al. 2012). It's not yet known whether TREX1 is also involved in regulation of host responses to DNA viruses.
Detection of nucleic acids is known to launch signaling cascades leading to induction of type I interferons, which in turn orchestrate an immune response that involves the expression of hundreds of interferon-stimulated genes (ISGs). It is interesting to note that interferon(IFN)-independent activation of a subset of ISGs was detected in mouse and human cells lacking functional TREX1 (Hasan M et al. 2012). Hasan et al. have also observed that TREX1-deficiency resulted in an increased lysosomal compartment. Trex1 was found to control mTORC1 activity in mouse embryonic fibroblasts (MEF), which in turn negatively regulates translocation of transcription factor EB (TFEB) to the nucleus thereby controlling lysosomal biogenesis (Hasan M et al. 2012; Roczniak-Ferguson A et al. 2012). The authors linked the altered lysosomal compartment to innate immune responses by suggesting that lysosomal biogenesis (regulated by TFEB and mTORC1) acted upstream of IFN-independent ISG expression (regulated by IRF3 and IRF7) (Hasan M et al. 2012). R-HSA-3371378 Regulation by c-FLIP c-FLIP proteins (CASP8 and FADD-like apoptosis regulators or c-FLICE inhibitory proteins) are death effector domain (DED)-containing proteins that are recruited to the death-inducing signaling complex (DISC) to regulate activation of caspases-8. Three out of 13 distinct spliced variants of c-FLIP had been found to be expressed at the protein level, the 26 kDa short form FLIP(S), the 24 kDa form FLIP(R), and the 55 kDa long form FLIP(L) (Irmler M et al. 1997; Shu HB et al. 1997; Srinivasula SM et al. 1997; Scaffidi C et al. 1999; Golks A et al. 2005; Haag C et al. 2011)
All c-FLIP proteins carry two DEDs at their N termini, which can bind FADD and procaspase-8. In addition to two DEDs, FLIP(L) contains a large (p20) and a small (p12) caspase-like domain without catalytic activity. FLIP(S) and FLIP(R) consist of two DEDs and a small C terminus. Depending on its level of expression FLIP(L) may function as an anti-apoptotic or pro-apoptotic factor, while FLIP(S) and FLIP(R) protect cells from apoptosis by blocking the processing of caspase-8 at the receptor level (Scaffidi C et al. 1999; Golks A et al. 2005; Toivonen HT et al. 2011; Fricker N et al. 2010).
R-HSA-176408 Regulation of APC/C activators between G1/S and early anaphase The APC/C is activated by either Cdc20 or Cdh1. While both activators associate with the APC/C, they do so at different points in the cell cycle and their binding is regulated differently (see Zachariae and Nasmyth, 1999). Cdc20, whose protein levels increase as cells enter into mitosis and decrease upon mitotic exit, only associates with the APC/C during M phase. Cdh1 associates with the APC/C in G1. This interaction is inhibited at other times by Cdk1 phosphorylation.
R-HSA-169911 Regulation of Apoptosis A regulated balance between cell survival and apoptosis is essential for normal development and homeostasis of multicellular organisms (see Matsuzawa, 2001). Defects in control of this balance may contribute to autoimmune disease, neurodegeneration and cancer. Protein ubiquitination and degradation is one of the major mechanisms that regulate apoptotic cell death (reviewed in Yang and Yu 2003).
R-HSA-9708530 Regulation of BACH1 activity The transcription factor BTB and CNC homology 1 (BACH1) is widely expressed in most mammalian tissues and functions primarily as a transcriptional suppressor by heterodimerizing with small Maf proteins and binding to Maf recognition elements in the promoters of targeted genes. It has a key regulatory role in the production of reactive oxygen species (ROS), cell cycle, heme homeostasis, hematopoiesis, and immunity and has been shown to suppress ischemic angiogenesis and promote breast cancer metastasis (Zhang et al, 2018; Okada et al, 2010).
R-HSA-9759475 Regulation of CDH11 Expression and Function CDH11 gene encodes Cadherin-11, also known as osteoblast cadherin (OB-cadherin). The CDH11 gene maps to chromosome 16, chromosomal band 16q22, which is a subject to recurrent genomic loss in some types of cancer. The CDH11 gene consists of 14 exons, which are known to encode two splicing isoforms. Both splicing isoforms are expressed in the heart, brain, placenta, lung and bone, but not in the kidney, skeletal muscle, pancreas and liver (Okazaki et al. 1994; Kawaguchi et al. 1999). Several transcription factors have been shown to directly regulate CDH11 gene transcription, including HOXC8 (Lei et al. 2005; Lei et al. 2006; Li et al. 2014), ILF3 (Zhang et al. 2017), ZEB2 (Nam et al. 2012; Nam et al. 2014), HEYL (Liu et al. 2020), FOXF1 (Black et al. 2018), and BHLHE22 (Ross et al. 2012), and the transcription of CDH11 has also been shown to be influenced by a number of growth factors and hormones, such as FGF2 (Strutz et al. 2002; James et al. 2008), TNF (Wu et al. 2013), TGFB1 (Schneider et al. 2012; Schulte et al. 2013; Hahn et al. 2016; Cheng et al. 2018; Ruan et al. 2019; Doolin et al. 2021; Wilson et al. 2022), TGFB2 (Wecker et al. 2013; Theodossiou et al. 2019), GNRH1 (Peng et al. 2015), PTH (Yao et al. 2014), dexamethasone (Lecanda et al. 2000), and progesterone (Chen et al. 1999). CDH11 can also affect TGFB1 signaling, thereby possibly creating a feedback loop (Passanha et al. 2022). Expression of mouse Cdh11 in mouse osteoblast-like cell line (MC3T3-E1) is not affected by osteogenic hormones triiodothyronine (T3) and 1,25-dihydroxyvitamin D3 at either mRNA or protein levels (Leugmayr et al. 2000). CDH11 mRNA has been identified as the target of several microRNAs, such as miR-200c-3p (Luo et al. 2013; Van der Goten et al. 2014) and miR-451a (Yamada et al. 2018; Wang et al. 2020; Wang et al. 2021).
Like other classical cadherins, CDH11 associates with several catenin proteins through its intracellular domain, which is thought to play a role in the establishment and regulation of adherens junctions: CTNND1 (also known as p120 catenin or delta-catenin), CTNNB1 (beta-catenin), JUP (Junction Plakoglobin, also known as gamma-catenin), and CTNNA1 (alpha-catenin) (Straub et al. 2003; Kiener et al. 2006; Ortiz et al. 2015; Lee et al. 2018).
CDH11, through its C-terminus, also forms a complex with angiomotin (AMOT) isoform p80 (AMOT-2), which is implicated in CDH11-mediated cell migration and tumor cell invasiveness (Levchenko et al. 2004; Jiang et al. 2006; Yi et al. 2011; Oritz et al. 2015; Lee et al. 2018).
Through its extracellular region, CDH11 binds to the C-terminal fragment of ANGPTL4 (Angiopoietin-like-4), commonly known as cANGPTL4, which is implicated in the regulation of wound healing. The variant isoform of CDH11 (CDH11v), an 85 kDa membrane-bound fragment produced as a consequence of alternative splicing (Kawaguchi et al. 1999), can compete with the canonical CDH11 for cANGPTL4 binding, leading to diminished CTNNB1 release (Teo et al. 2017).
During normal development, CDH11 is implicated as a regulator of stem cell fate decisions, especially in mesodermal cell lineages (reviewed in Alimperti and Andreadis 2015), being particularly important for skeleton formation (reviewed in Marie et al. 2014).
Besides cancer (reviewed in Blaschuk and Devemy 2009, Niit et al. 2015, Chen et al. 2021), CDH11 has been implicated in several other diseases, such as rheumatoid arthritis (reviewed in Chang et al. 2010, Dou et al. 2013, Sfikakis et al. 2017, Senolt et al. 2019, Nygaard and Firestein 2020), fibrosis (reviewed in Agarwal 2014), cardiovascular diseases (reviewed in Boda-Heggemann et al. 2009, Huynh 2017, Du et al. 2021), and neuropsychiatric disorders (reviewed in Redies et al. 2012).
R-HSA-9762292 Regulation of CDH11 function Like other classical cadherins, CDH11 associates with several catenin proteins through its intracellular domain, which is thought to play a role in the establishment and regulation of adherens junctions. These catenin proteins include CTNND1 (also known as p120 catenin or delta-catenin), CTNNB1 (beta-catenin), JUP (Junction Plakoglobin, also known as gamma-catenin), and CTNNA1 (alpha-catenin) (Straub et al. 2003; Kiener et al. 2006; Ortiz et al. 2015; Lee et al. 2018).
CDH11, through its C terminus, also forms a complex with angiomotin (AMOT) isoform p80 (AMOT-2), which is implicated in CDH11-mediated cell migration and tumor cell invasiveness (Levchenko et al. 2004; Jiang et al. 2006; Yi et al. 2011; Ortiz et al. 2015; Lee et al. 2018).
Through its extracellular region, CDH11 binds to the C terminal fragment of ANGPTL4 (Angiopoietin-like-4), commonly known as cANGPTL4, which is implicated in the regulation of wound healing. The variant isoform of CDH11 (CDH11v), an 85 kDa membrane-bound protein produced as a result of alternative splicing (Kawaguchi et al. 1999), can compete with the canonical CDH11 for cANGPTL4 binding (Teo et al. 2017).
R-HSA-9762293 Regulation of CDH11 gene transcription The CDH11 gene consists of 14 exons, which encode two splice isoforms. Both splicing isoforms are expressed in the heart, brain, placenta, lung and bone, but not in the kidney, skeletal muscle, pancreas and liver (Okazaki et al. 1994; Kawaguchi et al. 1999). Several transcription factors have been shown to directly regulate CDH11 gene transcription, including HOXC8 (Lei et al. 2005; Lei et al. 2006; Li et al. 2014), ILF3 (Zhang et al. 2017), ZEB2 (Nam et al. 2012; Nam et al. 2014), HEYL (Liu et al. 2020), FOXF1 (Black et al. 2018), and BHLHE22 (Ross et al. 2012), and the transcription of CDH11 has also been shown to be influenced by a number of growth factors and hormones, such as FGF2 (Strutz et al. 2002; James et al. 2008), TNF (Wu et al. 2013), TGFB1 (Schneider et al. 2012; Schulte et al. 2013; Hahn et al. 2016; Cheng et al. 2018; Ruan et al. 2019; Doolin et al. 2021; Wilson et al. 2022), TGFB2 (Wecker et al. 2013; Theodossiou et al. 2019), GNRH1 (Peng et al. 2015), PTH (Yao et al. 2014), dexamethasone (Lecanda et al. 2000), progesterone (Chen et al. 1999). CDH11 can also affect TGFB1 signaling, thereby possibly creating a feedback loop (Passanha et al. 2022). Expression of mouse Cdh11 in mouse osteoblast-like cell line (MC3T3-E1) is not affected by osteogenic hormones triiodothyronine (T3) and 1,25-dihydroxyvitamin D3 at either mRNA or protein levels (Leugmayr et al. 2000).
R-HSA-9759811 Regulation of CDH11 mRNA translation by microRNAs Several microRNAs are implicated in posttranscriptional regulation of CDH11 gene expression. The diagram only shows microRNAs reported to downregulate CDH11 mRNA and/or protein levels by at least 2 studies, with at least one study providing human evidence, and at least one study providing mechanistic evidence in the form of luciferase reporter assay and/or formation of the microRNA-mRNA complex. For a more detailed description of criteria for microRNA annotation please refer to Huntely et al. 2016.
The following CDH11-targeting microRNAs are strongly supported by experimental evidence and directly shown in the diagram:
miR-200c-3p (Luo et al. 2013; Van der Goten et al. 2014)
miR-451a (Yamada et al. 2018; Wang et al. 2020; Wang et al. 2021)
The following microRNAs probably target CDH11, but additional evidence is needed to directly represent them in the diagram:
miR-103-2-5p (Gao et al. 2020)
miR-127-3p (Dong et al. 2021)
miR-148-5p (Kawagoe et al. 2020)
R-HSA-9764302 Regulation of CDH19 Expression and Function Cadherin-19 (CDH19, also known as CDH7L2) is a classical type II cadherin. The human CDH19 gene is a part of the cadherin gene cluster at the chromosomal bands 18q22-q23, together with CDH7 and CDH20 (Kools et al. 2000). At the plasma membrane, CDH19 associates with alpha-catenin (CTNNA1), beta-catenin (CTNNB1), gamma-catenin (JUP) and delta catenin (CTNND1) (Huang et al. 2022), like other classical type I and type II cadherins. CDH19 possesses five extracellular cadherin domains and, like other classical cadherins, is thought to play a role in the establishment of homotypic cell-cell adhesions during formation of adherens junctions.
In rat, the expression of Cdh19 overlaps with the expression of the neural crest cell marker Sox10 (Takahashi and Osumi 2005). In mouse, it was shown that Sox10 transcription factor, essential for migration of neural crest cells during formation of the enteric nervous system, binds to the Cdh19 gene promoter and stimulates Cdh19 transcription. Cdh19 knockdown results in retarded sacral migration of neural crest cells, while re-expression of Cdh19 partially rescues retarded migration of Sox10-null neural crest cells (Huang et al. 2022). CDH19 is a specific marker of Schwann cell precursors (Takahashi and Osumi 2005, Iribar et al. 2016, Stratton et al. 2017, George et al. 2018, Woods et al. 2021).
During angiogenesis, in response to monocyte chemotactic protein 1 (MCP-1, also known as CCL2 or C-C motif chemokine 2), CDH19 transcription is directly stimulated by ZC3H12A (MCPIP, for MCP-1 induced protein) (Niu et al. 2008, Niu et al. 2013). CDH19 was found to be a target of microRNA miR-197-5p. The circular RNA hsa_circ_006220 was shown to sponge miR-197-5p and lead to upregulation of CDH19 mRNA and protein levels (Shi et al. 2021). Circular RNAs that possess multiple microRNA binding sites act as sponges that, by binding to microRNAs, prevent these microRNAs from associating with their target mRNAs.
Both upregulation and downregulation of CDH19 have been reported in cancer and it has been proposed to play both oncogenic and tumor-suppressive roles, depending on the cancer type. CDH19 mRNA is upregulated in clear-cell sarcoma and correlates with a hypomethylated profile (Dermawan et al. 2022). In glioblastoma, CDH19 is upregulated in cancer stem-like cells (Zorniak et al. 2015). In colorectal tumors, CDH19 is upregulated compared to normal tissue (Bujko et al. 2015). Downregulation of CDH19 is an independent prognostic biomarker of the outcome of lung adenocarcinoma (Li et al. 2022). In triple negative breast cancer, CDH19 was proposed to play a tumor suppressor role (Shi et al. 2021). A homozygous deletion of the CDH19 gene was reported in a portion of chondrosarcoma tumor samples (Niini et al. 2012).
R-HSA-977606 Regulation of Complement cascade Two inherent features of complement activation make its regulation very important:
1. There is an inherent positive feedback loop because the product of C3 activation forms part of an enzyme that causes more C3 activation.
2. There is continuous low-level activation of the alternative pathway (see Spontaneous hydrolysis of C3 thioester).
Complement cascade activation is regulated by a family of related proteins termed the regulators of complement activation (RCA). These are expressed on healthy host cells. Most pathogens do not express RCA proteins on their surface, but many have found ways to evade the complement system by stably binding the RCA that circulates in human plasma (Lambris et al. 2008); trapping RCA is by far the most widely employed strategy for avoiding the complement response. RCA recruitment is common in bacteria such as E. coli and streptococci (Kraiczy & Wurzner 2006) and has also been described for viruses, fungi and parasites. RCA deposition and the complement system also have an important role in tissue homeostasis, clearing dead cells and debris, and preventing damage from oxidative stress (Weismann et al. 2011).
RCA proteins control complement activation in two different ways; by promoting the irreversible dissociation (decay acceleration) of complement convertases and by acting as cofactors for Complement factor I (CFI)-mediated cleavage of C3b and C4b.
Decay accelerating factor (DAF, CD55), Complement factor H (FH), Membrane Cofactor Protein (MCP) and Complement receptor 1 (CR1) are composed of arrays of tandem globular domains termed CCPs (complement control protein repeats) or SCRs (short consensus repeats). CR1, MCP and FH are cofactors for the CFI-mediated cleavage of C3b, generating iC3b. CR1 and MCP are also cofactors for C4b cleavage.
C4BP is an additional cofactor for the CFI-mediated cleavage of C4b.
R-HSA-9764260 Regulation of Expression and Function of Type II Classical Cadherins Type II classical cadherins are comprised of five extracellular cadherin (EC) repeats in their ectodomain. The first cadherin repeat (EC1) of type II classical cadherins has two conserved tryptophan residues, at positions 2 and 4. The conserved tryptophan residues are critical for dimerization. Trans dimerization of classical cadherins occurs through a unique mechanism, called 'strand swapping', where one set of interactions in two monomers is replaced with an equivalent set of interactions in a dimer, through exchange of an N-terminal beta-strand facilitating docking of the Trp residues into a hydrophobic receptor pocket of the binding partner. This strand-swapping mechanism is aided by an intermediate non-swapped dimer, called X dimer, in accordance with the induced fit model. Type II classical cadherins include CDH5 (cadherin-5, also known as VE-cadherin, an atypical type II cadherin), CDH6 (cadherin-6, also known as K-cadherin), CDH7 (cadherin-7), CDH8 (cadherin-8), CDH9 (cadherin-9, also known as T1-cadherin), CDH10 (cadherin-10, also known as T2-cadherin), CDH11 (cadherin-11, also known as OB-cadherin), CDH12 (cadherin-12, also known as N-cadherin 2), CDH18 (cadherin-18), CDH19 (cadherin-19), CDH20 (cadherin-20), CDH22 (cadherin-22), and CDH24 (cadherin-24). For review, refer to Brasch et al. 2012, Gul et al. 2017.
Type II classical cadherins are predominantly expressed in the nervous system where they govern formation of neuronal circuits (e.g. cold perception, motor neuron bundling). In addition to homotypic dimer formation, type II classical cadherins form heterotypic dimers with other type II classical cadherins and can be divided into three specificity subgroups based on their binding preferences. The specificity subgroups correspond to the branches of the phylogenetic tree where binding between members has been retained. The first specificity subgroup includes CDH8 and CDH11, and likely CDH24, the second specificity subgroup includes CDH6, CDH9 and CDH10, and the third specificity subgroup includes CDH7, CDH12, CDH18, CDH20 and CDH22. The CDH8, CDH11, and CDH24 group does not bind to the others, while binding interactions are found within the other branches of the phylogenetic tree. Divergent type II cadherin CDH5 and CDH19 could not be placed in these specificity subgroups (Brasch et al. 2018).
R-HSA-9617629 Regulation of FOXO transcriptional activity by acetylation Oxidative stress induces acetylation of FOXO transcription factors, which changes the preference of FOXO transcription factors for target DNA sequences. Histone deacetylases SIRT1 and SIRT3 deacetylate FOXO transcription factors (Brunet et al. 2004, Daitoku et al. 2004, Motta et al. 2004, Dansen et al. 2009, Kim et al. 2010, Tseng et al. 2013, reviewed by Hisahara et al. 2005).
Acetylation can also regulate FOXO localization, overriding phosphorylation (Frescas et al. 2005, Bertaggia et al. 2012).
R-HSA-4641263 Regulation of FZD by ubiquitination WNT responsiveness is influenced by expression levels of FZD and LRP proteins. Levels of these receptors at the cell surface are regulated in part by endocytosis, but the mechanisms are not fully elucidated (Garliardi et al, 2008). A number of recent studies have identified a role for ubiquitination in the localization and turnover of WNT receptors at the plasma membrane. ZNRF3 and RNF43 are E3 ligases that have been shown to ubiquitinate FZD proteins and promote their lysosomal degradation, while the deubiquitinating enzyme USP8 promotes recycling of the receptor back to the plasma membrane (Hao et al, 2012; Mukai et al, 2010). This balance of ubiquitination and deubiquitination is in turn regulated by the R-spondin (RSPO) proteins, agonists of WNT signaling which appear to act by downregulating ZNRF3 and RNF43, thus potentiating both canonical and non-canonical pathways (Hao et al, 2012; reviewed in Abo and Clevers, 2012; Fearon and Spence, 2012, Papartriantafyllou, 2012).
R-HSA-170822 Regulation of Glucokinase by Glucokinase Regulatory Protein Glucokinase (GCK1) is negatively regulated by glucokinase regulatory protein (GKRP), which reversibly binds the enzyme to form an inactive complex. Binding is stimulated by fructose 6-phosphate and sorbitol 6-phosphate (hence high concentrations of these molecules tend to reduce GCK1 activity) and inhibited by fructose 1-phosphate (hence a high concentration of this molecule tends to increase GCK1 activity). Once formed, the complex is translocated to the nucleus. In the presence of high glucose concentrations, the nuclear GCK1:GKRP complex dissociates, freeing GCK1 to return to the cytosol. The free GKRP is thought also to return to the cytosol under these conditions, but this return has not been confirmed experimentally. Possible physiological roles for this sequestration process are to decrease futile cycling between glucose and glucose 6 phosphate in hepatocytes under low-glucose conditions, and to decrease the lag between a rise in intracellular glucose levels and the onset of glucose phosphorylation in both hepatocytes and pancreatic beta cells (Brocklehurst et al. 2004; Shiota et al. 1999).
R-HSA-9707587 Regulation of HMOX1 expression and activity Heme oxygenase 1 (HMOX1) is regulated at the level of gene transcription, mRNA translation, localization and degradation. Its gene is often activated under a wide range of stressful conditions. The transcriptional control of HMOX1 is determined by inducible regulatory elements localized in the 5′ region of the promoter, so called antioxidant response elements (ARE)(Raghunath et al, 2018).
AREs on the HMOX1 gene are ultimately controlled by the enhancing NFE2L2:MAFK dimer and the repressing BACH1:MAFK dimer, both of which are influenced by a multitude of processes. Less specific enhancement occurs via AP-1 (FOS:JUN) dimers (Funes et al, 2020).
HMOX1 activity depends on dimerization in the ER membrane. Its membrane localization is abandoned by cleavage of the membrane domain by HM13. The resulting soluble enzyme is found in the cytosol, mitochondria, and the nucleus (Schaefer et al, 2017).
R-HSA-3371453 Regulation of HSF1-mediated heat shock response The ability of HSF1 to respond to cellular stresses is under negative regulation by chaperones, modulation of nucleocytoplasmic shuttling, post-translational modifications and transition from monomeric to trimeric state.
R-HSA-9759476 Regulation of Homotypic Cell-Cell Adhesion Adherens junctions depend on formation of dimers between extracellular domains of cadherins presented on the surface of neighboring apposed cells, bridging the intermembrane space. The cadherin dimers are stabilized by interaction of intracellular domains of cadherins with cytoplasmic catenins that further associate with cytoskeletal proteins, such as actin and microtubules. The dimers are largely homotypic (homophilic), involving identical cadherin proteins, but heterotypic (heterophilic) interactions, involving different cadherin proteins, also occur. Heterotypic cadherin interactions contribute to formation of asymmetric adherens junctions which may serve to sense differences in cytoskeletal geometry between neighboring cells during development. One mechanism for regulation of homotypic cell-cell adhesion is the regulation of expression of cadherin genes. For review, refer to Yap et al. 1997, Meng and Takeichi 2009, Brasch et al. 2012, Malinova and Huveneers 2018).
Cadherins are a family of evolutionarily conserved calcium-dependent single-pass transmembrane proteins characterized by the presence of an N-terminal ectodomain composed of tandem extracellular cadherin (EC) repeats that engage in extracellular interactions mediating cell-cell adhesion through dimerization, and a C-terminal cytoplasmic tail that interacts with catenins and links extracellular adhesion to the cytoskeleton. Based on their sequence similarity, cadherins can be grouped into type I classical cadherins, type II classical cadherins, clustered and non-clustered protocadherins, 7D cadherins, and CELSR cadherins; CDH13 and CDH26 have not been grouped so far. Type I and II classical cadherins are comprised of five extracellular cadherin (EC) repeats in their ectodomains. The first, membrane distal cadherin repeat (EC1) of type I classical cadherins possesses a conserved tryptophan residue at position 2, while the EC1 of type II classical cadherins has two conserved tryptophan residues, at positions 2 and 4. The conserved tryptophan residues are involved in dimerization. 7D cadherins have 7 cadherin repeats in their ectodomains and a conserved tryptophan residue in the third cadherin repeat. CELSR cadherins possess 6-9 cadherin repeats in their ectodomains and no conserved tryptophan residues. Calcium ions bind to cadherins at conserved sites in between consecutive EC repeats, commonly each site binding three calcium ions (Ca2+), and plays an important role in formation of strand-swapped trans dimers in classical cadherins, and protein rigidity in others. For review, refer to Brasch et al. 2012, Gul et al. 2017.
R-HSA-912694 Regulation of IFNA/IFNB signaling There are several proteins and mechanisms involved in controlling the extent of ligand stimulation of IFNA/B signaling. These mechanisms can effect every step of the IFNA/B cascade. Dephosphorylation of JAK and STAT by SHP protein phosphatases, inhibition of STAT function in the nucleus by protein inhibitors of activated STATs (PIAS) proteins, inhibition of tyrosine kinase activity of JAKs by SOCS as well as inhibition of JAK and IFNAR2 interaction by UBP43 are few of the negative regulation mechanisms in controling type I IFN signaling.
R-HSA-877312 Regulation of IFNG signaling At least three different classes of negative regulators exist to control the extent of INFG stimulation and signaling. These include the feedback inhibitors belonging to protein family suppressors of cytokine signaling (SOCS), the Scr-homology 2 (SH2)-containing protein tyrosine phosphatases (SHPs), and the protein inhibitors of activated STATs (PIAS). The induction of these regulators seems to be able to stop further signal transduction by inhibiting various steps in IFNG cascade.
R-HSA-381426 Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) The family of Insulin like Growth Factor Binding Proteins (IGFBPs) share 50% amino acid identity with conserved N terminal and C terminal regions responsible for binding Insulin like Growth Factors I and II (IGF I and IGF II). Most circulating IGFs are in complexes with IGFBPs, which are believed to increase the residence of IGFs in the body, modulate availability of IGFs to target receptors for IGFs, reduce insulin like effects of IGFs, and act as signaling molecules independently of IGFs. About 75% of circulating IGFs are in 1500 220 KDa complexes with IGFBP3 and ALS. Such complexes are too large to pass the endothelial barrier. The remaining 20 25% of IGFs are bound to other IGFBPs in 40 50 KDa complexes. IGFs are released from IGF:IGFBP complexes by proteolysis of the IGFBP. IGFs become active after release, however IGFs may also have activity when still bound to some IGFBPs. IGFBP1 is enriched in amniotic fluid and is produced in the liver under control of insulin (insulin suppresses production). IGFBP1 binding stimulates IGF function. It is unknown which if any protease degrades IGFBP1. IGFBP2 is enriched in cerebrospinal fluid; its binding inhibits IGF function. IGFBP2 is not significantly degraded in circulation. IGFB3, which binds most IGF in the body is enriched in follicular fluid and found in many other tissues. IGFBP 3 may be cleaved by plasmin, thrombin, Prostate specific Antigen (PSA, KLK3), Matrix Metalloprotease-1 (MMP1), and Matrix Metalloprotease-2 (MMP2). IGFBP3 also binds extracellular matrix and binding lowers its affinity for IGFs. IGFBP3 binding stimulates the effects of IGFs. IGFBP4 acts to inhibit IGF function and is cleaved by Pregnancy associated Plasma Protein A (PAPPA) to release IGF. IGFBP5 is enriched in bone matrix; its binding stimulates IGF function. IGFBP5 is cleaved by Pregnancy Associated Plasma Protein A2 (PAPPA2), ADAM9, complement C1s from smooth muscle, and thrombin. Only the cleavage site for PAPPA2 is known. IGFBP6 is enriched in cerebrospinal fluid. It is unknown which if any protease degrades IGFBP6.
R-HSA-1433559 Regulation of KIT signaling SCF induced proliferation is negatively regulated by various proteins including SHP1, PKC, CBL, SOCS1, SOCS6 and LNK.
R-HSA-9022692 Regulation of MECP2 expression and activity Transcription of the MECP2 gene is known to be regulated by methylation of the promoter and the first intron, but the responsible methyltransferases are not known (Nagarajan et al. 2008, Franklin et al. 2010, Liyanage et al. 2013).
Translation of MECP2 mRNA is negatively regulated by the microRNA miR-132. Transcription of miR-132 is regulated by BDNF signaling, through an unknown mechanism (Klein et al. 2007, Su et al. 2015).
Binding of MECP2 to other proteins and to DNA is regulated by posttranslational modifications, of which phosphorylation has been best studied. Calcium dependent protein kinases, PKA and CaMK IV, activated by neuronal membrane depolarization, phosphorylate MECP2 at threonine residue T308 (corresponding to T320 in the longer MECP2 splicing isoform, MECP2_e1). Phosphorylation at T308 correlates with neuronal activity and inhibits binding of MECP2 to the nuclear receptor co-repressor complex (NCoR/SMRT) (Ebert et al. 2013). In resting neurons, MECP2 is phosphorylated at serine residue S80, which results in a decreased association of MECP2 with chromatin. Nuclear serine/threonine protein kinase HIPK2 phosphorylates MECP2 on serine residue S80 (Bracaglia et al. 2009). In activity-induced neurons, upon neuronal membrane depolarization, MECP2 S80 becomes dephosphorylated, and MECP2 acquires phosphorylation on serine S423 (corresponding to mouse Mecp2 serine S421). CaMK IV is one of the kinases that can phosphorylate MECP2 on S423. Phosphorylation of MECP2 at S423 increases MECP2 binding to chromatin (Zhou et al. 2006, Tao et al. 2009, Qiu et al. 2012). AURKB phosphorylates MECP2 at serine residue S423 in dividing adult neuronal progenitor cells (Li et al. 2014).
Besides binding to the NCoR/SMRT co-repressor complex (Lyst et al. 2013, Ebert et al. 2013), MECP2 binds the SIN3A co-repressor complex. This interaction involves the transcriptional repressor domain of MECP2 and the amino terminal part of the HDAC interaction domain (HID) of SIN3A. HDAC1 and HDAC2 are part of the SIN3A co-repressor complex that co-immunoprecipitates with MECP2 (Nan et al. 1998). While binding of MECP2 to SIN3A at target genes is associated with transcriptional repression, binding to CREB1 at target genes is associated with transcriptional activation (Chahrour et al. 2008, Chen et al. 2013). Function of MECP2 can be affected by binding to FOXG1, another gene mutated in Rett syndrome besides MECP2 and CDKL5 (Dastidar et al. 2012), and HTT (Huntingtin) (McFarland et al. 2013). The subnuclear localization of MECP2 may be affected by binding to the Lamin B receptor (LBR) (Guarda et al. 2009). R-HSA-9854909 Regulation of MITF-M dependent genes involved in invasion Targets of MITF such as CEACAM1, GMPR and DIAPH1 contribute to cellular mobility and invasion by affecting cellular adhesion and regulating the actin cytoskeleton (Ullrich et al, 1995; Bianchi-Smiraglia et al, 2017; Carreira et al, 2006). MITF also regulates expression of genes involved in EMT such as SNAI2 (Sanchez-Martin et al, 2002; Strub et al, 2011). MITF-dependent changes in invasiveness are of particular interest in the context of melanoma (reviewed in Goding and Arnheiter, 2019; Cheli et al, 2010; White and Zon, 2008). R-HSA-9854907 Regulation of MITF-M dependent genes involved in metabolism MITF contributes to cellular energetics by regulating the expression of genes such as PPARGC1A, a regulator of mitochondrial biogenesis. MITF-dependent PPARGC1A expression shifts cells towards oxidative phosphorylation (Haq et al, 2013; Vazquez et al, 2013). MITF also promotes the expression of SIRT1, an NAD-dependent deacetylase that acts as a rheostat for cellular energetics. SIRT1 contributes to proliferation and inhibition of senescence in part through its regulation of p300 (Ohanna et al, 2014; Bouras et al, 2005). R-HSA-9825895 Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence MITF target genes are involved in DNA replication, damage repair and chromosome maintenance and stability (Strub et al, 2011; Giuliano et al, 2010; Seoane et al, 2019; reviewed in Cheli et al, 2010; Goding and Arnheiter, 2019). Cells depleted of MITF through siRNA can undergo senescence as a result of accumulating DNA damage. In contrast, cells that are depleted of MITF by overexpression of ATF4 undergo reversible cell cycle arrest but do not undergo senescence, suggesting that ATF4 and translational reprogramming may block the senescence pathway (Giuliano et al, 2010; Falletta et al, 2017; reviewed in Goding and Arnheiter, 2019). R-HSA-9824594 Regulation of MITF-M-dependent genes involved in apoptosis MITF contributes to cellular survival through regulation of anti-apoptotic factors such as BCL2 and BIRC7 (McGill et al, 2002; Dynek et al, 2008; Strub et al, 2011; reviewed in Cheli et al, 2010). Consistent with this, MITF is required for survival of melanoblasts during embryogenesis (Hodgkinson et al, 1993; Opdecamp et al, 1997; Nakayama et al, 1998). MITF may also contribute to survival through regulation of DICER, which in turn regulates expression of a number of genes by virtue of its processing of microRNAs (Levy et al, 2010). R-HSA-9825892 Regulation of MITF-M-dependent genes involved in cell cycle and proliferation Depending on the overall level of activity, MITF may have a proliferative or antiproliferative role. In what has been termed a rheostat model of action, low-levels of MITF activity are associated with dedifferentiation, invasion, p27kip (CDKN1B)-dependent cell cycle arrest and low proliferative rates, while higher MITF activity drive proliferation by upregulation of cell-cycle and mitotic genes such as CDK2, CCNB1, CCND1, MET, PLK1, CENPA and NDC80 (Carreira et al, 2006; Strub et al, 2011; McGill et al, 2006; Beuret et al, 2007; Webster et al, 2014). At even higher MITF levels, cell-cycle is arrested by virtue of expression of p21 (CDKN1A) and p16 (CDKN2A) (Carreira et al, 2005; Loercher et al, 2005; reviewed in Goding and Arnheiter, 2019). This rheostat model of MITF activity and target gene expression can also be used to describe the role of MITF in the development of melanoma, with activation of different groups of target genes driving proliferation and invasion without activation of pigmentation genes (Hoek and Goding, 2010; reviewed in Mort et al, 2015; White and Zon, 2008). R-HSA-9857377 Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy MITF regulates biogenesis of organelles such as the lysosome and endosomes through its regulation of components of the V-ATPase that is required for organelle acidification and function (Zhang et al, 2015; Ploper et al, 2015a; reviewed in Ploper et al, 2015b). MITF-dependent targets also contribute to autophagy when cells are stressed for nutrients (Möller et al, 2019). MITF additionally controls expression of the lysosome-resident acid ceramidase ASAH1 that has roles in sphingolipid metabolism and cellular proliferation in melanoma (Leclerc et al, 2019; Realini et al, 2016). R-HSA-9824585 Regulation of MITF-M-dependent genes involved in pigmentation Genes involved in pigmentation and melanocyte structure and organization were among the first identified targets of MITF. Expression of enzymes TYR, DCT and TYRP1, which work sequentially to eventually convert tyrosine into eumelanin and pheomelanin, is regulated in part by the binding of MITF to M-boxes in the promoters (Bentley et al, 1994; Bertolotto et al, 1998; Yavuzer et al, 1995; reviewed in Cheli et al, 2010; Goding and Arnheiter, 2019). MITF additionally regulates the expression of structural components of the melanosome such as MLANA, SLC24A5, SILV and GPR143, although direct binding and regulation has not been demonstrated in all cases (Du et al, 2003; Cortese et al, 2005; Schiaffino and Tacchetti, 2005; reviewed in Cheli et al, 2010; Goding and Arnheiter, 2019). Genes encoding RAB27A and MYO5A, which regulate the localization and trafficking of melanosomes, are also targets of MITF (Chiaverini et al, 2008; Alves et al, 2017; reviewed in Cheli et al, 2010; Goding and Arnheiter, 2019). R-HSA-9758274 Regulation of NF-kappa B signaling Nuclear factor kappa B (NF-kappa-B, NF-κB) is activated by a diverse range of stimuli including cytokines, ligands of pattern-recognition receptors (PRRs) such as Toll-like receptors (TLRs) in myeloid cells, antigen-activated TCR in T-cells and by DNA damage (reviewed in Yu H et al. 2020; Zhang T et al. 2021). NF-kappa-B regulates the transcription of genes that are involved in immune and inflammatory responses, cell cycle, cell proliferation and apoptosis (Bhatt D & Ghosh S 2014; Liu T et al. 2017; Yu H et al. 2020). In unstimulated cells, NF-κB is sequestered in the cytosol through interactions with a class of inhibitor proteins, called NF-κB inhibitors (IkBs, such as NFKBIA or NFKBIB) (Jacobs MD & Harrison SC 1998). IkBs mask the nuclear localization signal (NLS) of NF-κB preventing its nuclear translocation (Cervantes CF et al. 2011). A key event in NF-κB activation involves phosphorylation of IkBs by the IκB kinase (IKK) complex which consists of CHUK, IKBKB and IKBKG subunits (Israël A 2010). The activated NF-κB signaling is tightly controlled at multiple levels (Dorrington MG & Fraser IDC 2019; Prescott JA et al. 2021). Dysregulated NF-κB activity can cause tissue damage associated with inflammatory diseases and is also linked to tumorigenesis (Aggarwal BB & Sung B 2011; Liu T et al.2017; Barnabei L et al. 2021). The regulation of NF-κB is cell-type-, context- , and stimulus-dependent and is crucial for orchestrating specific cellular responses (Mussbacher M et al. 2019).
This Reactome module describes several molecular mechanisms that regulate TLR-mediated NF-κB signaling at the level of the IKK signaling complex.
R-HSA-9818749 Regulation of NFE2L2 gene expression Sub-pathway represents a collection of events involved in the expression of the NFE2L2 gene. The NFE2L2 gene is transcriptionally regulated by multiple transcription factors like Myc, NFKB, NFE2L2 itself and many more. This diverse regulation of NFE2L2 connects its regulation with other signalling pathways (He et al, 2020)
R-HSA-9768759 Regulation of NPAS4 gene expression NPAS4 is predominantly expressed in neuronal cells. In neurons, expression of NPAS4 is regulated by Ca2+, which ties NPAS4 level to neuronal activity (Lin et al. 2008; Zhang et al. 2009; Kim et al. 2010; Mellström et al. 2014; Lobos et al. 2021).
NPAS4 expression is regulated by signaling pathways activated downstream of the N-methyl-D-aspartate (NMDA) receptor and L-type Ca2+ channel (Coba et al. 2008; Lin et al. 2008; Horvath et al. 2021).
In vivo, NPAS4 expression is activated by visual stimulation (Lin et al. 2008), contextual learning (Ramamoorthi et al. 2011), as well as pharmacologically induced generalized seizure (Flood et al. 2004). Chronic stress induces downregulation of NPAS4 gene expression in the hippocampus (Furukawa-Hibi et al. 2015), so does social isolation (Ibi et al. 2008). Adult female mice who were exposed to early maternal separation (early life stress) show upregulation of NPAS4 in the prefrontal cortex later in life (Ryabushkina et al. 2020). NPAS4 is thought to have a neuroprotective effect and is downregulated during neurodegeneration (Ooe et al. 2009; Zhang et al. 2009; Louis Sam Titus et al 2019). NPAS4 level is reduced in the hippocampus of aged, memory-impaired mice (Qiu et al. 2016). Studies in mice indicate that NPAS4 affects synaptic connections in excitatory and inhibitory neurons, neural circuit plasticity, and memory formation (reviewed by Sun and Lin 2016). NPAS4 may be involved in the functioning of the circadian system (Unfried et al. 2010; West et al. 2013; Xu et al. 2021).
Npas4 mRNA levels are downregulated upon infection with Zika virus through an unknown mechanism (Alpuche-Lazcano et al. 2021).
Besides neuronal cells, NPAS4 is also expressed in pancreatic beta cells, where its levels are regulated by intracellular calcium, as in the nervous system (Speckmann et al. 2016).
R-HSA-9768777 Regulation of NPAS4 gene transcription Transcription of the NPAS4 gene is positively regulated by neuronal stimulation-related increase in intracellular calcium levels (Lin et al. 2008; Zhang et al. 2009, Mellström et al. 2014; Lobos et al. 2021).
In the absence of neuronal activity induced calcium influx, KCNIP3 (DREAM) binds to the promoter of the NPAS4 gene and represses NPAS4 transcription (Mellström et al. 2014). In non-neuronal cells, REST protein represses transcription of the NPAS4 gene (Bersten et al. 2014). In neuronal cells, REST may have a dual effect on NPAS4 expression: acting as a positive regulator of NPAS4 transcription early upon neuronal excitation and as a negative regulator at later time points, allowing NPAS4 to return to basal levels (Prestigio et al. 2021). Binding of agonist activated glucocorticoid receptor NR3C1 (also known as GR) to evolutionarily conserved glucocorticoid response elements (GREs) upstream of the NPAS4 gene transcription start site is responsible for stress-induced repression of NPAS4 gene transcription (Furukawa Hibi et al. 2012). Chronic restraint stress as well as corticosterone injection also reduce Npas4 gene expression in the mouse hippocampus (Yun et al. 2010). Though mechanisms remain to be delineated, HDAC5 was reported by multiple studies to contribute to NPAS4 gene repression (Taniguchi et al. 2017, Hashikawa-Hobara et al. 2021; Lv et al. 2021; Rein et al. 2022). In addition, HDAC3 was reported as the NPAS4 gene repressor during neurodegeneration (Louis Sam Titus et al. 2019).
SRF (Serum response factor) stimulates NPAS4 gene transcription upon neuronal excitation (Kuzniewska et al. 2016, Lösing et al. 2017, Förstner and Knöll 2019). NPAS4 gene transcription is positively regulated by PI3K/AKT signaling (Ooe et al. 2009; Speckmann et al. 2016), and only partially dependent on ERK (MAPK) signaling (Blüthgen et al. 2017). NPAS4 may be one of the EGR1 target genes (Han et al. 2014). Neuronal activity stimulation may trigger the formation of DNA double strand breaks (DSBs) in the promoters of a subset of early-response genes, including FOS, NPAS4, and EGR1, which may contribute to their transcriptional activation (Madabushi et al. 2015). NPAS4 appears to be a downstream target involved in amyloid precursor protein (APP)-dependent regulation of inhibitory synaptic transmission (Opsomer et al. 2020). TET1, a methylcytosine dioxygenase that catalyzes oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and promotes DNA demethylation is implicated in transcriptional activation of NPAS4 gene through demethylation of hypermethylated CpG dinucleotides in the NPAS4 gene promoter region (Rudenko et al. 2013). Transcriptional activation of the NPAS4 gene is associated with the appearance of H3K4me3 mark and 5hmC mark at the NPAS4 gene promoter (Webb et al. 2017).
R-HSA-9768778 Regulation of NPAS4 mRNA translation The 3'UTR of NPAS4 mRNA is highly conserved between mouse, rat and human (>95% identity across ~700 bp of the 3'UTR sequence). Of the three putative microRNAs, miR-224, miR-203 and miR-132/212, that were predicted to target the 3'UTR of NPAS4 mRNA by multiple computational algorithms, miR-224 and miR-203 were able to significantly downregulate expression of the NPAS4 3’UTR reporter construct (Bersten et al. 2014). Downregulation of Npas4 expression by miR-224 was also shown in mouse (Choy et al. 2017). Npas4 was also reported as a target gene of miR-1 (Forget et al. 2021), miR-142 (Ji et al. 2019) and miR-744 (Choy et al. 2017). Only microRNAs that were reported to target Npas4 mRNA by at least two studies are shown in the diagram. The circulatory RNA circ_0003420 was also reported to target NPAS4 mRNA and contribute to its degradation (Xiong et al. 2021).
R-HSA-211728 Regulation of PAK-2p34 activity by PS-GAP/RHG10 PS-GAP (RGH10) interacts specifically with caspase-activated PAK-2p34 reducing the ability of PAK-2p34 to induce cell death. This interaction inhibits the kinase activity of PAK-2p34 and changes the localization of PAK-2p34 from the nucleus to the perinuclear region (Koeppel et al., 2004).
R-HSA-2565942 Regulation of PLK1 Activity at G2/M Transition The kinase activity of PLK1 is required for cell cycle progression as PLK1 phosphorylates and regulates a number of cellular proteins during mitosis. Centrosomic AURKA (Aurora A kinase), catalytically activated through AJUBA facilitated autophosphorylation on threonine residue T288 at G2/M transition (Hirota et al. 2003), activates PLK1 on centrosomes by phosphorylating threonine residue T210 of PLK1, critical for PLK1 activity (Jang et al. 2002), in the presence of BORA (Macurek et al. 2008, Seki et al. 2008). Once activated, PLK1 phosphorylates BORA and targets it for ubiquitination mediated degradation by SCF-beta-TrCP ubiquitin ligases. Degradation of BORA is thought to allow PLK1 to interact with other substrates (Seki, Coppinger, Du et al. 2008, Seki et al. 2008).
The interaction of PLK1 with OPTN (optineurin) provides a negative-feedback mechanism for regulation of PLK1 activity. Phosphorylated PLK1 binds and phosphorylates OPTN associated with the Golgi membrane GTPase RAB8, promoting dissociation of OPTN from Golgi and translocation of OPTN to the nucleus. Phosphorylated OPTN facilitates the mitotic phosphorylation of the myosin phosphatase subunit PPP1R12A (MYPT1) and myosin phosphatase activation (Kachaner et al. 2012). The myosin phosphatase complex dephosphorylates threonine residue T210 of PLK1 and inactivates PLK1 (Yamashiro et al. 2008).
R-HSA-8943724 Regulation of PTEN gene transcription Transcription of the PTEN gene is regulated at multiple levels. Epigenetic repression involves the recruitment of Mi-2/NuRD upon SALL4 binding to the PTEN promoter (Yang et al. 2008, Lu et al. 2009) or EVI1-mediated recruitment of the polycomb repressor complex (PRC) to the PTEN promoter (Song et al. 2009, Yoshimi et al. 2011). Transcriptional regulation is also elicited by negative regulators, including NR2E1:ATN1 (atrophin-1) complex, JUN (c-Jun), SNAIL and SLUG (Zhang et al. 2006, Vasudevan et al. 2007, Escriva et al. 2008, Uygur et al. 2015) and positive regulators such as TP53 (p53), MAF1, ATF2, EGR1 or PPARG (Stambolic et al. 2001, Virolle et al. 2001, Patel et al. 2001, Shen et al. 2006, Li et al. 2016).
R-HSA-8948747 Regulation of PTEN localization When monoubiquitinated by E3 ubiquitin ligases XIAP and NEDD4, PTEN translocates from the cytosol to the nucleus (Trotman et al. 2007, Van Themsche et al. 2009). USP7 (HAUSP)-mediated deubiquitination of monoubiquitinated nuclear PTEN promotes relocalization of PTEN to the cytosol (Song et al. 2008).
R-HSA-8943723 Regulation of PTEN mRNA translation MicroRNAs miR-17, miR-19a, miR-19b, miR-20a, miR-20b, miR-21, miR-22, miR-25, miR 26A1, miR 26A2, miR-93, miR-106a, miR-106b, miR 205, and miR 214 and bind PTEN mRNA and inhibit its translation into protein. These microRNAs are altered in cancer and can account for changes in PTEN levels. There is evidence that PTEN mRNA translation is also inhibited by other microRNAs, such as miR-302 and miR-26B, and these microRNAs will be annotated when additional experimental details become available (Meng et al. 2007, Xiao et al. 2008, Yang et al. 2008, Huse et al. 2009, Kim et al. 2010, Poliseno, Salmena, Riccardi et al. 2010, Zhang et al. 2010, Tay et al. 2011, Qu et al. 2012, Cai et al. 2013). In addition, coding and non coding RNAs can prevent microRNAs from binding to PTEN mRNA. These RNAs are termed competing endogenous RNAs or ceRNAs. Transcripts of the pseudogene PTENP1 and mRNAs transcribed from SERINC1, VAPA and CNOT6L genes exhibit this activity (Poliseno, Salmena, Zhang et al. 2010, Tay et al. 2011, Tay et al. 2014).
R-HSA-8948751 Regulation of PTEN stability and activity PTEN protein stability is regulated by ubiquitin ligases, such as NEDD4, WWP2, STUB1 (CHIP), XIAP, MKRN1 and RNF146, which polyubiquitinate PTEN in response to different stimuli and thus target it for proteasome-mediated degradation (Wang et al. 2007, Van Themsche et al. 2009, Maddika et al. 2011, Ahmed et al. 2012, Lee et al. 2015, Li et al. 2015). Several ubiquitin proteases, such as USP13 and OTUD3, can remove polyubiquitin chains from PTEN and rescue it from degradation (Zhang et al. 2013, Yuan et al. 2015). TRIM27 (RFP) is an E3 ubiquitin ligase that polyubiquitinates PTEN on multiple lysines in the C2 domain of PTEN using K27 linkage between ubiquitin molecules. TRIM27 mediated ubiquitination inhibits PTEN lipid phosphatase activity, but does not affect PTEN protein localization or stability (Lee et al. 2013).
PTEN phosphorylation by the tyrosine kinase FRK (RAK) inhibits NEDD4 mediated polyubiquitination and subsequent degradation of PTEN, thus increasing PTEN half life. FRK mediated phosphorylation also increases PTEN enzymatic activity (Yim et al. 2009). Casein kinase 2 (CK2) mediated phosphorylation of the C-terminus of PTEN on multiple serine and threonine residues increases PTEN protein stability (Torres and Pulido 2001) but results in ~30% reduction in PTEN lipid phosphatase activity (Miller et al. 2002).
PREX2, a RAC1 guanine nucleotide exchange factor (GEF) can binds to PTEN and inhibit its catalytic activity (Fine et al. 2009).
R-HSA-5658442 Regulation of RAS by GAPs The intrinsic GTPase activity of RAS proteins is stimulated by the GAP proteins, of which there are at least 10 in the human genome (reviewed in King et al, 2013).
R-HSA-8934593 Regulation of RUNX1 Expression and Activity At the level of transcription, expression of the RUNX1 transcription factor is regulated by two alternative promoters: a distal promoter, P1, and a proximal promoter, P2. P1 is more than 7 kb upstream of P2 (Ghozi et al. 1996). In mice, the Runx1 gene is preferentially transcribed from the proximal P2 promoter during generation of hematopoietic cells from hemogenic endothelium. In fully committed hematopoietic progenitors, the Runx1 gene is preferentially transcribed from the distal P1 promoter (Sroczynska et al. 2009, Bee et al. 2010). In human T cells, RUNX1 is preferentially transcribed from P1 throughout development, while developing natural killer cells transcribe RUNX1 predominantly from P2. Developing B cells transcribe low levels of RUNX1 from both promoters (Telfer and Rothenberg 2001).
RUNX1 mRNAs transcribed from alternative promoters differ in their 5'UTRs and splicing isoforms of RUNX1 have also been described. The function of alternative splice isoforms and alternative 5'UTRs has not been fully elucidated (Challen and Goodell 2010, Komeno et al. 2014).
During zebrafish hematopoiesis, RUNX1 expression increases in response to NOTCH signaling, but direct transcriptional regulation of RUNX1 by NOTCH has not been demonstrated (Burns et al. 2005). RUNX1 transcription also increases in response to WNT signaling. BothTCF7 and TCF4 bind the RUNX1 promoter (Wu et al. 2012, Hoverter et al. 2012), and RUNX1 transcription driven by the TCF binding element (TBE) in response to WNT3A treatment is inhibited by the dominant-negative mutant of TCF4 (Medina et al. 2016). In developing mouse ovary, Runx1 expression is positively regulated by Wnt4 signaling (Naillat et al. 2015).
Studies in mouse hematopoietic stem and progenitor cells imply that RUNX1 may be a direct transcriptional target of HOXB4 (Oshima et al. 2011).
Conserved cis-regulatory elements were recently identified in intron 5 of RUNX1. The RUNX1 breakpoints observed in acute myeloid leukemia (AML) with translocation (8;21), which result in expression of a fusion RUNX1-ETO protein, cluster in intron 5, in proximity to these not yet fully characterized cis regulatory elements (Rebolledo-Jaramillo et al. 2014).
At the level of translation, RUNX1 expression is regulated by various microRNAs which bind to the 3'UTR of RUNX1 mRNA and inhibit its translation through endonucleolytic and/or nonendonucleolytic mechanisms. MicroRNAs that target RUNX1 include miR-378 (Browne et al. 2016), miR-302b (Ge et al. 2014), miR-18a (Miao et al. 2015), miR-675 (Zhuang et al. 2014), miR-27a (Ben-Ami et al. 2009), miR-17, miR-20a, miR106 (Fontana et al. 2007) and miR-215 (Li et al. 2016).
At the posttranslational level, RUNX1 activity is regulated by postranslational modifications and binding to co-factors. SRC family kinases phosphorylate RUNX1 on multiple tyrosine residues in the negative regulatory domain, involved in autoinhibition of RUNX1. RUNX1 tyrosine phosphorylation correlates with reduced binding of RUNX1 to GATA1 and increased binding of RUNX1 to the SWI/SNF complex, leading to inhibition of RUNX1-mediated differentiation of T-cells and megakaryocytes. SHP2 (PTPN11) tyrosine phosphatase binds to RUNX1 and dephosphorylates it (Huang et al. 2012).
Formation of the complex with CBFB is necessary for the transcriptional activity of RUNX1 (Wang et al. 1996). Binding of CCND3 and probably other two cyclin D family members, CCND1 and CCND2, to RUNX1 inhibits its association with CBFB (Peterson et al. 2005), while binding to CDK6 interferes with binding of RUNX1 to DNA without affecting formation of the RUNX1:CBFB complex. Binding of RUNX1 to PML plays a role in subnuclear targeting of RUNX1 (Nguyen et al. 2005).
RUNX1 activity and protein levels vary during the cell cycle. RUNX1 protein levels increase from G1 to S and from S to G2 phases, with no increase in RUNX1 mRNA levels. CDK1-mediated phosphorylation of RUNX1 at the G2/M transition is implicated in reduction of RUNX1 transactivation potency and may promote RUNX1 protein degradation by the anaphase promoting complex (reviewed by Friedman 2009).
R-HSA-8939902 Regulation of RUNX2 expression and activity Several transcription factors have been implicated in regulation of the RUNX2 gene transcription. Similar to the RUNX1 gene, the RUNX2 gene expression can be regulated from the proximal P2 promoter or the distal P1 promoter (reviewed in Li and Xiao 2007).
Activated estrogen receptor alpha (ESR1) binds estrogen response elements (EREs) in the P2 promoter and stimulates RUNX2 transcription (Kammerer et al. 2013). Estrogen-related receptor alpha (ERRA) binds EREs or estrogen-related response elements (ERREs) in the P2 promoter of RUNX2. When ERRA is bound to its co-factor PPARG1CA (PGC1A), it stimulates RUNX2 transcription. When bound to its co-factor PPARG1CB (PGC1B), ERRA represses RUNX2 transcription (Kammerer et al. 2013).
TWIST1, a basic helix-loop-helix (bHLH) transcription factor, stimulates RUNX2 transcription by binding to the E1-box in the P2 promoter (Yang, Yang et al. 2011). TWIST proteins also interact with the DNA-binding domain of RUNX2 to modulate its activity during skeletogenesis (Bialek et al. 2004). Schnurri-3 (SHN3) is another protein that interacts with RUNX2 to decrease its availability in the nucleus and therefore its activity (Jones et al. 2006). In contrast, RUNX2 and SATB2 interact to enhance the expression of osteoblast-specific genes (Dobreva et al. 2006). Formation of the heterodimer with CBFB (CBF-beta) also enhances the transcriptional activity of RUNX2 (Kundu et al. 2002, Yoshida et al. 2002, Otto et al. 2002).
Transcription of RUNX2 from the proximal promoter is inhibited by binding of the glucocorticoid receptor (NR3C1) activated by dexamethasone (DEXA) to a glucocorticoid receptor response element (GRE), which is also present in the human promoter (Zhang et al. 2012).
NKX3-2 (BAPX1), required for embryonic development of the axial skeleton (Tribioli and Lufkin 1999), binds the distal (P1) promoter of the RUNX2 gene and inhibits its transcription (Lengner et al. 2005). RUNX2-P1 transcription is also autoinhibited by RUNX2-P1, which binds to RUNX2 response elements in the P1 promoter of RUNX2 (Drissi et al. 2000). In contrast, binding of RUNX2-P2 to the proximal P2 promoter autoactivates transcription of RUNX2-P2 (Ducy et al. 1999). Binding of a homeodomain transcription factor DLX5, and possibly DLX6, to the RUNX2 P1 promoter stimulates RUNX2 transcription (Robledo et al. 2002, Lee et al. 2005). The homeobox transcription factor MSX2 can bind to DLX5 sites in the promoter of RUNX2 and inhibit transcription of RUNX2-P1 (Lee et al. 2005).
Translocation of RUNX2 protein to the nucleus is inhibited by binding to non-activated STAT1 (Kim et al. 2003).
Several E3 ubiquitin ligases were shown to polyubiquitinate RUNX2, targeting it for proteasome-mediated degradation: STUB1 (CHIP) (Li et al. 2008), SMURF1 (Zhao et al. 2003, Yang et al. 2014), WWP1 (Jones et al. 2006), and SKP2 (Thacker et al. 2016).
R-HSA-8941858 Regulation of RUNX3 expression and activity RUNX3, like other RUNX family members, is transcribed from two promoters - the proximal P2 promoter and the distal P1 promoter. The P2 promoter is positioned within a large CpG island that is frequently methylated in solid tumors, resulting in epigenetic inactivation of the RUNX3 gene (reviewed by Levanon and Groner 2004). RUNX3 transcription is affected by SMAD4 levels. RUNX3 may directly upregulate its own transcription through a positive feedback loop (Whittle et al. 2015). Under hypoxic conditions, RUNX3 transcription is downregulated. Hypoxic silencing of RUNX3 involves hypoxia-induced upregulation of the histone methyltransferase G9a and histone deacetylase HDAC1, which leads to increased dimethylation of histone H3 at lysine residue K9 (K10 when taking into account the initiator methionine) and reduced acetylation of histone H3 at the RUNX3 promoter (Lee et al. 2009).
RUNX3 protein levels are inversely related to the levels of microRNA miR-130b. Based on in silico analysis, RUNX3 is predicted to be the target of miR-130b, but binding assays and 3'UTR reporter assays have not been done to confirm this (Lai et al. 2010, Paudel et al. 2016).
Similar to RUNX1 and RUNX2, RUNX3 forms a transcriptionally active heterodimer with CBFB (CBF-beta) (Kim et al. 2013). RUNX3 activity can be regulated by changes in RUNX3 localization. SRC protein tyrosine kinase phosphorylates RUNX3 on multiple tyrosine residues, inhibiting its translocation from the cytosol to the nucleus and thus inhibiting RUNX3-mediated transcription (Goh et al. 2010). Subcellular localization of RUNX3 may be affected by PIM1-mediated phosphorylation (Kim et al. 2008).
The P1 and P2 promoters regulate RUNX3 transcription in a cell-type/differentiation dependent manner, giving rise to the p44 and p46 isoforms of RUNX3, respectively. Several splicing isoforms have also been reported. One example is the generation of a 33 kDa protein isoform (p33) by alternative splicing. The RUNX3 p33 isoform lacks the Runt domain and is unable to transactivate the regulatory regions of integrin genes. The p33 isoform is induced during maturation of monocyte-derived dendritic cells (MDDC), leading to reduced expression of genes involved in inflammatory responses, such as IL8 (interleukin-8) (Puig-Kroger et al. 2010).
E3 ubiquitin ligases MDM2 (Chi et al. 2009), SMURF1 and SMURF2 (Jin et al. 2004) are implicated in RUNX3 polyubiquitination and degradation.
R-HSA-9824878 Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 Production of type I IFN genes in response to Toll-like receptor 3 (TLR3) and TLR4 ligands is mediated by TANK-binding kinase 1 (TBK1) or I-kappa-B kinase epsilon (IKKε, IKBKE), which phosphorylate IFN regulatory factor 3 (IRF3) and IRF7. The activity of TBK1 and/or IRF3, IRF7 is regulated by multiple mechanisms including post-translational modifications, protein-protein interactions, and protein degradation (Zhao W et al., 2013; Runde AP et al., 2022).
This Reactome module describes regulation of TBK1, IKKε activity by K63-linked ubiquitination of TBK1 and IKKε, and TBK1 interaction with OPTN.
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R-HSA-9828211 Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation Production of type I IFN genes in response to Toll-like receptor 3 (TLR3) and TLR4 ligands is mediated by TANK-binding kinase 1 (TBK1) or I-kappa-B kinase epsilon (IKKε, IKBKE), which phosphorylate IFN regulatory factor 3 (IRF3) and IRF7. The activity of TBK1 and/or IRF3, IRF7 is regulated by multiple mechanisms including post-translational modifications, protein-protein interactions, and protein degradation (Zhao W et al., 2013; Runde AP et al., 2022).
This Reactome module describes regulation of TBK1, IKKε activity by K63-linked ubiquitination of TBK1 and IKKε, and TBK1 interaction with OPTN. R-HSA-5686938 Regulation of TLR by endogenous ligand Diverse molecules of host-cell origin may serve as endogenous ligands of Toll-like receptors (TLRs) (Erridge C 2010; Piccinini AM & Midwood KS 2010). These molecules are known as damage-associated molecular patterns (DAMPs). DAMPs are immunologically silent in healthy tissues but become active upon tissue damage during both infectious and sterile insult. DAMPs are released from necrotic cells or secreted from activated cells in response to tissue damage to mediate tissue repair by promoting inflammatory responses. However, DAMPs have also been implicated in the pathogenesis of many inflammatory and autoimmune diseases, including rheumatoid arthritis (RA), cancer, and atherosclerosis. The mechanism underlying the switch from DAMPs that initiate controlled tissue repair, to those that mediate chronic, uncontrolled inflammation is still unclear. Recent evidence suggests that an abnormal increase in protein citrullination is involved in disease pathophysiology (Anzilotti C et al. 2010; Sanchez-Pernaute O et al. 2013; Sokolove J et al. 2011; Sharma P et al. 2012). Citrullination is a post-translational modification event mediated by peptidyl-arginine deaminase enzymes which catalyze the deimination of proteins by converting arginine residues into citrullines in the presence of calcium ions. R-HSA-5357905 Regulation of TNFR1 signaling Tumor necrosis factor-alpha (TNFα) is an inflammatory cytokine, that activates either cell survival (e.g.,inflammation, proliferation) or cell death upon association with TNF receptor 1 (TNFR1). Stimuli and the cellular context dictate cell fate decisions between survival and death which rely on tightly regulated mechanisms with checkpoints on many levels. The TNFR1 signaling is controlled by the interplay between post-translational modifications such as proteolytic processing by active caspases or ubiquitination/deubiquitination by LUBAC or CYLD ubiquitin-editing complexes. TNFR1-mediated NFkappaB activation leads to the pro-survival transcriptional program that is both anti-apoptotic and highly proinflammatory. The constitutive NFkappaB or AP1 activation may lead to excessive inflammation which has been associated with a variety of aggressive tumor types (Jackson-Bernitsas DG et al. 2007; Zhang JY et al. 2007). Thus, the tight regulation of TNFα:TNFR1 signaling is required to ensure the appropriate cell response to stimuli. R-HSA-5633007 Regulation of TP53 Activity Protein stability and transcriptional activity of TP53 (p53) tumor suppressor are regulated by post-translational modifications that include ubiquitination, phosphorylation, acetylation, methylation, sumoylation and prolyl-isomerization (Kruse and Gu 2009, Meek and Anderson 2009, Santiago et al. 2013, Mantovani et al. 2015). In addition to post-translational modifications, the activity of TP53 is also regulated by binding of transcription co-factors.
In unstressed cells, TP53 protein levels are low due to MDM2-mediated ubiquitination of TP53, which triggers proteasome-mediated degradation. In response to stress, TP53 undergoes stabilizing phosphorylation, mainly at serine residues S15 and S20. Several different kinases can phosphorylate TP53 at these sites, but the main S15 kinases are considered to be ATM and ATR, while the main S20 kinases are considered to be CHEK2 and CHEK1. Additional phosphorylation of TP53 at serine residue S46 promotes transcription of pro-apoptotic, rather than cell cycle arrest genes.
Acetylation mainly has a positive impact on transcriptional activity of TP53, while methylation can both positively and negatively regulate TP53.
Some posttranslational modifications regulate interaction of TP53 with transcriptional co-factors, some of which are themselves transcriptional targets of TP53.
For review of the complex network of TP53 regulation, please refer to Kruse and Gu 2009, and Meek and Anderson 2009. R-HSA-6804758 Regulation of TP53 Activity through Acetylation Transcriptional activity of TP53 is positively regulated by acetylation of several of its lysine residues. BRD7 binds TP53 and promotes acetylation of TP53 lysine residue K382 by acetyltransferase EP300 (p300). Acetylation of K382 enhances TP53 binding to target promoters, including CDKN1A (p21), MDM2, SERPINE1, TIGAR, TNFRSF10C and NDRG1 (Bensaad et al. 2010, Burrows et al. 2010. Drost et al. 2010). The histone acetyltransferase KAT6A, in the presence of PML, also acetylates TP53 at K382, and, in addition, acetylates K120 of TP53. KAT6A-mediated acetylation increases transcriptional activation of CDKN1A by TP53 (Rokudai et al. 2013). Acetylation of K382 can be reversed by the action of the NuRD complex, containing the TP53-binding MTA2 subunit, resulting in inhibition of TP53 transcriptional activity (Luo et al. 2000). Acetylation of lysine K120 in the DNA binding domain of TP53 by the MYST family acetyltransferases KAT8 (hMOF) and KAT5 (TIP60) can modulate the decision between cell cycle arrest and apoptosis (Sykes et al. 2006, Tang et al. 2006). Studies with acetylation-defective knock-in mutant mice indicate that lysine acetylation in the p53 DNA binding domain acts in part by uncoupling transactivation and transrepression of gene targets, while retaining ability to modulate energy metabolism and production of reactive oxygen species (ROS) and influencing ferroptosis (Li et al. 2012, Jiang et al. 2015). R-HSA-6804759 Regulation of TP53 Activity through Association with Co-factors Association of TP53 (p53) with various transcriptional co-factors can promote, inhibit or provide specificity towards either transcription of cell cycle arrest genes or transcription of cell death genes. Binding of the zinc finger protein ZNF385A (HZF), which is a transcriptional target of TP53, stimulates transcription of cell cycle arrest genes, such as CDKN1A (Das et al. 2007). Binding of POU4F1 (BRN3A) to TP53 also stimulates transcription of cell cycle arrest genes while inhibiting transcription of pro-apoptotic genes (Budhram-Mahadeo et al. 1999, Hudson et al. 2005).
Binding of ASPP family proteins PPP1R13B (ASPP1) or TP53BP2 (ASPP2) to TP53 stimulates transcription of pro-apoptotic TP53 targets (Samuels-Lev et al. 2001, Bergamaschi et al. 2004). Binding of the ASPP family member PPP1R13L (iASSP) inhibits TP53-mediated activation of pro-apoptotic genes probably by interfering with binding of stimulatory ASPPs to TP53 (Bergamaschi et al. 2003). Transcription of pro-apoptotic genes is also stimulated by binding of TP53 to POU4F2 (BRN3B) (Budrham-Mahadeo et al. 2006, Budhram-Mahadeo et al. 2014) or to hCAS/CSE1L (Tanaka et al. 2007).
Binding of co-factors to TP53 can also affect protein stability. For example, PHF20 binds to TP53 dimethylated on lysine residues K370 and K382 by unidentified protein lysine methyltransferase(s) and interferes with MDM2 binding, resulting in prolonged TP53 half-life (Cui et al. 2012). Long noncoding RNAs can contribute to p53-dependent transcriptional responses (Huarte et al. 2010). For a general review on this topic, see Espinosa 2008, Beckerman and Prives 2010, Murray-Zmijewski et al. 2008, An et al. 2004 and Barsotti and Prives 2010. R-HSA-6804760 Regulation of TP53 Activity through Methylation TP53 (p53) undergoes methylation on several lysine and arginine residues, which modulates its transcriptional activity.
PRMT5, recruited to TP53 as part of the ATM-activated complex that includes TTC5, JMY and EP300 (p300), methylates TP53 arginine residues R333, R335 and R337. PRMT5-mediated methylation promotes TP53-stimulated expression of cell cycle arrest genes (Shikama et al. 1999, Demonacos et al. 2001, Demonacos et al. 2004, Adams et al. 2008, Adams et al. 2012). SETD9 (SET9) methylates TP53 at lysine residue K372, resulting in increased stability and activity of TP53 (Chuikov et al. 2004, Couture et al. 2006, Bai et al. 2011).
TP53 transcriptional activity is repressed by SMYD2-mediated methylation of TP53 at lysine residue K370 (Huang et al. 2006). Dimethylation of TP53 at lysine residue K373 by the complex of methyltransferases EHMT1 and EHMT2 also represses TP53-mediated transcription (Huang et al. 2010). The chromatin compaction factor L3MBTL1 binds TP53 monomethylated at lysine K382 by SETD8 (SET8) and, probably through changing local chromatin architecture, represses transcription of TP53 targets (West et al. 2010). The histone lysine-specific demethylase LSD1 interacts with TP53 and represses p53-mediated transcriptional activation (Huang et al. 2007). PRMT1 and CARM1 can also modulate p53 functions in a cooperative manner (An et al. 2004). R-HSA-6804756 Regulation of TP53 Activity through Phosphorylation Phosphorylation of TP53 (p53) at the N-terminal serine residues S15 and S20 plays a critical role in protein stabilization as phosphorylation at these sites interferes with binding of the ubiquitin ligase MDM2 to TP53. Several different kinases can phosphorylate TP53 at S15 and S20. In response to double strand DNA breaks, S15 is phosphorylated by ATM (Banin et al. 1998, Canman et al. 1998, Khanna et al. 1998), and S20 by CHEK2 (Chehab et al. 1999, Chehab et al. 2000, Hirao et al. 2000). DNA damage or other types of genotoxic stress, such as stalled replication forks, can trigger ATR-mediated phosphorylation of TP53 at S15 (Lakin et al. 1999, Tibbetts et al. 1999) and CHEK1-mediated phosphorylation of TP53 at S20 (Shieh et al. 2000). In response to various types of cell stress, NUAK1 (Hou et al. 2011), CDK5 (Zhang et al. 2002, Lee et al. 2007, Lee et al. 2008), AMPK (Jones et al. 2005) and TP53RK (Abe et al. 2001, Facchin et al. 2003) can phosphorylate TP53 at S15, while PLK3 (Xie, Wang et al. 2001, Xie, Wu et al. 2001) can phosphorylate TP53 at S20.
Phosphorylation of TP53 at serine residue S46 promotes transcription of TP53-regulated apoptotic genes rather than cell cycle arrest genes. Several kinases can phosphorylate S46 of TP53, including ATM-activated DYRK2, which, like TP53, is targeted for degradation by MDM2 (Taira et al. 2007, Taira et al. 2010). TP53 is also phosphorylated at S46 by HIPK2 in the presence of the TP53 transcriptional target TP53INP1 (D'Orazi et al. 2002, Hofmann et al. 2002, Tomasini et al. 2003). CDK5, in addition to phosphorylating TP53 at S15, also phosphorylates it at S33 and S46, which promotes neuronal cell death (Lee et al. 2007).
MAPKAPK5 (PRAK) phosphorylates TP53 at serine residue S37, promoting cell cycle arrest and cellular senescence in response to oncogenic RAS signaling (Sun et al. 2007).
NUAK1 phosphorylates TP53 at S15 and S392, and phosphorylation at S392 may contribute to TP53-mediated transcriptional activation of cell cycle arrest genes (Hou et al. 2011). S392 of TP53 is also phosphorylated by the complex of casein kinase II (CK2) bound to the FACT complex, enhancing transcriptional activity of TP53 in response to UV irradiation (Keller et al. 2001, Keller and Lu 2002).
The activity of TP53 is inhibited by phosphorylation at serine residue S315, which enhances MDM2 binding and degradation of TP53. S315 of TP53 is phosphorylated by Aurora kinase A (AURKA) (Katayama et al. 2004) and CDK2 (Luciani et al. 2000). Interaction with MDM2 and the consequent TP53 degradation is also increased by phosphorylation of TP53 threonine residue T55 by the transcription initiation factor complex TFIID (Li et al. 2004).
Aurora kinase B (AURKB) has been shown to phosphorylate TP53 at serine residue S269 and threonine residue T284, which is possibly facilitated by the binding of the NIR co-repressor. AURKB-mediated phosphorylation was reported to inhibit TP53 transcriptional activity through an unknown mechanism (Wu et al. 2011). A putative direct interaction between TP53 and AURKB has also been described and linked to TP53 phosphorylation and S183, T211 and S215 and TP53 degradation (Gully et al. 2012). R-HSA-6804757 Regulation of TP53 Degradation In unstressed cells, TP53 (p53) has a short half-life as it undergoes rapid ubiquitination and proteasome-mediated degradation. The E3 ubiquitin ligase MDM2, which is a transcriptional target of TP53, plays the main role in TP53 protein down-regulation (Wu et al. 1993). MDM2 forms homodimers and homo-oligomers, but also functions as a heterodimer/hetero-oligomer with MDM4 (MDMX) (Sharp et al. 1999, Cheng et al. 2011, Huang et al. 2011, Pant et al. 2011). The heterodimers of MDM2 and MDM4 may be especially important for downregulation of TP53 during embryonic development (Pant et al. 2011).
The nuclear localization of MDM2 is positively regulated by AKT- or SGK1- mediated phosphorylation (Mayo and Donner 2001, Zhou et al. 2001, Amato et al. 2009, Lyo et al. 2010). Phosphorylation of MDM2 by CDK1 or CDK2 decreases affinity of MDM2 for TP53 (Zhang and Prives 2001). ATM and CHEK2 kinases, activated by double strand DNA breaks, phosphorylate TP53, reducing its affinity for MDM2 (Banin et al. 1998, Canman et al. 1998, Khanna et al. 1998, Chehab et al. 1999, Chehab et al. 2000). At the same time, ATM phosphorylates MDM2, preventing MDM2 dimerization (Cheng et al. 2009, Cheng et al. 2011). Both ATM and CHEK2 phosphorylate MDM4, triggering MDM2-mediated ubiquitination of MDM4 (Chen et al. 2005, Pereg et al. 2005). Cyclin G1 (CCNG1), transcriptionally induced by TP53, targets the PP2A phosphatase complex to MDM2, resulting in dephosphorylation of MDM2 at specific sites, which can have either a positive or a negative impact on MDM2 function (Okamoto et al. 2002).
In contrast to MDM2, E3 ubiquitin ligases RNF34 (CARP1) and RFFL (CARP2) can ubiquitinate phosphorylated TP53 (Yang et al. 2007).
In addition to ubiquitinating MDM4 (Pereg et al. 2005), MDM2 can also undergo auto-ubiquitination (Fang et al. 2000). MDM2 and MDM4 can be deubiquitinated by the ubiquitin protease USP2 (Stevenson et al. 2007, Allende-Vega et al. 2010). The ubiquitin protease USP7 can deubiquitinate TP53, but in the presence of DAXX deubiquitinates MDM2 (Li et al. 2002, Sheng et al. 2006, Tang et al. 2006).
The tumor suppressor p14-ARF, expressed from the CDKN2A gene in response to oncogenic or oxidative stress, forms a tripartite complex with MDM2 and TP53, sequesters MDM2 from TP53, and thus prevents TP53 degradation (Zhang et al. 1998, Parisi et al. 2002, Voncken et al. 2005).
For review of this topic, please refer to Kruse and Gu 2009. R-HSA-6804754 Regulation of TP53 Expression Transcription of the TP53 (p53) gene is negatively regulated by the TP53 transcriptional target PRDM1 (BLIMP1), which binds to the promoter region of TP53 and probably induces repressive methylation (Yan et al. 2007).
TP53 functions as a homotetramer (Jeffrey et al. 1995, Waterman et al. 1995). R-HSA-6806003 Regulation of TP53 Expression and Degradation TP53 (p53) tumor suppressor protein is a transcription factor that functions as a homotetramer (Jeffrey et al. 1995). The protein levels of TP53 are low in unstressed cells due to MDM2-mediated ubiquitination that triggers proteasome-mediated degradation of TP53 (Wu et al. 1993). The E3 ubiquitin ligase MDM2 functions as a homodimer/homo-oligomer or a heterodimer/hetero-oligomer with MDM4 (MDMX) (Linares et al. 2003, Toledo and Wahl 2007, Cheng et al. 2011, Wade et al. 2013).
Activating phosphorylation of TP53 at serine residues S15 and S20 in response to genotoxic stress disrupts TP53 interaction with MDM2. In contrast to MDM2, E3 ubiquitin ligases RNF34 (CARP1) and RFFL (CARP2) can ubiquitinate phosphorylated TP53 (Yang et al. 2007). Binding of MDM2 to TP53 is also inhibited by the tumor suppressor p14-ARF, transcribed from the CDKN2A gene in response to oncogenic signaling or oxidative stress (Zhang et al. 1998, Parisi et al. 2002, Voncken et al. 2005). Ubiquitin-dependant degradation of TP53 can also be promoted by PIRH2 (Leng et al. 2003) and COP1 (Dornan et al. 2004) ubiquitin ligases. HAUSP (USP7) can deubiquitinate TP53, contributing to TP53 stabilization (Li et al. 2002).
While post-translational regulation plays a prominent role, TP53 activity is also controlled at the level of promoter function (reviewed in Saldana-Meyer and Recillas-Targa 2011), mRNA stability and translation efficiency (Mahmoudi et al. 2009, Le et al. 2009, Takagi et al. 2005). R-HSA-2029482 Regulation of actin dynamics for phagocytic cup formation The actin cytoskeleton is fundamental for phagocytosis and members of the Rho family GTPases RAC and CDC42 are involved in actin cytoskeletal regulation leading to pseudopod extension. Active RAC and CDC42 exert their action through the members of WASP family proteins (WASP/N-WASP/WAVE) and ARP2/3 complex. Actin filaments move from the bottom toward the top of the phagocytic cup during pseudopod extension. R-HSA-211733 Regulation of activated PAK-2p34 by proteasome mediated degradation Stimulation of cell death by PAK-2 requires the generation and stabilization of the caspase-activated form, PAK-2p34 (Walter et al., 1998;Jakobi et al., 2003). Levels of proteolytically activated PAK-2p34 protein are controlled by ubiquitin-mediated proteolysis. PAK-2p34 but not full-length PAK-2 is degraded by the 26 S proteasome (Jakobi et al., 2003). It is not known whether ubiquitination and degradation of PAK-2p34 occurs in the cytoplasm or in the nucleus. R-HSA-186712 Regulation of beta-cell development The normal development of the pancreas during gestation has been intensively investigated over the past decade especially in the mouse (Servitja and Ferrer 2004; Chakrabarti and Mirmira 2003). Studies of genetic defects associated with maturity onset diabetes of the young (MODY) has provided direct insight into these processes as they take place in humans (Fajans et al. 2001). During embryogenesis, committed epithelial cells from the early pancreatic buds differentiate into mature endocrine and exocrine cells. It is helpful to schematize this process into four consecutive cellular stages, to begin to describe the complex interplay of signal transduction pathways and transcriptional networks. The annotations here are by no means complete - factors in addition to the ones described here must be active, and even for the ones that are described, only key examples of their regulatory effects and interactions have been annotated.
It is also important to realize that in the human, unlike the mouse, cells of the different stages can be present simultaneously in the developing pancreas and the linear representation of these developmental events shown here is an over-simplification of the actual developmental process (e.g., Sarkar et al. 2008).
The first stage of this process involves the predifferentiated epithelial cells of the two pancreatic anlagen that arise from the definitive endoderm at approximately somite stages 11-15 and undergo budding from somite stages 20-22. This period corresponds to gestational days 8.75-9.5 in the mouse, and 26 in the human.
Pancreatic buds subsequently coalesce to form a single primitive gland, while concomitantly a ductal tree lined by highly proliferative epithelial cells is formed. A subset of such epithelial cells is thought to differentiate into either endocrine or acinar exocrine cells. A third cellular stage is defined by the endocrine-committed progenitors that selectively express the basic helix-loop-helix transcription factor NEUROG3. NEUROG3 is known to activate a complex transcriptional network that is essential for the specification of endocrine cells. Many transcription factors that are activated by NEUROG3 are also involved in islet-subtype cellular specification and in subsequent stages of differentiation of endocrine cells. This transient cellular stage thus leads to the generation of all known pancreatic endocrine cells, including insulin-producing beta-cells, and glucagon-producing alpha cells, the final stage of this schematic developmental process.
The diagram below summarizes interactions that take place between transcription factors and transcription factor target genes during these cellular stages, and shows cases where there is both functional evidence that a transcription factor is required for the target gene to be expressed, and biochemical evidence that this interaction is direct. We also describe instances where a signaling pathway is known to regulate a transcription factor gene in this process, even if the intervening signaling pathway is not fully understood.
R-HSA-1655829 Regulation of cholesterol biosynthesis by SREBP (SREBF) Sterol regulatory element binding proteins (SREBPs, SREBFs) respond to low cholesterol concentrations by transiting to the nucleus and activating genes involved in cholesterol and lipid biosynthesis (reviewed in Brown and Goldstein 2009, Osborne and Espenshade 2009, Weber et al. 2004).
Newly synthesized SREBPs are transmembrane proteins that bind SCAP in the endoplasmic reticulum (ER) membrane. SCAP binds cholesterol which causes a conformational change that allows SCAP to interact with INSIG, retaining the SCAP:SREBP complex in the ER. INSIG binds oxysterols, which cause INSIG to bind SCAP and retain SCAP:SREBP in the endoplasmic reticulum.
In low cholesterol (below about 5 mol%) SCAP no longer interacts with cholesterol or INSIG and binds Sec24 of the CopII coat complex instead. Thus SCAP:SREBP transits with the CopII complex from the ER to the Golgi. In the Golgi SREBP is cleaved by S1P and then by S2P, releasing the N-terminal fragment of SREBP into the cytosol. The N-terminal fragment is imported to the nucleus by importin-beta and then acts with other factors, such as SP1 and NF-Y, to activate transcription of target genes. Targets of SREBP include the genes encoding all enzymes of cholesterol biosynthesis and several genes involved in lipogenesis. SREBP2 most strongly activates cholesterol biosynthesis while SREBP1C most strongly activates lipogenesis.
R-HSA-428542 Regulation of commissural axon pathfinding by SLIT and ROBO Commissural axons project to the floor plate, attracted by the interaction of their DCC receptors with Netrin-1 (NTN1) produced by floor plate cells (Dickson and Gilestro 2006) and radial glia (Dominici et al. 2017, Varadarajan et al. 2017). Once an axon enters the floor plate, it must be efficiently expelled on the contralateral side. A switch from attraction to repulsion allows commissural axons to enter and then leave the CNS midline. Based on studies in Xenopus neurons and by yeast two hybrid screens, it is observed that the attractive response of axons to netrins is silenced by activation of ROBO. SLIT bound ROBO binds to DCC, preventing it from transducing an attractive response to netrin. The sensitivity of axons to the repulsive action of SLIT does not only depend on repulsive SLIT receptors (ROBO1 and ROBO2), but is also influenced by expression of ROBO3, a SLIT receptor that suppresses the activity of ROBO1 and ROBO2. Upon crossing the midline, commissural axons downregulate expression of ROBO3 and increase expression of ROBO1/ROBO2 (reviewed by Dickson and Gilestro, 2006). Two transcript variants of ROBO3, ROBO3.1 and ROBO3.2 are considered to play different roles in midline crossing. ROBO3.1 is expressed in the pre-crossing and crossing commissural axons, while ROBO3.2, generated by alternative splicing, is expressed after midline crossing and thought to block midline re-crossing (Chen et al. 2008). In addition to SLITs, a secreted ligand NELL2 also acts as an axonal guidance cue that, by acting through ROBO3 receptors, helps to steer commissural axons to the midline. Both ROBO3.1 and ROBO3.2 can bind to a secreted ligand NELL2. Pre-crossing commissural axons, which express ROBO3.1, are repelled by NELL2. Post-crossing axons, which express ROBO3.2 are not repelled by NELL2 (Jaworski et al. 2015). .
R-HSA-8985801 Regulation of cortical dendrite branching Besides being involved in axon repulsion during neuronal system development, SLIT-ROBO signaling is also involved in dendrite branching. Based on studies in mice, SLIT1 triggers cortical dendrite branching by activating receptors ROBO1 and/or ROBO2. ROBO effector NCK2 is needed for SLIT1-mediated dendrite branching (Round and Sun 2011).
R-HSA-446388 Regulation of cytoskeletal remodeling and cell spreading by IPP complex components The PINCH-ILK-Parvin complexes function in transducing diverse signals from ECM to intracellular effectors. Interacting partners for components of these complexes have been identified, a number of which regulate and/or mediate its functions in cytoskeletal remodeling and cell spreading (reviewed in Wu, 2004).
R-HSA-9842860 Regulation of endogenous retroelements Transposable elements (TEs) constitute about 48.34% of the human genome (Osmanski et al. 2023) and can be classified by their transposition mechanisms: DNA transposons (about 3% of the human genome) transpose by excising a DNA intermediate and inserting it into a new location; retrotransposons (about 33% of the human genome) transpose by transcribing an element, reverse transcribing the RNA to DNA, and inserting the DNA copy into a new location.
Retrotransposons can be divided into those that contain long terminal repeats (LTRs) and those that lack LTRs. Retrotransposons that contain LTRs are believed to be remnants of retroviruses, are therefore called endogenous retroviruses, and constitute about 9.45% of the human genome (Lander et al. 2001, Osmanski et al. 2023). No endogenous retroviruses are known to be currently transpositionally active in humans, with the most recent transpositions estimated to have occurred about 0.67 million years ago (Wildschutte et al. 2016).
Retrotransposons that lack LTRs constitute about 34% of the human genome and mostly have uncertain origins: Long interspersed nuclear elements (LINEs, about 18,99% of the genome) encode two proteins, an RNA-binding protein (ORF1p) and a reverse transcriptase/endonuclease (ORF2p), that confer autonomous transposition activity; short interspersed nuclear elements (SINEs, about 14.66% of the genome) do not encode proteins and require proteins produced in trans by LINEs for transposition (Lander et al. 2001). Of the 3 families of LINEs, only the LINE1 family is known to be currently active (Lander et al. 2001, Beck et al. 2010). Of the SINEs, only Alu elements, which evolved from the 7SL RNA of the signal recognition particle, are known to be currently active (Lander et al. 2001, Bennett et al. 2008).
Surprisingly, although retroelements can cause deleterious mutations due to insertions and recombination, their genomic elements and expression are required for embryogenesis. The envelope proteins ERVW-1 (Syncytin-1) of the HERV-W endogenous retrovirus and ERVFRD-1 (Syncytin-2) of the HERV-FRD endogenous retrovirus act to fuse cells in the trophoblast (reviewed in Gholami Barzoki et al. 2023). TEs contain binding sites for pluripotency factors (for example OCT4, SOX2, and NANOG) as well as cell lineage-specific factors (Pontis et al. 2022), In humans, a hominid-specific TE family, LTR5Hs, become transcriptionally active during specification of primordial germ cells (PGCs) and serve to bind PGC transcription factors (Xiang et al. 2022). In mice, the retroviral MERVL element is transcribed in cleavage-stage embryos and during this time MERVL regulatory DNA elements activate expression of more than one hundred genes involved in zygotic genome activation (Macfarlan et al. 2012, Sakashita et al. 2023, Yang et al. 2024). In mouse embryos, transcripts from LINE1 retroelements are required to exit the 2-cell stage by serving as scaffolds for Nucleolin (NCL) and TRIM28 (KAP1) to repress Dux expression and activate rRNA expression (Percharde et al. 2018, Chen et al. 2021). LINE1 elements are also active in expressing cell type-specific transcripts in the developing and adult human brain (Garza et al. 2023). By binding transcription activators, retroelements such as LTR5 and LTR7 can also act as cis-regulatory networks in somatic cells (reviewed in Sundaram and Wysocka 2020, Low et al. 2021, Fueyo et al. 2022).
Retroelements are generally silenced transcriptionally by DNA methylation and histone modifications (reviewed in Geis and Goff 2020, Carotti et al. 2023, Stamidis and Zylicz 2023) or post-transcriptionally by RNA interference (reviewed in Geis and Goff 2020), however repressive chromatin marks are lost and retroelements are transcribed at two points during mammalian development: in early germ cells prior to meiosis and in zygotes immediately after fertilization (reviewed in Low et al. 2021). In germ cells, small RNAs of 24-31 nucleotides known as PIWI-interacting RNAs (piRNAs) are generated from transcripts of retroelements and, when bound to PIWI proteins, guide post-transcriptional decay of retroelement transcripts and re-impose chromatin modifications that repress transcription of retroelements.
Endogenous retroelements are also transcriptionally silenced by zinc finger-containing proteins, KRAB-ZFPs, that bind specific DNA sequences (reviewed in Yang et al. 2017). The human genome contains 423 KRAB-ZFP genes that encode 742 KRAB-ZFP proteins that appear to evolve in response to invasion by retroelements (reviewed in Huntley et al. 2006, Lupo et al. 2013). Specific KRAB-ZFPs bind specific families of retroelements and recruit the TRIM28 scaffold protein (also known as KAP1), which assembles a complex containing the histone methylase SETDB1 and the NuRD repressor complex to silence transcription of the retroelements (reviewed in Almeida et al. 2022).
The Human Silencing Hub (HUSH) complex directly binds RNA of LINE1 elements and trimethylates lysine-9 of histone H3 (H3K9) of nucleosomes assembled on the LINE1 that produced the RNA (reviewed in Seczynska and Lehner 2023). Trimethyl H3K9 (H3K9me3) is a repressive mark thus the result is de novo formation of heterochromatin at LINE1 elements. The HUSH complex also binds H3K9me3 and trimethylates H3K9 of adjacent nucleosomes, resulting in propagation of heterochromatin (reviewed in Seczynska and Lehner 2023).
In mice, N6 methylation of adenosine residues in RNAs can cause destabilization of the RNA (Chelmicki et al. 2021) and transcriptional silencing of the locus that produced the RNA (Xu et al. 2021, Liu et al. 2021). The effect of N6-methyladenosine on expression of human retroelements is less clear. Xiong et al. (2021) observed that N6-methyladenosine in transcripts of young LINE1 elements increased RNA expression while N6-methyladenosine in transcripts of ancient LINE1 elements decreased RNA expression. The mechanism responsible for the difference may involve the promotion of translation of young LINE1 elements by N6-methyladenosine residues located in the 5' untranslated region (Hwang et al. 2021).
R-HSA-9843940 Regulation of endogenous retroelements by KRAB-ZFP proteins Krüppel-associated box domain (KRAB) zinc finger proteins (KRAB-ZFPs) contain a transcriptionally repressive N-terminal domain, the KRAB domain, and a C-terminal domain, the ZFP domain, that contains 2-40 zinc fingers and binds specific sequences of DNA (reviewed in Ecco et al. 2017, Yang et al. 2017). The human genome contains about 352 (Lukic et al. 2014), 378 (de Tribolet-Hardy et al. 2023), or 423 (Huntley et al. 2006) KRAB-ZFP genes, making them the largest family of transcription regulators.
About two thirds or more of KRAB-ZFPs bind transposable elements (Schmitges et al. 2016, Imbeault et al. 2017, de Tribolet-Hardy et al. 2023) and KRAB-ZFPs appear to coevolve with retroelements such that a KRAB-ZFP binds and transcriptionally silences a specific set of retroelements (reviewed in Ecco et al. 2017). The number of KRAB-ZFP genes correlates with the number of retroelements in mammalian genomes and younger retroelements bind fewer KRAB-ZFPs, suggesting an "arms race" in which the evolution of new KRAB-ZFPs is driven by and lags the appearance of new transposable elements (Thomas and Schneider 2011, Jacobs et al. 2014, Imbeault et al. 2017, reviewed in Ecco et al. 2017, Yang et al. 2017).
The repressive action of KRAB-ZFPs is mediated by the scaffold protein TRIM28 (also called KAP1), the RBCC domain of which binds the N-terminal KRAB domains of KRAB-ZFPs (Friedman et al. 1996). TRIM28 autoSUMOylates and recruits effectors, such as the histone H3 lysine-9 trimethyltransferase SETDB1 (also called ESET) (Schultz et al. 2002) and the NuRD repressor complex (Schultz et al. 2001).
The HUSH complex (MPHOSPH8:TASOR:PPHLN1) plays a nonredundant role with TRIM28 in silencing some young LINE1 retroelements, which are only weakly repressed by TRIM28 or HUSH alone (Robbez-Masson et al. 2018).
R-HSA-9845323 Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) PIWI-interacting RNAs (piRNAs) are short RNAs of 24-31 nucleotides that are produced by cleavage of longer RNAs and amplification by a "ping-pong" mechanism involving rounds of strand hybridization and cleavage (reviewed in Sun et al. 2022). The piRNAs are loaded onto PIWI proteins (PIWIL1, PIWIL2, PIWIL4) that are then guided by base-pairing of the piRNAs to nascent and mature transcripts, where the PIWI:piRNA complexes initiate transcriptional and post-transcriptional silencing, respectively (reviewed in Czech et al. 2018, Onishi et al. 2021, Wang et al. 2023).
In mice, sources of piRNAs include transposon RNAs, long non-coding RNAs, exon transcripts, and RNAs from unannotated regions of the genome (Aravin et al. 2007, 2008). Two populations of piRNAs are observed during mouse development: pre-pachytene piRNAs and pachytene piRNAs (Aravin et al. 2008, Gan et al. 2011). Pre-pachytene piRNAs are present prenatally in prospermatogonial cells and postnatally in spermatogonial cells. Pachytene piRNAs are present in more mature postnatal spermatocytes and spermatids. The piRNAs derived from retroelements comprise about half (Aravin et al. 2008) or less (Gan et al. 2011) of the total pre-pachytene piRNAs and the portion falls sharply from pre-pachytene to pachytene (Gan et al. 2011).
In mice, PIWIL2 (MILI, Piwil2 gene) is first detected in primordial germ cells that have reached the genital ridge and expression persists through meiosis in adults. PIWIL4 (MIWI2, PIWIl4 gene) is present in mouse germ cells during de novo DNA methylation shortly before and after birth. PIWIL1 (MIWI, PIWIL1 gene) is present during later stages of meiosis after birth (Aravin et al. 2008). PIWIL4 and PIWIL2 participate in re-methylation of the genome in mouse germ cells and consequent repression of transposable elements (Carmell et al. 2007, Aravin et al. 2008, Kuramochi-Miyagawa et al. 2008, Zoch et al. 2020). In mice, the piRNAs bound by PIWIL4 bind nascent transcripts of transposable elements and connects to the de novo DNA methylation machinery via SPOCD1 and C19ORF84 to direct DNA methylation to the transposable elements (Zoch et al. 2020, 2024). Mutations in SPOCD1 are associated with infertility in men (Zoch et al. 2024)
R-HSA-9843970 Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex The Human Silencing Hub (HUSH) complex comprises MPHOSPH8 (MPP8), Periphilin (PHPLN1), and TASOR, which appears to act as a scaffold that binds the other subunits (reviewed in Seczynska and Lehner 2023). The HUSH complex preferentially represses transcription of young LINE1 retroelements (Liu et al. 2018, Robbez-Masson et al. 2018) and some HIV integrants (Tchasovnikarova et al. 2015, Zhu et al. 2018, Chougui and Margottin-Goguet 2019).
The HUSH complex creates repressive chromatin in two ways (reviewed in Seczynska and Lehner 2023). Firstly, HUSH can cause spreading of existing heterochromatin by binding existing trimethylated H3K9 and recruiting SETDB1 to trimethylate H3K9 of adjacent nucleosomes (Tchasovnikarova et al. 2015). Secondly, HUSH can initiate heterochromatin by binding nascent transcripts via its PHPLN1 subunit and recruiting SETDB1 to trimethylate lysine-9 of histone H3 (H3K9) at the locus being transcribed (Seczynska et al. 2022).
By an uncharacterized mechanism, the HUSH complex targets long intronless cDNAs, such as those produced by retroelements, as well as unusually long exons of normal cellular genes (Seczynska et al. 2022). Introns somehow protect against silencing by HUSH, though actual splicing is not required (Seczynska et al. 2022). In mice, ZNF638 (NP220, Znf638 gene) recruits the HUSH complex to unintegrated murine leukemia virus (MLV) (Zhu et al. 2018) and in human cells ZNF638 (NP220) and HUSH silence recombinant adeno-associated viruses (Das et al. 2022). The potential recruitment of HUSH by ZNF638 to human retroelements is not yet demonstrated.
R-HSA-9010553 Regulation of expression of SLITs and ROBOs Expression of SLIT and ROBO proteins is regulated at the level of transcription, translation and protein localization and stability. LIM-homeodomain transcription factors LHX2, LHX3, LHX4, LHX9 and ISL1 have so far been implicated in a cell type-dependent transcriptional regulation of ROBO1, ROBO2, ROBO3 and SLIT2 (Wilson et al. 2008, Marcos-Mondejar et al. 2012, Kim et al. 2016). Homeobox transcription factor HOXA2 is involved in transcriptional regulation of ROBO2 (Geisen et al. 2008). Transcription of SLIT1 during optic tract development in Xenopus is stimulated by FGF signaling and may also involve the transcription factor HOXA2, but the mechanism has not been established (Atkinson-Leadbeater et al. 2010). PAX6 and the homeodomain transcription factor NKX2.2 are also implicated in regulation of SLIT1 transcription (Genethliou et al. 2009). An RNA binding protein, MSI1, binds ROBO3 mRNA and promotes its translation, thus increasing ROBO3 protein levels (Kuwako et al. 2010). A poorly studied E3 ubiquitin ligase ZSWIM8 promotes degradation of ROBO3 (Wang et al. 2013). ROBO1 is protein half-life is increased via deubiquitination of ROBO1 by a ubiquitin protease USP33 (Yuasa-Kawada et al. 2009, Huang et al. 2015). Interaction of SLIT2 with DAG1 (dystroglycan) is important for proper localization of SLIT2 at the floor plate (Wright et al. 2012). Interaction of SLIT1 with a type IV collagen COL4A5 is important for localization of SLIT1 to the basement membrane of the optical tectum (Xiao et al. 2011).
R-HSA-191650 Regulation of gap junction activity Src is believed to suppress gap junction communication by phosphorylating Cx43. The kinases c-Src (Giepmans et al. 2001; Sorgen et al. 2004), PKc (Lin et al. 2003) and MAPK (Mograbi et al. 2003) play an essential role in the phosphorylation of Cx which leads to its degradation. c-Src appears to associate with and phosphorylate Cx43 leading to closure of gap junctions. Evidence suggests that v-src may activate MAPK, which in turn phosphorylates Cx43 on serine sites leading to channel gating (Zhou et al. 1999).
R-HSA-1234158 Regulation of gene expression by Hypoxia-inducible Factor HIF-alpha (HIF1A, HIF2A (EPAS1), HIF3A) is translocated to the nucleus, possibly by two pathways: importin 4/7 (Chachami et al. 2009) and importin alpha/beta (Depping et al. 2008). Once in the nucleus HIF-alpha heterodimerizes with HIF-beta (ARNT) (Wang et al. 1995, Jiang et al. 1996, Tian et al. 1997, Gu et al. 1998, Erbel et al. 2003) and recruits CBP and p300 to promoters of target genes (Ebert and Bunn 1998, Kallio et al. 1998, Ema et al. 1999, Gu et al. 2001, Dames et al. 2002, Freedman et al. 2002).
R-HSA-210745 Regulation of gene expression in beta cells Two transcription factors, PDX1 and HNF1A, play key roles in maintaining the gene expression pattern characteristic of mature beta cells in the endocrine pancreas. Targets of these regulatory molecules include genes encoding insulin, the GLUT2 glucose transporter, the liver- (and pancreas) specific form of pyruvate kinase and other transcription factors including HNF4A, HNF4G, and FOXA3. PDX1 expression in turn is controlled by the activities of MAFA, FOXA2, and PAX6, and negatively regulated via AKT (Chakrabarti and Mirmira 2003; Servitja and Ferrer 2004).
R-HSA-210747 Regulation of gene expression in early pancreatic precursor cells The properties of transcriptional networks early in the differentiation of human pancreatic cells are inferred from the properties of well-studied networks in mouse models. In mice, the first visible sign of pancreatic development is the appearance of pancreatic buds at about embryonic day 9. The cells in these buds are already committed to differentiate into specialized cells of the exocrine and endocrine pancreas. Expression of transcription factors including Hnf1b, Hnf6, and Pdx1, as well as responsiveness to Fgf10 (fibroblast growth factor 10), up-regulates the expression of factors including Ptf1, Onecut3, Lrh1, and Nkx6.1 (Servitja and Ferrer 2004; Chakrabarti and Mirmira 2003).
R-HSA-210746 Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells Studies in mouse model systems indicate that the transcription factor neurogenin 3 plays a central role in the induction of endocrine differentiation in the developing pancreas (Servitja and Ferrer 2004; Chakrabarti and Mirmira 2003). In both mice and humans critical events in this induction process include the neurogenin 3 (NEUROG3)-dependent transcription of PAX4, NEUROD1, NKX2-2, and INSM1.
R-HSA-210744 Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells The properties of transcriptional networks in late stage (branching morphogenesis) pancreatic bud precursor cells are inferred from the properties of well-studied networks in mouse models. In mice, committed but undifferentiated epithelial cells are organized into branching ductal structures. At a molecular level, expression of Pdx1, Nkx2.2, and Nkx6.1 is reduced while Hnf6 expression remains high. Hnf6 mediates the continued expression of Onecut3 and Hnf1 beta and epithelial cell proliferation. As expression of Ngn3 (corresponds to human NEUROG3) rises, endocrine differentiation of the epithelial cells begins (Servitja and Ferrer 2004; Chakrabarti and Mirmira 2003).
R-HSA-9634600 Regulation of glycolysis by fructose 2,6-bisphosphate metabolism The committed step of glycolysis is the phosphorylation of D-fructose 6-phosphate (Fru(6)P) to form D-fructose 1,6-bisphosphate, catalyzed by phosphofructokinase 1 (PFK) tetramer. PFK can be allosterically activated by D-fructose 2,6-bisphosphate whose levels are increased in response to insulin signaling and decreased in response to glucagon signaling, through the reactions annotated here (Pilkis et al. 1995).
R-HSA-3134975 Regulation of innate immune responses to cytosolic DNA Innate immune responses are coordinated and regulated to provide an efficient first line of defense against pathogens and at the same time to prevent host self-damage. Here we present some regulatory events involved in the detection of cytosolic nucleic acids.
R-HSA-422356 Regulation of insulin secretion Pancreatic beta cells integrate signals from several metabolites and hormones to control the secretion of insulin. In general, glucose triggers insulin secretion while other factors can amplify or inhibit the amount of insulin secreted in response to glucose. Factors which increase insulin secretion include the incretin hormones Glucose-dependent insulinotropic polypeptide (GIP and glucagon-like peptide-1 (GLP-1), acetylcholine, and fatty acids. Factors which inhibit insulin secretion include adrenaline and noradrenaline.
Increased blood glucose levels from dietary carbohydrate play a dominant role in insulin release from the beta cells of the pancreas. Glucose catabolism in the beta cell is the transducer that links increased glucose levels to insulin release. Glucose uptake and glycolysis generate cytosolic pyruvate; pyruvate is transported to mitochondria and converted both to oxaloacetate which increases levels of TCA cycle intermediates, and to acetyl-CoA which is oxidized to CO2 via the TCA cycle. The rates of ATP synthesis and transport to the cytosol increase, plasma membrane ATP-sensitive inward rectifying potassium channels (KATP channels) close, the membrane depolarizes, and voltage-gated calcium channels in the membrane open (Muoio and Newgard 2008; Wiederkehr and Wollheim 2006).
Elevated calcium concentrations near the plasma membrane cause insulin secretion in two phases: an initial high rate within minutes of glucose stimulation and a slow, sustained release lasting longer than 30 minutes. In the initial phase, 50-100 insulin granules already docked at the membrane are exocytosed. Exocytosis is rendered calcium-dependent by Synaptotagmin V/IX, a calcium-binding membrane protein located in the membrane of the docked granule, although the exact action of Synapototagmin in response to calcium is unknown. Calcium also causes a translocation of reserve granules within the cell towards the plasma membrane for release in the second, sustained phase of secretion. Human cells contain L-type (continually reopening), P/Q-type (long burst), R-type (long burst), and T-type (short burst) calcium channels and these partly account for differences between the two phases of secretion. Other factors that distinguish the two phases are not yet fully known (Bratanova-Tochkova et al. 2002; Henquin 2000; MacDonald et al. 2005).
R-HSA-400206 Regulation of lipid metabolism by PPARalpha Peroxisome proliferator-activated receptor alpha (PPAR-alpha) is the major regulator of fatty acid oxidation in the liver. PPARalpha is also the target of fibrate drugs used to treat abnormal plasma lipid levels.
PPAR-alpha is a type II nuclear receptor (its subcellular location does not depend on ligand binding). PPAR-alpha forms heterodimers with Retinoid X receptor alpha (RXR-alpha), another type II nuclear receptor. PPAR-alpha is activated by binding fatty acid ligands, especially polyunsaturated fatty acids having 18-22 carbon groups and 2-6 double bonds.
The PPAR-alpha:RXR-alpha heterodimer binds peroxisome proliferator receptor elements (PPREs) in and around target genes. Binding of fatty acids and synthetic ligands causes a conformational change in PPAR-alpha such that it releases the corepressors and binds coactivators (CBP-SRC-HAT complex, ASC complex, and TRAP-Mediator complex) which initiate transcription of the target genes.
Target genes of PPAR-alpha participate in fatty acid transport, fatty acid oxidation, triglyceride clearance, lipoprotein production, and cholesterol homeostasis.
R-HSA-9614399 Regulation of localization of FOXO transcription factors Localization of FOXO transcription factors FOXO1, FOXO3 and FOXO4 is regulated by AKT-mediated phosphorylation. In the absence of PI3K/AKT signaling, FOXO1, FOXO3 and FOXO4 localize to the nucleus. AKT-mediated phosphorylation induces a conformational change that exposes a nuclear export signal (NES) and promotes translocation of FOXO1, FOXO3 and FOXO4 to the cytosol (Rena et al. 1999, Brunet et al. 1999, Kops et al. 1999). AKT-phosphorylated FOXO1, FOXO3 and FOXO4 bind to 14-3-3 proteins, which contributes to their retention in the cytosol (Rena et al. 2001, Brunet et al. 1999, Arimoto Ishida et al. 2004, Obsilova et al. 2005, Boura et al. 2007, Silhan et al. 2009). FOXO6 lacks the NES sequence and is exclusively nuclear, but phosphorylation in response to PI3K/AKT signaling affects the transcriptional activity of FOXO6 (Jacobs et al. 2003, van der Heide et al. 2005).
R-HSA-450531 Regulation of mRNA stability by proteins that bind AU-rich elements RNA elements rich in adenine and uracil residues (AU-rich elements) bind specific proteins which either target the RNA for degradation or, more rarely, stabilize the RNA. The activity of the AU-element binding proteins is regulated, usually by phosphorylation but also by subcellular localization.
R-HSA-453276 Regulation of mitotic cell cycle Regulation of mitotic cell cycle currently covers APC/C-mediated degradation of cell cycle proteins.
R-HSA-5675482 Regulation of necroptotic cell death A regulated balance between cell survival and cell death is essential for normal development and homeostasis of multicellular organisms. Defects in control of this balance may contribute to autoimmune disease, neurodegeneration, ischemia/reperfusion injury, non alcoholic steatohepatitis (NASH) and cancer.
R-HSA-350562 Regulation of ornithine decarboxylase (ODC) Polyamines increase the production of antizyme (AZ). The carboxy-terminal half of antizyme interacts with ODC, generating an inactive AZ:ODC heterodimer complex. A carboxy-terminal domain of ODC is exposed only within the heterodimer, and is the target for subsequent degradation. A domain within the amino-terminal portion of antizyme provides a function needed for efficient degradation of ODC by the proteasome.
The proteasome cycle starts with the processing of AZ:ODC, sequestering ODC and then degrading it to peptides but releasing AZ. AZ participates in additional rounds of binding and degradation. Antizyme-mediated inhibition and destruction of ODC reduces synthesis of polyamines. Additionally, antizyme also inhibits polyamine transport into the cell. Antizyme production is reduced, completing the regulatory circuit (Coffino, 2001).
The following illustration is adapted from a minireview by Pegg, 2006; J. Biol. Chem., Vol. 281, Issue 21, 14529-14532.
R-HSA-204174 Regulation of pyruvate dehydrogenase (PDH) complex The mitochondrial pyruvate dehydrogenase (PDH) complex catalyzes the oxidative decarboxylation of pyruvate, linking glycolysis to the tricarboxylic acid cycle and fatty acid synthesis. PDH inactivation is crucial for glucose conservation when glucose is scarce, while adequate PDH activity is required to allow both ATP and fatty acid production from glucose. The mechanisms that control human PDH activity include its phosphorylation (inactivation) by pyruvate dehydrogenase kinases (PDK 1-4) and its dephosphorylation (activation, reactivation) by pyruvate dehydrogenase phosphate phosphatases (PDP 1 and 2). Isoform-specific differences in kinetic parameters, regulation, and phosphorylation site specificity of the PDKs introduce variations in the regulation of PDC activity in differing endocrine and metabolic states (Sugden and Holness 2003). Further, PDH is inhibited by SIRT4 and the drug dichloroacetic acid (DCA).
R-HSA-9861718 Regulation of pyruvate metabolism This subpathway collects reactions regulating pyruvate metabolism.
R-HSA-912631 Regulation of signaling by CBL Cbl is an E3 ubiquitin-protein ligase that negatively regulates signaling pathways by targeting proteins for ubiquitination and proteasomal degradation (Rao et al. 2002). Cbl negatively regulates PI3K via this mechanism (Dufour et al. 2008). The binding of Cbl to the p85 subunit of PI3K is mediated at least in part by tyrosine phosphorylation at Y731 (Dufour et al. 2008). Fyn and the related kinases Hck and Lyn are known to be associated with Cbl (Anderson et al. 1997, Hunter et al. 1999). Fyn is proven capable of Cbl Y731 phosphorylation (Hunter et al. 1999).The association of Fyn and Cbl has been described as constitutive (Hunter et al. 1999). CBL further associates with the p85 subunit of PI3K (Hartley et al. 1995, Anderson et al. 1997, Hunter et al. 1997), this also described as constitutive and mediated by the SH3 domain of p85. Binding of the SH2 domain of p85 to a specific phosphorylation site in Cbl is postulated to explain the the increase in Cbl/p85 association seen in activated cells (Panchamoorthy et al 1996) which negatively regulates PI3K activity (Fang et al. 2001). The negative effect of increased Cbl-PI3K interaction is mediated by Y731 of Cbl. Cbl binding increases PI3K ubiquitination and proteasome degradation (Dufour et al. 2008).
Cbl is constitutively associated with Grb in resting hematopoietic cells (Anderson et al. 1997, Odai et al. 1995, Park et al. 1998, Panchamoorthy et al. 1996). Both the SH2 and SH3 domains of Grb2 are involved. Cbl has 2 distinct C-terminal domains, proximal and distal. The proximal domain binds Grb2 in resting and stimulated cells, and in stimulated cells also binds Shc. The distal domain binds the adaptor protein CRKL. Tyrosine phosphorylation of Cbl in response to IL-3 releases the SH3 domain of Grb2 which then is free to bind other molecules (Park et al. 1998). Cbl is tyrosine phosphorylated in response to many cytokines including IL-3, IL-2 (Gesbert et al. 1998) and IL-4 (Ueno et al. 1998).
R-HSA-1433617 Regulation of signaling by NODAL Mature NODAL can form heterodimers with LEFTY1, LEFTY2, or CERBERUS. The heterodimers do not activate the NODAL receptor. LEFTY1 and LEFTY2 also bind CRIPTO and CRYPTIC coreceptors and prevent them from interacting with other components of the NODAL receptor. By these mechanisms LEFTY1, LEFTY2, and CERBERUS negatively regulate NODAL signaling (reviewed in Shen 2007, Schier 2009).
R-HSA-9627069 Regulation of the apoptosome activity Apoptosis is a controlled process of cell death, which must be tightly regulated to ensure that potentially dangerous cells are efficiently removed, while cells that are transiently stressed by environmental conditions can recover and survive (Bratton SB & Salvesen GS 2010). Defects in the regulation of apoptosis have been associated with the pathogenesis of disease states such as neurodegeneration and cancer (Favaloro B et al. 2012). The mitochondrial or intrinsic apoptotic pathway is regulated at multiple steps, including apoptosome formation and caspase‑9 activation.
R-HSA-350864 Regulation of thyroid hormone activity The iodothyronine deiodinases (DIO) are dimeric, membrane-bound enzymes that regulate the activity of thyroid hormone by removal of specific iodines from the precursor T4. There are three types of DIOs in humans; types I, II and III (D1, D2 and D3 respectively) which are proteins of about 250 residues that contain a selenocysteine at their active site. Signaling by thyroid hormone can change in individual tissues by this activation or inactivation process, even when serum concentrations of the hormone remain normal. Generally, cell types express just one type of DIO at any one time. The exception is the pituitary gland which expresses all three.
R-HSA-444821 Relaxin receptors Relaxins are part of a family of peptide hormones that diverged from insulin in early vertebrate evolution to form the insulin-like peptides and relaxins, now often referred to as the relaxin peptide family. All are heterodimers; both chains are cleaved from a common propeptide and cross-linked by 2 disulphide bonds. Humans have 3 true relaxins encoded by 3 related genes, plus several more distantly related insulin-like peptide genes. Non-primates have 2 relaxin genes. The major circulating form of relaxin in humans is relaxin-2, equivalent to relaxin-1 in non-primates. Relaxin-3 is very highly conserved. Little is known about human relaxin-1; several of the insulin-like peptides have no known receptor or function.
There are 4 human G-protein coupled receptors for relaxin family peptides. Relaxin receptor 1 (RXFP1) and relaxin receptor 2 (RXFP2) are also known as LGR7 and LGR8 respectively, members of the LRR-containing G protein-coupled receptors (LGRs). Relaxin-3 receptor 1 (RXFP3) and Relaxin-3 receptor 2 (RXFP4) are unrelated, having more homology with small peptide receptors such as the somatostatin receptors.
R-HSA-168298 Release Once the viral envelope has separated from the cell membrane Influenza virus particles are actively released to complete the budding process. HA (hemagglutinin) anchors the virus to the cell by binding to sialic acid-containing receptors on the cell surface. The enzymatic activity of the neuraminidase (NA) protein removes the sialic acid and releases the virus from the host cell. NA activity is also required to remove sialic acid from the carbohydrates present on the viral glycoproteins to prevent the viral particles from aggregating.
R-HSA-5362798 Release of Hh-Np from the secreting cell Cholesterol and palmitoyl-modification of Hh-Np render the ligand highly hydrophobic and results in its close association with the plasma membrane of the producing cell after secretion. Hh-Np tethered in this way may cluster in sterol-rich lipid rafts where it is competent for short-range signaling. Cell surface Hh-Np also interacts with glypican components of the extracellular matrix and this interaction stabilizes the ligand and is required for its lateral spread. Together, clustering into lipid rafts and interaction with HSPGs may favour packaging of ligand into higher order forms required for ligand dispersal.
Long-range signaling requires release of Hh-Np from the secreting cell. Release is achieved through a number of possibly overlapping mechanisms. These include oligomerization into micelle-like structures, packaging into lipoprotein particles and interaction with cholesterol-binding adaptor proteins such as DISP and SCUBE2. In addition, Hh-Np can be released from the plasma membrane through proteolytic cleavage: NOTUM is a secreted enzyme that is thought to promote the release of Hh-Np by cleaving the GPI anchor of Hh-associated glypicans, while the transmembrane metalloprotease ADAM17 promotes long-range Hh signaling by removing the palmitoyl- and cholesterol-modified N- and C-termini of the membrane-associated ligand. How all these mechanisms are coordinated remains to be elucidated (reviewed in Briscoe and Therond, 2013; Gallet, 2011).
R-HSA-111457 Release of apoptotic factors from the mitochondria Apoptotic factors released from the mitochondria promote apoptosis through several different mechanisms. Cytochrome C participates in Apoptosome driven effector caspase activation while SMAC relieves IAP mediated caspase inhibition.
R-HSA-159782 Removal of aminoterminal propeptides from gamma-carboxylated proteins Furin is an endopeptidase localized to the Golgi membrane that cleaves many proteins on the carboxyterminal side of the sequence motif Arg-[any residue]-(Lys or Arg)-Arg (Jones et al. 1995; Leduc et al. 1992). In the case of gamma-carboxylated proteins, if this cleavage does not occur, the proteins are still secreted but do not function properly (Bristol et al. 1993; Lind et al. 1997; Wasley et al. 1993). The aminoterminal fragments, "propeptides", generated in this reaction have no known function; the carboxylated, cleaved proteins are delivered to the cell membrane or secreted from the cell.
R-HSA-69166 Removal of the Flap Intermediate Two endonucleases, Dna2 and flap endonuclease 1 (FEN-1), are responsible for resolving the nascent flap structure (Tsurimoto and Stillman 1991). The Dna2 endonuclease/helicase in yeast is a monomer of approximately 172 kDa. Human FEN-1 is a single polypeptide of approximately 42 kDa. Replication Protein A regulates the switching of endonucleases during the removal of the displaced flap (Tsurimoto et al.1991).
R-HSA-174437 Removal of the Flap Intermediate from the C-strand Two endonucleases, Dna2 and flap endonuclease 1 (FEN-1), are responsible for resolving the nascent flap structure (Tsurimoto and Stillman 1991). The Dna2 endonuclease/helicase in yeast is a monomer of approximately 172 kDa. Human FEN-1 is a single polypeptide of approximately 42 kDa. Replication Protein A regulates the switching of endonucleases during the removal of the displaced flap (Tsurimoto et al.1991).
R-HSA-9821993 Replacement of protamines by nucleosomes in the male pronucleus In human sperm, about 85 to 90% of the genome is associated with protamines rather than histones (reviewed in Torres-Flores and Hernández-Hernández 2020, Ribas-Maynou et al. 2022). Protamines provide a much higher packing density of DNA in the nucleus but there are few reports of epigenetic marks on protamines (Brunner et al. 2014). After fertilization, protamines in the male pronucleus are replaced with histones provided by the oocyte cytoplasm (reviewed in Yang et al. 2015, Okada and Yamaguchi 2017). The result is a decondensation of sperm chromatin that produces a chromatin state that is permissive for transcription.
Dissociation of protamines from DNA appears to be controlled by phosphorylation of the protamines PRM1 and PRM2 (inferred from mouse homologs in Gou et al. 2020). The kinase SRPK1 phosphorylates both PRM1 and PRM2, which recruit the histone chaperones Nucleoplasmin 2 (NPM2) and HIRA (inferred from mouse homologs in Gou et al. 2020). NPM2 then dissociates the phosphorylated PRM1 from DNA. By inference NPM1 and NPM3, which are also present in the zygote, may also dissociate PRM1 and PRM2 from DNA (Okuwaki et al. 2012).
Nucleosomes in the zygote are characterized by H3.3 and H2AX (H2A.X) (reviewed in Martire and Banaszynski 2020). HIRA chaperones histone H3.3 and acts together with NPM proteins to assemble nucleosomes from individual histone proteins. Asymmetric dimethylation of H3.3 arginine-17 catalyzed by METTL23 is required for assembly of H3.3 into chromatin in the male pronucleus (inferred from mouse homologs in Hatanaka et al. 2017) . The oocyte-specific histone H1, H1FOO (H1.8, H1-8), is also deposited on the newly formed chromatin at this time and persists until the 8-cell stage (McGraw et al. 2006). In mouse embryos, H1foo is not required for development (Sánchez-Sáez et al. 2022).
R-HSA-9682706 Replication of the SARS-CoV-1 genome The plus strand RNA genome of the human SARS coronavirus 1 (SARS-CoV-1) is replicated by the viral replication-transcription complex (RTC) composed of nonstructural proteins nsp3-nsp16, encoded by open reading frames ORF1a and ORF1b. Two RTC proteins, nsp8 and nsp12, possess 5'-3' RNA-dependent RNA polymerase activity. nsp12 is the main RNA polymerase, while nsp8 is thought to act as an RNA primase. nsp14 acts as a 3'-5' exonuclease, increasing the fidelity of the RTC. nsp14 also has the RNA capping activity and, in concert with nsp16, it caps viral plus strand and minus strand genomic and subgenomic RNAs, which confers stability to viral RNAs by enabling them to escape interferon-mediated innate immune responses of the host. nsp13 is an RNA helicase which is thought to melt secondary structures in the genomic RNA during replication and transcription. The plus strand genomic RNA is first used to synthesize the minus strand genomic RNA complement, which is subsequently used as a template for synthesis of plus strand viral RNA genomes that are packaged into mature virions. For review, please refer to Yang and Leibowitz 2015, Snijder et al. 2016, Fung and Liu 2019.
R-HSA-9694686 Replication of the SARS-CoV-2 genome This COVID-19 pathway has been created by a combination of computational inference from SARS-CoV-1 data (https://reactome.org/documentation/inferred-events) and manual curation, as described in the summation for the overall SARS-CoV-2 infection pathway. Steps of SARS-CoV-2 genome replication that have been studied directly include binding of the replication transcription complex (RTC) to the RNA template and the polymerase activity of nsp12 (Hillen et al. 2020, Wang et al. 2020, Yin et al. 2020), helicase activity of nsp13 (Chen et al. 2020, Ji et al. 2020, Shu et al. 2020), capping activity of nsp16 (Viswanathan et al. 2020), and polyadenylation of SARS-CoV-2 genomic RNA (Kim et al. 2020). Replication is localized in double-membrane vesicles (DMVs) that are created by distortion of ER membranes (Cortese et al, 2020; Snijder et al, 2020). One host factor needed for formation of these replication organelles is phosphatidic acid (Tabata et al, 2021). Other steps have been inferred from previous studies in SARS-CoV-1 and related coronaviruses.
The plus strand RNA genome of the human SARS coronavirus 1 (SARS-CoV-1) is replicated by the viral replication-transcription complex (RTC) composed of nonstructural proteins nsp3-nsp16, encoded by open reading frames ORF1a and ORF1b. Two RTC proteins, nsp8 and nsp12, possess 5'-3' RNA-dependent RNA polymerase activity. nsp12 is the main RNA polymerase, while nsp8 is thought to act as an RNA primase. nsp14 acts as a 3'-5' exonuclease, increasing the fidelity of the RTC. nsp14 also has the RNA capping activity and, in concert with nsp16, it caps viral plus strand and minus strand genomic and subgenomic RNAs, which confers stability to viral RNAs by enabling them to escape interferon-mediated innate immune responses of the host. nsp13 is an RNA helicase which is thought to melt secondary structures in the genomic RNA during replication and transcription. The plus strand genomic RNA is first used to synthesize the minus strand genomic RNA complement, which is subsequently used as a template for synthesis of plus strand viral RNA genomes that are packaged into mature virions. For review, please refer to Yang and Leibowitz 2015, Snijder et al. 2016, Fung and Liu 2019.
R-HSA-4641265 Repression of WNT target genes In the absence of a WNT signal, many WNT target genes are repressed by Groucho/TLE. Groucho was initially identified in Drosophila, where it has been shown to interact with a variety of proteins to repress transcription (reviewed in Turki-Judeh and Courey, 2012). Groucho proteins, including the 4 human homologues (transducin-like enhancer of split (TLE) 1-4), do not bind DNA directly but instead are recruited to target genes through interaction with DNA-binding transcription factors including TCF/LEF (Brantjes et al, 2001; reviewed in Chen and Courey, 2000). Groucho proteins are believed to oligomerize in a manner that depends on an N-terminal glutamine-rich Q domain, and oligomerization may be important for function (Song et al, 2004; Pinto and Lobe, 1996). Groucho/TLE proteins affect levels of gene expression by interacting with the core transcriptional machinery as well as by modfiying chromatin structure through direct interaction with histones and recruitment of histone deacetylases, among other mechanisms (reviewed in Turki-Judeh and Courey, 2012). In addition to the four TLE proteins, human cells also include a truncated TLE-like protein called amino-terminal enhancer of split (AES) which contains the N-terminal Q domain but lacks much of the C-terminal sequence of TLE proteins, including the WD domain which is important for many protein-protein interactions. AES is believed to act as a dominant negative, since it is able to heter-oligomerize with full-length TLE proteins to form non-functional complexes (Brantjes et al, 2001; reviewed in Beagle and Johnson, 2010).
R-HSA-1474165 Reproduction Human reproduction mixes the genomes of two individuals, creating a new organism. The offspring individuals produced by sexual reproduction differ from their parents and from their siblings. Reproduction includes the reproductive system, sperm and egg production (haploid cells), fertilization, and the early stages embryo development.
R-HSA-9665250 Resistance of ERBB2 KD mutants to AEE788 This pathway describes resistance of ERBB2 KD mutants to tyrosine kinase inhibitor AEE788 (Kancha et al. 2011).
R-HSA-9665249 Resistance of ERBB2 KD mutants to afatinib This pathway describes resistance of ERBB2 KD mutants to tyrosine kinase inhibitor afatinib (Rexer et al. 2013, Hanker et al. 2017).
R-HSA-9665251 Resistance of ERBB2 KD mutants to lapatinib This pathway describes resistance of ERBB2 KD mutants to tyrosine kinase inhibitor lapatinib (Trowe et al. 2008, Kancha et al. 2011, Bose et al. 2013, Rexer et al. 2013, Yang et al. 2015, Hanker et al. 2017, Cocco et al. 2018, Nagano et al. 2018).
R-HSA-9665246 Resistance of ERBB2 KD mutants to neratinib This pathway describes resistance of ERBB2 KD mutants to tyrosine kinase inhibitor neratinib (Hanker et al. 2017).
R-HSA-9665247 Resistance of ERBB2 KD mutants to osimertinib This pathway describes resistance of ERBB2 KD mutants to tyrosine kinase inhibitor osimertinib (Hanker et al. 2017).
R-HSA-9665244 Resistance of ERBB2 KD mutants to sapitinib This pathway describes resistance of ERBB2 KD mutants to tyrosine kinase inhibitor sapitinib (Nagano et al. 2018).
R-HSA-9665245 Resistance of ERBB2 KD mutants to tesevatinib This pathway describes resistance of ERBB2 KD mutants to tyrosine kinase inhibitor tesevatinib (Trowe et al. 2018).
R-HSA-9665233 Resistance of ERBB2 KD mutants to trastuzumab This pathway describes resistance of ERBB2 KD mutants to therapeutic antibody trastuzumab (herceptin) (Bose et al. 2013, Rexer et al. 2013, Hanker et al. 2017, Nagano et al. 2018).
R-HSA-110373 Resolution of AP sites via the multiple-nucleotide patch replacement pathway While the single nucleotide replacement pathway appears to facilitate the repair of most damaged bases, an alternative BER pathway is evoked when the structure of the 5'-terminal sugar phosphate is such that it cannot be cleaved through the AP lyase activity of DNA polymerase beta (POLB). Under these circumstances, a short stretch of residues containing the abasic site is excised and replaced (Dianov et al., 1999). Following DNA glycosylase-mediated cleavage of the damaged base, the endonuclease APEX1 is recruited to the site of damage where it cleaves the 5' side of the abasic deoxyribose residue, as in the single nucleotide replacement pathway. However, POLB then synthesizes the first replacement residue without prior cleavage of the 5'-terminal sugar phosphate, hence displacing this entity. Long-patch BER can be completed by continued POLB-mediated DNA strand displacement synthesis in the presence of PARP1 or PARP2, FEN1 and DNA ligase I (LIG1) (Prasad et al. 2001). When the PCNA-containing replication complex is available, as is the case with cells in the S-phase of the cell cycle, DNA strand displacement synthesis is catalyzed by DNA polymerase delta (POLD) or DNA polymerase epsilon (POLE) complexes, in the presence of PCNA, RPA, RFC, APEX1, FEN1 and LIG1 (Klungland and Lindahl 1997, Dianova et al. 2001). In both POLB-dependent and PCNA-dependent DNA displacement synthesis, the displaced DNA strand containing the abasic sugar phosphate creates a flap structure that is recognized and cleaved by the flap endonuclease FEN1. The replacement residues added by POLB or POLD/POLE are then ligated by the DNA ligase I (LIG1) (Klungland and Lindahl, 1997; Matsumoto et al., 1999).
R-HSA-110381 Resolution of AP sites via the single-nucleotide replacement pathway The single nucleotide replacement pathway of base excision repair appears to facilitate the repair of most damaged bases. Following DNA glycosylase mediated cleavage of the damaged base, the endonuclease APEX1 is recruited to the site of damage where it cleaves the 5' side of the abasic (AP) deoxyribose residue. DNA polymerase beta (POLB) then cleaves the 3' side of the AP sugar phosphate, thus excising the AP residue. APEX1 is subsequently released, the XRCC1:LIG3 complex is recruited, and POLB mediates the synthesis of the replacement residue. Following LIG3 mediated ligation of the replaced residue, the XRCC1:LIG3 complex dissociates from DNA (Lindahl and Wood, 1999). An alternative BER pathway is employed when the structure of the terminal sugar phosphate is such that it cannot be cleaved by the AP lyase activity of POLB.
R-HSA-73933 Resolution of Abasic Sites (AP sites) Resolution of AP sites can occur through the single nucleotide replacement pathway or through the multiple nucleotide patch replacement pathway, also known as the long-patch base excision repair (BER). Except for the APEX1-independent resolution of AP sites via single nucleotide base excision repair mediated by NEIL1 or NEIL2 (Wiederhold et al. 2004, Das et al. 2006), single nucleotide and multiple-nucleotide patch replacement pathways are both initiated by APEX1-mediated displacement of DNA glycosylases and cleavage of the damaged DNA strand by APEX1 immediately 5' to the AP site (Wilson et al. 1995, Bennett et al. 1997, Masuda et al. 1998). The BER proceeds via the single nucleotide replacement when the AP (apurinic/apyrimidinic) deoxyribose residue at the 5' end of the APEX1-created single strand break (SSB) (5'dRP) can be removed by the 5'-exonuclease activity of DNA polymerase beta (POLB) (Bennett et al. 1997). POLB fills the created single nucleotide gap by adding a nucleotide complementary to the undamaged DNA strand to the 3' end of the SSB. The SSB is subsequently ligated by DNA ligase III (LIG3) which, in complex with XRCC1, is recruited to the BER site by an XRCC1-mediated interaction with POLB (Kubota et al. 1996). BER proceeds via the multiple-nucleotide patch replacement pathway when the AP residue at the 5' end of the APEX1-created SSB undergoes oxidation-related damage (5'ddRP) and cannot be cleaved by POLB (Klungland and Lindahl 1997). Long-patch BER can be completed by POLB-mediated DNA strand displacement synthesis in the presence of PARP1 or PARP2, FEN1 and DNA ligase I (LIG1) (Prasad et al. 2001). When the PCNA-containing replication complex is available, as is the case with cells in S-phase of the cell cycle, DNA strand displacement synthesis is catalyzed by DNA polymerase delta (POLD) or DNA polymerase epsilon (POLE) complexes, in the presence of PCNA, RPA, RFC, APEX1, FEN1 and LIG1 (Klungland and Lindahl 1997, Dianova et al. 2001). It is likely that the 9-1-1 repair complex composed of HUS1, RAD1 and RAD9 interacts with and coordinates components of BER, but the exact mechanism and timing have not been elucidated (Wang et al. 2004, Smirnova et al. 2005, Guan et al. 2007, Balakrishnan et al. 2009).
R-HSA-5693537 Resolution of D-Loop Structures Once repair synthesis has occurred, the D-loop structure may be resolved either through Holliday junction intermediates or through synthesis-dependent strand-annealing (SDSA) (Prado and Aguilera 2003, Ciccia and Elledge 2010).
R-HSA-5693568 Resolution of D-loop Structures through Holliday Junction Intermediates D-loops generated after strand invasion and DNA repair synthesis during homologous recombination repair (HRR) can be resolved through Holliday junction intermediates.
A D-loop can be cleaved by the complex of MUS81 and EME1 (MUS81:EME1) or MUS81 and EME2 (MUS81:EME2) and resolved without the formation of double Holliday junctions, generating cross-over products. All steps involved in this process have not been elucidated (Osman et al. 2003, Schwartz et al. 2012, Pepe and West 2014).
Alternatively, double Holliday junctions can be created by ligation of crossed-strand intermediates. Double Holliday junctions can then be resolved through the action of the BLM helicase complex known as BTRR (BLM:TOP3A:RMI1:RMI2) (Wan et al. 2013, Bocquet et al. 2014). BLM-mediated resolution of Holliday junction intermediates prevents sister chromatid exchange (SCE) between mitotic chromosomes and generates non-crossover products. SPIDR enables recruitment of the BTTR complex to the ionizing radiation-induced foci. The complex of FIGNL1 and FIRRM, which, through FIGNL1, simultaneously interacts with SPIDR (Yuan and Chen 2013) and RAD51 (Yuan and Chen 2013, Fernandes et al. 2018), may facilitate the function of SPIDR in promoting the no cross-over route of homologous recombination repair. Mitotic SCE can result in the loss-of-heterozygosity (LOH), which can make the cell homozygous for deleterious recessive mutations (e.g. in tumor suppressor genes) (Wu and Hickson 2003). Double Holliday junctions can also be resolved by cleavage, mediated by GEN1 or the SLX-MUS complex (composed of SLX1A:SLX4 heterodimer and a heterodimer of MUS81 and EME1 or, possibly, EME2). The resolvase activity of GEN1 and SLX-MUS predominantly results in crossover products, with SCE (Fekairi et al. 2009, Wyatt et al. 2013, Sarbajna et al. 2014).
R-HSA-5693554 Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) In the synthesis-dependent strand-annealing (SDSA) model of D-loop resolution, D-loop strands extended by DNA repair synthesis dissociate from their sister chromatid complements and reanneal with their original complementary strands, resulting in non-crossover products (Mitchel et al. 2010). SDSA is promoted by the DNA helicase RTEL1 (Barber et al. 2008, Uringa et al. 2012). Additional DNA synthesis occurs to fill the remaining single strand gap present in the reannealed DNA duplex. DNA polymerase alpha has been implicated in this late step of DNA repair synthesis (Levy et al. 2009), although RTEL1-mediated recruitment of PCNA-bound DNA polymerases may also be involved (Vannier et al. 2013). The remaining single strand nicks are closed by DNA ligases, possibly LIG1 or LIG3 (Mortusewicz et al. 2006, Puebla-Osorio et al. 2006).
R-HSA-2500257 Resolution of Sister Chromatid Cohesion The resolution of sister chromatids in mitotic prometaphase involves removal of cohesin complexes from chromosomal arms, with preservation of cohesion at centromeres (Losada et al. 1998, Hauf et al. 2001, Hauf et al. 2005).
CDK1-mediated phosphorylation of cohesin-bound CDCA5 (Sororin) at threonine T159 provides a docking site for PLK1, enabling PLK1-mediated phosphorylation of cohesin subunits STAG2 (SA2) and RAD21 (Hauf et al. 2005, Dreier et al. 2011, Zhang et al. 2011). Further phosphorylation of CDCA5 by CDK1 results in dissociation of CDCA5 from cohesin complex, which restores the activity of WAPAL in removing STAG2-phosphorylated cohesin from chromosomal arms (Hauf et al. 2005, Gandhi et al. 2006, Kueng et al. 2006, Shintomi and Hirano 2006, Nishiyama et al. 2010, Zhang et al. 2011).
At centromeres, kinetochore proteins shugoshins (SGOL1 and SGOL2) enable PP2A-B56 (also a kinetochore constituent) to dephosphorylate the STAG2 subunit of centromeric cohesin. Dephosphorylation of STAG2 enables maintenance of centromeric cohesion, thus preventing separation of sister chromatids until anaphase (Salic et al. 2004, Kitajima et al. 2004, Kitajima et al. 2005, Kitajima et al. 2006).
R-HSA-9820952 Respiratory Syncytial Virus Infection Pathway Infection with human respiratory syncytial virus (hRSV) is transmitted through close contact, fomites, and aerosolized droplets. RSV first infects the epithelial lining of the upper respiratory tract and nasopharynx where the virus begins to replicate, and from there it may spread to the lower respiratory tract - bronchioles and alveoli - especially in infants. Immune response to RSV infection increases mucus production which, in combination with inflammation, leads to the narrowing of airways and bronchiolitis. Experimental vaccination with a formalin-inactivated RSV has been associated with vaccine-enhanced disease, which has hindered vaccine development and led to advancement of costly and modestly effective therapies based on monoclonal antibodies (mAb) and small molecules, which act to block RSV entry and have been reserved for high-risk patients (reviewed in Battles and McLellan 2019, and Pandya et al. 2019). Recently, a prophylactic mAb Nirsevimab was approved for use in all infants (reviewed in Keam 2023). Some of the preF vaccines, which elicit immune response against the pre-fusion conformation of the F protein (pre-F), are in the late stages of clinical trial or undergoing approval for being used in elderly patients and pregnant women (reviewed in Jenkins et al. 2023).
RSV is classified into two distinct subtypes, RSV A and RSV B, predominantly based on antigenic and sequence-based variations in the viral envelope protein G, involved in virus attachment to the host cells. Multiple RSV genotypes are often in co-circulation with a dominance shift between RSV A and RSV B subtypes occurring every 1-2 years. The majority of RSV molecular studies use a limited number of historical isolates, the so-called laboratory strains, of which hRSV A substrain A2 is the most commonly used. If not indicated otherwise, the events described in this pathway refer to findings from hRSV A2-based studies.
For review, please refer to Battles and McLellan 2019, and Pandya et al. 2019.
R-HSA-611105 Respiratory electron transport Mitochondria are often described as the "powerhouse" of a cell as it is here that energy is largely released from the oxidation of food. Reducing equivalents generated from beta-oxidation of fatty acids and from the Krebs cycle enter the electron transport chain (also called the respiratory chain). During a series of redox reactions, electrons travel down the chain releasing their energy in controlled steps. These reactions drive the active transport of protons from the mitochondrial matrix , through the inner membrane to the intermembrane space. The respiratory chain consists of five main types of carrier; flavins, iron-sulfur centres, quinones, cytochromes (heme proteins) and copper. The two main reducing equivalents entering the respiratory chain are NADH and FADH2. NADH is linked through the NADH-specific dehydrogenase whereas FADH2 is reoxidised within succinate dehydrogenase and a ubiquinone reductase of the fatty acid oxidation pathway. Oxygen is the final acceptor of electrons and with protons, is converted to form water, the end product of aerobic cellular respiration. A proton electrochemical gradient (often called protonmotive force) is established across the inner membrane, with positive charge in the intermembrane space relative to the matrix. Protons driven by the proton-motive force, can enter ATP synthase thus returning to the mitochondrial matrix. ATP synthases use this exergonic flow to form ATP in the matrix, a process called chemiosmotic coupling. A by-product of this process is heat generation.
An antiport, ATP-ADP translocase, preferentially exports ATP from the matrix thereby maintaining a high ADP:ATP ratio in the matrix. The tight coupling of electron flow to ATP synthesis means oxygen consumption is dependent on ADP availability (termed respiratory control). High ADP (low ATP) increases electron flow thereby increasing oxygen consumption and low ADP (high ATP) decreases electron flow and thereby decreases oxygen consumption. There are many inhibitors of mitochondrial ATP synthesis. Most act by either blocking the flow of electrons (eg cyanide, carbon monoxide, rotenone) or uncoupling electron flow from ATP synthesis (eg dinitrophenol). Thermogenin is a natural protein found in brown fat. Newborn babies have a large amount of brown fat and the heat generated by thermogenin is an alternative to ATP synthesis (and thus electron flow only produces heat) and allows the maintenance of body temperature in newborns.
The electron transport chain is located in the inner mitochondrial membrane and comprises some 80 proteins organized in four enzymatic complexes (I-IV). Complex V generates ATP but has no electron transfer activity. In addition to these 5 complexes, there are also two electron shuttle molecules; Coenzyme Q (also known as ubiquinone, CoQ) and Cytochrome c (Cytc). These two molecules shuttle electrons between the large complexes in the chain.
How many ATPs are generated by this process? Theoretically, for each glucose molecule, 32 ATPs can be produced. As electrons drop from NADH to oxygen in the chain, the number of protons pumped out and returning through ATP synthase can produce 2.5 ATPs per electron pair. For each pair donated by FADH2, only 1.5 ATPs can be formed. Twelve pairs of electrons are removed from each glucose molecule;
10 by NAD+ = 25 ATPs
2 by FADH2 = 3 ATPs.
Making a total of 28 ATPs. However, 2 ATPs are formed during the Krebs' cycle and 2 ATPs formed during glycolysis for each glucose molecule therefore making a total ATP yield of 32 ATPs. In reality, the energy from the respiratory chain is used for other processes (such as active transport of important ions and molecules) so under conditions of normal respiration, the actual ATP yield probably does not reach 32 ATPs.
The reducing equivalents that fuel the electron transport chain, namely NADH and FADH2, are produced by the Krebs cycle (TCA cycle) and the beta-oxidation of fatty acids. At three steps in the Krebs cycle (isocitrate conversion to oxoglutarate; oxoglutarate conversion to succinyl-CoA; Malate conversion to oxaloacetate), a pair of electrons (2e-) are removed and transferred to NAD+, forming NADH and H+. At a single step, a pair of electrons are removed from succinate, reducing FAD to FADH2. From the beta-oxidation of fatty acids, one step in the process forms NADH and H+ and another step forms FADH2.
Cytoplasmic NADH, generated from glycolysis, has to be oxidized to reform NAD+, essential for glycolysis, otherwise glycolysis would cease to function. There is no carrier that transports NADH directly into the mitochondrial matrix and the inner mitochondrial membrane is impermeable to NADH so the cell uses two shuttle systems to move reducing equivalents into the mitochondrion and regenerate cytosolic NAD+.
The first is the glycerol phosphate shuttle, which uses electrons from cytosolic NADH to produce FADH2 within the inner membrane. These electrons then flow to Coenzyme Q. Complex I is bypassed so only 1.5 ATPs can be formed per NADH via this route. The overall balanced equation, summing all the reactions in this system, is
NADH (cytosol) + H+ (cytosol) + NAD+ (mito.) = NAD+ (cytosol) + NADH (mito.) + H+ (mito.)
The malate-aspartate shuttle uses the oxidation of malate to generate NADH in the mitochondrial matrix. This NADH can then be fed directly to complex I and thus can form 3 ATPs via the respiratory chain. The overall balanced equation is
NADH (cytosol) + H+ (cytosol) + FAD (inner memb.) = NAD+ (cytosol) + FADH2 (inner memb.)
Both of these shuttle systems regenerate cytosolic NAD+.
The entry point for NADH is complex I (NADH dehydrogenase) and the entry point for FADH2 is Coenzyme Q. The input of electrons from fatty acid oxidation via ubiquinone is complicated and not shown in the diagram.
R-HSA-9820960 Respiratory syncytial virus (RSV) attachment and entry The entry of human respiratory syncytial virus (RSV) into host cells involves attachment of the virion to the host cell surface, through interaction of viral envelope proteins with host cell attachment factors, and fusion of the viral membrane with the host cell membrane. The G glycoprotein is the attachment protein that interacts with surface molecules of the host cells, enabling the RSV virions to bind to their target cells. While the F glycoprotein may facilitate attachment, its primary function is to promote fusion of the viral and host cell membranes. The SH protein is dispensable for entry. For review, please refer to Battles and McLellan 2019.
Using human primary airway epithelial cell cultures, it was established that RSV efficiently infects the airway epithelium from the luminal surface and specifically targets ciliated airway epithelial cells. In the absence of immune response, RSV causes no obvious cytopathology (Zhang et al. 2002).
In addition to ciliated respiratory epithelial cells, RSV may infect granulocytes and cause a delay in constitutive apoptosis of neutrophils and eosinophils (Lindemans et al. 2006). RSV can also infect neonatal-specific regulatory B cells, which may contribute to high viral load and disease severity in infants (Zhivaki et al. 2017).
R-HSA-9820965 Respiratory syncytial virus (RSV) genome replication, transcription and translation After the human respiratory syncytial virus A (hRSV A) enters host cells, an initial round of transcription and translation of virally-encoded mRNAs ensues, which is followed by genome replication.
The negative sense, single-stranded RNA (-ssRNA) genome of the human respiratory syncytial virus (RSV) A is 15.2 kb long and contains 10 genes that encode 11 proteins. The 10 genes, going from the 3' end to the 5' end of the -ssRNA are: 1C (NS1), 1B (NS2), N, P, M, SH, G, F, M2, and L. Except for the M2 gene, each gene encodes one protein. The two overlapping open reading frames (ORFs) of the M2 gene encode proteins M2-1 and M2-2.
The N gene encodes the nucleoprotein, which forms decameric and hendecameric (11-fold) rings around which viral genomic RNA is packaged. The L and P genes encode the large polymerase subunit and the phosphoprotein polymerase cofactor subunit, respectively, of the RNA-dependent RNA polymerase complex (RdRP) (reviewed in Battles and McLellan 2019). The L protein contains three conserved enzymatic domains: the RNA-dependent RNA polymerase (RdRp) domain, the polyribonucleotidyl transferase (PRNTase or capping) domain, and the methyltransferase (MTase) domain (reviewed in Sutto-Ortiz et al. 2023). The M2-1 product of the M2 gene is a transcription processivity factor, while the M2-2 product of the M2 gene is a nonstructural protein that regulates the switch between transcription and genome replication. The SH, G, and F genes encode three proteins that are embedded in the viral envelope: small hydrophobic protein, attachment protein, and fusion protein, respectively. The secreted isoform of G protein (sG) mediates immune evasion. The NS1 and NS2 genes encode nonstructural proteins that function together to inhibit apoptosis and interferon response in infected cells. For review, please refer to Battles and McLellan 2019.
The genomic -ssRNA and the antigenome RNA are encapsidated as they are synthesized, and the association of the nascent RNA with the N protein is likely what causes the replicating polymerase to be processive, with the processivity being further augmented by the M2-1 processivity factor (reviewed in Fearns and Deval 2016). The C-terminal arm of the N protein, known to interact with the P protein subunit of RdRP complex, extends above the plane of N decamers. The interaction between N and P proteins may allow the RdRP complex to distort the helical conformation of the nucleocapsid during RNA synthesis. A long beta-hairpin in the N-terminal region of the N protein may be the site of contact with the catalytic L subunit of the RdRP complex. The proposed model for RNA synthesis in RSV is that the RdRP complex induces a hinge movement of the N-terminal region with respect to the C-terminal region of the N protein that allows the polymerase to thread through the template RNA without the need to disassemble the nucleocapsid (Tawar et al. 2009). The hinge movement would enable 11 bases available for readout at a time (Tawar et al. 2009), consistent with the accumulation of abortive transcripts 9-11 nucleotides in length in P protein phosphorylation mutants that impair transcript elongation (Dupuy et al. 1999).
The M2-2 protein regulates the shift from positive to negative sense RNA synthesis. While the mechanism has not been fully elucidated, M2-2 was shown to directly bind to the L protein and to inhibit positive sense RNA synthesis (reviewed in Noton and Fearns 2015).
For review, please refer to Collins et al. 2013.
R-HSA-9834752 Respiratory syncytial virus genome replication Replication of the negative sense genomic RNA of the human respiratory syncytial virus (RSV) occurs through the positive sense intermediate, also known as antigenomic RNA. RNA synthesis is performed by the RNA-dependent RNA polymerase (RdRP) complex composed at a minimum of the L protein, which is the catalytic subunit of RdRP, and P protein. Protein M2-1 that acts as a processivity factor is described as a consitutive RdRP subunit by some and as an accessory RdRP subunit by other studies (reviewed in Fearns and Deval 2016). Replication of both genomic and antigenomic RNA depends on encapsidation by protein N, which has regions that interact with both protein P and protein L. Encapsidation protects genomic and antigenomic RNA from degradation as these RNAs do not possess the 5' cap and the poly(A) tail. Replication occurs after primary transcription. Accumulation of the protein M2-2 is responsible for the shift of RNA synthesis from transcription to replication through a mechanism that has not been fully elucidated (For review, refer to Collins and Melero 2011, Battles and McLellan 2019).
R-HSA-9828642 Respiratory syncytial virus genome transcription The negative sense, single-stranded RNA (-ssRNA) genome of the respiratory syncytial virus (RSV) is transcribed into 10 positive sense messenger RNAs that encode 11 viral proteins. The 10 viral mRNAs, going from the 3' end, are: 1C (NS1) mRNA,1B (NS2) mRNA, N mRNA, P mRNA, M mRNA, SH mRNA, G mRNA, F mRNA, M2 mRNA, and L mRNA. Except for the M2 mRNA, each mRNA contains a single open reading frame (ORF). The two overlapping open reading frames (ORFs) of the M2 mRNA are translated into two distinct proteins, M2-1 and M2-2.
The N mRNA encodes the nucleoprotein, while the L and P mRNAs encode the large polymerase subunit and the phosphoprotein polymerase cofactor subunit, respectively, of the RNA-dependent RNA polymerase complex (RdRP). The M2-1 mRNA encodes a transcription processivity factor, while the M2-2 mRNA encodes a nonstructural protein that regulates the switch between transcription and genome replication. The SH, G and F mRNAs encode three proteins that are embedded in the viral envelope: small hydrophobic protein, attachment protein and fusion protein, respectively. The secreted isoform of G protein (sG), involved in mediation of immune evasion, and the truncated form of SH (SHt), are translated from G mRNA and SH mRNA, respectively, through the usage of an alternative start codon. The NS1 and NS2 mRNAs encode nonstructural proteins that function together to inhibit apoptosis and interferon response in infected cells. All RSV mRNAs undergo 5' capping and 3' polyadenylation, performed by the viral RdRP. For review, please refer to Battles and McLellan 2019.
R-HSA-9648895 Response of EIF2AK1 (HRI) to heme deficiency The kinases of the integrated stress response phosphorylate EIF2S1 (eIF2-alpha) to regulate cellular translation. The kinases comprise PERK (also called EIF2AK3), which responds to unfolded protein in the endoplasmic reticulum; EIF2AK2 (also called PKR), which responds to cytosolic double-stranded RNA; EIF2AK4 (also called GCN2), which responds to amino acid deficiency; and EIF2AK1 (also called heme-regulated inhibitor, HRI, and heme-controlled repressor, HCR), which responds to heme deficiency and cytosolic unfolded protein. Each molecule of EIF2AK1 binds two molecules of heme, one bound near the N-terminus and one bound at the kinase insert (KI) domain that inhibits the kinase activity of EIF2AK1 (inferred from the rabbit homolog in Chefalo et al. 1998, Rafie-Kolpin et al. 2000, inferred from the mouse homolog in Misanova et al. 2006, Hirai et al. 2007, Igarashi et al. 2008). Dissociation of heme from the KI domain activates the kinase activity of EIF2AK1, which autophosphorylates (inferred from the mouse homolog in Bauer et al. 2001, Rafie-Kolpin et al. 2003, Igarashi et al. 2011) and then phosphorylates EIF2S1 (Bhavnani et al. 2018, inferred from the rabbit homologs in Chefalo et al. 1998, Rafie-Kolpin et al. 2000, inferred from the mouse homologs in Lu et al. 2001, Rafie-Kolpin et al. 2003, Igarashi et al. 2011).
Phosphorylated EIFS1 causes a reduction in general cellular translation and thereby coordinates globin synthesis with heme availability during erythropoiesis (inferred from mouse knockout in Han et al. 2001, reviewed in Chen et al. 2014). Translation of mitochondrial and cytosolic ribosomal proteins is most severely reduced, causing a decrease in cellular protein synthesis (inferred from mouse homologs in Zhang et al. 2019). Lack of EIF2AK1 causes accumulation of unfolded globins devoid of heme and consequent anemia in iron-deficient mice (inferred from mouse knockout in Han et al. 2001). Activation of the cytoplasmic unfolded protein response and impaired mitochondrial respiration are also observed in HRI deficiency (inferred from mouse homologs in Zhang et al. 2019).
Phosphorylation of EIFS1 activates translation of certain mRNAs such as ATF4, ATF5, and DDIT3 (CHOP) that have upstream ORFs (inferred from mouse homologs in Harding et al. 2000). ATF4 in turn activates programs of gene expression that ameliorate effects of the stress to maintain mitochondrial function, redox homeostasis, and erythroid differentiation (inferred from mouse homologs in Zhang et al. 2019). Unresolved stress, however, can eventually lead to apoptosis regulated by DDIT3. EIF2AK1 also represses mTORC1 (mechanistic target of mechanistic target of rapamycin complex 1) signaling via ATF4-mediated induction of GRB10 as a feedback mechanism to attenuate erythropoietin-mTORC1-stimulated ineffective erythropoiesis in iron deficiency anemia (inferred from mouse homologs in Zhang et al. 2018 and Zhang et. al. 2019).
EIF2AK1 is also activated by heat shock, arsenite (oxidative stress), and osmotic stress (inferred from mouse homologs in Lu et al. 2001). The mechanisms by which these stresses act on EIF2AK1 are independent of heme but are not yet fully elucidated. Furthermore, EIF2AK1 is involved in the production of human fetal hemoglobin, and EIF2AK1-mediated stress response has emerged as a potential therapeutic target for hemoglobinopathies (reviewed in Chen and Zhang 2019).
In addition to regulation of erythropoiesis, EIF2AK1 shows effects outside of the erythroid lineage, including requirement for the maturation and functions of macrophages (inferred from mouse homologs in Liu et al. 2007), reduction in endoplasmic reticulum stress in hepatocytes, activation of hepatic expression of fibroblast growth factor, and mediation of translation of GRIN2B (GluN2B. a subunit of the NMDA receptor) and BACE1 in the nervous system (reviewed in Burwick and Aktas 2017). HRI-integrated stress response is activated in human cancer cell lines and primary multiple myeloma cells, and has emerged as a molecular target of anticancer agents (reviewed in Burwick and Aktas 2017; reviewed in Chen and Zhang 2019).
R-HSA-9633012 Response of EIF2AK4 (GCN2) to amino acid deficiency EIF2AK4 (GCN2) senses amino acid deficiency by binding uncharged tRNAs near the ribosome and responds by phosphorylating EIF2S1, the alpha subunit of the translation initiation factor EIF2 (inferred from yeast homologs and mouse homologs, reviewed in Chaveroux et al. 2010, Castilho et al. 2014, Gallinetti et al. 2013, Bröer and Bröer 2017, Wek 2018). Phosphorylated EIF2S1 reduces translation of most mRNAs but increases translation of downstream ORFs in mRNAs such as ATF4 that contain upstream ORFs (inferred from mouse homologs in Vattem and Wek 2004, reviewed in Hinnebusch et al. 2016, Sonenberg and Hinnebusch 2009). ATF4, in turn, activates expression of genes involved in responding to amino acid deficiency such as DDIT3 (CHOP), ASNS (asparagine synthetase), CEBPB, and ATF3 (reviewed in Kilberg et al. 2012, Wortel et al. 2017). In mice, EIF2AK4 in the brain may responsible for avoidance of diets lacking essential amino acids (Hao et al. 2005, Maurin et al. 2005, see also Leib and Knight 2015, Gietzen et al. 2016, reviewed in Dever and Hinnebusch 2005).
EIF2AK4 is bound to both the ribosome and GCN1, which is required for activation of EIF2AK4 and may act by shuttling uncharged tRNAs from the A site of the ribosome to EIF2AK4. Upon binding tRNA, EIF2AK4 trans-autophosphorylates. Phosphorylated EIF2AK4 then phosphorylates EIF2S1 on serine-52, the same serine residue phosphorylated by other kinases of the integrated stress response: EIF2AK1 (HRI, activated by heme deficiency and other stresses), EIF2AK2 (PKR, activated by double-stranded RNA), and EIF2AK3 (PERK, activated by unfolded proteins) (reviewed in Hinnebusch 1994, Wek et al. 2006, Donnelly et al. 2013, Pakos-Zebrucka et al. 2016, Wek 2018),
R-HSA-9637690 Response of Mtb to phagocytosis Mycobacterium tuberculosis (Mtb) encounters a vastly changed environment shortly after being internalized by macrophages. The compartment it resides in, the phagosome, is acidified and devoid of important metal ions and is flooded with reactive oxygen and nitrogen species. Steps will be soon taken by the macrophage to "mature" the phagosome with all kinds of lysosomal digestive enzymes. However, unlike most other bacteria species, Mtb has evolved solutions to each of these threats. As a last resort to a strong immune response, some bacteria will enter a dormant state (de Chastellier 2009, Flannagan et al. 2009). To what extent this is true is still unclear (McDaniel et al. 2016). Upon weakening of the immune defense, Mtb reawakens from its dormant state and starts to multiply inside the phagocyte (Repasy et al. 2013).
R-HSA-9860931 Response of endothelial cells to shear stress Vascular endothelial cells experience shear stress produced by the flow of blood across their apical surfaces. Different types of shear stress have been identified based on the type of flow and the response of the endothelial cells: low volume laminar flow, high volume laminar flow, and turbulent (disturbed, oscillatory) flow (reviewed in Davis et al. 2023, Rahaman et al. 2023, Lim and Harraz 2024). A key difference between the responses of cells to the different types of flow is the absence or presence of inflammation (reviewed in Davis et al. 2023, Wang et al. 2023). Whereas high volume laminar flow produces vasodilation and cytoskeletally based streamlining without inflammation, both turbulent flow and low volume laminar flow activate the inflammatory NF-kB and YAP1 pathways.
All types of flow activate the mechanosensitive cation channel PIEZO1, resulting in an influx of calcium ions (Li et al. 2014, reviewed in Fang et al. 2021, Davis et al. 2023, Xiao et al. 2023). Calcium binds and activates the Calpain2 protease complex which acts on cytoskeletal proteins near the inner face of the plasma membrane, causing alterations to the morphology of the cell (Miyazaki et al. 2020). In the case of high volume laminar flow, cells become ellipsoid with their long axes parallel with the flow of blood.
In addition to optimization of cell shape, high volume laminar flow activates AKT1 via ligand-independent KDR (VEGFR2) signaling, ATP-dependent P2RY2 signaling, and Adrenomedullin (ADM) signaling (Tzima et al. 2005, Wang et al. 2015, Iring et al. 2019, reviewed in Xiao et al. 2023). AKT1 and other kinases then phosphorylate NOS3 (eNOS), resulting in increased production of nitric oxide and vasodilation (Dimmeler et al. 1999, Jin et al. 2021). High volume laminar flow is thus atheroprotective.
In contrast, turbulent flow activates signaling by integrin alpha5:beta1 (ITGA5:ITGB1) that causes the phosphodiesterase PDE4D5 to hydrolyze cAMP (Yun et al. 2016) and the phosphatase PP2A to dephosphorylate and hence activate the transcription factor YAP1 (Jiang et al. 2021). YAP1 positively regulates expression of pro-inflammatory genes. Also during turbulent flow, Focal adhesion kinase (PTK2, FAK) is activated by phosphorylation and causes phosphorylation and nuclear translocation of the pro-inflammatory transcription factor complex NF-kB (Albarrán-Juárez et al. 2018).
R-HSA-76005 Response to elevated platelet cytosolic Ca2+ Activation of phospholipase C enzymes results in the generation of second messengers of the phosphatidylinositol pathway. The events resulting from this pathway are a rise in intracellular calcium and activation of Protein Kinase C (PKC). Phospholipase C cleaves the phosphodiester bond in PIP2 to form 1,2 Diacylglycerol (DAG) and 1,4,5-inositol trisphosphate (IP3). IP3 opens Ca2+ channels in the platelet dense tubular system, raising intracellular Ca2+ levels. DAG is a second messenger that regulates a family of Ser/Thr kinases consisting of PKC isozymes (Nishizuka 1995). DAG achieves activation of PKC isozymes by increasing their affinity for phospholipid. Most PKC enzymes are also calcium-dependent, so their activation is in synergy with the rise in intracellular Ca2+. Platelets contain several PKC isoforms that can be activated by DAG and/or Ca2+ (Chang 1997).
R-HSA-5660526 Response to metal ions Though metals such as zinc, copper, and iron are required as cofactors for cellular enzymes they can also catalyze damaging metal substitution or unspecific redox reactions if they are not sequestered. The transcription factor MTF1 directs the major cellular response to zinc, cadmium, and copper. MTF1 activates gene expression to up-regulate genes encoding proteins, such as metallothioneins and glutamate-cysteine ligase (GCLC), involved in sequestering metals. MTF1 represses gene expression to down-regulate genes encoding transporters that import the metals into the cell (reviewed in Laity and Andrews 2007, Jackson et al. 2008, Günther et al. 2012, Dong et al. 2015). During activation MTF1 in the cytosol binds zinc ions and is translocated into the nucleus, where it binds metal response elements in the promoters of target genes. Activation of MTF1 by cadmium and copper appears to be indirect as these metals displace zinc from metallothioneins and the displaced zinc then binds MTF1.
Metallothioneins bind metals and participate in detoxifying heavy metals, storing and transporting zinc, and redox biochemistry.
R-HSA-2453864 Retinoid cycle disease events The gene defects which cause diseases related to the retinoid cycle are described here (Travis et al. 2007, Palczewski 2010, Fletcher et al. 2011, den Hollander et al. 2008).
R-HSA-975634 Retinoid metabolism and transport Vitamin A (all-trans-retinol) must be taken up, either as carotenes from plants, or as retinyl esters from animal food. The most prominent carotenes are alpha-carotene, lycopene, lutein, beta-cryptoxanthine, and especially beta-carotene. After uptake they are mostly broken down to retinal. Retinyl esters are hydrolysed like other fats. In enterocytes, retinoids bind to retinol-binding protein (RBP). Transport from enterocytes to the liver happens via chylomicrons (Harrison & Hussain 2001, Harrison 2005).
R-HSA-6809583 Retinoid metabolism disease events Retinol binding protein (RBP4) delivers all-trans-retinol (atROL) from liver stores to peripheral tissues. Defects in RBP4 cause retinol-binding protein deficiency (RBP deficiency, MIM:180250), causing night vision problems and a typical 'xerophthalmic fundus' with progressive atrophy of the retinal pigment epithelium (RPE) (Seeliger et al. 1999, Biesalski et al. 1999).
R-HSA-177504 Retrograde neurotrophin signalling Neurotrophin-TRK complexes can be internalized and enter signalling vesicles, which travel retrogradely over long distances from distal nerve terminals to neuronal cell bodies. Such retrograde signalling by neurotrophin-TRK complexes regulates survival, synaptogenesis and maintenance of proper neural connectivity. The neurotrophin-TRK complex may use three distinct internalization pathways. Although Clathrin-mediated endocytosys appears to be the major internalization route, it is controversial whether it also represents the dominant pathway for retrograde transport and signalling. Pyncher-mediated endocytosis might be more relevant in this regard. Moreover, also caveolin-mediated endocytosis may play a role in NGF-TrkA internalization.
Retrograde transport of TRKs is microtubule-dependent: TRKs remain activated and bound to neurotrophins during retrograde transport. The current view is reflected in the signalling endosome model. It is a specialized vesicle containing ligand (NGF, BDNF) bound to its activated TRK receptor, together with activated downstream signalling proteins, transported by motor proteins (dyneins) from nerve terminals to remote cell bodies, where the receptors trigger signalling cascades.
R-HSA-6811440 Retrograde transport at the Trans-Golgi-Network The trans-Golgi network is the docking site for retrograde cargo from the endolysosomal system and the plasma membrane. Typical cargo includes recycling resident TGN proteins such as TGOLN2 (also known as TGN46), receptors such as the mannose-6-phosphate receptors and toxins like Shiga, cholera and ricin which use the retrograde trafficking machinery to 'hitchhike' back through the secretory system for release into the cytoplasm (reviewed in Johannes and Popoff, 2008; Pfeffer, 2011; Sandvig et al, 2013). These cargo are trafficked from the endocytic system in a clathrin- and AP1-dependent manner that is described in more detail in the "Trans-Golgi network budding pathway" (just not yet). In general, it appears that vesicles are uncoated prior to their tethering and fusion at the TGN. At the TGN, at least 2 distinct tethering pathways exist. A RAB6-dependent pathway contributes to the fusion and docking of vesicles from the early endocytic pathway. These vesicles, which carry cargo such as TGOLN2 and toxins, dock at the TGN through interactions with TGN-localized Golgin tethers and with the multisubunit tethering complexes COG and GARP (reviewed in Bonafacino and Rojas, 2006; Bonafacino and Hierro, 2011; Pfeffer, 2011). In contrast, mannose-6-phosphate receptors appear to traffic from late endosomes to the TGN through a RAB9- and PLIN3-dependent pathway. Vesicles are recruited to the TGN through interaction of RAB9 with the atypical RHO GTPase RHOBTB3, and tethered by virtue of interaction with TGN-localized Golgins and the GARP complex (Perez-Victoria et al, 2008; Perez-Victoria et al, 2009; Diaz et al, 1999; reviewed in Pfeffer, 2011; Chia and Gleeson, 2014)
R-HSA-888593 Reuptake of GABA Reuptake of GABA from the synapse terminates the action of GABA thus regulating GABA action. GABA taken up from the synapse into the neurons is reused for synaptic loading. GABA taken up by astrocytes is degraded into C02 and glutamine. Glutamine is transported into the neurons for glutamate and GABA synthesis.
R-HSA-165054 Rev-mediated nuclear export of HIV RNA The HIV-1 genome contains 9 genes encoded by a single transcript. In order for the virus to replicate, unspliced, singly-spliced and fully spliced viral mRNA must be exported from the nucleus. The HIV-1 mRNA splice sites are inefficient resulting it the accumulation of a pool of incompletely spliced RNAs (Staffa and Cochrane, 1994). In the early stages of the viral life cycle, or in the absence of the viral Rev protein, completely spliced viral mRNA which encode the regulatory proteins Tat, Nef and Rev are exported from the nucleus while the incompletely spliced structural protein encoding transcripts are held within the nucleus by cellular proteins that normally function in preventing the nuclear export of cellular pre-mRNA. Export of both unspliced and partially spliced mRNA is mediated by the viral protein Rev which is recruited, along with cellular cofactors, to the Rev Response Element (RRE) within the HIV-1 mRNA sequence (Malim et al., 1990; Fischer et al., 1994). The cellular hRIP protein is essential for correct Rev-mediated export of viral RNAs to the cytoplasm (Sanchez-Velar et al., 2004; Yu et al., 2005).
R-HSA-73943 Reversal of alkylation damage by DNA dioxygenases DNA in cells is susceptible to different types of cytotoxic and mutagenic damage caused by alkylating agents. These genotoxic chemicals generate major lesions like 1-methyladenine, 3-methyladenine, 3-methylcytosine and O6-methylguanine in DNA. Cells have built in repair mechanisms against such toxic molecules. For example, 3-methyladeninie-DNA glycosylases excise some methylated bases while MGMT/hAGT protein transfers alkyl groups from others lesions onto cysteine residues. E.coli AlkB protein has a unique function wherein 1-methyladenine and 3-methylcytosine are demethylated by a combination of oxidative decarboxylation and hydroxylation activities. AlkB and its human orthologs, ALKBH2 (ABH2) and ALKBH3 (ABH3) belong to alpha-ketoglutarate deoxygenase family of enzymes that oxidize chemically inert compounds in the presence of alpha-ketoglutarate, oxygen and ferrous ions. As a byproduct of these chemical reactions, formaldehyde is released in the case of methylated lesions and acetaldehyde in the case 1-ethyladenine in DNA. CO2 and succinate are also released in an intermediate step not shown in the following illustration. Unlike other mechanisms which involve some kind of nuclease activities, this type of repair mechanism leaves the repaired bases intact by just removing the reactive alkyl groups that get bound to the bases thereby effecting accurate restoration of damaged DNA sequences (Trewick et al. 2002, Duncan et al. 2002, Sedgwick 2004).
R-HSA-162589 Reverse Transcription of HIV RNA The RNA genome of HIV-1, like that of other retroviruses, is reverse-transcribed (Baltimore 1970; Temin and Mizutani 1970) into double-stranded DNA, which is then integrated into a host cell chromosome and transcribed to yield both viral mRNAs and viral genomic RNAs. HIV-1 reverse transcription takes place in the cytosol of a newly infected host cell and involves multiple steps of RNA synthesis and degradation of the RNA strand of RNA:DNA duplexes mediated by the HIV-1 RT protein, as well as two template switches, to yield a DNA duplex colinear with the viral genomic RNA but with additional Long Terminal Repeat (LTR) sequence motifs at both ends (Telesnitsky and Goff 1997; Jonckheere et al. 2000).
HIV-1 RT has two catalytic activities essential for transcription of a DNA duplex copy of the viral genomic RNA: a reverse transcriptase activity and an RNase H activity. The reverse transcriptase is primer dependent and can transcribe both RNA and DNA templates in a 5'-3' direction. The RNaseH acts on the RNA strand of RNA:DNA duplexes and can catalyze both endo- and exonucleolytic cleavage of such an RNA strand. RT is a heterodimer of 66 and 51 kD polypeptides, both generated by cleavage of the HIV-1 Pol gene product: p66 contains Pol amino acid residues 599-1158; p51 contains residues 599-1038. Both active sites of the HIV-1 RT enzyme are contained in the p66 polypeptide, the polymerase activity in its aminoterminal region, and the RNase in its carboxyterminus. The p51 subunit lacks an RNaseH domain, and while its polymerase domain is intact, its conformation in the p66:p51 heterodimer occludes the active site (Hughes et al. 1996; Jacobo-Molina et al. 1993; Kohlstaedt et al. 1992; Wang et al. 1994).
The process of reverse transcription is outlined in the figure below: viral genomic RNA and primer tRNA are shown in black, "minus" strand DNA is shown in red, and "plus" strand DNA is shown in blue.
R-HSA-9729902 Reversible DNA damage induced by alkylating chemotherapeutic drugs This pathway describes how chemotherapeutic drugs commonly used in cancer treatment produce alkylating DNA damage that is repaired through the DNA damage reversal pathway. For review, please refer to Fu et al. 2012.
R-HSA-1475029 Reversible hydration of carbon dioxide Carbonic anhydrases reversibly catalyze the hydration of carbon dioxide and directly produce bicarbonate and protons, bypassing the formation of carbonic acid (reviewed in Lindskog 1997, Breton 2001, Esbaugh and Tufts 2006, Boron 2010, Gilmour 2010). Carbonic anhydrase deprotonates water to yield a zinc-hydroxyl group and a proton which is transferred to external buffer molecules via histidine or glutamate residues in carbonic anhydrase. The hydroxyl group reacts with carbon dioxide in the active site to yield bicarbonate. A water molecule displaces the bicarbonate and the reaction cycle begins again. There are currently 12 known active carbonic anhydrases in humans.
R-HSA-9037628 Rhesus blood group biosynthesis The Rhesus (Rh) blood group system (including the Rh factor) is the second most important blood group system after the ABO blood group system. The Rh blood type was first discovered in 1937 by Karl Landsteiner and Alexander S. Wiener who named it after the rhesus macaque whose RBCs were used to generate the rabbit immune serum that first detected the human blood group system. Subsequent studies by them and Philip Levine and Rufus Stetson identified the antigen that induced this immunization as the "Rh factor" and also its association with hemolytic disease of the newborn (Levine & Stetson 1984, Landsteiner & Wiener 1941). Of the 50 defined Rh blood group antigens, five (D, C/c and E/e) are the major types expressed by the RHD and RHCE genes in the RH gene complex. Rh antigens are expressed on red cell (RBC) membranes in association with other membrane proteins and this whole complex interacts with the spectrin-based skeleton and contributes to the maintenance of the mechanical properties of the RBC membrane (Van Kim et al. 2006).
The RHD gene produces the D antigen, the most immunogenic Rh antigen. The term "Rh factor" refers only to the D antigen; Rh positive (Rh+) individuals have the D antigen on their RBC membranes whereas Rh negative (Rh-) individuals don't. Humans are not born with antibodies towards the D antigen in their blood, they have to be exposed to it (through blood transfusion or placental exposure during pregnancy) at some point in their lives before antibodies are made against it. Once exposed, however, Rh+ individuals remain sensitive for the rest of their lives. Importantly, if individuals are Rh+ and are exposed to Rh- blood, no immune response is mounted. Anti-D antibodies are only seen if an individual is lacking the D antigen (Rh-) and is exposed to Rh+ blood. The RHCE gene produces polypeptides with C/c and E/e antigens.
These polypeptides are the core components of their respective antigens but by themselves are devoid of the immunoreactivity which defines the Rh antigens. The remaining antigens are produced by partial deletion, recombination, mutation, or polymorphisms of one or both RHD and RHCE genes (Cartron 1999). Together, these antigens form the most complex and polymorphic blood group system based on the multitude of phenotypes that can be expressed on the RBC surface. The Fisher-Race system, the nomenclature used most commonly, uses the CDE system to depict the notation of Rh genotypes (Race 1948). The most common group of 3 genes inherited is CDe with ce (D negative) being the second most common. Rh genotyping is used in blood transfusion, paternity testing and to determine the risk of hemolytic disease of the newborn.
R-HSA-444411 Rhesus glycoproteins mediate ammonium transport The Rhesus (Rh) glycoproteins were originally described in human blood cells as potent immunogens. There are three Rh glycoproteins in humans; an erythroid-specific Rh-associated glycoprotein (RhAG) and two non-erythroid Rh glycoproteins, RhBG and RhCG. These proteins are related to ammonium (NH4+) transporters of yeast and bacteria (methylammonium and ammonium permease and ammonium transporter, MEP/Amt) (Nakhoul NL and Hamm LL, 2004; Planelles G, 2007).
R-HSA-9755088 Ribavirin ADME Ribavirin (RBV) is a synthetic nucleoside analog structurally related to guanine. It is given orally as part of the treatment of HCV infection, and by inhalation for the treatment of RSV infection. According to the WHO, ribavirin can also be used for the treatment of viral hemorrhagic fevers (WHO 2015).
RBV is administered orally in doses of 400 to 600 mg. It is highly soluble in water and a typical dose is dissolved completely over a wide range of acidities. RBV is rapidly absorbed into the circulation. After the oral administration of 600 mg radiolabeled ribavirin, approximately 61% of the drug was detected in the urine and 12% was detected in the feces. 17% of an administered dose was in unchanged form. RBV accumulates in human erythrocytes and remains in the body for weeks, with a halflife of >100 hours (Goodarzi et al, 2016). A consequence of the accumulation in erythrocytes is the well-known side effect of hemolytic anemia, which is reversible by cessation of administration (FDA label Rebetol, 2013).
Ribavirin is a prodrug. It is metabolized through two different paths: phosphorylation, yielding the active triphosphate (RBV-TP), and degradation via de-ribosylation and hydrolysis of the amide group. The GI tract, and not the liver, appears to be the major site of first-pass elimination (Dixit and Perelson, 2006).
R-HSA-72702 Ribosomal scanning and start codon recognition The 80S ribosome bound to the mRNA moves along the mRNA molecule from its initial site to the initiation codon and forms a 48S complex, in which the initiation codon is base paired to the anticodon of the Met-tRNAi. Proper recognition of the AUG initiation codon depends on base pairing with the anticodon of the Met-tRNAi and requires eIF1, eIF1A, eIF2 and eIF5.
R-HSA-428890 Role of ABL in ROBO-SLIT signaling ABL (ABL1 or ABL2) plays a dual role in the ROBO pathway. As a key enzymatic component in the signaling pathway, ABL supports repellent signaling (by recruiting the necessary actin binding proteins) and also feeds back on the receptor (by down regulating through phosphorylation) to adjust the sensitivity of the pathway.
ABL cooperates with multiple effectors, including the actin binding protein Capulet (Capt) and Orbit/MAST/CLASP, suggesting that ABL simultaneously coordinates the dynamics of two major cytoskeletal systems to achieve growth cone repellent guidance.
R-HSA-2730905 Role of LAT2/NTAL/LAB on calcium mobilization The lipid raft resident adaptor molecules LAT1 and Non-T cell activation linker (NTAL), also known as linker for activation of B cells (LAB)/LAT2 are known participants in the regulation of mast cell calcium responses. Both LAT and NTAL are expressed and phosphorylated following engagement of FCERI on mast cells. NTAL is functionally and topographically different from LAT. There is a considerable debate on the role of NTAL in mast cell. Depending on the circumstances, NTAL appears to have a dual role as positive and negative regulator of MC responses elicited via FCERI. Studies conducted in bone marrow-derived mast cells (BMMCs) of mice lacking NTAL displayed enhanced FCERI-mediated tyrosine phosphorylation of several substrates, calcium response, degranulation, and cytokine production. This indicated that NTAL negatively regulates FCERI-mediated degranulation. However, in mice lacking both LAT and NTAL showed severe block in FCERI-mediated signaling than BMMCs deficient in LAT alone, suggesting that NTAL also shares a redundant function with LAT to play a positive role (Draberova et al. 2007, Orr & McVicar. 2011, Zhu et al. 2004, Volna et al. 2004). The major steps in NTAL mediated Ca+2 influx involves NTAL--> GAB2--> PI3K
R-HSA-2029485 Role of phospholipids in phagocytosis Phospholipases play an integral role in phagocytosis by generating essential second messengers. An early step in phagocytic signaling is the association of PIP2 and IP3 with the phagocytic cup. These are formed by the activity of phosphoinositol kinases and phospholipases. PI3K is has been shown to accumulate at phagocytic cups and converts PI (4,5)P2 to PI (3,4,5)P3. These phosphoinositides are capable of binding and increasing the activity of proteins that regulate the actin cytoskeleton. Phospholipases are lipid modifying enzymes that produce lipid mediators such as diacylglycerol (DAG), arachidonic acid (AA) and IP3. Phopsholipases PLA, PLC and PLD have been shown to be involved in antibody (IgG) mediated phagocytosis. The PLC product IP3 stimulates release of calcium from the endoplasmic reticulum. This Ca+2 concentration increase is greatest in the cytoplasm surrounding the phagocytic cup. Calcium is involved in the various stages of phagosome formation, including phagocytic ingestion and phagosome maturation.
R-HSA-418890 Role of second messengers in netrin-1 signaling The levels of second messengers such as Ca+2, cAMP and cGMP may regulate the response of the growth cone to a particular cue. Netrin-1 as a guidance molecule depends on intracellular Ca+2 concentration, coactivation of PI3K and PLCgamma, and the type of response depends on the levels of cAMP. Netrin first stimulates its receptor DCC, resulting in the activation of the enzyme phospholipase C. This then produces the messenger molecules, inositol-1,4,5-trisphosphate (IP3) and DAG, which in turn causes the release of Ca+2 from intracellular stores. Ca+2 release from the stores then activates TRPC channels on the cell surface. DAG activates TRPC3 and TRPC6 in a direct, membrane delimited manner, and IP3 may activate TRPC channels by depleting the ER Ca+2 levels.
R-HSA-69242 S Phase DNA synthesis occurs in the S phase, or the synthesis phase, of the cell cycle. The cell duplicates its hereditary material, and two copies of the chromosome are formed. As DNA replication continues, the E type cyclins shared by the G1 and S phases, are destroyed and the levels of the mitotic cyclins rise.
R-HSA-9679506 SARS-CoV Infections Coronaviruses (CoVs) are large, enveloped, positive strand RNA viruses that can be classified into four genera: alpha, beta, delta, and gamma. Coronaviruses are ecologically diverse, infecting animals including camels, cattle, cats, and bats, with the greatest variety seen in bats, suggesting that bats are the reservoirs for many of these viruses. Rarely, A and B lineage beta coronaviruses of non-human origin can infect people and then spread directly between people. Four human coronaviruses (HCoVs), HCoV 229E, NL63, OC43, and HKU1, are endemic globally and account for 10% to 30% of upper respiratory tract infections in adults, typically presenting as common colds (van der Hoek 2007). However, in the 21st century, three highly pathogenic HCoVs - severe acute respiratory syndrome coronavirus (SARS-CoV-1) in 2003, Middle East Respiratory Syndrome coronavirus (MERS CoV) in 2012, and SARS-CoV-2 in 2019 - emerged from animal reservoirs to cause global epidemics with alarming morbidity and mortality (De Wit et al. 2016; Fung & Liu 2019; Marra et al. 2003; Paules et al. 2020).
During the 2003 outbreak of SARS-CoV-1, 8,098 people worldwide became sick. Of these, 774 died. In the United States, only eight people had laboratory evidence of SARS-CoV-1 infection. All of these people had traveled to other parts of the world where the disease was spreading. Community spread was not observed in the United States (De Wit et al. 2016; WHO - SARS). A second human coronavirus, MERS-CoV, first observed in 2012, has been identified in 2,494 patients with respiratory distress of whom 858 have died. Human-to-human transmission of the virus appears to be limited (De Wit et al. 2016; WHO – MERS).
In December 2019, yet another pathogenic HCoV, 2019 novel coronavirus (2019 nCoV), was recognized, initially in Wuhan, China. The World Health Organization has named the disease caused by the 2019 novel coronavirus COronaVIrus Disease 2019, or COVID-19. The disease has also been referred to as 2019 novel coronavirus or 2019 nCoV.
SARS-CoV-1 and SARS-CoV-2 viral infection pathways are annotated in this section, as are drugs that potentially modulate the infection processes. Many of the steps of SARS-CoV-1 infection have been characterized experimentally in the past 15 years (Fung & Liu 2019; Masters 2006), and this experimental work has allowed the annotation here of the infection process and interactions with host proteins in molecular detail. Less comparable data is yet available for SARS-CoV-2 infection, but the similarity in the genomes and predicted proteomes of the two viruses allows the inference of a detailed infection pathway for SARS-CoV-2 that has been manually annotated as well with experimental results published in the first half of 2020.
R-HSA-9679514 SARS-CoV-1 Genome Replication and Transcription Using the genomic RNA as a template, the coronavirus replicase synthesizes full-length negative-sense antigenome, which in turn serves as a template for the synthesis of new genomic RNA (Masters 2006). The polymerase can also switch template during discontinuous transcription of the genome at specific sites called transcription-regulated sequences, thereby producing a 5'-nested set of negative-sense sgRNAs, which are used as templates for the synthesis of a 3'-nested set of positive-sense sgRNAs (Masters 2006). Although genome replication/transcription is mainly mediated by the viral replicase and confines in the replication-transcription complex (RTC), the involvement of various additional viral and host factors has been implicated. For instance, coronavirus N protein is known to serve as an RNA chaperone and facilitate template switching (Zúñiga et al. 2007, Zúñiga et al. 2010). Importantly, the N protein of SARS-CoV-1 and mouse hepatitis virus (MHV-JHM) is also phosphorylated by the host glycogen synthase kinase 3 (GSK3), and inhibition of GSK3 was shown to inhibit viral replication in Vero E6 cells infected with SARS-CoV-1 (Wu et al. 2009). Additionally, GSK3-mediated phosphorylation of the MHV-JHM N protein recruited an RNA-binding protein DEAD-box helicase 1 (DDX1), which facilitates template read-through, favoring the synthesis of genomic RNA and longer sgRNAs (Wu et al. 2014). Another RNA-binding protein called heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) can also bind tightly to SARS-CoV N protein and potentially regulate viral RNA synthesis (Luo et al. 2005). Host RNA-binding proteins could also bind directly to untranslated regions (UTRs) of the coronavirus genome to modulate replication/transcription, such as zinc finger CCHC-type and RNA-binding motif 1 (ZCRB1) binding to the 5-UTR of IBV (Tan et al. 2012), mitochondrial aconitase binding to the 3' UTR of MHV (Nanda and Leibowitz 2001), and poly(A)-binding protein (PABP) to the poly(A) tail of bovine coronavirus (Spagnolo and Hogue 2000). For review, please refer to Snijder et al. 2016 and Fung and Liu 2019.
R-HSA-9678108 SARS-CoV-1 Infection The SARS-CoV-1 coronavirus is the causative agent of the outbreak of severe acute respiratory syndrome in 2003 that caused 8,098 known cases of the disease and 774 deaths. The molecular events involved in viral infection and the response of the human host to it have since been studied in detail and are annotated here (de Wit et al. 2016; Marra et al. 2003). The SARS-CoV-1 viral infection pathway here uses entries listed in the UniProt "Human SARS coronavirus (SARS-CoV) (Severe acute respiratory syndrome coronavirus)" taxonomy.
SARS-CoV-1 infection begins with the binding of viral S (spike) protein to cell surface angiotensin converting enzyme 2 (ACE2) and endocytosis of the bound virion. Within the endocytic vesicle, host proteases mediate cleavage of S protein into S1 and S2 fragments, leading to S2-mediated fusion of the viral and host endosome membranes and release of the viral capsid into the host cell cytosol. The capsid is uncoated to free the viral genomic RNA, whose cap-dependent translation produces polyprotein pp1a and, by means of a 1-base frameshift, polyprotein pp1ab. Autoproteolytic cleavage of pp1a and pp1ab generates 15 or 16 nonstructural proteins (nsps) with various functions. Importantly, the RNA dependent RNA polymerase (RdRP) activity is encoded in nsp12. Nsp3, 4, and 6 induce rearrangement of the cellular endoplasmic reticulum membrane to form cytosolic double membrane vesicles (DMVs) where the viral replication transcription complex is assembled and anchored. With viral genomic RNA as a template, viral replicase-transcriptase synthesizes a full length negative sense antigenome, which in turn serves as a template for the synthesis of new genomic RNA. The replicase-transcriptase can also switch template during discontinuous transcription of the genome at transcription regulated sequences to produce a nested set of negative-sense subgenomic (sg) RNAs, which are used as templates for the synthesis of positive-sense sgRNAs that are translated to generate viral proteins. Finally, viral particle assembly occurs in the ER Golgi intermediate compartment (ERGIC). Viral M protein provides the scaffold for virion morphogenesis (Fung & Liu 2019; Masters 2006).
R-HSA-9692916 SARS-CoV-1 activates/modulates innate immune responses Coronaviruses (CoVs) are positive-sense RNA viruses that replicate in the interior of double membrane vesicles (DMV) in the cytoplasm of infected cells (Stertz S et al. 2007; Knoops K et al. 2008). The viral replication and transcription are facilitated by virus-encoded non-structural proteins (SARS-CoV-1 nsp1–nsp16) that assemble to form a DMV-bound replication-transcription complex (RTC). The replication strategy of CoVs can generate both single-stranded RNA (ssRNA) and double-stranded RNA (dsRNA) species, that may act as pathogen-associated molecular patterns (PAMPs) recognized by pattern recognition receptor (PRR) such as toll-like receptor 7 (TLR7) and TLR8, antiviral innate immune response receptor RIG-I (also known as DEAD box protein 58, DDX58) and interferon-induced helicase C domain-containing protein 1 (IFIH1, also known as MDA5) (Cervantes-Barragan L et al. 2007; Chen Y et al. 2009, 2011; Daffis S et al. 2010; Li Y et al. 2013). The activated PRRs trigger signaling pathways to produce type I and type III interferons IFNs and proinflammatory mediators that perform antiviral functions. This Reactome module describes the mechanisms underlying PRR-mediated sensing of the severe acute respiratory syndrome coronavirus type 1 (SARS-CoV-1) infection. First, endosomal recognition of viral ssRNA occurs by means of TLR7 and TLR8 which detect GU-rich ssRNA sequences. Specifically, GU-rich ssRNA oligonucleotides derived from SARS-CoV-1 stimulated mononuclear phagocytes to release considerable levels of pro‑inflammatory cytokines TNF‑a, IL‑6 and IL‑12 via TLR7 and TLR8 (Li Y et al. 2013). Second, SARS-CoV-1 dsRNA replication intermediates can be recognized by cytoplasmic receptors DDX58 and IFIH1 which bind to mitochondrial antiviral-signaling protein (MAVS, IPS-1) to induce the IFN-mediated antiviral response. In addition, the module shows an antiviral function of interferon-induced protein with tetratricopeptide repeats 1 (IFIT1) that directly binds and sequesters viral single-stranded uncapped 5′-ppp RNA and cap-0 RNA (Daffis S et al. 2010). This module also describes several strategies developed by SARS-CoV-1 to evade or alter host immunity, including escaping innate immune sensors, inhibiting IFN production and signaling, and evading antiviral function of IFN stimulated gene (ISG) products. For example, viral dsRNA replication intermediates derived from SARS‑CoV‑1 were shown to associate with RTC bound to double membrane vesicles, which protected viral RNA from sensing by DDX58 or IFIH1 (Stertz S et al. 2007; Knoops K et al. 2008). Further, SARS-CoV-1 encodes nsp14 and nsp16 which possess guanine-N7-methyltransferase activity and 2’-O-methyl-transferase activity respectively (Chen Y et al. 2009, 2011). SARS-CoV-1 nsp14 generates 5' cap-0 viral RNA (m7GpppN, guanine N7-methylated) and nsp16 further methylates cap-0 viral RNA. These viral RNA modifications mimic the 5'-cap structure of host mRNAs allowing the virus to efficiently evade recognition by cytosolic DDX58 and IFIH1 (Chen Y et al. 2009, 2011; Daffis S et al. 2010). The nsp16-mediated ribose 2′-O-methylation of viral RNA also blocks the antiviral function of IFIT1 complexes (Menachery VD et al. 2014). Further, the uridylate‐specific endoribonuclease (EndoU) activity of viral nsp15 degrades viral RNA to hide it from innate immune sensors (Bhardwaj K et al. 2006; Ricagno S et al. 2006). Moreover, SARS-CoV-1 encodes several proteins that directly bind to host targets associated with SARS‑CoV‑1 infection and cytokine production (Frieman M et al. 2009; Hu Y et al. 2017; Kopecky-Bromberg SA et al. 2007; Lindner H et al. 2005; Siu KL et al. 2009). This Reactome module describes several such binding events and their consequences. For example, as a de-ubiquitinating enzyme, viral nsp3 binds to and removes polyubiquitin chains of signaling proteins such as TRAF3, TRAF6, STING, IkBA, and IRF3 thereby modulating the formation of signaling complexes and the activation of IRF3/7 and NFkappaB (Sun L et al. 2012; Chen X et al. 2014; Li SW et al. 2016). This inhibits IFN production downstream of TLR7/8, DDX58, IFIH1, MAVS and STING signaling pathways. Binding of SARS-CoV-1 nucleocapsid (N) protein to E3 ubiquitin ligase TRIM25 inhibits TRIM25-mediated DDX58 ubiquitination and DDX58-mediated signaling pathway (Hu Y et al. 2017). Next, SARS‑CoV‑1 membrane (M) protein targets IBK1/IKBKE and TRAF3 to prevent the formation of the TRAF3:TANK:TBK1/IKBKE complex and thereby inhibits TBK1/IKBKE‑dependent activation of IRF3/IRF7 transcription factors downstream of DDX58, IFIH1 and adaptor MAVS (Siu KL et al. 2009; 2014). The ion channel activities of open reading frame 3a (orf3a or 3a) and E contribute to activation of the NLRP3 inflammasome leading to highly inflammatory pyroptotic cell death (Nieto‑Torres JL et al. 2015; Chen IY et al. 2019; Yue Y et al. 2018). Viral 3a promoted the NLRP3-mediated formation of PYCARD (ASC) speck by interaction with both TRAF3 and PYCARD (ASC) (Siu KL et al. 2019). Binding of 3a to caspase-1 (CASP1) enhanced CASP1-mediated cleavage of interleukin 1 beta (IL‑1β) downstream of the NLRP3 inflammasome pathway (Yue Y et al. 2018). Like 3a, SARS-CoV-1 8b was found to bind to NLRP3 activating the NLRP3 inflammasome and triggering IL‑1β release (Shi CS et al. 2019). 8b was also shown to bind IRF3, inhibiting subsequent IRF3 dimerization (Wong et al. 2018). At the plasma membrane, binding of SARS-CoV-1 7a to host BST2 disrupts the antiviral tethering function of BST2 which restricts the release of diverse mammalian enveloped viruses (Taylor JK et al. 2015). SARS-CoV-1 9b (orf9b) inhibits the MAVS-mediated production of type I IFNs by targeting TOMM70 on the mitochondria (Jiang HW et al. 2020). SARS-CoV-1 6 (orf6) inhibits the IFN signaling pathway by tethering karyopherins KPNA2 and KPNB1 to the endoplasmic reticulum (ER)/Golgi intermediate compartment (ERGIC) and thus blocking the KPNA1:KPNB1-dependent nuclear import of STAT1 (Frieman M et al. 2007). Binding of SARS-CoV-1 nsp1 to peptidyl-prolyl isomerases (PPIases) and calcipressin-3 (RCAN3) significantly activates the cyclophilin A/NFAT pathway, ultimately enhancing the induction of the IL-2 promoter (Pfefferle et al, 2011; Law et al, 2007). At last, SARS‑CoV‑1 3b, after translocating to the nucleus, binds to transcription factor RUNX1 and increases its promoting activity (Varshney et al, 2012).
R-HSA-9735869 SARS-CoV-1 modulates host translation machinery Severe acute respiratory syndrome coronavirus type 1 (SARS-CoV-1) nonstructural protein 1 (nsp1) and nucleocapsid protein (N) disrupt mRNA translation upon SARS-CoV-1 infection in human cells.
R-HSA-9692912 SARS-CoV-1 targets PDZ proteins in cell-cell junction PDZ domains are protein‑protein recognition sequences, consisting of 80–90 amino acids that bind to a PDZ‑binding motif (PBM), usually located at the carboxy‑terminus of a target protein (Hung AY & Sheng M 2002; Gerek ZN et al. 2009; Munz M et al. 2012). Proteins containing PDZ domains are typically found in the cell cytoplasm or in association with the plasma membrane and play a role in cell‑cell junction formation, establishment of cellular polarity, and signal transduction pathways. The multidomain structure of PDZ-containing proteins enables them to interact with multiple binding partners simultaneously, thereby assembling larger protein complexes (Harris BZ & Lim WA 2001). Viruses also encode PBM-containing proteins that bind to cellular PDZ proteins. Viral PBMs target cellular PDZ-containing proteins involved in tight junction formation, cell polarity establishment, and apoptosis (Javier RT & Rice AP 2011).
R-HSA-9735871 SARS-CoV-1 targets host intracellular signalling and regulatory pathways Severe acute respiratory syndrome coronavirus type 1 (SARS‑CoV‑1) encodes several proteins that modulate host intracellular signaling and regulatory pathways. Among them are nucleocapsid N, membrane M and 3a proteins that directly bind to host targets associated with SARS‑CoV‑1 infection and cytokine production. This Reactome module describes several such binding events and their consequences. First, SARS‑CoV‑1 M binds to 3‑phosphoinositide‑dependent protein kinase 1 (PDPK1) to inhibit PKB/Akt activation (Chan et al. 2007; Tsoi et al. 2014). Second, SARS‑CoV‑1 N binds to SMAD3 to alter transforming growth factor‑β (TGF‑β) signaling (Zhao et al. 2008). This interaction prevents SMAD3 from complexing with SMAD4, thereby blocking TGF-β-sensitized apoptosis. The association of N with SMAD3 also enhances the TGF-β-induced expression of PAI-1 (SERPINE1) promoting tissue fibrosis (Zhao et al. 2008). Third, N protein binding to proteasome subunit p42 (PSMC6) modulates proteasome‑regulated degradation of proteins (Wang et al. 2010). Fourth, SARS‑CoV‑1 N binds SUMO-conjugating enzyme UBC9 (UBE2I) to regulate the activity of UBE2I, affecting downstream signaling factors involved in the cell cycle, in addition to its function in the process of sumoylation (Fan et al. 2006). Finally, binding of viral 3a to the regulator and scaffolding protein caveolin‑1 (CAV1) may regulate virus uptake as well as the trafficking of viral structural proteins (Padhan et al. 2007).
R-HSA-9692914 SARS-CoV-1-host interactions Coronaviruses are a group of enveloped viruses with single‑stranded, positive‑sense RNA genomes. Each of the steps of viral replication - attachment and entry, translation of viral replicase, genome transcription and replication, translation of structural proteins, and virion assembly and release - involves host factors. These interactions can cause alterations in cellular structure and physiology, and activate host stress responses, autophagy, cell death, and processes of innate immunity (Fung TS & Liu DX 2019). This Reactome module describes molecular mechanisms by which severe acute respiratory syndrome coronavirus type 1 (SARS-CoV-1) modulates host cell death pathways, innate immune responses, translation, intracellular signaling and regulatory pathways, and PDZ-mediated cell-cell junctions.
R-HSA-9692913 SARS-CoV-1-mediated effects on programmed cell death Programmed cell death (PCD) pathways, including pyroptosis, apoptosis, and necroptosis, are induced in infected host cells as an integral part of host defense to restrict microbial infections and regulate inflammatory responses (reviewed in Jorgensen I et al. 2017; Galluzzi L et al. 2018). Apoptosis is a noninflammatory form of cell death driven by the initiator caspase‑mediated cleavage of executioner caspase‑3 and ‑7. It facilitates degradation of the cellular contents but these are not released to the extracellular space. Necroptosis and pyroptosis are highly inflammatory forms of cell death that lead to cell lysis and release of pro‑inflammatory cytokines such as interleukin (IL)‑1β, tumour necrosis factor alpha (TNF‑α), IL6, IL18 and cellular contents, which can cause severe inflammation (reviewed in Jorgensen I et al. 2017; Galluzzi L et al. 2018; Pasparakis M & Vandenabeele P 2015). Gasdermins (GSDMs) exert pore‑forming activity in inflammasome‑dependent pyroptosis, while the mixed lineage kinase domain‑like (MLKL) protein functions as the executioner during necroptosis (Shi J et AL. 2015; Upton JW et al. 2017). Inflammation is a fundamental protective mechanism in elimination of microorganisms, and is normally tightly regulated by certain mediators, in particular IL10, to promote resolution of inflammation (reviewed in Sugimoto MA et al. 2016). Microbial pathogens are able to trigger and/or modulate host PCD and inflammatory response through multiple mechanisms.
This Reactome module describes the roles of severe acute respiratory syndrome‑associated coronavirus type 1 (SARS‑CoV‑1) 3a, E, and 7a proteins in the induction of host cell death pathways. SARS‑CoV‑1 open reading frame‑3a (3a) binds host receptor interacting serine/threonine protein kinase 3 (RIPK3), facilitating RIPK3 oligomerization and the ion channel functionality of viral 3a, inducing inflammatory cell death and release of cellular contents (Yue Y et al. 2018). Enhanced production and release of proinflammatory cytokines leads to the cytokine storm that is considered to play a major role in SARS‑CoV type 1and 2 infections (reviewed in Channappanavar R & Perlman S 2017; Yang L et al. 2020). The module also describes induction of apoptosis by SARS‑CoV‑1 E and 7a proteins through their interaction with anti‑apoptotic BCL2L1 (Yang Y et al. 2005; Tan YX et al. 2007). Low levels of BCL2L1 may lead to enhanced function of pro‑apoptotic molecules, contributing to the depletion of T lymphocytes by apoptosis (Yang Y et al. 2005). This may lead to the lymphopenia observed in SARS patients, particularly in severe cases (Diao B et al. 2020; Chen Z & Wherry EJ 2020).
R-HSA-9694682 SARS-CoV-2 Genome Replication and Transcription This COVID-19 pathway has been created by a combination of computational inference from SARS-CoV-1 data (https://reactome.org/documentation/inferred-events) and manual curation, as described in the summation for the overall SARS-CoV-2 infection pathway. Specifically, binding of the replication-transcription complex (RTC) to the RNA template and the polymerase activity of nsp12 (Hillen et al. 2020, Wang et al. 2020, Yin et al. 2020), helicase activity of nsp13 (Chen et al. 2020, Ji et al. 2020, Shu et al. 2020), capping activity of nsp16 (Viswanathan et al. 2020), and polyadenylation of SARS-CoV-2 genomic RNA and transcripts (Kim et al. 2020, Ravindra et al. 2020) have been studied directly, and the remaining steps have been inferred from previous studies in SARS-CoV-1 and related coronaviruses.
Using the genomic RNA as a template, the coronavirus replicase synthesizes full-length negative-sense antigenome, which in turn serves as a template for the synthesis of new genomic RNA (Masters 2006). The polymerase can also switch template during discontinuous transcription of the genome at specific sites called transcription-regulated sequences, thereby producing a 5'-nested set of negative-sense sgRNAs, which are used as templates for the synthesis of a 3'-nested set of positive-sense sgRNAs (Masters 2006). Although genome replication/transcription is mainly mediated by the viral replicase and confines in the RTC, the involvement of various additional viral and host factors has been implicated. For instance, coronavirus N protein is known to serve as an RNA chaperone and facilitate template switching (Zúñiga et al. 2007, Zúñiga et al. 2010). Importantly, the N protein of SARS-CoV-1 and mouse hepatitis virus (MHV-JHM) is also phosphorylated by the host glycogen synthase kinase 3 (GSK3), and inhibition of GSK3 was shown to inhibit viral replication in Vero E6 cells infected with SARS-CoV-1 (Wu et al. 2009). Additionally, GSK3-mediated phosphorylation of the MHV-JHM N protein recruits an RNA-binding protein DEAD-box helicase 1 (DDX1), which facilitates template read-through, favoring the synthesis of genomic RNA and longer sgRNAs (Wu et al. 2014). Another RNA-binding protein called heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) can also bind tightly to SARS-CoV-1 N protein and potentially regulate viral RNA synthesis (Luo et al. 2005). Host RNA-binding proteins could also bind directly to untranslated regions (UTRs) of the coronavirus genome to modulate replication/transcription, such as zinc finger CCHC-type and RNA-binding motif 1 (ZCRB1) binding to the 5-UTR of IBV (Tan et al. 2012), mitochondrial aconitase binding to the 3' UTR of MHV (Nanda and Leibowitz 2001), and poly(A)-binding protein (PABP) to the poly(A) tail of bovine coronavirus (Spagnolo and Hogue 2000). For review, please refer to Snijder et al. 2016 and Fung and Liu 2019.
R-HSA-9694516 SARS-CoV-2 Infection This pathway, SARS-CoV-2 infection of human cells (COVID-19), was initially generated via electronic inference from the manually curated and reviewed Reactome SARS-CoV-1 (Human SARS coronavirus) infection pathway. The inference process created SARS-CoV-2 events corresponding to each event in the SARS-CoV-1 pathway and populated those events with SARS-CoV-2 protein-containing physical entities based on orthology to SARS-CoV-1 proteins (https://reactome.org/documentation/inferred-events). All of these computationally created events and entities have been reviewed by Reactome curators and modified as appropriate where recently published experimental data indicate the existences of differences between the molecular details of the SARS-CoV-1 and SARS-CoV-2 infection pathways.
SARS‑CoV‑2 infection begins with the binding of viral S (spike) protein to cell surface angiotensin converting enzyme 2 (ACE2) and endocytosis of the bound virion. Within the endocytic vesicle, host proteases mediate cleavage of S protein into S1 and S2 fragments, leading to S2‑mediated fusion of the viral and host endosome membranes and release of the viral capsid into the host cell cytosol. The capsid is uncoated to free the viral genomic RNA, whose cap‑dependent translation produces polyprotein pp1a and, by means of a 1‑base frameshift, polyprotein pp1ab. Autoproteolytic cleavage of pp1a and pp1ab generates 15 or 16 nonstructural proteins (nsps) with various functions. Importantly, the RNA dependent RNA polymerase (RdRP) activity is encoded in nsp12. Nsp3, 4, and 6 induce rearrangement of the cellular endoplasmic reticulum membrane to form cytosolic double membrane vesicles (DMVs) where the viral replication transcription complex is assembled and anchored. With viral genomic RNA as a template, viral replicase‑transcriptase synthesizes a full length negative sense antigenome, which in turn serves as a template for the synthesis of new genomic RNA. The replicase‑transcriptase can also switch template during discontinuous transcription of the genome at transcription regulated sequences to produce a nested set of negative‑sense subgenomic (sg) RNAs, which are used as templates for the synthesis of positive‑sense sgRNAs that are translated to generate viral proteins. Finally, viral particle assembly occurs in the ER Golgi intermediate compartment (ERGIC). Viral M protein provides the scaffold for virion morphogenesis (Hartenian et al. 2020; Fung & Liu 2019; Masters 2006).
This Reactome module also describes molecular mechanisms by which SARS-CoV-2 modulates innate and adaptive immune responses, autophagy, host translation, intracellular signaling and regulatory pathways, and PDZ-mediated cell-cell junctions, mostly annotated from studies of cells infected with SARS-CoV-2.
R-HSA-9705671 SARS-CoV-2 activates/modulates innate and adaptive immune responses Coronaviruses (CoVs) are positive-sense RNA viruses that replicate in the interior of double membrane vesicles (DMV) in the cytoplasm of infected cells (Stertz S et al. 2007; Knoops K et al. 2008; V'kovski P et al. 2021). The viral replication and transcription are facilitated by virus-encoded non-structural proteins (SARS-CoV-2 nsp1–nsp16) that assemble to form a DMV-bound replication-transcription complex (RTC) (V'kovski P et al. 2021). The replication strategy of CoVs can generate both single-stranded RNA (ssRNA) and double-stranded RNA (dsRNA) species, that may act as pathogen-associated molecular patterns (PAMPs) recognized by pattern recognition receptor (PRR) such as toll-like receptor 7 (TLR7) and TLR8, antiviral innate immune response receptor RIG-I (also known as DEAD box protein 58, DDX58) and interferon-induced helicase C domain-containing protein 1 (IFIH1, also known as MDA5) (Salvi V et al. 2021; Campbell GR et al. 2021; Rebendenne A et al. 2021). The activated PRRs trigger signaling pathways to produce type I and type III interferons IFNs and proinflammatory mediators that perform antiviral functions. This Reactome module describes the mechanisms underlying PRR-mediated sensing of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection. First, endosomal recognition of viral ssRNA occurs by means of TLR7 and TLR8, which detect GU-rich ssRNA sequences (Salvi V et al. 2021; Campbell GR et al. 2021). Second, SARS-CoV-2 dsRNA replication intermediates can be recognized by cytoplasmic receptors DDX58 and IFIH1 which bind to mitochondrial antiviral-signaling protein (MAVS, IPS-1) to induce the IFN-mediated antiviral response (Rebendenne A et al. 2021; Yin X et al. 2021). In addition, SARS-CoV-2 E can be sensed by TLR2 (Zheng M et al. 2021). Further, cellular nucleic acid-binding protein (CNBP) and La-related protein 1 (LARP1) can directly bind SARS-CoV-2 gRNA to repress SARS-CoV-2 replication (Schmidt N et al. 2021). This module also describes several strategies developed by SARS-CoV-2 to evade or alter host immunity, including escaping innate immune sensors, inhibiting IFN production and signaling, and evading antiviral function of IFN stimulated gene (ISG) products. For example, SARS-CoV-2 encodes nsp14 and nsp16 which possess guanine-N7-methyltransferase activity and 2’-O-methyl-transferase activity respectively (Ogando NS et al. 2020; Krafcikova P et al. 2020; Viswanatha T et al. 2020; Lin S et al. 2021; Yan L et al. 2021). In human coronaviruses nsp14 generates 5' cap-0 viral RNA (m7GpppN, guanine N7-methylated) and nsp16 further methylates cap-0 viral RNA. These viral RNA modifications mimic the 5'-cap structure of host mRNAs allowing the virus to efficiently evade recognition by cytosolic DDX58 and IFIH1 (Chen Y et al. 2009, 2011; Daffis S et al. 2010, shown for CoVs such as SARS-CoV-1 and MERS-CoV). Structural studies and computational analysis suggest that properties and biological functions of SARS-CoV-2 nsp14 and nsp16 could be very similar to these of SARS-CoV-1 (Rosas-Lemus M et al. 2020; Lin S et al. 2020; Viswanathan T et al. 2020; Krafcikova P et al. 2020; Jiang Y et al. 2020; Wilamowski M et al. 2021). Further, the uridylate‐specific endoribonuclease (EndoU) activity of SARS-CoV-2 nsp15 degrades viral RNA to hide it from innate immune sensors (Frazier MN et al. 2021). Moreover, SARS-CoV-2 encodes several proteins that directly bind to host targets associated with SARS‑CoV‑2 infection and cytokine production (Shin D et al. 2020; Viswanathan T et al. 2020; Xia H et al. 2020; Matsuyama T et al. 2020; Yuen CK et al. 2020; reviewed by Park A & Iwasaki A 2020). This Reactome module describes several such binding events and their consequences. For example, as a deubiquitinating and deISGylating enzyme, viral nsp3 binds to and removes ISG15 from signaling proteins such as IRF3 and IFIH1 thereby modulating the formation of signaling complexes and the activation of IRF3/7 and NF-kappaB (Liu CQ et al. 2021). Binding of SARS-CoV-2 nsp6, nsp13 or membrane (M) protein to cytosolic TBK1 prevents IRF3/7 activation and inhibits IFN production downstream of DDX58, IFIH1, MAVS and STING signaling pathways (Xia H et al. 2020; Sui L et al. 2021). Next, M protein targets MAVS to prevent the formation of the MAVS signalosome complex and thereby inhibits downstream signaling pathways of DDX58 and IFIH1 (Fu YZ et al. 2021). Binding of SARS-CoV-2 nucleocapsid (N) protein to E3 ubiquitin ligase TRIM25 inhibits TRIM25-mediated DDX58 ubiquitination and the DDX58 signaling pathway (Gori SG et al. 2021). N interacts with NLRP3 to promote the assembly and activation of the NLRP3 inflammasome (Pan P et al. 2021). The interaction between viral N and MASP2 promotes MASP2-mediated cleavage of C4 (Ali YM et al. 2021) and C2 (Kang S et al. 2021) leading to the hyperactivation of the complement system. Besides, viral N promotes NF-kappaB activation by targeting signaling complexes of TAK1 and IKK (Wu Y et al. 2021). The ion channel activities of accessory protein ORF3a or 3a (open reading frame 3a) and SARS‑CoV‑2 envelope (E) protein contribute to activation of the NLRP3 inflammasome leading to highly inflammatory pyroptotic cell death (based on findings for SARS-CoV-1, Siu KL et al. 2019). SARS-CoV-2 nsp5 protease (3CLpro) cleaves TAB1, a component of the TAK1 complex, thus inhibiting NF-kappaB activation (Moustaqil M et al .2021). 3CLpro targets NLRP12 which modulates the expression of inflammatory cytokines through the regulation of the NFkappaB and MAPK pathways (Moustaqil M et al. 2021). SARS-CoV-2 6 (ORF6) interacts with importin KPNA2 and components of the nuclear pore complex, NUP98 and RAE1, to block nuclear translocation of IRF3, STAT1 and STAT2 (Xia H et al. 2020; Miorin L et al. 2020). SARS-CoV-2 9b (ORF9b) inhibits the MAVS-mediated production of type I IFNs by targeting TOMM70 on the mitochondria (Jiang HW et al. 2020). Binding of mitochondrial viral 9 to IKBKG prevents MAVS-dependent NF-kappaB activation (Wu J et al. 2021). Although the evasion mechanisms are mainly conserved between SARS-CoV-1 and SARS-CoV-2 (Gordon DE et al. 2020), studies identified SARS-CoV-2-specific modulations of host immune response that may contribute to pathophysiological determinants of COVID-19 (Gordon DE et al. 2020; Schiller HB et al. 2021). This Reactome module describes several virus-host interactions identified in cells during SARS-CoV-2, but not SARS-CoV-1, infection. For example, SARS-CoV-2 8 (ORF8) regulates the expression of class I MHC on the surface of the infected cells through an autophagy-dependent lysosomal degradation of class I MHC (Zhang Y et al. 2021). At the plasma membrane, binding of secreted viral 8 to IL17RA activates IL17 signaling pathway leading to an increased secretion of cytokines/chemokines thus contributing to cytokine storm during SARS-CoV-2 infection (Lin X et al. 2021). Furthermore, SARS-CoV-2-host interactome and proteomics studies identified various human proteins that are targeted by SARS-CoV-2 proteins (Gordon DE et al. 2020a, b; Bojkova D et al. 2020; Stukalov A et al. 2021; Li J et al. 2021; Messina F et al. 2021). This Reactome module does not cover all identified SARS-CoV-2–human interactions; the module describes those associations that were functionally validated.
R-HSA-9754560 SARS-CoV-2 modulates autophagy Autophagy is activated during microbial infection to exert antimicrobial defense mechanisms by targeting pathogen-associated components for lysosomal degradation. Pathogens evolved various strategies to manipulate autophagy responses. This Reactome module describes the impact of SARS-CoV-2 infection on autophagy. SARS-CoV-2-encoded proteins, such as open reading frame 3a (ORF3a, 3a) and ORF7a (7a), were shown to colocalize with markers of late endosomal membrane, lysosomal membrane and trans-Golgi network (Hayn M et al. 2021; Koepke L et al. 2021; Zhang Y et al. 2021). Both 3a and 7a block autophagic flux in human cells, but use different strategies (Hayn M et al. 2021; Koepke L et al. 2021). While 7a lowers the acidity of lysosome (Koepke L et al. 2021), ORF3a prevents autophagosome-lysosome fusion (Zhang Y et al. 2021; Qu Y et al. 2021; Miao G et al. 2021). Thus, the SARS-CoV-2 infection stimulates autophagy and leads to an accumulation of autophagosomes but blocks fusion between autophagosome and lysosome thereby preventing degradation of the cargo. In addition, SARS-CoV-2 membrane (M) protein associates with the mitochondrion to promote mitophagy (Hui X et al. 2021).
R-HSA-9754678 SARS-CoV-2 modulates host translation machinery SARS-CoV-2 encodes several proteins that have been implicated in shutting off host expression (Banerjee AK et al. 2020; Finkel Y et al. 2021). This Reactome module describes SARS-CoV-2 nonstructural protein 1 (nsp1)-mediated shutdown of host protein translation by binding to the mRNA entrance channel on the 40S subunit (Banerjee AK et al. 2020), SARS-CoV-2 nsp16-mediated disruption of global mRNA splicing via binding to the 5′ splice site recognition sequence of U1 snRNA and the branchpoint recognition site of U2 snRNA, both parts of the spliceosome (Banerjee et al, 2020), and SARS-CoV-2 nsp8, nsp9-mediated suppression of protein integration into the cell membrane (Banerjee et al, 2020).
R-HSA-9705677 SARS-CoV-2 targets PDZ proteins in cell-cell junction PSD95/Dlg1/ZO-1 (PDZ) domains are protein-protein recognition sequences, consisting of 80–90 amino acids that bind to a PDZ-binding motif (PBM), usually located at the end of the carboxy-terminus of a target protein (Hung AY & Sheng M 2002; Gerek ZN et al. 2009; Munz M et al. 2012). Proteins containing PDZ domains are typically found in the cell cytoplasm or in association with the plasma membrane and play a role in a variety of cellular processes such as cell-cell junctions, cellular polarity, and signal transduction pathways. The multidomain structure of PDZ-containing proteins enables them to interact with multiple binding partners simultaneously, thereby assembling larger protein complexes (Harris BZ & Lim WA 2001). Viruses also encode PBM-containing proteins that bind to cellular PDZ proteins. Viral PBMs target cellular PDZ-containing proteins involved in tight junction formation, cell polarity establishment, and apoptosis (Javier RT & Rice AP 2011).
R-HSA-9755779 SARS-CoV-2 targets host intracellular signalling and regulatory pathways Severe acute respiratory syndrome coronavirus type 2 (SARS‑CoV‑2) encodes several proteins that modulate host intracellular signaling and regulatory pathways. Among them are membrane M, nucleocapsid N and 3a proteins that directly bind to host targets associated with SARS‑CoV‑2 infection and cytokine production. This Reactome module describes several such binding events and their consequences. First, SARS‑CoV‑2 M binds to 3‑phosphoinositide‑dependent protein kinase 1 (PDPK1) to inhibit PKB/Akt activation (Ren Y et al. 2021). Second, SARS‑CoV‑1 N binds to the host 14-3-3 protein, which regulates nucleocytoplasmic shuttling and other functions of N (Tugaeva KV et al. 2021). Third, binding of viral 3a to the regulator and scaffolding protein caveolin‑1 (CAV1) may regulate virus uptake as well as the trafficking of viral structural proteins (inferred from the orthologous protein in SARS-CoV-1).
R-HSA-9705683 SARS-CoV-2-host interactions Coronaviruses are a group of enveloped viruses with single‑stranded, positive‑sense RNA genomes. Each of the steps of viral replication - attachment and entry, translation of viral replicase, genome transcription and replication, translation of structural proteins, and virion assembly and release - involves host factors. These interactions can cause alterations in cellular structure and physiology, and activate host stress responses, autophagy, cell death, and processes of innate immunity (Fung TS & Liu DX 2019). This Reactome module describes molecular mechanisms by which severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) modulates innate and adaptive immune responses, autophagy, host translation, intracellular signaling and regulatory pathways, and PDZ-mediated cell-cell junctions, mostly annotated from studies of cells infected with SARS-CoV-2.
R-HSA-187577 SCF(Skp2)-mediated degradation of p27/p21 During G1, the activity of cyclin-dependent kinases (CDKs) is kept in check by the CDK inhibitors (CKIs) p27 and p21, thereby preventing premature entry into S phase (see Guardavaccaro and Pagano, 2006). These two CKIs are degraded in late G1 phase by the ubiquitin pathway (Pagano et al., 1995; Bloom et al., 2003) involving the ubiquitin ligase SCF(Skp2) (Tsvetkov et al., 1999; Carrano et al., 1999; Sutterluty et al., 1999, Bornstein et al., 2003) and the cell-cycle regulatory protein Cks1 (Ganoth et al., 2001; Spruck et al 2001; Bornstein et al., 2003). Recognition of p27 by SCF(Skp2) and its subsequent ubiquitination is dependent upon Cyclin E/A:Cdk2- mediated phosphorylation at Thr 187 of p27 (Montagnoli et al., 1999). There is evidence that Cyclin A/B:Cdk1 complexes can also bind and phosphorylate p27 on Th187 (Nakayama et al., 2004). Degradation of polyubiquitinated p27 by the 26S proteasome promotes the activity of CDKs in driving cells into S phase. (Montagnoli et al., 1999; Tsvetkov et al., 1999, Carrano et al 1999). The mechanism of SCF(Skp2)-mediated degradation of p21 is similar to that of p27 in terms of its requirements for the presence of Cks1 and of Cdk2/cyclin E/A (Bornstein et al.,2003; Wang et al., 2005). In addition, as observed for p27, p21 phosphorylation at a specific site (Ser130) stimulates its ubiquitination. In contrast to p27, however, ubiquitination of p21 can take place in the absence of phosphorylation, although with less efficiency (Bornstein et al.,2003). SCF(Skp2)-mediated degradation of p27/p21 continues from late G1 through M-phase. During G0 and from early G1 to G1/S, Skp2 is degraded by the anaphase promoting complex/Cyclosome and its activator Cdh1 [APC/C(Cdh1)] (Bashir et al, 2004; Wei et al, 2004). The tight regulation of APC/C(Cdh1) activity ensures the timely elimination Skp2 and, thus, plays a critical role in controlling the G1/S transition. APC/C(Cdh1) becomes active in late M-phase by the association of unphosphorylated Cdh1 with the APC/C. APC/C(Cdh1) remains active until the G1/S phase at which time it interacts with the inhibitory protein, Emi1 (Hsu et al., 2002). Inhibition of APC/C(Cdh1) activity results in an accumulation of cyclins, which leads to the phosphorylation and consequently to a further inactivation of Cdh1 at G1/S (Lukas et al., 1999). Finally, to make the inactivation of APC/C(Cdh1) permanent, Cdh1 and its E2, namely Ubc10, are eliminated in an auto-ubiquitination event (Listovsky et al., 2004; Rape and Kirschner, 2004). At G1/S, Skp2 reaccumulates as Cdh1 is inactivated, thus allowing the ubiquitination of p21 and p27 and resulting in a further increase in CDK activity.
R-HSA-174113 SCF-beta-TrCP mediated degradation of Emi1 Emi1 destruction in early mitosis requires the SCF beta-TrCP ubiquitin ligase complex. Binding of beta-TrCP to Emi1 occurs in late prophase and requires phosphorylation at the DSGxxS consensus motif as well as Cdk mediated phosphorylation. A two-step mechanism has been proposed in which the phosphorylation of Emi1 by Cdc2 occurs after the G2-M transition followed soon after by binding of beta-TrCP to the DSGxxS phosphorylation sites. Emi1 is then poly-ubiquitinated and degraded by the 26S proteasome.
R-HSA-373756 SDK interactions Sidekick-1 (SDK1) and sidekick-2 (SDK2) are cell adhesion molecules of the immunoglobulin superfamily expressed by nonoverlapping subsets of retinal neurons. They have been shown to function as neuronal targeting molecules, guiding developing neurons to specific synapses.
SDKs are concentrated at synapses that connect SDK-expressing pre- and postsynaptic partners, suggesting that their homophilic adhesion properties promote formation or stabilization of synapses.
SDKs promotes lamina-specific synaptic connections in the retina and are specifically required for the formation of neuronal circuits that detect motion (Krishnaswamy et al. 2015).
R-HSA-399955 SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion Sema3A, a prototypical semaphorin, acts as a chemorepellent or a chemoattractant for axons by activating a receptor complex comprising neuropilin-1 as the ligand-binding subunit and plexin-A1 as the signal-transducing subunit. Sema3A inhibits cell migration by inhibiting integrin ligand-binding activity.
R-HSA-5654688 SHC-mediated cascade:FGFR1 The exact role of SHC1 in FGFR signaling remains unclear. Numerous studies have shown that the p46 and p52 isoforms of SHC1 are phosphorylated in response to FGF stimulation, but direct interaction with the receptor has not been demonstrated. Co-precipitation of p46 and p52 with the FGFR2 IIIc receptor has been reported, but this interaction is thought to be indirect, possibly mediated by SRC. Consistent with this, co-precipitation of SHC1 and FGFR1 IIIc is seen in mammalian cells expressing v-SRC. The p66 isoform of SHC1 has also been co-precipitated with FGFR3, but this occurs independently of receptor stimulation, and the p66 isoform not been shown to undergo FGF-dependent phosphorylation. SHC1 has been shown to associate with GRB2 and SOS1 in response to FGF stimulation, suggesting that the recruitment of SHC1 may contribute to activation of the MAPK cascade downstream of FGFR.
R-HSA-5654699 SHC-mediated cascade:FGFR2 The exact role of SHC1 in FGFR signaling remains unclear. Numerous studies have shown that the p46 and p52 isoforms of SHC1 are phosphorylated in response to FGF stimulation, but direct interaction with the receptor has not been demonstrated. Co-precipitation of p46 and p52 with the FGFR2 IIIc receptor has been reported, but this interaction is thought to be indirect, possibly mediated by SRC. Consistent with this, co-precipitation of SHC1 and FGFR1 IIIc is seen in mammalian cells expressing v-SRC. The p66 isoform of SHC1 has also been co-precipitated with FGFR3, but this occurs independently of receptor stimulation, and the p66 isoform not been shown to undergo FGF-dependent phosphorylation. SHC1 has been shown to associate with GRB2 and SOS1 in response to FGF stimulation, suggesting that the recruitment of SHC1 may contribute to activation of the MAPK cascade downstream of FGFR.
R-HSA-5654704 SHC-mediated cascade:FGFR3 The exact role of SHC1 in FGFR signaling remains unclear. Numerous studies have shown that the p46 and p52 isoforms of SHC1 are phosphorylated in response to FGF stimulation, but direct interaction with the receptor has not been demonstrated. Co-precipitation of p46 and p52 with the FGFR2 IIIc receptor has been reported, but this interaction is thought to be indirect, possibly mediated by SRC. Consistent with this, co-precipitation of SHC1 and FGFR1 IIIc is seen in mammalian cells expressing v-SRC. The p66 isoform of SHC1 has also been co-precipitated with FGFR3, but this occurs independently of receptor stimulation, and the p66 isoform not been shown to undergo FGF-dependent phosphorylation. SHC1 has been shown to associate with GRB2 and SOS1 in response to FGF stimulation, suggesting that the recruitment of SHC1 may contribute to activation of the MAPK cascade downstream of FGFR.
R-HSA-5654719 SHC-mediated cascade:FGFR4 The exact role of SHC1 in FGFR signaling remains unclear. Numerous studies have shown that the p46 and p52 isoforms of SHC1 are phosphorylated in response to FGF stimulation, but direct interaction with the receptor has not been demonstrated. Co-precipitation of p46 and p52 with the FGFR2 IIIc receptor has been reported, but this interaction is thought to be indirect, possibly mediated by SRC. Consistent with this, co-precipitation of SHC1 and FGFR1 IIIc is seen in mammalian cells expressing v-SRC. The p66 isoform of SHC1 has also been co-precipitated with FGFR3, but this occurs independently of receptor stimulation, and the p66 isoform not been shown to undergo FGF-dependent phosphorylation. SHC1 has been shown to associate with GRB2 and SOS1 in response to FGF stimulation, suggesting that the recruitment of SHC1 may contribute to activation of the MAPK cascade downstream of FGFR.
R-HSA-2428933 SHC-related events triggered by IGF1R Phosphorylated IGF1R binds and phosphorylates SHC1 (reviewed in Pavelic et al. 2007, Chitnis et al. 2008, Maki et al. 2010, Parrella et al. 2010, Siddle et al. 2012). Phosphorylated SHC then binds GRB:SOS, which activates RAS-RAF-MAPK signaling.
R-HSA-180336 SHC1 events in EGFR signaling GRB2 can bind EGFR directly or through another SH2-containing protein, SHC1. This association leads to RAS activation.
R-HSA-1250196 SHC1 events in ERBB2 signaling All ERBB2 heterodimers, ERBB2:EGFR, ERBB2:ERBB3 and ERBB2:ERBB4, are able to activate RAF/MAP kinase cascade by recruiting SHC1 (Pinkas-Kramarski et al. 1996, Sepp-Lorenzino et al. 1996) to phosphorylated C-tail tyrosine residues in either EGFR (Y1148 and Y1173), ERBB2 (Y1196, Y1221, Y1222 and Y1248), ERBB3 (Y1328) or ERBB4 (Y1188 and Y1242 in JM-A CYT1 isoform, Y1178 and Y1232 in JM-B CYT1 isoform, Y1172 and Y1226 in JM-A CYT2 isoform). SHC1 recruitment is followed by phosphorylation (Segatto et al. 1993, Soler et al. 1994), and the phosphorylated SHC1 recruits GRB2:SOS1 complex (Xie et al. 1995), which leads to SOS1-mediated guanyl-nucleotide exchange on RAS (Xie et al. 1995) and downstream activation of RAF and MAP kinases.
R-HSA-1250347 SHC1 events in ERBB4 signaling All splicing isoforms of ERBB4 possess two tyrosine residues in the C-tail that serve as docking sites for SHC1 (Kaushansky et al. 2008, Pinkas-Kramarski et al. 1996, Cohen et al. 1996). Once bound to ERBB4, SHC1 becomes phosphorylated on tyrosine residues by the tyrosine kinase activity of ERBB4, which enables it to recruit the complex of GRB2 and SOS1, resulting in the guanyl-nucleotide exchange on RAS and activation of RAF and MAP kinase cascade (Kainulainen et al. 2000).
R-HSA-9726840 SHOC2 M1731 mutant abolishes MRAS complex function This pathway describes the effect of a loss-of-function mutation in SHOC2 on RAF activation (Rodriguez-Viciano et al, 2006; Hannig et al, 2014). How both loss- and gain-of-function SHOC2 mutants can contribute to RAF pathway activation remains to be elucidated.
R-HSA-427359 SIRT1 negatively regulates rRNA expression Expression of rRNA genes is coupled to the overall metabolism of the cell by the NAD-dependent histone deacetylase SIRT1, a component of the Energy-dependent Nucleolar Silencing Complex (eNoSC) (Murayama et al. 2008, reviewed in Salminen and Kaarniranta 2009, Grummt and Voit 2010). eNoSC comprises Nucleomethylin (NML), SIRT1, and the histone methylase SUV39H1 (Murayama et al. 2008). Deacetylation and methylation of histone H3 in the chromatin of a rRNA gene by eNoSC causes reduced expression of the gene. When glucose is low, NAD is high (NADH is low), activity of SIRT1 is high, and activity of rRNA genes is reduced. It is hypothesized that eNoSC forms on a nucleosome containing dimethylated lysine-9 on histone H3 (H3K9me2) and then eNoSC deacetylates and dimethylates the adjacent nucleosome, thus catalyzing spreading of H3K9me2 throughout the gene.
R-HSA-77588 SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs There are two well-documented trans-acting factors required for histone pre-mRNA processing. These are:
1 Stem-loop binding protein (SLBP), also termed hairpin binding protein (HBP). This 32 kDa protein is likely the first protein that binds to the histone pre-mRNA as it is being transcribed.
The U7 snRNP. This particle contains the U7 snRNA, the smallest of the snRNAs which varies from 57-70 nts long depending on the species. The 5' end of U7 snRNA binds to a sequence 3' of the stemloop, termed the histone downstream element (HDE). There are a number of proteins found in the U7 snRNP. There are 7 Sm proteins, as are present in the spliceosomal snRNP. Five of these proteins are the same as ones found in the spliceosomal snRNPs and there are 2, Lsm10 and Lsm11 that are unique to U7 snRNP.
A third protein joins the U7 snRNP, ZFP100, a large zinc finger protein. ZFP100 interacts with SLBP bound to the histone pre-mRNA and with Lsm11 and likely plays a critical role in recruiting U7 snRNP to the histone pre-mRNA.
It should be noted that there must be other trans-acting factors, including the factor that catalyzes the cleavage reaction. The cleavage occurs in the presence of EDTA as does the cleavage reaction in polyadenylation, it is likely that this reaction is catalyzed by a protein. There may well be additional proteins associated with U7 snRNP, and since under some conditions in vitro processing occurs in the absence of SLBP, it is possible that all of the other factors required for processing are associated with the active form of U7 snRNP.
R-HSA-111367 SLBP independent Processing of Histone Pre-mRNAs This class of mRNAs is expressed from genes that lack introns yet the transcripts end in polyA tails. These tails are formed by a mechanism similar to that for pre-mRNAs containing introns. It is believed that there is a cis-element that replaces the 3' splice site that normally serves to activate polyadenylation of intron containing pre-mRNAs.
R-HSA-5619102 SLC transporter disorders The solute-carrier gene (SLC) superfamily encodes membrane-bound transporters comprising 55 gene families with at least 362 putatively functional protein-coding genes. The gene products include passive transporters, symporters and antiporters and are located in all cellular and organelle membranes. Curated here is a list of SLCs, where mutations within them can result in disease (Hediger et al. 2013).
R-HSA-425407 SLC-mediated transmembrane transport Proteins with transporting functions can be roughly classified into 3 categories: ATP-powered pumps, ion channels, and transporters. Pumps utilize the energy released by ATP hydrolysis to power the movement of the substrates across the membrane, against their electrochemical gradient. Channels at the open state can transfer the substrates (ions or water) down their electrochemical gradient, at an extremely high efficiency (up to 108 s-1). Transporters facilitate the movement of a specific substrate either against or following their concentration gradient, at a lower speed (about 102 -104 s-1); as generally believed, conformational change of the transporter protein is involved in the transfer process.
According to the Human Genome Organization (HUGO) Gene Nomenclature Committee, all human transporters can be grouped into the solute-carrier (SLC) superfamily (http://www.genenames.org/genefamilies/SLC). Currently, there are 55 SLC families in the superfamily, with a total of at least 362 putatively functional protein-coding genes (Hediger et al. 2004, He et al. 2009; http://www.bioparadigms.org/slc/intro.htm). At least 20-25% amino-acid sequence identity is shared by members belonging to the same SLC family. No homology is shared between different SLC families. While the HUGO nomenclature system by definition only includes human genes, the nomenclature system has been informally extended to include rodent species through the use of lower cases letters (e.g., Slc1a1 denotes the rodent ortholog of the human SLC1A1 gene). And it's worthwhile to mention that pumps, channels and aquaporins are not included in SLC superfamily.
To date, nine SLC gene families (SLC4, SLC5, SLC8, SLC9, SLC12, SLC20, SLC24, SLC26 and SLC34) comprise the group that exclusively transports inorganic cations and anions across membranes. A further eight SLC gene families (SLC1, SLC6, SLC7, SLC16, SLC25, SLC36, SLC38 and SLC43) are involved in the transport of amino acids and oligopeptides (He et al. 2009). Two gene families are responsible for glucose transport in humans. SLC2 (encoding GLUTs) and SLC5 (encoding SGLTs) families mediate glucose absorption in the small intestine, glucose reabsorption in the kidney, glucose uptake by the brain across the blood-brain barrier and glucose release by all cells in the body (Wood & Trayhurn 2003).
SLC transporters are able to transport bile salts, organic acids, metal ions and amine compounds. Myo-Inositol is a precursor to phosphatidylinositols (PtdIns) and to the inositol phosphates (IP), which serve as second messengers and also act as key regulators of many cell functions (Schneider 2015). Mono-, di- and tri-carboxylate transporters mediate the transport of these acids across cellular membranes (Pajor 2006, Morris & Felmlee 2008). Essential metals are transported by metal-transporting proteins, which also control their efflux to avoid toxic build-up (Bressler et al. 2007). The SLC6 gene family encodes proteins that mediate neurotransmitter uptake in the central nervous system (CSN) and peripheral nervous system (PNS), thus terminating a synaptic signal (Chen et al. 2004). Urea transport is particularly important in the process of urinary concentration and for rapid urea equilibrium in non-renal tissues (Olives et al. 1994). Choline uptake is the rate-limiting step in the synthesis of the neurotransmitter acetylcholine. SLC genes SLC5A7 and the SLC44 family encode choline transporters (Traiffort et al. 2005). The SLC22 gene family of solute carriers function as organic cation transporters (OCTs), cation/zwitterion transporters (OCTNs) and organic anion transporters (OATs). They play important roles in drug absorption and excretion. Substrates include xenobiotics, drugs, and endogenous amine compounds (Koepsell & Endou 2004).
The human SLC5A6 encodes the Na+-dependent multivitamin transporter SMVT (Prasad et al. 1999). SMVT co-transports biotin (vitamin B7), D-Pantothoate (vitamin B5) and lipoic acid into cells with Na+ ions electrogenically. Four SLC gene families encode transporters that play key roles in nucleoside and nucleobase uptake for salvage pathways of nucleotide synthesis, and in the cellular uptake of nucleoside analogues used in the treatment of cancers and viral diseases (He et al. 2009). The human gene SLC33A1 encodes acetyl-CoA transporter AT1 (Kanamori et al. 1997). Acetyl-CoA is transported to the lumen of the Golgi apparatus, where it serves as the substrate of acetyltransferases that O-acetylates sialyl residues of gangliosides and glycoproteins. Nucleotide sugars are used as sugar donors by glycosyltransferases to create the sugar chains for glycoconjugates such as glycoproteins, polysaccharides and glycolipids. The human solute carrier family SLC35 encode nucleotide sugar transporters (NSTs), localised on Golgi and ER membranes, which can mediate the antiport of nucleotide sugars in exchange for the corresponding nucleoside monophosphates (eg. UMP for UDP-sugars) (Handford et al. 2006). Long chain fatty acids (LCFAs) can be used for energy sources and steroid hormone synthesis and regulate many cellular processes such as inflammation, blood pressure, the clotting process, blood lipid levels and the immune response. The SLC27A family encode fatty acid transporter proteins (FATPs) (Anderson & Stahl 2013). The SLC gene family members SLCO1 SLCO2 and SLCO3 encode organic anion transporting polypeptides (OATPs). OATPs are membrane transport proteins that mediate the sodium-independent transport of a wide range of amphipathic organic compounds including bile salts, steroid conjugates, thyroid hormones, anionic oligopeptides and numerous drugs (Hagenbuch & Meier 2004).
R-HSA-9860276 SLC15A4:TASL-dependent IRF5 activation This Reactome module describes the Toll-like receptor 7 (TLR7), TLR8, or TLR9 – induced activation of interferon regulatory factor 5 (IRF5) via the SLC15A4:TASL axis.
Solute carrier family 15, member 4 (SLC15A4, also known as PHT1) is a proton-coupled L-histidine/oligopeptide transporter. In addition to its function as a transporter, SLC15A4 regulates TLR7-9 signaling pathways in late endosomes/lysosomes (Heinz LX. et al., 2020; Kobayashi T et al., 2021). SLC15A4 acts as a signaling scaffold, recruiting the protein TLR adaptor interacting with SLC15A4 on the lysosome (TASL) to the cytosolic surface of endolysosomes (Heinz LX. et al., 2020; Custodio TF et al., 2023; Chen X et al., 2023). Upon activation of endosomal TLR signaling, TASL undergoes phosphorylation and recruits IRF5 to its pLxIS motif (Heinz LX. et al., 2020). The SLC15A4:TASL complex facilitates IRF5 phosphorylation by IKBKB (IKKβ) and subsequent IRF5 homodimerization downstream of TLR7-TLR9 (Heinz LX. et al., 2020; Zhang H et al., 2023; Chen X et al., 2023; Boeszoermeny A et al., 2023). Once activated, IRF5 translocates to the nucleus to induce the transcription of genes encoding type I interferons (IFNs) and pro-inflammatory cytokines. Hyperactivation of the SLC15A4:TASL:IRF5 pathway, often caused by the detection of endogenous nucleic acids, leads to increased production of type I IFNs and is associated with pathogenesis of inflammatory diseases such as systemic lupus erythematosus (SLE) (Odhams CA et al., 2019; Heinz LX. et al., 2020; Kobayashi T et al., 2021).
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R-HSA-8985586 SLIT2:ROBO1 increases RHOA activity ROBO1 receptor, activated by SLIT2, binds to MYO9B and inhibits its RHOA GAP activity. SLIT2-ROBO1 signaling thus results in increased RHOA activity, which is thought to negatively regulate invasiveness of lung cancer cells (Kong et al. 2015). ROCK-mediated signaling and phosphorylation of the myosin regulatory light chain (MLRC) downstream of activated RHOA is needed for SLIT-mediated axon pathfinding in cranial motor neurons (Murray et al. 2010).
R-HSA-111463 SMAC (DIABLO) binds to IAPs Second mitochondria‑derived activator of caspases protein (SMAC, also known as direct IAP binding protein with low pI or DIABLO) in its dimeric form interacts and antagonizes X‑linked inhibitor of apoptosis protein (XIAP) by concurrently targeting both BIR2 and BIR3 domains of XIAP (Chai J et al. 2000; Liu Z et sl. 2000; Burke SP & Smith JB 2010). XIAP inhibits apoptosis by binding to and inhibiting the effectors caspase‑3 and ‑7 and an initiator caspase‑9 (Deveraux QL et al. 1997; Paulsen M et al. 2008). During apoptosis, SMAC (DIABLO) is released from the mitochondria (Du C et al. 2000). In the cytosol, SMAC binds to XIAP displacing it from caspase:XIAP complexes liberating the active caspases (Wu G et al. 2000; Abhari BA & Davoodi J 2008).
R-HSA-111464 SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes Second mitochondria derived activator of caspase/direct inhibitor of apoptosis binding protein with low pI (SMAC, also known as DIABLO) regulates XIAP function and potentiates caspase-3, -7 and -9 activity by disrupting the interaction of caspases with XIAP. Residues 56-59 of SMAC (DIABLO) are homologous to the amino-terminal motif that is used by caspase-9 (CASP9) to bind to the BIR3 domain of XIAP. SMAC (DIABLO) competes with CASP9 for binding to BIR3 domain of XIAP promoting the release of XIAP from the CASP9:apoptosome complex (Srinivasula SM et al. 2001; Salvesen et al. 2002). The binding of SMAC to the BIR2 and BIR3 regions of XIAP creates a steric hindrance that is essential for preventing binding of XIAP linker region with effector caspases CASP3 and CASP7 thus achieving neutralization of XIAP inhibition. The strong affinity for XIAP allows SMAC (DIABLO) to displace caspase-3, -7 from the XIAP:caspase complexes (Wu G et al. 2000; Chai J et al. 2001; Huang Y et al. 2003; Abhari BA & Davoodi J 2008).
R-HSA-111469 SMAC, XIAP-regulated apoptotic response Once released from the mitochondria, SMAC binds to IAP family proteins displacing them from Caspase:IAP complexes liberating the active caspases.
R-HSA-3315487 SMAD2/3 MH2 Domain Mutants in Cancer Mutations in the MH2 domain of SMAD2 and SMAD3 affect their ability to form heterotrimers with SMAD4, thereby impairing TGF-beta signaling (Fleming et al. 2013).
The SMAD2 and SMAD3 MH2 domain residues most frequently targeted by missense mutations are those that are homologous to SMAD4 MH2 domain residues shown to be involved in the formation of SMAD heterotrimers. Asp300 of SMAD2 and Asp258 of SMAD3 correspond to the frequently mutated Asp351 of SMAD4. Pro305 of SMAD2 corresponds to the frequently mutated Pro356 of SMAD4, while Ala354 of SMAD2 corresponds to Ala406 of SMAD4. Arg268 of SMAD3 corresponds to the frequently mutated Arg361 of SMAD4. SMAD2 and SMAD3 MH2 domain mutations have been examined in most detail in colorectal cancer (Fleming et al. 2013).
R-HSA-3304356 SMAD2/3 Phosphorylation Motif Mutants in Cancer The conserved phosphorylation motif Ser-Ser-X-Ser at the C-terminus of SMAD2 and SMAD3 is subject to disruptive mutations in cancer. The last two serine residues in this conserved motif, namely Ser465 and Ser467 in SMAD2 and Ser423 and Ser425 in SMAD3, are phosphorylated by the activated TGF beta receptor complex (Macias Silva et al. 1996, Nakao et al. 1997). Once phosphorylated, SMAD2 and SMAD3 form transcriptionally active heterotrimers with SMAD4 (Chacko et al. 2001, Chacko et al. 2004). Phosphorylation motif mutants of SMAD2 and SMAD3 cannot be activated by the TGF-beta receptor complex either because serine residues are substituted with amino acid residues that cannot be phosphorylated or because the phosphorylation motif is deleted from the protein sequence or truncated (Fleming et al. 2013).
R-HSA-2173796 SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription After phosphorylated SMAD2 and/or SMAD3 form a heterotrimer with SMAD4, SMAD2/3:SMAD4 complex translocates to the nucleus (Xu et al. 2000, Kurisaki et al. 2001, Xiao et al. 2003). In the nucleus, linker regions of SMAD2 and SMAD3 within SMAD2/3:SMAD4 complex can be phosphorylated by CDK8 associated with cyclin C (CDK8:CCNC) or CDK9 associated with cyclin T (CDK9:CCNT). CDK8/CDK9-mediated phosphorylation of SMAD2/3 enhances transcriptional activity of SMAD2/3:SMAD4 complex, but also primes it for ubiquitination and consequent degradation (Alarcon et al. 2009).
The transfer of SMAD2/3:SMAD4 complex to the nucleus can be assisted by other proteins, such as WWTR1. In human embryonic cells, WWTR1 (TAZ) binds SMAD2/3:SMAD4 heterotrimer and mediates TGF-beta-dependent nuclear accumulation of SMAD2/3:SMAD4. The complex of WWTR1 and SMAD2/3:SMAD4 binds promoters of SMAD7 and SERPINE1 (PAI-1 i.e. plasminogen activator inhibitor 1) genes and stimulates their transcription (Varelas et al. 2008). Stimulation of SMAD7 transcription by SMAD2/3:SMAD4 represents a negative feedback loop in TGF-beta receptor signaling. SMAD7 can be downregulated by RNF111 ubiquitin ligase (Arkadia), which binds and ubiquitinates SMAD7, targeting it for degradation (Koinuma et al. 2003).
SMAD2/3:SMAD4 heterotrimer also binds the complex of RBL1 (p107), E2F4/5 and TFDP1/2 (DP1/2). The resulting complex binds MYC promoter and inhibits MYC transcription. Inhibition of MYC transcription contributes to anti-proliferative effect of TGF-beta (Chen et al. 2002). SMAD2/3:SMAD4 heterotrimer also associates with transcription factor SP1. SMAD2/3:SMAD4:SP1 complex stimulates transcription of a CDK inhibitor CDKN2B (p15-INK4B), also contributing to the anti-proliferative effect of TGF-beta (Feng et al. 2000).
MEN1 (menin), a transcription factor tumor suppressor mutated in a familial cancer syndrome multiple endocrine neoplasia type 1, forms a complex with SMAD2/3:SMAD4 heterotrimer, but transcriptional targets of SMAD2/3:SMAD4:MEN1 have not been elucidated (Kaji et al. 2001, Sowa et al. 2004, Canaff et al. 2012).
JUNB is also an established transcriptional target of SMAD2/3:SMAD4 complex (Wong et al. 1999).
R-HSA-3311021 SMAD4 MH2 Domain Mutants in Cancer The MH2 domain of SMAD4 is the most frequently mutated SMAD4 region in cancer. MH2 domain mutations result in the loss of function of SMAD4 by abrogating the formation of transcriptionally active heterotrimers of SMAD4 and TGF-beta receptor complex-activated R-SMADs - SMAD2 and SMAD3 (Shi et al. 1997, Chacko et al. 2001, Chacko et al. 2004, Fleming et al. 2013).
The hotspot MH2 domain amino acid residues that are targeted by missense mutations are Asp351 (D351), Pro356 (P356) and Arg361 (R361). These three hotspot residues map to the L1 loop which is conserved in SMAD2 and SMAD3 and is involved in intermolecular interactions that contribute to the formation of SMAD heterotrimers and homotrimers (Shi et al. 1997, Fleming et al. 2013). Other frequently mutated residues in the MH2 domain of SMAD4 - Ala406 (A406), Lys428 (K428) and Arg515 (R515) - are involved in binding the phosphorylation motif (Ser-Ser-X-Ser) of SMAD2 and SMAD3, with Arg515 in the L3 loop being critical for this interaction (Chacko et al. 2001, Chacko et al. 2004, Fleming et al. 2013).
R-HSA-112412 SOS-mediated signalling SOS is recruited to the plasma membrane and mediates activation of Ras.
R-HSA-1799339 SRP-dependent cotranslational protein targeting to membrane The process for translation of a protein destined for the endoplasmic reticulum (ER) branches from the canonical cytoslic translation process at the point when a nascent polypeptide containing a hydrophobic signal sequence is exposed on the surface of the cytosolic ribosome:mRNA:peptide complex. The signal sequence mediates the interaction of this complex with a cytosolic signal recognition particle (SRP) to form a complex which in turn docks with an SRP receptor complex on the ER membrane. There the ribosome complex is transferred from the SRP complex to a translocon complex embedded in the ER membrane and reoriented so that the nascent polypeptide protrudes through a pore in the translocon into the ER lumen. Translation, which had been halted by SRP binding, now resumes, the signal peptide is cleaved from the polypeptide, and elongation proceeds, with the growing polypeptide oriented into the ER lumen.
R-HSA-9701898 STAT3 nuclear events downstream of ALK signaling Activation of the STAT3 pathway downstream of ALK signaling contributes to cellular survival by modulating expression of a number of genes involved in apoptosis, immune response and angiogenesis (reviewed in Werner et al, 2009). The STAT3 pathway is particularly important in ALK+ cancers that express ALK fusion proteins, where STAT3 contributes to the repression of a number of tumor suppressor genes, highlighting its role as a critical oncogene (reviewed in Yu et al, 2014; Guanizo et al, 2018).
R-HSA-9645135 STAT5 Activation Signal transducer and activator of transcription (STAT) constitutes a family of universal transcription factors. STAT5 refers to two highly related proteins, STAT5A and STAT5B, with critical function in cell survival and proliferation. Several upstream signals including cytokines and growth factors can trigger STAT5 activation.
R-HSA-9702518 STAT5 activation downstream of FLT3 ITD mutants STAT5 signaling appears to be preferentially activated downstream of FLT3 ITD mutants relative to the wild-type or FLT3 TKD mutants, although this is subject to some debate (Choudhary et al, 2005; Reindl et al, 2006; Bagrintseva et al, 2005; Grundler et al, 2003; Choudhary et al, 2007; Marhall et al, 2018; reviewed in Choudhary et al, 2005). STAT5 activation contributes to oncogenesis by promoting the transcription of a number of factors involved in regulating cell cycle progression, proliferation and apoptosis, among others (Kim et al, 2005; Nabinger et al, 2013; Takahashi et al, 2004; Godfrey et al, 2012; Hayakawa et al, 2000; reviewed in Murphy and Rani, 2015).
R-HSA-3249367 STAT6-mediated induction of chemokines Signal transducer and activator of transcription 6 (STAT6) may function as a signaling molecule and as a transcription factor. The canonical activation of STAT6 in IL4 and IL13 signaling pathways is mediated by the tyrosine kinases JAK (Hebenstreit D et al. 2006). Virus-induced STAT6 activation was found to be cytokine- and JAK-independent (Chen H et al. 2011). Infection of human cells with RNA or DNA viruses resulted in an interaction of STAT6 with STING. The kinase TBK1 was shown to phosphorylate STAT6, which in turn induced STAT6 dimerization and translocation to the nucleus, leading to induction of chemokines CCL2, CCL20, and CCL26 in IFN-independent manner (Chen H et al. 2011).
RNA virus infection triggers STAT6 activation through STING, TBK1 and adaptor protein MAVS interaction (Chen H et al. 2011). R-HSA-1834941 STING mediated induction of host immune responses STING (stimulator of IFN genes; also known as MITA/ERIS/MPYS/TMEM173) is an endoplasmic reticulum (ER) resident, which is required for effective type I IFN production in response to nucleic acids. Indeed, select pathogen-derived DNA or RNA were shown to activate STING in human and mouse cells (Ishikawa H and Barber GN 2008; Ishikawa H et al. 2009; Sun W et al. 2009; Prantner D et al. 2010). Importantly, in vitro studies have shown that STING is essential for Mycobacterium tuberculosis (Manzanillo PS et al. 2012), Plasmodium falciparum (Sharma S et al. 2011) and human immunodeficiency virus (HIV) induced type I IFN production [Yan N et al 2010]. Mycobacterium tuberculosis, plasmodium falciparum and HIV are three deadliest pathogens, which kill millions of people each year worldwide.
STING has been also implicated in type I IFN response which was stimulated by fusion of viral and target-cell membrane in a manner independent of DNA, RNA and viral capsid [Holm CK et al 2012].
Under steady state conditions, STING is positioned at the translocon complex within the ER membrane. However upon stimulation with intracellular DNA it translocates from ER to perinuclear vesicles via the Golgi by mechanisms that remain unclear (Ishikawa H and Barber GN 2008; Sun W et al. 2009; Ishikawa H et al. 2009; Saitoh T et al. 2009). Mouse Sting trafficking in dsDNA-stimulated mouse embryonic fibroblasts (MEF) cells was found to depend on autophagy-related gene 9a (Atg9a) (Saitoh T et al. 2009).
STING was reported to function as a signaling adaptor or coreceptor in response to cytosolic dsDNA (Unterholzner L et al. 2010; Zhang Z et al. 2011). STING was also shown to function as a direct DNA sensor to induce the innate immune response in human telomerase fibroblasts (hTERT-BJ1) and murine embryonic fibroblasts (MEFs) (Abe T et al. 2013). Additionally, STING is thought to function as a direct sensor of cyclic dinucleotides. STING was shown to interact directly with c-di-GMP in human embryonic kidney HEK293T cell lysates (Burdette DL et al. 2011). Once STING is stimulated, its C-terminus serves as a signaling scaffold to recruit IRF3 and TBK1, which leads to TBK1-dependent phosphorylation of IRF3 (Tanaka Y and Chen ZJ 2012).
Mouse, but not human STING, can also bind vascular disrupting agents 5,6-dimethylxanthenone-4-acetic acid (DMXAA) and the antiviral small molecule 10-carboxymethyl-9-acridanone (CMA) to induce type I IFN production, suggesting a species-specific drug effect on the STING-mediated host response (Conlon J et al. 2013; Cavlar T et al. 2013).
R-HSA-3108232 SUMO E3 ligases SUMOylate target proteins SUMO proteins are conjugated to lysine residues of target proteins via an isopeptide bond with the C-terminal glycine of SUMO (reviewed in Zhao 2007, Gareau and Lima 2010, Hannoun et al. 2010, Citro and Chiocca 2013, Yang and Chiang 2013). Proteomic analyses indicate that SUMO is conjugated to hundreds of proteins and most targets of SUMOylation are nuclear (Vertegal et al. 2006, Bruderer et al. 2011, Tatham et al. 2011, Da Silva et al. 2012, Becker et al. 2013). Within the nucleus SUMOylation targets include transcription factors (TFs), transcription cofactors (TCs), intracellular (nuclear) receptors, RNA binding proteins, RNA splicing proteins, polyadenylation proteins, chromatin organization proteins, DNA replication proteins, DNA methylation proteins, DNA damage response and repair proteins, immune response proteins, SUMOylation proteins, and ubiquitinylation proteins. Mitochondrial fission proteins are SUMOylated at the mitochondrial outer membrane.
UBE2I (UBC9), the E2 activating enzyme of the SUMO pathway, is itself also a SUMO E3 ligase. Most SUMOylation reactions will proceed with only the substrate protein and the UBE2I:SUMO thioester conjugate. The rates of some reactions are further enhanced by the action of other E3 ligases such as RANBP2. These E3 ligases catalyze SUMO transfer to substrate by one of two basic mechanisms: they interact with both the substrate and UBE2I:SUMO thus bringing them into proximity or they enhance the release of SUMO from UBE2I to the substrate.
In the cell SUMO1 is mainly concentrated at the nuclear membrane and in nuclear bodies. Most SUMO1 is conjugated to RANGAP1 near the nuclear pore. SUMO2 is at least partially cytosolic and SUMO3 is located mainly in nuclear bodies. Most SUMO2 and SUMO3 is unconjugated in unstressed cells and becomes conjugated to target proteins in response to stress (Golebiowski et al. 2009). Especially notable is the requirement for recruitment of SUMO to sites of DNA damage where conjugation to targets seems to coordinate the repair process (Flotho and Melchior 2013).
Several effects of SUMOylation have been described: steric interference with protein-protein interactions, interference with other post-translational modifications such as ubiquitinylation and phosphorylation, and recruitment of proteins that possess a SUMO-interacting motif (SIM) (reviewed in Zhao 2007, Flotho and Melchior 2013, Jentsch and Psakhye 2013, Yang and Chiang 2013). In most cases SUMOylation inhibits the activity of the target protein.
The SUMOylation reactions included in this module have met two criteria: They have been verified by assays of individual proteins (as opposed to mass proteomic assays) and the effect of SUMOylation on the function of the target protein has been tested.
R-HSA-3065676 SUMO is conjugated to E1 (UBA2:SAE1) The UBA2:SAE1 complex catalyzes the formation of a thioester linkage between the C-terminal glycine of the mature SUMO and a cysteine residue (cysteine-173) in UBA2 (SAE2) (reviewed in Wang and Dasso 2009, Wilkinson and Henley 2010, Hannoun et al. 2010, Gareau and Lima 2010). During the process the C-terminal glycine residue of SUMO is reacted with ATP to yield pyrophosphate and a transient intermediate, SUMO adenylate. The SUMO adenylate then reacts with the thiol group of the cysteine residue of UBA2 (Olsen et al. 2010).
R-HSA-3065679 SUMO is proteolytically processed SUMO1, 2, and 3 are initially expressed as propeptides containing extra residues at the C-terminus. (SUMO1 has 4 residues, SUMO2 has 2 residues, and SUMO3 has 11 residues,) SENP1, 2, and 5 are endoproteases that process the precursors to produce the mature peptides (reviewed in Wang and Dasso 2009, Wilkinson and Henley 2010, Hannoun et al. 2010, Gareau and Lima 2010). SENP1 processes SUMO1 with greater efficiency than SUMO2 or SUMO3. SENP2 and SENP5 process SUMO2 with greater efficiency than SUMO1 or SUMO3 (Gong and Yeh 2006, Mikolajczyk et al. 2007). SENP1 shuttles between the cytosol and nuceoplasm and is predominantly nuclear (Bailey and O'hare 2004, Kim et al. 2005). SENP2 also shuttles (Itahana et al. 2006) and is mainly located on nucleoplasmic filaments of the nuclear pore complex (Hang and Dasso 2002, Zhang et al. 2002). SENP5 is located mostly in the nucleolus (Di Bacco et al. 2006, Gong and Yeh 2006).
R-HSA-3065678 SUMO is transferred from E1 to E2 (UBE2I, UBC9) SUMO is transferred from cysteine-173 of UBA2 to cysteine-93 of UBC9 (UBE2I) in a transthiolation reaction (reviewed in Wang and Dasso 2009, Wilkinson and Henley 2010, Hannoun et al. 2010, Gareau and Lima 2010). UBC9 is the only known E2 enzyme for SUMO and on certain substrates such as RanGAP1 may act without the requirement of an E3 ligase.
R-HSA-2990846 SUMOylation Small Ubiquitin-like MOdifiers (SUMOs) are a family of 3 proteins (SUMO1,2,3) that are reversibly conjugated to lysine residues of target proteins via a glycine-lysine isopeptide bond (reviewed in Hay 2013, Hannoun et al. 2010, Gareau and Lima 2010, Wilkinson and Henley 2010, Wang and Dasso 2009). Proteomic methods have yielded estimates of hundreds of target proteins. Targets are mostly located in the nucleus and therefore SUMOylation disproportionately affects gene expression.
SUMOs are initially translated as proproteins possessing extra amino acid residues at the C-terminus which are removed by the SUMO processing endoproteases SENP1,2,5 (Hay 2007). Different SENPs have significantly different efficiencies with different SUMOs. The processing exposes a glycine residue at the C-terminus that is activated by ATP-dependent thiolation at cysteine-173 of UBA2 in a complex with SAE1, the E1 complex. The SUMO is transferred from E1 to cysteine-93 of a single E2 enzyme, UBC9 (UBE2I). UBC9 with or, in some cases, without an E3 ligase conjugates the glycine C-terminus of SUMO to an epsilon amino group of a lysine residue on the target protein. SUMO2 and SUMO3 may then be further polymerized, forming chains. SUMO1 is unable to form polymers.
Conjugated SUMO can act as a biinding site for proteins possessing SUMO interaction motifs (SIMs) and can also directly affect the formation of complexes between the target protein and other proteins.
Conjugated SUMOs are removed by cleavage of the isopeptide bond by processing enzymes SENP1,2,3,5. The processing enzymes SENP6 and SENP7 edit chains of SUMO2 and SUMO3.
R-HSA-3108214 SUMOylation of DNA damage response and repair proteins Several factors that participate in DNA damage response and repair are SUMOylated (reviewed in Dou et al. 2011, Bekker-Jensen and Mailand 2011, Ulrich 2012, Psakhye and Jentsch 2012, Bologna and Ferrari 2013, Flotho and Melchior 2013, Jackson and Durocher 2013). SUMOylation can alter enzymatic activity and protein stability or it can serve to recruit additional factors. For example, SUMOylation of Thymine DNA glycosylase (TDG) causes TDG to lose affinity for its product, an abasic site opposite a G residue, and thus increases turnover of the enzyme. During repair of double-strand breaks SUMO1, SUMO2, SUMO3, and the SUMO E3 ligases PIAS1 and PIAS4 accumulate at double-strand breaks where BRCA1, HERC1, RNF168, MDC1, and TP53BP1 are SUMOylated. SUMOylation of BRCA1 may increase its ubiquitin ligase activity while SUMOylation of MDC1 and HERC2 appears to play a role in recruitment of proteins such as RNF4 and RNF8 to double strand breaks. Similarly SUMOylation of RPA1 (RPA70) recruits RAD51 in the homologous recombination pathway.
R-HSA-4655427 SUMOylation of DNA methylation proteins The known DNA methyltransferases (DNMT1, DNMT3A, and DNMT3B) can be SUMOylated (reviewed in Xu et al. 2010, Denis et al. 2011). SUMOylation affects the catalytic activity of DNMT1 and the protein interactions of DNMT3A.
R-HSA-4615885 SUMOylation of DNA replication proteins The sliding clamp protein PCNA, Aurora-A, Aurora-B, Borealin, and various topoisomerases can be SUMOylated (reviewed in Wan et al. 2012). SUMOylation of PCNA appears to reduce formation of double-strand breaks and inappropriate recombination (reviewed in Watts 2006, Watts 2007, Dieckman et al. 2012, Gazy and Kupiec 2012). SUMOylation of Aurora-A, Aurora-B, and Borealin is necessary for proper chromosome segregation. SUMOylation of topoisomerases is observed in response to damage caused by inhibitors of topoisomerases.
R-HSA-4570464 SUMOylation of RNA binding proteins SUMOylation of RNA-binding proteins (Li et al. 2004, reviewed in Filosa et al. 2013) alters their interactions with nucleic acids and with proteins. Whereas SUMOylation of HNRNPC decreases its affinity for nucleic acid (ssDNA), SUMOylation of NOP58 is required for binding of snoRNAs. SUMOylation of HNRNPK is required for its coactivation of TP53-dependent transcription.
R-HSA-4085377 SUMOylation of SUMOylation proteins SUMOylation processes themselves can be controlled by SUMOylation (reviewed in Wilkinson and Henley 2010). The SUMO E3 ligases PIAS4, RANBP2, and TOPORS are SUMOylated, as is the single SUMO E2 enzyme, UBE2I (UBC9). SUMOylation affects the subcellular location of PIAS4 and TOPORS and affects the activity of PIAS4 and UBE2I.
R-HSA-4551638 SUMOylation of chromatin organization proteins SUMOylation of proteins involved in chromatin organization regulates gene expression in several ways: direct influence on catalytic activity of enzymes that modify chromatin, recruitment of proteins that form repressive (e.g. PRC1) or activating complexes on chromatin, recruitment of proteins to larger bodies (e.g PML bodies) in the nucleus (reviewed in Cubenas-Potts and Matunis 2013).
R-HSA-4755510 SUMOylation of immune response proteins NF-kappaB transcription factors are sequestered in the cytosol due to their association with IkappaB. During activation of NF-kappaB, IKK phosphorylates IkappaB, releasing NF-kappaB for importation into the nucleus. NF-kappaB transcription factors, the NFKBIA component of IkappaB, and subunits of the IKK complex can be SUMOylated (reviewed in Kracklauer and Schmidt 2003, Liu et al. 2013). SUMOylations of IkappaB, NFKBIA, and RELA inhibit NF-kappaB signaling; SUMOylation of NFKB2 is required for proteolytic processing.
R-HSA-4090294 SUMOylation of intracellular receptors At least 17 nuclear receptors have been discovered to be SUMOylated (reviewed in Treuter and Venteclef 2011, Wadosky et al. 2012, Knutson and Lange 2013). In all but a few cases (notably AR and RORA) SUMOylation causes transcriptional repression. Repression by SUMOylation is believed to occur through several mechanisms: interference with DNA binding, recruitment of corepressors, retention of corepressors at non-target promoters (transrepression), re-localization of nuclear receptors within the nucleus, interference with dimerization of receptors, and interference (crosstalk) with other post-translational modifications. SUMOylation of receptors affects inflammation and disease processes (Anbalagan et al. 2012).
R-HSA-9793242 SUMOylation of nuclear envelope proteins SUMOylation of RANGAP1 (Mahajan et al. 1997, Lee et al. 1998, Knipscheer et al. 2008) and LMNA (Zhang and Sarge 2008) affect their localization at the nuclear envelope. SUMOylation of NUP153 has unknown consequences (Chow et al. 2012).
R-HSA-3899300 SUMOylation of transcription cofactors SUMO1,2, and 3 are predominantly located in the nucleus and targets of SUMOylation are predominantly nuclear. Transcription cofactors are nuclear proteins that generally do not bind DNA themselves but interact with DNA-bound factors and influence transcription. SUMOylation of transcription cofactors usually inhibits the activity of the cofactor (reviewed in Girdwood et al. 2004, Gill 2005, Lyst and Stancheva 2007, Garcia-Dominguez and Reyes 2009). In the cases of coactivators such as PPARGC1A (PGC-1alpha) this results in decreased transcription; in the cases of corepressors such as MBD1 this results in increased transcription.
R-HSA-3232118 SUMOylation of transcription factors Proteins classified as transcription factors constitute a disproportionate number of SUMOylation targets. In most cases SUMOylation inhibits transcriptional activation, however in some cases such as TP53 (p53) SUMOylation can enhance activation. Inhibition of transcription by SUMOylation may be due to interference with DNA binding, re-localization to inactive nuclear bodies, or recruitment of repressive cofactors such as histone deacetylases (reviewed in Girdwood et al. 2004, Gill 2005).
R-HSA-3232142 SUMOylation of ubiquitinylation proteins Several ubiquitin E3 ligases are regulated by SUMOylation (reviewed in Wilson and Heaton 2008). SUMOylation appears to be necessary for nuclear import of MDM2, the E3 ligase that ubiquitinylates TP53 (p53). SUMOylation of VHL abolishes its ubiquitin ligase activity. HERC2, RNF168, and BRCA1 are ubiquitin ligases that are SUMOylated during DNA damage response and repair.
R-HSA-3000480 Scavenging by Class A Receptors Class A scavenger receptors contain an intracellular domain, a transmembrane region, a coiled-coil domain, a collagenous domain, and the SR cysteine-rich domain (reviewed in Areschoug and Gordon 2009, Bowdish and Gordon 2009). The coiled coil domains interact to form trimers. The collagenous domain (Rohrer et al. 1990, Acton et al. 1993) and/or the SR cysteine-rich domain (Brannstrom et al. 2002) bind ligands and determine the specificity of the receptor.
R-HSA-3000471 Scavenging by Class B Receptors Class B receptors have two transmembrane domains separated by an extracellular loop (reviewed in Adachi and Tsujimoto 2006, Areschoug and Gordon 2009).
R-HSA-3000484 Scavenging by Class F Receptors SCARF1 (SREC-I) and SCARF2 (SREC-II) are transmembrane proteins that contain multiple extracellular EGF-like domains (Ishii et al. 2002, reviewed in Areschoug and Gordon 2009). SCARF2 may be involved in cell adhesion rather than ligand binding.
R-HSA-3000497 Scavenging by Class H Receptors STAB1 (FEEL-1) and STAB2 (FEEL-2) are very large transmambrane proteins containing fasciclin domains, EGF-like domains, and hyaluronan-like domains (Politz et al. 2002, reviewed in Areschoug and Gordon 2009).
R-HSA-2168880 Scavenging of heme from plasma Free heme is damaging to tissues as it intercalates into biologic membranes, perturbing lipid bilayers and promoting the conversion of low-density lipoprotein to cytotoxic oxidized products. Moreover, it represents a source of redox-active iron that, participating in the Fenton reaction, generates oxygen radicals (reviewed in Gutteridge 1989). Free heme in plasma is mainly generated from hemoglobin released by circulating erythrocytes in pathologic conditions associated with intravascular hemolysis. Free hemoglobin in plasma is scavenged by the extracellular protein haptoglobin. Haptoglobin is produced by the liver and secreted into the plasma. Haptoglobin binds dimers of hemoglobin subunits rather than the intact tetramer (reviewed in Nielsen et al. 2010, Levy et al. 2010, Ascenzi et al. 2005, Madsen et al. 2001). The resulting haptoglobin:hemoglobin complex is then bound by CD163, expressed on plasma membranes of monocytes and macrophages, and endocytosed. When the buffering capacity of plasma haptoglobin is overwhelmed, heme is released from methemoglobin and it is bound by albumin and then transferred to hemopexin (reviewed in Chiabrando et al. 2011, Nielsen et al. 2010, Tolosano et al. 2010, Ascenzi et al. 2005, Tolosano and Altruda 2002). Hemopexin is produced mainly in the liver. Once secreted into the plasma, hemopexin binds heme and the hemopexin:heme complex is then preferentially delivered to liver hepatocytes, bound by LRP1 (CD91) and endocytosed.
R-HSA-9668328 Sealing of the nuclear envelope (NE) by ESCRT-III During telophase, the double membrane of the reforming NE, which is derived from fenestrated sheets and tubules of the mitotic ER, is sealed to reestablish the nucleocytoplasmic permeability barrier (reviewed by Otsuka and Ellenberg 2018). Some of the holes in the reforming nuclear envelope close around forming nuclear pore complexes (NPCs) (reviewed by Otsuka and Ellenberg 2018). Other fenestrations are sealed by the formation of filamentous ESCRT-III assemblies and their disassembly by the AAA+ ATPase VPS4 (VPS4A/VPS4B) (reviewed by Schoneberg et al. 2017). The ESCRT-III/VPS4 machinery has a general role in “reverse topology” membrane scission (i.e., involving the fusion of cytoplasmic membrane surfaces (reviewed by Schoneberg et al. 2017). In concert with these events, microtubules connected to the kinetochore and to other chromosomal regions are severed (reviewed by Schoneberg et al. 2017).
R-HSA-9663891 Selective autophagy Autophagy can be a selective process where specific cargo (organelles/proteins) are targetted to degradation in the lysosome. In general, selective autophagy is initiated when a cellular signal tags the cargo organelle for degradation. Subsequently, cargo recognition proteins detect and recruit the organelle to interact directly or indirectly with Atg proteins forming the phagophore. The next steps involve formation of the autophagosome and fusion with the lysosome for degradation. Depending upon the organelle, different molecules are used to for the autophagy mechanism (Andling AL et al. 2017). Consequently, the different mechanisms are known by the organelle degraded such as mitophagy for mitochondia, lipophagy for lipid droplets, pexophagy for peroxisomes and aggrephagy for aggregated proteins.
R-HSA-2408522 Selenoamino acid metabolism Selenium (Se) is a trace element essential for the normal function of the body. Selenoamino acids are defined as those amino acids where selenium has been substituted for sulphur. Selenium and sulphur share many chemical properties and so the substitution of normal amino acids with selenoamino acids has little effect on protein structure and function. Both inorganic (selenite, SeO3(2-); and selenate, SeO4(2-)) and organic (selenocysteine, Sec; and selenomethionine, SeMet) forms of selenium can be introduced in the diet where they are transformed into the intermediate selenide (Se(2-)) and then utilized for the de novo synthesis of Sec through a phosphorylated intermediate in a tRNA-dependent fashion. The final step of Sec formation is catalyzed by O-phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SEPSECS) that converts phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec).
All nutritional selenium is metabolised into selenide directly or through methylselenol (MeSeH). Sec liberated from selenoproteins is transformed to Se(2-) by selenocysteine lyase (SCLY). SeMet liberated from general proteins and from free SeMet sources is transformed into Se(2-) either through MeSeH by cystathionine gamma-lyase (CTH) followed by demethylation (SeMet to CH3SeH to H2Se), or through Sec by SCLY after the trans-selenation pathway (SeMet to Sec to H2Se). MeSec is hydrolysed into MeSeH by CTH. Methylseleninic acid (MeSeO2H) is reduced to methylselenol. MeSeH is demethylated to Se(2-) for further utilization for selenoprotein synthesis or oxidised to selenite (SeO3(2-)) for excretion in the form of selenosugar. Additionally, MeSeH is further methylated to dimethylselenide (Me2Se) and trimethylselenonium (Me3Se+) for excretion.
R-HSA-2408557 Selenocysteine synthesis Selenocysteine, the 21st genetically encoded amino acid, is the major form of the antioxidant trace element selenium in the human body. In eukaryotes and archaea its synthesis proceeds through a phosphorylated intermediate in a tRNA-dependent fashion. The final step of selenocysteine formation is catalyzed by O-phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SEPSECS) that converts phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec).
R-HSA-399954 Sema3A PAK dependent Axon repulsion Activated Rac1 bound to plexin-A might modulate actin dynamics through the sequential phosphorylation and activation of PAK, LIMK1 and cofilin.
R-HSA-400685 Sema4D in semaphorin signaling Semaphorin 4D (Sema 4D/CD100) is an axon guidance molecule with two disulfide-linked 150-kDa subunits. SEMA4D is structurally defined by a conserved 500-amino acid extracellular domain with 16 cysteines (sema domain) and also an Ig-like domain C-terminal to the sema domain. Sema4D is expressed on the cell surface as a homodimer; cysteine 679 within the sema domain is required for this dimerization.
The main receptors for Sema4D are plexin-B1 and CD72. The activation of plexins by semaphorins initiates a variety of signaling processes that involve several small GTPases of the Ras and Rho families. Sema4D-Plexin-B1 interaction appears to mediate different and sometimes opposite effects depending on the cellular context. Plexin-B1 activation inhibits integrin-mediated cell attachment and cell migration through the activation of the R-RasGAP activity inherent to plexin-B1 or through the inhibition of RhoA. However, activation of plexin-B1 by Sema4D stimulates the migration of endothelial cells by mediating the activation of RhoA.
R-HSA-416572 Sema4D induced cell migration and growth-cone collapse Sema4D-mediated attraction of endothelial cells requires Rho, but not R-Ras, signaling. Sema4D-mediated plexinB1 activation activates Rho and its downstream effector ROCK. ROCK then phosphorylates MLC to induce actomyosin stress fiber contraction and to direct the assembly of focal adhesion complexes and integrin-mediated adhesion.
R-HSA-416550 Sema4D mediated inhibition of cell attachment and migration Repulsive Sema4D-Plexin-B1 signaling involves four GTPases, Rnd1, R-Ras, Rho and Rac1. Sema4D-Plexin-B1 binding promotes Rnd1-dependent activation of the plexin-B1 GAP domain and transient suppression of R-Ras activity. R-Ras inactivation promotes PI3K and Akt inactivation followed by GSK-3beta activation and CRMP2 inactivation. Plexin-B1 also transiently associates with and activates p190Rho-GAP, triggering a transient decrease in activated Rho.
R-HSA-373755 Semaphorin interactions Semaphorins are a large family of cell surface and secreted guidance molecules divided into eight classes on the basis of their structures. They all have an N-terminal conserved sema domain. Semaphorins signal through multimeric receptor complexes that include other proteins such as plexins and neuropilins.
R-HSA-2559582 Senescence-Associated Secretory Phenotype (SASP) The culture medium of senescent cells in enriched in secreted proteins when compared with the culture medium of quiescent i.e. presenescent cells and these secreted proteins constitute the so-called senescence-associated secretory phenotype (SASP), also known as the senescence messaging secretome (SMS). SASP components include inflammatory and immune-modulatory cytokines (e.g. IL6 and IL8), growth factors (e.g. IGFBPs), shed cell surface molecules (e.g. TNF receptors) and survival factors. While the SASP exhibits a wide ranging profile, it is not significantly affected by the type of senescence trigger (oncogenic signalling, oxidative stress or DNA damage) or the cell type (epithelial vs. mesenchymal) (Coppe et al. 2008). However, as both oxidative stress and oncogenic signaling induce DNA damage, the persistent DNA damage may be a deciding SASP initiator (Rodier et al. 2009). SASP components function in an autocrine manner, reinforcing the senescent phenotype (Kuilman et al. 2008, Acosta et al. 2008), and in the paracrine manner, where they may promote epithelial-to-mesenchymal transition (EMT) and malignancy in the nearby premalignant or malignant cells (Coppe et al. 2008). Interleukin-1-alpha (IL1A), a minor SASP component whose transcription is stimulated by the AP-1 (FOS:JUN) complex (Bailly et al. 1996), can cause paracrine senescence through IL1 and inflammasome signaling (Acosta et al. 2013).
Here, transcriptional regulatory processes that mediate the SASP are annotated. DNA damage triggers ATM-mediated activation of TP53, resulting in the increased level of CDKN1A (p21). CDKN1A-mediated inhibition of CDK2 prevents phosphorylation and inactivation of the Cdh1:APC/C complex, allowing it to ubiquitinate and target for degradation EHMT1 and EHMT2 histone methyltransferases. As EHMT1 and EHMT2 methylate and silence the promoters of IL6 and IL8 genes, degradation of these methyltransferases relieves the inhibition of IL6 and IL8 transcription (Takahashi et al. 2012). In addition, oncogenic RAS signaling activates the CEBPB (C/EBP-beta) transcription factor (Nakajima et al. 1993, Lee et al. 2010), which binds promoters of IL6 and IL8 genes and stimulates their transcription (Kuilman et al. 2008, Lee et al. 2010). CEBPB also stimulates the transcription of CDKN2B (p15-INK4B), reinforcing the cell cycle arrest (Kuilman et al. 2008). CEBPB transcription factor has three isoforms, due to three alternative translation start sites. The CEBPB-1 isoform (C/EBP-beta-1) seems to be exclusively involved in growth arrest and senescence, while the CEBPB-2 (C/EBP-beta-2) isoform may promote cellular proliferation (Atwood and Sealy 2010 and 2011). IL6 signaling stimulates the transcription of CEBPB (Niehof et al. 2001), creating a positive feedback loop (Kuilman et al. 2009, Lee et al. 2010). NF-kappa-B transcription factor is also activated in senescence (Chien et al. 2011) through IL1 signaling (Jimi et al. 1996, Hartupee et al. 2008, Orjalo et al. 2009). NF-kappa-B binds IL6 and IL8 promoters and cooperates with CEBPB transcription factor in the induction of IL6 and IL8 transcription (Matsusaka et al. 1993, Acosta et al. 2008). Besides IL6 and IL8, their receptors are also upregulated in senescence (Kuilman et al. 2008, Acosta et al. 2008) and IL6 and IL8 may be master regulators of the SASP.
IGFBP7 is also an SASP component that is upregulated in response to oncogenic RAS-RAF-MAPK signaling and oxidative stress, as its transcription is directly stimulated by the AP-1 (JUN:FOS) transcription factor. IGFBP7 negatively regulates RAS-RAF (BRAF)-MAPK signaling and is important for the establishment of senescence in melanocytes (Wajapeyee et al. 2008).
Please refer to Young and Narita 2009 for a recent review.
R-HSA-5693548 Sensing of DNA Double Strand Breaks Detection of DNA double-strand breaks (DSBs) involves sensor proteins of the MRN complex, composed of MRE11A, RAD50 and NBN (NBS1). Binding of the MRN complex to DNA DSBs activates ATM-dependent DNA damage signaling cascade, by promoting KAT5 (Tip60) mediated acetylation of ATM and subsequent ATM autophosphorylation. Activated ATM triggers and coordinates recruitment of repair proteins to DNA DSBs (Beamish et al. 2002, Thompson and Schild 2002, Bakkenist et al. 2003, Lee and Paull 2005, Sun et al. 2005, Sun et al. 2007, Ciccia and Elledge 2010).
R-HSA-9709957 Sensory Perception Sensory perception includes the reactions and physical events that are required to receive a stimulus, convert the stimulus to a molecular signal, and sense the signal. This module includes pathways describing the sensory perception of light (visual transduction, reviewed in Grossniklaus et al. 2015, Molday and Moritz 2015, Lankford et al. 2020), volatile chemicals (olfaction, reviewed in Glezer and Malnic 2019, Lankford et al. 2020), tastants (chemicals that activate taste receptors, reviewed in Roper and Chaudhari et al. 2017), and sound (reviewed in Fettiplace 2017).
R-HSA-9730628 Sensory perception of salty taste Initially, type I taste bud cells were suggested to be responsible for tasting low concentrations of salt, however a subset of type II taste bud cells are now thought to be responsible (Nomura et al. 2020). The identity of salt-tasting cells remains a subject of current research. The ability to taste low concentrations of salt is at least partially due to an amiloride-sensitive sodium channel believed to be an SCNN channel (ENaC channel). SCNN complexes contain the pore-forming subunit SCNN1A or SCNN1D, and the modulatory subunits SCNN1B and SCNN1G, all of which have been detected in human taste buds (Rossier et al. 2004, Stähler et al. 2008). Knockout of SCNN1A in mice abolished amiloride-sensitive salt taste and attraction to low concentrations of salt, however SCNN1B and SCNN1G do not colocalize with SCNN1A in taste cells of mice (Lossow et al. 2020), raising the question of the subunit composition of the SCNN complex. SCNN1D is present in human taste cells but not in mouse taste cells.
In humans, a SCNN channel containing SCNN1A or SCNN1D located in the plasma membrane is believed to transport sodium ions from the extracellular region into the cytosol, resulting in depolarization that causes CALHM1:CALHM3 channels to open and release ATP, a neurotransmitter, from the cytosol to the extracellular region.
R-HSA-9729555 Sensory perception of sour taste The sour taste channel OTOP1 is located in type III taste bud cells where it transports H+ ions from the extracellular region into the cytosol (reviewed in Liman and Kinnamon 2021). Organic acids such as acetic acid and citric acid are believed to also enter type III taste bud cells by passive diffusion of the protonated (uncharged) form of the acid across the plasma membrane. The increase in cytosolic H+ ions inhibits the KCNJ2 potassium channel and may also open unidentified sodium channels to further depolarize the cell. The resulting depolarization is adequate to generate an action potential which eventually results in release of the neurotransmitters serotonin (5-HT) and gamma-butyric acid (GABA) (inferred from mouse type III cells in Huang et al. 2005, Huang et al. 2009, Huang et al. 2011). Mice lacking both P2x2 and P2x3 ATP receptors do not produce nerve activity in response to sour tastants so ATP may play a role in transmission of sour taste (Eddy et al. 2009).
R-HSA-9717207 Sensory perception of sweet, bitter, and umami (glutamate) taste Taste receptors for bitter compounds, sweet compounds, and umami compounds (L-glutamate in humans, several amino acids in mice) are G protein-coupled receptors located in type II taste bud cells that signal through a common downstream pathway (reviewed in Margolskee 2002, Kinnamon 2009, Kurihara 2015, Roper and Chauhari et al. 2017, Kinnamon and Finger 2019, Servant et al. 2020). Umami ("savoury", L-glutamate) taste receptors are heterodimers of the plasma membrane proteins TAS1R1 and TAS1R3. TAS1R1:TAS1R3 heterodimers also bind 5' nucleotides such as 5' IMP which synergistically augment umami taste. The glutamate receptors GRM1 (mGluR1) and GRM4 (mGluR4) act in an alternative pathway for sensing glutamate in taste cells (reviewed in Chaudhari et al. 2009). Sweet taste receptors are heterodimers of the plasma membrane proteins TAS1R2 and TAS1R3 (reviewed in Yang et al. 2021). The glucose transporters SGLT1 and GLUT4 are expressed in type II taste cells and may provide an alternative pathway for sensing glucose (reviewed in von Molitor et al. 2020). Bitter receptors are a large family of monomeric plasma membrane proteins, the TAS2R proteins.
TAS1R-containing sweet and umami receptors and TAS2R bitter receptors are each physically associated with a particular heterotrimeric G protein complex, the gustducin complex, containing GNAT3 (gustducin), GNB1 or GNB3, and GNG13. Upon binding an agonist ligand, the receptor activates the alpha subunit, GNAT3, to exchange GDP for GTP, which results in a conformational change in GNAT3 that causes the receptor-gustducin complex to dissociate, yielding GNAT3:GTP, GNB1,3:GNG13, and the receptor:ligand. The GNB1,3:GNG13 complex binds and activates Phospholipase C beta-2 (PLCB2), which then hydrolyzes phosphoinositol 4,5-bisphosphate (PI(4,5)P2) to yield diacylglycerol and inositol 1,4,5-trisphosphate (I(1,4,5)P3). I(1,4,5)P3 binds and activates the calcium channel IP3-gated Ca-channel type 3 (ITPR3) and ITPR3 then releases calcium ions from the endoplasmic reticulum into the cytosol. The increased cytosolic calcium activates the TRPM5 cation channels, which then transport sodium ions along the concentration gradient from the extracellular region to the cytosol (reviewed in Aroke et al. 2020). The depolarization activates SCN2A, SCN3A, and SCN9A channels, which transport further sodium ions from the extracellular region to the cytosol. The depolarization of the plasma membrane opens CALHM1:CALHM3 channels, which transport ATP, a neurotransmitter in the olfactory system, from the cytosol to the extracellular region.
Taste receptors were initially discovered in taste buds of the tongue and have now been found in several other tissues including nasal epithelium (Barnham et al. 2015, inferred from rodent homologs in Tizzano et al. 2011), the respiratory system, pancreatic islet cells, sperm (Governini et al. 2020), leukocytes (Malki et al. 2015), and enteroendocrine cells of the gut (inferred from rat and mouse homologs in Wu et al. 2002).
R-HSA-9717189 Sensory perception of taste Taste buds contain at least 3 types of cells: type I cells appear to have a support (glial-like) function; type II cells are responsible for tasting sweet compounds, bitter compounds, and umami (savoury, amino acid) compounds; and type III cells are responsible for tasting sour (acidic) compounds (reviewed in Liman et al. 2014, Roper and Chaudhari 2017, Kinnamon and Finger 2019, Taruno et al. 2021). Recently identified sodium sensing cells expressing the epithelial sodium channel (ENaC) and POU2F3 are thought to be responsible for tasting low concentrations of salt and may be a subset of type II cells or a novel type of taste cell (Chandrashekar et al. 2010, reviewed in Taruno et al. 2021). High concentrations of salt appear to be detected by both type II and type III cells.
Receptors for sweet compounds, bitter compounds, and umami compounds contain an intracellular domain, transmembrane domains, and an extracellular domain that binds the ligand. The extracellular domains of receptors for sweet and umami ligands have a distinctive "venus flytrap"-shaped domain. Upon binding ligand, sweet taste receptors (TAS1R2:TAS1R3 heterodimers), bitter taste receptors (TAS2R class receptors), and umami receptors (TAS1R1:TAS1R3 heterodimers) then signal through a common downstream pathway: the receptor-ligand complex activates an associated heterotrimeric G protein complex (GNAT3:GNB1 or GNB3:GNG13) to exchange GDP for GTP, the heterotrimeric G protein complex dissociates and the resulting GNB1,3:GNG13 complex activates Phospholipase C beta-2 (PLCB2) which hydrolyzes phosphoinositol 4,5-bisphosphate (PI(4,5)P2) to yield inositol 1,4,5-trisphosphate (I(1,4,5)P3) and diacylglycerol (DAG). I(1,4,5)P3 binds and activates ITPR3 to release calcium ions from the endoplasmic reticulum into the cytosol. Cytosolic Ca2+ causes TRPM5 sodium channels to open and depolarize the cell. SCN2A, SCN3A, and SCN9A sodium channels also appear to augment the depolarization. Depolarization causes opening of CALHM1:CALHM3 channels which transport ATP from the cytosol to the extracellular region. ATP then acts as a neurotransmitter in the taste sensing system.
Alternative pathways exist for sensing sugars and glutamate, as evidenced by residual signaling activity in the absence of TAS1R1 or TAS1R3. Glutamate is sensed by the glutamate receptors GRM1 (mGluR1) and GRM4 (mGluR4) expressed in type II taste cells. GRM1 and GRM4 activate calcium channels by an incompletely characterized mechanism that probably involves heterotrimeric G proteins. Glucose may be sensed by a pathway comprising transport into type II taste cells via the glucose transporters SGLT1 and GLUT4, generation of ATP, and inhibition of KATP potassium channels by ATP.
Protons (H+ ions) from acidic compounds translocate from the extracellular region to the cytosol of type III taste cells through the OTOP1 channel. Weak acids such as acetic acid and citric acid are also able to enter type III cells by diffusing through the membrane in their protonated, uncharged forms, Once in the cytosol, the H+ ions inhibit KCNJ2 inwardly rectifying potassium channels, depolarizing the cell. The H+ ions may also open unidentified sodium channels to further depolarize the cell. Depolarization causes exocytosis of the neurotransmitters serotonin (5-HT) and gamma-aminobutyric acid (GABA).
Low concentrations of salt appear to be sensed in specific salt-sensing cells that may be a subset of type II cells. Low concentrations of salt are believed to enter the cell through an epithelial sodium channel (ENaC, SCNN) and the ability to taste low concentrations of salt is dependent on the SCNN1A pore-containing subunit of the SCNN complex in mice. Human taste cells express both SCNN1A and SCNN1D pore-containing subunits. The composition of other subunits of the complex is less certain. The transport of sodium ions (Na+) into the cells depolarizes the plasma membrane and eventually leads to opening of CALHM1:CALHM3 channels which transport ATP from the cytosol to the extracellular region.
R-HSA-9659379 Sensory processing of sound In mammals, sounds are processed in the cochlea, a spiral-shaped organ in the inner ear (reviewed in Basch et al. 2016, Fettiplace 2017, Koppl and Manley 2019). Low frequency sounds are sensed at the distal end (apex) of the cochlea; high frequency sounds are sensed at the proximal end (base) of the cochlea (reviewed in Dallos 1992, Manley 2018). Sound vibrations are transmitted from the eardrum through the three bones of the inner ear (malleus, incus, stapes) and the oval window of the cochlea to the fluids within the cochlea. Within the organ of Corti in the cochlea there are 3 rows of outer hair cells (OHCs) on the external side of the tunnel of Corti and 1 row of inner hair cells (IHCs) on the internal side (Spoendlin 1967). Each IHC synapses with approximately 20 afferent myelinated type I spiral ganglion neurons and functions as a sensory receptor to convert the energy of sound waves to secretion of glutamate neurotransmitter. Multiple OHCs synapse with each unmyelinated type II afferent neuron and OHCs are also synapsed with efferent medial olivocochlear fibers (Spoendlin 1967). The primary function of OHCs, however, is amplification of organ of Corti motions in response to sound (Ryan and Dallos 1975). Amplification is produced by changes in receptor-potential driven cell length caused by changes in the conformation of the unusual membrane protein prestin (SLC26A5, Zheng et al. 2000).
IHCs and OHCs sense the sonic vibrations by deflection of stereocilia on their apical surfaces (reviewed in Fettiplace et al. 2017, McPherson 2018). The stereocilia are arranged in rows of increasing height, with a stereocilium of one row connected to a stereocilium of another row by a tip link composed of a CDH23 dimer on the taller stereocilium joined at its N-termini to the N-termini of a PCDH15 dimer on the shorter stereocilium. CDH23 is connected to the cytoskeleton of the taller stereocilium via MYO7A (MyoVIIa), USH1C (Harmonin), and USH1G (Sans) (reviewed in Peng et al. 2011, Cosgrove and Zallocchi 2014, Barr-Gillespie 2015, Fettiplace 2017, McGrath et al. 2017, Cunningham and Müller 2019, Ó Maoiléidigh and Ricci 2019, Velez-Ortega and Frolenkov 2019) while PCDH15 on the shorter stereocilium interacts with LHFPL5, an auxiliary subunit of the mechanoelectrical transduction channel (MET channel, also known as the mechanotransduction channel), which contains at least TMC1 or TMC2, TMIE, and the auxiliary subunits LHFPL5 and CIB2 (reviewed in Fettiplace 2016, Qiu and Müller 2018, Corey et al. 2019). Deflection of stereocilia in the direction that increases tension on the tip link causes depolarization of the cell by increasing the open probability of the MET channel, which then transports calcium and potassium into the hair cell according to the gradient of those ions between the scala media (containing endolymph at 154 mM K+ and <1 mM Ca2+) at the apex of the cell and the scala tympani (containing perilymph at 7 mM K+) at the base (reviewed in Fettiplace and Kim 2014). Similarly, compression of the tip link by deflection of the stereocilia in the opposite direction decreases the open probability of the MET channel and causes hyperpolarization of the cell.
Depolarization of IHCs causes opening of voltage-gated calcium channels arrayed in stripes on the basolateral membrane close to ribbon synapses formed between the IHC and the afferent fiber of a myelinated type I spiral ganglion neuron. This results in a localized increase in cytosolic calcium ions which interact with Otoferlin (OTOF) on glutamate-containing synaptic vesicles at the ribbon structure to activate exocytosis of glutamate into the synapse formed with the afferent neuron (reviewed in Wichmann 2015, Pangrsic and Vogl 2018). Ribbon synapses are distinguished by electron-dense ribbon structures projecting from the presynaptic membrane into the cytosol and comprising at least BASSOON, RIBEYE (an isoform of CTBP2), and PICCOLINO (an isoform of PICCOLO). The ribbon structures appear to transiently bind synaptic vesicles and facilitate resupply of synaptic vesicles at active zones to refill the pool of readily releasable vesicles (reviewed in Moser et al. 2006, Moser et al. 2020).
In contrast with IHCs, OHCs mainly function in sound amplification by decreasing up to about 4% in length in response to depolarization caused by opening of the MET channel and increasing in length in response to hyperpolarization caused by channel closing, resulting in alternating compression and decompression between the reticular lamina and the basilar membrane. The changes in the length of the OHC are caused by very rapid (microseconds), voltage-sensitive changes in the conformation of the membrane protein prestin (SLC26A5). Stereociliary ATP2B2 (PMCA2) extrudes calcium ions and basally located KCNQ4 extrudes potassium ions to repolarize the OHC.
OHCs are synapsed with efferent cholinergic medial olivocochlear fibers (reviewed in Fritzsch and Elliott 2017, Fuchs and Lauer 2019). Acetylcholine released at the synapse binds an unusual, nicotine-antagonized, nicotinic receptor comprising CHRNA9 and CHRNA10. Upon binding acetylcholine, CHRNA9:CHRNA10 transports calcium ions into the OHC. The calcium activates SK2 potassium channels (KCNN2) and BK potassium channels (KCNMA1:KCNMB1) which extrude potassium ions, hyperpolarize the OHC, and inhibit activation of the OHC.
Loud sounds can cause a temporary threshold shift (temporary loss of hearing) caused by damage to stereocilia and synapses or permanent threshold shift (permanent loss of hearing) caused by damage or death of hair cells and neurons (reviewed in Kurabi et al. 2017).
R-HSA-9662360 Sensory processing of sound by inner hair cells of the cochlea Inner hair cells (IHCs) of the cochlea transduce sound waves into an ionic (mainly potassium) current that leads to exocytosis of glutamate from the IHC and activation of postsynaptic type I afferent fibers of the radial ganglion (reviewed in Meyer and Moser 2010, Moser and Vogl 2016, Fettiplace 2017). IHCs have stereocilia on their apical surface that are arranged in rows of increasing height, a "staircase" arrangement. Stereocilia of different rows are connected by a tip link comprising a CDH23 dimer on the taller stereocilium bound to a PCDH15 dimer on the shorter stereocilium. PCDH15 interacts with LHFPL5, an auxiliary subunit of the mechanoelectrical transduction channel (MET channel, also called the mechanotransduction channel), which contains at least TMC1 (adults) or TMC2 (newborns), TMIE, and the auxiliary subunits LHFPL5 and CIB2 (reviewed in Fettiplace and Kim 2014, Fettiplace 2016).
Deflection of the stereocilia by sound waves creates tension on the tip link that increases the open probability of the MET channel, which then transports calcium and potassium ions from the scala media into the IHC, depolarizing the IHC (reviewed in Fettiplace 2017). The potassium channel KCNQ4 located in the neck region of the cell may also participate in depolarization. The depolarization of the IHC opens voltage-gated Cav1.3 channels (CACNA1D:CACA2D2:CACNB2) located in stripes near ribbon synapses on the basolateral surface of the IHC. The resulting localized influx of calcium ions activates exocytosis of glutamate into the synapse by an interaction between calcium and Otoferlin (OTOF) on glutamate-loaded vesicles in the IHC (reviewed in Wichmann 2015).
Ribbon synapses are characterized by a multiprotein complex, the ribbon, that contains at least BASSOON, RIBEYE (an isoform of CTBP2), and PICCOLINO (a small isoform of PICCOLO) and appears to act to transiently tether vesicles near the synapse and thereby increase the pool of readily releasable vesicles (reviewed in Safieddine et al. 2012, Wichman and Moser 2015, Pangrsic and Vogl 2018, Moser et al. 2020).
ATP2B1 calcium channels, ATP2B2 calcium channels, KCNMA1:KCNMB1:LRRC52 potassium channels, and basolateral KCNQ4 potassium channels transport cations out of the IHC and thereby act to repolarize the cell and limit the duration of the synaptic potentials (reviewed in Patuzzi 2011, Oak and Yi 2014).
R-HSA-9662361 Sensory processing of sound by outer hair cells of the cochlea Outer hair cells (OHCs) produce amplification of sound waves in the cochlea by shortening and lengthening in response to sound, a phenomenon called electromotility (reviewed in Kim and Fettiplace 2014, Fettiplace 2016, Fettiplace 2017, Fritzsch et al. 2017, Ashmore 2019). Like inner hair cells, OHCs possess apical stereocilia arranged in rows of ascending height. A taller stereocilium is connected to a shorter stereocilium by a tip link comprising a CDH23 dimer onthe side of the taller stereocilium and a PCDH15 dimer on theapex of the shorter stereocilium. PCDH15 interacts with LHFPL5, a subunit of the mechanoelectrical transduction channel complex (MET channel, also called the mechanotransduction channel), which contains TMC1 or TMC2, TMIE, CIB2, and LHFPL5 (reviewed in Fettiplace 2016). Deflection of the stereocilia in one direction produces tension on the tip link that increases the open probability of the MET channel, resulting in depolarization of the OHC. Deflection of the stereocilia in the opposite direction produces compression on the tip link that decreases the the open probability of the MET channel, resulting in hyperpolarization of the OHC.
Sound causes micromechanical motions of the organ of Corti that result in alternating tension and compression in the tip link that produce excitatory-inhibitory cycles of MET channel openings and closings relative to the MET channel's resting open probability. This causes directionally alternating fluxes of K+ and Ca2+, yielding depolarization-hyperpolarization cycles that cause conformational changes in prestin (SLC26A5). These cycles are asymmetrical, with contraction caused by depolarization dominating elongation caused by hyperpolarization due to the asymmetry of the open probability of MET channels. Stereociliary ATP2B2 (PMCA2) extrudes calcium ions and basally located KCNQ4 extrudes potassium ions to repolarize the OHC.
Depolarization of the OHC causes a decrease in length of the OHC due to a very rapid, voltage-sensitive change in conformation of the membrane protein prestin (SLC26A5), an unusual member of the anion transporter family located in the lateral membrane (Mahendrasingam et al, 2010) that appears to respond to cytosolic chloride by altering its conformation in the plane of the plasma membrane (reviewed in Dallos et al. 2006, Dallos 2008, Hudspeth 2014, Reichenbach and Hudspeth 2014, Ashmore 2019, Santos-Sacchi 2019). Prestin also appears to act as a weak chloride-bicarbonate antiporter (Mistrik et al. 2012). Changes in length of the OHCs cause movement of the reticular lamina toward and away from the basilar membrane.
R-HSA-2467813 Separation of Sister Chromatids While sister chromatids resolve in prometaphase, separating along chromosomal arms, the cohesion of sister centromeres persists until anaphase. At the anaphase onset, the anaphase promoting complex/cyclosome (APC/C) ubiquitinates PTTG1 (securin), targeting it for degradation (Hagting et al. 2002). PTTG1 acts as an inhibitor of ESPL1 (known as separin i.e. separase). Hence, PTTG1 removal initiated by APC/C, enables ESPL1 to become catalytically active (Zou et al. 1999, Waizenegger et al. 2002). ESPL1 undergoes autoleavage (Waizenegger et al. 2002) and also cleaves RAD21 subunit of centromeric cohesin (Hauf et al. 2001). RAD21 cleavage promotes dissociation of cohesin complexes from sister centromeres, leading to separation of sister chromatids. Subsequent movement of sister chromatids to opposite poles of the mitotic spindle segregates replicated chromosomes to two daughter cells (Waizenegger et al. 2000, Hauf et al. 2001, Waizenegger et al. 2002).
R-HSA-977347 Serine biosynthesis L-Serine is needed in human brain in large amounts as precursor to important biomolecules such as nucleotides, phospholipids and the neurotransmitters glycine and D-serine. The pathway for its synthesis starts with 3-phosphoglycerate and it later needs glutamate as an amination agent. Deficiencies in the participating enzymes lead to severe neurological symptoms that are treatable with serine if treatment starts early (de Koning & Klomp 2004).
R-HSA-181429 Serotonin Neurotransmitter Release Cycle Serotonin is synthesized in the serotonergic neurons in the central nervous system and the enterochrommaffin cells of the gastroinetstinal system. Serotonin is loaded into the clathrin sculpted monoamine transport vesicles. The vesicles are docked, primed and release after the change in the membrane potential that activates voltage gated calcium channels and the reponse by several proetins to the changes in intracellular Ca2+ increase leads to fusion of the vesicle and release of serotonin into the synapse.
R-HSA-209931 Serotonin and melatonin biosynthesis Serotonin (5-HT) is a hormone and neurotransmitter used for regulatory purposes in animal CNS. In the human brain, serotonin is involved in many physiological functions such as sleep, pain, mood and is the precursor to melatonin, a hormone produced in the pineal gland.
R-HSA-380615 Serotonin clearance from the synaptic cleft Serotonergic neurotransmission affects a wide range of behaviors, from food intake and reproductive activity, to sensory processing and motor activity, to cognition and emotion. One such key regulator is the serotonin transporter (5-HTT), which is observed to remove serotonin released into the synaptic cleft.
R-HSA-390666 Serotonin receptors Serotonin (5-HT) is a monoamine neurotransmitter that plays an important role as a modulator of anger, aggression, body temperature, mood, sleep, sexuality, appetite, metabolism, as well as stimulating vomiting. Several classes of drugs target the 5-HT system including some antidepressants, antipsychotics, anxiolytics, antiemetics and antimigraine drugs. The activity of 5-HT is modulated by 5-HT receptors, made up of seven families (5-HT1-7). All but 5-HT3 (ligand-gated ion channel) are GPCRs and these receptors bind different G proteins resulting in differing outcomes (Hoyer D et al, 1994; Kitson SL, 2007).
R-HSA-3282872 Severe congenital neutropenia type 4 (G6PC3) Glucose-6-phosphatase 3 (G6PC3) associated with the endoplasmic reticulum membrane normally catalyzes the hydrolysis of glucose-6-phosphate to glucose and orthophosphate. In the body, this enzyme is ubiquitously expressed; mutations that inactivate it are associated with severe congenital neutropenia (but not with fasting hypoglycemia or lactic acidemia) (Boztug et al. 2009, 2012).
R-HSA-4085001 Sialic acid metabolism Sialic acids are a family of 9 carbon alpha-keto acids that are usually present in the non reducing terminal of glycoconjuates on the cell surface of eukaryotic cells. These sialylated conjugates play important roles in cell recognition and signaling, neuronal development, cancer metastasis and bacterial or viral infection. More than 50 forms of sialic acid are found in nature, the most abundant being N-acetylneuraminic acid (Neu5Ac, N-acetylneuraminate) (Li & Chen 2012, Wickramasinghe & Medrano 2011). The steps below describe the biosynthesis, transport, utilization and degradation of Neu5Ac in humans.
R-HSA-162582 Signal Transduction Signal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such as hormones and growth factors, or reacting to other types of stimuli, such as light. Stimulation of transmembrane receptors leads to their conformational change which propagates the signal to the intracellular environment by activating downstream signaling cascades. Depending on the cellular context, this may impact cellular proliferation, differentiation, and survival. On the organism level, signal transduction regulates overall growth and behavior.
Receptor tyrosine kinases (RTKs) transmit extracellular signals by phosphorylating their protein partners on conserved tyrosine residues. Some of the best studied RTKs are EGFR (reviewed in Avraham and Yarden, 2011), FGFR (reviewed in Eswarakumar et al, 2005), insulin receptor (reviewed in Saltiel and Kahn, 2001), NGF (reviewed in Reichardt, 2006), PDGF (reviewed in Andrae et al, 2008) and VEGF (reviewed in Xie et al, 2004). RTKs frequently activate downstream signaling through RAF/MAP kinases (reviewed in McKay and Morrison, 2007 and Wellbrock et al 2004), AKT (reviewed in Manning and Cantley, 2007) and PLC- gamma (reviewed in Patterson et al, 2005), which ultimately results in changes in gene expression and cellular metabolism.
Receptor serine/threonine kinases of the TGF-beta family, such as TGF-beta receptors (reviewed in Kang et al. 2009) and BMP receptors (reviewed in Miyazono et al. 2009), transmit extracellular signals by phosphorylating regulatory SMAD proteins on conserved serine and threonine residues. This leads to formation of complexes of regulatory SMADs and SMAD4, which translocate to the nucleus where they act as transcription factors.
WNT receptors transmit their signal through beta-catenin. In the absence of ligand, beta-catenin is constitutively degraded in a ubiquitin-dependent manner. WNT receptor stimulation releases beta-catenin from the destruction complex, allowing it to translocate to the nucleus where it acts as a transcriptional regulator (reviewed in MacDonald et al, 2009 and Angers and Moon, 2009). WNT receptors were originally classified as G-protein coupled receptors (GPCRs). Although they are structurally related, GPCRs primarily transmit their signals through G-proteins, which are trimers of alpha, beta and gamma subunits. When a GPCR is activated, it acts as a guanine nucleotide exchange factor, catalyzing GDP to GTP exchange on the G-alpha subunit of the G protein and its dissociation from the gamma-beta heterodimer. The G-alpha subunit regulates the activity of adenylate cyclase, while the gamma-beta heterodimer can activate AKT and PLC signaling (reviewed in Rosenbaum et al. 2009, Oldham and Hamm 2008, Ritter and Hall 2009).
NOTCH receptors are activated by transmembrane ligands expressed on neighboring cells, which results in cleavage of NOTCH receptor and release of its intracellular domain. NOTCH intracellular domain translocates to the nucleus where it acts as a transcription factor (reviewed in Kopan and Ilagan, 2009).
Integrins are activated by extracellular matrix components, such as fibronectin and collagen, leading to conformational change and clustering of integrins on the cell surface. This results in activation of integrin-linked kinase and other cytosolic kinases and, in co-operation with RTK signaling, regulates survival, proliferation and cell shape and adhesion (reviewed in Hehlgans et al, 2007) .
Besides inducing changes in gene expression and cellular metabolism, extracellular signals that trigger the activation of Rho GTP-ases can trigger changes in the organization of cytoskeleton, thereby regulating cell polarity and cell-cell junctions (reviewed in Citi et al, 2011).
R-HSA-392518 Signal amplification In the initial response to injury, platelets adhere to damaged blood vessels, responding to the exposure of collagen from the vascular epithelium. Once adhered they degranulate, releasing stored secondary agents such as ADP and ATP, and synthesized thromboxane A2. These amplify the response, activating and recruiting further platelets to the area and promoting platelet aggregation. Adenosine nucleotides secreted following platelet activation signal through P2 purinergic receptors on the platelet membrane. ADP activates P2Y1 and P2Y12 while ATP activates the ionotropic P2X1 receptor (Kunapuli et al. 2003). Activation of these receptors initiates a complex signaling cascade that ultimately results in platelet activation and thrombus formation (Kahner et al. 2006). ADP stimulation of P2Y1 and P2Y12 involves signaling via both the alpha and gamma:beta components of the heterotrimeric G-protein (Hirsch et al. 2001, 2006).
R-HSA-74749 Signal attenuation Now with the complete receptor-ligand dissociation and subsequent degradation of insulin in the endosomal lumen, the endosomally associated protein tyrosine phosphatases (PTPs) complete the receptor dephosphorylation. So too are all the receptor substrates dephosphorylated leading to the collapse of the signalling complexes and signal attenuation.
R-HSA-391160 Signal regulatory protein family interactions Signal regulatory protein alpha (SIRPA, SHPS1, CD172a) is a transmembrane protein expressed mostly on myeloid cells. CD47, a widely expressed transmembrane protein, is a ligand for SIRP alpha, with the two proteins constituting a cell-cell communication system. The interaction of SIRPA with CD47 is important for the regulation of migration and phagocytosis. SIRPA functions as a docking protein to recruit and activate PTPN6 (SHP-1) or PTPN11 (SHP-2) at the cell membrane in response to extracellular stimuli. SIRPA also binds other intracellular proteins including the adaptor molecules Src kinase-associated protein (SKAP2 SKAP55hom/R), Fyn-binding protein/SLP-76-associated phosphoprotein (FYB/SLAP-130) and the tyrosine kinase PYK2. SIRPA also binds the extracellular proteins, surfactant-A (SP-A) and surfactant-D (SP-D).
The SIRP family members SIRPB and SIRPG show high sequence similarity and similar extracellular structural topology, including three Ig domains, but their ligand binding topology might differ. SIRPB is expressed on myeloid cells, including monocytes, granulocytes and DCs. It has no known natural ligand. SIRPG can bind CD47 but with lower affinity than SIRPA.
R-HSA-445144 Signal transduction by L1 Besides adhesive roles in cell cell interaction, L1 functions as a signal transducing receptor providing neurons with cues from their environment for axonal growth and guidance. L1 associates with beta1 integrins on the cell surface to induce a signaling pathway involving sequential activation of pp60csrc, Vav2 -GEF, Rac1, PAK1, MEK and ERK1/2. L1 stimulates cell migration and neurite outgrowth through the MAP kinases ERK1/2. CHL1 also associates with integrins and activates a MAPK signaling pathway via pp60c-src, MEK and ERK1/2.
L1 also binds the Sema3A receptor neuropilin1 and acts as an obligate coreceptor to mediate Sema3A induced growth cone collapse and axon repulsion. This repulsion can be converted to attraction by homophilic binding of L1 on an apposing cell in trans with L1 complexed with Neuropilin1 (NP1) in the responding neuron.
L1 also interacts with FGF receptor and activates PLC gamma and DAG, resulting in the production of arachidonic acid and subsequent opening of voltage-gated channels.
R-HSA-201556 Signaling by ALK The anaplastic lymphoma kinase (ALK) is a transmembrane receptor tyrosine kinase that, along with related receptor LTK (leukocyte tyrosine kinase receptor) is a member of the insulin receptor superfamily (Iwahara et al, 1997). ALK was discovered as an oncogene in anaplastic large cell lymphomas (ALCLs), but also plays an oncogenic role in other cancer types, such as non-small-cell lung cancer (NSCLC), inflammatory myofibroblastic tumours (IMT), melanoma, neuroblastoma and glioblastoma. In cancer, the chromosomal region encoding ALK frequently undergoes genomic rearrangements, resulting in the formation of ALK fusion proteins, such as NPM‑ALK (the result of a translocation event, t(2;5)(p23;q35) which is predominant in ALCL) and EML4‑ALK (an inversion event on chromosome 2) (Morris et al, 1994; Couts et al, 2018). These fusion proteins consist of the C‑terminal region of ALK, encompassing the kinase domain and the effector protein binding domain (with loss of the transmembrane domain), while the N‑terminus of the fusion protein contains the dimerization domain of the partner gene. Fusion proteins of ALK are therefore capable of ligand‑independent dimerization, resulting in constitutive ALK signaling (reviewed in Duyster et al, 2001; Chiarle et al, 2008; Della Corte et al, 2018; Hallberg and Palmer, 2013; Hallberg and Palmer, 2016; Janoueix-Larousey et al, 2018; Ducray et al, 2019). Additionally, amplification of ALK and/or point mutations leading to its constitutive activation have been detected in neuroblastoma (reviewed in McDuff et al, 2011).
Many of the functional studies on ALK have been conducted in the context of oncogenic forms of the protein. In contrast, fewer studies have been conducted on the wild type protein under normal physiological conditions, and indeed, ALK was initially classed as an orphan receptor with no identified ligand. Two small heparin-binding growth factors, pleiotrophin (PTN) and midkine (MDK), were initially identified as potential ligands however subsequent studies failed to support this (Stoica et al, 2001; Stoica et al, 2002; Mathivet et al, 2007; Moog-Lutz et al, 2005; Motegi et al, 2004; reviewed in Wellstein et al, 2012; Winkler et al, 2014; Herradon and Perez-Garcia, 2014). More recently, ALKAL1 and ALKAL2 (also known as FAM150A and FAM150B) have been identified as ligands for both ALK and the related LTK receptor, albeit with differing potencies (Zhang et al, 2014; Guan et al, 2015; Reshetnyak et al, 2015; Reshetnyak et al, 2018; Fadeev et al, 2018; Reshetnyak et al, 2021; De Munck et al, 2021; Borenas et al, 2021; reviewed in Hallberg and Palmer, 2016). Whereas LTK receptor is potently activated by both ALKAL1 and ALKAL2, ALK is only weakly stimulated by ALKAL1 (Reshetnyak et al, 2015; Reshetnyak et al, 2018). Ligand binding induces the dimerization of the receptor and transautophosphorylation, resulting in a fully activated receptor that triggers downstream signaling cascades such as RAS, PI3K and IRS1 signaling. ALK may also undergo ligand-independent activation through RPTPB/RPTPZ (Deuel et al, 2013).
ALK is mainly expressed in the developing central and peripheral nervous system and plays a role in differentiation during development (Souttou et al, 2001; Gouzi et al, 2005; Degoutin et al, 2007). In Drosophila and mice, ALK is a thinness gene involved in the resistance to weight gain (Orthofer et al, 2020). Through activation of STAT3 targets, ALK also appears to play a role in response to ethanol (Hamada et al, 2021).
R-HSA-9725370 Signaling by ALK fusions and activated point mutants ALK is activated in a range of cancers as a result of amplification or overexpression, fusion event or activating point mutations, resulting, in general, in constitutive activation of intracellular signaling. The major pathways initiated downstream of activated ALK are STAT3 and, to a lesser extent, STAT5 signaling and signaling through the MAP kinase, PI3K/AKT and PLC gamma cascades (reviewed in Della Corte et al, 2018; Hallberg and Palmer, 2013; Hallberg and Palmer, 2016; Chiarle et al, 2008).
R-HSA-9700206 Signaling by ALK in cancer Anaplastic lymphoma kinase (ALK) was first identified in the context of an oncogenic fusion with nucleophosmin (NPM) in anaplastic large cell lymphoma (ALCL) (Morris et al, 1994). NPM-ALK fusions occur in approximately 75-80% of ALCL cases and at lower frequencies in other cancers, including non-small cell lung cancer, neuroblastoma and inflammatory myofibroblastic tumors (IFTs) (Morris et al, 1994; Shiota et al, 1994; reviewed in Della Corte et al, 2018; Werner et al, 2017).
In addition to NPM, fusions of ALK with nearly 30 other 5' partners have since been identified, although these tend to occur at lower frequencies in the cancers in which they appear (reviewed in Chiarle et al, 2008; Della Corte et al, 2018; Roskoski, 2013; Hallberg and Palmer, 2016). In general, ALK fusions combine the 5' end of the partner gene which contributes a dimerization domain with the intracellular portion of the ALK receptor including the kinase domain, and lead to constitutive signaling by virtue of the partner-domain mediated dimerization (reviewed in Roskoski, 2013; Della Corte et al, 2018).
In addition to translocation events that lead to fusion proteins, the ALK gene also contributes to oncogenesis as a result of gene amplification and overexpression events, as well as being subject to activating missense mutations (reviewed in Della Corte et al, 2018; Hallberg and Palmer, 2016).
Oncogenic ALK activity can be targeted with tyrosine kinase inhibitors, although resistance often arises due to secondary mutations or activation of bypass pathways (reviewed in Roskoski, 2013; Della Corte et al, 2018; Hallberg and Palmer, 2016; Werner et al, 2017; Lovly and Pao, 2012).
R-HSA-4839748 Signaling by AMER1 mutants AMER1/WTX is a component of the destruction complex that interacts directly with beta-catenin through its C-terminal half. Depletion of AMER1 through siRNA stabilizes cellular beta-catenin levels and increases transcriptional activity in a reporter assay consistent with a role for AMER1 in the degradation of beta-catenin (Major et al, 2007). Deletions of the entire AMER1 gene have been reported in Wilms tumor, as have nonsense and missense mutations that truncate the protein before the beta-catenin interaction domain. These mutations are predicted to stabilize beta-catenin and increase WNT signaling (reviewed in Saito-Diaz et al, 2013; Huff, 2011).
R-HSA-4839744 Signaling by APC mutants APC is a large and central component of the destruction complex, which limits signaling in the absence of WNT ligand by promoting the ubiquitin-mediated degradation of beta-catenin. APC interacts with numerous components of the destruction complex, including AXINs (AXIN1 and AXIN2), GSK3s (GSK3alpha and GSK3beta), CK1, PP2A and beta-catenin, and these interactions are critical for the phosphorylation and degradation of beta-catenin (reviewed in Saito-Diaz et al, 2013). APC is itself the target of phosphorylation and K63 ubiquitination in the absence of WNT signaling and these modifications are required for its interactions with other components of the destruction complex (Tran and Polakis, 2012; Ha et al, 2004; reviewed in Stamos and Weis, 2013).
More than 85% of sporadic and hereditary colorectal tumors carry loss-of-function mutations in APC. Most of the mutations are frameshifts and result in truncated proteins that lack the SAMP motifs and the 15 and 20 aa repeats that are implicated in binding AXIN and regulating beta-catenin binding and degradation (Miyoshi et al, 1992; Nagase and Nakamura, 1993; reviewed in Segditas and Tomlinson, 2006). Cancers expressing truncated APC have high levels of cytoplasmic beta-catenin and deregulated expression of WNT target genes (Korinek et al, 1997). Approximately 15% of the colorectal tumors with wild-type APC harbor phosphodegron mutations of beta-catenin; interestingly, mutations in APC and beta-catenin are mutually exclusive events. Similar to APC-mutant tumors, beta-catenin is stabilized in these tumors and constitutive WNT target activation is detected (Morin et al, 1997; reviewed in Polakis, 2000).
R-HSA-4839735 Signaling by AXIN mutants AXIN1 and AXIN2 are critical scaffolding proteins of the beta-catenin destruction complex and make protein-protein interactions with several of the other complex components including APC, GSK3, CK1 and beta-catenin itself through specific domains (reviewed in Saito-Diaz et al, 2013). Because of its role in promoting the degradation of beta-catenin and thereby restricting WNT signaling, AXIN1 is regarded as a tumor suppressor; consistent with this, biallelic mutations in AXIN1 that abrogate its expression or result in the production of truncated proteins have been identified in some human cancers, notably in hepatocellular and colorectal carcinomas and medullobalstoma (Satoh et al, 2000; Taniguchi et al, 2002; Shimizu et al, 2002; Dahmen et al, 2001; reviewed in Salahshor and Woodgett, 2005).
R-HSA-1502540 Signaling by Activin Activin was initially discovered as an activator of follicle stimulating hormone in the pituitary gland. It has since been shown to be an important participant in the differentiation of embryonic cells into mesodermal and endodermal layers. Activin binds the Activin receptor and triggers downstream events: phosphorylation of SMAD2 and SMAD3 followed by activation of gene expression (reviewed in Attisano et al. 1996, Willis et al. 1996, Chen et al. 2006, Hinck 2012). Activins are dimers comprising activin A (INHBA:INHBA), activin AB (INHBA:INHBB), and activin B (INHBB:INHBB). Activin first binds the type II receptor (ACVR2A, ACVR2B) and this complex then interacts with the type I receptor (ACVR1B, ACVR1C) (Attisano et al. 1996). The type II receptor phosphorylates the type I receptor and then the phosphorylated type I receptor phosphorylates SMAD2 and SMAD3. Dimers of phosphorylated SMAD2/3 bind SMAD4 and the resulting ternary complex enters the nucleus and activates target genes.
R-HSA-201451 Signaling by BMP Bone morphogenetic proteins (BMPs) have many biological activities in various tissues, including bone, cartilage, blood vessels, heart, kidney, neurons, liver and lung. They are members of the Transforming growth factor-Beta (TGFB) family. They bind to type II and type I serine-threonine kinase receptors, which transduce signals through SMAD and non-SMAD signalling pathways. BMP signalling is linked to a wide variety of clinical disorders, including vascular diseases, skeletal diseases and cancer. BMPs typically activate BMP type I receptors and signal via SMAD1, 5 and 8. They can be classified into several subgroups, including the BMP2/4 group, the BMP5-8 osteogenic protein-1 (OP1) group, the growth and differentiation factor (GDF) 5-7 group and the BMP9/10 group. Most of the proteins of the BMP2/4, OP1 and BMP9/10 groups induce formation of bone and cartilage tissues in vivo, while the GDF5-7 group induce cartilage and tendon-like, but not bone-like, tissues (Miyazono et al. 2010). Members of the TGFB family bind to two types of serine-threonine kinase receptors, type I and type II (Massagué 2012). BMPs can bind type I receptors in the absence of type II receptors, but both types are required for signal transduction. The presence of both types dramatically increases binding affinity (Rozenweig et al. 1995). The type II receptor kinase transphosphorylates the type I receptor, which transmits specific intracellular signals. Type I and type II receptors share similar structural properties, comprised of a relatively short extracellular domain, a single membrane-spanning domain and an intracellular domain containing a serine-threonine kinase domain. Seven receptors, collectively referred to as the Activin receptor-like kinases (ALK), have been identified as type I receptors for the TGFB family in mammals. ALKs are classified into three groups based on their structure and function, the BMPRI group (Bone morphogenetic protein receptor type-1A, ALK3, BMPR1A and Bone morphogenetic protein receptor type-1B, ALK6, BMPR1B), the ALK1 group (Serine/threonine-protein kinase receptor R3, ALK1, ACVRL1 and Activin receptor type-1, ALK2, ACVR1) and the TBetaR1 group (Activin receptor type-1B, ALK4, ACVR1B and TGF-beta receptor type-1, ALK5, TGFBR1 and Activin receptor type-1C, ALK7, ACVR1C) (Kawabata et al. 1998). ALK1 group and BMPRI group activate SMAD1/5/8 and transduce similar intracellular signals. The TBetaR1 group activate SMAD2/3. BMPR1A and ACVR1 are widely expressed. BMPR1B shows a more restricted expression profile. ACVRL1 is limited to endothelial cells and a few other cell types. The binding specificities of BMPs to type I receptors is affected by the type II receptors that are present (Yu et al. 2005). Typically, BMP2 and BMP4 bind to BMPR1A and BMPR1B (ten Dijke et al. 1994). BMP6 and BMP7 bind strongly to ACVR1 and weakly to BMPR1B. Growth/differentiation factor 5 (BMP14, GDF5) preferentially binds to BMPR1B, but not to other type I receptors (Nishitoh et al. 1995). BMP9 and BMP10 bind to ACVRL1 and ACVRL (Scharpfenecker et al. 2007). BMP type I receptors are shared by other members of the TGFB family. Three receptors, Bone morphogenetic protein receptor type-2 (BMPR2), Activin receptor type-2A (ACVR2A) and Activin receptor type-2B (ACVR2B) are the type II receptors for mammalian BMPs. They are widely expressed in various tissues. BMPR2 is specific for BMPs, whereas ACVR2A and ACVR2B are shared with activins and myostatin. BMP binding and signalling can be affected by coreceptors. Glycosylphosphatidylinositol (GPI)-anchored proteins of the repulsive guidance molecule (RGM) family, including RGMA, RGMB (DRAGON) and Hemojuvelin (HFE2, RGMC) are coreceptors for BMP2 and BMP4, enhancing signaling (Samad et al. 2005, Babitt et al. 2005, 2006). They interact with BMP type I and/or type II receptors and bind BMP2 and BMP4, but not BMP7 or TGFB1. BMP2/4 signalling normally involves BMPR2, not ACVR2A or ACVR2B. Cells transfected with RGMA use both BMPR2 and ACVR2A for BMP-2/4 signalling, suggesting that RGMA facilitates the use of ACVR2A by BMP2/4 (Xia et al. 2007). Endoglin (ENG) is a transmembrane protein expressed in proliferating endothelial cells. It binds various ligands including TGFB1/3, Activin-A and BMP2/7 (Barbara et al. 1999). It inhibits TGFB-induced responses and enhances BMP7-induced responses (Scherner et al. 2007). Mutations in ENG result in hereditary haemorrhagic telangiectasia (HHT1), also known as OslerWeberRendu disease, while mutations in ACVRL1 lead to HHT2, suggesting that they act in a common signalling pathway (McAllister et al. 1994, Johnson et al. 1996). BMP2 is a dimeric protein, having two receptor-binding motifs. One is a high-affinity binding site for BMPR1A, the other is a low-affinity binding site for BMPR2 (Kirsch et al. 2000). In the absence of ligand stimulation, small fractions of type II and type I receptors are present as preexisting homodimers and heterodimers on the cell surface. Ligand-binding increases oligomerization. The intracellular domains of type I receptors have a characteristic GS domain (glycine and serine-rich domain) located N-terminal to the serine-threonine kinase domains. Type II receptor kinases are constitutively active in the absence of ligand. Upon ligand binding, the type II receptor kinase phosphorylates the GS domain of the type I receptor, a critical event in signal transduction by the serine/threonine kinase receptors (Miyazono et al. 2010). Activation of the TGFBR1 receptor has been studied in detail. The inactive conformation is maintained by interaction between the GS domain, the N-terminal lobe and the activation loop of the kinase (Huse et al. 1999). When the GS domain is phosphorylated by the type II receptor kinase, the TGFBR1 kinase is converted to an active conformation. Mutations of Thr-204 in TGFBR1 and the corresponding Gln in BMP type I receptors lead to their constitutive activation. The L45 loop, in the kinase domain of type I receptors, specifically interacts with receptor-regulated Smads (R-Smads). Neurotrophic tyrosine kinase receptor type 3 (NT-3 growth factor receptor, TrkC, NTRK3) directly binds BMPR2, interfereing with its interaction with BMPR1A, which inhibits downstream signalling (Jin et al. 2007). Tyrosine-protein kinase transmembrane receptor ROR2 and BMPR1B form a heteromeric complex in a ligand independent fashion that modulatesGDF5-BMPR1B signalling by inhibition of Smad1/5 signalling (Sammar et al. 2004). Type I receptor kinases activated by the type II receptor kinases, phosphorylate R-Smads. R-Smads then form a complex with common-partner Smad (co-Smad) and translocate to the nucleus. The oligomeric Smad complexes regulate the transcription of target genes through interaction with various transcription factors and transcriptional coactivators or corepressors. Inhibitory Smads (I-Smads) negatively regulate the action of R-Smads and/or co-Smads. Eight different Smads have been identified in mammals. Smad1, Smad5 and Smad8 are R-Smads in BMP signalling pathways (BMP-specific R-Smads). Smad2 and Smad3 are R-Smads in TGFB/activin
signalling pathways. BMP receptors can phosphorylate Smad2 in certain types of cells (Murakami et al. 2009). Smad1, Smad5 and Smad8 are structurally highly similar to each other. The functional differences between them are largely unknown. Smad4 is the only co-Smad in mammals, shared by both BMP and TGFB/activin signalling pathways. Smad6 and Smad7 are I-Smads.
R-HSA-6802952 Signaling by BRAF and RAF1 fusions In addition to the more prevalent point mutations, BRAF and RAF1 are also subject to activation as a result of translocation events that yield truncated or fusion products (Jones et al, 2008; Cin et al, 2011; Palanisamy et al, 2010; Ciampi et al, 2005; Stransky et al, 2014; Hutchinson et al, 2013; Zhang et al, 2013; Lee et al, 2012; Ricarte-Filho et al, 2013; reviewed in Lavoie and Therrien et al, 2015). In general these events put the C-terminal kinase domain of BRAF or RAF1 downstream of an N-terminal sequence provided by a partner protein. This removes the N-terminal region of the RAF protein, relieving the autoinhibition imposed by this region of the protein. In addition, some but not all of the fusion partner proteins have been shown to contain coiled-coil or other dimerization domains. Taken together, the fusion proteins are thought to dimerize constitutively and activate downstream signaling (Jones et al, 2008; Lee et al, 2012; Hutchinson et al, 2013; Ciampi et al, 2005; Cin et al, 2011; Stransky et al, 2014).
R-HSA-9680350 Signaling by CSF1 (M-CSF) in myeloid cells Colony stimulating factor-1 (CSF1, CSF-1, also called macrophage colony stimulating factor, M-CSF) is a disulfide-linked dimer that stimulates the proliferation and differentiation of mononuclear phagocytes and the survival, proliferation, motility, and anti-inflammatory activity of macrophages (reviewed in Mouchemore et al. 2012, Stanley and Chitu 2014, Ushach and Zlotnik 2016, Dwyer et al. 2017 and inferred from mouse homologs in Caescu et al. 2015). The unliganded CSF1 receptor, CSF1R (CSF-1R) is either clustered or undergoing rapid dimer-monomer transitions at the cell surface (Li and Stanley 1991). The CSF1 dimer initially binds the D2 and D3 extracellular domains of a monomer of CSF1R (Wang et al. 1993, Chihara et al. 2010, Ma et al. 2012, Felix et al. 2015, and inferred from mouse homologs). A second monomer of CSF1R then binds the CSF1:CSF1R complex and the resulting dimerization of CSF1R activates its kinase activity (Elegheert et al. 2011, Felix et al. 2015, and inferred from mouse homologs). CSF1R initially trans-autophosphorylates tyrosine-561 in the juxtamembrane domain, relieving negative autoinhibition of kinase activity, resulting in the trans-autophosphorylation of 7 more tyrosine residues in its cytoplasmic domain (Rohrschneider et al. 1997, Chihara et al. 2010, and inferred from mouse homologs in Xiong et al. 2011).
The PIK3R1 (p85alpha) regulatory subunit of phosphatidylinositol 3-kinase (PI3K) binds phosphotyrosine-723 of CSF1R, phosphorylated SRC binds phosphotyrosine-561 of CSF1R, phosphorylated CBL binds CSF1R associated with SHC, and GRB2:SOS binds CSF1R (Saleem et al. 1995, and inferred from mouse homologs). The resulting activation of the catalytic subunit of PI3K (PIK2CA,B,G) produces phosphatidylinositol 3,4,5-trisphosphate which recruits effectors containing pleckstrin homology domains (PH domains) such as PKB (also called Akt) to the plasma membrane. Pathways activated by PI3K appear to both enhance proliferation, survival, and migration of macrophages (reviewed in Dwyer et al. 2017) and, via induction of miR21, suppress the inflammatory response by targeting mRNAs encoding multiple proinflammatory molecules.
Phospholipase C gamma2 (PLCG2) binds phosphotyrosine-723 of CSF1R, hydrolyzes phosphatidylcholine to yield choline phosphate (phosphocholine) and diacylglycerol, and promotes survival and differentiation of macrophages via PKCdelta (PRKCD) (inferred from mouse homologs).
GRB2 bound to SOS1 (GRB2:SOS1) transiently interacts with phosphotyrosine-699 of CSF1R. SOS1 promotes the exchange of GDP for GTP by KRAS, activating the RAS-RAF-ERK1,2 pathway that causes proliferation of macrophage precursors (inferred from mouse homologs). CBL transiently associates with and ubiquitinates the CSF1R, then is deubiquitinated and returned to the cytoplasm (inferred from mouse homologs).
Phosphorylated CSF1R also recruits STAT1 and STAT3, which are then phosphorylated (inferred from mouse homologs). The role of phosphorylated STAT1,3 in signaling by CSF1R is incompletely characterized.
CSF1R is a target for therapeutics, such as imatinib (reviewed in Kumari et al. 2018).
R-HSA-9674555 Signaling by CSF3 (G-CSF) CSF3 (GCSF) is a cytokine that regulates production of neutrophils and granulocytes (reviewed in Panopoulos and Watowich 2008). CSF3 circulates extracellularly as a dimer and binds to the monomeric receptor CSF3R (GCSFR) on neutrophil precursors and mature neutrophils (reviewed in Futosi et al. 2013). CSF3R possesses no catalytic activity of its own and is constitutively associated with the kinases LYN (Corey et al. 1994) and JAK1 (Nicholson et al. 1994). Upon binding the CSF3 dimer, CSF3R dimerizes, is phosphorylated, and activates JAK-STAT signaling, RAS-RAF-MEK-ERK signaling, and PI3K signaling (reviewed in Basu et al. 2002, Roberts et al. 2005, Kendricks and Bogoyevitch 2007, Touw and van de Geijn 2007).
After dimerization of CSF3R, JAK1 associated with CSF3R is required for phosphorylation of tyrosine residues in the cytosolic domain of CSF3R which recruit further kinases such as JAK2, SYK, HCK, and TYK2 (reviewed in Sampson et al. 2007). Phosphorylated JAK1 and JAK2 then appear to act redundantly to phosphorylate STAT proteins (STAT1, STAT3, STAT5) which dimerize and transit to the nucleus to activate gene expression.
CSF3 signaling also activates the RAS pathway, resulting in activation of ERK1 and ERK2 and cellular proliferation. Phosphorylated CSF3R recruits both GRB2, which can act as a scaffold for RAS guanyl exchange factors SOS and VAV, and PTPN11 (SHP2), which activates RAS by dephosphorylating tyrosine-32 of RAS (Bunda et al. 2015). Association of SOS or VAV with the phosphorylated CSF3R has not yet been shown. The pathway to activation of PI3K is uncertain but appears to proceed via GAB2 bound to CSF3R.
Mutations in CSF3R can occur during the course of Kostmann disease, a severe congenital neutropenia (reviewed in Zeidler and Welte 2002, Zeidler 2005, Ward 2007, Vandenberghe and Beel 2011). Somatic mutations in CSF3R, principally truncations of the C-terminal region, are involved in the pathogenesis of severe congenital neutropenia and are associated with progression to acute myeloid leukemia (Dong et al. 1995, reviewed in Ward 2007, Beekman and Touw 2010, Xing and Zhao 2016). Loss or mutation of the C-terminal region of CSF3R interferes with inhibition and turnover of the receptor. Mutation of Thr-618 to Ile-618 in CSF3R causes spontaneous dimerization and consequent autoactivation leading to CSF3-independent signaling and chronic neutrophilic leukemia (Maxson et al. 2013).
R-HSA-4839743 Signaling by CTNNB1 phospho-site mutants Mutations in exon 3 of the beta-catenin gene have been identified in a number of human cancers (Morin et al, 1997; Rubinfeld et al, 1997; reviewed in Polakis, 2000; Polakis, 2007). These mutations generally affect serine and threonine residues (S33, S37, T41, S45) that are the sites of phosphorylation by CK1 and GSK3; phosphorylation of these residues is required for the ubiquitin-mediated degradation of beta-catenin. Hence mutation of these phospho-acceptor sites stabilizes beta-catenin, allowing it to accumulate, translocate to the nucleus and activate WNT signaling through association with LEF1/TCF DNA binding partners (Hart et al, 1999; Peifer and Polakis, 2000; Laurent-Puig et al, 2001; reviewed in Saito-Diaz et al, 2013).
R-HSA-177929 Signaling by EGFR The epidermal growth factor receptor (EGFR) is one member of the ERBB family of transmembrane glycoprotein tyrosine receptor kinases (RTK). Binding of EGFR to its ligands induces conformational change that unmasks the dimerization interface in the extracellular domain of EGFR, leading to receptor homo- or heterodimerization at the cell surface. Dimerization of the extracellular regions of EGFR triggers additional conformational change of the cytoplasmic EGFR regions, enabling the kinase domains of two EGFR molecules to achieve the catalytically active conformation. Ligand activated EGFR dimers trans-autophosphorylate on tyrosine residues in the cytoplasmic tail of the receptor. Phosphorylated tyrosines serve as binding sites for the recruitment of signal transducers and activators of intracellular substrates, which then stimulate intracellular signal transduction cascades that are involved in regulating cellular proliferation, differentiation, and survival. Recruitment of complexes containing GRB2 and SOS1 to phosphorylated EGFR dimers either directly, through phosphotyrosine residues that serve as GRB2 docking sites, or indirectly, through SHC1 recruitment, promotes GDP to GTP exchange on RAS, resulting in the activation of RAF/MAP kinase cascade. Binding of complexes of GRB2 and GAB1 to phosphorylated EGFR dimers leads to formation of the active PI3K complex, conversion of PIP2 into PIP3, and activation of AKT signaling. Phospholipase C-gamma1 (PLCG1) can also be recruited directly, through EGFR phosphotyrosine residues that serve as PLCG1 docking sites, which leads to PLCG1 phosphorylation by EGFR and activation of DAG and IP3 signaling. EGFR signaling is downregulated by the action of ubiquitin ligase CBL. CBL binds directly to the phosphorylated EGFR dimer through the phosphotyrosine Y1069 (i.e. Y1045 in the mature protein) in the C-tail of EGFR, and after CBL is phosphorylated by EGFR, it becomes active and ubiquitinates phosphorylated EGFR dimers, targeting them for degradation. Positive regulation of EGFR signaling by direct association of EGFR with accessory proteins such as AAMP and FAM83B is being investigated. For review of EGFR signaling, please refer to Carpenter 1999, Wells 1999, Schlessinger 2002, Herbst 2004, Avraham and Yarden, 2011, Bartel et al. 2016, Uribe et al. 2021, Keflee et al. 2022.
R-HSA-1643713 Signaling by EGFR in Cancer The pathway "Signaling by EGFR in Cancer" shows signaling by constitutively active EGFR cancer variants in the context of "Signaling by EGFR", allowing users to compare cancer events with the wild-type EGFR events. Red lines emphasize cancer related events and physical entities, while wild-type entities and events are shaded. Please refer to "Signaling by Ligand-Responsive EGFR Variants in Cancer", "Signaling by EGFRvIII in Cancer" and "Signaling by Overexpressed Wild-Type EGFR in Cancer" for detailed pathway summations.
R-HSA-5637812 Signaling by EGFRvIII in Cancer EGFRvIII (EGFR V30_R297delinsG) is the most prevalent EGFR variant in glioblastoma, but it is also found in other cancer types. In-frame deletion of the ligand binding domain in EGFRvIII is frequently accompanied with genomic amplification, resulting in over-expression of EGFRvIII. EGFRvIII dimerizes and autophosphorylates spontaneously and is therefore constitutively active (Fernandes et al. 2001)
R-HSA-1227986 Signaling by ERBB2 ERBB2, also known as HER2 or NEU, is a receptor tyrosine kinase (RTK) belonging to the EGFR family. ERBB2 possesses an extracellular domain that does not bind any known ligand, contrary to other EGFR family members, a single transmembrane domain, and an intracellular domain consisting of an active kinase and a C-tail with multiple tyrosine phosphorylation sites. Inactive ERBB2 is associated with a chaperone heat shock protein 90 (HSP90) and its co-chaperone CDC37 (Xu et al. 2001, Citri et al. 2004, Xu et al. 2005). In addition, ERBB2 is associated with ERBB2IP (also known as ERBIN or LAP2), a protein responsible for proper localization of ERBB2. In epithelial cells, ERBB2IP restricts expression of ERBB2 to basolateral plasma membrane regions (Borg et al. 2000).
ERBB2 becomes activated by forming a heterodimer with another ligand-activated EGFR family member, either EGFR, ERBB3 or ERBB4, which is accompanied by dissociation of chaperoning proteins HSP90 and CDC37 (Citri et al. 2004), as well as ERBB2IP (Borg et al. 2000) from ERBB2. ERBB2 heterodimers function to promote cell proliferation, cell survival and differentiation, depending on the cellular context. ERBB2 can also be activated by homodimerization when it is overexpressed, in cancer for example.
In cells expressing both ERBB2 and EGFR, EGF stimulation of EGFR leads to formation of both ERBB2:EGFR heterodimers (Wada et al. 1990, Karunagaran et al. 1996) and EGFR homodimers. Heterodimers of ERBB2 and EGFR trans-autophosphorylate on twelve tyrosine residues, six in the C-tail of EGFR and six in the C-tail of ERBB2 - Y1023, Y1139, Y1196, Y1221, Y1222 and Y1248 (Margolis et al. 1989, Hazan et al. 1990,Walton et al. 1990, Helin et al. 1991, Ricci et al. 1995, Pinkas-Kramarski 1996). Phosphorylated tyrosine residues in the C-tail of EGFR and ERBB2 serve as docking sites for downstream signaling molecules. Three key signaling pathways activated by ERBB2:EGFR heterodimers are RAF/MAP kinase cascade, PI3K-induced AKT signaling, and signaling by phospholipase C gamma (PLCG1). Downregulation of EGFR signaling is mediated by ubiquitin ligase CBL, and is shown under Signaling by EGFR.
In cells expressing ERBB2 and ERBB3, ERBB3 activated by neuregulin NRG1 or NRG2 binding (Tzahar et al. 1994) forms a heterodimer with ERBB2 (Pinkas-Kramarski et al. 1996, Citri et al. 2004). ERBB3 is the only EGFR family member with no kinase activity, and can only function in heterodimers, with ERBB2 being its preferred heterodimerization partner. After heterodimerization, ERBB2 phosphorylates ten tyrosine residues in the C-tail of ERBB3, Y1054, Y1197, Y1199, Y1222, Y1224, Y1260, Y1262, Y1276, Y1289 and Y1328 (Prigent et al. 1994, Pinkas-Kramarski et al. 1996, Vijapurkar et al. 2003, Li et al. 2007) that subsequently serve as docking sites for downstream signaling molecules, resulting in activation of PI3K-induced AKT signaling and RAF/MAP kinase cascade. Signaling by ERBB3 is downregulated by the action of RNF41 ubiquitin ligase, also known as NRDP1.
In cells expressing ERBB2 and ERBB4, ligand stimulated ERBB4 can either homodimerize or form heterodimers with ERBB2 (Li et al. 2007), resulting in trans-autophosphorylation of ERBB2 and ERBB4 on C-tail tyrosine residues that will subsequently serve as docking sites for downstream signaling molecules, leading to activation of RAF/MAP kinase cascade and, in the case of ERBB4 CYT1 isoforms, PI3K-induced AKT signaling (Hazan et al. 1990, Cohen et al. 1996, Li et al. 2007, Kaushansky et al. 2008). Signaling by ERBB4 is downregulated by the action of WWP1 and ITCH ubiquitin ligases, and is shown under Signaling by ERBB4.
R-HSA-9665348 Signaling by ERBB2 ECD mutants ERBB2 extracellular domain (ECD) mutants harbor missense mutations that lead to substitutions of amino acid residues in the heterodimerization arm contact surface, involved in formation of ERBB2 heterodimers. The functionally studied ERBB2 ECD mutants, ERBB2 G309A (Bose et al. 2013), ERBB2 G309E (Greulich et al. 2012) and ERBB2 S310F (Greulich et al. 2012) seem to preferntially heterodimerize with EGFR. Heterodimerization of ERBB2 G309E involves formation of disulfide bonds (Greulich et al. 2012). ERBB2 S310F shows stronger activation of downstream signaling than ERBB2 G309A and ERBB2 G309E, and is hyperphosphorylated on tyrosine residues in the C-tail (Greulich et al. 2012), while the C-tail phosphorylation of ERBB2 G309A (Bose et al. 2013) and ERBB2 G309E (Greulich et al. 2012) is comparable to the wild type ERBB2.
RAS signaling and PLCgamma1 signaling are activated dowsntream of all three ERBB2 ECD mutants, ERBB2 G309A (Bose et al. 2013), ERBB2 G309E (Greulich et al. 2012) and ERBB2 S310F (Greulich et al. 2012), as evidenced by activating phosphorylation on ERKs (MAPK1 and MAPK3) and PLCG1, respectively. ERBB2 G309E and ERBB2 S310F also activate PI3K/AKT signaling, demonstrated by activating phosphorylation of AKT1 (Greulich et al. 2012). Activation of PI3K/AKT signaling downstream of ERBB2 G309A has not been tested. Signaling downstream of ERBB2 S310Y has been poorly characterized and it is annotated as a candidate. Many regulators of cell migration show increased phosphorylation in cells expressing ERBB2 G309E and ERBB2 S310F (Greulich et al. 2012).
Comapred with the wild type ERBB2, ERBB2 G309E, ERBB2 S310F and ERBB2 S310Y are more sensitive to the ERBB2-directed therapeutic antibody trastuzumab (herceptin) and to tyrosine kinase inhibitors lapatinib, neratinib and afatinib (Greulich et al. 2012). ERBB2 G309A was also responsive to trastuzumab, lapatinib and neratinib (Bose et al. 2013).
R-HSA-9664565 Signaling by ERBB2 KD Mutants Mutations in the kinase domain (KD) of ERBB2 result in constitutive activation of ERBB2 signaling, facilitate heterodimerization of ERBB2 with other EGFR family members and increase the signaling intensity, leading to cellular transformation (Kancha et al. 2011).
Only a subset of potential heterodimerization partners has been tested for most ERBB2 KD mutant proteins, so our annotations here are correspondingly limited. ERBB2 L755S and ERBB2 V777L cancer variants were shown to heterodimerize with ERBB3 (HER3) at a higher rate than wild type ERBB2 (Croessmann et al. 2019). Increased activity of ERBB2 L755S, ERBB2 L755P, ERBB2 V777L, ERBB2 D769H, ERBB2 D769Y, ERBB2 V842I, ERBB2 R896C and ERBB2 G778_P780dup in the presence of either EGFR (Kancha et al. 2011, Bose et al. 2013) or ERBB3 (Kancha et al. 2011, Bose et al. 2013, Collier et al. 2013) as a heterodimerization partner was also observed. The interplay of ERBB2 G778_P780dup, ERBB2 I767M and ERBB2 R896C with ERBB3 has not been tested. ERBB2 L869R mutant shows increased activity in the presence of ERBB3, which is further augmented in the presence of dimerization-facilitating ERBB3 E928G mutants (Hanker et al. 2017). The interplay of ERBB2 L869R with EGFR has not been tested. Heterodimerization of ERBB2 KD mutants with ERBB4 has not been tested and ERBB4 is a candidate heterodimerization partner for these KD variants.
ERBB2 H878Y mutant has ten times higher kinase activity than the wild type ERBB2 (Hu, Wan et al. 2015; Hu, Hu et al. 2015), but its heterodimerization properties have not been studied and it is therefore annotated as a candidate.
Ligand requirements have not been studied in the context of heterodimerization of ERBB2 KD mutants, but it is assumed that ligands are required.
The signaling properties of ERBB2 L755M (Gonzalez-Alonso et al. 2015), ERBB2 L755W (COSMIC database: Forbes et al. 2017), ERBB2 V777E (Dietz et al. 2017), ERBB2 V777M (Lee et al. 2006, Ross et al. 2016, Zehir et al. 2017), ERBB2 D769N (Tschui et al. 2015), ERBB2 V842E (Siroy et al. 2015), ERBB2 R896H (Cancer Genome Atlas Research Network 2011), ERBB2 L869Q (Lee et al. 2006) and ERBB2 H878R (Trowe et al. 2008, Zehir et al. 2017) have not been experimentally tested, but they are predicted to be pathogenic (COSMIC database: Forbes et al. 2017) and they are annotated as candidates. ERBB2 T733I (Trowe et al. 2008), ERBB2 T798I (Trowe et al. 2008, Hanker et al. 2017) and ERBB2 T798M (Hanker et al. 2017) usually occur as secondary ERBB2 mutations and are responsible for treatment failure. On their own, ERBB2 T733I and ERBB2 T798I appear to be weakly transforming compared with the other ERBB2 KD mutants. As their signaling properties have been poorly studied, ERBB2 T733I, ERBB2 T798I and ERBB2 T798M are annotated as candidates.
The binding of ERBB2 KD mutants to ERBIN and the HSP90:CDC37 chaperone:co-chaperone complex has not been tested but is assumed to occur similarly to the wild type ERBB2.
Signaling by ERBB2 KD mutants has been organized into subpathways based on the current knowledge of biology of these mutants (heterodimerization, downstream signaling, drug interaction) and on the sequence similarity of their mutations.
R-HSA-9665686 Signaling by ERBB2 TMD/JMD mutants Recurrent missense mutations in regions encoding the transmembrane domain (TMD) and the juxtamembrane domain (JMD) are frequently reported in cancer. The ERBB2 TMD mutants include ERBB2 V659E, ERBB2 V659K, ERBB2 G660D, ERBB2 G660R, ERBB2 S653C, ERBB2 R677L and ERBB2 R678Q. The ERBB2 JMD mutants include ERBB2 E693K and ERBB2 Q709L. ERBB2 TMD mutants ERBB2 V659E, ERBB2 G660D and S653C (de Martino et al. 2014) are known to be activating. ERBB2 TMD/JMD mutants ERBB2 R678Q, ERBB2 E693K, and ERBB2 Q709L mutations may be activating when co-expressed with a wild type ERBB2 receptor (Pahuja et al. 2018). TMD and JMD mutations can activate ERBB2 signaling by improving the active dimer interface or by stabilizing the active conformation. TMD/JMD mutants that are activating in the presence of wild type ERBB2, such as ERBB2 R678Q, may form homodimers with the wild type ERBB2 (Pahuja et al. 2018).
Based on trans-autophosphorylation of ERBB2 and its dimerization partners EGFR and ERBB3, the following ERBB2 TMD/JMD mutants are assumed to form heterodimers with EGFR and ERBB3:
ERBB2 S653C (de Martino et al. 2014)
ERBB2 R678Q (Bose et al. 2013, Pahuja et al. 2018).
Phosphorylation of tyrosine residues in the C-tail of ERBB2 was shown for the following ERBB2 TMD/JMD mutants:
ERBB2 V659E (Pahuja et al. 2018);
ERBB2 V659K (Pahuja et al. 2018);
ERBB2 G660D (Pahuja et al. 2018);
ERBB2 G660R (Pahuja et al. 2018);
ERBB2 S653C (de Martino et al. 2014 - phosphorylation at Y1248 demonstrated);
ERBB2 R677L (Pahuja et al. 2018);
ERBB2 R678Q (Bose et al. 2013; de Martino et al. 2014 - phosphorylation at Y1248 demonstrated; Pahuja et al. 2018); ERBB2 Q709L (Pahuja et al. 2018)
Phosphorylation of tyrosine residues in the C-tail of EGFR was demonstrated for ERBB2 S653C (de Martino et al. 2014 - phosphorylation at Y1068) and ERBB2 R678Q (Bose et al. 2013; de Martino et al. 2014 - phosphorylation at Y1068).
Phosphorylation of tyrosine residues in the C-tail of ERBB3 was demonstrated for ERBB2 S653C (de Martino et al. 2014 - phosphorylation at Y1197) and ERBB2 R678Q (Bose et al. 2013; de Martino et al. 2014 - phosphorylation at Y1197).
Activation of downstream RAS signaling was shown for ERBB2 S653C (de Martino et al. 2014) and ERBB2 R678Q (Bose et al. 2013, de Martino et al. 2014) through activating tyrosine phosphorylation on ERKs (MAPK1 and MAPK3) and SHC1.
Activation of downstream PLCG1 signaling was demonstrated for ERBB2 R678Q, through activating tyrosine phosphorylation on PLCG1 (Bose et al. 2013).
Activation of PI3K/AKT signaling by ERBB2 TMD/JMD mutants has not been tested.
Signaling by ERBB2 V659K, ERBB2 G660D, ERBB2 G660R, ERBB2 R677L, ERBB2 E693K and ERBB2 Q709L has not been sufficiently studied and they are annotated as candidates.
The following ERBB2 TMD/JMD mutants are sensitive to the therapeutic antibody trastuzumab (herceptin):
ERBB2 V659E (Pahuja et al. 2018);
ERBB2 G660D (Pahuja et al. 2018);
ERBB2 G660R (Pahuja et al. 2018);
ERBB2 R678Q (Bose et al. 2013, Pahuja et al. 2018);
ERBB2 Q709L (Pahuja et al. 2018);
With respect to pertuzumab, a therapeutic antibody that block ligand-driven heterodimerization of ERBB2, ERBB2 R678Q is sensitive to pertuzumab, while ERBB2 V659E, ERBB2 G660D, ERBB2 G660R and probably ERBB2 Q709L are resistant (Pahuja et al. 2018).
The following ERBB2 TMD/JMD mutants are sensitive to lapatinib:
ERBB2 S653C (de Martino et al. 2014);
ERBB2 R678Q (Bose et al. 2013);
The following ERBB2 TMD/JMD mutants are sensitive to neratinib:
ERBB2 V659E (Pahuja et al. 2018);
ERBB2 G660D (Pahuja et al. 2018);
ERBB2 G660R (Pahuja et al. 2018);
ERBB2 R678Q (Bose et al. 2013, Pahuja et al. 2018);
ERBB2 Q709L (Pahuja et al. 2018);
The following ERBB2 TMD/JMD mutants are sensitive to afatinib:
ERBB2 G660D (Pahuja et al. 2018);
ERBB2 G660R (Pahuja et al. 2018);
ERBB2 S653C (de Martino et al. 2014);
ERBB2 R678Q (Pahuja et al. 2018);
ERBB2 Q709L (Pahuja et al. 2018).
R-HSA-1227990 Signaling by ERBB2 in Cancer Gene amplification of the ERBB2 (HER2) oncogene is observed across various different cancer types. In addition to HER2 gene amplification, sequencing of tumour samples have revealed HER2 mutations, which fall within three major regions: the extracellular domain (ECD), transmembrane domain/ juxtamembrane domain (TMD/JMD) and kinase domain (KD). Based on the functional studies of their catalytic activity, signaling and drug sensitivity, as well as their time of occurence with respect to treatment, these mutation can be classified as primary mutations, that can be activating or silent, and may confer drug resistance, and secondary mutations, associated with development of drug resistance upon initial response to targeted therapy.
Overexpression of ERBB2 (HER2) protein, usually as a consequence of ERBB2 gene amplification, leads to formation of constitutively active, growth factor independent, ERBB2 homodimers, which are sensitive to the therapeutic antibody trastuzumab (herceptin) (Pickl and Ries 2009).
Co-overexpression of ERBB2 and its dimerization partner ERBB3 leads to formation of both ERBB2 homodimers and ERRB2:ERBB3 heterodimers and is associated with chemotherapy resistance and reduced relapse-free and overall survival (Spears et al. 2012).
Mutations in the kinase domain (KD) of ERBB2 result in constitutive activation of ERBB2 signaling, facilitate heterodimerization of ERBB2 with other EGFR family members and increase the signaling intensity (Kancha et al. 2011). Functionally studied ERBB2 KD mutants include ERBB2 L755S, ERBB2 L755P, ERBB2 I767M, ERBB2 D769H, ERBB2 V777L, ERBB2 G778_P780dup, ERBB2 T798I, ERBB2 T798M, ERBB2 V842I, ERBB2 T862A, ERBB2 L869R, ERBB2 H878Y and ERBB2 R896C (Kancha et al. 2011, Bose et al. 2013, Collier et al. 2013, Hu, Wan et al. 2015; Hu, Hu et al. 2015, Hanker et al. 2017, Croessmann et al. 2019).
Sensitivity to tyrosine kinase inhibitors (TKIs) and the therapeutic antibody trastuzumab (herceptin) differs between different ERBB2 KD mutants (Bose et al. 2013, Rexer et al. 2013, Nagano et al. 2018).
ERBB2 extracellular domain (ECD) mutants harbor missense mutations that lead to substitutions of amino acid residues in the heterodimerization arm contact surface, involved in formation of ERBB2 heterodimers (Greulich et al. 2012).
Recurrent missense mutations in regions encoding the transmembrane domain (TMD) and the juxtamembrane domain (JMD) are frequently reported in cancer. TMD and JMD mutations can activate ERBB2 signaling by improving the active dimer interface or by stabilizing the active conformation (Ou et al. 2017, Pahuja et al. 2018).
ERBB2 TMD/JMD mutants differ in their sensitivity to the therapeutic antibody pertuzumab, which blocks ligand-driven heterodimerization of ERBB2 (Pahuja et al. 2018).
R-HSA-1236394 Signaling by ERBB4 ERBB4, also known as HER4, belongs to the ERBB family of receptors, which also includes ERBB1 (EGFR/HER1), ERBB2 (HER2/NEU) and ERBB3 (HER3). Similar to EGFR, ERBB4 has an extracellular ligand binding domain, a single transmembrane domain and a cytoplasmic domain which contains an active tyrosine kinase and a C-tail with multiple phosphorylation sites. At least three and possibly four splicing isoforms of ERBB4 exist that differ in their C-tail and/or the extracellular juxtamembrane regions: ERBB4 JM-A CYT1, ERBB4 JM-A CYT2 and ERBB4 JM-B CYT1 (the existence of ERBB4 JM-B CYT2 has not been confirmed).
ERBB4 becomes activated by binding one of its seven ligands, three of which, HB-EGF, epiregulin EPR and betacellulin BTC, are EGF-like (Elenius et al. 1997, Riese et al. 1998), while four, NRG1, NRG2, NRG3 and NRG4, belong to the related neuregulin family (Tzahar et al. 1994, Carraway et al. 1997, Zhang et al. 1997, Hayes et al. 2007). Upon ligand binding, ERBB4 forms homodimers (Sweeney et al. 2000) or it heterodimerizes with ERBB2 (Li et al. 2007). Dimers of ERBB4 undergo trans-autophosphorylation on tyrosine residues in the C-tail (Cohen et al. 1996, Kaushansky et al. 2008, Hazan et al. 1990, Li et al. 2007), triggering downstream signaling cascades. The pathway Signaling by ERBB4 only shows signaling by ERBB4 homodimers. Signaling by heterodimers of ERBB4 and ERBB2 is shown in the pathway Signaling by ERBB2. Ligand-stimulated ERBB4 is also able to form heterodimers with ligand-stimulated EGFR (Cohen et al. 1996) and ligand-stimulated ERBB3 (Riese et al. 1995). Dimers of ERBB4 with EGFR and dimers of ERBB4 with ERBB3 were demonstrated in mouse cell lines in which human ERBB4 and EGFR or ERBB3 were exogenously expressed. These heterodimers undergo trans-autophosphorylation. The promiscuous heteromerization of ERBBs adds combinatorial diversity to ERBB signaling processes. As ERBB4 binds more ligands than other ERBBs, but has restricted expression, ERBB4 expression channels responses to ERBB ligands. The signaling capabilities of the four receptors have been compared (Schulze et al. 2005).
As for other receptor tyrosine kinases, ERBB4 signaling effectors are largely dictated through binding of effector proteins to ERBB4 peptides that are phosphorylated upon ligand binding. All splicing isoforms of ERBB4 possess two tyrosine residues in the C-tail that serve as docking sites for SHC1 (Kaushansky et al. 2008, Pinkas-Kramarski et al. 1996, Cohen et al. 1996). Once bound to ERBB4, SHC1 becomes phosphorylated on tyrosine residues by the tyrosine kinase activity of ERBB4, which enables it to recruit the complex of GRB2 and SOS1, resulting in the guanyl-nucleotide exchange on RAS and activation of RAF and MAP kinase cascade (Kainulainen et al. 2000).
The CYT1 isoforms of ERBB4 also possess a C-tail tyrosine residue that, upon trans-autophosphorylation, serves as a docking site for the p85 alpha subunit of PI3K (Kaushansky et al. 2008, Cohen et al. 1996), leading to assembly of an active PI3K complex that converts PIP2 to PIP3 and activates AKT signaling (Kainulainen et al. 2000).
Besides signaling as a conventional transmembrane receptor kinase, ERBB4 differs from other ERBBs in that JM-A isoforms signal through efficient release of a soluble intracellular domain. Ligand activated homodimers of ERBB4 JM-A isoforms (ERBB4 JM-A CYT1 and ERBB4 JM-A CYT2) undergo proteolytic cleavage by ADAM17 (TACE) in the juxtamembrane region, resulting in shedding of the extracellular domain and formation of an 80 kDa membrane bound ERBB4 fragment known as ERBB4 m80 (Rio et al. 2000, Cheng et al. 2003). ERBB4 m80 undergoes further proteolytic cleavage, mediated by the gamma-secretase complex, which releases the soluble 80 kDa ERBB4 intracellular domain, known as ERBB4 s80 or E4ICD, into the cytosol (Ni et al. 2001). ERBB4 s80 is able to translocate to the nucleus, promote nuclear translocation of various transcription factors, and act as a transcription co-factor. For example, in mammary cells, ERBB4 binds SH2 transcription factor STAT5A. ERBB4 s80 shuttles STAT5A to the nucleus, and actsa as a STAT5A co-factor in binding to and promoting transcription from the beta-casein (CSN2) promoter, and may be involved in the regulation of other lactation-related genes (Jones et al. 1999, Williams et al. 2004, Muraoka-Cook et al. 2008). ERBB4 s80 binds activated estrogen receptor in the nucleus and acts as a transcriptional co-factor in promoting transcription of some estrogen-regulated genes, including progesterone receptor gene NR3C3 and CXCL12 (SDF1) (Zhu et al. 2006). In neuronal precursors, ERBB4 s80 binds the complex of TAB and NCOR1, helps to move the complex into the nucleus, and is a co-factor of TAB:NCOR1-mediated inhibition of expression of astrocyte differentiation genes GFAP and S100B (Sardi et al. 2006).
The C-tail of ERBB4 possesses several WW-domain binding motifs (three in CYT1 isoform and two in CYT2 isoform), which enable interaction of ERBB4 with WW-domain containing proteins. ERBB4 s80, through WW-domain binding motifs, interacts with YAP1 transcription factor, a known proto-oncogene, and is a co-regulator of YAP1-mediated transcription in association with TEAD transcription factors (Komuro et al. 2003, Omerovic et al. 2004). Hence, the WW binding motif couples ERBB4 to the major effector arm of the HIPPO signaling pathway. The tumor suppressor WWOX, another WW-domain containing protein, competes with YAP1 in binding to ERBB4 s80 and prevents translocation of ERBB4 s80 to the nucleus (Aqeilan et al. 2005).
WW-domain binding motifs in the C-tail of ERBB4 play an important role in the downregulation of ERBB4 receptor signaling, enabling the interaction of intact ERBB4, ERBB4 m80 and ERBB4 s80 with NEDD4 family of E3 ubiquitin ligases WWP1 and ITCH. The interaction of WWP1 and ITCH with intact ERBB4 is independent of receptor activation and autophosphorylation. Binding of WWP1 and ITCH ubiquitin ligases leads to ubiquitination of ERBB4 and its cleavage products, and subsequent degradation through both proteasomal and lysosomal routes (Omerovic et al. 2007, Feng et al. 2009). In addition, the s80 cleavage product of ERBB4 JM-A CYT-1 isoform is the target of NEDD4 ubiquitin ligase. NEDD4 binds ERBB4 JM-A CYT-1 s80 (ERBB4jmAcyt1s80) through its PIK3R1 interaction site and mediates ERBB4jmAcyt1s80 ubiquitination, thereby decreasing the amount of ERBB4jmAcyt1s80 that reaches the nucleus (Zeng et al. 2009).
ERBB4 also binds the E3 ubiquitin ligase MDM2, and inhibitor of p53 (Arasada et al. 2005). Other proteins that bind to ERBB4 intracellular domain have been identified by co-immunoprecipitation and mass spectrometry (Gilmore-Hebert et al., 2010), and include transcriptional co-repressor TRIM28/KAP1, which promotes chromatin compaction. DNA damage signaling through ATM releases TRIM28-associated heterochromatinization. Interactions of ERBB4 with TRIM28 and MDM2 may be important for integration of growth factor responses and DNA damage responses.
In human breast cancer cell lines, ERBB4 activation enhances anchorage-independent colony formation in soft agar but inhibits cell growth in a monolayer culture. Different ERBB4 ligands induce different gene expression changes in breast cancer cell lines. Some of the genes induced in response to ERBB4 signaling in breast cancer cell lines are RAB2, EPS15R and GATA4. It is not known if these gene are direct transcriptional targets of ERBB4 (Amin et al. 2004).
Transcriptome and ChIP-seq comparisons of full-length and intracellular domain isoforms in isogenic MCF10A mammary cell background have revealed the diversification of ERBB4 signaling engendered by alternative splicing and cleavage (Wali et al., 2014). ERBB4 broadly affected protease expression, cholesterol biosynthesis, HIF1-alpha signaling, and HIPPO signaling pathways, and other pathways were differentially activated by CYT1 and CYT2 isoforms. For example, CYT1 promoted expression of transcription factors TWIST1 and SNAIL1 that promote epithelial-mesenchymal transition. HIF1-alpha and HIPPO signaling are mediated, respectively, by binding of ERBB4 to HIF1-alpha and to YAP (Paatero et al., 2012, Komuro et al., 2003). ERBB4 increases activity of the transcription factor SREBF2, resulting in increased expression of SREBF2-target genes involved in cholesterol biosynthesis. The mechanism is not known and may involve facilitation of SREBF2 cleavage through ERBB4-mediated PI3K signaling (Haskins et al. 2016).
In some contexts, ERBB4 promotes growth suppression or apoptosis (Penington et al., 2002). Activation of ERBB4 in breast cancer cell lines leads to JNK dependent increase in BRCA1 mRNA level and mitotic cell cycle delay, but the exact mechanism has not been elucidated (Muraoka Cook et al. 2006). The nature of growth responses may be connected with the spliced isoforms expressed. In comparisons of CYT1 vs CYT2 (full-length and ICD) expression in mammary cells, CYT1 was a weaker growth inducer, associated with attenuated MAPK signaling relative to CYT2 (Wali et al., 2014). ERBB4 s80 is also able to translocate to the mitochondrial matrix, presumably when its nuclear translocation is inhibited. Once in the mitochondrion, the BH3 domain of ERBB4, characteristic of BCL2 family members, may enable it to act as a pro apoptotic factor (Naresh et al. 2006).
ERBB4 plays important roles in the developing and adult nervous system. Erbb4 deficiency in somatostatin-expressing neurons of the thalamic reticular nucleus alters behaviors dependent on sensory selection (Ahrens et al. 2015). NRG1-activated ERBB4 signaling enhances AMPA receptor responses through PKC-dependent AMPA receptor exocytosis. This results in an increased excitatory input to parvalbumin-expressing inhibitory neurons in the visual cortex and regulates visual cortical plasticity (Sun et al. 2016). NRG1-activated ERBB4 signaling is involved in GABAergic activity in amygdala which mediates fear conditioning (fear memory) (Lu et al. 2014). Conditional Erbb4 deletion from fast-spiking interneurons, chandelier and basket cells of the cerebral cortex leads to synaptic defects associated with increased locomotor activity and abnormal emotional, social and cognitive function that can be linked to some of the schizophrenia features. The level of GAD1 (GAD67) protein is reduced in the cortex of conditional Erbb4 mutants. GAD1 is a GABA synthesizing enzyme. Cortical mRNA levels of GAD67 are consistently decreased in schizophrenia (Del Pino et al. 2014). Erbb4 is expressed in the GABAergic neurons of the bed nucleus stria terminalis, a part of the extended amygdala. Inhibition of NRG1-triggered ERBB4 signaling induces anxiety-like behavior, which depends on GABAergic neurotransmission. NRG1-ERBB4 signaling stimulates presynaptic GABA release, but the exact mechanism is not known (Geng et al. 2016). NRG1 protects cortical interneurons against ischemic brain injury through ERBB4-mediated increase in GABAergic transmission (Guan et al. 2015). NRG2-activated ERBB4 can reduce the duration of GABAergic transmission by binding to GABA receptors at the postsynaptic membrane via their GABRA1 subunit and promoting endocytosis of GABA receptors (Mitchell et al. 2013). NRG1 promotes synchronization of prefrontal cortex interneurons in an ERBB4 dependent manner (Hou et al. 2014). NRG1-ERBB4 signaling protects neurons from the cell death induced by a mutant form of the amyloid precursor protein (APP) (Woo et al. 2012).
Clinical relevance of ERBB4 has been identified in several contexts. In cancer, putative and validated gain-of-function mutations or gene amplification that may be drivers have been identified at modest frequencies, and may also contribute to resistance to EGFR and ERBB2-targeted therapies. This is noteworthy as ERBB4 kinase activity is inhibited by pan-ERBB tyrosine kinase inhibitors, including lapatinib, which is approved by the US FDA. The reduced prevalence relative to EGFR and ERBB2 in cancer may reflect more restricted expression of ERBB4, or differential signaling, as specific ERBB4 isoforms have been linked to growth inhibition or apoptosis in experimental systems. ERBB2/ERBB4 heterodimers protect cardiomyocytes, so reduced activity of ERBB4 in patients treated with the ERBB2-targeted therapeutic antibody trastuzumab may contribute to the cardiotoxicity of this agent when used in combination with (cardiotoxic) anthracyclines.
With the importance of ERBB4 in developing and adult nervous system, NRG1 and/or ERBB4 polymorphisms, splicing aberrations and mutations have been linked to nervous system disorders including schizophrenia and amyotrophic lateral sclerosis, although these findings are not yet definitive.
R-HSA-9006335 Signaling by Erythropoietin Erythropoietin (EPO) is a cytokine that serves as the primary regulator of erythropoiesis, the differentiation of erythrocytes from stem cells in the liver of the fetus and the bone marrow of adult mammals (reviewed in Ingley 2012, Zhang et al. 2014, Kuhrt and Wojchowski 2015). EPO is produced in the kidneys in response to low oxygen tension and binds a receptor, EPOR, located on progenitor cells: burst forming unit-erythroid (BFU-e) cells and colony forming unit-erythroid (CFU-e) cells.
The erythropoietin receptor (EPOR) exists in lipid rafts (reviewed in McGraw and List 2017) as a dimer pre-associated with proteins involved in downstream signaling: the tyrosine kinase JAK2, the tyrosine kinase LYN, and the scaffold protein IRS2. Binding of EPO to the EPOR dimer causes a change in conformation (reviewed in Watowich et al. 2011, Corbett et al. 2016) that activates JAK2, which then transphosphorylates JAK2 and phosphorylates the cytoplasmic domain of EPOR. The phosphorylated EPOR serves directly or indirectly as a docking site for signaling molecules such as STAT5, phosphatidylinositol 4,5-bisphosphate 3-kinase (PI3K), phospholipase C gamma (PLCG1, PLCG2), and activators of RAS (SHC1, GRB2:SOS1, GRB2:VAV1).
EPO activates 4 major signaling pathways: STAT5-activated transcription, PI3K-AKT, RAS-RAF-ERK, and PLC-PKC. JAK2-STAT5 activates expression of BCL2L1 (Bcl-xL) and therefore appears to be important for anti-apoptosis. PI3K-AKT appears to be important for both anti-apoptosis and proliferation. The roles of other signaling pathways are controversial but both RAS-RAF-MEK-ERK and PLCgamma-PKC have mitogenic effects. Phosphatases such as SHP1 are also recruited and downregulate the EPO signal.
EPO also has effects outside of erythropoiesis. The EPOR is expressed in various tissues such as endothelium where it can act to stimulate growth and promote cell survival (Debeljak et al. 2014, Kimáková et al. 2017). EPO and EPOR in the neurovascular system act via Akt, Wnt1, mTOR, SIRT1, and FOXO proteins to prevent apoptotic cell injury (reviewed in Ostrowski and Heinrich 2018, Maiese 2016) and EPO may have therapeutic value in the nervous system (Ma et al. 2016).
R-HSA-190236 Signaling by FGFR The 22 members of the fibroblast growth factor (FGF) family of growth factors mediate their cellular responses by binding to and activating the different isoforms encoded by the four receptor tyrosine kinases (RTKs) designated FGFR1, FGFR2, FGFR3 and FGFR4. These receptors are key regulators of several developmental processes in which cell fate and differentiation to various tissue lineages are determined. Unlike other growth factors, FGFs act in concert with heparin or heparan sulfate proteoglycan (HSPG) to activate FGFRs and to induce the pleiotropic responses that lead to the variety of cellular responses induced by this large family of growth factors. An alternative, FGF-independent, source of FGFR activation originates from the interaction with cell adhesion molecules, typically in the context of interactions on neural cell membranes and is crucial for neuronal survival and development.
Upon ligand binding, receptor dimers are formed and their intrinsic tyrosine kinase is activated causing phosphorylation of multiple tyrosine residues on the receptors. These then serve as docking sites for the recruitment of SH2 (src homology-2) or PTB (phosphotyrosine binding) domains of adaptors, docking proteins or signaling enzymes. Signaling complexes are assembled and recruited to the active receptors resulting in a cascade of phosphorylation events.
This leads to stimulation of intracellular signaling pathways that control cell proliferation, cell differentiation, cell migration, cell survival and cell shape, depending on the cell type or stage of maturation.
R-HSA-1226099 Signaling by FGFR in disease A number of skeletal and developmental diseases have been shown to arise as a result of mutations in the FGFR1, 2 and 3 genes. These include dwarfism syndromes (achondroplasia, hypochondroplasia and the neonatal lethal disorders thanatophoric dysplasia I and II), as well as craniosynostosis disorders such as Pfeiffer, Apert, Crouzon, Jackson-Weiss and Muenke syndromes (reviewed in Webster and Donoghue 1997; Burke, 1998, Cunningham, 2007; Harada, 2009). These mutations fall into four general regions of the receptor: a) the immunoglobulin (Ig)-like domain II-III linker region, b) the alternatively spliced second half of the Ig III domain, c) the transmembrane domain and d) the tyrosine kinase domain (reviewed in Webster and Donoghue, 1997). With the exception of mutations in class b), which affect only the relevant splice variant, these mutations may be present in either the 'b' or 'c' isoforms. These activating mutations affect FGFR function by altering or expanding the ligand-binding range of the receptors (see for instance Ibrahimi, 2004a), by promoting ligand-independent dimerization (for instance, Galvin,1996; Neilson and Friesel, 1996; d'Avis,1998) or by increasing the activity of the kinase domain (for instance, Webster, 1996; Naski, 1996; Tavormina, 1999; Bellus, 2000). Thus, a number of the point mutations found in FGFR receptors alter their activity without altering their intrinsic kinase activity. Many of the mutations that promote constitutive dimerization do so by creating or removing cysteine residues; the presence of an unpaired cysteine in the receptor is believed to promote dimerization through the formation of intramolecular disulphide bonds (Galvin, 1996; Robertson, 1998). Paralogous mutations at equivalent positions have been identified in more than one FGF receptor, sometimes giving rise to different diseases. For instance, mutation of the highly conserved FGFR2 Ser252-Pro253 dipeptide in the region between the second and third Ig domain is responsible for virtually all cases of Apert Syndrome (Wilkie, 1995), while paralogous mutations in FGFR1 (S252R) and FGFR3 (P250R) are associated with Pfeiffer and Crouzon syndromes, respectively (Bellus, 1996). FGFR4 is unique in that mutations of this gene are not known to be associated with any developmental disorders.
Recently, many of the same activating mutations in the FGFR genes that have been characterized in skeletal and developmental disorders have begun to be identified in a range of cancers (reviewed in Turner and Gross, 2010; Greulich and Pollock, 2011; Wesche, 2011). The best established link between a somatic mutation of an FGFR and the development of cancer is in the case of FGFR3, where 50% of bladder cancers have mutations in the FGFR3 coding sequence. Of these mutations, which largely match the activating mutations seen in thanatophoric dysplasias, over half occur at a single residue (S249C) (Cappellen, 1999; van Rhijn, 2002). Activating mutations have also been identified in the coding sequences of FGFR1, 2 and 4 (for review, see Wesche, 2011)
In addition to activating point mutations, the FGFR1, 2 and 3 genes are subject to misregulation in cancer through gene amplification and translocation events, which are thought to lead to overexpression and ligand-independent dimerization (Weiss, 2010; Turner, 2010; Kunii, 2008; Takeda, 2007; Chesi, 1997; Avet-Loiseau, 1998; Ronchetti, 2001). It is important to note, however, that in each of these cases, the amplification or translocation involve large genomic regions encompassing additional genes, and the definitive roles of the FGFR genes in promoting oncogenesis has not been totally established. In the case of FGFR1, translocation events also give rise to FGFR1 fusion proteins that contain the intracellular kinase domain of the receptor fused to a dimerization domain from the partner gene. These fusions, which are expressed in a pre-leukemic myeloproliferative syndrome, dimerize constitutively based on the dimerization domain provided by the fusion partner and are constitutively active (reviewed in Jackson, 2010).
R-HSA-5654736 Signaling by FGFR1 The 22 members of the fibroblast growth factor (FGF) family of growth factors mediate their cellular responses by binding to and activating the different isoforms encoded by the four receptor tyrosine kinases (RTKs) designated FGFR1, FGFR2, FGFR3 and FGFR4. These receptors are key regulators of several developmental processes in which cell fate and differentiation to various tissue lineages are determined. Unlike other growth factors, FGFs act in concert with heparin or heparan sulfate proteoglycan (HSPG) to activate FGFRs and to induce the pleiotropic responses that lead to the variety of cellular responses induced by this large family of growth factors. An alternative, FGF-independent, source of FGFR activation originates from the interaction with cell adhesion molecules, typically in the context of interactions on neural cell membranes and is crucial for neuronal survival and development.
Upon ligand binding, receptor dimers are formed and their intrinsic tyrosine kinase is activated causing phosphorylation of multiple tyrosine residues on the receptors. These then serve as docking sites for the recruitment of SH2 (src homology-2) or PTB (phosphotyrosine binding) domains of adaptors, docking proteins or signaling enzymes. Signaling complexes are assembled and recruited to the active receptors resulting in a cascade of phosphorylation events.
This leads to stimulation of intracellular signaling pathways that control cell proliferation, cell differentiation, cell migration, cell survival and cell shape, depending on the cell type or stage of maturation.
R-HSA-1839120 Signaling by FGFR1 amplification mutants Amplification or activation of FGFR1 has been reported in lung cancer (Weiss, 2001; Marek, 2009; Dutt, 2011), breast cancer (Reis-Filho, 2006; Turner, 2010), oral squamous carcinoma (Freier, 2007), esophageal squamous cell carcinomas (Ishizuka, 2002), ovarian cancer (Gorringe, 2007), bladder cancer (Simon, 2001), prostate cancer (Edwards, 2003; Acevedo, 2007) and rhabodomyosarcoma (Missiaglia, 2009). Unlike the case for FGFR2 amplifications, FGFR1 amplifications are not associated with additional point mutations and affect signaling without altering the intrinsic kinase activity of the receptor. Overexpressed FGFR1 appears to signal at a basal level in a ligand-independent fashion, but is also able to be stimulated by exogenous ligand. Downstream activation may be the result of aberrant paracrine or autocrine stimulation (reviewed in Turner and Gross, 2010; Greulich and Pollock, 2011). FGFR1 amplification has not been conclusively demonstrated to be the causative oncogenic agent in all of the cancer types mentioned above, and other genes in the 8p11 region may also be candidates in some cases (Bass, 2009; Bernard-Pierrot, 2008; Ray, 2004).
R-HSA-5655302 Signaling by FGFR1 in disease The FGFR1 gene has been shown to be subject to activating mutations, chromosomal rearrangements and gene amplification leading to a variety of proliferative and developmental disorders depending on whether these events occur in the germline or arise somatically (reviewed in Webster and Donoghue, 1997; Burke, 1998; Cunningham, 2007; Wesche, 2011; Greulich and Pollock, 2011).
Activating mutation P252R in FGFR1 is associated with the development of Pfeiffer syndrome, characterized by craniosynostosis (premature fusion of several sutures in the skull) and broadened thumbs and toes (Muenke, 1994; reviewed in Cunningham, 2007). This residue falls in a highly conserved Pro-Ser dipeptide between the second and third Ig domains of the extracellular region of the receptor. The mutation is thought to increase the number of hydrogen bonds formed with the ligand and to thereby increase ligand-binding affinity (Ibrahimi, 2004a). Unlike other FGF receptors, few activating point mutations in the FGFR1 coding sequence have been identified in cancer. Point mutations in the Ig II-III linker analagous to the P252R Pfeiffer syndrome mutation have been identified in lung cancer and melanoma (Ruhe, 2007; Davies, 2005), and two kinase-domain mutations in FGFR1 have been identified in glioblastoma (Rand, 2005, Network TCGA, 2008).
In contrast, FGFR1 is a target of chromosomal rearrangements in a number of cancers. FGFR1 has been shown to be recurrently translocated in the 8p11 myeloproliferative syndrome (EMS), a pre-leukemic condition also known as stem cell leukemia/lymphoma (SCLL) that rapidly progresses to leukemia. This translocation fuses the kinase domain of FGFR1 with the dimerization domain of one of 10 identified fusion partners, resulting in the constitutive dimerization and activation of the kinase (reviewed in Jackson, 2010).
Amplification of the FGFR1 gene has been implicated as a oncogenic factor in a range of cancers, including breast, ovarian, bladder, lung, oral squamous carcinomas, and rhabdomyosarcoma (reviewed in Turner and Grose, 2010; Wesche, 2011; Greulich and Pollock, 2011), although there are other candidate genes in the amplified region and the definitive role of FGFR1 has not been fully established.
More recently, FGFR1 fusion proteins have been identified in a number of cancers; these are thought to undergo constitutive ligand-independent dimerization and activation based on dimerization motifs found in the fusion partners (reviewed in Parker, 2014).
R-HSA-5654738 Signaling by FGFR2 The 22 members of the fibroblast growth factor (FGF) family of growth factors mediate their cellular responses by binding to and activating the different isoforms encoded by the four receptor tyrosine kinases (RTKs) designated FGFR1, FGFR2, FGFR3 and FGFR4. These receptors are key regulators of several developmental processes in which cell fate and differentiation to various tissue lineages are determined. Unlike other growth factors, FGFs act in concert with heparin or heparan sulfate proteoglycan (HSPG) to activate FGFRs and to induce the pleiotropic responses that lead to the variety of cellular responses induced by this large family of growth factors. An alternative, FGF-independent, source of FGFR activation originates from the interaction with cell adhesion molecules, typically in the context of interactions on neural cell membranes and is crucial for neuronal survival and development.
Upon ligand binding, receptor dimers are formed and their intrinsic tyrosine kinase is activated causing phosphorylation of multiple tyrosine residues on the receptors. These then serve as docking sites for the recruitment of SH2 (src homology-2) or PTB (phosphotyrosine binding) domains of adaptors, docking proteins or signaling enzymes. Signaling complexes are assembled and recruited to the active receptors resulting in a cascade of phosphorylation events.
This leads to stimulation of intracellular signaling pathways that control cell proliferation, cell differentiation, cell migration, cell survival and cell shape, depending on the cell type or stage of maturation.
R-HSA-8851708 Signaling by FGFR2 IIIa TM A soluble truncated form of FGFR2 is aberrantly expressed in an Apert Syndrome mouse model and inhibits FGFR signaling in vitro and in vivo. This variant, termed FGFR IIIa TM, arises from an misspliced transcript that fuses exon 7 to exon 10 and that escapes nonsense-mediated decay. FGFR2 IIIa TM may inhibit signaling by sequestering FGF ligand and/or by forming nonfunctional heterodimers with full-length receptors at the cell surface (Wheldon et al, 2011).
R-HSA-2023837 Signaling by FGFR2 amplification mutants FGFR2 amplifications have been identified in 10% of gastric cancers, where they are associated with poor prognosis diffuse cancers (Hattori, 1996; Ueda, 1999; Shin, 2000; Kunii, 2008) , and in ~1% of breast cancers (Turner, 2010; Tannheimer, 2000). FGFR2 amplification often occur in conjunction with deletions of C-terminal exons, resulting in expression of a internalization- and degradation-resistant form of the receptor (Takeda, 1999; Cha, 2008, 2009). Amplification affects signaling without altering the intrinsic kinase activity of the receptor. Signaling through overexpressed FGFR2 also shows evidence of being ligand-independent and sensitive to FGFR inhibitors (Lorenzi, 1997; Takeda, 1999; Cha, 2009).
R-HSA-8853333 Signaling by FGFR2 fusions FGFR2 fusions have been identified in cancers such as lung, breast, thyroid and cholangiocarcinoma (Wu et al, 2013; Seo et al, 2012; Arai et al, 2013). Of all the FGF receptors, FGFR2 shows the broadest range of 3' fusion partners, including BICC1, AHCYL1, CIT, CCDC6, CASP7, AFF3, OFD1 and CCAR2. Many of these fusion partners contain dimerization domains, suggesting that the resulting fusions may demonstrate constitutive ligand-independent activation (Wu et al, 2013; Arai et al, 2013; Seo et al, 2012; reviewed in Parker et al, 2014).
R-HSA-5655253 Signaling by FGFR2 in disease The FGFR2 gene has been shown to be subject to activating mutations and gene amplification leading to a variety of proliferative and developmental disorders depending on whether these events occur in the germline or arise somatically. Activating FGFR2 mutations in the germline give rise to a range of craniosynostotic conditions including Pfeiffer, Apert, Jackson-Weiss, Crouzon and Beare-Stevensen Cutis Gyrata syndromes. These autosomal dominant skeletal disorders are characterized by premature fusion of several sutures in the skull, and in some cases also involve syndactyly (abnormal bone fusions in the hands and feet) (reviewed in Webster and Donoghue, 1997; Burke, 1998; Cunningham, 2007).
Activating FGFR2 mutations arising somatically have been linked to the development of gastric and endometrial cancers (reviewed in Greulich and Pollock, 2011; Wesche, 2011). Many of these mutations are similar or identical to those that contribute to the autosomal disorders described above. Notably, loss-of-function mutations in FGFR2 have also been recently described in melanoma (Gartside, 2009). FGFR2 may also contribute to tumorigenesis through overexpression, as FGFR2 has been identified as a target of gene amplification in gastric and breast cancers (Kunii, 2008; Takeda, 2007).
R-HSA-5654741 Signaling by FGFR3 The 22 members of the fibroblast growth factor (FGF) family of growth factors mediate their cellular responses by binding to and activating the different isoforms encoded by the four receptor tyrosine kinases (RTKs) designated FGFR1, FGFR2, FGFR3 and FGFR4. These receptors are key regulators of several developmental processes in which cell fate and differentiation to various tissue lineages are determined. Unlike other growth factors, FGFs act in concert with heparin or heparan sulfate proteoglycan (HSPG) to activate FGFRs and to induce the pleiotropic responses that lead to the variety of cellular responses induced by this large family of growth factors. An alternative, FGF-independent, source of FGFR activation originates from the interaction with cell adhesion molecules, typically in the context of interactions on neural cell membranes and is crucial for neuronal survival and development.
Upon ligand binding, receptor dimers are formed and their intrinsic tyrosine kinase is activated causing phosphorylation of multiple tyrosine residues on the receptors. These then serve as docking sites for the recruitment of SH2 (src homology-2) or PTB (phosphotyrosine binding) domains of adaptors, docking proteins or signaling enzymes. Signaling complexes are assembled and recruited to the active receptors resulting in a cascade of phosphorylation events.
This leads to stimulation of intracellular signaling pathways that control cell proliferation, cell differentiation, cell migration, cell survival and cell shape, depending on the cell type or stage of maturation.
R-HSA-8853334 Signaling by FGFR3 fusions in cancer In recent years, recurrent fusions of FGFR3 have been identified in a number of cancers, including glioblastoma and cancers of the lung and bladder, among others (Singh et al, 2012; Parker et al, 2013; Williams et al, 2013; Wu et al, 2013; Capelletti et al, 2014; Yuan et al, 2014; Wang et al, 2014; Carneiro et al, 2015; reviewed in Parker et al, 2014). The most common fusion partner of FGFR3 is TACC3 (transforming acidic coiled coil protein 3), a protein involved in mitotic spindle assembly and chromosome segregation (Lin et al, 2010; Burgess et al, 2015). FGFR3 fusions are constitutively active and may form oligomers in a ligand-independent manner based on dimerization domains provided by the fusion partner (Singh et al, 2012; Williams et al, 2013; Parker et al, 2013; reviewed in Parker et al, 2014). Transformation and proliferation appear to be promoted through activation of the ERK and AKT signaling pathways. In contrast, PLC gamma signaling is not stimulated downstream of FGFR3 fusions, as the PLC gamma docking site is not present in the fusion. FGFR3 fusions are sensitive to protein kinase inhibitors, suggesting their potential as therapeutic targets (Singh et al, 2012; Williams et al, 2013; Wu et al, 2013; reviewed in Parker et al, 2014).
R-HSA-5655332 Signaling by FGFR3 in disease The FGFR3 gene has been shown to be subject to activating mutations and gene amplification leading to a variety of proliferative and developmental disorders depending on whether these events occur in the germline or arise somatically.
Activating mutations in FGFR3 are associated with the development of a range of skeletal dysplasias that result in dwarfism (reviewed in Webster and Donoghue, 1997; Burke et al, 1998; Harada et al, 2009). The most common form of human dwarfism is achondroplasia (ACH), which is caused by mutations G380R and G375C in the transmembrane domain of FGFR3 that are thought to promote ligand-independent dimerization (Rousseau et al, 1994; Shiang et al, 1994; Bellus et al, 1995a) Hypochondroplasia (HCH) is a milder form dwarfism that is the result of mutations in the tyrosine kinase domain of FGFR3 (Bellus et al, 1995b). Two neonatal lethal conditions, thanatophoric dysplasia type I and II (TDI and TDII) are also the result of mutations in FGFR3; TDI arises from a range of mutations that either result in the formation of unpaired cysteine residues in the extracellular region that promote aberrant ligand-independent dimerization or by mutations that introduce stop codons (Rousseau et al, 1995; Rousseau et al, 1996, D'Avis et al,1998). A single mutation, K650E in the second tyrosine kinase domain of FGFR3 is responsible for all identified cases of TDII (Tavormina et al, 1995a, b). Other missense mutations at the same K650 residue give rise to Severe Achondroplasia with Developmental Disorders and Acanthosis Nigricans (SADDAN) syndrome (Tavormina et al, 1999; Bellus et al, 1999). The severity of the phenotype arising from many of the activating FGFR3 mutations has recently been shown to correlate with the extent to which the mutations activate the receptor (Naski et al, 1996; Bellus et al, 2000)
In addition to mutations that cause dwarfism syndromes, a Pro250Arg mutation in the conserved dipeptide between the IgII and IgIII domains has been identified in an atypical craniosynostosis condition (Bellus et al, 1996; Reardon et al, 1997). This mutation, which is paralogous to mutations seen in FGFR1 and 2 in Pfeiffer and Apert Syndrome, respectively, results in an increase in ligand-binding affinity for the receptor (Ibrahimi et al, 2004b).
Of all the FGF receptors, FGFR3 has perhaps the best established link to the development in cancer. 50% of bladder cancers have somatic mutations in the coding sequence of FGFR3; of these, more than half occur in the extracellular region at a single position (S249C) (Cappellen et al, 1999; Naski et al, 1996; di Martino et al, 2009, Sibley et al, 2001). Activating mutations are also seen in the juxta- and trans-membrane domains, as well as in the kinase domain (reviewed in Weshe et al, 2011). As is the case for the other receptors, many of the activating mutations that are seen in FGFR3-related cancers mimic the germline FGFR3 mutations that give rise to autosomal skeletal disorders and include both ligand-dependent and independent mechanisms (reviewed in Webster and Donoghue, 1997; Burke et al, 1998). In addition to activating mutations, the FGFR3 gene is subject to a translocation event in 15% of multiple myelomas (Avet-Loiseau et al, 1998; Chesi et al, 1997). This chromosomal rearrangement puts the FGFR3 gene under the control of the highly active IGH promoter and promotes overexpression and constitutive activation of FGFR3. In a small proportion of multiple myelomas, the translocation event is accompanied by activating mutations in the FGFR3 coding sequence (Chesi et al, 1997).
More recently, a number of fusion proteins of FGFR3 have been identified in various cancers (Singh et al, 2012; Williams et al, 2013; Parker et al, 2013; Wu et al, 2013; Wang et al, 2014; Yuan et al, 2014; reviewed in Parker et al, 2014). The most common fusion protein is TACC3, a coiled coil protein involved in mitotic spindle assembly. FGFR3 fusion proteins are constitutively active and appear to contribute to proliferation and tumorigenesis through activation of the ERK and AKT signaling pathways (reviewed in Parker et al, 2014).
R-HSA-5654743 Signaling by FGFR4 The 22 members of the fibroblast growth factor (FGF) family of growth factors mediate their cellular responses by binding to and activating the different isoforms encoded by the four receptor tyrosine kinases (RTKs) designated FGFR1, FGFR2, FGFR3 and FGFR4. These receptors are key regulators of several developmental processes in which cell fate and differentiation to various tissue lineages are determined. Unlike other growth factors, FGFs act in concert with heparin or heparan sulfate proteoglycan (HSPG) to activate FGFRs and to induce the pleiotropic responses that lead to the variety of cellular responses induced by this large family of growth factors. An alternative, FGF-independent, source of FGFR activation originates from the interaction with cell adhesion molecules, typically in the context of interactions on neural cell membranes and is crucial for neuronal survival and development.
Upon ligand binding, receptor dimers are formed and their intrinsic tyrosine kinase is activated causing phosphorylation of multiple tyrosine residues on the receptors. These then serve as docking sites for the recruitment of SH2 (src homology-2) or PTB (phosphotyrosine binding) domains of adaptors, docking proteins or signaling enzymes. Signaling complexes are assembled and recruited to the active receptors resulting in a cascade of phosphorylation events.
This leads to stimulation of intracellular signaling pathways that control cell proliferation, cell differentiation, cell migration, cell survival and cell shape, depending on the cell type or stage of maturation.
R-HSA-5655291 Signaling by FGFR4 in disease FGFR4 is perhaps the least well studied of the FGF receptors, and unlike the case for the other FGFR genes, mutations in FGFR4 are not known to be associated with any developmental disorders. Recently, however, somatically arising mutations in the FGFR4 coding sequence have begun to be identified in some cancers. 8% of rhabdomyosarcomas have activating mutations in the kinase domain of FGFR4. Two of these mutations - N535K (paralogous to the FGFR2 N550K allele found in endometrial cancers) and V550E - have been shown to support the oncogenic transformation of NIH 3T3 cells (Taylor, 2009). An FGFR4 Y367C mutation has also been identified in breast cancers (Ruhe, 2007; Roidl, 2010); mutations of paralogous residues in FGFR2 and FGFR3 are associated with both skeletal dysplasias and the development of diverse cancers (Pollock, 2007; Ruhe, 2007; Rousseau, 1996; Chesi, 1997, 2001).
Finally, a SNP at position 388 of FGFR4 is associated with aggressive disease development. Expression of the G388R allele in breast, colorectal and prostate cancers is correlated with rapid progression times and increased rates of recurrence and metastasis (Bange, 2002; Spinola, 2005; Wang, 2004).
R-HSA-9703648 Signaling by FLT3 ITD and TKD mutants FLT3 is subject to internal tandem duplications (ITDs) of lengths varying from 3 to 1236 base pairs (Nakao et al, 1996; Kiyoi et al 1997, Meshinchi et al, 2008; reviewed in Kazi and Roonstrand, 2019). These ITDs are generally found in the juxtamembrane domain, or more rarely, the first tyrosine kinase domain (TKD) and disrupt the autoinhibitory loop of the receptor, constitutively activating it (Kiyoi et al, 2002; Griffith et al, 2004; reviewed in Lagunas-Rangel and Chavez-Valencia, 2017; Kazi and Roonstrand, 2019). FLT3 ITDs are found in ~25% of acute myeloid leukemias (AMLs) and represent the most frequent mutation of this cancer (reviewed in Kazi and Roonstrand, 2019, Klug et al, 2018)
At lower frequency, FLT3 is subject to activating point mutations (~7% of AML cases). These mutations tend to cluster in the TKD, with mutation of the activation loop residue D835 and the gatekeeper F691 residue the most common sites (Griffin et al, 2001; Jiang et al, 2004; reviewed in Kazi and Roonstrand, 2019).
FLT3 ITD and TKD mutants support cellular transformation through activation of downstream signaling pathways such as the MAP kinase, PI3K/AKT and STAT5 cascades. There is some debate about the extent to which the pathways activated by the ITD and TKD mutants are distinct, with some evidence that STAT5 signaling, in particular, is more characteristic of FLT3 ITD activation (Hayakawa et al, 2000; Choudhary et al, 2005; Grundler et al, 2005; Choudhary et al, 2007; Yoshimoto et al, 2009; Leischner et al, 2012; Janke et al, 2014; Marhall et al, 2018; reviewed in Chan, 2011; Kazi and Roonstrand, 2019).
R-HSA-9703465 Signaling by FLT3 fusion proteins In addition to internal tandem duplications and activating point mutations, FLT3 is also subject at low frequency to translocations that generate fusion proteins. These fusion proteins occur in some chronic myeloid leukemias as well as myeloid neoplasms with eosinophilia, and generate constitutively active proteins by virtue of fusing a N-terminal partner encoding a dimerization domain with the intracellular region of FLT3 (reviewed in Reiter and Gotlib, 2017; Kazi and Roonstrand, 2019). To date, 6 fusion partner genes of FLT3 have been identified: ETV6, TRIP11, MYO18A, SPTBN1, GOLGB1 and ZMYM2 (Balwin et al, 2007; Vu et al, 2006; Walz et al, 2011; Falchi et al, 2014; Chung et al, 2017; Troadec et al, 2017; Grand et al, 2007; Jawhar et al, 2017; Zhang et al, 2018).
R-HSA-372790 Signaling by GPCR G protein-coupled receptors (GPCRs; 7TM receptors; seven transmembrane domain receptors; heptahelical receptors; G protein-linked receptors [GPLR]) are the largest family of transmembrane receptors in humans, accounting for more than 1% of the protein-coding capacity of the human genome. All known GPCRs share a common architecture of seven membrane-spanning helices connected by intra- and extracellular loops. The extracellular loops contain two highly-conserved cysteine residues that form disulphide bonds to stabilize the structure of the receptor. They recognize diverse messengers such as light, odorants, small molecules, hormones and neurotransmitters. Most GPCRs act as guanine nucleotide exchange factors; activated by ligand binding, they promote GDP-GTP exchange on associated heterotrimeric guanine nucleotide-binding (G) proteins. There are two models for GPCR-G Protein interactions: 1) ligand-GPCR binding first, then binding to G Proteins; 2) "Pre-coupling" of GPCRs and G Proteins before ligand binding (review Oldham WM and Hamm HE, 2008). These in turn activate effector enzymes or ion channels. GPCRs are involved in a range of physiological roles which include the visual sense, smell, behavioural regulation, functions of the autonomic nervous system and regulation of the immune system and inflammation.
GPCRs are divided into classes based on sequence homology and functional similarity. The main mammalian classes, in order of size, are the Rhodopsin-like family A, the Secretin receptor family B, and the Metabotropic glutamate/pheromone receptor family C.
R-HSA-5339716 Signaling by GSK3beta mutants GSK3beta is subject to in-frame missplicing in CML stem cells resulting in the production of mutant protein that lacks the AXIN and FRAT binding domains. Cells containing this mutant GSK3beta show elevated levels of nuclear beta-catenin and enhanced TCF-dependent reporter activity (Jamieson et al, 2008; Abrahamsson et al, 2009).
R-HSA-5358351 Signaling by Hedgehog Hedgehog (Hh) is a secreted morphogen that regulates developmental processes in vertebrates including limb bud formation, neural tube patterning, cell growth and differentiation (reviewed in Hui and Angers, 2011). Hh signaling also contributes to stem cell homeostasis in adult tissues. Downregulation of Hh signaling can lead to neonatal abnormalities, while upregulation of signaling is associated with the development of various cancers (Beachy et al, 2004; Jiang and Hui, 2008; Hui and Angers, 2011).
Hh signaling is switched between 'off' and an 'on' states to differentially regulate an intracellular signaling cascade that targets the Gli transcription factors. In the absence of Hh ligand, cytosolic Gli proteins are cleaved to yield a truncated form that translocates into the nucleus and represses target gene transcription. Binding of Hh to the Patched (PTC) receptor on the cell surface stabilizes the Gli proteins in their full-length transcriptional activator form, stimulating Hh-dependent gene expression (reviewed in Hui and Angers, 2011; Briscoe and Therond, 2013).
R-HSA-2028269 Signaling by Hippo Human Hippo signaling is a network of reactions that regulates cell proliferation and apoptosis, centered on a three-step kinase cascade. The cascade was discovered by analysis of Drosophila mutations that lead to tissue overgrowth, and human homologues of its components have since been identified and characterized at a molecular level. Data from studies of mice carrying knockout mutant alleles of the genes as well as from studies of somatic mutations in these genes in human tumors are consistent with the conclusion that in mammals, as in flies, the Hippo cascade is required for normal regulation of cell proliferation and defects in the pathway are associated with cell overgrowth and tumorigenesis (Oh and Irvine 2010; Pan 2010; Zhao et al. 2010). This group of reactions is also notable for its abundance of protein:protein interactions mediated by WW domains and PPxY sequence motifs (Sudol and Harvey 2010).
There are two human homologues of each of the three Drosophila kinases, whose functions are well conserved: expression of human proteins rescues fly mutants. The two members of each pair of human homologues have biochemically indistinguishable functions. Autophosphorylated STK3 (MST2) and STK4 (MST1) (homologues of Drosophila Hippo) catalyze the phosphorylation and activation of LATS1 and LATS2 (homologues of Drosophila Warts) and of the accessory proteins MOB1A and MOB1B (homologues of Drosophila Mats). LATS1 and LATS2 in turn catalyze the phosphorylation of the transcriptional co-activators YAP1 and WWTR1 (TAZ) (homologues of Drosophila Yorkie).
In their unphosphorylated states, YAP1 and WWTR1 freely enter the nucleus and function as transcriptional co-activators. In their phosphorylated states, however, YAP1 and WWTR1 are instead bound by 14-3-3 proteins, YWHAB and YWHAE respectively, and sequestered in the cytosol.
Several accessory proteins are required for the three-step kinase cascade to function. STK3 (MST2) and STK4 (MST1) each form a complex with SAV1 (homologue of Drosophila Salvador), and LATS1 and LATS2 form complexes with MOB1A and MOB1B (homologues of Drosophila Mats).
In Drosophila a complex of three proteins, Kibra, Expanded, and Merlin, can trigger the Hippo cascade. A human homologue of Kibra, WWC1, has been identified and indirect evidence suggests that it can regulate the human Hippo pathway (Xiao et al. 2011). A molecular mechanism for this interaction has not yet been worked out and the molecular steps that trigger the Hippo kinase cascade in humans are unknown.
Four additional processes related to human Hippo signaling, although incompletely characterized, have been described in sufficient detail to allow their annotation. All are of physiological interest as they are likely to be parts of mechanisms by which Hippo signaling is modulated or functionally linked to other signaling processes. First, the caspase 3 protease cleaves STK3 (MST2) and STK4 (MST1), releasing inhibitory carboxyterminal domains in each case, leading to increased kinase activity and YAP1 / TAZ phosphorylation (Lee et al. 2001). Second, cytosolic AMOT (angiomotin) proteins can bind YAP1 and WWTR1 (TAZ) in their unphosphorylated states, a process that may provide a Hippo-independent mechanism to down-regulate the activities of these proteins (Chan et al. 2011). Third, WWTR1 (TAZ) and YAP1 bind ZO-1 and 2 proteins (Remue et al. 2010; Oka et al. 2010). Fourth, phosphorylated WWTR1 (TAZ) binds and sequesters DVL2, providing a molecular link between Hippo and Wnt signaling (Varelas et al. 2010). R-HSA-74752 Signaling by Insulin receptor Insulin binding to its receptor results in receptor autophosphorylation on tyrosine residues and the tyrosine phosphorylation of insulin receptor substrates (e.g. IRS and Shc) by the insulin receptor tyrosine kinase. This allows association of IRSs with downstream effectors such as PI-3K via its Src homology 2 (SH2) domains leading to end point events such as Glut4 (Slc2a4) translocation. Shc when tyrosine phosphorylated associates with Grb2 and can thus activate the Ras/MAPK pathway independent of the IRSs.
Signal transduction by the insulin receptor is not limited to its activation at the cell surface. The activated ligand-receptor complex initially at the cell surface, is internalised into endosomes itself a process which is dependent on tyrosine autophosphorylation. Endocytosis of activated receptors has the dual effect of concentrating receptors within endosomes and allows the insulin receptor tyrosine kinase to phosphorylate substrates that are spatially distinct from those accessible at the plasma membrane. Acidification of the endosomal lumen, due to the presence of proton pumps, results in dissociation of insulin from its receptor. (The endosome constitutes the major site of insulin degradation). This loss of the ligand-receptor complex attenuates any further insulin-driven receptor re-phosphorylation events and leads to receptor dephosphorylation by extra-lumenal endosomally-associated protein tyrosine phosphatases (PTPs). The identity of these PTPs is not clearly established yet.
R-HSA-449147 Signaling by Interleukins Interleukins are low molecular weight proteins that bind to cell surface receptors and act in an autocrine and/or paracrine fashion. They were first identified as factors produced by leukocytes but are now known to be produced by many other cells throughout the body. They have pleiotropic effects on cells which bind them, impacting processes such as tissue growth and repair, hematopoietic homeostasis, and multiple levels of the host defense against pathogens where they are an essential part of the immune system.
R-HSA-9669938 Signaling by KIT in disease KIT signaling is important in several processes including stem cell maintenance, erythropoiesis, mast cell development, lymphopoiesis, melanogenesis and maintenance of interstitial cell of Cajal (Hirota et al, 1998; Chi et al, 2010). Gain-of-function mutations in KIT have been identified at low frequency in a number of diseases, including AML, melanoma and mast and germ cell tumors, and at higher frequency in gastrointesinal stromal tumors (reviewed in Lennartsson and Roonstrand, 2012; Abbaspour Babaei et al, 2016; Roskoski, 2018).
R-HSA-5339717 Signaling by LRP5 mutants LRP5 is subject to an in-frame missplicing event in breast and parathyroid cancers that renders the protein insensitive to inhibition by the WNT antagonist DKK1. Expression of the mutant protein results in elevated levels of active, unphosphorylated beta-catenin and enhanced TCF-dependent WNT-signaling, promoting cellular proliferation (Bjorklund et al 2007a, b; Bjorklund et al, 2009).
R-HSA-9842663 Signaling by LTK Leukocyte tyrosine kinase (LTK) is a transmembrane receptor tyrosine kinase that is a member of the insulin growth factor receptor superfamily. LTK is most closely related to the ALK receptor, and may have originated as a result of a duplication event of the ALK gene (Krowelski and Dalla-Favera, 1991; Dornburg et al, 2021). The extracellular domains of ALK and LTK are characterized by a membrane proximal EGF-like (EGFL) module, a unique 250 amino acid glycine rich (GR) domain that, in Drosophila, is essential for function (Englund et al, 2003), as well as a TNF-like (TNFL) module. The ALK ECD additionally contains two MAM domains, an LDLa domain and a heparin-binding domain (HBD) that are not present in the LTK receptor (Iwahara et al, 1997; Morris et al, 1997; DeMunck et al, 2021). These differences in ECD may contribute to differences in the ligand binding affinities of the two receptors.
LTK is activated by the binding of cytokines ALKAL1 and ALKAL2 to the ECD (Zhang et al, 2014; Reshetnyak et al, 2015; Reshetnyak et al, 2018). Ligand binding induces trans-autophosphorylation in the intracellular domain of the receptor and promotes the interaction and activation of downstream signaling molecules such as SHC, IRS1, CBL and PI3K with the phosphorylated receptor (Kozutsumi et al, 1994; Honda et al, 1994; Ueno et al, 1995; Ueno et al, 1996; Ueno et al, 1997; Li et al, 2004; Yamada et al, 2008). Note however that much of the early functional studies on LTK were conducted before the identification of ALKAL1 and 2 as physiological ligands. In consequence, many of these studies were carried out using chimeric receptors consisting of the ECD (and stimulating ligands) of well-characterized receptors fused to the intracellular domain of LTK.
The exact role of LTK signaling is likewise not fully elucidated. Expression of the chimeric LTK proteins described above promotes neurite outgrowth and cell survival (Ueno et al, 1997; Yamada et al, 2008). A role for LTK in the regulation of transport from the ER to the Golgi has also been proposed, and one study suggests that LTK may actually bean ER-resident protein (Farhan et al, 2010; Centonze et al, 2019). More recently, fusions of LTK have been identified in non-small cell lung cancer (Izumi et al, 2021).
R-HSA-9842640 Signaling by LTK in cancer LTK is a member of the anaplastic lymphoma kinase (ALK)/LTK subfamily within the insulin receptor superfamily of RTKs. LTK encodes an 864-amino-acid protein consisting of extracellular, transmembrane, and tyrosine kinase domains and a short carboxy terminus. The LTK kinase domain shares 80% identity with ALK (Roll and Reuther, 2012). The biological role of LTK is not well defined under normal physiological conditions, and unlike ALK, a clear role for LTK in cancer is also not yet well established. LTK is overexpressed in leukemia, and high expression of LTK in early-stage non-small cell lung cancer (NSCLC) has been associated with greater risk of metastasis (Mueller-Tidow et al, 2005; Roll and Reuther, 2012). More recently, a novel CLIP1-LTK fusion protein has been identified in a small proportion of NSCLC cases (Izumi et al, 2021).
R-HSA-2586552 Signaling by Leptin Leptin (LEP, OB, OBS), a circulating adipokine, and its receptor LEPR (DB, OBR) control food intake and energy balance and are implicated in obesity-related diseases (recently reviewed in Amitani et al. 2013, Dunmore and Brown 2013, Cottrell and Mercer 2012, La Cava 2012, Marroqui et al. 2012, Paz-Filho et al. 2012, Denver et al. 2011, Lee 2011, Marino et al. 2011, Morton and Schwartz 2011, Scherer and Buettner 2011, Shan and Yeo 2011, Wauman and Tavernier 2011, Dardeno et al. 2010, Bjorbaek 2009, Morris and Rui 2009, Myers et al. 2008), including cancer (Guo et al. 2012), inflammation (Newman and Gonzalez-Perez 2013, Iikuni et al. 2008), and angiogenesis (Gonzalez-Perez et al. 2013).
The identification of spontaneous mutations in the leptin gene (ob or LEP) and the leptin receptor gene (Ob-R, db or LEPR) genes in mice opened up a new field in obesity research. Leptin was discovered as the product of the gene affected by the ob (obesity) mutation, which causes obesity in mice. Likewise LEPR is the product of the gene affected by the db (diabetic) mutation. Leptin binding to LEPR induces canonical (JAK2/STATs; MAPK/ERK 1/2, PI-3K/AKT) and non-canonical signaling pathways (PKC, JNK, p38 MAPK and AMPK) in diverse cell types. The binding of leptin to the long isoform of LEPR (OB-Rl) initiates a phosphorylation cascade that results in transcriptional activation of target genes by STAT5 and STAT3 and activation of the PI3K pathway(not shown here), the MAPK/ERK pathway, and the mTOR/S6K pathway. Shorter LEPR isoforms with truncated intracellular domains are unable to activate the STAT pathway, but can transduce signals by way of activation of JAK2, IRS-1 or ERKs, including MAPKs.
LEPR is constitutively bound to the JAK2 kinase. Binding of LEP to LEPR causes a conformational change in LEPR that activates JAK2 autophosphorylation followed by phosphorylation of LEPR by JAK2. Phosphorylated LEPR binds STAT3, STAT5, and SHP2 which are then phosphorylated by JAK2. Phosphorylated JAK2 binds SH2B1 which then binds IRS1/2, resulting in phosphorylation of IRS1/2 by JAK2. Phosphorylated STAT3 and STAT5 dimerize and translocate to the nucleus where they activate transcription of target genes (Jovanovic et al. 2010). SHP2 activates the MAPK pathway. IRS1/2 activate the PI3K/AKT pathway which may be the activator of mTOR/S6K.
Several isoforms of LEPR have been identified (reviewed in Gorska et al. 2010). The long isoform (LEPRb, OBRb) is expressed in the hypothalamus and all types of immune cells. It is the only isoform known to fully activate signaling pathways in response to leptin. Shorter isoforms (LEPRa, LEPRc, LEPRd, and a soluble isoform LEPRe) are able to interact with JAK kinases and activate other pathways, however their roles in energy homeostasis are not fully characterized.
R-HSA-5637815 Signaling by Ligand-Responsive EGFR Variants in Cancer Ligand-responsive EGFR cancer variants harbor mutations in the kinase domain or point mutations in the extracellular domain. These altered EGFR proteins are able to signal in the absence of ligands, but their ligand binding ability is preserved and downstream signaling is potentiated when ligand is available (Greulich et al. 2005, Lee et al. 2006).
R-HSA-9652169 Signaling by MAP2K mutants Activating mutations in MAP2K1 and MAP2K2, the genes encoding MEK1 and MEK2, have been identified at low frequency in a variety of cancers as well as in germline diseases such as Noonan syndrome, cardiofaciocutaneous syndromes and other RASopathies (reviewed in Samatar and Poulikakos, 2014; Bezniakow et al, 2014; Rauen, 2013).
R-HSA-9652817 Signaling by MAPK mutants Mutations in ERK proteins (MAPK1 and MAPK2) are rare, with mutations reported in ~8% of cervical cancers and 1.5% of head and neck squamous cell carcinomas (Ojesina et al, 2014; Cancer Genome Atlas, 2015; reviewed in Najafi et al, 2019). MAPK proteins with activating mutations are often still dependent on upstream phosphorylation by MAP2K proteins, but support sustained downstream signaling by virtue of being resistant to inactivating dephosphorylations (reviewed in Samatar and Poulikakos, 2014; Liu et al, 2018).
R-HSA-6806834 Signaling by MET MET is a receptor tyrosine kinase (RTK) (Cooper et al. 1984, Park et al. 1984) activated by binding to its ligand, Hepatocyte growth factor/Scatter factor (HGF/SF) (Bottaro et al. 1991, Naldini et al. 1991). Similar to other related RTKs, such as EGFR, ligand binding induces MET dimerization and trans-autophosphorylation, resulting in the active MET receptor complex (Ferracini et al. 1991, Longati et al. 1994, Rodrigues and Park 1994, Kirchhofer et al. 2004, Stamos et al. 2004, Hays and Watowich 2004). Phosphorylated tyrosines in the cytoplasmic tail of MET serve as docking sites for binding of adapter proteins, such as GRB2, SHC1 and GAB1, which trigger signal transduction cascades that activate PI3K/AKT, RAS, STAT3, PTK2, RAC1 and RAP1 signaling (Ponzetto et al. 1994, Pelicci et al. 1995, Weidner et al. 1995, Besser et al. 1997, Shen and Novak 1997, Beviglia and Kramer 1999, Rodrigues et al. 2000, Sakkab et al. 2000, Schaeper et al. 2000, Lamorte et al. 2002, Wang et al. 2002, Chen and Chen 2006, Palamidessi et al. 2008, Chen et al. 2011, Murray et al. 2014).
Activation of PLC gamma 1 (PLCG1) signaling by MET remains unclear. It has been reported that PLCG1 can bind to MET directly (Ponzetto et al. 1994) or be recruited by phosphorylated GAB1 (Gual et al. 2000). Tyrosine residue Y307 of GAB1 that serves as docking sites for PLCG1 may be phosphorylated either by activated MET (Watanabe et al. 2006) or SRC (Chan et al. 2010). Another PCLG1 docking site on GAB1, tyrosine residue Y373, was reported as the SRC target, while the kinase for the main PLCG1 docking site, Y407 of GAB1, is not known (Chan et al. 2010).
Signaling by MET promotes cell growth, cell survival and motility, which are essential for embryonic development (Weidner et al. 1993, Schmidt et al. 1995, Uehara et al. 1995, Bladt et al. 1995, Maina et al. 1997, Maina et al. 2001, Helmbacher et al. 2003) and tissue regeneration (Huh et al. 2004, Borowiak et al. 2004, Liu 2004, Chmielowiec et al. 2007). MET signaling is frequently aberrantly activated in cancer, through MET overexpression or activating MET mutations (Schmidt et al. 1997, Pennacchietti et al. 2003, Smolen et al. 2006, Bertotti et al. 2009).
Considerable progress has recently been made in the development of HGF-MET inhibitors in cancer therapy. These include inhibitors of HGF activators, HGF inhibitors and MET antagonists, which are protein therapeutics that act outside the cell. Kinase inhibitors function inside the cell and have constituted the largest effort towards MET-based therapeutics (Gherardi et al. 2012).
Pathogenic bacteria of the species Listeria monocytogenes, exploit MET receptor as an entryway to host cells (Shen et al. 2000, Veiga and Cossart 2005, Neimann et al. 2007).
For review of MET signaling, please refer to Birchmeier et al. 2003, Trusolino et al. 2010, Gherardi et al. 2012, Petrini 2015.
R-HSA-9660537 Signaling by MRAS-complex mutants A complex of MRAS, SHOC2 and the phosphatase PP1 contributes to the activation of RAF proteins by removing an inhibitory phosphorylation that mediates binding to 14-3-3 (also known as YWHAB) proteins (Rodriguez-Viciano et al, 2006; Young et al, 2013;reviewed in Simanshu et al, 2017; Lavoie and Therrien, 2015). Activating and inactivating mutations in each of the components of this dephosphorylating complex have been identified in RASopathies as well as at low frequency in some cancers (Cordeddu et al, 2009; Hannig et al, 2014; Gripp et al, 2016; Higgin et al, 2017; Motta et al, 2016; Motta et al, 2019a,b).
R-HSA-8852405 Signaling by MST1 Inflammatory mediators such as growth factors produced by macrophages play an important role in the inflammatory response occurring during bacterial infection, tissue injury and immune responses. Many growth factors and their receptor-type protein tyrosine kinases (RTKs) play a critical role in inflammation, wound healing and tissue remodelling. The growth factor hepatocyte growth factor-like protein (MST1, also known as macrophage-stimulating protein, MSP) binds to a specific receptor, macrophage-stimulating protein receptor (MST1R, also known as RON, recepteur d'origine nantais). MST1 belongs to the kringle protein family, which includes HGF and plasminogen. It is produced by the liver and circulates in the blood as a biologically-inactive single chain precursor (pro-MST1). Proteolytic cleavage of pro-MST1 into the biologically-active MST1 dimer is necessary for receptor binding. Cleavage occurs during blood coagulation and at inflammatory sites, the resultant MST1 dimer then binds MST1R receptors on local macrophages. MST1R is ubiquitously expressed but mainly in epithelial cells.
MST1 binding to MST1R promotes receptor homodimerisation which in turn allows autophosphorylation of two tyrosine residues within the catalytic site which regulates kinase activity and allows phosphorylation of the carboxy-terminal binding site of the receptor. The docking site is essential for downstream signaling through direct and indirect binding of SH2 domain-containing adaptor proteins such as GRB2, PI3K, and SRC. MST1/MST1R signaling plays a dual role in regulating inflammation; initially stimulating chemotaxis and phagocytosis (macrophage activation) and then exerts broad inhibitory effects on macrophages, limiting the extent of inflammtory responses (Wang et al. 2002). MST1R is upregulated in many epithelial cancers where it is thought to play a role in the progression of these types of cancer (Kretschmann et al. 2010).
R-HSA-1181150 Signaling by NODAL Signaling by NODAL is essential for patterning of the axes of the embryo and formation of mesoderm and endoderm (reviewed in Schier 2009, Shen 2007). The NODAL proprotein is secreted and cleaved extracellularly to yield mature NODAL. Mature NODAL homodimerizes and can also form heterodimers with LEFTY1, LEFTY2, or CERBERUS, which negatively regulate NODAL signaling. NODAL also forms heterodimers with GDF1, which increases NODAL activity. NODAL dimers bind the NODAL receptor comprising a type I Activin receptor (ACVR1B or ACVR1C), a type II Activin receptor (ACVR2A or ACVR2B), and an EGF-CFC coreceptor (CRIPTO or CRYPTIC). After binding NODAL, the type II activin receptor phosphorylates the type I activin receptor which then phosphorylates SMAD2 and SMAD3 (R-SMADs). Phosphorylated SMAD2 and SMAD3 form hetero-oligomeric complexes with SMAD4 (CO-SMAD) and transit from the cytosol to the nucleus. Within the nucleus the SMAD complexes interact with transcription factors such as FOXH1 to activate transcription of target genes.
R-HSA-157118 Signaling by NOTCH The Notch Signaling Pathway (NSP) is a highly conserved pathway for cell-cell communication. NSP is involved in the regulation of cellular differentiation, proliferation, and specification. For example, it is utilised by continually renewing adult tissues such as blood, skin, and gut epithelium not only to maintain stem cells in a proliferative, pluripotent, and undifferentiated state but also to direct the cellular progeny to adopt different developmental cell fates. Analogously, it is used during embryonic development to create fine-grained patterns of differentiated cells, notably during neurogenesis where the NSP controls patches such as that of the vertebrate inner ear where individual hair cells are surrounded by supporting cells.
This process is known as lateral inhibition: a molecular mechanism whereby individual cells within a field are stochastically selected to adopt particular cell fates and the NSP inhibits their direct neighbours from doing the same. The NSP has been adopted by several other biological systems for binary cell fate choice. In addition, the NSP is also used during vertebrate segmentation to divide the growing embryo into regular blocks called somites which eventually form the vertebrae. The core of this process relies on regular pulses of Notch signaling generated from a molecular oscillator in the presomatic mesoderm.
The Notch receptor is synthesized in the rough endoplasmic reticulum as a single polypeptide precursor. Newly synthesized Notch receptor is proteolytically cleaved in the trans-golgi network, creating a heterodimeric mature receptor comprising of non-covalently associated extracellular and transmembrane subunits. This assembly travels to the cell surface ready to interact with specific ligands. Following ligand activation and further proteolytic cleavage, an intracellular domain is released and translocates to the nucleus where it regulates gene expression.
R-HSA-1980143 Signaling by NOTCH1 NOTCH1 functions as both a transmembrane receptor presented on the cell surface and as a transcriptional regulator in the nucleus.
NOTCH1 receptor presented on the plasma membrane is activated by a membrane bound ligand expressed in trans on the surface of a neighboring cell. In trans, ligand binding triggers proteolytic cleavage of NOTCH1 and results in release of the NOTCH1 intracellular domain, NICD1, into the cytosol.
NICD1 translocates to the nucleus where it associates with RBPJ (also known as CSL or CBF) and mastermind-like (MAML) proteins (MAML1, MAML2 or MAML3; possibly also MAMLD1) to form NOTCH1 coactivator complex. NOTCH1 coactivator complex activates transcription of genes that possess RBPJ binding sites in their promoters.
R-HSA-2691230 Signaling by NOTCH1 HD Domain Mutants in Cancer NOTCH1 heterodimerization domain mutations are frequently found in T-cell acute lymphoblastic leukemia (T-ALL) (Weng et al. 2004) and result in constitutive activity of NOTCH1 mutants (Malecki et al. 2006).
R-HSA-2894858 Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer Mutations in the heterodimerization domain (HD) and PEST domain of NOTCH1 are frequently found in cis in T-cell acute lymphoblastic leukemia. While HD mutations alone result in up to ~10-fold increase in NOTCH1 transcriptional activity and PEST domain mutations alone result in up to ~2-fold increase in NOTCH1 transcriptional activity, in cis mutations of HD and PEST domains act synergistically, increasing NOTCH1 transcriptional activity up to ~40-fold (Weng et al. 2004).
R-HSA-2644602 Signaling by NOTCH1 PEST Domain Mutants in Cancer NOTCH1 PEST domain mutations are frequently found in T-cell acute lymphoblastic leukemia (T-ALL). PEST domain mutations interfere with ubiquitination-mediated NOTCH1 downregulation and result in prolonged half-life of the intracellular NOTCH1 fragment, NICD1, and increased NICD1 transcriptional activity (Weng et al. 2004, Thompson et al. 2007, O'Neil et al. 2007).
R-HSA-2644603 Signaling by NOTCH1 in Cancer Human NOTCH1 was cloned as a chromosome 9 gene, translocated to the T-cell beta receptor (TCBR) promoter on chromosome 7 in T-cell acute lymphoblastic leukemia (T-ALL) (Ellisen et al. 1991). This translocation, present in only a small percentage of T-ALL patients, results in the overexpression of a truncated NOTCH1 receptor, which lacks almost the entire extracellular domain, in T lymphocytes. Oncogenic NOTCH1 mutations were subsequently found to be present in >50% of T-ALL patients, with hotspots in the heterodimerization domain (HD domain) and PEST domain of NOTCH1 (Weng et al. 2004).
Normal NOTCH1 becomes activated by binding DLL (DLL1 or DLL4) or JAG (JAG1 or JAG2) ligands expressed on the surface of a neighboring cell, which leads to proteolytic cleavage of NOTCH1 by ADAM10/17 and gamma-secretase, and release of the NOTCH1 intracellular domain (NICD1) which regulates expression of genes that play important roles in the development of T lymphocytes (Washburn et al. 1997. Radtke et al. 1999, Maillard et al. 2004, Sambandam et al. 2005, Tan et al. 2005). Mutations in the HD domain, responsible for association of NOTCH1 extracellular and transmembrane regions after furin-mediated cleavage of NOTCH1 precursor, as well as the truncation of the NOTCH1 extracellular domain by the rare T-ALL translocation, enable constitutive production of NICD1, in the absence of ligand binding (Malecki et al. 2006, Ellisen et al. 1991).
Mutations in the NOTCH1 PEST domain interfere with FBXW7 (FBW7)-mediated ubiquitination and degradation of NICD1, resulting in prolonged half-life and increased transcriptional activity of NICD1, which promotes growth and division of T-lymphocytes (Weng et al. 2004, Thompson et al. 2007, O'Neil et al. 2007).
Mutations in the HD domain and PEST domain of NOTCH1 are frequently found in cis in T-ALL. While HD mutations alone result in up to ~10-fold increase in NOTCH1 transcriptional activity and PEST domain mutations alone result in up to ~2-fold increase in NOTCH1 transcriptional activity, in cis mutations of HD and PEST domains act synergistically, increasing NOTCH1 transcriptional activity up to ~40-fold (Weng et al. 2004).
FBXW7 (FBW7), a component of the SCF (SKP1, CUL1, and F-box protein) ubiquitin ligase complex SCF-FBW7 involved in the degradation of NOTCH1 (Oberg et al. 2001, Wu et al. 2001, Fryer et al. 2004), is subject to loss of function mutations in T-ALL (Akhoondi et al. 2007, Thompson et al. 2007, O'Neil et al. 2007) which are mutually exclusive with NOTCH1 PEST domain mutations (Thompson et al. 2007, O'Neil et al. 2007).
Although gamma-secretase inhibitors (GSIs) are successfully used in vitro to inhibit NOTCH1 signaling in T-ALL cell lines, the gamma-secretase complex has many other substrates besides NOTCH. The specificity of GSIs is therefore limited and, as they are not considered to be particularly promising drugs for the clinical treatment of T-ALL (reviewed by Purow, 2012), they have not been annotated.
For a recent review of NOTCH1 signaling in cancer, please refer to Grabher et al. 2006.
R-HSA-2660825 Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant Human NOTCH1 was cloned as a chromosome 9 gene, translocated to the T-cell beta receptor (TCBR) promoter on chromosome 7 in T-cell acute lymphoblastic leukemia (T-ALL) (Ellisen et al. 1991). The translocated gene was found to be homologous to Drosophila Notch, and was initially named TAN-1 (translocation-associated Notch homolog). Although the translocation t(7;9)(q34;q34.3) is present in a small percentage of T-ALL patients, the mutant protein is highly oncogenic and its overexpression causes T-ALL-like illness in mice (Pear et al. 1996).
R-HSA-1980145 Signaling by NOTCH2 NOTCH2 is activated by binding Delta-like and Jagged ligands (DLL/JAG) expressed in trans on neighboring cells (Shimizu et al. 1999, Shimizu et al. 2000, Hicks et al. 2000, Ji et al. 2004). In trans ligand-receptor binding is followed by ADAM10 mediated (Gibb et al. 2010, Shimizu et al. 2000) and gamma secretase complex mediated cleavage of NOTCH2 (Saxena et al. 2001, De Strooper et al. 1999), resulting in the release of the intracellular domain of NOTCH2, NICD2, into the cytosol. NICD2 traffics to the nucleus where it acts as a transcriptional regulator. For a recent review of the cannonical NOTCH signaling, please refer to Kopan and Ilagan 2009, D'Souza et al. 2010, Kovall and Blacklow 2010. CNTN1 (contactin 1), a protein involved in oligodendrocyte maturation (Hu et al. 2003) and MDK (midkine) (Huang et al. 2008, Gungor et al. 2011), which plays an important role in epithelial-to-mesenchymal transition, can also bind NOTCH2 and activate NOTCH2 signaling.
In the nucleus, NICD2 forms a complex with RBPJ (CBF1, CSL) and MAML (mastermind). The NICD2:RBPJ:MAML complex activates transcription from RBPJ binding promoter elements (RBEs) (Wu et al. 2000). NOTCH2 coactivator complexes directly stimulate transcription of HES1 and HES5 genes (Shimizu et al. 2002), both of which are known NOTCH1 targets. NOTCH2 but not NOTCH1 coactivator complexes, stimulate FCER2 transcription. Overexpression of FCER2 (CD23A) is a hallmark of B-cell chronic lymphocytic leukemia (B-CLL) and correlates with the malfunction of apoptosis, which is thought be an underlying mechanism of B-CLL development (Hubmann et al. 2002). NOTCH2 coactivator complexes together with CREBP1 and EP300 stimulate transcription of GZMB (granzyme B), which is important for the cytotoxic function of CD8+ T cells (Maekawa et al. 2008).
NOTCH2 gene expression is differentially regulated during human B-cell development, with NOTCH2 transcripts appearing at late developmental stages (Bertrand et al. 2000).
NOTCH2 mutations are a rare cause of Alagille syndrome (AGS). AGS is a dominant congenital multisystem disorder characterized mainly by hepatic bile duct abnormalities. Craniofacial, heart and kidney abnormalities are also frequently observed in the Alagille spectrum (Alagille et al. 1975). AGS is predominantly caused by mutations in JAG1, a NOTCH2 ligand (Oda et al. 1997, Li et al. 1997), but it can also be caused by mutations in NOTCH2 (McDaniell et al. 2006).
Hajdu-Cheney syndrome, an autosomal dominant disorder characterized by severe and progressive bone loss, is caused by NOTCH2 mutations that result in premature C-terminal NOTCH2 truncation, probably leading to increased NOTCH2 signaling (Simpson et al. 2011, Isidor et al. 2011, Majewski et al. 2011).
R-HSA-9012852 Signaling by NOTCH3 Similar to NOTCH1, NOTCH3 is activated by delta-like and jagged ligands (DLL/JAG) expressed in trans on a neighboring cell. The activation triggers cleavage of NOTCH3, first by ADAM10 at the S2 cleavage site, then by gamma-secretase at the S3 cleavage site, resulting in the release of the intracellular domain of NOTCH3, NICD3, into the cytosol. NICD3 subsequently traffics to the nucleus where it acts as a transcriptional regulator. NOTCH3 expression pattern is more restricted than the expression patterns of NOTCH1 and NOTCH2, with predominant expression of NOTCH3 in vascular smooth muscle cells, lymphocytes and the nervous system (reviewed by Bellavia et al. 2008). Based on the study of Notch3 knockout mice, Notch3 is not essential for embryonic development or fertility (Krebs et al. 2003).
Germline gain-of-function NOTCH3 mutations are an underlying cause of the CADASIL syndrome - cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy. CADASIL is characterized by degeneration and loss of vascular smooth muscle cells from the arterial wall, predisposing affected individuals to an early onset stroke (Storkebaum et al. 2011). NOTCH3 promotes survival of vascular smooth muscle cells at least in part by induction of CFLAR (c FLIP), an inhibitor of FASLG activated death receptor signaling. The mechanism of NOTCH3 mediated upregulation of CFLAR is unknown; it is independent of the NOTCH3 coactivator complex and involves an unelucidated crosstalk with the RAS/RAF/MAPK pathway (Wang et al. 2002).
In rat brain, NOTCH3 and NOTCH1 are expressed at sites of adult neurogenesis, such as the dentate gyrus (Irvin et al. 2001). NOTCH3, similar to NOTCH1, promotes differentiation of the rat adult hippocampus derived multipotent neuronal progenitors into astroglia (Tanigaki et al. 2001). NOTCH1, NOTCH2, NOTCH3, and their ligand DLL1 are expressed in neuroepithelial precursor cells in the neural tube of mouse embryos. Together, they signal to inhibit neuronal differentiation of neuroepithelial precursors. Expression of NOTCH3 in mouse neuroepithelial precursors is stimulated by growth factors BMP2, FGF2, Xenopus TGF beta5 - homologous to TGFB1, LIF, and NTF3 (Faux et al. 2001).
In mouse telencephalon, NOTCH3, similar to NOTCH1, promotes radial glia and neuronal progenitor phenotype. This can, at least in part be attributed to NOTCH mediated activation of RBPJ-dependent and HES5-dependent transcription (Dang et al. 2006).
In mouse spinal cord, Notch3 is involved in neuronal differentiation and maturation. Notch3 knockout mice have a decreased number of mature inhibitory interneurons in the spinal cord, which may be involved in chronic pain conditions (Rusanescu and Mao 2014).
NOTCH3 amplification was reported in breast cancer, where NOTCH3 promotes proliferation and survival of ERBB2 negative breast cancer cells (Yamaguchi et al. 2008), and it has also been reported in ovarian cancer (Park et al. 2006). NOTCH3 signaling is involved in TGF beta (TGFB1) signaling-induced eptihelial to mesenchimal transition (EMT) (Ohashi et al. 2011, Liu et al. 2014)
NOTCH3 indirectly promotes development of regulatory T cells (Tregs). NOTCH3 signaling activates pre-TCR-dependent and PKC-theta (PRKCQ)-dependent NF-kappaB (NFKB) activation, resulting in induction of FOXP3 expression (Barbarulo et al. 2011). Deregulated NOTCH3 and pre-TCR signaling contributes to development of leukemia and lymphoma (Bellavia et al. 2000, Bellavia et al. 2002).
R-HSA-9013694 Signaling by NOTCH4 The NOTCH4 gene locus was discovered as a frequent site of insertion for the proviral genome of the mouse mammary tumor virus (MMTV) (Gallahan and Callahan 1987). MMTV-insertion results in aberrant expression of the mouse mammary tumor gene int-3, which was subsequently discovered to represent the intracellular domain of Notch4 (Robbins et al. 1992, Uyttendaele et al. 1996).
NOTCH4 is prevalently expressed in endothelial cells (Uyttendaele et al. 1996). DLL4 and JAG1 act as ligands for NOTCH4 in human endothelial cells (Shawber et al. 2003, Shawber et al. 2007), but DLL4- and JAG1-mediated activation of NOTCH4 have not been confirmed in all cell types tested (Aste-Amezaga et al. 2010, James et al. 2014). The gamma secretase complex cleaves activated NOTCH4 receptor to release the intracellular domain fragment (NICD4) (Saxena et al. 2001, Das et al. 2004). NICD4 traffics to the nucleus where it acts as a transcription factor and stimulates expression of NOTCH target genes HES1, HES5, HEY1 and HEY2, as well as VEGFR3 and ACTA2 (Lin et al. 2002, Raafat et al.2004, Tsunematsu et al. 2004, Shawber et al. 2007, Tang et al. 2008, Bargo et al. 2010). NOTCH4 signaling can be downregulated by AKT1 phosphorylation-induced cytoplasmic retention (Ramakrishnan et al. 2015) as well as proteasome-dependent degradation upon FBXW7-mediated ubiquitination (Wu et al. 2001, Tsunematsu et al. 2004).
NOTCH4 was reported to inhibit NOTCH1 signaling in-cis, by binding to NOTCH1 and interfering with the S1 cleavage of NOTCH1, thus preventing production of functional NOTCH1 heterodimers at the cell surface (James et al. 2014).
NOTCH4 is involved in development of the vascular system. Overexpression of constitutively active Notch4 in mouse embryonic vasculature results in abnormal vessel structure and patterning (Uyttendaele et al. 2001). NOTCH4 may act to inhibit apoptosis of endothelial cells (MacKenzie et al. 2004).
Expression of int-3 interferes with normal mammary gland development in mice and promotes tumorigenesis. The phenotype of mice expressing int-3 in mammary glands is dependent on the presence of Rbpj (Raafat et al. 2009). JAG1 and NOTCH4 are upregulated in human ER+ breast cancers resistant to anti-estrogen therapy, which correlates with elevated expression of NOTCH target genes HES1, HEY1 and HEY2, and is associated with increased population of breast cancer stem cells and distant metastases (Simoes et al. 2015). Development of int-3-induced mammary tumours in mice depends on Kit and Pdgfra signaling (Raafat et al. 2006) and on int-3-induced activaton of NFKB signaling (Raafat et al. 2017). In head and neck squamous cell carcinoma (HNSCC), high NOTCH4 expression correlates with elevated HEY1 levels, increased cell proliferation and survival, epithelial-to-mesenchymal transition (EMT) phenotype and cisplatin resistance (Fukusumi et al. 2018). In melanoma, however, exogenous NOTCH4 expression correlates with mesenchymal-to-epithelial-like transition and reduced invasiveness (Bonyadi Rad et al. 2016). NOTCH4 is frequently overexpressed in gastric cancer. Increased NOTCH4 levels correlate with activation of WNT signaling and gastric cancer progression (Qian et al. 2015).
NOTCH4 is expressed in adipocytes and may promote adipocyte differentiation (Lai et al. 2013).
During Dengue virus infection, DLL1, DLL4, NOTCH4 and HES1 are upregulated in interferon-beta (INFB) dependent manner (Li et al. 2015). NOTCH4 signaling may be affected by Epstein-Barr virus (EBV) infection, as the EBV protein BARF0 binds to NOTCH4 (Kusano and Raab-Traub 2001).
R-HSA-187037 Signaling by NTRK1 (TRKA) Trk receptors signal from the plasma membrane and from intracellular membranes, particularly from early endosomes. Signalling from the plasma membrane is fast but transient; signalling from endosomes is slower but long lasting. Signalling from the plasma membrane is annotated here. TRK signalling leads to proliferation in some cell types and neuronal differentiation in others. Proliferation is the likely outcome of short term signalling, as observed following stimulation of EGFR (EGF receptor). Long term signalling via TRK receptors, instead, was clearly shown to be required for neuronal differentiation in response to neurotrophins.
R-HSA-9006115 Signaling by NTRK2 (TRKB) NTRK2 (TRKB) belongs to the family of neurotrophin tyrosine kinase receptors, also known as NTRKs or TRKs. Besides NTRK2, the family includes NTRK1 (TRKA) and NTRK3 (TRKC). Similar to other receptor tyrosine kinases (RTKs), NTRK2 is activated by ligand binding to its extracellular domain. Ligand binding induces receptor dimerization, followed by trans-autophosphorylation of dimerized receptors on conserved tyrosine residues in the cytoplasmic region. Phosphorylated tyrosines in the intracellular domain of the receptor serve as docking sites for adapter proteins, triggering downstream signaling cascaded. Brain-derived neurotrophic factor (BDNF) and neurotrophin-4 (NTF4, also known as NT-4) are two high affinity ligands for NTRK2. Neurotrophin-3 (NTF3, also known as NT-3), a high affinity ligand for NTRK3, binds to NTRK2 with low affinity and it is not clear if it the low level of activation of NTRK2 by NTF3 plays a physiologically relevant role. Nerve growth factor (NGF), a high affinity ligand for NTRK1, does not interact with NTRK2. NTRK2 activation triggers downstream RAS, PI3K, and PLCgamma signaling cascades, thought to be involved in neuronal development in both the peripheral (PNS) and central nervous system (CNS). In addition, NTRK2 plays an important, but poorly elucidated, role in long-term potentiation (LTP) and learning (reviewed by Minichiello 2009). NTRK2 may modify neuronal excitability and synaptic transmission by directly phosphorylating voltage gated channels (Rogalski et al. 2000).
It was recently demonstrated that the protein tyrosine phosphatase PTPN12 negatively regulates NTRK2 signaling and neurite outgrowth. In the presence of PTPN12, NTRK2 phosphorylation at tyrosine Y816 decreases. It has not yet been demonstrated that PTPN12 acts directly to dephosphorylate Y816 (and possibly other phosphotyrosines) of NTRK2 (Ambjorn et al. 2013).
Binding of SH2D1A (SAP) to NTRK2 attenuates NTRK2 trans autophosphorylation and downstream signaling through an unknown mechanism (Lo et al. 2005).
Little is known about downregulation of NTRK2 (TRKB) receptor via ubiquitin dependent pathways (Sanchez Sanchez and Arevalo 2017). CBL, a ubiquitin ligase involved in degradation of many receptor tyrosine kinases, was shown to ubiquitinate and, unexpectedly, increase stability of NTRK2 (Pandya et al. 2014). NTRK2 undergoes ubiquitination by the TRAF6 E3 ubiquitin ligase complex. While ubiquitination by the TRAF6 complex negatively regulates NTRK2 induced AKT activation, the effect of TRAF6 mediated ubiquitination on NTRK2 protein levels has not been examined (Jadhav et al. 2008).
Downregulation of the TRKB receptor may depend on the activating ligand, with BDNF inducing more rapid ubiquitination and degradation compared to NTF4 (NT 4). NTRK2 undergoes both lysosome dependent and proteasome dependent degradation upon stimulation by BDNF, while stimulation by NTF4 may protect NTRK2 from the lysosome degradation route (Proenca et al. 2016). R-HSA-9034015 Signaling by NTRK3 (TRKC) NTRK3 (TRKC) belongs to the family of neurotrophin receptor tyrosine kinases, which also includes NTRK1 (TRKA) and NTRK2 (TRKB). Neurotrophin-3 (NTF3, also known as NT-3) is the ligand for NTRK3. Similar to other NTRK receptors and receptor tyrosine kinases in general, ligand binding induces receptor dimerization followed by trans-autophosphorylation on conserved tyrosines in the intracellular (cytoplasmic) domain of the receptor (Lamballe et al. 1991, Philo et al. 1994, Tsoulfas et al. 1996, Yuen and Mobley 1999, Werner et al. 2014). These conserved tyrosines serve as docking sites for adaptor proteins that trigger downstream signaling cascades. Signaling through PLCG1 (Marsh and Palfrey 1996, Yuen and Mobley 1999, Huang and Reichardt 2001), PI3K (Yuen and Mobley 1999, Tognon et al. 2001, Huang and Reichardt 2001, Morrison et al. 2002, Lannon et al. 2004, Jin et al. 2008) and RAS (Marsh and Palfrey 1996, Gunn-Moore et al. 1997, Yuen and Mobley 1999, Gromnitza et al. 2018), downstream of activated NTRK3, regulates cell survival, proliferation and motility.
In the absence of its ligand, NTRK3 functions as a dependence receptor and triggers BAX and CASP9-dependent cell death (Tauszig-Delamasure et al. 2007, Ichim et al. 2013).
NTRK3 was reported to activate STAT3 through JAK2, but the exact mechanism has not been elucidated (Kim et al. 2016). NTRK3 was reported to interact with the adaptor protein SH2B2, but the biological role of this interaction has not been determined (Qian et al. 1998).
Receptor protein tyrosine phosphatases PTPRO and PTPRS (PTPsigma) negatively regulate NTRK3 signaling by dephosphorylating NTRK3 (Beltran et al. 2003, Faux et al. 2007, Hower et al. 2009, Tchetchelnitski et al. 2014). In addition to dephosphorylation of NTRK3 in-cis, the extracellular domain of pre-synaptic PTPRS can bind in-trans to extracellular domain of post-synaptic NTRK3, contributing to synapse formation (Takahashi et al. 2011, Coles et al. 2014). R-HSA-166520 Signaling by NTRKs Neurotrophins (NGF, BDNF, NTF3 and NTF4) play pivotal roles in survival, differentiation, and plasticity of neurons in the peripheral and central nervous system. They are produced, and secreted in minute amounts, by a variety of tissues. They signal through two types of receptors: NTRK (TRK) tyrosine kinase receptors (TRKA, TRKB, TRKC), which differ in their preferred neurotrophin ligand, and p75NTR death receptor, which interacts with all neurotrophins. Besides the nervous system, TRK receptors and p75NTR are expressed in a variety of other tissues. For review, please refer to Bibel and Barde 2000, Poo 2001, Lu et al. 2005, Skaper 2012, Park and Poo 2013.
NTRK receptors, NTRK1 (TRKA), NTRK2 (TRKB) and NTRK3 (TRKC) are receptor tyrosine kinases activated by ligand binding to their extracellular domain. Ligand binding induces receptor dimerization, followed by trans-autophosphorylation of dimerized receptors on conserved tyrosine residues in the cytoplasmic region. Phosphorylated tyrosines in the intracellular domain of the receptor serve as docking sites for adapter proteins, triggering downstream signaling cascades.
NTRK1 (TRKA) is the receptor for the nerve growth factor (NGF). NGF is primarily secreted by tissues that are innervated by sensory and sympathetic neurons. NTRK1 signaling promotes growth and survival of neurons during embryonic development and maintenance of neuronal cell integrity in adulthood (reviewed by Marlin and Li 2015).
Brain-derived neurotrophic factor (BDNF) and neurotrophin-4 (NTF4, also known as NT-4) are two high affinity ligands for NTRK2 (TRKB). Neurotrophin-3 (NTF3, also known as NT-3) binds to NTRK2 with low affinity and may not be a physiologically relevant ligand. Nerve growth factor (NGF), a high affinity ligand for NTRK1, does not interact with NTRK2. NTRK2 signaling is implicated in neuronal development in both the peripheral (PNS) and central nervous system (CNS) and may play a role in long-term potentiation (LTP) and learning (reviewed by Minichiello 2009). NTRK2 may modify neuronal excitability and synaptic transmission by directly phosphorylating voltage gated channels (Rogalski et al. 2000).
NTF3 (NT-3) is the ligand for NTRK3 (TRKC). Signaling downstream of activated NTRK3, regulates cell survival, proliferation and motility. In the absence of its ligand, NTRK3 functions as a dependence receptor and triggers BAX and CASP9-dependent cell death (Tauszig-Delamasure et al. 2007, Ichim et al. 2013).
R-HSA-9006927 Signaling by Non-Receptor Tyrosine Kinases In addition to receptor tyrosine kinases, the human genome encodes at least 32 non-receptor tyrosine kinases (non-RTKs). These cytosolic tyrosine kinases lack a transmembrane domain but are recruited into signal transduction cascades through interaction with other plasma-bound receptors, which may or may not themselves have intrinsic catalytic activity. In this way, non-RTKs essentially function as an (additional) enzymatic subunit of the signaling complex and contribute to many of the same downstream signaling pathways. The non-RTKs can be grouped into 9 families (ABL, SYK, JAK, TEC, FAK, ACK, SRC, BRK/PTK6 and CSK) based on their domain structure (reviewed in Neet and Hunter, 1996).
R-HSA-9006931 Signaling by Nuclear Receptors Nuclear receptors (NRs) are ligand-activated transcription factors that bind to small lipid based molecules to regulate gene expression and other cellular process. This family includes receptors for steroid hormones and derivatives (such as estrogen, progesterone, glucocorticoids, Vitamin D, oxysterols and bile acids, among others) as well as receptors for retinoic acids, thyroid hormones and fatty acids and their derivatives. These ligands are able to diffuse directly through cellular membranes as a result of their lipophilic nature (reviewed in Beato et al, 1996; Holzer et al, 2017). The 48 human nuclear receptors share a conserved modular structure that consists of a sequence specific DNA-binding domain and a ligand-binding domain, in addition to various other protein-protein interaction domains. Upon interaction with ligand, NRs bind to the regulatory regions of target genes as homo- or heterodimers, or more rarely, as monomers. At the promoter, NRs interact with other activators and repressors to regulate gene expression (reviewed Beato et al, 1996; Simons et al, 2014; Hah and Kraus, 2010). A number of nuclear receptors are cytoplasmic in the absence of ligand and exist as part of a heat shock protein complex that regulates their cellular location, protein stability, competency to bind steroid hormones and transcriptional activity (Echeverria and Picard, 2010). Ligand-binding to these receptors promotes dimerization and nuclear translocation. Other nuclear receptors are contstitutively nuclear and their chromatin-modifying activities are regulated by ligand binding (reviewed in Beato et al, 1996). In addition to the classic transcriptional response, NRs also have a role in rapid, non-nuclear signaling originating from receptors localized at the plasma membrane. Ligand-binding to these receptors intitiates downstream phospholipase- and kinase-based signaling cascades (reviewed in Schwartz et al, 2016; Levin and Hammes, 2016). Signaling by estrogen, liver X and retinoic acid receptors are currently described here.
R-HSA-5638302 Signaling by Overexpressed Wild-Type EGFR in Cancer Signaling by EGFR is frequently activated in cancer through genomic amplification of the EGFR locus, resulting in over-expression of the wild-type protein (Wong et al. 1987).
R-HSA-186797 Signaling by PDGF Platelet-derived Growth Factor (PDGF) is a potent stimulator of growth and motility of connective tissue cells such as fibroblasts and smooth muscle cells as well as other cells such as capillary endothelial cells and neurons.The PDGF family of growth factors is composed of four different polypeptide chains encoded by four different genes. The classical PDGF chains, PDGF-A and PDGF-B, and more recently discovered PDGF-C and PDGF-D. The four PDGF chains assemble into disulphide-bonded dimers via homo- or heterodimerization, and five different dimeric isoforms have been described so far; PDGF-AA, PDGF-AB, PDGF-BB, PDGF-CC and PDGF-DD. It is notable that no heterodimers involving PDGF-C and PDGF-D chains have been described. PDGF exerts its effects by binding to, and activating, two protein tyrosine kinase (PTK) receptors, alpha and beta. These receptors dimerize and undergo autophosphorylation. The phosphorylation sites then attract downstream effectors to transduct the signal into the cell.
R-HSA-9671555 Signaling by PDGFR in disease PDGFRA and PDGFRB are type III receptor tyrosine kinases that promote development and maintenance of mesenchymal tissues, including vascular smooth muscle, kidney, intestine, skin and lung, among others (reviewed in Tallquist and Kazlauskas, 2004; reviewed in Wang et al, 2016). Signaling through PDGF receptors stimulates cell proliferation and survival through activation of downstream signaling pathways including the RAS-MAP kinase cascade, PI3K signaling and STAT signaling (reviewed in Roskoski, 2018). Aberrant signaling through PDGF receptors is implicated in a number of human diseases. Point mutations in PDGFRA and, to a lesser extent, PDGFRB are implicated in a number of cancers, such as gastrointestinal stromal tumors (GIST; 5-10% mutation frequency in PDGFRA) and haematological cancers (Corless et al, 2005; Wang et al, 2016; reviewed in Klug et al, 2018). In addition, amplified signaling through the PDGF pathway can arise through gene fusion events or overexpression of ligand or receptor through gene amplification (Ozawa et al, 2010; Verhaak et al, 2010; reviewed in Appiah-Kubi et al, 2017).
R-HSA-9673770 Signaling by PDGFRA extracellular domain mutants Mutations in the extracellular domain of receptor tyrosine kinases like PDGRFA have the potential to interfere with glycosylation, which is required for proper trafficking to the cell surface. Versions of PDGFRA bearing mutations in the extracellular domain have been identified in some cancers, and while some of these are inactive, some have also been shown to signal constitutively from the endoplasmic reticulum (Ip et al, 2018; Velghe et al, 2014; Ozawa et al, 2010; Paugh et al, 2013; Clarke et al, 2003). PDGFRA Y288C carries a mutation in the extracellular domain of the receptor that prevents the normal trafficking of the protein to the plasma membrane. PDGFRA Y288C is trapped in the endoplasmic reticulum membrane, from where it is able to signal constitutively in the absence of ligand (Ip et al, 2018). Similarly, a version of PDGFRA bearing an in-frame deletion of exons 8 and 9 has been identified in glioblastoma. The resulting protein is constitutively active in the absence of ligand despite the low fraction of protein expressed at the cell surface (Clarke et al, 2003; Ozawa et al, 2010).
R-HSA-9673767 Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants PDGFRA is a type III transmembrane receptor tyrosine kinase. The extracellular domain consists of 5 immunoglobulin (IG) domains that contribute to dimerization and ligand binding. The intracellular region has a juxtamembrane domain that plays a role in autoinhibiting the receptor in the absence of ligand, and a bi-lobed kinase region with an activation loop and the catalytic cleft (reviewed in Klug et al, 2018). Upon ligand binding, PDGFRA undergoes dimerization and transautophosphorylation at at least 11 tyrosine residues in the intracellular domain. These phosphorylated residues are binding sites for downstream effectors of PDGFRA-responsive signaling pathways (reviewed in Klug et al, 2018; Roskoski, 2018).
PDGFRA is subject to activating mutations in a number of cancers, including gastrointestinal stromal tumors (GIST), melanoma and haematological cancers (reviewed in Corless et al, 2011; Wang et al, 2016; Roskoski, 2018). The most prevalent mutations in PDGFRA are at residue V561 in the juxtamembrane domain, N659 in the small lobe of the kinase domain and D842 in the activation loop of the kinase domain. PDGFRA is also subject to short deletions in the activation loop segment (reviewed in Roskoski, 2018). Acitvated forms of the protein may signal from the plasma membrane, similar to the wild type receptor, however there is also evidence that some mutants, notably D842V and V561D localize primarily to the Golgi membrane (Bahlawane et al, 2014). Activated PDGFRA mutants signal constitutively in the absence of ligand (reviewed in Roskoski, 2018; Wang et al, 2016; Klug et al, 2018).
R-HSA-8848021 Signaling by PTK6 PTK6 (BRK) is an oncogenic non-receptor tyrosine kinase that functions downstream of ERBB2 (HER2) (Xiang et al. 2008, Peng et al. 2015) and other receptor tyrosine kinases, such as EGFR (Kamalati et al. 1996) and MET (Castro and Lange 2010). Since ERBB2 forms heterodimers with EGFR and since MET can heterodimerize with both ERBB2 and EGFR (Tanizaki et al. 2011), it is not clear if MET and EGFR activate PTK6 directly or act through ERBB2. Levels of PTK6 increase under hypoxic conditions (Regan Anderson et al. 2013, Pires et al. 2014). The kinase activity of PTK6 is negatively regulated by PTPN1 phosphatase (Fan et al. 2013) and SRMS kinase (Fan et al. 2015), as well as the STAT3 target SOCS3 (Gao et al. 2012).
PTK6 activates STAT3-mediated transcription (Ikeda et al. 2009, Ikeda et al. 2010) and may also activate STAT5-mediated transcription (Ikeda et al. 2011). PTK6 promotes cell motility and migration by regulating the activity of RHO GTPases RAC1 (Chen et al. 2004) and RHOA (Shen et al. 2008), and possibly by affecting motility-related kinesins (Lukong and Richard 2008). PTK6 crosstalks with AKT1 (Zhang et al. 2005, Zheng et al. 2010) and RAS signaling cascades (Shen et al. 2008, Ono et al. 2014) and may be involved in MAPK7 (ERK5) activation (Ostrander et al. 2007, Zheng et al. 2012). PTK6 enhances EGFR signaling by inhibiting EGFR down-regulation (Kang et al. 2010, Li et al. 2012, Kang and Lee 2013). PTK6 may also enhance signaling by IGF1R (Fan et al. 2013) and ERBB3 (Kamalati et al. 2000).
PTK6 promotes cell cycle progression by phosphorylating and inactivating CDK inhibitor CDKN1B (p27) (Patel et al. 2015).
PTK6 activity is upregulated in osteopontin (OPN or SPP1)-mediated signaling, leading to increased VEGF expression via PTK6/NF-kappaB/ATF4 signaling path. PTK6 may therefore play a role in VEGF-dependent tumor angiogenesis (Chakraborty et al. 2008).
PTK6 binds and phosphorylates several nuclear RNA-binding proteins, including SAM68 family members (KHDRSB1, KHDRSB2 and KHDRSB3) (Derry et al. 2000, Haegebarth et al. 2004, Lukong et al. 2005) and SFPQ (PSF) (Lukong et al. 2009). The biological role of PTK6 in RNA processing is not known.
For a review of PTK6 function, please refer to Goel and Lukong 2015.
R-HSA-9656223 Signaling by RAF1 mutants RAF1, also known as CRAF, is mutated in a number of germline RASopathies including Noonan Syndrome, Costello Syndrome and others, and also at low frequency in a number of cancers (reviewed in Rauen, 2013; Samatar and Poulikakos, 2015). Activating mutations cluster around conserved region 2 (CR2) which is required for regulation of the protein and the activation segment in CR3 (reviewed in Rauen, 2013).
R-HSA-9753510 Signaling by RAS GAP mutants This pathway describes RAS mutants whose intrinsic GTPase activity can't be stimulated by GTPase activating proteins (GAPs). These RAS mutants therefore support increased RAS pathway activity (reviewed in Prior et al, 2012; Pylayeva and Gupta, 2011, King et al, 2013; Cox and Der, 2010).
R-HSA-9753512 Signaling by RAS GTPase mutants This pathway describes RAS mutants with decreased intrinsic GTPase activity that therefore support increased RAS pathway activity (reviewed in Prior et al, 2012; Pylayeva and Gupta, 2011, King et al, 2013; Cox and Der, 2010).
R-HSA-6802949 Signaling by RAS mutants Members of the RAS gene family were the first oncogenes to be identified, and mutations in RAS are present in ~20-30% of human cancers (reviewed in Prior et al, 2012). Mutations in the KRAS gene are the most prevalent, and are found with high frequency in colorectal cancer, non-small cell lung cancer and pancreatic cancer, among others. The reasons for the lower prevalence of HRAS and NRAS mutations in human cancers are not fully understood, but may reflect gene-specific functions as well as differential codon usage and spatio-temporal regulation (reviewed in Prior et al, 2012; Stephen et al, 2014; Pylayeva-Gupta et al, 2011). Activating RAS mutations contribute to cellular proliferation, transformation and survival by activating the MAPK signaling pathway, the AKT pathway and the RAL GDS pathway, among others (reviewed in Stephen et al, 2014; Pylayeva-Gupta et al, 2011).
Although the frequency and distribution varies between RAS genes and cancer types, the vast majority of activating RAS mutations occur at one of three residues - G12, G13 and Q61. Mutations at these sites favour the RAS:GTP bound form and yield constitutively active versions of the protein (reviewed in Prior et al, 2012).
R-HSA-5340588 Signaling by RNF43 mutants RNF43 and related protein ZNRF3 are E3 ubiquitin ligases that negatively regulate WNT signaling by downregulating FZD receptors at the cell surface (Mukai et al, 2010; Hao et al, 2012). Frameshift loss-of-function mutations in RNF43 that enhance WNT signaling have been identified in pancreatic and colorectal cancers; the proliferation of these cells is dependent on the presence of secreted WNT, as their growth is abrogated by treatment of cells with the Porcupine inhibitor LGK974 (Koo et al, 2012; Jiang et al, 2013).
R-HSA-376176 Signaling by ROBO receptors The Roundabout (ROBO) family encodes transmembrane receptors that regulate axonal guidance and cell migration. The major function of the Robo receptors is to mediate repulsion of the navigating growth cones. There are four human Robo homologues, ROBO1, ROBO2, ROBO3 and ROBO4. Most of the ROBOs have the similar ectodomain architecture as the cell adhesion molecules, with five Ig domains followed by three FN3 repeats, except for ROBO4. ROBO4 has two Ig and two FN3 repeats. The cytoplasmic domains of ROBO receptors are in general poorly conserved. However, there are four short conserved cytoplasmic sequence motifs, named CC0-3, that serve as binding sites for adaptor proteins. The ligands for the human ROBO1 and ROBO2 receptors are the three SLIT proteins SLIT1, SLIT2, and SLIT3; all of the SLIT proteins contain a tandem of four LRR (leucine rich repeat) domains at the N-terminus, termed D1-D4, followed by six EGF (epidermal growth factor)-like domains, a laminin G like domain (ALPS), three EGF-like domains, and a C-terminal cysteine knot domain. Most SLIT proteins are cleaved within the EGF-like region by unknown proteases (reviewed by Hohenster 2008, Ypsilanti and Chedotal 2014, Blockus and Chedotal 2016). NELL2 is a ligand for ROBO3 (Jaworski et al. 2015).
SLIT protein binding modulates ROBO interactions with the cytosolic adaptors. The cytoplasmic domain of ROBO1 and ROBO2 determines the repulsive responses of these receptors. Based on the studies from both invertebrate and vertebrate organisms it has been inferred that ROBO induces growth cone repulsion by controlling cytoskeletal dynamics via either Abelson kinase (ABL) and Enabled (Ena), or RAC1 activity (reviewed by Hohenster 2008, Ypsilanti and Chedotal 2014, Blockus and Chedotal 2016). While there is some redundancy in the function of ROBO receptors, ROBO1 is implicated as the predominant receptor for axon guidance in ventral tracts, and ROBO2 is the predominant receptor for axon guidance in dorsal tracts. ROBO2 also repels neuron cell bodies from the floor plate (Kim et al. 2011).
In addition to regulating axon guidance, ROBO1 and ROBO2 receptors are also implicated in regulation of proliferation and transition of primary to intermediate neuronal progenitors through a poorly characterized cross-talk with NOTCH-mediated activation of HES1 transcription (Borrell et al. 2012).
Thalamocortical axon extension is regulated by neuronal activity-dependent transcriptional regulation of ROBO1 transcription. Lower neuronal activity correlates with increased ROBO1 transcription, possibly mediated by the NFKB complex (Mire et al. 2012).
It is suggested that the homeodomain transcription factor NKX2.9 stimulates transcription of ROBO2, which is involved in regulation of motor axon exit from the vertebrate spinal code (Bravo-Ambrosio et al. 2012).
Of the four ROBO proteins, ROBO4 is not involved in neuronal system development but is, instead, involved in angiogenesis. The interaction of ROBO4 with SLIT3 is involved in proliferation, motility and chemotaxis of endothelial cells, and accelerates formation of blood vessels (Zhang et al. 2009).
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases Receptor tyrosine kinases (RTKs) are a major class of cell surface proteins involved in Signal Transduction. Human cells contain ~60 RTKs, grouped into 20 subfamilies based on their domain architecture. All RTK subfamilies are characterized by an extracellular ligand-binding domain, a single transmembrane region and an intracellular region consisting of the tyrosine kinase domain and additional regulatory and protein interaction domains. In general, RTKs associate into dimers upon ligand binding and are activated by autophosphorylation on conserved intracellular tyrosine residues. Autophosphorylation increases the catalytic efficiency of the receptor and provides binding sites for the assembly of downstream signaling complexes (reveiwed in Lemmon and Schlessinger, 2010). Common signaling pathways activated downstream of RTK activation include RAF/MAP kinase cascades (reviewed in McKay and Morrison, 2007 and Wellbrock et al 2004), AKT signaling (reviewed in Manning and Cantley, 2007) and PLC-gamma mediated signaling (reviewed in Patterson et al). Activation of these pathways ultimately results in changes in gene expression and cellular metabolism.
R-HSA-5362517 Signaling by Retinoic Acid Vitamin A (retinol) can be metabolised into active retinoid metabolites that function either as a chromophore in vision or in regulating gene expression transcriptionally and post-transcriptionally. Genes regulated by retinoids are essential for reproduction, embryonic development, growth, and multiple processes in the adult, including energy balance, neurogenesis, and the immune response. The retinoid used as a cofactor in the visual cycle is 11-cis-retinal (11cRAL). The non-visual cycle effects of retinol are mediated by retinoic acid (RA), generated by two-step conversion from retinol (Napoli 2012). All-trans-retinoic acid (atRA) is the major activated metabolite of retinol. An isomer, 9-cis-retinoic acid (9cRA) has biological activity, but has not been detected in vivo, except in the pancreas. An alternative route involves BCO1 cleavage of carotenoids into retinal, which is then reduced into retinol in the intestine (Harrison 2012). The two isomers of RA serve as ligands for retinoic acid receptors (RAR) that regulate gene expression. (Das et al. 2014). RA is catabolised to oxidised metabolites such as 4-hydroxy-, 18-hydroxy- or 4-oxo-RA by CYP family enzymes, these metabolites then becoming substrates for Phase II conjugation enzymes (Ross & Zolfaghari 2011).
R-HSA-194315 Signaling by Rho GTPases The Rho family of small guanine nucleotide binding proteins is one of seven phylogenetic branches of the Ras superfamily (Bernards 2005), which, besides Rho, Miro and RHOBTB3 also includes Ran, Arf, Rab and Ras families (Boureux et al. 2007). Miro GTPases and RHOBTB3 ATPase are sometimes described as Rho family members, but they are phylogenetically distinct (Boureux et al. 2007). Phylogenetically, RHO GTPases can be grouped into four clusters. The first cluster consists of three subfamilies: Rho, RhoD/RhoF and Rnd. The second cluster consists of three subfamilies: Rac, Cdc42 and RhoU/RhoV. The third cluster consists of the RhoH subfamily. The fourth cluster consists of the RhoBTB subfamily. Based on their activation type, RHO GTPases can be divided into classical (typical) and atypical (reviewed by Haga and Ridley 2016, and Kalpachidou et al. 2019). Classical RHO GTPases cycle between active GTP-bound states and inactive GDP-bound states through steps that are tightly controlled by members of three classes of proteins: (1) guanine nucleotide dissociation inhibitors or GDIs, which maintain Rho proteins in an inactive state in the cytoplasm, (2) guanine nucleotide exchange factors or GEFs, which destabilize the interaction between Rho proteins and their bound nucleotide, the net result of which is the exchange of bound GDP for the more abundant GTP, and (3) GTPase activating proteins or GAPs, which stimulate the low intrinsic GTP hydrolysis activity of Rho family members, thus promoting their inactivation. GDIs, GEFs, and GAPs are themselves subject to tight regulation, and the overall level of Rho activity reflects the balance of their activities. Many of the Rho-specific GEFs, GAPs, and GDIs act on multiple Rho GTPases, so that regulation of these control proteins can have complex effects on the functions of multiple Rho GTPases (reviewed by Van Aelst and D'Souza-Schorey 1997, Schmidt and Hall 2002, Jaffe and Hall 2005, Bernards 2005, and Hodge and Ridley 2016). Classical RHO GTPases include four subfamilies: Rho (includes RHOA, RHOB and RHOC), Rac (includes RAC1, RAC2, RAC3 and RHOG), Cdc42 (includes CDC42, RHOJ and RHOQ) and RhoD/RhoF (includes RHOD and RHOF) (reviewed in Haga and Ridley 2016). Atypical RHO GTPases do not possess GTPase activity. They therefore constitutively exist in the active GTP-bound state. Atypical RHO GTPases include three subfamilies: Rnd (includes RND1, RND2 and RND3), RhoBTB (includes RHOBTB1 and RHOBTB2), RhoH (RHOH is the only member) and RhoU/RhoV (includes RHOU and RHOV). Members of the Rho family have been identified in all eukaryotes. Among Rho GTPases, RHOA, RAC1 and CDC42 have been most extensively studied.
RHO GTPases regulate cell behavior by activating a number of downstream effectors that regulate cytoskeletal organization, intracellular trafficking and transcription (reviewed by Sahai and Marshall 2002). They are best known for their ability to induce dynamic rearrangements of the plasma membrane-associated actin cytoskeleton (Aspenstrom et al. 2004; Murphy et al. 1999; Govek et al. 2005). Beyond this function, Rho GTPases also regulate actomyosin contractility and microtubule dynamics. Rho mediated effects on transcription and membrane trafficking are believed to be secondary to these functions. At the more macroscopic level, Rho GTPases have been implicated in many important cell biological processes, including cell growth control, cytokinesis, cell motility, cell-cell and cell-extracellular matrix adhesion, cell transformation and invasion, and development (Govek et al., 2005). One of the best studied RHO GTPase effectors are protein kinases ROCK1 and ROCK2, which phosphorylate many proteins involved in the stabilization of actin filaments and generation of actin-myosin contractile force, such as LIM kinases and myosin regulatory light chains (MRLC) (reviewed in Riento and Ridley 2003). The p21-activated kinase family, which includes PAK1, PAK2 and PAK3, is another well characterized family of RHO GTPase effectors involved in cytoskeleton regulation (reviewed in Daniels and Bokoch 1999, Szczepanowska 2009). Protein kinase C related kinases (PKNs), PKN1, PKN2 and PKN3 play important roles in cytoskeleton organization (Hamaguchi et al. 2000), regulation of cell cycle (Misaki et al. 2001), receptor trafficking (Metzger et al. 2003), apoptosis (Takahashi et al. 1998), and transcription (Metzger et al. 2003, Metzger et al. 2005, Metzger et al. 2008). Citron kinase (CIT) is involved in Golgi apparatus organization through regulation of the actin cytoskeleton (Camera et al. 2003) and in the regulation of cytokinesis (Gruneberg et al. 2006, Bassi et al. 2013, Watanabe et al. 2013). Kinectin (KTN1), a kinesin anchor protein, is a RHO GTPase effector involved in kinesin-mediated vesicle motility (Vignal et al. 2001, Hotta et al. 1996), including microtubule-dependent lysosomal transport (Vignal et al. 2001). IQGAP proteins, IQGAP1, IQGAP2 and IQGAP3, are RHO GTPase effectors that modulate cell shape and motility through regulation of G-actin/F-actin equilibrium (Brill et al. 1996, Fukata et al. 1997, Bashour et al. 1997, Wang et al. 2007, Pelikan-Conchaudron et al. 2011), regulate adherens junctions (Kuroda et al. 1998, Hage et al. 2009), and contribute to cell polarity and lamellipodia formation (Fukata et al. 2002, Suzuki and Takahashi 2008). WASP and WAVE proteins (reviewed by Lane et al. 2014), as well as formins (reviewed by Kuhn and Geyer 2014), are RHO GTPase effectors that regulate actin polymerization and play important roles in cell motility, organelle trafficking and mitosis. Rhotekin (RTKN) and rhophilins (RHPN1 and RHPN2) are RHO GTPase effectors that regulate the organization of the actin cytoskeleton and are implicated in the establishment of cell polarity, cell motility and possibly endosome trafficking (Sudo et al. 2006, Watanabe et al. 1996, Fujita et al. 2000, Peck et al. 2002, Mircescu et al. 2002). Cytoskeletal changes triggered by the activation of formins (Miralles et al. 2003) and RTKN (Reynaud et al. 2000) may lead to stimulation of SRF-mediated transcription. NADPH oxidase complexes 1, 2 and 3 (NOX1, NOX2 and NOX3), membrane associated enzymatic complexes that use NADPH as an electron donor to reduce oxygen and produce superoxide (O2-), are also regulated by RHO GTPases (Knaus et al. 1991, Roberts et al. 1999, Kim and Dinauer 2001, Jyoti et al. 2014, Cheng et al. 2006, Miyano et al. 2006, Ueyama et al. 2006). Every RHO GTPase activates multiple downstream effectors and most effectors are regulated by multiple RHO GTPases, resulting in an elaborate cross-talk.
R-HSA-9716542 Signaling by Rho GTPases, Miro GTPases and RHOBTB3 RAS-like proteins are small GTP binding proteins characterized structurally by 5 G boxes that are involved in nucleotide binding and hydrolysis. RAS-like proteins are typically active when bound to GTP and inactive when bound to GDP. Conversion between the two states is mediated by effector proteins: among others, GTPase activating proteins (GAPs) enable hydrolysis of bound GTP to form GDP, which remains bound, and guanine nucleotide exchange factors (GEFs) enable exchange of bound GDP for free GTP (intracellular GTP concentrations are typically an order of magnitude higher than GDP concentrations) (reviewed in Tetlow and Tamanoi, 2013).
The human genome includes over 150 members of the RAS superfamily grouped into five main subfamilies: RAS, RHO, ARF, RAB and RAN. These small GTPases affect a wide range of critical processes including gene expression, signal transduction, cell morphology, vesicle and nuclear trafficking, cellular proliferation and motility, among others (reviewed in Tetlow and Tamanoi, 2013).
The RHO family of GTPases is large and diverse, with many of its members considered to be master regulators of actin cytoskeleton, involved in the regulation of cellular processes that depend on dynamic reorganization of the cytoskeleton, including cell migration, cell adhesion, cell division, establishment of cellular polarity and intracellular transport (reviewed in Hodge and Ridley 2016, and Olson 2018).
MIRO proteins and RHOBTB3 protein, sometimes called atypical RHO proteins, show a high degree of overall sequence similarity to members of the five RAS-like subfamilies but diverge in their functions enough to constitute two separate subfamilies (Boureux et al. 2007). MIRO proteins have intrinsically high GTPase activity and do not require GTPase activator proteins (Peters et al. 2018). They play an important role mitochondrial biogenesis, maintenance and organization (reviewed in Birsa et al. 2013). The GTPase domain of RHOBTB3 is divergent from other Ras like superfamily members and displays ATPase activity (Espinosa et al. 2009). RHOBTB3 is involved in CUL3 dependent protein ubiquitination (Berthold et al. 2008; Ji and Rivero 2016), retrograde transport from endosomes to the Golgi apparatus (Espinosa et al. 2009), regulation of the cell cycle and in modulating the adaptive response to hypoxia (Ji and Rivero 2016).
R-HSA-1433557 Signaling by SCF-KIT Stem cell factor (SCF) is a growth factor with membrane bound and soluble forms. It is expressed by fibroblasts and endothelial cells throughout the body, promoting proliferation, migration, survival and differentiation of hematopoetic progenitors, melanocytes and germ cells.(Linnekin 1999, Ronnstrand 2004, Lennartsson and Ronnstrand 2006). The receptor for SCF is KIT, a tyrosine kinase receptor (RTK) closely related to the receptors for platelet derived growth factor receptor, colony stimulating factor 1 (Linnekin 1999) and Flt3 (Rosnet et al. 1991). Four isoforms of c-Kit have been identified in humans. Alternative splicing results in isoforms of KIT differing in the presence or absence of four residues (GNNK) in the extracellular region. This occurs due to the use of an alternate 5' splice donor site. These GNNK+ and GNNK- variants are co-expressed in most tissues; the GNNK- form predominates and was more strongly tyrosine-phosphorylated and more rapidly internalized (Ronnstrand 2004). There are also splice variants that arise from alternative usage of splice acceptor site resulting in the presence or absence of a serine residue (Crosier et al., 1993). Finally, there is an alternative shorter transcript of KIT expressed in postmeiotic germ cells in the testis which encodes a truncated KIT consisting only of the second part of the kinase domain and thus lackig the extracellular and transmembrane domains as well as the first part of the kinase domain (Rossi et al. 1991). Binding of SCF homodimers to KIT results in KIT homodimerization followed by activation of its intrinsic tyrosine kinase activity. KIT stimulation activates a wide array of signalling pathways including MAPK, PI3K and JAK/STAT (Reber et al. 2006, Ronnstrand 2004). Defects of KIT in humans are associated with different genetic diseases and also in several types of cancers like mast cell leukaemia, germ cell tumours, certain subtypes of malignant melanoma and gastrointestinal tumours.
R-HSA-5339700 Signaling by TCF7L2 mutants ~50% of colorectal cancers with microsatellite instability show frameshift mutations in TCF7L2 that result in the loss of the CTBP-binding region (Duval et al, 1999; Cuillliere-Dartigues et al, 2006). These cancer cells show decreased colocalization of CTBP and TCF7L2 and have increased expression of a TCF-dependent reporter gene (Cuilliere-Dartigues et al, 2006).
R-HSA-170834 Signaling by TGF-beta Receptor Complex The TGF-beta/BMP pathway incorporates several signaling pathways that share most, but not all, components of a central signal transduction engine. The general signaling scheme is rather simple: upon binding of a ligand, an activated plasma membrane receptor complex is formed, which passes on the signal towards the nucleus through a phosphorylated receptor SMAD (R-SMAD). In the nucleus, the activated R-SMAD promotes transcription in complex with a closely related helper molecule termed Co-SMAD (SMAD4). However, this simple linear pathway expands into a network when various regulatory components and mechanisms are taken into account. The signaling pathway includes a great variety of different TGF-beta/BMP superfamily ligands and receptors, several types of the R-SMADs, and functionally critical negative feedback loops. The R-SMAD:Co-SMAD complex can interact with a great number of transcriptional co-activators/co-repressors to regulate positively or negatively effector genes, so that the interpretation of a signal depends on the cell-type and cross talk with other signaling pathways such as Notch, MAPK and Wnt. The pathway plays a number of different biological roles in the control of embryonic and adult cell proliferation and differentiation, and it is implicated in a great number of human diseases.
TGF beta (TGFB1) is secreted as a homodimer, and as such it binds to TGF beta receptor II (TGFBR2), inducing its dimerization. Binding of TGF beta enables TGFBR2 to form a stable hetero-tetrameric complex with TGF beta receptor I homodimer (TGFBR1). TGFBR2 acts as a serine/threonine kinase and phosphorylates serine and threonine residues within the short GS domain (glycine-serine rich domain) of TGFBR1.
The phosphorylated heterotetrameric TGF beta receptor complex (TGFBR) internalizes into clathrin coated endocytic vesicles where it associates with the endosomal membrane protein SARA. SARA facilitates the recruitment of cytosolic SMAD2 and SMAD3, which act as R-SMADs for TGF beta receptor complex. TGFBR1 phosphorylates recruited SMAD2 and SMAD3, inducing a conformational change that promotes formation of R-SMAD trimers and dissociation of R-SMADs from the TGF beta receptor complex.
In the cytosol, phosphorylated SMAD2 and SMAD3 associate with SMAD4 (known as Co-SMAD), forming a heterotrimer which is more stable than the R-SMAD homotrimers. R-SMAD:Co-SMAD heterotrimer translocates to the nucleus where it directly binds DNA and, in cooperation with other transcription factors, regulates expression of genes involved in cell differentiation, in a context-dependent manner.
The intracellular level of SMAD2 and SMAD3 is regulated by SMURF ubiquitin ligases, which target R-SMADs for degradation. In addition, nuclear R-SMAD:Co-SMAD heterotrimer stimulates transcription of inhibitory SMADs (I-SMADs), forming a negative feedback loop. I-SMADs bind the phosphorylated TGF beta receptor complexes on caveolin coated vesicles, derived from the lipid rafts, and recruit SMURF ubiquitin ligases to TGF beta receptors, leading to ubiquitination and degradation of TGFBR1. Nuclear R-SMAD:Co-SMAD heterotrimers are targets of nuclear ubiquitin ligases which ubiquitinate SMAD2/3 and SMAD4, causing heterotrimer dissociation, translocation of ubiquitinated SMADs to the cytosol and their proteasome-mediated degradation. For a recent review of TGF-beta receptor signaling, please refer to Kang et al. 2009.
R-HSA-3304351 Signaling by TGF-beta Receptor Complex in Cancer Signaling by the TGF-beta receptor complex is tumor suppressive, as it inhibits cell growth and promotes cell differentiation and apoptosis (Shipley et al. 1986, Hannon et al. 1994, Datto et al. 1995, Chen et al. 2002, Azar et al. 2009). TGF-beta signaling is frequently impaired in cancer, mostly through SMAD4 gene deletion or loss-of-function mutations (described in the pathway Loss of Function of SMAD4 in Cancer), which are especially frequent in pancreatic cancer (Hahn et al. 1996, Shi et al. 1997, Fleming et al. 2013). Signaling by TGF-beta receptor complex can also be disrupted by loss-of-function mutations in SMAD2 and SMAD3 (Fleming et al. 2013), as described in the pathway Loss of Function of SMAD2/SMAD3 in Cancer, or loss-of-function mutations in TGFBR2 (TGF-beta receptor II) (Markowitz et al. 1995, Garrigue-Antar et al. 1995, Parsons et al. 1995, Grady et al. 1999), as described in the pathway Loss of Function of TGFBR2 in Cancer, or TGFBR1 (TGF-beta receptor I) (Chen et al. 1998, Chen et al. 2001, Goudie et al. 2011), as described in the pathway Loss of Function of TGFBR1 in Cancer.
In advanced cancer, signaling by TGF-beta may be tumor promoting, as it induces epithelial-to-mesenchymal transition (EMT), thereby increasing invasiveness (Cui et al. 1996, Guasch et al. 2007, reviewed by Heldin et al. 2012).
R-HSA-9006936 Signaling by TGFB family members The human genome encodes 33 TGF-beta family members, including TGF-beta itself, as well as bone morphogenetic protein (BMP), activin, nodal and growth and differentiation factors (GDFs). This superfamily of ligands generally binds as dimers to hetero-tetrameric cell-surface receptor serine/threonine kinases to activate SMAD-dependent and SMAD-independent signaling (reviewed in Morikawa et al, 2016; Budi et al, 2017).
Signaling by the TGF-beta receptor complex is initiated by TGF-beta. TGF-beta (TGFB1), secreted as a homodimer, binds to TGF-beta receptor II (TGFBR2), inducing its dimerization and formation of a stable hetero-tetrameric complex with TGF-beta receptor I homodimer (TGFBR1). TGFBR2-mediated phosphorylation of TGFBR1 triggers internalization of the heterotetrameric TGF beta receptor complex (TGFBR) into clathrin coated endocytic vesicles and recruitment of cytosolic SMAD2 and SMAD3, which act as R-SMADs for TGF beta receptor complex. TGFBR1 phosphorylates SMAD2 and SMAD3, promoting their association with SMAD4 (known as Co-SMAD). In the nucleus, the SMAD2/3:SMAD4 heterotrimer binds target DNA elements and, in cooperation with other transcription factors, regulates expression of genes involved in cell differentiation. For a review of TGF-beta receptor signaling, please refer to Kang et al. 2009.
Signaling by BMP is triggered by bone morphogenetic proteins (BMPs). BMPs can bind type I receptors in the absence of type II receptors, but the presence of both types dramatically increases binding affinity. The type II receptor kinase transphosphorylates the type I receptor, leading to recruitment and phosphorylation of SMAD1, SMAD5 and SMAD8, which function as R-SMADs in BMP signalling pathways. Phosphorylated SMAD1, SMAD5 and SMAD8 form heterotrimeric complexes with SMAD4, the only Co-SMAD in mammals. The SMAD1/5/8:SMAD4 heterotrimer regulates transcription of genes involved in development of many tissues, including bone, cartilage, blood vessels, heart, kidney, neurons, liver and lung. For review of BMP signaling, please refer to Miyazono et al. 2010.
Signaling by activin is triggered when an activin dimer (activin A, activin AB or activin B) binds the type II receptor (ACVR2A, ACVR2B). This complex then interacts with the type I receptor (ACVR1B, ACVR1C) and phosphorylates it. The phosphorylated type I receptor phosphorylates SMAD2 and SMAD3. Dimers of phosphorylated SMAD2/3 bind SMAD4 and the resulting ternary complex enters the nucleus and activates target genes. For a review of activin signaling, please refer to Chen et al. 2006.
R-HSA-9839373 Signaling by TGFBR3 TGFBR3, also known as betaglycan, is a member of the proteoglycan family (Zhang et al., 2020) and plays a key role in regulating TGF-beta receptor-mediated signaling (Esparza-Lopez et al., 2001, Blobe et al., 2001) as well as TGF-beta-independent signaling (Wiater et al.,2003, Andres et al., 1992). TGFBR3 is expressed in abundance in normal cells (Wang et al, 1991) and is known to be down-regulated in multiple cancers due to its function as a tumor suppressor (Zhang et al.,2020, Fang et al.,2020, Cook et al.,2019). TGFBR3 is a transmembrane protein but lacks kinase activity in its cytoplasmic domain (López-Casillas et al.,1991). TGFBR3 primarily works as a co-receptor for different signaling pathways and can either facilitate or inhibit them (Wiater et al.,2003, Andres et al., 1992, Esparza-Lopez et al., 2001). TGFBR3 binds to TGF-beta ligands, facilitates their presentation to the TGFBR2 receptor, and helps in complex formation between TGFBR2 and TGFBR1 (Esparza-Lopez et al., 2001, Blobe et al., 2001). TGFBR3 also facilitates FGF:FGFR receptor complex stability and functions in FGFR1-mediated signaling as a co-receptor (Andres et al., 1992). TGBFR3 regulates signaling by other TGF-beta family members, including BMP2/7 and Activin (Wiater et al.,2003). Thus, TGFBR3 is involved in normal cell signaling and plays an important role in cancer, inflammatory diseases (Santiago et al, 2020), and Alzheimer's (Song et al., 2022).
R-HSA-2404192 Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) Binding of IGF1 (IGF-I) or IGF2 (IGF-II) to the extracellular alpha peptides of the type 1 insulin-like growth factor receptor (IGF1R) triggers the activation of two major signaling pathways: the SOS-RAS-RAF-MAPK (ERK) pathway and the PI3K-PKB (AKT) pathway (recently reviewed in Pavelic et al. 2007, Chitnis et al. 2008, Maki et al. 2010, Parella et al. 2010, Annunziata et al. 2011, Siddle et al. 2012, Holzenberger 2012).
R-HSA-194138 Signaling by VEGF In normal development vascular endothelial growth factors (VEGFs) are crucial regulators of vascular development during embryogenesis (vasculogenesis) and blood-vessel formation in the adult (angiogenesis). In tumor progression, activation of VEGF pathways promotes tumor vascularization, facilitating tumor growth and metastasis. Abnormal VEGF function is also associated with inflammatory diseases including atherosclerosis, and hyperthyroidism. The members of the VEGF and VEGF-receptor protein families have distinct but overlapping ligand-receptor specificities, cell-type expression, and function. VEGF-receptor activation in turn regulates a network of signaling processes in the body that promote endothelial cell growth, migration and survival (Hicklin and Ellis, 2005; Shibuya and Claesson-Welsh, 2006).
Molecular features of the VGF signaling cascades are outlined in the figure below (from Olsson et al. 2006; Nature Publishing Group). Tyrosine residues in the intracellular domains of VEGF receptors 1, 2,and 3 are indicated by dark blue boxes; residues susceptible to phosphorylation are numbered. A circled R indicates that phosphorylation is regulated by cell state (VEGFR2), by ligand binding (VEGFR1), or by heterodimerization (VEGFR3). Specific phosphorylation sites (boxed numbers) bind signaling molecules (dark blue ovals), whose interaction with other cytosolic signaling molecules (light blue ovals) leads to specific cellular (pale blue boxes) and tissue-level (pink boxes) responses in vivo. Signaling cascades whose molecular details are unclear are indicated by dashed arrows. DAG, diacylglycerol; EC, endothelial cell; eNOS, endothelial nitric oxide synthase; FAK, focal adhesion kinase; HPC, hematopoietic progenitor cell; HSP27, heat-shock protein-27; MAPK, mitogen-activated protein kinase; MEK, MAPK and ERK kinase; PI3K, phosphatidylinositol 3' kinase; PKC, protein kinase C; PLCgamma, phospholipase C-gamma; Shb, SH2 and beta-cells; TSAd, T-cell-specific adaptor.
In the current release, the first events in these cascades - the interactions between VEGF proteins and their receptors - are annotated.
R-HSA-195721 Signaling by WNT WNT signaling pathways control a wide range of developmental and adult process in metozoans including cell proliferation, cell fate decisions, cell polarity and stem cell maintenance (reviewed in Saito-Diaz et al, 2013; MacDonald et al, 2009). The pathway is named for the WNT ligands, a large family of secreted cysteine-rich glycoproteins. At least 19 WNT members have been identified in humans and mice with distinct expression patterns during development (reviewed in Willert and Nusse, 2012). These ligands can activate at least three different downstream signaling cascades depending on which receptors they engage.
In the so-called 'canonical' WNT signaling pathway, WNT ligands bind one of the 10 human Frizzled (FZD) receptors in conjunction with the LRP5/6 co-receptors to activate a transcriptional cascade that controls processes such as cell fate, proliferation and self-renenwal of stem cells. Engagement of the FZD-LRP receptor by WNT ligand results in the stabilization and translocation of cytosolic beta-catenin to the nucleus where it is a co-activator for LEF (lymphoid enhancer-binding factor)- and TCF (T cell factor) -dependent transcription. In the absence of WNT ligand, cytosolic beta-catenin is phosphorylated by a degradation complex consisting of glycogen synthase kinase 3 (GSK3), casein kinase 1 (CK1), Axin and Adenomatous polyposis coli (APC), and subsequently ubiquitinated and degraded by the 26S proteasome (reviewed in Saito-Diaz et al, 2013; Kimmelman and Xu, 2006).
In addition to the beta-catenin-dependent transcriptional response, WNT signaling can also activate distinct non-transcriptional pathways that regulate cell migration and polarity. These beta-catenin-independent 'non-canonical' pathways signal through Frizzled receptors independently of LRP5/6, or occur through the tyrosine kinase receptors ROR and RYK (reviewed in Veeman et al, 2003; James et al, 2009). Non-canonical WNT pathways are best studied in Drosophila where the planar cell polarity (PCP) pathway controls the orientation of wing hairs and eye facets, but are also involved in processes such as convergent extension, neural tube closure, inner ear development and hair orientation in vertebrates and mammals(reviewed in Seifert and Mlodzik, 2007; Simons and Mlodzik, 2008). In the PCP pathway, binding of WNT ligand to the FZD receptor leads to activation of small Rho GTPases and JNK, which regulate the cytoskeleton and coordinate cell migration and polarity (reviewed in Lai et al, 2009; Schlessinger et al, 2009). In some cases, a FZD-WNT interaction increases intracellular calcium concentration and activates CaMK II and PKC; this WNT calcium pathway promotes cell migration and inhibits the canonical beta-catenin dependent transcriptional pathway (reviewed in Kuhl et al, 2000; Kohn and Moon, 2005; Rao et al 2010). Binding of WNT to ROR or RYK receptors also regulates cell migration, apparently through activation of JNK or SRC kinases, respectively, however the details of these pathways remain to be worked out (reviewed in Minami et al, 2010).
Although the WNT signaling pathways were originally viewed as discrete, linear pathways controlled by defined subsets of 'canonical' or 'non-canonical' ligands and receptors, the emerging evidence is challenging this notion. Instead, the specificity and the downstream response appear to depend on the particular cellular context and vary with species, tissue and stage of development (reviewed in van Amerongen and Nusse, 2009; Rao et al, 2010).
R-HSA-4791275 Signaling by WNT in cancer The WNT signaling pathway has been linked with cancer ever since the identification of the first WNT as a gene activated by integration of mouse mammary tumor virus proviral DNA in virally-induced breast tumors (Nusse et al, 1984). The most well known example of aberrant WNT signaling in cancer is in colorectal cancer, where an activating mutation in a WNT pathway component is seen in 90% of sporadic cases. Inappropriate WNT pathway activation has also been implicated in most other solid human cancers but is not always associated with mutations in WNT pathway components (reviewed in Polakis, 2012).
Both tumor suppressors and oncogenes have been identified in the so-called canonical WNT pathway, which regulates WNT-dependent transcription by promoting the degradation of beta-catenin in the absence of ligand (reviewed in Polakis, 2012). Loss-of-function mutations in the destruction complex components APC, Axin and AMER1 and gain-of-function mutations in beta-catenin itself cause constitutive signaling and are found in cancers of the intestine, kidney, liver and stomach, among others (Polakis, 1995; Segiditsas and Tomlinson, 2006; Peifer and Polakis, 2000; Laurent-Puig et al, 2001; Liu et al, 2000; Satoh et al, 2000; Major et al, 2007; Ruteshouser et al, 2008). WNTs and WNT pathway components are also frequently over- or under-expressed in various cancers, and these changes are correlated with epigenetic regulation of promoter activity. In some contexts, both the canonical and non-canonical WNT signaling, which governs processes such as cell polarity and morphogenesis, may also contribute to tumor formation by promoting cell migration, invasiveness and metastasis.
R-HSA-1839122 Signaling by activated point mutants of FGFR1 Unlike FGFR2 and FGFR3, FGFR1 appears not to be a frequent target of activating point mutations (reviewed in Wesche, 2011; Turner and Grose, 2010). Germline point mutations at residue P252 have been identified in Pfeiffer syndrome (reviewed in Webster and Donoghue, 1997; Burke, 1998; Cunningham, 2007) while mutation of the same residue arising somatically has been identified in melanoma and lung cancer (Ruhe, 2007; Davies, 2005). Two kinase domain mutations have been characterized in glioblastoma (Rand, 2005; Network TCGA, 2008), both at positions that are also mutated in an autosomal disorder in one of the FGFR family members (Muenke, 1994; Bellus, 1995a; Bellus, 2000; Tavormina, 1995a; Tavormina, 1999).
R-HSA-1839130 Signaling by activated point mutants of FGFR3 Activating point mutations in FGFR3 are found in the extracellular ligand-binding domain, the transmembrane region and the tyrosine kinase domain and are believed to result in ligand-independent activation of the receptor (Webster and Donoghue, 1996; Wenbster, 1997). These mutations, although initially characterized in the context of autosomal skeletal disorders, are now being identified in a range of cancers including bladder, cervical, breast, prostate, head and neck, and multiple myeloma (reviewed in Wesche, 2011).
R-HSA-1839117 Signaling by cytosolic FGFR1 fusion mutants 8p11 myeloproliferative syndrome (EMS) is an aggressive disorder that is associated with a translocation event at the FGFR1 gene on chromosome 8p11. Typical symptoms upon diagnosis include eosinophilia and associated T-cell lymphoblastic lymphoma; the disease rapidly advances to acute leukemia, usually of myeloid lineage. At present the only effective treatment is allogenic stem cell transplantation (reviewed in Jackson, 2010).
At the molecular level, EMS appears to be caused by translocation events on chromosome 8 that create gene fusions between the intracellular domain of FGFR1 and an N-terminal partner gene that encodes a dimerization domain. The resulting fusion protein dimerizes in a ligand-independent fashion based the N-terminal domain provided by the partner protein and stimulates constititutive downstream FGFR1 signaling without altering the intrisic kinase activity of the receptor. To date, 11 partner genes have been identified: ZMYM2, FGFR1OP, FGFR1OP2, HERVK, TRIM24, CUX1, BCR, CEP110, LRRFIP1, MYO18A and CPSF6, although not all have been functionally characterized (reviewed in Jackson, 2010, Turner and Grose, 2010; Wesche, 2011).
Where examined, cell lines carrying FGFR1 fusion genes have been shown to be transforming and to support IL3-independent proliferation through anti-apoptotic, prosurvival pathways(Lelievre, 2008; Ollendorff, 1999; Chase, 2007; Guasch, 2001; Wasag 2011; Roumiantsev, 2004; Demiroglu, 2001; Smedley, 1999). Signaling appears to occur predominantly through PLCgamma, PI3K and STAT signaling, with a more minor contribution from MAPK activation. Because the fusion proteins lack the FRS2-binding site, the mechanism of MAPK activation is unclear. Recruitment of GRB2:SOS1 through recruitment of SHC is one possibility (Guasch, 2001).
R-HSA-9673766 Signaling by cytosolic PDGFRA and PDGFRB fusion proteins In addition to activating missense mutations and in-frame deletions, PDGFRA and PDGFRB are also subject to gene fusion events arising from chromosomal rearrangements. PDGFR fusions often consist of the cytosolic domain of the receptor tyrosine kinase fused to the N-terminal oligomerization domain of an intracellular protein, leading to ligand-independent dimerization and constitutive activation (reviewed in Wang et al, 2016; Appiah-Kubi et al, 2017). To date there are about 35 identified PDGFR fusion partners, most of which form fusions with PDGFRB (reviewed in Appiah-Kubi et al, 2017). The most common cytosolic fusion partners of PDGFRA is FIP1L1, an RNA processing factor (Cools et al, 2003; Stover et al, 2006; Simon et al, 2008; Andrae et al, 2008; Ozawa et al, 2010; Appiah-Kubi et al, 2017). Fusion partners with PDGFRB are numerous but occurrence of these proteins is rare (Hidalgo-Curtis et al, 2010; reviewed in Wang et al, 2016; Appiah-Kubi et al, 2017).
R-HSA-9680187 Signaling by extracellular domain mutants of KIT Many of the described KIT mutations are located in the fifth Ig-like domain, encoded by exon 8 and 9. The fifth Ig-like domain of KIT plays a critical role in stabilizing the receptor dimers formed upon SCF binding, allowing these mutations to support constitutive activation of the receptor (Yuzawa et al, 2007; reviewed in Lennartsson and Ronnstrand, 2012)
R-HSA-6802948 Signaling by high-kinase activity BRAF mutants BRAF is mutated in about 8% of human cancers, with high prevalence in hairy cell leukemia, melanoma, papillary thyroid and ovarian carcinomas, colorectal cancer and a variety of other tumors (Davies et al, 2002; reviewed in Samatar and Poulikakos, 2014). Most BRAF mutations fall in the activation loop region of the kinase or the adjacent glycine rich region. These mutations promote increased kinase activity either by mimicking the effects of activation loop phosphorylations or by promoting the active conformation of the enzyme (Davies et al, 2002; Wan et al, 2004). Roughly 90% of BRAF mutants are represented by the single missense mutation BRAF V600E (Davies et al, 2002; Wan et al, 2004). Other highly active kinase mutants of BRAF include BRAF G469A and BRAF T599dup. G469 is in the glycine rich region of the kinase domain which plays a role in orienting ATP for catalysis, while T599 is one of the two conserved regulatory phosphorylation sites of the activation loop. Each of these mutants has highly enhanced basal kinase activities, phosphorylates MEK and ERK in vitro and in vivo and is transforming when expressed in vivo (Davies et al, 2002; Wan et al, 2004; Eisenhardt et al, 2011). Further functional characterization shows that these highly active mutants are largely resistant to disruption of the BRAF dimer interface, suggesting that they are able to act as monomers (Roring et al, 2012; Brummer et al, 2006; Freeman et al, 2013; Garnett et al, 2005). Activating BRAF mutations occur for the most part independently of RAS activating mutations, and RAS activity levels are generally low in BRAF mutant cells. Moreover, the kinase activity of these mutants is only slightly elevated by coexpression of G12V KRAS, and biological activity of the highly active BRAF mutants is independent of RAS binding (Brummer et al, 2006; Wan et al, 2004; Davies et al, 2002; Garnett et al, 2005). Although BRAF V600E is inhibited by RAF inhibitors such as vemurafenib, resistance frequently develops, in some cases mediated by the expression of a splice variant that lacks the RAS binding domain and shows elevated dimerization compared to the full length V600E mutant (Poulikakos et al, 2011; reviewed in Lito et al, 2013).
R-HSA-9669935 Signaling by juxtamembrane domain KIT mutants Mutations in the juxtamembrane region of KIT, encoded by exon 11, are especially prevalent as initiating events in gastrointestinal stromal tumors (GIST), but are also found at lower frequency in other cancers such as AML and melanoma (reviewed in Antonescu, 2006; Roskoski, 2018). Mutations in this region of KIT are believed to disrupt an auto-inhibitory function, leading to constitutive enzyme activation (Ma et al, 1999; Chan et al, 2003; Mol et al, 2004; reviewed in Roskoski, 2018). Unlike kinase domain mutants, juxtamembrane domain KIT mutants still undergo dimerization, although in a ligand-independent manner (Hirota et al, 1998; Furitsu et al, 1993; reviewed in Lennartsson and Roonstrand, 2012).
R-HSA-9669933 Signaling by kinase domain mutants of KIT Activating mutations in the kinase domain of KIT are found in a small number of cases of AML and melanoma, as well as in myeloproliferative syndromes, mastocytosis and germ cell tumors (Longley et al, 1996; 1999; Nagata et al, 1995; Beghini et al, 2000; Ning et al, 2001; Tian et al, 1999; Kemmer et al, 2004; reviewed in Roskoski, 2018; Meng and Carvajal, 2019). Mutations in the kinase domain and activation loop of KIT (encoded by exons 13, 14 and 17) also arise in gastrointestinal stromal tumors (GIST) as primary mutations (<1%) and as secondary resistance mutations in response to treatment with imatinib (Chen et al, 2004; Serrano et al, 2019; Gajiwala et al, 2008; McLean et al, 2008; reviewed in Antonescu, 2006; Roskoski, 2018; Wu et al, 2019; Corless et al, 2011). Activating kinase mutants of KIT are constitutively active in the absence of ligand and can be tyrosine phosphorylated in the absence of dimerization (Furitsu et al, 1993; Hirota et al, 1998; Tsujimura et al, 1994).
R-HSA-9673768 Signaling by membrane-tethered fusions of PDGFRA or PDGFRB In addition to activating missensse and in-frame deletion mutations, PDGFRA and PDGFRB are also subject to low frequency gene fusion events arising from chromosomal rearrangements. To date there are about 35 identified PDGFRA or B fusion partners, with PDGFRB being the more common partner (reviewed in Appiah-Kubi et al, 2017). Although some of the PDGF fusions proteins are cytosolic by virtue of removal of the PDGFR transmembrane region (TMD), a number of fusions retain the TMD and are linked to the plasma membrane (Hidalgo-Curtis et al, 2010; Ozawa et al, 2010; Curtis et al, 2007; Medves et al, 2010; reviewed in Appiah-Kubi et al, 2017). The most common transmembrane fusion partner of PDGFRA and PDGFRB is ETV6 (also known as TEL1), a transcriptional repressor with known ability to homodimerize (Curtis et al, 2007; Golub et al, 1994; Andrae et al, 2008; reviewed in de Braekeleer et al, 2012; Wang et al, 2016; Appiah-Kubi et al, 2017).
R-HSA-6802946 Signaling by moderate kinase activity BRAF mutants In addition to the highly prevalent and activating V600E BRAF mutations, numerous moderately activating and less common mutations have also been identified in human cancers (Forbes et al, 2015). Unlike the case for their highly activating counterparts, signaling through these mutant versions of BRAF depends both upon RAS binding and RAF dimerization (Wan et al, 2004; Freeman et al, 2013; Roring et al, 2012; reviewed in Lito et al, 2013; Lavoie and Therrien, 2015)
R-HSA-9670439 Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants Activation of the PI3K/mTOR, RAS/MAPK and STAT signaling pathways has been observed downstream of activated extracellular, juxtamembrane and kinase domain mutants of KIT, although downstream signaling has not been studied in great detail in all cases. Activation of these pathways contributes to cellular proliferation, avoidance of apoptosis, and actin cytoskeletal organization (Dunesing et al, 2004; Bauer et al, 2007; Chi et al, 2010; Bosbach et al, 2017; reviewed in Lennartsson and Roonstrand, 2012; Corless et al, 2011).
R-HSA-8853336 Signaling by plasma membrane FGFR1 fusions In addition to the cytosolic FGFR1 fusions identified in 8 myeloproliferative syndrome, plasma membrane localized FGFR1 fusions have been identified in glioblastoma, breast cancer and non small cell lung cancers (Singh et al, 2012; Wu et al, 2013; Wang et al, 2014). A FGFR1:TACC1 fusion identified in glioblastoma promotes anchorage independent growth when expressed in Rat1A cells, while an ERLIN2:FGFR1 fusion in breast cancer shows constitutive autophosphorylation when expressed in HEK 293 cells (Singh et al, 2012; Wu et al, 2013). All FGFR1 fusions tested also shown increased sensitivity to growth inhibition upon treatment with kinase inhibitors (Singh et al, 2012; Wu et al, 2013; Wang et al, 2014; reviewed in Parker et al, 2014).
R-HSA-983705 Signaling by the B Cell Receptor (BCR) Mature B cells express IgM and IgD immunoglobulins which are complexed at the plasma membrane with Ig-alpha (CD79A, MB-1) and Ig-beta (CD79B, B29) to form the B cell receptor (BCR) (Fu et al. 1974, Fu et al. 1975, Kunkel et al. 1975, Van Noesel et al. 1992, Sanchez et al. 1993, reviewed in Brezski and Monroe 2008). Binding of antigen to the immunoglobulin activates phosphorylation of immunoreceptor tyrosine-based activation motifs (ITAMs) in the cytoplasmic tails of Ig-alpha and Ig-beta by Src family tyrosine kinases, including LYN, FYN, and BLK (Nel et al. 1984, Yamanashi et al. 1991, Flaswinkel and Reth 1994, Saouaf et al. 1994, Hata et al. 1994, Saouaf et al. 1995, reviewed in Gauld and Cambier 2004, reviewed in Harwood and Batista 2010).
The protein kinase SYK binds the phosphorylated immunoreceptor tyrosine-activated motifs (ITAMs) on the cytoplasmic tails of Ig-alpha (CD79A, MB-1) and Ig-beta (CD79B, B29) (Wienands et al. 1995, Rowley et al. 1995, Tsang et al. 2008). The binding causes the activation and autophosphorylation of SYK (Law et al. 1994, Baldock et al. 2000, Irish et al. 2006, Tsang et al. 2008, reviewed in Bradshaw 2010).
Activated SYK and other kinases phosphorylate BLNK (SLP-65), BCAP, and CD19 which serve as scaffolds for the assembly of large complexes, the signalosomes, by recruiting phosphoinositol 3-kinase (PI3K), phospholipase C gamma (predominantly PLC-gamma2 in B cells, Coggeshall et al. 1992), NCK, BAM32, BTK, VAV1, and SHC. The effectors are phosphorylated by SYK and other kinases.
PLC-gamma associated with BLNK hydrolyzes phosphatidylinositol-4,5-bisphosphate to yield inositol-1,4,5-trisphosphate (IP3) and diacylglycerol (Carter et al. 1991, Kim et al. 2004). IP3 binds receptors on the endoplasmic reticulum and causes release of calcium ions from the ER into the cytosol. The depletion of calcium from the ER in turn activates STIM1 to interact with ORAI and TRPC1 channels in the plasma membrane, resulting in an influx of extracellular calcium ions (Muik et al. 2008, Luik et al. 2008, Park et al. 2009, Mori et al. 2002). PI3K associated with BCAP and CD19 phosphorylates phosphatidylinositol 4,5-bisphosphate to yield phosphatidyinositol 3,4,5-trisphosphate.
Second messengers (calcium, diacylglycerol, inositol 1,4,5-trisphosphate, and phosphatidylinositol 3,4,5-trisphosphate) trigger signaling pathways: NF-kappaB is activated via protein kinase C beta, RAS is activated via RasGRP proteins, NF-AT is activated via calcineurin, and AKT (PKB) is activated via PDK1 (reviewed in Shinohara and Kurosaki 2009, Stone 2006).
R-HSA-9649948 Signaling downstream of RAS mutants Disease-causing mutations in RAS favour the active RAS:GTP bound form and yield constitutively active forms of the protein (reviewed in Prior et al, 2011; Maertens and Cichowski, 2014). Mutations in RAS contribute to cellular proliferation, transformation and survival by activating the MAPK signaling pathway, the AKT pathway and the RAL GDS pathway, among others (reviewed in Stephen et al, 2014; Pylayeva-Gupta et al, 2011)
R-HSA-198765 Signalling to ERK5 The location of neurotrophin stimulation appears to determine the nature of the transcriptional response through differential uses of individual MAP kinases. The ERK5 pathway has a unique function in retrograde signalling; in contrast, ERK1/2, which mediate nuclear responses following direct cell body stimulation, does not transmit a retrograde signal. Following neurotrophin stimulation of distal axons, phosphorylated TRK receptors are endocytosed and transported to the cell bodies, where MEK5 phosphorylates ERK5, leading to ERK5 nuclear translocation, phosphorylation of transcription factors, and neuronal survival. In contrast, neurotrophin stimulation of the cell bodies causes concurrent activation and nuclear transport of ERK1/2 as well as ERK5. Several distinctive features of the ERK5 pathway might be important for retrograde signalling. The ERK5 cascade does not depend on activation of the G-protein RAS. Instead, this pathway may use other G-proteins such as RAP that are associated with vesicles, or may not require any G-protein intermediate. Another distinctive feature is that the MEK5 isoform, which is expressed in the nervous system, exhibits a punctate staining pattern, suggesting a vesicular localization. ERK5 itself significantly differs from ERK1/2, and its substrate specificity also differs from ERK1/2. For instance, ERK5 directly activates transcription factors, including MEF2, that are not phosphorylated by ERK1/2. Conversely, ERK1/2, but not ERK5, activate transcription factors such as ELK1 and MITF.
R-HSA-187687 Signalling to ERKs Neurotrophins utilize multiple pathways to activate ERKs (ERK1 and ERK2), a subgroup of the large MAP kinase (MAPK) family, from the plasma membrane. The major signalling pathways to ERKs are via RAS, ocurring from caveolae in the plasma membrane or from clathrin-coated vesicles, and via RAP1, taking place in early endosomes. Whereas RAS activation by NGF is transient, RAP1 activation by NGF is sustained for hours.
R-HSA-167044 Signalling to RAS Signalling through Shc adaptor proteins appears to be identical for both NGF and EGF. It leads to a fast, but transient, MAPK/ERK activation, which is insufficient to explain the prolonged activation of MAPK found in NGF-treated cells.
R-HSA-198745 Signalling to STAT3 Neurotrophin-induced increase in Signal transducer and activator of transcription 3 (STAT3; acute-phase response factor) activation appears to underly several downstream functions of neurotrophin signalling, such as transcription of immediate early genes, proliferation arrest, and neurite outgrowth.
R-HSA-187706 Signalling to p38 via RIT and RIN RIT and RIN are two small guanine nucleotide binding proteins that share more than 50% sequence identity with RAS, including highly conserved core effector domains. Unlike RAS, the C termini of RIT and RIN lack a typical prenylation motif (CAAX, XXCC, or CXC) required for the association of RAS proteins with the plasma membrane. RIT is expressed in all tissues, whereas RIN is neuron-specific. They have similar signalling properties and are activated by NGF through unknown exchange factors. They signal to ERKs and p38 MAP kinase. They mainly lead to p38 activation via the BRAF-MEK kinase cascade.
R-HSA-426486 Small interfering RNA (siRNA) biogenesis Small interfering RNAs (siRNAs) are 21-25 nucleotide single-stranded RNAs produced by cleavage of longer double-stranded RNAs by the enzyme DICER1 within the RISC loading complex containing DICER1, an Argonaute protein, and either TARBP2 or PRKRA (PACT). Typically the long double-stranded substrates originate from viruses or repetitive elements in the genome and the two strands of the substrate are exactly complementary.
After cleavage by DICER1 the 21-25 nucleotide double-stranded product is loaded into an Argonuate protein (humans contain 4 Argonautes) and rendered single-stranded by a mechanism that is not well characterized.
siRNA-loaded AGO2 is predominantly located at the cytosolic face of the rough endoplasmic reticulum and has also been observed in the nucleus.
R-HSA-445355 Smooth Muscle Contraction Layers of smooth muscle cells can be found in the walls of numerous organs and tissues within the body. Smooth muscle tissue lacks the striated banding pattern characteristic of skeletal and cardiac muscle. Smooth muscle is triggered to contract by the autonomic nervous system, hormones, autocrine/paracrine agents, local chemical signals, and changes in load or length.
Actin:myosin cross bridging is used to develop force with the influx of calcium ions (Ca2+) initiating contraction. Two separate protein pathways, both triggered by calcium influx contribute to contraction, a calmodulin driven kinase pathway, and a caldesmon driven pathway.
Recent evidence suggests that actin, myosin, and intermediate filaments may be far more volatile then previously suspected, and that changes in these cytoskeletal elements along with alterations of the focal adhesions that anchor these proteins may contribute to the contractile cycle.
Contraction in smooth muscle generally uses a variant of the same sliding filament model found in striated muscle, except in smooth muscle the actin and myosin filaments are anchored to focal adhesions, and dense bodies, spread over the surface of the smooth muscle cell. When actin and myosin move across one another focal adhesions are drawn towards dense bodies, effectively squeezing the cell into a smaller conformation. The sliding is triggered by calcium:caldesmon binding, caldesmon acting in an analogous fashion to troponin in striated muscle. Phosphorylation of myosin light chains also is involved in the initiation of an effective contraction.
R-HSA-427652 Sodium-coupled phosphate cotransporters Phosphorus is an essential element that is critical for structural and metabolic roles in all living organisms. Cells obtain phosphorus in the form of negatively-charged inorganic phosphate (Pi). Two SLC families transport phosphate in mammals; SLC34 (Murer H et al, 2004) and SLC20 (Collins JF et al, 2004). Both are secondary-active, Na+-coupled transporter systems which use the inward Na+ gradient (from the Na+-K+-ATPase) to drive phosphate influx into cells (Virkki LV et al, 2007).
R-HSA-433137 Sodium-coupled sulphate, di- and tri-carboxylate transporters Five human SLC13 genes encode sodium-coupled sulphate, di- and tri-carboxylate transporters located on the plasma membrane. Two transporters (NaS1 and NaS2) co-transport sulphate with sodium. The other members (NaDC1, NaDC3, and NaCT) co-transport sodium with di- and tri-carboxylates such as succinate, citrate and alpha-ketoglutarate (Pajor AM, 2006).
R-HSA-425561 Sodium/Calcium exchangers Calcium ions are used by cells as ubiquitous signalling molecules that control diverse physiological events. Three mammalian gene families control Ca2+ transport across plasma membranes and intracellular compartments (Lytton J, 2007). They are the Na+/Ca2+ exchanger family designated NCX (SLC8) (three members NCX1-3) (Quednau BD et al, 2004), the Na+/Ca2+-K+ exchanger family designated NCKX (SLC24) (five members NCKX1-5) (Schnetkamp PP, 2004) and a Ca2+/cation exchanger (NCKX6, NCLX) whose physiological function remains unclear.
R-HSA-425986 Sodium/Proton exchangers The SLC9 gene family encode proteins (sodium/proton exchangers, NHE or NHX) which exchange sodium (influx) for protons (efflux) electroneutrally. This mechanism is important because many metabolic processes generate acids which need to be removed to maintain pH. This is the major proton extruding system in cells, driven by the inward sodium ion chemical gradient. To date, there are eleven NHE genes, NHE1-11. NHE1-5 exchange cations at the cell membrane. NHE6-9 exchange cations at endosomal membranes or the trans-golgi network membranes.
R-HSA-9824272 Somitogenesis Somites are bounded segments of mesenchyme that are periodically cleaved, or segmented, from the developing anterior paraxial mesoderm (Diaz-Cuadros et al. 2020). Somite formation is conceptualized using a clock and wavefront model (reviewed in Saga 2012). The clock is present in cells of the presomitic mesoderm and cycles between a permissive state in which segmentation can occur and a refractory state in which it cannot. The wavefront moves along the presomitic mesoderm and causes segmentation where and when it encounters cells in the permissive state, thus the size of the somites is determined by the periodicity of the clock and the migration speed of the wavefront.
The segmentation process is driven by WNY signaling, FGF signaling, and especially the Notch signaling (reviewed in Dunwoodie et al. 2009, Ferjentsik et al. 2009), Hubaud and Pourquie 2014). The intersection of posterior-anterior gradients of WNT and FGF signaling and an anterior-posterior gradient of retinoic acid signaling regulates the position of somite boundaries as perturbation of any of the gradients affects somite boundaries (reviewed in Gibb et al. 2010, Hubard and Pourquie et al. 2014). Thus WNT, FGF, and retinoic acid appear to form the wavefront, also called the determination front. Segmentation periodicity is controlled by HES7-mediated negative feedback loops in the Notch pathway, which constitute a molecular oscillator or segmentation clock (Bessho et al. 2003). Activation of LFNG expression by Notch and inhibition of Notch signaling by LFNG, possibly via regulation of the DLL3 ligand (Bochter et al. 2022), constitute another negative feedback loop that acts as a molecular oscillator (Dale et al. 2003, Falk et al. 2022). Clock oscillations are initiated in nascent presomitic mesoderm in the primitive streak of the gastrulating embryo (Falk et al. 2022) and posterior-to-anterior waves sweep to anterior paraxial mesoderm to regulate MESP2/RIPPLY2 expression to initiate segmentation. MESP2 activates expression of EPHA4 (Nakajima et al. 2006), an Eph receptor that participates in segment boundary formation. MESP2 also activates expression of RIPPLY2 (Morimoto et al. 2007), an inhibitor of TBX6 (Zhao et al. 2018). TBX6 is an activator of MESP2, therefore MESP2 indirectly inhibits its own expression via RIPPLY2.
Mutations in components of the segmentation clock, for example DLL3, MESP2, LFNG, and HES7, cause congenital vertebral defects in humans (Dunwoodie et al. 2009, Nóbrega et al. 2021).
R-HSA-9669936 Sorafenib-resistant KIT mutants Sorafenib is a type II tyrosine kinase inhibitor that is approved for use in hepatocellular and renal cell carcinoma. It is active against KIT receptors with mutations in the ATP-binding cleft and the activation loop, with the exception of substitutions at D816, which are resistant (Guida et al, 2007; Heinrich et al, 2012; Serrano et al, 2019; Weisberg et al, 2019; reviewed in Roskoski, 2018; Klug et al, 2012).
R-HSA-9674404 Sorafenib-resistant PDGFR mutants Sorafenib is a type II tyrosine kinase inhibitor that is approved for use in hepatocellular and renal cell carcinoma, and that is often used as a second-line treatment for imatinib-resistant tumors. Despite its initial efficacy, resistance to sorafenib often develops (reviewed in Molina-Ruiz et al, 2017).
R-HSA-9827857 Specification of primordial germ cells Primordial germ cells (PGCs), the progenitors of female gametes (oocytes) and male gametes (sperm), are specified and segregated from somatic cells early during mammalian development. In the mouse embryo, precursors of PGCs are present in the proximal epiblast adjacent to the extraembryonic ectoderm before gastrulation (E6.0, pre-streak stage) and PGCs, marked by high alkaline phosphatase activity (Ginsburg et al. 1990), are translocated to the extraembryonic mesoderm at the base of the developing allantois during gastrulation (Lawson and Hage 1994). Subsequently, PGCs are regionalised in the epithelium of the embryonic gut and migrate via the dorsal mesentery of the embryonic gut to the genital ridge. The post-migratory PGCs differentiate into oogonia and spermatogonia in the fetal gonad. In mouse embryos, PGCs are induced by Bmp4 emanating from extraembryonic ectoderm and Wnt3 from the visceral endoderm (reviewed in Bleckwehl and Rada Iglesias 2019). Less is known about the developmental origin of human PGCs and the sources of inducing signaling factors. In the non human primate (Cynomolgus monkey), PGCs are first observed in the amniotic epithelium of the amniotic sac of the pre-gastrulation embryo and remain in the early amnion for an extended period (6 days) (Sasaki et al. 2016). BMP4 is expressed in the amnion and WNT3A is expressed in the cytotrophoblast (Sasaki et al. 2016).
Ex vivo and in vitro studies have been performed to elucidate the specification of human PGCs (reviewed in Hancock et al. 2021). Putative PGCs, identified by immunofluorescence of PGC markers, are induced in ex vivo culture of early blastocysts (E6 days post fertilization, dpf) (Chen et al. 2019, Popovic et al. 2019) and in vitro differentiation of embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs) in the presence of BMP4 (Irie et al. 2015, Sasaki et al. 2015, Tang et al. 2015, Chen et al. 2017, Kojima et al. 2017). In both mouse embryos and cultured human cells, competence of the epiblast-like cells to form PGCs in response to BMP4 signals is transient during development, where, in the absence of BMP4, the epiblast-like cells acquire the mesendoderm cell fate (Tang et al. 2015).
For the induction of PGC-like cells from human pluripotent stem cells, the gene network activity that specifies human PGCs is different from that of mouse PGCs. Notably, SOX17, but not Prdm14, is a key factor for the specification of human PGCs. In human PGC precursors, Eomesodermin (EOMES) activates expression of SOX17, the most upstream factor in PGC specification. Similar molecular events are observed in the early PGCs isolated from human embryos and cynomolgus monkeys (Tyser et al. 2021). BMP4 signaling initiates the expression of TFAP2C and SOX17, that in turns initiates expression of PRDM1 (Tang et al. 2015, Kojima et al. 2017, Tang et al. 2022). Together these three key factors, SOX17, TFAP2C, and PRDM1, specify PGCs, activate the PGC program, and repress somatic cell programs, with SOX17 acting as an activator and PRDM1 as a repressor (Tang et al. 2015, Sasaki et al. 2015). Genes activated in PGCs include the pluripotency-related factors POU5F1 (OCT4) and NANOG (but not SOX2), the DNA demethylation factor TET2, and the regulators of cell migration PDPN and CXCR4 (Irie et al. 2015, Sasaki et al. 2015, Chen et al. 2018, Mishra et al. 2021, Tang et al. 2022). PRDM1 represses genes involved in DNA methylation leading to a genome wide DNA demethylation in human PGCs around week 10-11 of development (Guo et al. 2015). In mouse embryonal carcinoma cells, Prdm1 (Blimp1) binds and represses expression of the de novo DNA methylase Dnmt3b and Uhrf1, which interacts with the DNA methylase Dnmt1 (Magnusdottir et al. 2013). PRDM1 in human PGCs similarly represses expression of DNMT3B, DNMT1, and UHRF1 through yet uncharacterized mechanisms (Tang et al. 2015).
R-HSA-9834899 Specification of the neural plate border The neural plate border forms on the dorsal side of the embryo between the medial neural plate and the lateral epidermis. This region has intermediate BMP and FGF signaling, with WNT also playing a role in specification (reviewed in Patthey and Gunhaga 2011, Simoes-Costa and Bronner 2015, Thawani and Groves 2020). Within the neural plate border, FGF signaling appears to repress formation of epidermis while BMP appears to repress formation of neural cells (reviewed in Patthey and Gunhaga 2014). During neural plate border specification, the most anterior part is a WNT-free domain and the posterior part is exposed to WNT activity (reviewed in Patthey and Gunhaga 2011, Patthey and Gunhaga 2014).
As the neural plate folds to form the neural tube, the neural plate border contributes to the olfactory, lens, and hypophyseal placodes in the anterior region and the neural crest in the posterior region (reviewed in Singh and Groves 2016, Koontz et al. 2023). In addition, the otic placodes and cranial sensory placodes arise immediately lateral to the neural crest. The neural crest is a population of migratory cells located dorsal to the neural tube that is unique to vertebrates (reviewed in Cheung et al. 2019) and gives rise to several cell types, including neurons and glia of the peripheral nervous system, osteoblasts and chondrocytes of the craniofacial skeleton, adrenal medulla cells, and melanocytes (reviewed in Kalcheim and Kumar 2017). Placodes generate the olfactory epithelium, the lens of the eye, the inner ear, the endocrine adenohypophysis of the pituitary gland, and some neurons of the cranial sensory ganglia (reviewed in Alsina 2020).
The neural plate border is specified by a combination of transcription factors including GBX2, TFAP2A, MSX1, MSX2, ZIC1, ZIC3, DLX5/6, PAX3, and PAX7. These factors may also be expressed in additional, overlapping regions. For example ZIC1 is expressed in the neural plate border and more medially in the neural plate, where it is involved in neural induction. TFAP2A is expressed in the neural plate border and more laterally in the epidermis. Thus the neural plate border is defined by a combination of factors rather than by a single factor (reviewed in Prasad et al. 2019).
The order of expression of neural plate border specifiers is not completely characterized in humans. In human embryonic stem cells differentiated in vitro, GBX2 is expressed broadly in the posterior ectoderm, then TFAP2A, PAX3, PAX7, and MSX1 are expressed in a neural plate border state (Leung et al. 2016). The primacy of Gbx2 is also observed in Xenopus embryos (Li et al. 2009). These genes then cross-regulate each other's expression to create a self-reinforcing module.
R-HSA-1300642 Sperm Motility And Taxes A series of receptor signaling pathways potentially govern chemical communication between sperm and egg, chemotactically guiding incoming sperm towards the oocyte. Though several substances are confirmed as sperm chemoattractant, progesterone (P) seems to be the best chemoattractant candidate for human sperm. Ion channels control the sperm ability to fertilize the egg by regulating sperm maturation in the female reproductive tract and by triggering key sperm physiological responses required for successful fertilization such as hyperactivated motility, chemotaxis, and the acrosome reaction. CatSper, a pH regulated, calcium selective ion channel, potassium channel KSper (Slo3), and Hv1, the voltage gated proton channel are involved in regulation of sperm hyperactivated motility. While progesterone, secreted by ovulated cumulus oophorus, may act as a chemoattractant for sperm cells over the short distances, a major determinant of sperm guidance over long distances in the mammalian female reproductive tract is rheotaxis.
R-HSA-9845614 Sphingolipid catabolism The main steps involved in de novo sphingolipid synthesis are annotated here (Gault et al. 2010).
R-HSA-1660661 Sphingolipid de novo biosynthesis Glycosphingolipid biosynthesis is based on salvage of sphingolipids and de novo sphingolipid synthesis. Sphingoid-1-phosphate signalling molecules are synthesized through the same pathway, which starts with the transfer of a fatty acid onto serine. The diversity of products results from later dehydrogenation or hydroxylation of fatty acid moieties, as well as the usage of fatty acids of different lengths. Biosynthesis takes place in the endoplasmic reticulum lumen and the cytosol. Lipophilic products are transported to other membranes via a specialized transporter (CERT1) or the secretory pathway. Soluble sphingoid-1-phosphates are exported by multiple transporters in the plasma membrane (reviewed by Merrill 2002, Gault et al. 2010).
R-HSA-428157 Sphingolipid metabolism Sphingolipids are derivatives of long chain sphingoid bases such as sphingosine (trans-1,3-dihydroxy 2-amino-4-octadecene), an 18-carbon unsaturated amino alcohol which is the most abundant sphingoid base in mammals. Amide linkage of a fatty acid to sphingosine yields ceramides. Esterification of phosphocholine to ceramides yields sphingomyelin, and ceramide glycosylation yields glycosylceramides. Introduction of sialic acid residues yields gangliosides. These molecules appear to be essential components of cell membranes, and intermediates in the pathways of sphingolipid synthesis and breakdown modulate processes including apoptosis and T cell trafficking.
While sphingolipids are abundant in a wide variety of foodstuffs, these dietary molecules are mostly degraded by the intestinal flora and intestinal enzymes. The body primarily depends on de novo synthesis for its sphingolipid supply (Hannun and Obeid 2008; Merrill 2002). De novo synthesis proceeds in four steps: the condensation of palmitoyl-CoA and serine to form 3-ketosphinganine, the reduction of 3-ketosphinganine to sphinganine, the acylation of sphinganine with a long-chain fatty acyl CoA to form dihydroceramide, and the desaturation of dihydroceramide to form ceramide.
Other sphingolipids involved in signaling are derived from ceramide and its biosynthetic intermediates. These include sphinganine (dihydrosphingosine) 1-phosphate, phytoceramide, sphingosine, and sphingosine 1-phosphate.
Sphingomyelin is synthesized in a single step in the membrane of the Golgi apparatus from ceramides generated in the endoplasmic reticulum (ER) membrane and transferred to the Golgi by CERT (ceramide transfer protein), an isoform of COL4A3BP that is associated with the ER membrane as a complex with PPM1L (protein phosphatase 1-like) and VAPA or VAPB (VAMP-associated proteins A or B). Sphingomyelin synthesis appears to be regulated primarily at the level of this transport process through the reversible phosphorylation of CERT (Saito et al. 2008).
R-HSA-1295596 Spry regulation of FGF signaling Sprouty was initially characterized as a negative regulator of FGFR signaling in Drosophila. Human cells contain four genes encoding Sprouty proteins, of which Spry2 is the best studied and most widely expressed. Spry proteins modulate the duration and extent of signaling through the MAPK cascade after FGF stimulation, although the mechanism appears to depend on the particular biological context. Some studies have suggested that Sprouty binds to GRB2 and interferes with the recruitment of GRB2-SOS1 to the receptor, while others have shown that Sprouty interferes with the MAPK cascade at the level of RAF activation. In addition to modulating the MAPK pathway in response to FGF stimulation, Sprouty itself appears to be subject to complex post-translational modification that regulates its activity and stability.
R-HSA-69541 Stabilization of p53 Later studies pin-pointed that a single serine (Ser-15) was phosphorylated by ATM and phosphorylation of Ser-15 was rapidly-induced in IR-treated cells and this response was ATM-dependent (Canman et al, 1998; Banin et al, 1998 and Khanna et al, 1998). ATM also regulates the phosphorylation of p53 at other sites, especially Ser-20, by activating other serine/threonine kinases in response to IR (Chehab et al, 2000; Shieh et al, 2000; Hirao et al 2000). Phosphorylation of p53 at Ser-20 interferes with p53-MDM2 interaction. MDM2 is transcriptionally activated by p53 and is a negative regulator of p53 that targets it for degradation (Haupt et al, 1997; Kubbutat et al, 1997). In addition modification of MDM2 by ATM also affects p53 stabilization (Maya et al, 2001).
R-HSA-211994 Sterols are 12-hydroxylated by CYP8B1 Cytochrome P450 8B1 (CYP8B1, sterol 12-alpha- hydroxylase) has a broad substrate specificity including a number of 7-alpha- hydroxylated C27 steroids. It is also involved in bile acid synthesis and is responsible for the balance between the formation of cholic acid and chenodeoxycholic acid (Gafvels et al. 1999).
R-HSA-211736 Stimulation of the cell death response by PAK-2p34 In response to stress signals, the p21-activated protein kinase PAK-2 stimulates a cell death response characterized by increased cell rounding and apoptotic chromatin condensation (see Jakobi et al., 2003). PAK-2 is proteolytically cleaved by caspase-3 producing a constitutively active fragment, PAK-2p34. Following cleavage, PAK-2p34 is autophosphorylated at Thr 402 and transported to the nucleus where it accumulates due to the loss of its nuclear export signal motif (Jakobi et al., 2003). The activity of PAK-2p34 appears to be regulated both by proteosomal degradation (Jakobi et al., 2003) and by association with the GTPase-activating protein PS-GAP/ RHG-10. This interaction inhibits the kinase activity of PAK-2p34 and changes the localization of PAK-2p34 from the nucleus to the perinuclear region (Koeppel et al., 2004). PAK-2p34 may function in the down-regulation of translation initiation in apoptosis through phosphorylation of Mnk1 (Orton et al.,2004).
R-HSA-2672351 Stimuli-sensing channels Ion channels that mediate sensations such as pain, warmth, cold, taste pressure and vision. Channels that mediate these sensations include acid-sensing ion channels (ASICs) (Wang & Xu 2011, Qadri et al. 2012, Deval et al. 2010) and the transient receptor potential channels (TRPCs) (Takahashi et al. 2012, Numata et al. 2011 in "TRP Channels" Zhu, MX editor, CRC Press, 2011, Ramsey et al. 2006, Montell 2005). Many channels are sensitive to changes in calcium (Ca2+) levels, both inside and outside the cell. Examples are protein tweety homologs 2 and 3 (TTYH2, 3) (Suzuki 2006), bestrophins 1-4 (BEST1-4) (Sun et al. 2002, Tsunenari et al. 2003, Kunzelmann et al. 2009, Hartzell et al. 2008) and ryanodine receptor tetramers (RYRs) (Beard et al. 2009).
R-HSA-390522 Striated Muscle Contraction Striated muscle contraction is a process whereby force is generated within striated muscle tissue, resulting in a change in muscle geometry, or in short, increased force being exerted on the tendons. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Striated muscle is a type of muscle composed of myofibrils, containing repeating units called sarcomeres, in which the contractile myofibrils are arranged in parallel to the axis of the cell, resulting in transverse or oblique striations observable at the level of the light microscope.
Here striated muscle contraction is represented on the basis of calcium binding to the troponin complex, which exposes the active sites of actin. Once the active sites of actin are exposed, the myosin complex bound to ADP can bind actin and the myosin head can pivot, pulling the thin actin and thick myosin filaments past one another. Once the myosin head pivots, ADP is ejected, a fresh ATP can be bound and the energy from the hydrolysis of ATP to ADP is channeled into kinetic energy by resetting the myosin head. With repeated rounds of this cycle the sarcomere containing the thin and thick filaments effectively shortens, forming the basis of muscle contraction.
R-HSA-1614517 Sulfide oxidation to sulfate While the human body is very economical with sulfur amino acids (SAA), superfluous SAA are degraded via cysteine to toxic hydrogen sulfide which must be dealt with. The pathway to oxidize this gas is localized to mitochondria and is highly conserved, pointing back to a time when life was immersed in sulfide-rich waters.
The pathway for sulfide oxidation consists of five reactions, one of which, the sulfur transfer from thiosulfate to glutathione, is still to be characterized fully. A mutation in one enzyme has been identified that is associated with ethylmalonyl encephalopathy and where tissue sulfide is elevated (Stipanuk & Ueki 2011).
R-HSA-1614635 Sulfur amino acid metabolism The main sulfur amino acids are methionine, cysteine, homocysteine and taurine. Of these, the first two are proteinogenic.
This group of reactions contains all processes that 1) break down sulfur amino acids, 2) interconvert between them, and 3) synthesize them from solved sulfide which comes from sulfate assimilation and reduction. Only plants and microorganisms employ all processes. Humans cannot de novo synthesize any sulfur amino acid, nor convert cysteine to methionine (Brosnan & Brosnan, 2006).
R-HSA-9669934 Sunitinib-resistant KIT mutants Sunitinib is a class II tyrosine kinase inhibitor that is often used as a second line treatment in KIT-mutated cancers that develop resistance to imatinib (Heinrich et al, 2008; Serrano et al, 2017; reviewed in Roskoski, 2018; Corless et al, 2011).
R-HSA-9674401 Sunitinib-resistant PDGFR mutants Sunitinib is a class II TKI that is often used as a second-line treatment in PDGFR- and KIT-driven cancers that develop resistance to imatinib (reviewed in Corless et al, 2011; Klug et al, 2018). Sunintib is approved for the treatment of renal cell carcinoma, GIST and pancreatic tumors. A number of PDGFR mutations exhibit resistance to inhibition by sunitinib (Roskoski, 2007; reviewed in Roskoski, 2018; Klug et al, 2018).
R-HSA-9635465 Suppression of apoptosis In order to survive and grow within the phagocyte, Mtb has to inhibit programmed cell death. Several proteins are secreted by Mtb that block different pathways leading to complete arrest of apoptosis (Moraco & Kornfeld 2014).
R-HSA-9636569 Suppression of autophagy Autophagy, a distinct pathway of programmed cell death, is used by the phagocyte primarily to eradicate damaged cell organelles or unused proteins. As Mtb damages the phagosomal membrane it has to block autophagy processes to ensure maximum replication before exit from the cell (Jo 2013).
R-HSA-9637687 Suppression of phagosomal maturation The fate of phagosomes is usually directed by factors in the host phagocyte and involves flooding itself with superoxide, nitric oxide, and protons. Acidification is the prerequisite for later fusion with a lysosome. Mycobacterium tuberculosis (Mtb) releases substances that inhibit all of these processes, effectively arresting the phagosome in the present state and creating a protected niche for Mtb multiplication (Russell 2011, Stutz et al. 2018).
R-HSA-5683826 Surfactant metabolism The alveolar region of the lung creates an extensive epithelial surface that mediates the transfer of oxygen and carbon dioxide required for respiration after birth. Type I epithelial cells form the alveolar surface and mediate gaseous exchange. Type II epithelial cells secrete pulmonary surfactant, a lipoprotein complex that forms a thin interfacial film, lowering surface tension at the air-liquid interface in alveoli and maintaining the structural integrity of alveoli, preventing their collapse at low volumes (Agassandian & Mallampalli 2013). Surfactant production is increased prior to birth, in preparation for air breathing at birth (Hallman 2013). Pre-term infants, where type II epithelial cells are not fully differentiated yet, can produce insufficient surfactant and result in respiratory distress syndrome. Surfactant is composed primarily of phospholipids enriched in phosphatidylcholine (PC) and phosphatidylglycerol (PG) (Agassandian & Mallampalli 2013) and the pulmonary collectins, termed surfactant proteins A, B, C and D (SFTPA-D). They influence surfactant homeostasis, contributing to the physical structures of lipids in the alveoli and to the regulation of surfactant function and metabolism. They are directly secreted from alveolar type II cells into the airway to function as part of the surfactant. SFTPA and D are large, hydrophilic proteins while SFTPB and C are small, very hydrophobic proteins (Johansson et al. 1994). In addition to their surfactant functions, SFTPA and D play important roles in innate host defense by binding and clearing invading microbes from the lung (Kingma & Whitsett 2006). Nuclear regulation, transport, metabolism, reutilisation and degradation of surfactant are described here (Ikegami 2006, Boggaram 2009, Whitsett et al. 2010). Mutations in genes involved in these processes can result in respiratory distress syndrome, lung proteinosis, interstitial lung diseases and chronic lung diseases (Perez-Gil & Weaver 2010, Whitsett et al. 2010, Akella & Deshpande 2013, Jo 2014).
R-HSA-69052 Switching of origins to a post-replicative state Switching of origins to a post-replicative state involves the removal of Orc1 from chromatin, CDK-mediated phosphorylation and removal of Cdc6, and the rearrangement and mobilization of Mcm2-7.
R-HSA-8849932 Synaptic adhesion-like molecules Recruitment of receptors and ion channels to the postsynaptic membrane is the last step in synapse formation. Many of these proteins interact directly or indirectly with postsynaptic density-95 (PSD95)/Discs large/zona occludens-1 (PDZ) proteins, thus linking them to the postsynaptic scaffold and providing a mechanism for both retaining the protein at the synapse and keeping its proximity to signaling molecules known to associate with PDZ proteins (Wang et al. 2006, Morimura et al. 2006, Ko et al. 2006, Nourry et al. 2003, Kim & Sheng 2004, Montgomery et al. 2004, Sheng and Kim 2011). The synaptic adhesion-like molecules (SALM) family belongs to the superfamily of leucine-rich repeat (LRR)-containing adhesion molecules, alternatively referred to as LRFN (leucine-rich repeat and fibronectin III domain-containing) is synapse adhesion molecule linked to NMDA and AMPA receptors. It includes five known members (SALMs 1-5 or LRFN1-5), which have been implicated in the regulation of neurite outgrowth and branching, and synapse formation and maturation. SALM proteins are distributed to both dendrites and axons in neurons (Ko et al. 2006, Wang et al. 2006, Sebold et al. 2012). The family members, SALM1-SALM5, have a single transmembrane (TM) domain and contain extracellular leucine-rich repeats, an Ig C2 type domain, a fibronectin type III domain, and an intracellular postsynaptic density-95 (PSD-95)/Discs large/zona occludens-1 (PDZ) binding domain, which is present on all members except SALM4 and SALM5 (Ko et al. 2006, Wang et al.2006, Morimura et al. 2006).
R-HSA-3000170 Syndecan interactions Syndecans are type I transmembrane proteins, with an N-terminal ectodomain that contains several consensus sequences for glycosaminoglycan (GAG) attachment and a short C-terminal cytoplasmic domain. Syndecan-1 and -3 GAG attachment sites occur in two distinct clusters, one near the N-terminus and the other near the membrane-attachment site, separated by a proline and threonine-rich 'spacer'. Syndecan ectodomain sequences are poorly conserved in the family and between species, but the transmembrane and cytoplasmic domains are highly conserved. Syndecan-1 and -3 form a subfamily. Syndecan core proteins form dimers (Choi et al. 2007) and at least syndecan-3 and -4 form oligomers (Asundi & Carey 1995, Shin et al. 2012). Syndecan-1 is the major syndecan of epithelial cells including vascular endothelium. Syndecan-2 is present mostly in mesenchymal, neuronal and smooth muscle cells. Syndecan-3 is the major syndecan of the nervous system, while syndecan-4 is ubiquitously expressed but at lower levels than the other syndecans (refs in Alexopoulou et al. 2007). The core syndecan protein has three to five heparan sulfate or chondroitin sulfate chains, which interact with a variety of ligands including fibroblast growth factors, vascular endothelial growth factor, transforming growth factor-beta, fibronectin, collagen, vitronectin and several integrins. Syndecans may act as integrin coreceptors. Interactions between fibronectin and syndecans are modulated by tenascin-C. Syndecans bind a wide variety of soluble and insoluble ligands, inckluding extracellular matrix components, cell adhesion molecules, growth factors, cytokines, and proteinases. As the cleaved ectodomains of syndecans retain the ability to bind ligands, ectodomain shedding is a mechanism for releasing soluble effectors that may compete for ligands with their cell-bound counterparts (Kainulainen et al. 1998). Shed ectodomains are found in inflammatory fluids (Subramanian et al. 1997) and may induce the proliferation of cancer cells (Maeda et al. 2004).
R-HSA-174495 Synthesis And Processing Of GAG, GAGPOL Polyproteins Evidence suggests that the RNA molecules used for the synthesis of Gag and Gag-Pro-Pol are not the same molecules that are packaged into virions. Gag proteins do not appear to aggregate around and capture the RNA contained in the polyribosome from which they emerged, but rather bind to and ultimately encapsidate free transcripts elsewhere. During the replication of retroviruses, large numbers of Gag molecules must be generated to serve as precursors to the structural proteins of the virions. Retroviruses have developed a mechanism that permits expression of the Gag protein at high levels relative to the protein sequences encoded in the pro and pol genes, while retaining coregulated expression. This linkage results from the use of the same initiation codon in the same mRNA to express the gag, pro, and pol genes. Translation of this RNA leads occasionally to synthesis of a fusion protein that is usually called the Gag-Pol precursor but is now more appropriately called the Gag-Pro-Pol precursor
R-HSA-171286 Synthesis and processing of ENV and VPU The two viral membrane proteins, Env and the accessory protein Vpu, which are encoded by the same mRNA, are translated on the rough ER. All virion components need to traffic from their point of synthesis to sites of assembly on the plasma membrane. Env is an integral membrane protein. It is inserted cotranslationally into ER membranes and then travels through the cellular secretory pathway where it is glycosylated, assembled into trimeric complexes, processed into the gp41 and gp120 subunits by the cellular protease furin.
R-HSA-2142816 Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) Similar to the lipoxygenases, cytochrome P450 (CYP) enzymes catalyse the hydroxylation and epoxygenation of arachidonate. However, whereas lipoxygenases use an active non-heme iron to abstract hydrogen directly from arachidonate, CYPs contain a heme-iron active site that oxidizes its substrate by a different mechanism. They hydroxylate arachidonate between C-5 and C-15 to produce lipoxygenase-like hydroxyeicosatetraenoates (HETEs) and add a hydroxyl moiety to the sp3-hybridized omega-carbons to form a unique class of HETEs. The transfer of oxygen to the unstable arachidonate intermediate terminates the reaction by forming HETE or epoxy-eicosatrienoate (EETs), respectively (Capdevila et al. 2000, Buczynski et al. 2009, Vance & Vance 2008).
R-HSA-2142712 Synthesis of 12-eicosatetraenoic acid derivatives The 12-eicosatetraenoic acids: 12-hydroperoxy-eicosatetraenoate (12-HpETE), 12-hydroxyeicosatetraenoate (12-HETE) and 12-oxo-eicosatetraenoate (12-oxoETE) are formed after the initial step of arachidonate oxidation by the arachidonate 12 and 15 lipoxygenases (ALOX12, ALOX12B and ALOX15 respectively). This part of the pathway is bifurcated at the level of 12S-hydroperoxy-eicosatetraenoate (12S-HpETE), which can either be reduced to 12S-hydro-eicosatetraenoate (12S-HETE) or converted to hepoxilins (Buczynski et al. 2009, Vance & Vance 2008).
R-HSA-2142770 Synthesis of 15-eicosatetraenoic acid derivatives The 15-eicosatetraenoates: 15-hydroperoxy-eicosatetraenoate (15-HpETE), 15-hydroxyeicosatetraenoate (15-HETE) and 15-oxo-eicosatetraenoate (15-oxoETE) are formed after the initial step of arachidonate oxidation by the arachidonate 15-lipoxygenases (ALOX15 and ALOX15B) (Buczynski et al. 2009, Vance & Vance 2008).
R-HSA-2142688 Synthesis of 5-eicosatetraenoic acids 5-hydroperoxy-eicosatetraenoic acid (5-HpETE), 5-hydroxyeicosatetraenoic acid (5S-HETE) and 5-oxo-eicosatetraenoic acid (5-oxoETE) are formed after the initial step of Arachidonate oxidation by arachidonate 5-lipoxygenase (ALOX5) (Buczynski et al. 2009, Vance & Vance 2008).
R-HSA-1483171 Synthesis of BMP Lysobisphosphatidic acid, also known as bis(monoacylglycerol) hydrogen phosphate (BMP), is enriched in late endosomes and not found in the endoplasmic reticulum (ER) or mitochondria where phosphatidylglycerol (PG) is synthesized. Late endosomes form membrane contact sites with the ER, providing a means for PG to enter the late endosome and be converted to BMP via hydrolysis by a phospholipase A2, followed by acylation, and a reorientation of the phosphoryl ester (Poorthuis & Hostetler 1978, Heravi & Waite 1999, Hullin-Matsuda et al. 2007, Gallala & Sandhoff 2010).
R-HSA-1483076 Synthesis of CL Cardiolipin(CL) is synthesized in the inner mitochondrial membrane, when phosphatidylglycerol (PG) and cytidine diphosphate-diacylglycerol (CDP-DAG) are converted into CL. In addition to be synthesized in mitochondria, CDP-DAG may also be imported from ER to serve as the cardiolipin precursor pool. PGP (phosphatidylglycerol phosphate) catalyzes rate limiting step of cardiolipin biosynthesis.
R-HSA-69239 Synthesis of DNA The actual synthesis of DNA occurs in the S phase of the cell cycle. This includes the initiation of DNA replication, when the first nucleotide of the new strand is laid down during the synthesis of the primer. The DNA replication preinitiation events begin in late M or early G1 phase.
R-HSA-446199 Synthesis of Dolichyl-phosphate Dolichol is a polyisoprenol lipid comprised of five-carbon isoprene units linked linearly in a head-to-tail fashion. Almost all eukaryotic membranes contain dolichol and its phosphorylated form is used in the N-glycosylation of proteins where it is used as an anchor for the N-glycan sugar to the ER membrane, and as an initiation point for the synthesis. Dolichol biosynthesis occurs on the cytoplasmic face of the ER membrane, which is where N-glycosylation occurs too, so is perfectly placed to serve as a substrate for this process. Dolichyl phosphate can be obtained either from direct phosphorylation of dolichol, formed in a series of reactions from mevalonate 5-pyrophosphate, or a salvage reaction by de-phosphorylation of dolichyl diphosphate, released at the end of N-glycan biosynthesis (Cantagrel & Lefeber 2011).
R-HSA-446205 Synthesis of GDP-mannose GDP-mannose is the mannose donor for the first 5 mannose addition reactions in the N-glycan precursor synthesis, and also for the synthesis of Dolichyl-phosphate-mannose involved in other mannose transfer reactions. It is synthesized from fructose 6-phosphate and GTP in three steps.
R-HSA-2142696 Synthesis of Hepoxilins (HX) and Trioxilins (TrX) Hepoxilins are biologically relevant signalling molecules produced by certain arachidonate 12-lipoxygenase (ALOX12s). Hepoxilin A3 (HXA3) and B3 (HXB3) have been identified, both of which incorporate an epoxide across the C-11 and C-12 double bond, as well as an additional hydroxyl moiety. HXA3 has a C-8 hydroxyl, whereas the HXB3 hydroxyl occurs at C-10. The epoxy moiety is labile and can be hydrolyzed either by a hepoxilin specific epoxide hydrolase (HXEH) or in acidic aqueous solution to form the corresponding diol metabolites trioxilin A3 (TrXA3) and B3 (TrXB3) (Buczynski et al. 2009, Vance & Vance 2008).
R-HSA-1855183 Synthesis of IP2, IP, and Ins in the cytosol Inositol phosphates IP2, IP and the six-carbon cyclic alcohol inositol (Ins) are produced by various phosphatases and the inositol-3-phosphate synthase 1 (ISYNA1) (Ju et al. 2004, Ohnishi et al. 2007, Irvine & Schell 2001, Bunney & Katan 2010).
R-HSA-1855204 Synthesis of IP3 and IP4 in the cytosol An array of inositol trisphosphate (IP3) and tetrakisphosphate (IP4) molecules are synthesised by the action of various kinases and phosphatases in the cytosol (Irvine & Schell 2001, Bunney & Katan 2010).
R-HSA-1855231 Synthesis of IPs in the ER lumen In the endoplasmic reticulum (ER) lumen, inositol phosphates IP4, IP5, and IP6 are dephosphorylated by multiple inositol polyphosphate phosphatase 1 (MINPP1) (Caffrey et al. 1999, Chi et al. 1999, Deleu et al. 2006, Nogimori et al. 1991).
R-HSA-1855191 Synthesis of IPs in the nucleus Within the nucleus, inositol polyphosphate multikinase (IPMK), inositol-pentakisphosphate 2-kinase (IPPK), inositol hexakisphosphate kinase 1 (IP6K1) and 2 (IP6K2) produce IP5, IP6, IP7, and IP8 inositol phosphate molecules (Irvine & Schell 2001, Alcazar-Romain & Wente 2008, York 2006, Monserrate and York 2010, Nalaskowski et al. 2002, Chang et al. 2002, Chang & Majerus 2006, Saiardi et al. 2001, Saiardi et al. 2000, Draskovic et al. 2008, Mulugu et al. 2007).
R-HSA-77111 Synthesis of Ketone Bodies In a healthy, well-nourished individual, the production of ketone bodies occurs at a relatively low rate. During periods of normal physiological responses to carbohydrate shortages, the liver increases the production of ketone bodies from acetyl-CoA generated from fatty acid oxidation. This allows heart and skeletal muscle to use ketone bodies as the primary source of energy, thereby preserving the limited glucose supply for use in brain tissue.
In untreated diabetes mellitus, a huge buildup of ketone bodies occurs due to an increase in fatty acid oxidation. The production of ketone bodies exceeds the ability of peripheral tissues to oxidize them, and results in lowering the pH of blood. Blood acidification is dangerous, chiefly as it impairs the ability of hemoglobin to bind oxygen.
Ketone body synthesis proceeds via the synthesis of ccetoacetic acid in three steps from acetyl CoA, followed by the reduction of acetoacetic acid to beta-hydroxybutyrate. In the body, these reactions occur in the mitochondria of liver cells (Sass 2011).
R-HSA-2142691 Synthesis of Leukotrienes (LT) and Eoxins (EX) Leukotrienes (LTs) are biologically active molecules formed in response to inflammatory stimuli. They cause contraction of bronchial smooth muscles, stimulation of vascular permeability, and attraction and activation of leukocytes. LTs were discovered in 1938 and were termed the "slow release substance" (SRS) until their structures were determined in 1979 and they were then renamed to leukotrienes. LTs are derived from arachidonate through action by arachidonate 5-lipoxygenase (ALOX5). Cysteinyl leukotrienes (LTC4, LTD4, and LTE4) are generated as products derived from leukotriene A4 (LTA4). Eoxins are generated from leukotrienes (LTs) and resemble cysteinyl leukotrienes but have a different three-dimensional structure (Murphy & Gijon 2007, Hammarstrom 1983, MA.Claesson 2009, Vance & Vance 2008, Buczynski et al. 2009).
R-HSA-1483166 Synthesis of PA In the de novo synthesis of phosphatidic acid (PA), lysophosphatidic acid (LPA) is initially formed by the esterification of sn-1 by glycerol 3-phosphate acyltransferase (GPAT) from glycerol 3-phosphate (G3P). Next, LPA is converted to PA by a LPA acyltransferase (AGPAT, also known as LPAAT). In addition to this, PA is also formed when phosphatidylcholine (PC) is hydrolyzed by phospholipases D1 and D2 (PLD1 and 2). PA is involved in acyl chain remodeling via cleavage by phospholipases followed by reacylation by acyltransferases (Ghomashchi et al. 2010, Singer et al. 2002, Prasad et al. 2011, Shindou & Shimizu 2009, Cao et al. 2006).
R-HSA-1483191 Synthesis of PC De novo (Kennedy pathway) synthesis of phosphatidylcholine (PC) involves phosphorylation of choline (Cho) to phosphocholine (PCho) followed by condensing with cytidine triphosphate (CTP) to form CDP-choline (CDP-Cho). Diacylglycerol (DAG) and CDP-ETA together then form PC. Alternatively, PC is formed when phosphatidylethanolamine (PE) is methylated by phosphatidylethanolamine N-methyltransferase (PEMT) (Henneberry et al. 2002; Wright & McMaster 2002).
R-HSA-1483213 Synthesis of PE De novo (Kennedy pathway) synthesis of phosphatidylethanolamine (PE) involves phosphorylation of ethanolamine (ETA) to phosphoethanolamine (PETA) followed by condensing with cytidine triphosphate (CTP) to form CDP-ethanolamine (CDP-ETA). Diacylglycerol (DAG) and CDP-ETA together then form PE. Alternatively, PE is formed when phosphatidylserine (PS) is decarboxylated by phosphatidylserine decarboxylase proenzyme (PISD) (Henneberry et al. 2002, Vance 1991, Vance 1990).
R-HSA-1483148 Synthesis of PG Phosphatidylglycerol (PG) is synthesised at the inner mitochondrial (IM) membrane, phosphatidic acid (PA) and cytidine triphosphate (CTP) are converted into cytidine diphosphate-diacylglycerol (CDP-DAG), which in turn is converted with glycerol-3-phosphate (G3P) into phosphatidylglycerophosphate (PGP) and cytidine monophosphate (CMP). Finally, PGP is dephosphorylated to PG. In addition, PG can be synthesised at the endoplamic reticulum (ER) membrane when phospholipase D transphosphatidylates phosphatidylcholine (PC) with glycerol to displace choline (Cho) and form PG (Piazza & Marmer 2007, Stuhne-Sekalec et al. 1986, Lykidis et al. 1997, Cao & Hatch 1994).
R-HSA-1483226 Synthesis of PI Phosphatidylinositol (PI) is synthesized when phosphatidic acid (PA) and cytidine triphosphate (CTP) are converted into cytidine diphosphate-diacylglycerol (CDP-DAG) followed by conversion into PI and cytidine monophosphate (CMP) (Stuhne-Sekalec et al 1986, Lykidis et al. 1997).
R-HSA-1483248 Synthesis of PIPs at the ER membrane At the endoplasmic reticulum (ER) membrane, phosphatidylinositol (PI) and phosphatidylinositol 4-phosphate (PI4P) are interconverted (Wong et al. 1997, Gehrmann et al. 1999, Wei et al. 2002, Rohde et al. 2003).
R-HSA-1660514 Synthesis of PIPs at the Golgi membrane At the Golgi membrane, phosphatidylinositol 4-phosphate (PI4P) is primarily generated from phosphorylation of phosphatidylinositol (PI). Other phosphoinositides are also generated by the action of various kinases and phosphatases such as: phosphatidylinositol 3-phosphate (PI3P), phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2), phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) (Godi et al. 1999, Minogue et al. 2001, Rohde et al. 2003, Sbrissa et al. 2007, Sbrissa et al. 2008, Domin et al. 2000, Arcaro et al. 2000).
R-HSA-1660516 Synthesis of PIPs at the early endosome membrane At the early endosome membrane, phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) is generated in two steps from phosphatidylinositol 3,4-bisphosphate PI(3,4)P2 by the action of various kinases and phosphatases (Sbrissa et al. 2007, Sbrissa et al. 2008, Cao et al. 2007, Cao et al. 2008, Arcaro et al. 2000, Kim et al. 2002).
R-HSA-1660517 Synthesis of PIPs at the late endosome membrane At the late endosome membrane, the primary event is the dephosphorylation of the phosphoinositide phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) to phosphatidylinositol 3-phosphate (PI3P) and phosphatidylinositol 5-phosphate (PI5P) (Sbrissa et al. 2007, Sbrissa et al. 2008, Cao et al. 2007, Cao et al. 2008, Arcaro et al. 2000, Kim et al. 2002).
R-HSA-1660499 Synthesis of PIPs at the plasma membrane At the plasma membrane, subsequent phosphorylation of phosphatidylinositol 4-phosphate (PI4P) produces phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) and phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3) while the actions of various other kinases and phosphatases produces phosphatidylinositol 3-phosphate (PI3P), phosphatidylinositol 5-phosphate (PI5P), phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2), and phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) (Zhang et al. 1997, Gurung et al. 2003, Guo et al. 1999, Vanhaesebroeck et al. 1997, Tolias et al. 1998, Schaletzky et al. 2003, Kim et al. 2002, Clarke et al. 2010). Many of the phosphatidylinositol phosphatases that act at the plasma membrane belong to the myotubularin family. Enzymatically inactive myotubularin family members can heterodimerize with catalytically active mytotubularins to regulate their stability, activity and/or substrate specificity (Berger et al. 2006, Zou et al. 2012).
R-HSA-8847453 Synthesis of PIPs in the nucleus Under conditions of cellular stress, nuclear levels of phosphatidylinositol-5-phosphate (PI5P) increase. Type I phosphatidylinositol 4,5-bisphosphate 4-phosphatase TMEM55B translocates to the nucleus under stress via an unknown mechanism (Zou et al. 2007) and generates PI5P from the PI(4,5)P2 substrate. The level of PI5P in the nucleus is kept low because of the phosphatidylinositol-5-phosphate 4-kinase activity of nuclear PIP4K2 dimers, mainly dimers containing PIP4K2B (Ciruela et al. 2000). Under conditions of cellular stress, nuclear PIP4K2B is phosphorylated and inactivated by p38 MAP family kinases (Jones et al. 2006).
R-HSA-1483101 Synthesis of PS Phosphatidylserine (PS) is synthesized by facilitating the exchange of L-Serine (L-Ser) with the choline (Cho) head group in phosphatidylcholine (PC) and with the ethanolamine (ETA) head group in phosphatidylethanolamine (PE) (Saito et al. 1998, Tomohiro et al. 2009).
R-HSA-2162123 Synthesis of Prostaglandins (PG) and Thromboxanes (TX) The bioactive prostaglandin (PG) signalling molecules, including PGA2, PGE2, PGF2a, and PGI2 (prostacyclin) are synthesised from arachidonate and its products by various prostaglandin synthase type enzymes. Prostaglandin H2 (PGH2) is the starting point for the synthesis of Thromboxanes (TXs) (Buczynski et al. 2009, Vance & Vance 2008). PGs and TXs are collectively known as the prostanoids.
Two enzymes, PTGS1 and 2 (COX1 and 2) both catalyze the two-step conversion of arachidonate to PGH2. PTGS1 is constitutively expressed in many cell types while PTGS2 is induced in response to stress and mediates the syntheses of prostaglandins associated with pain, fever, and inflammation. Aspirin irreversibly inactivates both enzymes (though it acts more efficiently on PTGS1), explaining both its antiinflammatory effects and side effects like perturbed gastic acid secretion. Drugs like celecoxib, by specifically inhibiting PTGS2, have a strong anti-inflammatory effect with fewer side effects. These PTGS2-specific drugs, however, probably because of their effects on the balance of prostaglandin synthesis in platelets and endothelial cells, can also promote blood clot formation (Buczynski et al. 2009; Stables & Gilroy 2011).
R-HSA-446210 Synthesis of UDP-N-acetyl-glucosamine UDP-acetylglucosamine acts as a donor for the first two steps of the N-glycan precursor biosynthesis pathway, and is later used as a substrate for further modifications after the precursor has been attached to the protein. It is synthesized from fructose 6-phosphate, glutamine, acetyl-CoA, and UTP in four steps.
R-HSA-8866652 Synthesis of active ubiquitin: roles of E1 and E2 enzymes Ubiquitin monomers are processed from larger precursors and then activated by formation of a thiol ester bond between ubiquitin and a cysteine residue of an E1 activating enzyme (UBA1 or UBA6, Jin et al. 2007). The ubiquitin is then transferred to the active site cysteine residue of an E2 conjugating enzyme (reviewed in van Wijk and Timmers 2010, Kleiger and Mayor 2014, Stewart et al. 2016). Precursor proteins containing multiple ubiquitin monomers (polyubiquitins) are produced from the UBB and UBC genes. Precursors containing a single ubiquitin fused to a ribosomal protein are produced from the UBA52 and RPS27A genes. The proteases OTULIN and USP5 are very active in polyubiquitin processing, whereas the proteases UCHL3, USP7, and USP9X cleave the ubiquitin-ribosomal protein precursors yielding ubiquitin monomers (Grou et al. 2015). Other enzymes may also process ubiquitin precursors. A resultant ubiquitin monomer is activated by adenylation of its C-terminal glycine followed by conjugation of the C-terminus to a cysteine residue of the E1 enzymes UBA1 or UBA6 via a thiol ester bond (Jin et al. 2007, inferred from rabbit homologues in Haas et al. 1982, Hershko et al. 1983). The ubiquitin is then transferred from the E1 enzyme to a cysteine residue of one of several E2 enzymes (reviewed in van Wijk and Timmers 2010, Stewart et al. 2016).
R-HSA-192105 Synthesis of bile acids and bile salts In a healthy adult human, about 500 mg of cholesterol is converted to bile salts daily (Russell 2003). The major pathway for bile salt synthesis in the liver begins with the conversion of cholesterol to 7alpha-hydroxycholesterol. Bile salt synthesis can also begin with the synthesis of an oxysterol - 24-hydroxycholesterol or 27-hydroxycholesterol. In the body, the initial steps of these two pathways occur in extrahepatic tissues, generating intermediates that are transported to the liver and converted to bile salts via the 7alpha-hydroxycholesterol pathway. These extrahepatic pathways contribute little to the total synthesis of bile salts, but are thought to play important roles in cholesterol homeostasis (Javitt 2002).
R-HSA-193775 Synthesis of bile acids and bile salts via 24-hydroxycholesterol In the body, 24-hydroxycholesterol is synthesized in the brain, exported to the liver, and converted there to bile acids and bile salts. This pathway is only a minor source of bile acids and bile salts, but appears to be critical for the disposal of excess cholesterol from the brain (Bjorkhem et al. 1998; Javitt 2002).
In the liver, conversion of 24-hydroxycholesterol to bile acids and bile salts is initiated with hydroxylation and oxidoreductase reactions to form 4-cholesten-7alpha,24(S)-diol-3-one. The pathway then branches: hydroxylation of 4-cholesten-7alpha,24(S)-diol-3-one to 4-cholesten-7alpha,12alpha,24(S)-triol-3-one leads ultimately to the formation of cholate, while its reduction to 5beta-cholestan-7alpha,24(S)-diol-3-one leads to chenodeoxycholate formation. In both branches, reactions in the cytosol, the mitochondrial matrix, and the peroxisomal matrix result in modifications to the ring structure, shortening and oxidation of the side chain, conversion to a Coenzyme A derivative, and conjugation with the amino acids glycine or taurine (Russell 2003). These reactions are outlined in the figure below. The final three reactions are identical to ones of bile salt synthesis initiated by 7alpha-hydroxylation and are shown as arrows with no substrates. R-HSA-193807 Synthesis of bile acids and bile salts via 27-hydroxycholesterol In the body, 27-hydroxycholesterol is synthesized in multiple tissues, exported to the liver, and converted there to bile acids and bile salts. This pathway is only a minor source of bile acids and bile salts, but may play a significant role particularly in the mobilization of cholesterol from lung phagocytes (Bjorkhem et al. 1994; Babiker et al. 1999; Javitt 2002).
In the liver, conversion of 27-hydroxycholesterol to bile acids and bile salts is initiated with hydroxylation and oxidoreductase reactions to form 4-cholesten-7alpha,27-diol-3-one. The pathway then branches: hydroxylation of 4-cholesten-7alpha,27-diol-3-one to 4-cholesten-7alpha,12alpha,27-triol-3-one leads ultimately to the formation of cholate, while its reduction to 5beta-cholestan-7alpha,27-diol-3-one leads to chenodeoxycholate formation. In both branches, reactions in the cytosol, the mitochondrial matrix, and the peroxisomal matrix result in modifications to the ring structure, shortening and oxidation of the side chain, conversion to a Coenzyme A derivative, and conjugation with the amino acids glycine or taurine (Russell 2003). These reactions are outlined in the figure below. The final nine reactions are identical to ones of bile salt synthesis initiated by 7alpha-hydroxylation and are shown as arrows with no substrates. R-HSA-193368 Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol In the liver, synthesis of bile acids and bile salts is initiated with the conversion of cholesterol to 7alpha-hydroxycholesterol and of 7alpha-hydroxycholesterol to 4-cholesten-7alpha-ol-3-one. The pathway then branches: hydroxylation of 4-cholesten-7alpha-ol-3-one to 4-cholesten-7alpha, 12alpha-diol-3-one leads ultimately to the formation of cholate, while its reduction to 5beta-cholestan-7alpha-ol-3-one leads to chenodeoxycholate formation. The amounts of substrate following each branch appear to be determined by abundance of the hydroxylase enzyme: in human liver, cholate synthesis predominates.
In both branches, reactions in the cytosol, the mitochondrial matrix, and the peroxisomal matrix result in modifications to the ring structure, shortening and oxidation of the side chain, conversion to a Coenzyme A derivative, and conjugation with the amino acids glycine or taurine. In the body, glycocholate, taurocholate, glycochenodeoxycholate, and taurochenodeoxycholate are released from hepatocytes into the bile and ultimately into the lumen of the small intestine, where they function as detergents to solubilize dietary fats. The liver synthetic pathway also yields small amounts of bile acids, cholate and deoxycholate, which may play a feedback role in regulating the bile acid synthetic pathway (Russell 2003). These reactions are outlined in the figure below. R-HSA-5358493 Synthesis of diphthamide-EEF2 Eukaryotic elongation factor 2 (EEF2) catalyzes the GTP dependent ribosomal translocation step during translation elongation. This function requires the presence of a posttranslational modification, the conversion of histidine residue 715 to diphthamide (2' [3 carboxamido 3 (trimethylammonio)propyl] L histidine) (Van Ness et al. 1978). No other protein is known to undergo this modification. The diphthamide residue is also the target of ADP ribosylation catalyzed by diphtheria toxin, which inactivates EEF2 and leads to cell death (Collier 1975; Pappenheim 1977).
Diphthamide synthesis proceeds in four steps: the transfer of 3 amino 3 carboxypropyl group from S adenosylmethionine to histidine 715 of EEF2, the addition of four methyl groups to the 3 amino 3 carboxypropyl moiety, the demethylation of the methylated carboxylate group to form diphthine, and the amidation of the diphthine carboxyl group (Liu et al. 2004; Lin et al. 2014; Schaffrath et al. 2014; Su et al. 2013; Uthman et al. 2013). R-HSA-162699 Synthesis of dolichyl-phosphate mannose Dolichyl-phosphate-mannose (DPM, DOLPman) is the donor of mannose groups in the synthesis of the dolichyl pyrophosphate-linked precursor oligosaccharide in asparagine-linked glycosylation, in the synthesis of the glycosyl phosphatidylinositol (GPI) anchor precursor, in protein O-mannosylation and in protein C-mannosylation. Its synthesis proceeds in two steps. First, cytosolic GDP-mannose reacts with dolichyl phosphate exposed on the cytosolic face of the endoplasmic reticulum membrane to form DPM with its mannose moiety oriented toward the cytosol. The DPM molecule then flips in the endoplasmic reticulum membrane, so that its mannose moiety is in the endoplasmic reticulum lumen, accessible to the enzymes that catalyze its transfer to growing glycolipids and glycoproteins (Kinoshita and Inoue, 2000; Maeda et al, 2000). R-HSA-480985 Synthesis of dolichyl-phosphate-glucose Dolichyl-phosphate-glucose functions as a donor of glucose groups in reactions including three steps of N-glycan precursor biosynthesis. Dolichyl-phosphate-glucose itself is synthesized from UDP-glucose and dolichol phosphate on the cytosolic face of the endoplasmic reticulum membrane, then flipped to the luminal surface of that membrane. R-HSA-2142670 Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) The epoxidation of arachidonate by cytochrome P450s (CYPs) results in the formation of unique bioactive lipid mediators termed epoxyeicosatrienoates (EETs). Each double bond has been shown to be susceptible to oxidation, resulting in 5,6-EET, 8,9-EET, 11,12-EET, and 14,15-EET. The majority of the EET biological activities are diminished by the hydrolysis to the corresponding dihydroxyeicosatrienoates (DHET) (Capdevila et al. 2000, Buczynski et al. 2009, Vance & Vance 2008). R-HSA-162710 Synthesis of glycosylphosphatidylinositol (GPI) Glycosylphosphatidyl inositol (GPI) acts as a membrane anchor for many cell surface proteins. GPI is synthesized in the endoplasmic reticulum. In humans, a single pathway consisting of nine reactions appears to be responsible for the synthesis of the major GPI species involved in membrane protein anchoring. This pathway is shown in the figure. Two additional reactions, not shown, allow the synthesis of variant forms of GPI, one with an additional mannose residue and one with an additional ethanolamine (Tauron et al. 2004; Shishioh et al. 2005). These variant GPI molecules may be used for tissue-specific protein modifications, or may function independently.
The steps of GPI synthesis were first identified by isolating large numbers of mutant cell lines that had lost the ability to express GPI anchored proteins on their surfaces. Somatic cell hybrid analyses of these lines allowed the definition of complementation groups corresponding to distinct mutated genes, and cDNAs corresponding to normal forms of these genes were identified on the basis of their abilities to restore normal cell surface protein expression in mutant cells. Co-precipitation experiments with tagged cloned proteins have allowed the identification of additional proteins involved in GPI anchor biosynthesis.
R-HSA-1855167 Synthesis of pyrophosphates in the cytosol Inositol phosphates such as IP4, IP5 and IP6 are converted to an even wider variety of IPs including the di- and triphospho inositol phosphates, also known as pyrophosphates (Irvine & Schell 2001, Alcazar-Romain & Wente 2008, York 2006, Monserrate and York 2010, Ho et al. 2002, Saiardi et al. 2001, Draskovic et al. 2008, Choi et al. 2007, Caffrey et al. 2000, Leslie et al. 2002).
R-HSA-446219 Synthesis of substrates in N-glycan biosythesis Reactions for the synthesis of the small nucleotide-linked sugar substrates that are used in the synthesis of the N-glycan precursor and in the later steps of glycosylation are annotated here.
All these nucleotide-linked sugar donors are synthesized in the cytosol; however, to participate in the later reactions of N-glycan precursor biosynthesis (when the glycan is oriented toward the lumen of the endoplasmic reticulum (ER)), these substrates must be attached to a dolichyl-phosphate molecule and then flipped toward the luminal side of the ER, through a mechanism which is still not known but which involves a different protein than the one that mediates the flipping of the LLO itself (Sanyal et al. 2008). Two of the genes encoding enzymes involved in these reactions, MPI and PMM2, are known to be associated with Congenital Disorders of Glycosylation (CDG) diseases of type I. Of these, CDG-Ia, associated with defects in PMM2, is the most frequent CDG disease reported.
R-HSA-75876 Synthesis of very long-chain fatty acyl-CoAs Very long-chain fatty acids (VLCFA), ones with more than 20 carbon atoms, have diverse physiological roles, notably as components of ceramides in membrane lipids and as precursors of the eicosanoid hormones that play central roles in the generation and resolution of inflammatory responses. Saturated and monounsaturated VLCFAs can be synthesized by elongation of palmitic acid synthesized de novo or derived from the diet. Polyunsaturated VLCFAs are synthesized from dietary linoleic and linolenic acids - humans lack the desaturase enzymes to synthesize these molecules from stearate.
Chemically, the elongation process that yields VLCFA parallels the one by which palmitate (16 carbons) or stearate (18 carbons) are synthesized de novo from acetate. The starting fatty acid is activated by conjugation with coenzyme A (CoA-SH), condensed with malonyl-CoA to form a 3-oxoacyl CoA containing two more carbon atoms than the starting long chain fatty acyl CoA and CO2, reduced with NADPH to a 3-hydroxyacyl CoA, dehydrated to a trans 2,3-enoyl-CoA, and reduced with NADPH to yield a fatty acyl-CoA two carbons longer than the starting one.
The process differs from the de novo one in that the enzymatic activities resposible for each step are expressed by different proteins associated with the endoplasmic reticulum membrane, not by separate domains of a single multifunctional cytosolic protein. In humans, activation is catalyzed by one of five acyl-CoA synthetase long-chain (ACSL) enzymes, conjugation by one of seven elongation of very long chain fatty acids (ELOVL) proteins, reduction by one of two HSB17B estradiol dehydrogenases, dehydration by one of four protein tyrosine phosphatase-like / 3-hydroxyacyl-CoA dehydratase (PTPL / HACD) proteins, and reduction by one of two trans-2,3-enoyl-CoA reductase (TECR) proteins. Members of the four enzyme families differ in their tissue-specific expression patterns and in their substrate preferences (chain length, degree of saturation), leading to tissue-specific complements of VLCA (Jakobsson et al. 2006; Kihara 2012; Nugteren 1965; Sassa & Kihara 2014).
Here the full two-carbon elongation cycle to form stearate from palmitate is annotated, as well as the activation and condensation steps for elongation of arachidonate, the 20-carbon unsaturated fatty acid that plays a central role in the synthesis of prostaglandins and related hormones.
R-HSA-6782861 Synthesis of wybutosine at G37 of tRNA(Phe) Derivatives of wyosine are tricyclic bases found at nucleotide 37 of tRNA(Phe) in eukaryotes. The pathway of wybutosine synthesis begins with a templated guanosine residue and proceeds through 6 steps catalyzed by 5 enzymes: N1 methylation of guanosine, condensation of 1-methylguanosine with pyruvate to yield 4-demethylwyosine, addition of an aminocarboxypropyl group to yield yW-86, methylation of yW-86 to yield yW-72, methylation of yW-72 to yield yW-58, and methoxycarbonylation of yW-58 to yield wybutosine (reviewed in Young and Bandarian 2013, Perche-Letuvée et al. 2014). Wybutosine may further be modified by hydroxylation and methylation. Wyosine derivatives at position 37 of tRNAs participate in translational fidelity by stabilizing codon-anticodon pairing (Konevega et al. 2004) and preventing frameshifting (Waas et al. 2007).
R-HSA-422085 Synthesis, secretion, and deacylation of Ghrelin Ghrelin is a peptide hormone of 28 amino acid residues which is acylated at the serine-3 of the mature peptide. Ghrelin is synthesized in several tissues: X/A-like cells of the gastric mucosa (the major source of ghrelin), hypothalamus, pituitary, adrenal gland, thyroid, breast, ovary, placenta, fallopian tube, testis, prostate, liver, gall bladder, pancreas, fat tissue, human lymphocytes, spleen, kidney, lung, skeletal muscle, myocardium, vein and skin. Ghrelin binds the GHS-R1a receptor present in hypothalamus pituitary, and other tissues. Binding causes appetite stimulation and release of growth hormone. Levels of circulating ghrelin rise during fasting, peak before a meal, and fall according to the calories ingested.
Preproghrelin is cleaved to yield proghrelin which is then acylated by ghrelin O-acyltransferase to yield octanoyl ghrelin and decanoyl ghrelin. Only octanoyl ghrelin is able to bind and activate the GHS-R1a receptor. Unacylated ghrelin (des-acyl ghrelin) is also present in plasma but its function is controversial.
Acyl proghrelin is cleaved by prohormone convertase 1/3 to yield the mature acyl ghrelin and C-ghrelin. Secretion of ghrelin is inhibited by insulin, growth hormone (somatotropin), leptin, glucose, glucagon, and fatty acids. Secretion is stimulated by insulin-like growth factor-1 and muscarinic agonists.
In the bloodstream acyl ghrelin is deacylated by butyrylcholinesterase and platelet-activating factor acetylhydrolase. Other enzymes may also deacylate acyl ghrelin.
R-HSA-381771 Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) In L cells of the intestine the transcription factors TCF-4 (TCF7L2) and Beta-catenin form a heterodimer and bind the G2 enhancer of the Proglucagon gene GCG,activating its transcription to yield Proglucagon mRNA and, following translation, Proglucagon protein. The prohormone convertase PC1 present in the secretory granules of L cells cleaves Proglucagon at two sites to yield mostly Glucagon-like Peptide-1 (7-36) with a small amount of Glucagon-like Peptide-1 (7-37). Glucagon-like Peptide-1 (7-36 and 7-37) (GLP-1) is secreted into the bloodstream in response to glucose, fatty acids, insulin, leptin, gastrin-releasing peptide, cholinergic transmitters, beta-adrenergic transmitters, and peptidergic transmitters. The half-life of GLP-1 in the bloodstream is determined by Dipeptidyl Peptidase IV, which cleaves 2 amino acids at the amino terminus of GLP-1, rendering it biologically inactive.
R-HSA-400511 Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) In K cells of the intestine the transcription factors PAX6 and PDX-1 activate transcription of the gene encoding Glucose-dependent Insulinotropic Polypeptide (GIP, first called Gastric Inhibitory Peptide). ProGIP is cleaved in secretory granules by Prohormone Convertase 1 (PC1) at 2 sites to yield mature GIP. In response to fat the GIP is secreted into the bloodstream. The half-life of GIP in the bloodstream is determined by Dipeptidyl Peptidase IV, which cleaves 2 amino acids at the amino terminus of GIP, rendering it biologically inactive.
R-HSA-445989 TAK1-dependent IKK and NF-kappa-B activation NF-kappa-B is sequestered in the cytoplasm in a complex with inhibitor of NF-kappa-B (IkB). Almost all NF-kappa-B activation pathways are mediated by IkB kinase (IKK), which phosphorylates IkB resulting in dissociation of NF-kappa-B from the complex. This allows translocation of NF-kappa-B to the nucleus where it regulates gene expression.
R-HSA-6791462 TALDO1 deficiency: failed conversion of Fru(6)P, E4P to SH7P, GA3P Mutations in transaldolase 1 (TALDO1), an enzyme of the pentose phosphate pathway that normally mediates the reversible interconversion of D-fructose 6-phosphate and D-erythrose 4-phosphate to form sedoheptulose 7-phosphate and D-glyceraldehyde 3-phosphate, have been associated with congenital liver disease (Wamelink et al. 2008).
R-HSA-6791055 TALDO1 deficiency: failed conversion of SH7P, GA3P to Fru(6)P, E4P Mutations in transaldolase 1 (TALDO1), an enzyme of the pentose phosphate pathway that normally mediates the reversible interconversion of sedoheptulose 7-phosphate and D-glyceraldehyde 3-phosphate to form D-fructose 6-phosphate and D-erythrose 4-phosphate, have been associated with congenital liver disease (Wamelink et al. 2008).
R-HSA-8854214 TBC/RABGAPs Rab GTPases are peripheral membrane proteins involved in membrane trafficking. Often through their indirect interactions with coat components, motors, tethering factors and SNAREs, the Rab GTPases serve as multifaceted organizers of almost all membrane trafficking processes in eukaryotic cells. To perform these diverse processes, Rab GTPases interconvert between an active GTP-bound form and an inactive, GDP-bound form. The GTP-bound activated form mediates membrane transport through specific interaction with multiple effector molecules (Zerial & McBride 2001, Stenmark 2009, Zhen & Stenmark 2015, Cherfils & Zeghouf 2013). Conversion from the GTP- to the GDP-bound form occurs through GTP hydrolysis, which is not only driven by the intrinsic GTPase activity of the Rab protein but is also catalysed by GTPase-activating proteins (GAPs). GAPs not only increase the rate of GTP hydrolysis, but they are also involved in the inactivation of RABs, making sure they are inactivated at the correct membrane. Human cells contain as many as 70 Rabs and at least 51 putative Rab GAPs (Pfeffer 2005). Only a few of these GAPs have been matched to a specific Rab substrate. The Tre-2/Bub2/Cdc16 (TBC) domain-containing RAB-specific GAPs (TBC/RABGAPs) are a key family of RAB regulators, where the TBC domain facilitates the inactivation of RABs by facilitating activation of GTPase activity of the RAB (Pan et al. 2006, Frasa et al. 2012, Stenmark 2009). Studies suggest that TBC/RABGAPs are more than just negative regulators of RABs and can integrate signalling between RABs and other small GTPases, thereby regulating numerous cellular processes like intracellular trafficking (Frasa et al. 2012).
R-HSA-201681 TCF dependent signaling in response to WNT 19 WNT ligands and 10 FZD receptors have been identified in human cells; interactions amongst these ligands and receptors vary in a developmental and tissue-specific manner and lead to activation of so-called 'canonical' and 'non-canonical' WNT signaling. In the canonical WNT signaling pathway, binding of a WNT ligand to the Frizzled (FZD) and lipoprotein receptor-related protein (LRP) receptors results in the inactivation of the destruction complex, the stabilization and nuclear translocation of beta-catenin and subsequent activation of T-cell factor/lymphoid enhancing factor (TCF/LEF)-dependent transcription. Transcriptional activation in response to canonical WNT signaling controls processes such as cell fate, proliferation and self renewal of stem cells, as well as contributing to oncogenesis (reviewed in MacDonald et al, 2009; Saito-Diaz et al, 2013; Kim et al, 2013).
R-HSA-202403 TCR signaling The TCR is a multisubunit complex that consists of clonotypic alpha/beta chains noncovalently associated with the invariant CD3 delta/epsilon/gamma and TCR zeta chains. T cell activation by antigen presenting cells (APCs) results in the activation of protein tyrosine kinases (PTKs) that associate with CD3 and TCR zeta subunits and the co-receptor CD4. Members of the Src kinases (Lck), Syk kinases (ZAP-70), Tec (Itk) and Csk families of nonreceptor PTKs play a crucial role in T cell activation. Activation of PTKs following TCR engagement results in the recruitment and tyrosine phosphorylation of enzymes such as phospholipase C gamma1 and Vav as well as critical adaptor proteins such as LAT, SLP-76 and Gads. These proximal activation leads to reorganization of the cytoskeleton as well as transcription activation of multiple genes leading to T lymphocyte proliferation, differentiation and/or effector function.
R-HSA-5221030 TET1,2,3 and TDG demethylate DNA About 2-6% of all cytosine residues and 70-80% of cytosine residues in CG dinucleotides in mammalian cells are methylated at the 5 position of the pyrimidine ring. The cytosine residues are methylated by DNA methyltransferases after DNA replication and can be demethylated by passive dilution during subsequent replication or by active modification of the 5-methylcytosine base. Cytosine demethylation is developmentally regulated: one wave of demethylation occurs in primordial germ cells and one wave occurs by active demethylation in the male pronucleus after fertilization.
Some mechanisms of active demethylation remain controversial, however progressive oxidation of the methyl group of 5-methylcytosine followed by base excision by thymine DNA glycosylase (TDG) has been reproducibly demonstrated in vivo (reviewed in Wu and Zhang 2011, Franchini et al 2012, Cadet and Wagner 2013, Kohli and Zhang 2013, Ponnaluri et al. 2013, Rasmussen and Helin 2016). Ten-eleven translocation proteins TET1, TET2, and TET3 are dioxygenases that first oxidize 5-methylcytosine to 5-hydroxymethylcytosine (5-hmC) (Tahiliani et al. 2009, Ito et al. 2010), which is found in significant quantities and specific genomic locations in stem cells and neurons (Kinney and Pradhan 2013). TET proteins can further oxidize 5-hmC to 5-formylcytosine (5-fC) and then 5-carboxylcytosine (5-caC) (He et al. 2011, Ito et al. 2011). G:5-fC and G:5-caC base pairs are recognized by TDG, which excises the 5-fC or 5-caC and leaves an abasic site.
TET1 in mouse is expressed in neurons and its expression depends on neuronal activity (Guo et al. 2011, Kaas et al. 2013, Zhang et al. 2013). TET1 is also found in embryonic stem cells (Ficz et al. 2011, Koh et al. 2011, Wu et al. 2011) and in primordial germ cells of mice, where it plays a role in erasure of imprinting (Yamaguchi et al. 2013). TET3 is expressed in oocytes and zygotes of mice and is required for demethylation in the male pronucleus (Gu et al. 2011, Iqbal et al. 2011). TET2 is the most highly expressed TET family protein in hemopoietic stem cells and appears to act as a tumor suppressor. TET2 is also expressed in embryonic stem cells (Koh et al. 2011).
R-HSA-8866911 TFAP2 (AP-2) family regulates transcription of cell cycle factors TFAP2A and TFAP2C play opposing roles in transcriptional regulation of the CDKN1A (p21) gene locus. While TFAP2A stimulates transcription of the CDKN1A cyclin-dependent kinase inhibitor (Zeng et al. 1997, Williams et al. 2009, Scibetta et al. 2010), TFAP2C, in cooperation with MYC and histone demethylase KDM5B, represses CDKN1A transcription (Williams et al. 2009, Scibetta et al. 2010, Wong et al. 2012).
R-HSA-8866910 TFAP2 (AP-2) family regulates transcription of growth factors and their receptors TFAP2A and TFAP2C directly stimulate transcription of the estrogen receptor ESR1 gene (McPherson and Weigel 1999). TFAP2A expression correlates with ESR1 expression in breast cancer, and TFAP2C is frequently overexpressed in estrogen-positive breast cancer and endometrial cancer (deConinck et al. 1995, Turner et al. 1998). TFAP2A, TFAP2C, as well as TFAP2B can directly stimulate the expression of ERBB2, another important breast cancer gene (Bosher et al. 1996). Association of TFAP2A with the YY1 transcription factor significantly increases the ERBB2 transcription rate (Begon et al. 2005). In addition to ERBB2, the expression of another receptor tyrosine kinase, KIT, is also stimulated by TFAP2A and TFAP2B (Huang et al. 1998), while the expression of the VEGF receptor tyrosine kinase ligand VEGFA is repressed by TFAP2A (Ruiz et al. 2004, Li et al. 2012). TFAP2A stimulates transcription of the transforming growth factor alpha (TGFA) gene (Wang et al. 1997). TFAP2C regulates EGFR expression in luminal breast cancer (De Andrade et al. 2016). In placenta, TFAP2A and TFAP2C directly stimulate transcription of both subunits of the human chorionic gonadotropin, CGA and CGB (Johnson et al. 1997, LiCalsi et al. 2000).
R-HSA-8866906 TFAP2 (AP-2) family regulates transcription of other transcription factors Homodimers and possibly heterodimers of TFAP2A and TFAP2C, in complex with CITED2, stimulate transcription of the PITX2 gene, involved in left-right patterning and heart development (Bamforth et al. 2004, Li et al. 2012).
R-HSA-8869496 TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation During retinoic acid-induced cell differentiation, TFAP2A, in complex with NPM1 (nucleophosmin), represses transcription of HSPD1 (Hsp60), NOP2 (p120) and MYBL2 (b-Myb). The repression of gene expression probably involves the recruitment of histone deacetylases HDAC1 and HDCA2 to target promoters by NPM1. The complex of TFAP2A and NPM1 can also be detected at the NPM1 promoter, which is in agreement with decreased NPM1 expression after retinoic acid treatment. The level of TFAP2A increases in response to the retinoic acid treatment (Liu et al. 2007). NOP2 and MYBL2 are both proliferation markers (Valdez et al. 1992, Saville and Watson 1998).
R-HSA-2173789 TGF-beta receptor signaling activates SMADs Binding of transforming growth factor beta 1 (TGF beta 1, i.e. TGFB1) to TGF beta receptor type 2 (TGFBR2) activates TGF beta receptor signaling cascade. TGFB1 is posttranslationally processed by furin (Dubois et al. 1995) to form a homodimer and secreted to the extracellular space as part of the large latent complex (LLC). After the LLC disassembles in the extracellular space, dimeric TGFB1 becomes capable of binding to TGFBR2 (Annes et al. 2003, Keski Oja et al. 2004). Formation of TGFB1:TGFBR2 complex creates a binding pocket for TGF-beta receptor type-1 (TGFBR1) and TGFBR1 is recruited to the complex by binding to both TGFB1 and TGFBR2. This results in an active heterotetrameric TGF-beta receptor complex that consists of TGFB1 homodimer bound to two heterodimers of TGFBR1 and TGFBR2 (Wrana et al. 1992, Moustakas et al. 1993, Franzen et al. 1993). TGF-beta signaling can also occur through a single heterodimer of TGFBR1 and TGFBR2, although with decreased efficiency (Huang et al. 2011). TGFBR1 and TGFBR2 interact through their extracellular domains, which brings their cytoplasmic domains together. Ligand binding to extracellular receptor domains is cooperative, but no conformational change is seen from crystal structures of either TGFB1- or TGFB3-bound heterotetrameric receptor complexes (Groppe et al. 2008, Radaev et al. 2010).
Activation of TGFBR1 by TGFBR2 in the absence of ligand is prevented by FKBP1A (FKBP12), a peptidyl-prolyl cis-trans isomerase. FKBP1A forms a complex with inactive TGFBR1 and dissociates from it only after TGFBR1 is recruited by TGFB1-bound TGFBR2 (Chen et al. 1997).
Both TGFBR1 and TGFBR2 are receptor serine/threonine kinases. Formation of the hetero-tetrameric TGF-beta receptor complex (TGFBR) in response to TGFB1 binding induces receptor rotation, so that TGFBR2 and TGFBR1 cytoplasmic kinase domains face each other in a catalytically favourable configuration. TGFBR2 trans-phosphorylates serine residues at the conserved Gly-Ser-rich juxtapositioned domain (GS domain) of TGFBR1 (Wrana et al. 1994, Souchelnytskyi et al. 1996), activating TGFBR1.
In addition to phosphorylation, TGFBR1 may also be sumoylated in response to TGF-beta stimulation. Sumoylation enhances TGFBR1 kinase activity (Kang et al. 2008).
The activated TGFBR complex is internalized by clathrin-mediated endocytosis into early endosomes. With the assistance of SARA, an early endosome membrane protein, phosphorylated TGFBR1 within TGFBR complex recruits SMAD2 and/or SMAD3 , i.e. R-SMADs (Tsukazaki et al. 1998). TGFBR1 phosphorylates recruited SMAD2/3 on two C-terminal serine residues (Souchelnytskyi et al. 2001). The phosphorylation changes the conformation of SMAD2/3 MH2 domain, promoting dissociation of SMAD2/3 from SARA and TGFBR1 (Souchelnytskyi et al. 1997, Macias-Silva et al. 1996, Nakao et al. 1997) and formation of SMAD2/3 trimers (Chacko et al. 2004). The phosphorylated C-terminal tail of SMAD2/3 has high affinity for SMAD4 (Co-SMAD), inducing formation of SMAD2/3:SMAD4 heterotrimers, composed of two phosphorylated R-SMADs (SMAD2 and/or SMAD3) and SMAD4 (Co-SMAD). SMAD2/3:SMAD4 heterotrimers are energetically favored over R-SMAD trimers (Nakao et al. 1997, Qin et al. 2001, Kawabata et al. 1998, Chacko et al. 2004).
SMAD2/3:SMAD4 heterotrimers translocate to the nucleus where they act as transcriptional regulators.
R-HSA-2173791 TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) In normal cells and in the early stages of cancer development, signaling by TGF-beta plays a tumor suppressive role, as SMAD2/3:SMAD4-mediated transcription inhibits cell division by downregulating MYC oncogene transcription and stimulating transcription of CDKN2B tumor suppressor gene. In advanced cancers however, TGF-beta signaling promotes metastasis by stimulating epithelial to mesenchymal transition (EMT).
TGFBR1 is recruited to tight junctions by binding PARD6A, a component of tight junctions. After TGF-beta stimulation, activated TGFBR2 binds TGFBR1 at tight junctions, and phosphorylates both TGFBR1 and PARD6A. Phosphorylated PARD6A recruits SMURF1 to tight junctions. SMURF1 is able to ubiquitinate RHOA, a component of tight junctions needed for tight junction maintenance, leading to disassembly of tight junctions, an important step in EMT (Wang et al. 2003, Ozdamar et al. 2005).
R-HSA-3656532 TGFBR1 KD Mutants in Cancer Mutations in the kinase domain (KD) of TGF-beta receptor 1 (TGFBR1) have been found in Ferguson-Smith tumor i.e. multiple self-healing squamous epithelioma - MSSE (Goudie et al. 2011), breast cancer (Chen et al. 1998), ovarian cancer (Chen et al. 2001) and head-and-neck cancer (Chen et al. 2001). KD mutations reported in MSSE are nonsense and frameshift mutations that cause premature termination of TGFBR1 translation, resulting in truncated receptors that lack substantial portions of the kinase domain, or cause nonsense-mediated decay of mutant transcripts. A splice site KD mutation c.806-2A>C is predicted to result in the skipping of exon 5 and the absence of KD amino acid residues 269-324 from the mutant receptor. The splice site mutant is expressed at the cell surface but unresponsive to TGF-beta stimulation (Goudie et al. 2004).
TGFBR1 KD mutations reported in breast, ovarian and head-and-neck cancer are missense mutations, and it appears that these mutant proteins are partially functional but that their catalytic activity or protein stability is decreased (Chen et al. 1998, Chen et al. 2001a and b). These mutants are not shown.
R-HSA-3656535 TGFBR1 LBD Mutants in Cancer Mutations in the ligand-binding domain (LBD) of TGF-beta receptor 1 (TGFBR1) have been reported as germline mutations in Ferguson-Smith tumor (multiple self-healing squamous epithelioma - MSSE), an autosomal-dominant skin cancer condition (Ferguson-Smith et al. 1934, Ferguson-Smith et al. 1971), with tumors frequently showing loss of heterozygosity of the wild-type TGFBR1 allele (Goudie et al. 2011). Somatic mutations in the LBD of TGFBR1 have been reported in esophageal carcinoma (Dulak et al. 2013).
R-HSA-3645790 TGFBR2 Kinase Domain Mutants in Cancer Missense mutations in the kinase domain (KD) of TGF-beta receptor II (TGFBR2) are found in ~20% of microsatellite stable (MSS) colon cancers and make affected tumors resistant to TGF-beta (TGFB1)-mediated growth inhibition (Grady et al. 1999). While both alleles of TGFBR2 are affected by inactivating mutations in MSS colorectal cancer (Grady et al. 1999), a study of MSS esophageal carcinoma indicates that TGFBR2 KD mutations may function in a dominant-negative way (Tanaka et al. 2000). KD mutations in TGFBR2 are rarely reported in microsatellite instable (MSI) colorectal cancer (Parsons et al. 1995, Takenoshita et al. 1997).
R-HSA-3642279 TGFBR2 MSI Frameshift Mutants in Cancer The short adenine repeat in the coding sequence of TGF-beta receptor II (TGFBR2) gene is frequently targeted by loss-of-function frameshift mutations in colon cancers with microsatellite instability (MSI). The 1- or 2-bp deletions in the adenine stretch of TGFBR2 cDNA introduce a premature stop codon that leads to degradation of the majority of mutant transcripts through nonsense-mediated decay or to production of a truncated TGFBR2 that cannot be presented on the cell surface. Cells that harbor TGFBR2 MSI frameshift mutations are resistant to TGF-beta (TGFB1)-mediated growth inhibition.
R-HSA-9839383 TGFBR3 PTM regulation This subpathway includes the post-translation modification reactions of TGFBR3 including its plasma membrane localization and extracellular regulation by MT-MMPs and Gamma-secretase (Knappenberger et al.,2017, Velasco-loyden et al.,2004, Blari et al.,2011).
R-HSA-9839394 TGFBR3 expression This pathway describes the transcriptional and translational regulation of TGFBR3. Regulation of TGFBR3 expression includes different transcription factors (Sp1, MyoD and RAR) (Lopez-Casillas et al., 2003), epigenetic regulators such as HELLS (Hou et al., 2021) and KLP16 (Chen et al., 2022)), and translational regulation by miRNAs (Wang et al., 2019, Zhu et al., 2012).
R-HSA-9839397 TGFBR3 regulates FGF2 signaling This subpathway describes the regulation of FGF2:FGFR1 mediated signaling by the TGFBR3 receptor complex. TGFBR3 have binding affinity for FGF2 (Andres et al., 1992) and in presence of GIPC, FGF2/TGFBR3/GPIC enhances FGF2 signaling (Knelson et al.,2013).
R-HSA-9839389 TGFBR3 regulates TGF-beta signaling This subpathway describes the activation of TGFBR3 by TGF ligands and the subsequent regulation of TGF signaling by TGFBR3 (López‑Casillas et al.,1991,López‑Casillas et al.,1994, Blobe et al.,2001)
R-HSA-9839406 TGFBR3 regulates activin signaling This subpathway describes the regulation of activin signaling by TGFBR3. TGFBR3 binds with Inhibin A, which is also a ligand for TGFBR3 and inhibits activin/BMP signaling by binding competititively to ACVR2A receptor and BMPRII (Esparza-Lopez et al., 2001, Lewis et al., 2000, Wiater et al., 2003).
R-HSA-5602566 TICAM1 deficiency - HSE Inborn errors of interferon immunity due to defects in toll like receptor 3 (TLR3)-mediated signaling underlie pathogenesis of herpes simplex virus type 1 (HSV1) encephalitis (HSE) in some children (Netea MG et al. 2012). Autosomal dominant (AD) and recessive (AR) deficiencies of (TIR) domain-containing adaptor inducing IFN-beta (TRIF or TICAM1) are also associated with impaired IFN production and predisposition to HSE in the course of primary infection by HSV1 (Sancho-Shimizu V et al. 2011).
R-HSA-168927 TICAM1, RIP1-mediated IKK complex recruitment Receptor-interacting protein 1 (RIP1) mediates the activation of interferon-alpha/beta via intermediate activation of IKK/TBK1 or NFkB pathways.
R-HSA-9014325 TICAM1,TRAF6-dependent induction of TAK1 complex In human, together with ubiquitin-conjugating E2-type enzymes UBC13 and UEV1A (also known as UBE2V1), TRAF6 catalyses Lys63-linked ubiquitination. It is believed that auto polyubiquitination and oligomerization of TRAF6 is followed by binding the ubiquitin receptors of TAB2 or TAB3 (TAK1 binding protein 2 and 3), which stimulates phosphorylation and activation of TGF beta-activated kinase 1(TAK1).
TAK1 phosphorylates IKK alpha and IKK beta, which in turn phosphorylate NF-kB inhibitors - IkB and eventually results in IkB degradation and NF-kB translocation to the nucleus. Also TAK1 mediates JNK and p38 MAP kinases activation by phosphorylating MKK4/7 and MKK3/6 respectivly resulting in the activation of many transcription factors.
The role of TRAF6 is somewhat controversial and probably cell type specific. TRAF6 autoubiquitination was found to be dispensable for TRAF6 function to activate TAK1 pathway. These findings are consistent with the new mechanism of TRAF6-mediated NF-kB activation that was suggested by Xia et al. (2009). TRAF6 generates unanchored Lys63-linked polyubiquitin chains that bind to the regulatory subunits of TAK1 (TAB2 or TAB3) and IKK(NEMO), leading to the activation of the kinases.
Xia et al. (2009) demonstrated in vitro that unlike polyubiquitin chains covalently attached to TRAF6 or IRAK, TAB2 and NEMO-associated ubiquitin chains were found to be unanchored and susceptible to N-terminal ubiquitin cleavage. Only K63-linked polyubiquitin chains, but not monomeric ubiquitin, activated TAK1 in a dose-dependent manner. Optimal activation of the IKK complex was achieved using ubiquitin polymers containing both K48 and K63 linkages.
Furthermore, the authors proposed that the TAK1 complexes might be brougt in close proximity by binding several TAB2/3 to a single polyubiquitin chain to facilitate TAK1 kinase trans-phosphorylation. Alternativly, the possibility that polyUb binding promotes allosteric activation of TAK1 complex should be considered (Walsh et al 2008). R-HSA-9013973 TICAM1-dependent activation of IRF3/IRF7 Cell stimulation with viral double-stranded (ds) RNA and bacterial lipopolysaccharide (LPS) activate Toll-like receptors 3 (TLR3) and TLR4, respectively, triggering the activation the activation of two IKK-related serine/threonine kinases, TANK-binding kinase 1 (TBK1) and IκB kinase ε (IKKε, IKBKE) which directly phosphorylate interferon regulatory factor 3 (IRF3) and IRF7 promoting their dimerization and translocation into the nucleus. Although both kinases show structural and functional similarities, it seems that TBK1 and IKBKE differ in their regulation of downstream signaling events of TLR3/TLR4.
IRF3 activation and interferon β (IFNβ) production by poly(I:C), a synthetic analog of dsRNA, are decreased in TBK1-deficient mouse fibroblasts, whereas normal activation was observed in the IKBKE-deficient fibroblasts. However, in double-deficient mouse fibroblasts, the activation of IRF3 is completely abolished, suggesting a partially redundant functions of TBK1 and IKKε (IKBKE) (Hemmi H et al., 2004).
The poly(I:C)-induced phosphorylation of TBK1 and IRF3 was abolished in TRIF (TICAM1)-knockout human keratinocyte HACAT cells (Bakshi S et al., 2017). TICAM1 is utilized as an adaptor protein by TLR3 and TLR4 (Yamamoto M et al., 2003).
TLR3 recruits and activates PI3 kinase (PI3K), which activates the downstream kinase, Akt, leading to full phosphorylation and activation of IRF3 (Sarkar SN et al., 2004). When PI3K is not recruited to TLR3 or its activity is blocked, IRF3 is only partially phosphorylated and fails to bind the promoter of the target gene (Sarkar SN et al., 2004).
R-HSA-5602410 TLR3 deficiency - HSE Toll like receptor 3 (TLR3) recognizes double-stranded RNA (dsRNA), an intermediate product during viral replication for most viruses. TLR3 is expressed in various tissues and cells including cells of the central nervous system (CNS) (Bsibsi M et al. 2002). TLR3 activity in neurons and glial cells was found to be critical for controlling herpes simplex virus type 1 (HSV-1) infection in CNS (Lafaille FG et al. 2012). Children with inborn errors of TLR3-mediated immunity are prone to HSV-1 encephalitis (HSE), a rare life-threatening complication during HSV-1 infection (Casrouge A et al. 2006; Perez de Diego R et al. 2010; Zhang SY et al. 2007; Herman M et al. 2012; Lafaille FG et al. 2012). The functional defect in HSE patients with TLR3 deficiency is probably due to impaired induction of type I and III interferon (IFN) by cells of the CNS, which appears to be uniquely dependent upon TLR3 for protection against HSV1 (Zhang SY et al. 2007; Guo Y et al. 2011; Lafaille FG et al. 2012). Importantly, blood cells in the periphery produce normal amounts of interferons, even in TLR3-deficient patients, which perhaps can be explained by RIGI or MDA5-mediated antiviral responses.
R-HSA-9013957 TLR3-mediated TICAM1-dependent programmed cell death TLR3 and TLR4 trigger TRIF(TICAM1)-dependent programmed cell death in various human and mouse cells (Kalai M et al. 2002; Han KJ et al. 2004; Kaiser WJ and Offermann MK 2005; Estornes Y et al. 2012; He S et al. 2011). Apoptosis is a prevalent form of programmed cell death and is mediated by the activation of a set of caspases. In addition to apoptosis, TLR3/TLR4 activation induces RIP3-dependent necroptosis. These two programmed cell-death pathways may suppress each other. When the caspase activity is impaired or inhibited, certain cell types switch the apoptotic death program to necroptosis in response to various stimuli (TNF, Fas, viral infection and other stress stimuli) (Kalai M et al. 2002; Weber A et al. 2010; Feoktistova M et al. 2011, Tenev et al 2011).
R-HSA-5676594 TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway Activation of NF-kB is fundamental to signal transduction by members of the TNFRSF. Expression of NF-kB target genes is essential for mounting innate immune responses to infectious microorganisms but is also important for the proper development and cellular compartmentalization of secondary lymphoid organs necessary to orchestrate an adaptive immune response.
NF-kB transcription factor family is activated by two distinct pathways: the canonical pathway involving NF-kB1 and the non-canonical pathway involving NF-kB2. Unlike NF-kB1 signalling, which can be activated by a wide variety of receptors, the NF-kB2 pathway is typically activated by a subset of receptor and ligand pairs belonging to the tumor necrosis factor receptor (TNF) super family (TNFRSF) members. These members include TNFR2 (Rauert et al. 2010), B cell activating factor of the TNF family receptor (BAFFR also known as TNFRSF13C) (Kayagaki et al. 2002, CD40 (also known as TNFRSF5) (Coope et al. 2002, lymphotoxin beta-receptor (LTBR also known as TNFRSF3) (Dejardin et al. 2002), receptor activator for nuclear factor kB (RANK also known as TNFRSF11A) (Novack et al. 2003), CD27 and Fibroblast growth factor-inducible immediate-early response protein 14 (FN14 also known as TNFRSF12A) etc. These receptors each mediate specific biological roles of the non-canonical NF-kB. These non-canonical NF-kB-stimulating receptors have one thing in common and is the presence of a TRAF-binding motif, which recruits different TNF receptor-associated factor (TRAF) members, particularly TRAF2 and TRAF3, to the receptor complex during ligand ligation (Grech et al. 2004, Bishop & Xie 2007). Receptor recruitment of these TRAF members leads to their degradation which is a critical step leading to the activation of NIK and induction of p100 processing (Sun 2011, 2012).
R-HSA-75893 TNF signaling The inflammatory cytokine tumor necrosis factor alpha (TNF-α) is expressed in immune and nonimmune cell types including macrophages, T cells, mast cells, granulocytes, natural killer (NK) cells, fibroblasts, neurons, keratinocytes and smooth muscle cells as a response to tissue injury or upon immune responses to pathogenic stimuli (Köck A. et al. 1990; Dubravec DB et al. 1990; Walsh LJ et al. 1991; te Velde AA et al. 1990; Imaizumi T et al. 2000). TNF-α interacts with two receptors, namely TNF receptor 1 (TNFR1) and TNF receptor 2 (TNFR2). Activation of TNFR1 can trigger multiple signal transduction pathways inducing inflammation, proliferation, survival or cell death (Ward C et al. 1999; Micheau O and Tschopp J 2003; Widera D et al. 2006). Whether a TNF-α-stimulated cell will survive or die is dependent on autocrine/paracrine signals, and on the cellular context.
TNF binding to TNFR1 results initially in the formation of complex I that consists of TNFR1, TRADD (TNFR1-associated death domain), TRAF2 (TNF receptor associated factor-2), RIPK1 (receptor-interacting serin/threonine protein kinase 1), and E3 ubiquitin ligases BIRC2,BIRC3 (cIAP1/2,cellular inhibitor of apoptosis) and LUBAC (Micheau O and Tschopp J 2003). The conjugation of ubiquitin chains by BIRC2/3 and LUBAC (composed of HOIP, HOIL-1 and SHARPIN ) to RIPK1 allows further recruitment and activation of the TAK1 (also known as mitogen-activated protein kinase kinase kinase 7 (MAP3K7)) complex and IκB kinase (IKK) complex. TAK1 and IKK phosphorylate RIPK1 to limit its cytotoxic activity and activate both nuclear factor kappa‐light‐chain‐enhancer of activated B cells (NFkappaB) and mitogen‐activated protein (MAP) kinase signaling pathways promoting cell survival by induction of anti-apoptotic proteins such as BIRC, cellular FLICE (FADD-like IL-1β-converting enzyme)-like inhibitory protein (cFLIP) and secretion of pro-inflammatory cytokines (TNF and IL-6). When the survival pathway is inhibited, the TRADD:TRAF2:RIPK1 detaches from the membrane-bound TNFR1 signaling complex and recruits Fas-associated death domain-containing protein (FADD) and procaspase-8 (also known as complex II). Once recruited to FADD, multiple procaspase-8 molecules interact via their tandem death-effector domains (DED), thereby facilitating both proximity-induced dimerization and proteolytic cleavage of procaspase-8, which are required for initiation of apoptotic cell death (Hughes MA et al. 2009; Oberst A et al. 2010). When caspase activity is inhibited under certain pathophysiological conditions (e.g., expression of caspase-8 inhibitory proteins such as CrmA and vICA after infection with cowpox virus or CMV) or by pharmacological agents, deubiquitinated RIPK1 is physically and functionally engaged by its homolog RIPK3 leading to formation of the necrosome, a necroptosis-inducing complex consisting of RIPK1 and RIPK3 (Tewari M & Dixit VM 1995; Fliss PM & Brune W 2012; Sawai H 2013; Moquin DM et al. 2013; Kalai M et al. 2002; Cho YS et al. 2009, He S et al. 2009, Zhang DW et al., 2009). Within the complex II procaspase-8 can also form heterodimers with cFLIP isoforms, FLIP long (L) and FLIP short (S), which are encoded by the NFkappaB target gene CFLAR (Irmler M et al. 1997; Boatright KM et al. 2004; Yu JW et al. 2009; Pop C et al. 2011). FLIP(S) appears to act purely as an antagonist of caspase-8 activity blocking apoptotic but promoting necroptotic cell death (Feoktistova et al. 2011). The regulatory function of FLIP(L) has been found to differ depending on its expression levels. FLIP(L) was shown to inhibit death receptor (DR)-mediated apoptosis only when expressed at high levels, while low cell levels of FLIP(L) enhanced DR signaling to apoptosis (Boatright KM et al. 2004; Okano H et al. 2003; Yerbes R et al. 2011; Yu JW et al. 2009; Hughes MA et al. 2016). In addition, caspase-8:FLIP(L) heterodimer activity within the TRADD:TRAF2:RIPK1:FADD:CASP8:FLIP(L) complex allowed cleavage of RIPK1 to cause the dissociation of the TRADD:TRAF2:RIP1:FADD:CASP8, thereby inhibiting RIPK1-mediated necroptosis (Feoktistova et al. 2011, 2012). TNF-α can also activate sphingomyelinase (SMASE, such as SMPD2,3) proteins to catalyze hydrolysis of sphingomyeline into ceramide (Adam D et al.1996; Adam-Klages S et al. 1998; Ségui B et al. 2001). Activation of neutral SMPD2,3 leads to an accumulation of ceramide at the cell surface and has proinflammatory effects. However, TNF can also activate the pro-apoptotic acidic SMASE via caspase-8 mediated activation of caspase-7 which in turn proteolytically cleaves and activates the 72kDa pro-A-SMase form (Edelmann B et al. 2011). Ceramide induces anti-proliferative and pro-apoptotic responses. Further, ceramide can be converted by ceramidase into sphingosine, which in turn is phosphorylated by sphingosine kinase into sphingosine-1-phosphate (S1P). S1P exerts the opposite biological effects to ceramide by activating cytoprotective signaling to promote cell growth counteracting the apoptotic stimuli (Cuvillier O et al. 1996). Thus, TNF-α-induced TNFR1 activation leads to divergent intracellular signaling networks with extensive cross-talk between the pro-apoptotic/necroptotic pathway, and the other NFkappaB, and MAPK pathways providing highly specific cell responses initiated by various types of stimuli. R-HSA-5357956 TNFR1-induced NF-kappa-B signaling pathway Activation of tumor necrosis factor receptor 1 (TNFR1) can trigger multiple signal transduction pathways to induce inflammation, cell proliferation, survival or cell death (Ward C et al. 1999; Micheau O and Tschopp J 2003; Widera D et al. 2006). Whether a TNF-α-stimulated cell will survive or die is dependent on the cellular context. TNF-α-induced signals lead to the activation of transcriptional factors such as nuclear factor-kappa B (NFkappaB) and activator protein-1 (AP1) (Ward C et al. 1999; Widera D et al. 2006; Tsou HK et al. 2012).
The binding of TNF-α to TNFR1 leads to recruitment of the adapter protein TNFR1-associated death domain (TRADD) and of receptor‑interacting protein 1 (RIPK1). TRADD subsequently recruits also TNF receptor-associated factor 2 (TRAF2). RIPK1 is promptly K63-polyubiquitinated which results in the recruitment of the TAB2:TAK1 complex and the IkB kinase (IKK) complex to TNFR1. The activated IKK complex mediates phosphorylation of the inhibitor of NFkappaB (IkB), which targets IkB for ubiquitination and subsequent degradation. Released NFkappaB induces the expression of a variety of genes including inflammation-related genes and anti-apoptotic genes encoding proteins such as inhibitor of apoptosis proteins cIAP1/2, Bcl-2, Bcl-xL or cellular FLICE-like inhibitory protein (FLIP) (Blonska M et al. 2005; Ea CK et al. 2006; Wu CJ et al. 2006; Chen C et al. 2000; Manna SK et al. 2000; Kreuz S et al. 2001; Micheau O et al. 2001). NFkB-mediated inhibition of cell death also involves attenuating TNF-induced activation of c-Jun activating kinase (JNK). Whereas transient activation of JNK upon TNF treatment is associated with cellular survival, prolonged JNK activation contributes to cell death. However, as caspases activate JNK quite efficiently, JNKs are also regularly stimulated in course of apoptosis without being essential for cell death (Wicovsky A et al. 2007). AP1-mediated gene induction results from activation of JNK via TRAF2 (not shown here) (Tsou HK et al. 2012). While pro-survival signaling is initiated and regulated via the activated TNFR1 receptor complex at the cell membrane, cell death signals are induced by internalization-associated fashion upon the release of RIPK1 from the membrane complex (Micheau O and Tschopp J 2003; Schneider-Brachert W et al. 2004; Tchikov V et al. 2011).
TNFR1-mediated transcriptional activity of NFkB is both antiapoptotic and highly proinflammatory and thus must be tightly regulated to prevent constitutive activation that leads to persistent inflammation and cancer (Ward C et al. 1999; Fujihara S et al. 2002; Pekalski J et al. 2013; Kankaanranta H et al. 2014; Shukla S and Gupta S 2004; Jackson-Bernitsas DG et al. 2007; Zhang JY et al. 2007). Multiple mechanisms normally ensure the proper control of NFkappaB activation including two negative feedback loops mediated by NFkappaB inducible inhibitors, IkB-alpha (NFKBIA) and ubiquitin-editing protein A20 (He KL & Ting AT 2002; Wertz IE et al. 2004; Vereecke L et al. 2009; Pekalski J et al. 2013). R-HSA-5357786 TNFR1-induced proapoptotic signaling Activation of tumor necrosis factor receptor 1 (TNFR1) can trigger multiple signal transduction pathways to induce cell survival or cell death (Ward C et al. 1999; Micheau O and Tschopp J 2003; Widera D et al. 2006). While pro-survival signaling is initiated and regulated via the activated TNFR1 receptor complex at the cell membrane, cell death signals are induced upon the release of TRADD:TRAF2:RIP1 complex from the membrane to the cytosol where it forms death-inducing signaling complex (DISC) (Micheau O and Tschopp J 2003; Schneider-Brachert W et al. 2004). Upon apoptotic stimulation procaspase-8 or 10 is recruited into the DISC, and close proximity promotes the dimerization, autocatalytic processing, and activation of the initiator caspase-8 (and/or caspase-10) (Wang J et al. 2001; Boatright KM and Salvesen GS 2003). The initiator caspases then process and activate the downstream effector caspases such as caspase-3 in a proteolytic cascade (Stennicke HR et al. 1998). The effector caspases in turn cleave many diverse substrates, ultimately inducing cell death. R-HSA-5626978 TNFR1-mediated ceramide production TNF-alpha activates sphingomyelinase (SMASE) proteins to catalyze hydrolysis of sphingomyeline into ceramide. Two types of SMASE can be distinguished downstream of TNFR1 signaling, acid and neutral SMASEs (Adam-Klages S et al. 1996, 1998). Neutral SMASE (such as SMPD2,3) has a pH optimum of 7.4, requires Mg2+ ions and is found at the plasma membrane (Rao BG and Spence MW 1976). Acid SMASE is active at pH 4-5, is Zn2+-dependent and is mainly localized in the lysosomes. The death domain of TNFR1 that is responsible for the initiation of the apoptotic pathway also mediates activation of an acid SMASE. The two proapoptotic adaptor proteins TRADD and FADD are also involved in the activation of acid SMASE signaling events (Schwandner R et al. 1998). TNF-alpha can also activate the pro-apoptotic acidic SMASE via caspase-8 mediated activation of caspase-7 which in turn proteolytically cleaves and activates the 72kDa pro-acid SMASE form (Edelmann B et al. 2011). Neutral SMASE(SMPD) binds to adaptor protein NSMAF (FAN), which bridges it to NSMASE-activating domain (NSD) of TNFR1 (Adam D et al. 1996; Adam-Klages S et al. 1996; Ségui B et al. 2001). Activation of SMPD2,3 leads to an accumulation of ceramide at the cell surface.
Ceramide metabolism generates a cascade of bioactive lipids, all of which carry a specific signaling capacity. Ceramide can be converted by ceramidase into sphingosine, which in turn is phosphorylated by sphingosine kinase into sphingosine-1-phosphate (S1P). These lipids exert opposite biological effects: ceramide and sphingosine are able to induce anti-proliferative and pro-apoptotic responses, whereas S1P is a cytoprotective molecule that promotes cell growth and counteracts apoptotic stimuli (Cuvillier O et al.1996)
R-HSA-5668541 TNFR2 non-canonical NF-kB pathway Tumor necrosis factor-alpha (TNFA) exerts a wide range of biological effects through TNF receptor 1 (TNFR1) and TNF receptor 2 (TNFR2). Under normal physiological conditions TNFR2 exhibits more restricted expression, being found on certain subpopulation of immune cells and few other cell types (Grell et al. 1995 ). TNFR1 mediated signalling pathways have been very well characterized but, TNFR2 has been much less well studied. TNFR1 upon activation by TNFA activates apoptosis through two pathways, involving the adaptor proteins TNFR1-associated death domain (TRADD) and fas-associated death domain (FADD). In contrast, TNFR2 signalling especially in highly activated T cells, induces cell survival pathways that can result in cell proliferation by activating transcription factor NF-kB (nuclear factor-kB) via the alternative non-canonical route. TNFR2 signalling seems to play an important role, in particular for the function of regulatory T cells. It offers protective roles in several disorders, including autoimmune diseases, heart diseases, demyelinating and neurodegenerative disorders and infectious diseases (Faustman & Davis 2010).
Activation of the non-canonical pathway by TNFR2 is mediated through a signalling complex that includes TNF receptor-associated factor (TRAF2 and TRAF3), cellular inhibitor of apoptosis (cIAP1 and cIAP2), and NF-kB-inducing kinase (NIK). In this complex TRAF3 functions as a bridging factor between the cIAP1/2:TRAF2 complex and NIK. In resting cells cIAP1/2 in the signalling complex mediates K48-linked polyubiquitination of NIK and subsequent proteasomal degradation making NIK levels invisible. Upon TNFR2 stimulation, TRAF2 is recruited to the intracellular TRAF binding motif and this also indirectly recruits TRAF1 and cIAP1/2, as well as TRAF3 and NIK which are already bound to TRAF2 in unstimulated cells. TRAF2 mediates K63-linked ubiquitination of cIAP1/2 and this in turn mediates cIAP dependent K48-linked ubiquitination of TRAF3 leading to the proteasome-dependent degradation of the latter. As TRAF3 is degraded, NIK can no longer interact with TRAF1/2:cIAP complex. As a result NIK concentration in the cytosol increases and NIK gets stabilised and activated. Activated NIK phosphorylates IKKalpha, which in turn phosphorylates p100 (NFkB2) subunit. Phosphorylated p100 is also ubiquitinated by the SCF-beta-TRCP ubiquitin ligase complex and is subsequently processed by the proteaseome to p52, which is a transcriptionally competent NF-kB subunit in conjunction with RelB (Petrus et al. 2011, Sun 2011, Vallabhapurapu & Karin 2009).
R-HSA-5669034 TNFs bind their physiological receptors Members of the tumour necrosis factor superfamily (TNFSF) and TNF receptor superfamily (TNFRSF) have crucial roles in both innate and adaptive immunity. These members are implicated in various acquired or genetic human diseases, ranging from septic shock to autoimmune disorders, allograft rejection and cancer (So et al. 2006).
R-HSA-5628897 TP53 Regulates Metabolic Genes While the p53 tumor suppressor protein (TP53) is known to inhibit cell growth by inducing apoptosis, senescence and cell cycle arrest, recent studies have found that p53 is also able to influence cell metabolism to prevent tumor development. TP53 regulates transcription of many genes involved in the metabolism of carbohydrates, nucleotides and amino acids, protein synthesis and aerobic respiration.
TP53 stimulates transcription of TIGAR, a D-fructose 2,6-bisphosphatase. TIGAR activity decreases glycolytic rate and lowers ROS (reactive oxygen species) levels in cells (Bensaad et al. 2006). TP53 may also negatively regulate the rate of glycolysis by inhibiting the expression of glucose transporters GLUT1, GLUT3 and GLUT4 (Kondoh et al. 2005, Schwartzenberg-Bar-Yoseph et al. 2004, Kawauchi et al. 2008).
TP53 negatively regulates several key points in PI3K/AKT signaling and downstream mTOR signaling, decreasing the rate of protein synthesis and, hence, cellular growth. TP53 directly stimulates transcription of the tumor suppressor PTEN, which acts to inhibit PI3K-mediated activation of AKT (Stambolic et al. 2001). TP53 stimulates transcription of sestrin genes, SESN1, SESN2, and SESN3 (Velasco-Miguel et al. 1999, Budanov et al. 2002, Brynczka et al. 2007). One of sestrin functions may be to reduce and reactivate overoxidized peroxiredoxin PRDX1, thereby reducing ROS levels (Budanov et al. 2004, Papadia et al. 2008, Essler et al. 2009). Another function of sestrins is to bind the activated AMPK complex and protect it from AKT-mediated inactivation. By enhancing AMPK activity, sestrins negatively regulate mTOR signaling (Budanov and Karin 2008, Cam et al. 2014). The expression of DDIT4 (REDD1), another negative regulator of mTOR signaling, is directly stimulated by TP63 and TP53. DDIT4 prevents AKT-mediated inactivation of TSC1:TSC2 complex, thus inhibiting mTOR cascade (Cam et al. 2014, Ellisen et al. 2002, DeYoung et al. 2008). TP53 may also be involved, directly or indirectly, in regulation of expression of other participants of PI3K/AKT/mTOR signaling, such as PIK3CA (Singh et al. 2002), TSC2 and AMPKB (Feng et al. 2007).
TP53 regulates mitochondrial metabolism through several routes. TP53 stimulates transcription of SCO2 gene, which encodes a mitochondrial cytochrome c oxidase assembly protein (Matoba et al. 2006). TP53 stimulates transcription of RRM2B gene, which encodes a subunit of the ribonucleotide reductase complex, responsible for the conversion of ribonucleotides to deoxyribonucleotides and essential for the maintenance of mitochondrial DNA content in the cell (Tanaka et al. 2000, Bourdon et al. 2007, Kulawiec et al. 2009). TP53 also transactivates mitochondrial transcription factor A (TFAM), a nuclear-encoded gene important for mitochondrial DNA (mtDNA) transcription and maintenance (Park et al. 2009). Finally, TP53 stimulates transcription of the mitochondrial glutaminase GLS2, leading to increased mitochondrial respiration rate and reduced ROS levels (Hu et al. 2010).
The great majority of tumor cells generate energy through aerobic glycolysis, rather than the much more efficient aerobic mitochondrial respiration, and this metabolic change is known as the Warburg effect (Warburg 1956). Since the majority of tumor cells have impaired TP53 function, and TP53 regulates a number of genes involved in glycolysis and mitochondrial respiration, it is likely that TP53 inactivation plays an important role in the metabolic derangement of cancer cells such as the Warburg effect and the concomitant increased tumorigenicity (reviewed by Feng and Levine 2010). On the other hand, some mutations of TP53 in Li-Fraumeni syndrome may result in the retention of its wild-type metabolic activities while losing cell cycle and apoptosis functions (Wang et al. 2013). Consistent with such human data, some mutations of p53, unlike p53 null state, retain the ability to regulate energy metabolism while being inactive in regulating its classic gene targets involved in cell cycle, apoptosis and senescence. Retention of metabolic and antioxidant functions of p53 protects p53 mutant mice from early onset tumorigenesis (Li et al. 2012). R-HSA-6803207 TP53 Regulates Transcription of Caspase Activators and Caspases TP53 (p53) transcriptionally regulates cytosolic caspase activators, such as APAF1, PIDD1, and NLRC4, and caspases themselves, such as CASP1, CASP6 and CASP10. These caspases and their activators are involved either in the intrinsic apoptosis pathway or in the extrinsic apoptosis pathway triggerred by death receptors or the inflammation-related cell death pyroptosis (Lin et al. 2000, Robles et al. 2001, Gupta et al. 2001, MacLachlan and El-Deiry 2002, Rikhof et al. 2003, Sadasivam et al. 2005, Brough and Rothwell 2007). R-HSA-6791312 TP53 Regulates Transcription of Cell Cycle Genes Under a variety of stress conditions, TP53 (p53), stabilized by stress-induced phosphorylation at least on S15 and S20 serine residues, can induce the transcription of genes involved in cell cycle arrest. Cell cycle arrest provides cells an opportunity to repair the damage before division, thus preventing the transmission of genetic errors to daughter cells. In addition, it allows cells to attempt a recovery from the damage and survive, preventing premature cell death.
TP53 controls transcription of genes involved in both G1 and G2 cell cycle arrest. The most prominent TP53 target involved in G1 arrest is the inhibitor of cyclin-dependent kinases CDKN1A (p21). CDKN1A is one of the earliest genes induced by TP53 (El-Deiry et al. 1993). CDKN1A binds and inactivates CDK2 in complex with cyclin A (CCNA) or E (CCNE), thus preventing G1/S transition (Harper et al. 1993). Nevertheless, under prolonged stress, the cell destiny may be diverted towards an apoptotic outcome. For instance, in case of an irreversible damage, TP53 can induce transcription of an RNA binding protein PCBP4, which can bind and destabilize CDKN1A mRNA, thus alleviating G1 arrest and directing the affected cell towards G2 arrest and, possibly, apoptosis (Zhu and Chen 2000, Scoumanne et al. 2011). Expression of E2F7 is directly induced by TP53. E2F7 contributes to G1 cell cycle arrest by repressing transcription of E2F1, a transcription factor that promotes expression of many genes needed for G1/S transition (Aksoy et al. 2012, Carvajal et al. 2012). ARID3A is a direct transcriptional target of TP53 (Ma et al. 2003) that may promote G1 arrest by cooperating with TP53 in induction of CDKN1A transcription (Lestari et al. 2012). However, ARID3A may also promote G1/S transition by stimulating transcriptional activity of E2F1 (Suzuki et al. 1998, Peeper et al. 2002).
TP53 contributes to the establishment of G2 arrest by inducing transcription of GADD45A and SFN, and by inhibiting transcription of CDC25C. TP53 induces GADD45A transcription in cooperation with chromatin modifying enzymes EP300, PRMT1 and CARM1 (An et al. 2004). GADD45A binds Aurora kinase A (AURKA), inhibiting its catalytic activity and preventing AURKA-mediated G2/M transition (Shao et al. 2006, Sanchez et al. 2010). GADD45A also forms a complex with PCNA. PCNA is involved in both normal and repair DNA synthesis. The effect of GADD45 interaction with PCNA, if any, on S phase progression, G2 arrest and DNA repair is not known (Smith et al. 1994, Hall et al. 1995, Sanchez et al. 2010, Kim et al. 2013). SFN (14-3-3-sigma) is induced by TP53 (Hermeking et al. 1997) and contributes to G2 arrest by binding to the complex of CDK1 and CCNB1 (cyclin B1) and preventing its translocation to the nucleus. Phosphorylation of a number of nuclear proteins by the complex of CDK1 and CCNB1 is needed for G2/M transition (Chan et al. 1999). While promoting G2 arrest, SFN can simultaneously inhibit apoptosis by binding to BAX and preventing its translocation to mitochondria, a step involved in cytochrome C release (Samuel et al. 2001). TP53 binds the promoter of the CDC25C gene in cooperation with the transcriptional repressor E2F4 and represses CDC25C transcription, thus maintaining G2 arrest (St Clair et al. 2004, Benson et al. 2014).
Several direct transcriptional targets of TP53 are involved in cell cycle arrest but their mechanism of action is still unknown. BTG2 is induced by TP53, leading to cessation of cellular proliferation (Rouault et al. 1996, Duriez et al. 2002). BTG2 binds to the CCR4-NOT complex and promotes mRNA deadenylation activity of this complex. Interaction between BTG2 and CCR4-NOT is needed for the antiproliferative activity of BTG2, but the underlying mechanism has not been elucidated (Rouault et al. 1998, Mauxion et al. 2008, Horiuchi et al. 2009, Doidge et al. 2012, Ezzeddine et al. 2012). Two polo-like kinases, PLK2 and PLK3, are direct transcriptional targets of TP53. TP53-mediated induction of PLK2 may be important for prevention of mitotic catastrophe after spindle damage (Burns et al. 2003). PLK2 is involved in the regulation of centrosome duplication through phosphorylation of centrosome-related proteins CENPJ (Chang et al. 2010) and NPM1 (Krause and Hoffmann 2010). PLK2 is frequently transcriptionally silenced through promoter methylation in B-cell malignancies (Syed et al. 2006). Induction of PLK3 transcription by TP53 (Jen and Cheung 2005) may be important for coordination of M phase events through PLK3-mediated nuclear accumulation of CDC25C (Bahassi et al. 2004). RGCC is induced by TP53 and implicated in cell cycle regulation, possibly through its association with PLK1 (Saigusa et al. 2007). PLAGL1 (ZAC1) is a zinc finger protein directly transcriptionally induced by TP53 (Rozenfeld-Granot et al. 2002). PLAGL1 expression is frequently lost in cancer (Varrault et al. 1998) and PLAGL1 has been implicated in both cell cycle arrest and apoptosis (Spengler et al. 1997), but its mechanism of action remains unknown.
The zinc finger transcription factor ZNF385A (HZF) is a direct transcriptional target of TP53 that can form a complex with TP53 and facilitate TP53-mediated induction of CDKN1A and SFN (14-3-3 sigma) transcription (Das et al. 2007).
For a review of the role of TP53 in cell cycle arrest and cell cycle transcriptional targets of TP53, please refer to Riley et al. 2008, Murray-Zmijewski et al. 2008, Bieging et al. 2014, Kruiswijk et al. 2015.
R-HSA-5633008 TP53 Regulates Transcription of Cell Death Genes The tumor suppressor TP53 (p53) exerts its tumor suppressive role in part by regulating transcription of a number of genes involved in cell death, mainly apoptotic cell death. The majority of apoptotic genes that are transcriptional targets of TP53 promote apoptosis, but there are also several TP53 target genes that inhibit apoptosis, providing cells with an opportunity to attempt to repair the damage and/or recover from stress.
Pro-apoptotic transcriptional targets of TP53 involve TRAIL death receptors TNFRSF10A (DR4), TNFRSF10B (DR5), TNFRSF10C (DcR1) and TNFRSF10D (DcR2), as well as the FASL/CD95L death receptor FAS (CD95). TRAIL receptors and FAS induce pro-apoptotic signaling in response to external stimuli via extrinsic apoptosis pathway (Wu et al. 1997, Takimoto et al. 2000, Guan et al. 2001, Liu et al. 2004, Ruiz de Almodovar et al. 2004, Liu et al. 2005, Schilling et al. 2009, Wilson et al. 2013). IGFBP3 is a transcriptional target of TP53 that may serve as a ligand for a novel death receptor TMEM219 (Buckbinder et al. 1995, Ingermann et al. 2010).
TP53 regulates expression of a number of genes involved in the intrinsic apoptosis pathway, triggered by the cellular stress. Some of TP53 targets, such as BAX, BID, PMAIP1 (NOXA), BBC3 (PUMA) and probably BNIP3L, AIFM2, STEAP3, TRIAP1 and TP53AIP1, regulate the permeability of the mitochondrial membrane and/or cytochrome C release (Miyashita and Reed 1995, Oda et al. 2000, Samuels-Lev et al. 2001, Nakano and Vousden 2001, Sax et al. 2002, Passer et al. 2003, Bergamaschi et al. 2004, Li et al. 2004, Fei et al. 2004, Wu et al. 2004, Park and Nakamura 2005, Patel et al. 2008, Wang et al. 2012, Wilson et al. 2013). Other pro-apoptotic genes, either involved in the intrinsic apoptosis pathway, extrinsic apoptosis pathway or pyroptosis (inflammation-related cell death), which are transcriptionally regulated by TP53 are cytosolic caspase activators, such as APAF1, PIDD1, and NLRC4, and caspases themselves, such as CASP1, CASP6 and CASP10 (Lin et al. 2000, Robles et al. 2001, Gupta et al. 2001, MacLachlan and El-Deiry 2002, Rikhof et al. 2003, Sadasivam et al. 2005, Brough and Rothwell 2007).
It is uncertain how exactly some of the pro-apoptotic TP53 targets, such as TP53I3 (PIG3), RABGGTA, BCL2L14, BCL6, NDRG1 and PERP contribute to apoptosis (Attardi et al. 2000, Guo et al. 2001, Samuels-Lev et al. 2001, Contente et al. 2002, Ihrie et al. 2003, Bergamaschi et al. 2004, Stein et al. 2004, Phan and Dalla-Favera 2004, Jen and Cheung 2005, Margalit et al. 2006, Zhang et al. 2007, Saito et al. 2009, Davies et al. 2009, Giam et al. 2012).
TP53 is stabilized in response to cellular stress by phosphorylation on at least serine residues S15 and S20. Since TP53 stabilization precedes the activation of cell death genes, the TP53 tetramer phosphorylated at S15 and S20 is shown as a regulator of pro-apoptotic/pro-cell death genes. Some pro-apoptotic TP53 target genes, such as TP53AIP1, require additional phosphorylation of TP53 at serine residue S46 (Oda et al. 2000, Taira et al. 2007). Phosphorylation of TP53 at S46 is regulated by another TP53 pro-apoptotic target, TP53INP1 (Okamura et al. 2001, Tomasini et al. 2003). Additional post-translational modifications of TP53 may be involved in transcriptional regulation of genes presented in this pathway and this information will be included as evidence becomes available.
Activation of some pro-apoptotic TP53 targets, such as BAX, FAS, BBC3 (PUMA) and TP53I3 (PIG3) requires the presence of the complex of TP53 and an ASPP protein, either PPP1R13B (ASPP1) or TP53BP2 (ASPP2) (Samuels-Lev et al. 2001, Bergamaschi et al. 2004, Patel et al. 2008, Wilson et al. 2013), indicating how the interaction with specific co-factors modulates the cellular response/outcome.
TP53 family members TP63 and or TP73 can also activate some of the pro-apoptotic TP53 targets, such as FAS, BAX, BBC3 (PUMA), TP53I3 (PIG3), CASP1 and PERP (Bergamaschi et al. 2004, Jain et al. 2005, Ihrie et al. 2005, Patel et al. 2008, Schilling et al. 2009, Celardo et al. 2013).
For a review of the role of TP53 in apoptosis and pro-apoptotic transcriptional targets of TP53, please refer to Riley et al. 2008, Murray-Zmijewski et al. 2008, Bieging et al. 2014, Kruiswijk et al. 2015.
R-HSA-6796648 TP53 Regulates Transcription of DNA Repair Genes Several DNA repair genes contain p53 response elements and their transcription is positively regulated by TP53 (p53). TP53-mediated regulation probably ensures increased protein level of DNA repair genes under genotoxic stress.
TP53 directly stimulates transcription of several genes involved in DNA mismatch repair, including MSH2 (Scherer et al. 2000, Warnick et al. 2001), PMS2 and MLH1 (Chen and Sadowski 2005). TP53 also directly stimulates transcription of DDB2, involved in nucleotide excision repair (Tan and Chu 2002), and FANCC, involved in the Fanconi anemia pathway that repairs DNA interstrand crosslinks (Liebetrau et al. 1997). Other p53 targets that can influence DNA repair functions are RRM2B (Kuo et al. 2012), XPC (Fitch et al. 2003), GADD45A (Amundson et al. 2002), CDKN1A (Cazzalini et al. 2010) and PCNA (Xu and Morris 1999). Interestingly, the responsiveness of some of these DNA repair genes to p53 activation has been shown in human cells but not for orthologous mouse genes (Jegga et al. 2008, Tan and Chu 2002). Contrary to the positive modulation of nucleotide excision repair (NER) and mismatch repair (MMR), p53 can negatively modulate base excision repair (BER), by down-regulating the endonuclease APEX1 (APE1), acting in concert with SP1 (Poletto et al. 2016).
Expression of several DNA repair genes is under indirect TP53 control, through TP53-mediated stimulation of cyclin K (CCNK) expression (Mori et al. 2002). CCNK is the activating cyclin for CDK12 and CDK13 (Blazek et al. 2013). The complex of CCNK and CDK12 binds and phosphorylates the C-terminal domain of the RNA polymerase II subunit POLR2A, which is necessary for efficient transcription of long DNA repair genes, including BRCA1, ATR, FANCD2, FANCI, ATM, MDC1, CHEK1 and RAD51D. Genes whose transcription is regulated by the complex of CCNK and CDK12 are mainly involved in the repair of DNA double strand breaks and/or the Fanconi anemia pathway (Blazek et al. 2011, Cheng et al. 2012, Bosken et al. 2014, Bartkowiak and Greenleaf 2015, Ekumi et al. 2015). R-HSA-6803211 TP53 Regulates Transcription of Death Receptors and Ligands Pro-apoptotic transcriptional targets of TP53 are TRAIL death receptors TNFRSF10A (DR4), TNFRSF10B (DR5), TNFRSF10C (DcR1) and TNFRSF10D (DcR2), as well as the FASL/CD95L death receptor FAS (CD95). TRAIL receptors and FAS induce pro-apoptotic signaling in response to external stimuli via extrinsic apoptosis pathway (Wu et al. 1997, Takimoto et al. 2000, Guan et al. 2001, Liu et al. 2004, Ruiz de Almodovar et al. 2004, Liu et al. 2005, Schilling et al. 2009, Wilson et al. 2013). IGFBP3 is a transcriptional target of TP53 that may serve as a ligand for a novel death receptor TMEM219 (Buckbinder et al. 1995, Ingermann et al. 2010). R-HSA-6803204 TP53 Regulates Transcription of Genes Involved in Cytochrome C Release Apoptotic transcriptional targets of TP53 include genes that regulate the permeability of the mitochondrial membrane and/or cytochrome C release, such as BAX, BID, PMAIP1 (NOXA), BBC3 (PUMA) and probably BNIP3L, AIFM2, STEAP3, TRIAP1 and TP53AIP1 (Miyashita and Reed 1995, Oda et al. 2000, Samuels-Lev et al. 2001, Nakano and Vousden 2001, Sax et al. 2002, Passer et al. 2003, Bergamaschi et al. 2004, Li et al. 2004, Fei et al. 2004, Wu et al. 2004, Park and Nakamura 2005, Patel et al. 2008, Wang et al. 2012, Wilson et al. 2013), thus promoting the activation of the apoptotic pathway.
Transcriptional activation of TP53AIP1 requires phosphorylation of TP53 at serine residue S46 (Oda et al. 2000, Taira et al. 2007). Phosphorylation of TP53 at S46 is regulated by another TP53 pro-apoptotic target, TP53INP1 (Okamura et al. 2001, Tomasini et al. 2003). R-HSA-6804116 TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest The most prominent TP53 target involved in G1 arrest is the inhibitor of cyclin-dependent kinases CDKN1A (p21). CDKN1A is one of the earliest genes induced by TP53 (El-Deiry et al. 1993). CDKN1A binds and inactivates CDK2 in complex with cyclin A (CCNA) or E (CCNE), thus preventing G1/S transition (Harper et al. 1993). Considering its impact on the cell cycle outcome, CDKN1A expression levels are tightly regulated. For instance, under prolonged stress, TP53 can induce the transcription of an RNA binding protein PCBP4, which can bind and destabilize CDKN1A mRNA, thus alleviating G1 arrest and directing the affected cell towards G2 arrest and, possibly, apoptosis (Zhu and Chen 2000, Scoumanne et al. 2011). Expression of E2F7 is directly induced by TP53. E2F7 contributes to G1 cell cycle arrest by repressing transcription of E2F1, a transcription factor that promotes expression of many genes needed for G1/S transition (Aksoy et al. 2012, Carvajal et al. 2012). ARID3A is a direct transcriptional target of TP53 (Ma et al. 2003) that may promote G1 arrest by cooperating with TP53 in induction of CDKN1A transcription (Lestari et al. 2012). However, ARID3A may also promote G1/S transition by stimulating transcriptional activity of E2F1 (Suzuki et al. 1998, Peeper et al. 2002).
TP53 has co-factors that are key determinants of transcriptional selectivity within the p53 network. For instance, the zinc finger transcription factor ZNF385A (HZF) is a direct transcriptional target of TP53 that can form a complex with TP53 and facilitate TP53-mediated induction of CDKN1A, strongly favouring cell cycle arrest over apoptosis (Das et al. 2007). R-HSA-6804114 TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest TP53 contributes to the establishment of G2 arrest by inducing transcription of GADD45A and SFN, and by inhibiting transcription of CDC25C. TP53 induces GADD45A transcription in cooperation with chromatin modifying enzymes EP300, PRMT1 and CARM1 (An et al. 2004). GADD45A binds Aurora kinase A (AURKA), inhibiting its catalytic activity and preventing AURKA-mediated G2/M transition (Shao et al. 2006, Sanchez et al. 2010). GADD45A also forms a complex with PCNA. PCNA is involved in both normal and repair DNA synthesis. The effect of GADD45 interaction with PCNA, if any, on S phase progression, G2 arrest and DNA repair is not known (Smith et al. 1994, Hall et al. 1995, Sanchez et al. 2010, Kim et al. 2013). SFN (14-3-3-sigma) is induced by TP53 (Hermeking et al. 1997) and contributes to G2 arrest by binding to the complex of CDK1 and CCNB1 (cyclin B1) and preventing its translocation to the nucleus. Phosphorylation of a number of nuclear proteins by the complex of CDK1 and CCNB1 is needed for G2/M transition (Chan et al. 1999). While promoting G2 arrest, SFN can simultaneously inhibit apoptosis by binding to BAX and preventing its translocation to mitochondria, a step involved in cytochrome C release (Samuel et al. 2001). TP53 binds the promoter of the CDC25C gene in cooperation with the transcriptional repressor E2F4 and represses CDC25C transcription, thus maintaining G2 arrest (St Clair et al. 2004, Benson et al. 2014). The zinc finger transcription factor ZNF385A (HZF) is a direct transcriptional target of TP53 that can form a complex with TP53 and facilitate TP53-mediated induction of SFN transcription (Das et al. 2007). R-HSA-6804115 TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain BTG2 is induced by TP53, leading to cessation of cellular proliferation (Rouault et al. 1996, Duriez et al. 2002). BTG2 binds to the CCR4-NOT complex and promotes mRNA deadenylation activity of this complex. Interaction between BTG2 and CCR4-NOT is needed for the antiproliferative activity of BTG2, but the underlying mechanism has not been elucidated (Rouault et al. 1998, Mauxion et al. 2008, Horiuchi et al. 2009, Doidge et al. 2012, Ezzeddine et al. 2012). Two polo-like kinases, PLK2 and PLK3, are direct transcriptional targets of TP53. TP53-mediated induction of PLK2 may be important for prevention of mitotic catastrophe after spindle damage (Burns et al. 2003). PLK2 is involved in the regulation of centrosome duplication through phosphorylation of centrosome-related proteins CENPJ (Chang et al. 2010) and NPM1 (Krause and Hoffmann 2010). PLK2 is frequently transcriptionally silenced through promoter methylation in B-cell malignancies (Syed et al. 2006). Induction of PLK3 transcription by TP53 (Jen and Cheung 2005) may be important for coordination of M phase events through PLK3-mediated nuclear accumulation of CDC25C (Bahassi et al. 2004). RGCC is induced by TP53 and implicated in cell cycle regulation, possibly through its association with PLK1 (Saigusa et al. 2007). PLAGL1 (ZAC1) is a zinc finger protein directly transcriptionally induced by TP53 (Rozenfeld-Granot et al. 2002). PLAGL1 expression is frequently lost in cancer (Varrault et al. 1998) and PLAGL1 has been implicated in both cell cycle arrest and apoptosis (Spengler et al. 1997), but its mechanism of action remains unknown. R-HSA-6803205 TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain The exact mechanisms of action of several other pro-apoptotic TP53 (p53) targets, such as TP53I3 (PIG3), RABGGTA, BCL2L14, BCL6, NDRG1 and PERP, remain uncertain (Attardi et al. 2000, Guo et al. 2001, Samuels-Lev et al. 2001, Contente et al. 2002, Ihrie et al. 2003, Bergamaschi et al. 2004, Stein et al. 2004, Phan and Dalla-Favera 2004, Jen and Cheung 2005, Margalit et al. 2006, Zhang et al. 2007, Saito et al. 2009, Davies et al. 2009, Giam et al. 2012). R-HSA-5602571 TRAF3 deficiency - HSE TNF Receptor Associated Factor 3 (TRAF3) is a cytoplasmic adaptor protein utilized by the tumor necrosis factor receptor superfamily and toll-like receptors (TLRs). TRAF3 deficiency is thought to mimic the previously reported TLR3 deficiency in terms of susceptibility to herpes simplex virus type 1 (HSV1) encephalitis (HSE) via impaired TLR3-mediated immunity against HSV1 infection of central nervous system (CNS) (Pérez de Diego R et al. 2010; Guo Y et al. 2011). R-HSA-918233 TRAF3-dependent IRF activation pathway MAVS via its TRAF-interaction motif (TIM) directly interacts with TRAF3 and recruits TRAF3 to the signaling complex. TRAF3 acts as a scaffold for the assembly of a signaling complex composed of IKK epsilon/TBK1, leading to the activation of transcription factors IRF3/IRF7. R-HSA-933541 TRAF6 mediated IRF7 activation TRAF6 is crucial for both RIG-I- and MDA5-mediated antiviral responses. The absence of TRAF6 resulted in enhanced viral replication and a significant reduction in the production of type I IFNs and IL6 after infection with RNA virus. Activation of NF-kB and IRF7, but not that of IRF3, was significantly impaired during RIG-like helicases (RLHs) signaling in the absence of TRAF6. TRAF6-induced activation of IRF is likely to be specific for IRF7, while TRAF3 is thought to activate both IRF3 and IRF7. These results strongly suggest that the TRAF6- and TRAF3-dependent pathways are likely to bifurcate at IPS-1, but to converge later at IRF7 in order to co-operatively induce sufficient production of type I IFNs during RLH signaling. R-HSA-975110 TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling In plasmacytoid dendritic cell induction of type I IFNs critically depends on IFN regulatory factor 7 in TLR7 and 9 signaling (Honda et al 2005). IRF-7, but not IRF3, interacts with MyD88, TRAF6, and IRAKs and translocates to the nucleus upon phosphorylation (Kawai et al 2004; Uematsu et al 2005).
TLR7/8 signaling was shown to induce IRF5 activation along with IRF7 [Schoenemeyer et al 2005], while IRF8 [Tsujimura H et al 2004] and IRF1 were reported to be implicated in TLR9 signaling. R-HSA-933542 TRAF6 mediated NF-kB activation The TRAF6/TAK1 signal activates a canonical IKK complex, resulting in the activation of NF-kB as well as MAPK cascades leading to the activation of AP-1. Although TRAF6/TAK1 has been implicated in Tool like receptor (TLR) mediated cytokine production, the involvement of these molecules in the regulation of type I IFN induction mediated by RIG-I/MDA5 pathway is largely unknown. According to the study done by Yoshida et al RIG-I/IPS-1 pathway requires TRAF6 and MAP3K, MEKK1 to activate NF-kB and MAP Kinases for optimal induction of type I IFNs. R-HSA-975138 TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation TRAF6 mediates NFkB activation via canonical phosphorylation of IKK complex by TAK1. TRAF6 and TAK1 also regulate MAPK cascades leading to the activation of AP-1. R-HSA-937072 TRAF6-mediated induction of TAK1 complex within TLR4 complex In human, together with ubiquitin-conjugating E2-type enzymes UBC13 and UEV1A (also known as UBE2V1), TRAF6 catalyses Lys63-linked ubiquitination. It is believed that auto polyubiquitination and oligomerization of TRAF6 is followed by binding the ubiquitin receptors of TAB2 or TAB3 (TAK1 binding protein 2 and 3), which stimulates phosphorylation and activation of TGF beta-activated kinase 1(TAK1).
TAK1 phosphorylates IKK alpha and IKK beta, which in turn phosphorylate NF-kB inhibitors - IkB and eventually results in IkB degradation and NF-kB translocation to the nucleus. Also TAK1 mediates JNK and p38 MAP kinases activation by phosphorylating MKK4/7 and MKK3/6 respectivly resulting in the activation of many transcription factors.
The role of TRAF6 is somewhat controversial and probably cell type specific. TRAF6 autoubiquitination was found to be dispensable for TRAF6 function to activate TAK1 pathway. These findings are consistent with the new mechanism of TRAF6-mediated NF-kB activation that was suggested by Xia et al. (2009). TRAF6 generates unanchored Lys63-linked polyubiquitin chains that bind to the regulatory subunits of TAK1 (TAB2 or TAB3) and IKK(NEMO), leading to the activation of the kinases.
Xia et al. (2009) demonstrated in vitro that unlike polyubiquitin chains covalently attached to TRAF6 or IRAK, TAB2 and NEMO-associated ubiquitin chains were found to be unanchored and susceptible to N-terminal ubiquitin cleavage. Only K63-linked polyubiquitin chains, but not monomeric ubiquitin, activated TAK1 in a dose-dependent manner. Optimal activation of the IKK complex was achieved using ubiquitin polymers containing both K48 and K63 linkages.
Furthermore, the authors proposed that the TAK1 complexes might be brougt in close proximity by binding several TAB2/3 to a single polyubiquitin chain to facilitate TAK1 kinase trans-phosphorylation. Alternativly, the possibility that polyUb binding promotes allosteric activation of TAK1 complex should be considered (Walsh et al 2008).
R-HSA-75158 TRAIL signaling Tumor necrosis factor-related apoptosis-inducing ligand or Apo 2 ligand (TRAIL/Apo2L) is a member of the tumor necrosis factor (TNF) family. This group of apoptosis induction pathways all work through protein interactions mediated by the intracellular death domain (DD), encoded within the cytoplasmic domain of the receptor. TRAIL selectively induces apoptosis through its interaction with the Fas-associated death domain protein (FADD) and caspase-8/10 (Wang S & el-Deiry WS 2003; Sprick MR et al. 2002). TRAIL and its receptors, TRAIL-R1 and TRAIL-R2, were shown to be rapidly endocytosed via clathrin-dependent and -independent manner in human Burkitt's lymphoma B cells (BJAB) (Kohlhaas SL et al. 2007). However, FADD and caspase-8 were able to bind TRAIL-R1/R2 in TRAIL-stimulated BJAB cells at 4oC (at which membrane trafficking is inhibited), suggesting that the endocytosis was not required for an assembly of the functional TRAIL DISC complex. Moreover, blocking of clathrin-dependent endocytosis did not interfere with the capacity of TRAIL to promote apoptosis (Kohlhaas SL et al. 2007).
R-HSA-937061 TRIF (TICAM1)-mediated TLR4 signaling TRIF (TICAM1) was shown to induce IRF3/7 and NF-kappa-B activation as well as apoptosis through distinct intracellular signaling pathways (Yamamoto M et al., 2003; Fitzgerald KA et al., 2003; Han KJ et al., 2004; Kaiser WJ & Offermann MK 2005).
TRIF consists of an N-terminal domain (NTD) (1-153), an intermediate disordered proline-rich region, a TIR domain, and a C-terminal region (Mahita J & Sowdhamin R 2017). The disordered proline-rich region between NTD domain and the TIR domain of TICAM1 contains binding sites for TRAF (TNF receptor associated factor) family proteins, which, in turn, recruit protein kinases to promote activation of IRF3 and/or NF-kappa-B (Sato S et al., 2003; Fitzgerald KA et al., 2003). The C-terminal region of TICAM1 (TRIF) can recruit receptor-interacting serine/threonine-protein kinase 1 (RIPK1), and this event is followed by the activation of the IKK complex or the induction of programmed cell death (Han KJ et al., 2004; Kaiser WJ & Offermann MK 2005).
R-HSA-2562578 TRIF-mediated programmed cell death TLR3 and -4 trigger TRIF-dependent programmed cell death in various human and mouse cells (Kalai M et al. 2002; Han KJ et al. 2004; Kaiser WJ and Offermann MK 2005; Estornes Y et al. 2012; He S et al. 2011). Apoptosis is a prevalent form of programmed cell death and is mediated by the activation of a set of caspases. In addition to apoptosis, TLR3/TLR4 activation induces RIP3-dependent necroptosis. These two programmed cell-death pathways may suppress each other. When the caspase activity is impaired or inhibited, certain cell types switch the apoptotic death program to necroptosis in response to various stimuli (TNF, Fas, viral infection and other stress stimuli) (Kalai M et al. 2002; Weber A et al. 2010; Feoktistova M et al. 2011, Tenev et al 2011).
R-HSA-187042 TRKA activation by NGF Neurotrophin functions are mediated by binding of the secreted neurotrophin homodimers to their common neurotrophin receptor p75NTR, and to their cognate tropomyosin related kinase (TRK) receptor. NGF binds to TRKA, BDNF and NT4 bind to TRKB, NT3 binds to TRKC. A tri-molecular signalling complex (NGF-p75NTR-TRKA) might also be possible.
R-HSA-3295583 TRP channels Transient receptor potential (TRP) channel proteins were first discovered in Drosophila melanogaster and have many homologues in other species including humans. TRPs form cationic channels that can detect sensory stimuli such as temperature, pH or oxidative stress and transduce that into either electrical (change in membrane potential) or chemical signals (change in intracellular Ca2+ concentration). In humans, there are 28 TRP genes arranged into 6 subfamilies; TRPA, TRPC, TRPM, TRPML, TRPP, and TRPV (Wu et al. 2010). Each TRP channel subunit consists of six putative transmembrane-spanning segments (S1-S6) with a pore-forming loop between S5 and S6. These subunits assemble into tetramers to form functional channels. All functionally characterized TRP channels are permeable to Ca2+ except TRMP4 and 5 which are only permeable to monovalent cations such as Na+ (Latorre et al. 2009). Most TRPs can cause channelopathies which are risk factors for many disease states (Nilius & Owsianik 2010).
R-HSA-1299503 TWIK related potassium channel (TREK) TREK1 and TREK 2 are activated by physiochemical changes like stretch, convex deformation of the plasma membrane, depolarization, heat and intracellular acidosis. Polyunsaturated fatty acids (PUFA) including arachidonic acid open TREK channels.
R-HSA-1299361 TWIK-related alkaline pH activated K+ channel (TALK) TWIK related alkaline pH activated K+ channels are activated by increase in the extracellular pH. TALK1 and TALK 2 are members of the TALK subfamily and are both are activated by rise in extracellular pH. TALK 2 is expressed in proximal tubule cells and collecting duct cells. TASK 2 is involved in the resorption of bicarbonate.
R-HSA-1299344 TWIK-related spinal cord K+ channel (TRESK) TRESK subfamily of tandem domain K+ channels has one only member. TRESK is regulated by Ca/calmodulin dependent protein phosphatase, calcineurin.
R-HSA-1299316 TWIK-releated acid-sensitive K+ channel (TASK) TASK 1 and 3 are closely related both structurally and functionally. TASK1 and TASK3 are activated by extracellular acidification and inhibited by decrease in pH. TASK 1 and Task 3 form functional homodimers and heterodimers, however the biophysical properties of TAS1 and TASK3 heteromers are different form parent subunit properties.
R-HSA-9033500 TYSND1 cleaves peroxisomal proteins After proteins are imported into the peroxisome a subset of proteins are cleaved by the protease TYSND1 (Okumoto et al. 2011). Based onmutagenesis of human TYSND1 (Okumoto et al. 2011) and the homolog in Arabidopsis (Schuhmann et al. 2008), TYSND1 appears to be a trypsin-like serine protease containing a conserved histidine aspartate serine triad essential for catalysis. Mice lacking Tysnd1 have reduced peroxisomal localization of some peroxisomal enzymes and exhibit reduced beta-oxidation of fatty acids and metabolism of phytanic acid (Mizuno et al. 2013). Male mice lacking Tysnd1 are sterile due to sperm that lack acrosomal caps.
R-HSA-380095 Tachykinin receptors bind tachykinins Tachykinin peptides are one of the largest family of neuropeptides, so named due to their ability to rapidly induce contraction of gut tissue. Tachykinins excite neurons, elicit behavioural responses, are potent vasodilators and contract many smooth muscles. The tachykinin family is characterized by a common C-terminal sequence, Phe-X-Gly-Leu-Met-NH2 (where X can be either an aromatic or an aliphatic amino acid) and are ten to twelve residues long.
These peptides elicit their effects via the tachykinin receptors, of which there are three types in humans (NK1,2 and 3). There are two human tachykinin peptide genes in humans, TAC1 and TAC3. TAC1 encodes substance P and substance K while TAC3 encodes neurokinin B.
Antagonists of these receptors are promising candidates for classes of antidepressants, anxiolytics and antipsychotics.
R-HSA-1299308 Tandem of pore domain in a weak inwardly rectifying K+ channels (TWIK) TWIK channels exhibit very low current and comprise of TWIK1, TWIK2 and KCNK7 members. TWIK current may be low due to rapid recycling of the channels from the plasma membrane.
R-HSA-1299287 Tandem pore domain halothane-inhibited K+ channel (THIK) THIK channels are K+ leak channels that are not regulated by pH or temperature changes.
R-HSA-1296346 Tandem pore domain potassium channels Tandem pore domain K+ channels (K2p) produce leak K+ current which stabilizes negative membrane potential and counter balances depolarization. These channels are regulated by voltage independent mechanisms such as membrane stretch, pH, temperature. Tandem pore domain K+ channels have been classified into six subfamilies; tandem pore domains in weak rectifying K+ channel (TWIK), TWIK-related K+ channel (TREK), TWIK-related acid-sensitive K+ channel (TASK), TWIK-related alkaline pH-activated K+ channel (TALK), tandem pore domain halothane-inhibted K+ channel (THIK), TWIK-releated spinal cord K+ channel).
R-HSA-167243 Tat-mediated HIV elongation arrest and recovery RNA Pol II arrest is believed to be a result of irreversible backsliding of the enzyme by ~7-14 nucleotides. TFIIS reactivates arrested RNA Pol II by promoting the excision of nascent transcript ~7-14 nucleotides upstream of the 3' end.
R-HSA-167246 Tat-mediated elongation of the HIV-1 transcript The Tat protein is a viral transactivator protein that regulates HIV-1 gene expression by controlling RNA Pol II-mediated elongation (reviewed in Karn 1999; Taube et al. 1999; Liou et al. 2004; Barboric and Peterlin 2005). Tat appears to be required in order to overcome the arrest of RNA Pol II by the negative transcriptional elongation factors DSIF and NELF (Wada et al. 1998; Yamaguchi et al. 1999; Yamaguchi et al 2002; Fujinaga et al. 2004). While Pol II can associate with the proviral LTR and initiate transcription in the absence of Tat, these polymerase complexes are non-processive and dissociate from the template prematurely producing very short transcripts (Kao et al. 1987). Tat associates with the RNA element, TAR, which forms a stem loop structure in the leader RNA sequence (Dingwall et al. 1989). Tat also associates with the cellular kinase complex P-TEFb(Cyclin T1:Cdk9) and recruits it to the TAR stem loop structure (Herrmann, 1995) (Wei et al. 1998). This association between Tat, TAR and P-TEFb(Cyclin T1:Cdk9) is believed to bring the catalytic subunit of this kinase complex (Cdk9) in close proximity to Pol II where it hyperphosphorylates the CTD of RNA Pol II (Zhou et al. 2000). The RD subunits of NELF and the SPT5 subunit of DSIF, which associate through RD with the bottom stem of TAR, are also phosphorylated by P-TEFb(Cyclin T1:Cdk9) (Yamaguchi et al. 2002; Fujinaga et al. 2004; Ivanov et al. 2000). Phosphorylation of RD results in its dissociation from TAR. Thus, Tat appears to facilitate transcriptional elongation of the HIV-1 transcript by hyperphosphorylating the RNA Poll II CTD and by removing the negative transcription elongation factors from TAR. In addition, there is evidence that the association of Tat with P-TEFb(Cyclin T1:Cdk9) alters the substrate specificity of P-TEFb enhancing phosphorylation of ser5 residues in the CTD of RNA Pol II (Zhou et al. 2000).
R-HSA-174417 Telomere C-strand (Lagging Strand) Synthesis Due to the antiparallel nature of DNA, DNA polymerization is unidirectional, and one strand is synthesized discontinuously. This strand is called the lagging strand. Although the polymerase switching on the lagging strand is very similar to that on the leading strand, the processive synthesis on the two strands proceeds quite differently. Short DNA fragments, about 100 bases long, called Okazaki fragments are synthesized on the RNA-DNA primers first. Strand-displacement synthesis occurs, whereby the primer-containing 5'-terminus of the adjacent Okazaki fragment is folded into a single-stranded flap structure. This flap structure is removed by endonucleases, and the adjacent Okazaki fragments are joined by DNA ligase.
R-HSA-174430 Telomere C-strand synthesis initiation DNA polymerases are not capable of de novo DNA synthesis and require synthesis of a primer, usually by a DNA-dependent RNA polymerase (primase) to begin DNA synthesis. In eukaryotic cells, the primer is synthesized by DNA polymerase alpha:primase. First, the DNA primase portion of this complex synthesizes approximately 6-10 nucleotides of RNA primer and then the DNA polymerase portion synthesizes an additional 20 nucleotides of DNA. There have been reports that TRF1 inhibits this activity at telomeres, though the mechanism and physiological relevance of this inhibition remain to be elucidated.
R-HSA-171319 Telomere Extension By Telomerase Humans, like most eukaryotic organisms, add direct repeats to the telomere using a specialized DNA polymerase called telomerase. Telomerase is a ribonucleoprotein (RNP) complex minimally composed of a conserved protein subunit containing a reverse transcriptase domain (human telomerase reverse transcriptase, hTERT) and a template-containing RNA (human telomerase RNA component, hTERC, or hTR, hTER). The primer for telomerase is the G-rich single-strand overhang at the chromosome end.
Telomerase can perform multiple rounds of repeat synthesis. The reaction cycle has been inferred from in vitro studies of telomerase from multiple organisms and can be described as having four events: 1) DNA primer recognition, 2) RNA template alignment, 3) elongation, and 4) translocation. Telomeric DNA is recognized in part by a presumed "anchor site" in hTERT, which preferentially binds G-rich DNA, and this interaction can affect elongation and translocation steps. This interaction occurs 5' of the alignment of the RNA template with the end nucleotides of the chromosome. RNA alignment positions the template adjacent to the chromosome terminus. During elongation, the template directs sequential addition of nucleotides to the telomere end. After synthesis of a repeat is completed, relative movement of telomerase and the primer, termed translocation, repositions telomerase at the end of the newly added sequence to allow initiation of another round of repeat addition.
R-HSA-157579 Telomere Maintenance Telomeres are protein-DNA complexes at the ends of linear chromosomes that are important for genome stability. Telomeric DNA in humans, as in many eukaryotic organisms, consists of tandem repeats (Blackburn and Gall 1978; Moyzis et al. 1988; Meyne et al. 1989). The repeats at human telomeres are composed of TTAGGG sequences and stretch for several kilobase pairs. Another feature of telomeric DNA in many eukaryotes is a G-rich 3' single strand overhang, which in humans is estimated to be approximately 50-300 bases long (Makarov et al. 1997; Wright et al. 1997; Huffman et al. 2000). Telomeric DNA isolated from humans and several other organisms can form a lasso-type structure called a t-loop in which the 3' single-strand end is presumed to invade the double stranded telomeric DNA repeat tract (Griffith et al. 1999). Telomeric DNA is bound by multiple protein factors that play important roles in regulating telomere length and in protecting the chromosome end from recombination, non-homologous end-joining, DNA damage signaling, and unregulated nucleolytic attack (reviewed in de Lange 2005).
DNA attrition can occur at telomeres, which can impact cell viability. Attrition can occur owing to the "end-replication problem", a consequence of the mechanism of lagging-strand synthesis (Watson 1972; Olovnikov 1973). Besides incomplete replication, nucleolytic processing also likely contributes to telomere attrition (Huffman et al. 2000). If telomeres become critically shortened, replicative senescence can result (Harley et al. 1990). Thus, in order to undergo multiple divisions, cells need a mechanism to replenish the sequence at their chromosome ends.
The primary means for maintaining the sequence at chromosome ends in many eukaryotic organisms, including humans, is based on telomerase (Greider and Blackburn, 1985; Morin 1989). Telomerase is a ribonucleoprotein complex minimally composed of a conserved protein subunit containing a reverse transcriptase domain (telomerase reverse transcriptase, TERT) (Lingner et al. 1997; Nakamura et al. 1997) and a template-containing RNA (telomerase RNA component, TERC, TR, TER) (Greider and Blackburn, 1987; Feng et al 1995). Telomerase uses the RNA template to direct addition of multiple tandem repeats to the 3' G-rich single strand overhang. Besides extension by telomerase, maintenance of telomeric DNA involves additional activities, including C-strand synthesis, which fills in the opposing strand, and nucleolytic processing, which likely contributes to the generation of the 3' overhang.
R-HSA-166665 Terminal pathway of complement After cleavage of C5, C5b undergoes conformational changes and exposes a binding site for C6. C5b6 binds C7 resulting in the exposure of membrane binding sites and incorporation into target membranes. The membrane-bound C5b-7 complex can then bind C8. C5b-8 acts as a polymerizing agent for C9. The first C9 bound to C5b-8 undergoes major structural changes enabling formation of an elongated molecule and allows binding of additional C9 molecules and insertion of C9 cylinders into the target membrane. The number of C9 molecules varies from 1-12 in the membrane, although polymers containing up to fifteen C9 molecules are also possible.
R-HSA-977068 Termination of O-glycan biosynthesis O-glycan biosynthesis can be terminated (or modified) by the addition of sialic acid residues on Core 1 and 2 glycoproteins by sialyltransferases (Varki et al. 2009).
R-HSA-5656169 Termination of translesion DNA synthesis The initiation and extent of translesion DNA synthesis (TLS) has to be tightly controlled in order to limit TLS-induced mutagenesis, caused by the low fidelity of TLS-participating DNA polymerases. Since monoubiquitination of PCNA at lysine residue K164 is a prerequisite for the assembly of TLS complexes on damaged DNA templates, PCNA deubiquitination is a key step in TLS termination that allows DNA polymerase switching from Y family DNA polymerases involved in TLS to replicative DNA polymerases delta and epsilon (Povlsen et al. 2012, Park et al. 2014).
R-HSA-1474151 Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation Tetrahydrobiopterin (BH4) is an essential co-factor for the aromatic amino acid hydroxylases and glycerol ether monooxygenase and it regulates nitric oxide synthase (NOS) activity. Inherited BH4 deficiency leads to hyperphenylalaninemia, and dopamine and neurotransmitter deficiency in the brain. BH4 maintains enzymatic coupling to L-arginine oxidation to produce NO. Oxidation of BH4 to BH2 results in NOS uncoupling, resulting in superoxide (O2.-) formation rather than NO. Superoxide rapidly reacts with NO to produce peroxynitrite which can further uncouple NOS.
These reactive oxygen species (superoxide and peroxynitrite) can contribute to increased oxidative stress in the endothelium leading to atherosclerosis and hypertension (Thony et al. 2000, Crabtree and Channon 2011,Schulz et al. 2008, Schmidt and Alp 2007). The synthesis, recycling and effects of BH4 are shown here. Three enzymes are required for the de novo biosynthesis of BH4 and two enzymes for the recycling of BH4.
R-HSA-844615 The AIM2 inflammasome AIM2 is a member of the PYHIN or HIN200 family. It has a C-terminal HIN domain which can bind double-stranded DNA (dsDNA) and a PYD domain that can bind ASC via a PYD-PYD interaction. In cells expressing procaspase-1, The interaction of AIM2 with ASC leads to recruitment of procaspase-1 forming the ASC pyroptosome which induces pyroptotic cell death by generating active caspase-1. Data from AIM2 deficient mice indicates that the AIM2 inflammasome is a nonredundant sensor for dsDNA that regulates the caspase-1-dependent maturation of IL-1beta and IL-18 (Rathinam et al. 2010, Hornung & Latz, 2009).
R-HSA-844623 The IPAF inflammasome The IPAF (NLRC4) inflammasome can be activated by several stimuli, most notably by Gram-negative bacteria with either type III or type IV secretion systems that result in cytosolic flagellin, which is recognized by the IPAF inflammasome (Miao et al. 2006). IPAF also recognizes the rod-component of the type III secretion system which shares a sequence motif with flagellin that is essential for detection (Miao et al. 2010). Detection of Legionella and/or flagellin may also involve NAIP5 (Zamboni et al. 2006, Lightfield et al. 2008). IPAF contains a CARD domain and can interact directly with procaspase-1 (Poyet et al. 2001) but ASC increases the maximal activation of caspase-1 in response to S. typhimurium (Mariathasan et al. 2004), S. flexneri, and P. aeruginosa suggesting a possible collaboration with a PYD-containing NLRP for responses to these pathogens (Schroder & Tschopp, 2010). IPAF mediated caspase-1 activation can lead to a particular type of cell death called 'pyroptosis' (see Schroder & Tschopp 2010).
R-HSA-844455 The NLRP1 inflammasome NLRP1 is activated by MDP (Faustin et al. 2007). The NLRP1 inflammasome was the first to be characterized. It was described as a complex containing NALP1, ASC, caspase-1 and caspase-5 (Martinon et al. 2002). Unlike NLRP3, NLRP1 has a C-terminal extension containing a CARD domain, which has been reported to interact directly with procaspase-1, obviating a requirement for ASC (Faustin et al. 2007), though ASC was found to augment the interaction. Mouse NLRP1 has no PYD domain and would therefore not be expected to interact directly with procaspase-1. Like the NLRP3 inflammasome, K+ efflux appears to be essential for caspase-1 activation (Wickliffe et al. 2008). Ribonucleoside triphosphates (NTPs) are required for NALP1-mediated caspase-1 activation with ATP being the most efficient, Mg2+ was also required (Faustin et al. 2007). The human NLRP1 gene has 3 paralogues in mouse that are highly polymorphic. Differences between mouse strains underlie susceptibility to anthrax lethal toxin (Boyden & Dietrich 2006).
R-HSA-844456 The NLRP3 inflammasome The NLRP3 (Cryopyrin) inflammasome is currently the best characterized. It consists of NLRP3, ASC (PYCARD) and procaspase-1; CARD8 (Cardinal) is also suggested to be a component. It is activated by a number of pathogens and bacterial toxins as well as diverse PAMPs, danger-associated molecular patterns (DAMPS) such as hyaluronan and uric acid, and exogenous irritants such as silica and asbestos (see Table S1 Schroder & Tschopp, 2010).
Mutations in NLRP3 which lead to constitutive activation are linked to the human diseases Muckle-Wells syndrome, familial cold autoinflammatory syndrome and NOMID (Ting et al. 2006), characterized by skin rashes and other symptoms associated with generalized inflammation. The cause of these symptoms is uncontrolled IL-1 beta production. Multiple studies have shown that activation of the NLRP3 inflammasome by particulate activators (e.g. Hornung et al. 2008) requires phagocytosis, but this is not required for the response to ATP, which is mediated by the P2X7 receptor (Kahlenberg & Dubyak, 2004) and appears to involve the pannexin membrane channel (Pellegrin & Suprenenant 2006). Direct binding of activators to NLRP3 has not been demonstrated and the exact process of activation is unclear, though it is speculated to involve changes in conformation that free the NACHT domain for oligomerization (Inohara & Nunez 2001, 2003).
R-HSA-1663150 The activation of arylsulfatases Sulfatase activity requires a unique posttranslational modification (PTM) of a catalytic cysteine residue into a formylglycine. This modification is impaired in patients with multiple sulfatase deficiency (MSD) due to defects in the SUMF1 (sulfatase-modifying factor 1) gene responsible for this PTM. SUMF2 can inhibit the activity of SUMF1 thereby providing a mechanism for the regulation of sulfatase activation (Ghosh 2007, Diez-Roux & Ballabio 2005).
R-HSA-2453902 The canonical retinoid cycle in rods (twilight vision) The retinoid cycle (also referred to as the visual cycle) is the process by which the visual chromophore 11-cis-retinal (11cRAL) is released from light-activated opsins in the form all-trans-retinal and isomerized back to its 11-cis isomer ready for another photoisomerization reaction. This process involves oxidation, reduction and isomerization reactions and take place in the retinal pigment epithelium (RPE) and photoreceptor segments of the eye (von Lintig 2012, Blomhoff & Blomhoff 2006, von Lintig et al. 2010, D'Ambrosio et al. 2011). This section describes the retinoid cycle in rods during dark/twilight conditions.
R-HSA-167826 The fatty acid cycling model The "fatty acid cycling" hypothesis proposes that protonated fatty acids flip-flop in the membrane and deliver a proton to the matrix side. UCP1 catalyses the return of the fatty acid anion to the cytosolic side of the membrane, resulting in net proton transport catalysed by the protein.
R-HSA-2514856 The phototransduction cascade The visual pigment (rhodopsin in rods) consists of an 11-cis-retinal (11cRAL) chromophore covalently attached to a GPCR opsin family member via a Schiff base linkage. Upon photon absorption, 11cRAL isomerizes to all trans retinal (atRAL), changing the conformation of opsin to a form that can activate the regulatory G protein transducin (Gt). The alpha subunit of Gt activates phosphodiesterase which hydrolyses cGMP to 5'-GMP. A high level of cGMP keeps cGMP-gated cation channels open, so lower cGMP levels close these channels and hyperpolarize the cell. The hyperpolarization spreads passively to the synapse located at the opposite end of the rod, where it subsequently closes voltage-gated calcium channels. Vesicular release of the neurotransmitter glutamate subsides as the intracellular calcium levels drop. This diminution of neurotransmitter release relays the light signal to postsynaptic neurons. The events below describe activation, inactivation, recovery and regulation of the phototransduction cascade in rods (Burns & Pugh 2010, Korenbrot 2012, Smith 2010).
R-HSA-2187335 The retinoid cycle in cones (daylight vision) Rods and cones share the same mechanism for the phototransduction process but perform functionally different roles. Although cone photoreceptors make up around 5% of all photoreceptor cells and are outnumbered 20 to 1 by rod photoreceptors, they mediate daylight vision in the human eye whereas rods mediate twilight vision. Also, cones are around 100-times less light-sensitive than rods thereby depriving us of colour vision in dark conditions in which cones cannot function. Rod function saturates in even moderate amounts of light whereas cones can adjust to even very bright light conditions, a process called light adaptation. In bright conditions, rods can take up to one hour to regain their sensitivity whereas cones can recover in a few minutes, a process called dark adaptation and which allows us to retain visual perception in changing light conditions.
Cone cells express three types of opsin which allow colour discrimination. Long Wavelength Sensitive Opsin (OPN1LW) detects red , Short Wavelength Sensitive Opsin (OPN1SW) detects blue, and Medium Wavelength Sensitive Opsin (OPN1MW) detects green regions of the light spectrum.
In the canonical retinoid (visual) cycle, the visual chromophore is regenerated in reactions involving the rod outer segments (ROS) and the retinal pigment epithelium (RPE). For cones, chromophore recycling is independent of the RPE and instead involves Muller cells in the retina which supply the chromophore selectively to cones. The molecular steps of the cone retinoid (visual) cycle are outlined in this section. The ability of cones to react to bright and differing light conditions means it has to regenerate the chromophore much quicker than rods. All-trans-retinol (atROL) released from cone outer segments is taken up by Muller cells where it is directly isomerized back to 11-cis-retinol (11cROL) then esterified by LRAT. When required, these 11-cis-retinyl esters can be hydrolysed by 11-cis-RE hydrolases back to 11cROL then oxidised in the cone photoreceptor cell to regenerate 11-cis-retinal (11cRAL), the visual chromophore (see reviews von Lintig 2012, Wang & Kefalov 2011, Kefalov 2012, Wolf 2004).
R-HSA-8852276 The role of GTSE1 in G2/M progression after G2 checkpoint GTSE1 (B99) was identified as a microtubule-associated protein product of the mouse B99 gene, which exhibits both a cell cycle regulated expression, with highest levels in G2, and DNA damage triggered expression under direct control of TP53 (p53) (Utrera et al. 1998, Collavin et al. 2000). Human GTSE1, similar to the mouse counterpart, binds to microtubules, shows cell cycle regulated expression with a peak in G2 and plays a role in G2 checkpoint recovery after DNA damage but is not transcriptionally regulated by TP53 (Monte et al. 2003, Monte et al. 2004, Scolz et al. 2012).
In G1 cells, GTSE1 is found at the microtubule lattice, likely due to direct binding to tubulin. An evolutionarily conserved interaction between GTSE1 and MAPRE1 (EB1), a microtubule plus end protein, promotes GTSE1 localization to the growing tip of the microtubules, which contributes to cell migration and is likely involved in cancer cell invasiveness. Highly invasive breast cancer cell lines exhibit high GTSE1 levels in G1, while GTSE1 levels in G1 are normally low. At the beginning of mitotic prometaphase, GTSE1 is phosphorylated by mitotic kinase(s), possibly CDK1, in proximity to the MAPRE1-binding region, causing GTSE1 dissociation from the plus end microtubule ends (Scolz et al. 2012).
During G2 checkpoint recovery (cell cycle re-entry after DNA damage induced G2 arrest), GTSE1 relocates to the nucleus where it binds TP53 and, in an MDM2-dependent manner, promotes TP53 cytoplasmic translocation and proteasome mediated degradation (Monte et al. 2003, Monte et al. 2004). Relocation of GTSE1 to the nucleus in G2 phase depends on PLK1-mediated phosphorylation of GTSE1 (Liu et al. 2010).
GTSE1-facilitated down-regulation of TP53 in G2 allows cells to avoid TP53 mediated apoptosis upon DNA damage and to re-enter cell cycle (Monte et al. 2003). While TP53 down-regulation mediated by GTSE1 in G2 correlates with decreased expression of TP53 target genes involved in apoptosis and cell cycle arrest, GTSE1 can also increase the half-life of the TP53 target p21 (CDKN1A). GTSE1-mediated stabilization of CDKN1A involves interaction of GTSE1 with CDKN1A and its chaperone complex, consisting of HSP90 and FKBPL (WISp39), and may be involved in resistance to paclitaxel treatment (Bublik et al. 2010).
R-HSA-164952 The role of Nef in HIV-1 replication and disease pathogenesis The HIV-1 Nef protein is a 27-kDa myristoylated protein that is abundantly produced during the early phase of viral replication cycle. It is highly conserved in all primate lentiviruses, suggesting that its function is essential for survival of these pathogens. The protein name "Nef" was derived from early reports of its negative effect on viral replication, thus 'negative factor' or Nef. Subsequently it has been demonstrated that Nef plays an important role in several steps of HIV replication. In addition, it appears to be a critical pathogenic factor, as Nef-deficient SIV and HIV are significantly less pathogenic than the wild-type viruses, whereas Nef-transgenic mice show many features characteristic to HIV disease.
The role of Nef in HIV-1 replication and disease pathogenesis is determined by at least four independent activities of this protein. Nef affects the cell surface expression of several cellular proteins, interferes with cellular signal transduction pathways, enhances virion infectivity and viral replication, and regulates cholesterol trafficking in HIV-infected cells.
R-HSA-8849175 Threonine catabolism The degradation of L-threonine to glycine in both prokaryotes and eukaryotes takes place through a two-step biochemical pathway in mitochondria (Dale 1978). In the first step, L-threonine is oxidised to 2-amino-3-oxobutanoate. This reaction is catalysed by mitochondrial L-threonine 3-dehydrogenase tetramer (TDH tetramer). In the second step, mitochondrial 2-amino-3-ketobutyrate coenzyme A ligase (GCAT, aka KBL) catalyses the reaction between 2-amino-3-oxobutanoate and coenzyme A to form glycine and acetyl-CoA. GCAT resides on the mitochondrial inner membrane in dimeric form and requires pyridoxal 5-phosphate (PXLP) as cofactor. GCAT is thought to exist on the mitochondrial inner membrane in complex with TDH. With these two enzymes located together, it stops the rapid and spontaneous decarboxylation of 2A-3OBU to aminoacetone and carbon dioxide and instead, results in glycine formation (Tressel et al. 1986).
R-HSA-456926 Thrombin signalling through proteinase activated receptors (PARs) Thrombin activates proteinase activated receptors (PARs) that signal through heterotrimeric G proteins of the G12/13 and Gq families, thereby connecting to a host of intracellular signaling pathways. Thrombin activates PARs by cleaving an N-terminal peptide that then binds to the body of the receptor to effect transmembrane signaling. Intermolecular ligation of one PAR molecule by another can occur but is less efficient than self-ligation. A synthetic peptide of sequence SFLLRN, the first six amino acids of the new N-terminus generated when thrombin cleaves PAR1, can activate PAR1 independent of protease and receptor cleavage. PARs are key to platelet activation. Four PARs have been identified, of which PARs 1 ,3 and 4 are substrates for thrombin. In humans PAR 1 is the predominant thrombin receptor followed by PAR4 which is less responsive to thrombin. PAR 3 is not considered important for human platelet responses as it is minimally expressed, though this is not the case for mouse. PAR2 is not expressed in platelets. In mouse platelets, Gq is necessary for platelet secretion and aggregation in response to thrombin but is not necessary for thrombin-triggered shape change. G13 appears to contribute to platelet aggregation as well as shape change in response to low concentrations of thrombin but to be unnecessary at higher agonist concentrations; G12 appears to be dispensable for thrombin signaling in platelets. G alpha (q) activates phospholipase C beta thereby triggering phosphoinositide hydrolysis, calcium mobilization and protein kinase C activation. This provides a path to calcium-regulated kinases and phosphatases, GEFs, MAP kinase cassettes and other proteins that mediate cellular responses ranging from granule secretion, integrin activation, and aggregation in platelets. Gbeta:gamma subunits can activate phosphoinositide-3 kinase and other lipid modifying enzymes, protein kinases, and channels. PAR1 activation indirectly leads to activation of cell surface 'sheddases' that liberate ligands for receptor tyrosine kinases, providing a link between thrombin and receptor tyrosine kinases involved in cell growth and differentiation. The pleiotrophic effects of PAR activation are consistent with many of thrombin's diverse actions on cells.
R-HSA-428930 Thromboxane signalling through TP receptor Thromboxane (TXA2) binds to the thromboxane receptor (TP). There are 2 splice variant forms of TP, differing in their cytoplasmic carboxyl terminal tails. TP beta was first identified in endothelial cells. TP alpha was identified in platelets and placenta. The major signalling route for TP is Gq-mediated stimulation of PLC and consequent increase in cellular calcium. TP also couples to G13, leading to stimulation of Rho and Rac.
R-HSA-209968 Thyroxine biosynthesis Thyroxine (3,5,3',5'-tetraiodothyronine, T4) promotes normal growth and development. It also regulates heat and energy production. T4 is released from the thyroid gland, the largest endocrine organ in the human body. The primary hormone released is T4 although T3 (3,5,3'-triiodothyronine) is also released in small quantities. Tyrosine residues in thyroglobulin (a glycoprotein scaffold containing many tyrosine residues) are iodinated to form mono- or diiodo-tyrosine which can then couple to form either T3 or T4.
R-HSA-210993 Tie2 Signaling The Tie2/Tek receptor tyrosine kinase plays a pivotal role in vascular and hematopoietic development and is expressed exclusively on endothelial lineage. Tie2 interacts with a group of ligands belonging to angiopoietin family and undergoes activation.
These ligands show opposing actions, angiopoietin 1 and angiopoietin 4 stimulate the Tie2 phosphorylation and angiopoietin 2 inhibits it. Upon tyrosine phosphorylation Tie2 acts as a scaffold for various signaling proteins involved in different signal transduction cascades that can effect survival of endothelium and angiogenic sprout formation.
R-HSA-420029 Tight junction interactions Tight junctions (TJs) are the most apical component of the epithelial junctional complex forming a belt-like structure at the cellular junction. When visualized by freeze-fracture electron microscopy they appear as a branched network of intramembrane strands that correspond to the sites of direct membrane contacts and that are composed of the integral membrane claudin proteins. The TJs act as a primary barrier to the diffusion of solutes through the paracellular space (barrier function) (Tsukita et al., 2001). They also prevent the intermixing of intramembrane proteins and lipids and thus create a boundary between the apical and the basolateral membrane domains of polarized epithelial cells (fence function) (Tsukita et al., 2001). Interestingly, the fence function seems not to depend on TJ strands (Umeda et al., 2006). Recents evidence indicates that the TJs also participate in signal transduction mechanisms which regulate cell proliferation and morphogenesis (Matter and Balda, 2003; Matter and Balda, 2007). This module describes the major molecular interactions responsible for the formation of TJ strands and for the rectruitment of the PAR-3-PKC-PAR-6 and CRB3-Pals1-PATJ complexes that function in tight junction formation (Ebnet, 2008).
R-HSA-1222538 Tolerance by Mtb to nitric oxide produced by macrophages Reactive nitrogen species (RNS), like reactive oxygen species, have numerous target molecules in the bacterial cell, and Mtb has developed remedies to the most important ones of them. This is a key reason for its ability to stay alive in the hostile environment of the late phagosome within human macrophages.
Mtb repairs single-base DNA damage caused by DNA alkylation; it scavenges nitric oxide with large amounts of mycothiol and methionine-rich proteins (the nitroso compounds later being reduced). Nitric oxide and peroxynitrite are also directly reduced by a battery of hemoglobins and peroxiredoxins, supported by a network of thioredoxins and respective NADPH-dependent reductases (Fang. 2004).
R-HSA-1222387 Tolerance of reactive oxygen produced by macrophages The expression of AhpC in Mycobacteria does not correlate with virulence; instead, the most important parts of the antioxidant system in Mtb appear to be the lipid cell wall, the enzymes SodB/SodC (superoxide dismutases), and the catalase/peroxidase KatG. Together with the enzyme system that acts on nitrosative stress and the sequestration of iron, these appear to be critical in defending against the macrophage's production of ROS/RNS, and enable the bacterium to exist in the phagosome for extended periods (Zahrt & Deretic 2002).
R-HSA-168142 Toll Like Receptor 10 (TLR10) Cascade Little is known about TLR10 ligands. It has been established that the receptor homodimerizes upon binding and signals in an MyD88-dependent manner (Hasan U et al 2005; Nyman T et al 2008). It may also heterodimerize with TLRs 1 and 2. It is expressed in a restricted fashion as a highly N-glycosylated protein detectable in B cells and dendritic cells.
R-HSA-181438 Toll Like Receptor 2 (TLR2) Cascade TLR2 is involved in recognition of peptidoglycan from gram-positive bacteria, bacterial lipoproteins, mycoplasma lipoprotein and mycobacterial products. It is quite possible that recognition of at least some other TLR2 ligands may be assisted by additional accessory proteins, particularly in association with TLR1 or TLR6. TLR2 is expressed constitutively on macrophages, dendritic cells, and B cells, and can be induced in some other cell types, including epithelial cells. TLR1 and TLR6, on the other hand, are expressed almost ubiquitously (Muzio et al. 2000). TLR2 may be a sensor and inductor of specific defense processes, including oxidative stress and cellular necrosis initially spurred by microbial compounds.
R-HSA-168164 Toll Like Receptor 3 (TLR3) Cascade Toll-like receptor 3 (TLR3) as was shown for mammals is expressed in various tissues and cells, including myeloid dendritic cells, macrophages, respiratory and intestinal epithelium, neurons and microglial cells to induce antiviral and inflammatory responses of the innate immunity in combating viral infections.
TLR3 recognizes dsRNA in the endosome and that triggers the receptor dimerization. TLR3 recruits the adaptor TRIF (TICAM1), leading to the activation of NF-kappa-B and the production of type I interferons (IFNs). dsRNA-stimulated phosphorylation of two specific TLR3 tyrosine residues (Tyr759 and Tyr858) is essential for initiating TLR3 signaling pathways. R-HSA-166016 Toll Like Receptor 4 (TLR4) Cascade Toll-like Receptor 4 is a microbe associated molecular pattern receptor well known for it's sensitivity to bacterial lipopolysaccharides (LPS). LPS is assembled within diverse Gram-negative bacteria, many of which are human or plant pathogens. It is a component of the outer membrane of Gram-negative bacteria and consists of lipid A, a core polysaccharide and an O-polysaccharide of variable length (often more than 50 monosaccharide units). LPS is a potent activator of the innate immune response in humans, causing reactions including fever, headache, nausea, diarrhoea, changes in leukocyte and platelet counts, disseminated intravascular coagulation, multiorgan failure, shock and death. All these reactions are induced by cytokines and other endogenous mediators which are produced after interaction of LPS with the humoral and cellular targets of the host. In macrophages and dendritic cells, LPS-mediated activation of TLR4 triggers the biosynthesis of diverse mediators of inflammation, such as TNF-alpha and IL6, and activates the production of co-stimulatory molecules required for the adaptive immune response. In mononuclear and endothelial cells, LPS also stimulates tissue factor production. These events are desirable for clearing local infections, but when these various mediators and clotting factors are overproduced, they can damage small blood vessels and precipitate shock accompanied by disseminated intravascular coagulation and multiple organ failure. R-HSA-166016 Toll Like Receptor 4 (TLR4) Cascade TLR4 is unique among the TLR family in its ability to recruit four adapters to activate two distinct signaling pathways. One pathway is activated by the pair of the adapters Mal or TIRAP (Toll/interleukin-1-receptor (TIR)-domain-containing adapter protein) and MyD88, which leads to the NFkB activation and the induction of pro-inflammatory cytokines. The second pathway is activated by the adapters TRIF (TIR-domain-containing adapter protein inducing interferon-beta) and TRAM (TRIF-related adapter molecule). The combined use of TRIF and TRAM adapters is specific for TLR4 signaling pathway and leads to the induction of type I interferons and delayed activation of NFkB.
The previous model of TLR4 signaling pathway described the simultaneous activation of these two signaling pathways at the plasma membrane, however the later studies suggested that upon activation TLR4 first induces TIRAP-MyD88 signaling at the plasma membrane and is then endocytosed and activates TRAM-TRIF signaling from the early endosome [Kagan JC et al 2008; Tanimura N et al 2008; Zanoni I et al 2011]. R-HSA-168176 Toll Like Receptor 5 (TLR5) Cascade TLR5 is the receptor for flagellin, the protein that forms bacterial flagella. Unlike most other Pathogen-Associated Molecular Patterns (PAMPs), flagellin does not undergo any posttranslational modifications that would distinguish it from cellular proteins. However, flagellin is extremely conserved at its amino- and carboxyl-termini, which presumably explains why it was selected as a ligand for innate immune recognition. TLR5 is expressed on epithelial cells as well as on macrophages and dendritic cells. Expression of TLR5 on intestinal epithelium is polarized such that TLR5 is expressed only on the basolateral side of the cell, as pathogenic but not commensal microbes cross the epithelial barrier. This ensures that innate immune responses are confined to pathogenic but not commensal microbes (Paul 2004; Hayashi et al. 2001; Gewirtz et al. 2001). R-HSA-168181 Toll Like Receptor 7/8 (TLR7/8) Cascade RNA can serve as a danger signal, both in its double-stranded form as well as single-stranded RNA (ssRNA). Toll like receptor 7 (TLR7) and TLR8 are endosomal receptors that sense ssRNA oligonucleotides containing guanosine (G)- and uridine (U)-rich sequences from RNA viruses (Jurk M et al. 2002; Heil F et al. 2004; Diebold SS et al. 2004; Li Y et al. 2013; reviewed in Lester SN & Li K 2014). TLR7 is primarily expressed in plasmacytoid dendritic cells (pDCs) and, to some extent, in B cells, monocytes and macrophages, whereas TLR8 is mostly expressed in monocytes, macrophages and myeloid DCs. Upon engagement of ssRNAs in endosomes, TLR7/8 initiate the myeloid differentiation factor 88 (MyD88)-dependent pathway, culminating in synthesis of type I and type III IFNs and proinflammatory mediators via activation of IFN regulatory factors (IRF7, IRF5) and NF-kappaB, respectively, depending on the cell type (Takaoka A et al., 2005; Heinz LX et al., 2020; reviewed in Lester SN & Li K 2014). TLR7 and TLR8 are able to detect GU-rich ssRNA sequences from the viral genomes of influenza, human immunodeficiency virus-1 (HIV-1), vesicular stomatitis virus (VSV), coxsackie B virus, coronavirus and flaviviruses (hepatitis C virus, HCV and West Nile virus, WNV; reviewed in Lester SN & Li K 2014). Specifically, GU-rich ssRNA oligonucleotides derived from HIV-1, for example, stimulate dendritic cells (DC) and macrophages to secrete interferon-alpha and proinflammatory, as well as regulatory, cytokines (Heil F et al. 2004). This has been found to be mediated by TLR7, as well as TLR8. Similarly, severe acute respiratory syndrome-associated coronavirus type 1 (SARS-CoV-1) GU-rich ssRNAs had powerful immunostimulatory activities in mononuclear phagocytes to induce considerable level of pro-inflammatory cytokine TNF-a, IL-6 and IL-12 release via the TLR7 and TLR8 (Li Y et al. 2013). Further, mice deficient in either Tlr7 or the TLR adaptor protein Myd88 demonstrated reduced responses to in vivo infection with VSV (Lund JM et al. 2004), mouse-adapted SARS-CoV-1 (Sheahan et al. 2008; Totura et al., 2015). Upon Middle East respiratory syndrome-related coronavirus (MERS-CoV) infection, lack of MyD88 signaling resulted in delayed viral clearance and increased lung pathology in mice (Zhao et al. 2014). Consistently, another study showed that Tlr7-/- mice have reduced IFN expression compared with wild-type mice (Channappanavar et al. 2019). In addition, loss of function TLR7 variants identified in the patients with SARS-CoV-2 (COVID-19) resulted in defective upregulation of type I IFN–related genes in the TLR7 pathway (Figure 3) in response to the TLR7 agonist imiquimod as compared with controls (Van der Made CI et al. 2020). Separate studies showed that synthetic imidazoquinoline compounds (e.g. imiquimod and R-848, low-molecular-weight immune response modifiers that can induce the synthesis of interferon-alpha) also exert their effects in a MyD88-dependent fashion through TLR7 or TLR8 (Hemmi H et al. 2002; Jurk M et al. 2002; Diebold SS et al. 2004). Some viruses utilize multiple strategies to evade antiviral innate immune signaling, as is seen with influenza or SARS coronaviruses. TLR7-mediated innate immunity, for example, was associated with the negative regulation through removing Lys63-linked polyubiquitin chains of TRAF3/TRAF6 by papin-like protease (PLpro) catalytic domain of nsp3 from SARS-CoV-1 (Li SW et al. 2016). Thus, TLR7 and TLR8 play a critical role in sensing of viral ssRNA in the endosome. R-HSA-168138 Toll Like Receptor 9 (TLR9) Cascade CpG DNA is an unusual Pathogen-Associated Molecular Pattern (PAMP). Cytosine methylation exists in mammalian but not bacterial cells, and most (but not all) CpG in the mammalian genome is methylated. Therefore, unmethylated CpG DNA may signal the presence of microbial infection. Evidence of CpG recognition by TLR9 was demonstrated both in human and mouse, and this type of signaling requires its internalization into late endosomal/lysosomal compartments. TLR9 has been reported to be able to discern different types of CpG motifs, and therefore that it presumably recognizes CpG DNA directly. It appears that over evolutionary periods, TLR9 molecules expressed by different species have diverged. This has led to differences in the precise sequence motif (CpG dinucleotide plus flanking regions) that optimally stimulate the innate immune system of different animals. R-HSA-168179 Toll Like Receptor TLR1:TLR2 Cascade TLR1 is expressed by monocytes. TLR1 and TLR2 cotranslationally form heterodimeric complexes on the cell surface and in the cytosol. The TLR2:TLR1 complex recognizes Neisserial PorB and Mycobacterial triacylated lipoproteins and peptides, amongst others, triggering up-regulation of nuclear factor-kappaB production and apoptotic cascades. Such cooperation between TLR1 and TLR2 on the cell surface of normal human peripheral blood mononuclear cells, for instance, leads to the activation of pro-inflammatory cytokine secretion (Sandor et al. 2003). R-HSA-168188 Toll Like Receptor TLR6:TLR2 Cascade TLR2 and TLR4 recognize different bacterial cell wall components. While TLR4 is trained onto Gram-negative lipopolysaccharide components, TLR2 - in combination with TLR6 - plays a major role in recognizing peptidoglycan wall products from Gram-positive bacteria, as well as Mycobacterial diacylated lipopeptides. In particular, TLR6 appears to participate in discriminating the subtle differences between dipalmitoyl and tripalmitoyl cysteinyl residues (Okusawa et al. 2004). R-HSA-168898 Toll-like Receptor Cascades In human, ten members of the Toll-like receptor (TLR) family (TLR1-TLR10) have been identified (TLR11 has been found in mouse, but not in human). All TLRs have a similar Toll/IL-1 receptor (TIR) domain in their cytoplasmic region and an Ig-like domain in the extracellular region, where each is enriched with a varying number of leucine-rich repeats (LRRs). Each TLR can recognize specific microbial pathogen components. The binding pathogenic component to TLR initializes signaling pathways that lead to induction of Interferon alpha/beta and inflammatory cytokines. There are two main signaling pathways. The first is a MyD88-dependent pathway that is common to all TLRs, except TLR3; the second is a TRIF(TICAM1)-dependent pathway that is peculiar to TLR3 and TLR4. TLR4-mediated signaling pathway via TRIF requires adapter molecule TRAM (TRIF-related adapter molecule or TICAM2). TRAM is thought to bridge between the activated TLR4 complex and TRIF.(Takeda & Akira 2004; Akira 2003; Takeda & Akira 2005; Kawai 2005; Heine & Ulmer 2005). This pathway is organized as trafficking and processing of TLR, various TLR cascades (TLR10,TLR3,TLR5,TLR7/8,TLR9,TLR4,TLR2) and their regulation. R-HSA-5250968 Toxicity of botulinum toxin type A (botA) Botulinum toxin type A (botA, also known as BoNT/A), a disulfide bonded heavy chain (HC) - light chain (LC) heterodimer ("dichain"), enters the gut typically as a result of consuming contaminated food (Hatheway 1995), as a complex with nontoxic nonhemagglutinin protein (NTNHA, encoded by the C. botulinum ntnha gene) and multiple copies of three hemagglutinin proteins (HA, encoded by the C. botulinum ha17, ha34, and ha70 genes) (Lee et al. 2013). The complex protects the toxin from degradation in the gut and mediates its association with the gut epithelium and transcytosis to enter the circulation. Recent studies in vitro raise the possibility that the toxin may also directly disrupt the basolateral membrane of the gut epithelium (Fujinaga et al. 2013). Circulating toxin molecules associate with gangliosides and synaptic vesicle protein 2 (SV2) exposed by exocytosis at a synapse of a target neuron in the neuromuscular junction (Yowler & Schengrund 2004; Dong et al. 2006). Vesicle recycling brings the toxin into the neuron where the vesicle is acidified (Sudhoff 2004). The lowered pH induces a conformational change in the toxin: its HC forms a passage in the vesicle membrane through which its LC is extruded into the neuronal cytosol and released by reduction of the HC - LC disulfide bond (Montal 2010). The cytosolic LC then catalyzes the cleavage of synaptosomal associated protein 25 (SNAP25) on the cytosolic face of the neuronal plasma membrane (Binz et al. 1994; Schiavo et al. 1993), thereby inhibiting synaptic vesicle fusion with the plasma membrane and exocytosis. R-HSA-5250958 Toxicity of botulinum toxin type B (botB) Botulinum toxin type B (botB, also known as BoNT/B), a disulfide-bonded heavy chain (HC) - light chain (LC) heterodimer, enters the gut typically as a result of consuming contaminated food (Hatheway 1995), as a complex with nontoxic nonhemagglutinin protein (NTNHA, encoded by the C. botulinum ntnha gene) and multiple copies of three hemagglutinin proteins (HA, encoded by the C. botulinum ha17, ha34, and ha70 genes) (Amatsu et al. 2013). The complex protects the toxin from degradation in the gut and mediates its association with the gut epithelium and transcytosis to enter the circulation (Fujinaga et al. 2013). Circulating toxin molecules associate with gangliosides and synaptotagmin (SYT) proteins exposed by exocytosis at a synapse of a target neuron (Dong et al. 2003; Yowler & Schengrund 2004). Vesicle recycling brings the toxin into the neuron where the vesicle is acidified (Sudhoff 2004). The lowered pH induces a conformational change in the toxin: its HC forms a passage in the vesicle membrane through which its LC is extruded into the neuronal cytosol. Tthe HC - LC disulfide bond is reduced (Montal 2010). The LC then catalyzes the cleavage of vesicle-associated membrane protein 2 (VAMP2) on the cytosolic face of synaptic vesicle membranes (Foran et al. 1994; Schiavo et al. 1992), thereby inhibiting synaptic vesicle fusion with the plasma membrane and exocytosis. R-HSA-5250971 Toxicity of botulinum toxin type C (botC) Botulinum toxin type C (botC, also known as BoNT/C) is only very rarely associated with human disease (Hatheway 1995) and a pathway by which it might enter the circulation from the human gut has not been described. Nevertheless, the toxin itself, a disulfide-bonded heavy chain (HC) - light chain (LC) heterodimer (“dichain”), is capable of binding to neurons by interactions with cell surface gangliosides (Karalewitz et al. 2012), the bound toxin can enter synaptic vesicles and release its LC moiety into the cytosol of targeted cells (Montal 2010), and the botC LC can cleave synaptosomal associated protein 25 (SNAP25) and syntaxin 1 (STX1) on the cytosolic face of the neuronal plasma membrane (Foran et al. 1996). These four events are annotated here. R-HSA-5250955 Toxicity of botulinum toxin type D (botD) Botulinum toxin type D (botD) is only very rarely associated with human disease (Hatheway 1995) and a pathway by which it might enter the circulation from the human gut has not been described. Nevertheless, the toxin itself, a disulfide-bonded heavy chain (HC) - light chain (LC) heterodimer (“dichain”), is capable of binding to neurons by interactions with cell surface ganglioside (Kroken et al. 2011) and synaptic vesicle protein 2 (SV2) (Peng et al. 2011), the bound toxin can enter synaptic vesicles and release its LC moiety into the cytosol of targeted cells (Montal 2010), and the botD LC can cleave vesicle associated membrane proteins 1 and 2 (VAMP1 and 2) on the cytosolic face of the synaptic vesicle membrane (Schiavo et al. 1993; Yamasaki et al. 1994). These four events are annotated here. R-HSA-5250992 Toxicity of botulinum toxin type E (botE) Botulinum toxin type E (botE, also known as BoNT/E), a disulfide-bonded heavy chain (HC) - light chain (LC) heterodimer (“dichain”), enters the gut typically as a result of consuming contaminated food (Hatheway 1995), as a complex with nontoxic nonhemagglutinin protein (NTNHA, encoded by the C. botulinum ntnha gene) (Benefield et al. 2013). The complex protects the toxin from degradation in the gut and mediates its association with the gut epithelium and transcytosis to enter the circulation (Fujinaga et al. 2013). Circulating toxin molecules associate with gangliosides and synaptic vesicle protein 2 (SV2) exposed by exocytosis at a synapse of a target neuron (Dong et al. 2008; Yowler & Schengrund 2004). Vesicle recycling brings the toxin into the neuron where the vesicle is acidified (Sudhoff 2004). The lowered pH induces a conformational change in the toxin: its HC forms a passage in the vesicle membrane through which its LC is extruded into the neuronal cytosol and released by reduction of the HC - LC disulfide bond (Montal 2010). The LC then catalyzes the cleavage of synaptosome-associated protein 25 (SNAP25) on the cytosolic face of the neuronal plasma membrane (Binz et al. 1994; Schiavo et al. 1993), thereby inhibiting synaptic vesicle fusion with the plasma membrane and exocytosis. R-HSA-5250981 Toxicity of botulinum toxin type F (botF) Botulinum toxin type F (botF) is only very rarely associated with human disease (Hatheway 1995) and a pathway by which it might enter the circulation from the human gut has not been described. Nevertheless, the toxin itself, a disulfide-bonded heavy chain (HC) - light chain (LC) heterodimer ("dichain"), is capable of binding to neurons by interactions with cell-surface ganglioside and synaptic vesicle protein 2 (SV2) (Fu et al. 2009; Rummel et al. 2009), the bound toxin can enter synaptic vesicles and release its LC moiety into the cytosol of targeted cells (Montal 2010), and the botF LC can cleave vesicle-associated membrane proteins 1 and 2 (VAMP1 and 2) on the cytosolic face of the synaptic vesicle membrane (Yamasaki et al. 1994). These four events are annotated here. R-HSA-5250989 Toxicity of botulinum toxin type G (botG) Botulinum toxin type G (botG) is rarely if ever associated with human disease (Hatheway 1995) and a pathway by which it might enter the circulation from the human gut has not been described. Nevertheless, the toxin itself, a disulfide-bonded heavy chain (HC) - light chain (LC) heterodimer ("dichain"), is capable of binding to neurons by interactions with cell-surface ganglioside and syntagmin 1 (SYT1) (Peng et al. 2012; Willjes et al. 2013), the bound toxin can enter synaptic vesicles and release its LC moiety into the cytosol of targeted cells (Montal 2010), and the botG LC can cleave vesicle-associated membrane proteins 1 and 2 (VAMP1 and 2) on the cytosolic face of the synaptic vesicle membrane (Schiavo et al. 1994; Yamasaki et al. 1994). These four events are annotated here. R-HSA-5250982 Toxicity of tetanus toxin (tetX) Tetanus toxin (tetX, also known as TeNT), a disulfide-bonded heavy chain (HC) - light chain (LC) dimer, is secreted from bacteria growing in an infected wound directly into the circulation. Circulating toxin molecules associate with gangliosides at a synapse of a target neuron. The toxin is taken up into clathrin-coated vesicles that reach the neuron cell body by retrograde transport and then possibly other neurons before undergoing acidification. Vesicle acidification causes a conformational change in the toxin, allowing its HC part to function as a channel through which its LC part is extruded into the neuronal cytosol. Cleavage of the HC - LC disulfide bond releases the LC into the cytosol, where it functions as a zinc metalloprotease to cleave vesicle-associated membrane protein 2 (VAMP2), thereby blocking synaptic vesicle exocytosis (Lalli et al. 2003). R-HSA-1679131 Trafficking and processing of endosomal TLR Mammalian TLR3, TLR7, TLR8, TLR9 are endosomal receptors that sense nucleic acids that have been released from endocytosed/phagocytosed bacteria, viruses or parasites. These TLRs have a ligand-recognition domain that faces the lumen of the endosome (which is topologically equivalent to the outside of the cell), a transmembrane domain, and a signaling domain that faces the cytosol.
Under normal conditions, self nucleic acids are not recognized by TLRs due to multiple levels of regulation including receptor compartmentalization, trafficking and proteolytic processing (Barton GM et al 2006, Ewald SE et al 2008). At steady state TLR3, TLR7, TLR8, TLR9 reside primarily in the endoplasmic reticulum (ER), however, their activation by specific ligands only occurs within acidified endolysosomal compartments (Hacker H et al 1998, Funami K et al 2004, Gibbard RJ et al 2006). Several chaperon proteins associate with TLRs in the ER to provide efficient translocation to endolysosome. Upon reaching endolysosomal compartments the ectodomains of TLR7 and TLR9 are proteolytically cleaved by cysteine endoproteases. Both full-length and cleaved C-terminus of TLR9 bind CpG-oligodeoxynucleotides, however it has been proposed that only the processed receptor is functional.
Although similar cleavage of TLR3 has been reported by Ewald et al 2011, other studies demonstrated that the N-terminal region of TLR3 ectodomain was implicated in ligand binding, thus TLR3 may function as a full-length receptor (Liu L et al 2008, Tokisue T et al 2008).
There are no data on TLR8 processing, although the cell biology of TLR8 is probably similar to TLR9 and TLR7 (Gibbard RJ et al 2006, Wei T et al 2009).
R-HSA-399719 Trafficking of AMPA receptors Repetitive presynaptic activity causes long lasting changes in the postsynaptic transmission by changing the type and the number of AMPA receptors. These changes are brought about by trafficking mechanisms that are mainly controlled by activity dependent phosphorylation/desphosphorylation of the GluR1/GluR2 subunits.
R-HSA-416993 Trafficking of GluR2-containing AMPA receptors Trafficking of GluR2-containing receptors is governed by protein protein interactions that are regulated by phosphorylation events. GluR2 binds NSF and AP2 in the proximal C terminal region and binds PICK and GRIP1/2 in the extreme C terminal region. GluR2 interaction with NSF is necessary to maintain the synaptic levels of GluR2-containing AMPA receptors both at basal levels and under conditions of synaptic activity. GluR2 interaction with GRIP helps anchor AMPA receptors at the synapse. Phosphorylation of GluR2 at S880 disrupts GRIP interaction but allows binding of PICK. PICK is activated by Ca sensitive Protein kinase C (PKC). Under basal conditions, in hippocampal synapse, GluR2-containing AMPA receptors (GluR2/GluR3) constitutively recycle between the synapse and the endosome by endocytosis and exocytosis. GRIP anchors the receptors at the synapse while PICK interaction internalizes the receptors and NSF helps maintain the synaptic receptors. Cerebellar stellate cells mainly contain GluR3 homomers as Ca permeable receptors. The interaction of GluR3 and GRIP is disrupted by PICK interaction by phosphorylation of equivalent of S880 residue in GluR3. Under conditions of repetitive presynaptic activity, there is PICK dependent removal of GluR2-lacking AMPA receptors and selective incorporation of GluR2-containing AMPA receptors at the synapse. The GluR2-containing AMPA receptors are first delivered to the surface by PICK and mobilized to the synapse by NSF dependent mechanism (Liu SJ and Cull-Candy SG Nat Neurosci. 2005 Jun;8(6):768-75)
R-HSA-5624138 Trafficking of myristoylated proteins to the cilium A number of myristoylated proteins have been shown to traffic to the cilium in a myristoyl- and UNC119B:ARL3:RP2-dependent fashion. These include the ciliary proteins Nephrocystin 3 (NPHP3) and Cystin 1 (CYS1) (Wright et al, 2011; reviewed in Schwarz et al, 2012). Myristoyl-binding by the ARL3 effector UNC119B is required in an unknown fashion for the transport of the myristoylated cargo to the cilium. At the cilium, a GTPase cycle involving the ARF-like small GTPase ARL3 and its GAP protein RP2 promote the release of the myristoylated proteins into the ciliary membrane and the recycling and ciliary exit of UNC119B (Wright et al, 2011; reviewed in Schwarz et al, 2012). ARL3 plays additional roles in the cilium coordinating the association of IFT A and IFT B complexes with the kinesin motors (Li et al, 2010; reviewed in Li et al, 2012).
R-HSA-75944 Transcription from mitochondrial promoters Thirteen of the ~80 different proteins present in the respiratory chain of human mitochondria are encoded by the mitochondrial genome (mtDNA). The circular mtDNA, which is present in 1000 to 10000 copies in the human cell, also encodes for 2 ribosomal RNAs, and 22 transfer RNAs. The double-stranded mitochondrial genome lacks introns and the longer non-coding region contains the control elements for transcription and replication of mtDNA (Shadel and Clayton, 1997). The two mtDNA strands are referred to as the heavy (H-strand) and the light (L-strand) due to their differing G+T content. In human cells, each strand contains one single promoter for transcriptional initiation, the light-strand promoter (LSP) or the heavy-strand promoter (HSP). Transcription from the mitochondrial promoters produce polycistronic precursor RNA encompassing all the genetic information encoded in each of the specific strands. The primary transcripts are processed to produce the individual tRNA and mRNA molecules (Clayton, 1991; Ojala et al., 1981). There is likely a second initiation site for heavy strand transcription, which produces RNAs spanning the rDNA region. The resulting transcript including the genes for the two mitochondrial rRNAs and ends at the boundary between the 16 S rRNA and the tRNALeu(UUR) genes (Montoya et al., 1982; Montoya et al.,1983; Christianson and Clayton 1986). The existence of such a separate transcription unit may explain why the steady-state levels of rRNAs are much higher than the steady state levels of mRNAs.
R-HSA-1362277 Transcription of E2F targets under negative control by DREAM complex DREAM complex is evolutionarily conserved and is responsible for transcriptional repression of cell cycle-regulated genes in G0 and early G1.
R-HSA-1362300 Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 In G0 and early G1, expression of E2F target genes such as Cyclin A, E2F1, CDC2 and MYBL2 is inhibited by complexes containing p130 (RBL2) and p107 (RBL1), respectively, and histone deacetylase HDAC1.
R-HSA-9682708 Transcription of SARS-CoV-1 sgRNAs SARS-CoV-1 encodes eight subgenomic RNAs, mRNA2 to mRNA9. mRNA1 corresponds to the genomic RNA. The 5' and 3' ends of subgenomic RNAs are identical, in accordance with the template switch model of coronavirus RNA transcription (Snijder et al. 2003, Thiel et al. 2003, Yount et al. 2003). Genomic positive strand RNA is first transcribed into negative sense (minus strand) subgenomic mRNAs by template switching. Negative sense mRNAs subsequently serve as templates for the synthesis of positive strand subgenomic mRNAs. As shown in murine hepatitis virus (MHV), which is closely related to SARS-CoV-1, negative-sense viral RNAs are present in much smaller amounts than positive-sense RNAs (Irigoyen et al. 2016). Of the eight subgenomic mRNAs of SARS-CoV-1, mRNA2 encodes the S protein, mRNA3 is bicistronic and encodes proteins 3a and 3b, mRNA4 encodes the E protein, mRNA5 encodes the M protein, mRNA6 encodes protein 6, and bicistronic mRNA7, mRNA8 and mRNA9 encode proteins 7a and 7b (mRNA7), 8a and 8b (mRNA8), and 9a and N (mRNA9), respectively (Snijder et al. 2003, Thiel et al. 2003, Yount et al. 2003). The template switch model of coronavirus involves discontinuous transcription of subgenomic RNA, with the leader body joining occurring during the synthesis of minus strand RNAs. Each subgenomic RNA contains a leader transcription regulatory sequence (leader TRS) that is identical to the leader of the genome, appended via polymerase “jumping” during negative strand synthesis to the body transcription regulatory sequence (body TRS), a short, AU-rich motif of about 10 nucleotides found upstream of each ORF that is destined to become 5' proximal in one of the subgenomic mRNAs. The 3' and 5'UTRs may interact through RNA–RNA and/or RNA–protein plus protein–protein interactions to promote circularization of the coronavirus genome, placing the elongating minus strand in a favorable topology for leader-body joining. The host protein PABP was found to bind to the coronavirus 3' poly(A) tail and to interact with the host protein eIF-4G, a component of the three-subunit complex that binds to mRNA cap structures, which may promote the circularization of the coronavirus genome. Two viral proteins that bind to the coronavirus 5'UTR, the N protein and nsp1, may play a role in template switching. The poly(A) tail is necessary for the initiation of minus-strand RNA synthesis at the 3' end of genomic RNA. Elongation of nascent minus strand RNA continues until the first functional body TRS motif is encountered. A fixed proportion of replication-transcription complexes (RTCs) will either disregard the TRS motif and continue to elongate the nascent strand or stop synthesis of the nascent minus strand and relocate to the leader TRS, extending the minus strand by copying the 5' end of the genome. The completed minus-strand RNAs then serve as templates for positive strand mRNA synthesis (reviewed by Sawicki et al. 2007, Yang and Leibowitz 2015).
R-HSA-9694786 Transcription of SARS-CoV-2 sgRNAs This COVID‑19 pathway has been created by a combination of computational inference from SARS-CoV-1 data (https://reactome.org/documentation/inferred-events) and manual curation, as described in the summation for the overall SARS-CoV-2 infection pathway. Steps of SARS‑CoV‑2 transcription that have been studied directly include binding of the replication‑transcription complex (RTC) to the RNA template and the polymerase activity of nsp12 (Hillen et al. 2020, Wang et al. 2020, Yin et al. 2020), helicase activity of nsp13 (Chen et al. 2020, Ji et al. 2020, Shu et al. 2020), capping activity of nsp16 (Viswanathan et al. 2020), and polyadenylation of SARS‑CoV‑2 transcripts (Kim et al. 2020, Ravindra et al. 2020). Remaining steps have been inferred from previous studies in SARS‑CoV‑1 and related coronaviruses.
SARS-CoV-1 encodes eight subgenomic RNAs, mRNA2 to mRNA9. mRNA1 corresponds to the genomic RNA. The 5' and 3' ends of subgenomic RNAs are identical, in accordance with the template switch model of coronavirus RNA transcription (Snijder et al. 2003, Thiel et al. 2003, Yount et al. 2003). Genomic positive strand RNA is first transcribed into negative sense (minus strand) subgenomic mRNAs by template switching. Negative sense mRNAs subsequently serve as templates for the synthesis of positive strand subgenomic mRNAs. As shown in murine hepatitis virus (MHV), which is closely related to SARS-CoV-1, negative-sense viral RNAs are present in much smaller amounts than positive-sense RNAs (Irigoyen et al. 2016). Of the eight subgenomic mRNAs of SARS-CoV-1, mRNA2 encodes the S protein, mRNA3 is bicistronic and encodes proteins 3a and 3b, mRNA4 encodes the E protein, mRNA5 encodes the M protein, mRNA6 encodes protein 6, and bicistronic mRNA7, mRNA8 and mRNA9 encode proteins 7a and 7b (mRNA7), 8a and 8b (mRNA8), and 9a and N (mRNA9), respectively (Snijder et al. 2003, Thiel et al. 2003, Yount et al. 2003). The template switch model of coronavirus involves discontinuous transcription of subgenomic RNA, with the leader body joining occurring during the synthesis of minus strand RNAs. Each subgenomic RNA contains a leader transcription regulatory sequence (leader TRS) that is identical to the leader of the genome, appended via polymerase “jumping” during negative strand synthesis to the body transcription regulatory sequence (body TRS), a short, AU-rich motif of about 10 nucleotides found upstream of each ORF that is destined to become 5' proximal in one of the subgenomic mRNAs. The 3' and 5'UTRs may interact through RNA–RNA and/or RNA–protein plus protein–protein interactions to promote circularization of the coronavirus genome, placing the elongating minus strand in a favorable topology for leader-body joining. The host protein PABP was found to bind to the coronavirus 3' poly(A) tail and to interact with the host protein eIF-4G, a component of the three-subunit complex that binds to mRNA cap structures, which may promote the circularization of the coronavirus genome. Two viral proteins that bind to the coronavirus 5'UTR, the N protein and nsp1, may play a role in template switching. The poly(A) tail is necessary for the initiation of minus-strand RNA synthesis at the 3' end of genomic RNA. Elongation of nascent minus strand RNA continues until the first functional body TRS motif is encountered. A fixed proportion of replication-transcription complexes (RTCs) will either disregard the TRS motif and continue to elongate the nascent strand or stop synthesis of the nascent minus strand and relocate to the leader TRS, extending the minus strand by copying the 5' end of the genome. The completed minus-strand RNAs then serve as templates for positive strand mRNA synthesis (reviewed by Sawicki et al. 2007, Yang and Leibowitz 2015).
R-HSA-167172 Transcription of the HIV genome Expression of the integrated HIV-1 provirus is dependent on the host cell Pol II transcription machinery, but is regulated in critical ways by HIV-1 Tat and Rev proteins. The long terminal repeats (LTR) located at either end of the proviral DNA contain regulatory sequences that recruit cellular transcription factors. The U3 region of the 5' LTR contains numerous cis-acting elements that regulate Pol II-mediated transcription initiation. The full-length transcript, which encodes nine genes, functions as an mRNA and is packaged as genomic RNA. Smaller (subgenomic) viral mRNAs are generated by alternative splicing. The activities of Tat and Rev create two phases of gene expression (see Karn 1999; Cullen 1991). The Tat protein is an RNA specific trans-activator of LTR-mediated transcription. Association of Tat with TAR, a RNA stem-loop within the RNA leader sequence, is required for efficient elongation of the HIV-1 transcript. In the early phase of viral transcription, a multiply-spliced set of mRNAs is generated, producing the transcripts of the regulatory proteins, Tat, Rev, and Nef. In the late phase, Rev regulates nuclear export of HIV-1 mRNAs, repressing expression of the early regulatory mRNAs and promoting expression of viral structural proteins. Nuclear export of the unspliced and partially spliced late HIV-1 transcripts that encode the structural proteins requires the association of Rev with a cis-acting RNA sequence in the transcripts (Rev Response Element, RRE).
R-HSA-6781827 Transcription-Coupled Nucleotide Excision Repair (TC-NER) DNA damage in transcribed strands of active genes is repaired through a specialized nucleotide excision repair (NER) pathway known as transcription-coupled nucleotide excision repair (TC-NER). TC-NER impairment is the underlying cause of a severe hereditary disorder Cockayne syndrome, an autosomal recessive disease characterized by hypersensitivity to UV light.
TC-NER is triggered by helix distorting lesions that block the progression of elongating RNA polymerase II (RNA Pol II). Stalled RNA Pol II complex triggers the recruitment of ERCC6. ERCC6, commonly known as CSB (Cockayne syndrome protein B) recruits ERCC8, commonly known as CSA (Cockayne syndrome protein A). ERCC8 has 7 WD repeat motifs and is part of the ubiquitin ligase complex that also includes DDB1, CUL4A or CUL4B and RBX1. The ERCC8 ubiquitin ligase complex is one of the key regulators of TC-NER that probably exerts its role by ubiquitinating one or more factors involved in this repair process, including the RNA Pol II complex and ERCC6.
In addition to RNA Pol II, ERCC6 and the ERCC8 complex, the transcription elongation factor TFIIH, which is also involved in global genome nucleotide excision repair (GG-NER), is recruited to sites of TC-NER. The TC-NER pre-incision complex also includes XPA, XAB2 complex, TCEA1 (TFIIS), HMGN1, UVSSA in complex with USP7, and EP300 (p300). XPA probably contributes to the assembly and stability of the pre-incision complex, similar to its role in GG-NER. The XAB2 complex is involved in pre-mRNA splicing and may modulate the structure of the nascent mRNA hybrid with template DNA through its RNA-DNA helicase activity, allowing proper processing of DNA damage. TCEA1 may be involved in RNA Pol II backtracking, which allows repair proteins to gain access to the damage site. It also facilitates trimming of the 3' end of protruding nascent mRNA from the stalled RNA Pol II, enabling recovery of RNA synthesis after repair.
Deubiquitinating activity of the UVSSA:USP7 complex is needed for ERCC6 stability at repair sites. Non-histone nucleosomal binding protein HMGN1 and histone acetyltransferase p300 (EP300) remodel the chromatin around the damaged site, thus facilitating repair.
Dual incision of the lesion-containing oligonucleotide from the affected DNA strand is performed by two DNA endonucleases, the ERCC1:ERCC4 (ERCC1:XPF) complex and ERCC5 (XPG), which also participate in GG-NER. DNA polymerases delta, epsilon or kappa fill in the single stranded gap after dual incision and the remaining single strand nick is sealed by DNA ligases LIG1 or LIG3 (the latter in complex with XRCC1), similar to GG-NER. After the repair of DNA damage is complete, RNA Pol II resumes RNA synthesis.
For past and recent reviews, see Mellon et al. 1987, Svejstrup 2002, Hanawalt and Spivak 2008, Vermeulen and Fousteri 2013 and Marteijn et al. 2014.
R-HSA-69895 Transcriptional activation of cell cycle inhibitor p21 Both p53-independent and p53-dependent mechanisms of induction of p21 mRNA have been demonstrated. p21 is transcriptionally activated by p53 after DNA damage (el-Deiry et al., 1993).
R-HSA-8953750 Transcriptional Regulation by E2F6 E2F6, similar to other E2F proteins, possesses the DNA binding domain, the dimerization domain and the marked box. E2F6, however, does not have a pocket protein binding domain and thus does not interact with the retinoblastoma family members RB1, RBL1 (p107) and RBL2 (p130) (Gaubatz et al. 1998, Trimarchi et al. 1998, Cartwright et al. 1998). E2F6 lacks the transactivation domain and acts as a transcriptional repressor (Gaubatz et al. 1998, Trimarchi et al. 1998, Cartwright et al. 1998). E2F6 forms a heterodimer with TFDP1 (DP-1) (Trimarchi et al. 1998, Ogawa et al. 2002, Cartwright et al. 1998) or TFDP2 (DP-2) (Gaubatz et al. 1998, Trimarchi et al. 1998, Cartwright et al. 1998).
E2f6 knockout mice are viable and embryonic fibroblasts derived from these mice proliferate normally. Although E2f6 knockout mice appear healthy, they are affected by homeotic transformations of the axial skeleton, involving vertebrae and ribs. Similar skeletal defects have been reported in mice harboring mutations in polycomb genes, suggesting that E2F6 may function in recruitment of polycomb repressor complex(es) to target promoters (Storre et al. 2002).
E2F6 mediates repression of E2F responsive genes. While E2F6 was suggested to maintain G0 state in quiescent cells (Gaubatz et al. 1998, Ogawa et al. 2002), this finding has been challenged (Giangrande et al. 2004, Bertoli et al. 2013, Bertoli et al. 2016). Instead, E2F6-mediated gene repression in proliferating (non-quiescent) cells is thought to repress E2F targets involved in G1/S transition during S phase of the cell cycle. E2F6 does not affect E2F targets involved in G2/M transition (Oberley et al. 2003, Giangrande et al. 2004, Attwooll et al. 2005, Trojer et al. 2011, Bertoli et al. 2013). In the context of the E2F6.com-1 complex, E2F6 was shown to bind to promoters of E2F1, MYC, CDC25A and TK1 genes (Ogawa et al. 2002). E2F6 also binds the promoters of CDC6, RRM1 (RR1), PCNA and TYMS (TS) genes (Giangrande et al. 2004), as well as the promoter of the DHFR gene (Gaubatz et al. 1998). While transcriptional repression by the E2F6.com 1 complex may be associated with histone methyltransferase activity (Ogawa et al. 2002), E2F6 can also repress transcription independently of H3K9 methylation (Oberley et al. 2003).
During S phase, E2F6 is involved in the DNA replication stress checkpoint (Bertoli et al. 2013, Bertoli et al. 2016). Under replication stress, CHEK1-mediated phosphorylation prevents association of E2F6 with its target promoters, allowing transcription of E2F target genes whose expression is needed for resolution of stalled replication forks and restart of DNA synthesis. Inability to induce transcription of E2F target genes (due to CHEK1 inhibition or E2F6 overexpression) leads to replication stress induced DNA damage (Bertoli et al. 2013, Bertoli et al. 2016). E2F6 represses transcription of a number of E2F targets involved in DNA synthesis and repair, such as RRM2, RAD51, BRCA1, and RBBP8 (Oberley et al. 2003, Bertoli et al. 2013). R-HSA-8986944 Transcriptional Regulation by MECP2 MECP2 is an X chromosome gene whose loss-of-function mutations are an underlying cause of the majority of Rett syndrome cases. The MECP2 gene locus consists of four exons. Both exon 1 and exon 2 contain translation start sites. Alternative splicing of the second exon results in expression of two MECP2 transcript isoforms, MECP2_e1 (MECP2B or MECP2alpha) and MECP2_e2 (MECP2A or MECP2beta). The N-terminus of the MECP2_e1 isoform, in which exon 2 is spliced out, is encoded by exon 1. The N-terminus of the MECP2_e2 isoforms, which includes both exon 1 and exon 2, is encoded by exon 2, as the exon 2 translation start site is used. Exons 3 and 4 are present in both isoforms. The MECP2_e2 isoform was cloned first and is therefore more extensively studied. The MECP2_e1 isoform is more abundant in the brain (Mnatzakanian et al. 2004, Kriaucionis and Bird 2004, Kaddoum et al. 2013). Mecp2 isoforms show different expression patterns during mouse brain development and in adult brain regions (Dragich et al. 2007, Olson et al. 2014). While Rett syndrome mutations mainly occur in exons 3 and 4 of MECP2, thereby affecting both MECP2 isoforms (Mnatzakanian et al. 2004), some mutations occur in exon 1, affecting MECP2_e1 only. No mutations have been described in exon 2 (Gianakopoulos et al. 2012). Knockout of Mecp2_e1 isoform in mice, through a naturally occurring Rett syndrome point mutation which affects the first translation codon of MECP2_e1, recapitulates Rett-like phenotype. Knockout of Mecp2_e2 isoform in mice does not result in impairment of neurologic functions (Yasui et al. 2014). In Mecp2 null mice, transgenic expression of either Mecp2_e1 or Mecp2_e2 prevents development of Rett-like phenotype, with Mecp2_e1 rescuing more Rett-like symptoms than Mecp2_e2. This indicates that both splice variants can fulfill basic Mecp2 functions in the mouse brain (Kerr et al. 2012). Changes in gene expression upon over-expression of either MECP2_e1 or MECP2_e2 imply overlapping as well as distinct target genes (Orlic-Milacic et al. 2014).
Methyl-CpG-binding protein 2 encoded by the MECP2 gene binds to methylated CpG sequences in the DNA. The binding is not generic, however, but is affected by the underlying DNA sequence (Yoon et al. 2003). MECP2 binds to DNA containing 5 methylcytosine (5mC DNA), a DNA modification associated with transcriptional repression (Mellen et al. 2012), both in the context of CpG islands and outside of CpG islands (Chen et al. 2015). In addition, MECP2 binds to DNA containing 5 hydroxymethylcytosine (5hmC DNA), a DNA modification associated with transcriptional activation (Mellen et al. 2012). MECP2 binds to DNA as a monomer, occupying about 11 bp of the DNA. Binding of one MECP2 molecule facilitates binding of the second MECP2 molecule, and therefore clustering can occur at target sites. MECP2 binding to chromatin may be facilitated by nucleosome methylation (Ghosh et al. 2010).
MECP2 was initially proposed to act as a generic repressor of gene transcription. However, high throughput studies of MECP2-induced changes in gene expression in mouse hippocampus (Chahrour et al. 2008), and mouse and human cell lines (Orlic-Milacic et al. 2014) indicate that more genes are up-regulated than down-regulated when MECP2 is overexpressed. At least for some genes directly upregulated by MECP2, it was shown that a complex of MECP2 and CREB1 was involved in transcriptional stimulation (Chahrour et al. 2008, Chen et al. 2013).
MECP2 expression is the highest in postmitotic neurons compared to other cell types, with MECP2 being almost as abundant as core histones. Phosphorylation of MECP2 in response to neuronal activity regulates binding of MECP2 to DNA, suggesting that MECP2 may remodel chromatin in a neuronal activity-dependent manner. The resulting changes in gene expression would then modulate synaptic plasticity and behavior (reviewed by Ebert and Greenberg 2013). In human embryonic stem cell derived Rett syndrome neurons, loss of MECP2 is associated with a significant reduction in transcription of neuronally active genes, as well as the reduction in nascent protein synthesis. The reduction in nascent protein synthesis can at least in part be attributed to the decreased activity of the PI3K/AKT/mTOR signaling pathway. Neuronal morphology (reduced soma size) and the level of protein synthesis in Rett neurons can be ameliorated by treating the cells with growth factors which activate the PI3K/AKT/mTOR cascade or by inhibition of PTEN, the negative regulator of AKT activation. Mitochondrial gene expression is also downregulated in Rett neurons, which is associated with a reduced capacity of the mitochondrial electron transport chain (Ricciardi et al. 2011, Li et al. 2013). Treatment of Mecp2 null mice with IGF1 (insulin-like growth factor 1) reverses or ameliorates some Rett-like features such as locomotion, respiratory difficulties and irregular heart rate (Tropea et al. 2009).
MECP2 regulates expression of a number of ligands and receptors involved in neuronal development and function. Ligands regulated by MECP2 include BDNF (reviewed by Li and Pozzo-Miller 2014, and KhorshidAhmad et al. 2016), CRH (McGill et al. 2006, Samaco et al. 2012), SST (Somatostatin) (Chahrour et al. 2008), and DLL1 (Li et al. 2014). MECP2 also regulates transcription of genes involved in the synthesis of the neurotransmitter GABA – GAD1 (Chao et al. 2010) and GAD2 (Chao et al. 2010, He et al. 2014). MECP2 may be involved in direct stimulation of transcription from the GLUD1 gene promoter, encoding mitochondrial glutamate dehydrogenase 1, which may be involved in the turnover of the neurotransmitter glutamate (Livide et al. 2015). Receptors regulated by MECP2 include glutamate receptor GRIA2 (Qiu et al. 2012), NMDA receptor subunits GRIN2A (Durand et al. 2012) and GRIN2B (Lee et al. 2008), opioid receptors OPRK1 (Chahrour et al. 2008) and OPRM1 (Hwang et al. 2009, Hwang et al. 2010, Samaco et al. 2012), GPRIN1 (Chahrour et al. 2008), MET (Plummer et al. 2013), NOTCH1 (Li et al. 2014). Channels/transporters regulated by MECP2 include TRPC3 (Li et al. 2012) and SLC2A3 (Chen et al. 2013). MECP2 regulates transcription of FKBP5, involved in trafficking of glucocorticoid receptors (Nuber et al. 2005, Urdinguio et al. 2008). MECP2 is implicated in regulation of expression of SEMA3F (semaphorin 3F) in mouse olfactory neurons (Degano et al. 2009). In zebrafish, Mecp2 is implicated in sensory axon guidance by direct stimulation of transcription of Sema5b and Robo2 (Leong et al. 2015). MECP2 may indirectly regulate signaling by neuronal receptor tyrosine kinases by regulating transcription of protein tyrosine phosphatases, PTPN1 (Krishnan et al. 2015) and PTPN4 (Williamson et al. 2015).
MECP2 regulates transcription of several transcription factors involved in functioning of the nervous system, such as CREB1, MEF2C, RBFOX1 (Chahrour et al. 2008) and PPARG (Mann et al. 2010, Joss-Moore et al. 2011).
MECP2 associates with transcription and chromatin remodeling factors, such as CREB1 (Chahrour et al. 2008, Chen et al. 2013), the HDAC1/2-containing SIN3A co-repressor complex (Nan et al. 1998), and the NCoR/SMRT complex (Lyst et al. 2013, Ebert et al. 2013). There are contradictory reports on the interaction of MECP2 with the SWI/SNF chromatin-remodeling complex (Harikrishnan et al. 2005, Hu et al. 2006). Interaction of MECP2 with the DNA methyltransferase DNMT1 has been reported, with a concomitant increase in enzymatic activity of DNMT1 (Kimura and Shiota 2003).
In addition to DNA binding-dependent regulation of gene expression by MECP2, MECP2 may influence gene expression by interaction with components of the DROSHA microprocessor complex and the consequent change in the levels of mature microRNAs (Cheng et al. 2014, Tsujimura et al. 2015).
Increased MECP2 promoter methylation is observed in both male and female autism patients (Nagarajan et al. 2008). Regulatory elements that undergo methylation are found in the promoter and the first intron of MECP2 and their methylation was shown to regulate Mecp2 expression in mice (Liyanage et al. 2013). Mouse Mecp2 promoter methylation was shown to be affected by stress (Franklin et al. 2010).
The Rett-like phenotype of Mecp2 null mice is reversible (Guy et al. 2007), but appropriate levels of Mecp2 expression need to be achieved (Alvarez-Saavedra et al. 2007). When Mecp2 expression is restored in astrocytes of Mecp2 null mice, amelioration of Rett symptoms occurs, involving non-cell-autonomous positive effect on mutant neurons and increasing level of the excitatory glutamate transporter VGLUT1 (Lioy et al. 2011). Microglia derived from Mecp2 null mice releases higher than normal levels of glutamate, which has toxic effect on neurons. Increased glutamate secretion may be due to increased levels of glutaminase (Gls), involved in glutamate synthesis, and increased levels of connexin-32 (Gjb1), involved in glutamate release, in Mecp2 null microglia (Maezawa and Jin 2010). Targeted deletion of Mecp2 from Sim1-expressing neurons of the mouse hypothalamus recapitulates some Rett syndrome-like features and highlights the role of Mecp2 in feeding behavior and response to stress (Fyffe et al. 2008).
Mecp2 overexpression, similar to MECP2 duplication syndrome, causes neurologic phenotype similar to Rett (Collins et al. 2004, Luikenhuis et al. 2004, Van Esch et al. 2005, Alvarez-Saavedra 2007, Van Esch et al. 2012). The phenotype of the mouse model of the MECP2 duplication syndrome in adult mice is reversible when Mecp2 expression levels are corrected (Sztainberg et al. 2015).
R-HSA-9634815 Transcriptional Regulation by NPAS4 NPAS4 (Neuronal PAS domain containing protein 4) is a calcium dependent transcription factor predominantly expressed in neurons that regulates activation of genes involved in neuronal circuit formation, function, and plasticity (Ooe et al. 2004; Lin et al. 2008; Ramamoorthi et al. 2011; Maya-Vetencourt 2013; Sun and Lin 2016; Weng et al. 2018). NPAS4 possesses a conserved basic helix loop helix (bHLH) motif and a PAS domain (Fahim et al. 2018). NPAS4 is among the most rapidly induced immediate early genes (IEGs), which are activated after sensory and behavioral experience and thought to be crucial for formation of long term memory (Ramamoorthi et al. 2011; Sun et al. 2016; Heslin and Coutellier 2018; Weng et al. 2018). NPAS4 is activated within minutes of neuronal stimulation to regulate the formation of inhibitory synapses (Lin et al. 2008). NPAS4 enables gene regulation to be tailored to the type of depolarizing activity along the somato dendritic axis of a neuron (Brigidi et al. 2019). Transcriptional targets of NPAS4 include transcription factors and proteins involved in signal transduction and protein trafficking (Lin et al. 2008, Brigidi et al. 2019). NPAS4 regulates development of glutamatergic and GABAergic synapses essential for information processing and memory formation (Lin et al. 2008, Weng et al. 2018). NPAS4 induced gene expression programs differ between excitatory and inhibitory neurons (Spiegel et al. 2014), leading to a circuit wide homeostatic response. Besides directly regulating function of neurons, NPAS4 may be involved in the regulation of neuroinflammation and neuronal apoptosis (Zhang et al. 2009; Choy et al. 2015; Fan et al. 2016; Zhang et al. 2021). NPAS4 is expressed in the pancreatic beta cells and regulates their function under stress conditions (Sabatini et al. 2018). For review, please refer to Sun and Lin 2016, and Fu et al. 2020.
R-HSA-3700989 Transcriptional Regulation by TP53 The tumor suppressor TP53 (encoded by the gene p53) is a transcription factor. Under stress conditions, it recognizes specific responsive DNA elements and thus regulates the transcription of many genes involved in a variety of cellular processes, such as cellular metabolism, survival, senescence, apoptosis and DNA damage response. Because of its critical function, p53 is frequently mutated in around 50% of all malignant tumors. For a recent review, please refer to Vousden and Prives 2009 and Kruiswijk et al. 2015.
R-HSA-8853884 Transcriptional Regulation by VENTX The VENTX (also known as VENT homeobox or VENTX2) gene is a member of the homeobox family of transcription factors. The ortholog of VENTX was first described in Xenopus where it participates in BMP and Nanog signaling pathways and controls dorsoventral mesoderm patterning (Onichtchouk et al. 1996, Scerbo et al. 2012). The zebrafish ortholog of VENTX is also involved in dorsoventral patterning in the early embryo (Imai et al. 2001). Rodents lack the VENTX ortholog (Zhong and Holland 2011). VENTX is expressed in human blood cells (Moretti et al. 2001) and appears to play an important role in hematopoiesis. The role of VENTX in hematopoiesis was first suggested based on its role in mesoderm patterning in Xenopus and zebrafish (Davidson and Zon 2000). VENTX promotes cell cycle arrest and differentiation of hematopoietic stem cells and/or progenitor cells (Wu, Gao, Ke, Giese and Zhu 2011, Wu et al. 2014). Ventx suppression leads to expansion of hematopoietic stem cells and multi-progenitor cells (Gao et, J. Biol.Chem, 2012). VENTX induces transcription of cell cycle inhibitors TP53 (p53) and p16INK4A and activates tumor suppressor pathways regulated by TP53 and p16INK4A (Wu, Gao, Ke, Hager et al. 2011), as well as macrophage colony stimulating factor receptor (CSF1R) (Wu, Gao, Ke, Giese and Zhu 2011) and inhibits transcription of cyclin D1 (CCND1) (Gao et al. 2010) and Interleukin-6 (IL6) (Wu et al. 2014). Chromatin immunoprecipitation showed that EGR3 transcription factor directly binds to the promoter of IL6 and IL8 genes (Baron VT et al, BJC 2015). While VENTX expression may suppress lymphocytic leukemia (Gao et al. 2010), high levels of VENTX have been reported in acute myeloid leukemia cells, with a positive effect on their proliferation (Rawat et al. 2010). Another homeobox transcription factor that regulates differentiation of hematopoietic stemm cells is DLX4 (Bon et al. 2015). Studies on colon cancer showed that VentX regulates tumor associated macrophages and reverts immune suppression in tumor microenvironment (Le et al. 2018). MEK1 is required for Xenopus Ventx2 asymmetric distribution during blastula cell division. Ventx2 inhibition by MEK1 is required for embryonic cell commitment (Scerbo et al, eLife, 2017). VENTX induces TP53-independent apoptosis in cancer cells (Gao H, Oncotarget, 2016). During Xenopus embryonic development, VENTX ortholog regulates transcription of the sox3 gene (Rogers et al. 2007) as well as the early neuronal gene zic3 (Umair et al. 2018).
R-HSA-2151201 Transcriptional activation of mitochondrial biogenesis Phosphorylated PPARGC1A (PGC-1alpha) does not bind DNA directly but instead interacts with other transcription factors, notably NRF1 and NRF2 (via HCF1). NRF1 and NRF2 together with PPARGC1A activate the transcription of nuclear-encoded, mitochondrially targeted proteins such as TFB2M, TFB1M, and TFAM. PGC-1beta and PPRC appear to act similarly to PGC-1alpha but have not been as well studied. Transcription of PPARGC1A itself is upregulated by CREB1 (in response to calcium), MEF2C/D, ATF2, and PPARGC1A. Transcription of PPARGC1A is repressed by NR1D1 (REV-ERBA).
R-HSA-69560 Transcriptional activation of p53 responsive genes p53 causes G1 arrest by inducing the expression of a cell cycle inhibitor, p21 (El-Deiry et al, 1993; Harper et al, 1993; Xiong et al, 1993). P21 binds and inactivates Cyclin-Cdk complexes that mediate G1/S progression, resulting in lack of phosphorylation of Rb, E2F sequestration and cell cycle arrest at the G1/S transition. Mice with a homozygous deletion of p21 gene are deficient in their ability to undergo a G1/S arrest in response to DNA damage (Deng et al, 1995).
R-HSA-2173793 Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer In the nucleus, SMAD2/3:SMAD4 heterotrimer complex acts as a transcriptional regulator. The activity of SMAD2/3 complex is regulated both positively and negatively by association with other transcription factors (Chen et al. 2002, Varelas et al. 2008, Stroschein et al. 1999, Wotton et al. 1999). In addition, the activity of SMAD2/3:SMAD4 complex can be inhibited by nuclear protein phosphatases and ubiquitin ligases (Lin et al. 2006, Dupont et al. 2009).
R-HSA-9856649 Transcriptional and post-translational regulation of MITF-M expression and activity Melanocytes, neurons and glia all arise from precursor cells derived from neural crest cells. Cells that will give rise to neurons and glia migrate away from the neural crest earlier and in a ventral pattern, while cells that will give rise to melanocytes leave the neural crest later and migrate dorsolaterally. Nevertheless, melanocytes can also arise in an alternate pathway from dual Schwann cell/melanocyte precursors or by dedifferentiation from Schwann cells, a derivative of the glial lineage (reviewed in Mort et al, 2015). MITF-M is a key regulator of melanocyte development, and its expression distinguishes the melanocyte fate from that of glial and neural cells. MITF-M expression is repressed in precursors through the activity of FOXD3 and SOX2. Depending on the species, these transcription factors may either bind directly to elements in the MITF-M promoter to repress transcription, or may act independently of DNA binding by disrupting protein-protein interactions that promote transcriptional activity (Nitzan et al, 2013a,b; Curran et al, 2009, 2010; Adameyko et al, 2012; reviewed in Mort et al, 2015; White and Zon, 2008; Goding and Arnheiter, 2019). FOXD3 and SOX2 expression, in turn, are regulated by a cascade of other transcription factors, including ZIC1, PAX3, SNAIL2 and SOX9 (reviewed in Mort et al, 2015; Goding and Arnheiter, 2019).
Relief of FOXD3 mediated repression may depend in part on HDAC1, as well as on down regulation of SNAIL2 (Ignatius et al, 2008; Greenhill et al, 2011; Nitzan et al, 2013a, b). MITF-M expression in unpigmented but committed melanoblasts depends on PAX3 and SOX10 binding at the promoter as well as on WNT, EDNRB and KIT signaling (reviewed in Mort et al, 2015; White and Zon, 2008; Goding and Arnheiter, 2019). Initial expression of MITF-M also contributes to downregulation of FOXD3 and SOX2 establishing a positive feedback loop that reinforces commitment to the melanocyte fate (reviewed in Mort et al, 2015; Goding and Arnheiter, 2019).
In addition to transcriptional regulation, MITF-M activity is also controlled by post translational modifications, although the significance of these modifications is not always clear. SUMOylation, ubiquitination and phosphorylation downstream of MAPK, WNT and AKT signaling can all impact the stability, localization or activity of MITF-M (reviewed in Goding and Arnheiter, 2019), and acetylation regulates the occupancy of target promoters, decreasing occupancy at differentiation-specific promoters (Louphrasitthiphol et al, 2020, 2023).
R-HSA-8878171 Transcriptional regulation by RUNX1 The RUNX1 (AML1) transcription factor is a master regulator of hematopoiesis (Ichikawa et al. 2004) that is frequently translocated in acute myeloid leukemia (AML), resulting in formation of fusion proteins with altered transactivation profiles (Lam and Zhang 2012, Ichikawa et al. 2013). In addition to RUNX1, its heterodimerization partner CBFB is also frequently mutated in AML (Shigesada et al. 2004, Mangan and Speck 2011).
The core domain of CBFB binds to the Runt domain of RUNX1, resulting in formation of the RUNX1:CBFB heterodimer. CBFB does not interact with DNA directly. The Runt domain of RUNX1 mediated both DNA binding and heterodimerization with CBFB (Tahirov et al. 2001), while RUNX1 regions that flank the Runt domain are involved in transactivation (reviewed in Zhang et al. 2003) and negative regulation (autoinhibition). CBFB facilitates RUNX1 binding to DNA by stabilizing Runt domain regions that interact with the major and minor grooves of the DNA (Tahirov et al. 2001, Backstrom et al. 2002, Bartfeld et al. 2002). The transactivation domain of RUNX1 is located C-terminally to the Runt domain and is followed by the negative regulatory domain. Autoinhibiton of RUNX1 is relieved by interaction with CBFB (Kanno et al. 1998).
Transcriptional targets of the RUNX1:CBFB complex involve genes that regulate self-renewal of hematopoietic stem cells (HSCs) (Zhao et al. 2014), as well as commitment and differentiation of many hematopoietic progenitors, including myeloid (Friedman 2009) and megakaryocytic progenitors (Goldfarb 2009), regulatory T lymphocytes (Wong et al. 2011) and B lymphocytes (Boller and Grosschedl 2014).
RUNX1 binds to promoters of many genes involved in ribosomal biogenesis (Ribi) and is thought to stimulate their transcription. RUNX1 loss-of-function decreases ribosome biogenesis and translation in hematopoietic stem and progenitor cells (HSPCs). RUNX1 loss-of-function is therefore associated with a slow growth, but at the same time it results in reduced apoptosis and increases resistance of cells to genotoxic and endoplasmic reticulum stress, conferring an overall selective advantage to RUNX1 deficient HSPCs (Cai et al. 2015).
RUNX1 is implicated as a tumor suppressor in breast cancer. RUNX1 forms a complex with the activated estrogen receptor alpha (ESR1) and regulates expression of estrogen-responsive genes (Chimge and Frenkel 2013).
RUNX1 is overexpressed in epithelial ovarian carcinoma where it may contribute to cell proliferation, migration and invasion (Keita et al. 2013).
RUNX1 may cooperate with TP53 in transcriptional activation of TP53 target genes upon DNA damage (Wu et al. 2013).
RUNX1 is needed for the maintenance of skeletal musculature (Wang et al. 2005).
During mouse embryonic development, Runx1 is expressed in most nociceptive sensory neurons, which are involved in the perception of pain. In adult mice, Runx1 is expressed only in nociceptive sensory neurons that express the Ret receptor and is involved in regulation of expression of genes encoding ion channels (sodium-gated, ATP-gated and hydrogen ion-gated) and receptors (thermal receptors, opioid receptor MOR and the Mrgpr class of G protein coupled receptors). Mice lacking Runx1 show defective perception of thermal and neuropathic pain (Chen CL et al. 2006). Runx1 is thought to activate the neuronal differentiation of nociceptive dorsal root ganglion cells during embryonal development possibly through repression of Hes1 expression (Kobayashi et al. 2012). In chick and mouse embryos, Runx1 expression is restricted to the dorso-medial domain of the dorsal root ganglion, to TrkA-positive cutaneous sensory neurons. Runx3 expression in chick and mouse embryos is restricted to ventro-lateral domain of the dorsal root ganglion, to TrkC-positive proprioceptive neurons (Chen AI et al. 2006, Kramer et al. 2006). RUNX1 mediated regulation of neuronally expressed genes will be annotated when mechanistic details become available.
R-HSA-8878166 Transcriptional regulation by RUNX2 RUNX2 (CBFA1 or AML3) transcription factor, similar to other RUNX family members, RUNX1 and RUNX3, can function in complex with CBFB (CBF-beta) (Kundu et al. 2002, Yoshida et al. 2002, Otto et al. 2002). RUNX2 mainly regulates transcription of genes involved in skeletal development (reviewed in Karsenty 2008). RUNX2 is involved in development of both intramembraneous and endochondral bones through regulation of osteoblast differentiation and chondrocyte maturation, respectively. RUNX2 stimulates transcription of the BGLAP gene (Ducy and Karsenty 1995, Ducy et al. 1997), which encodes Osteocalcin, a bone-derived hormone which is one of the most abundant non-collagenous proteins of the bone extracellular matrix (reviewed in Karsenty and Olson 2016). RUNX2 directly controls the expression of most genes associated with osteoblast differentiation and function (Sato et al. 1998, Ducy et al. 1999, Roce et al. 2005). RUNX2-mediated transcriptional regulation of several genes involved in GPCR (G protein coupled receptor) signaling is implicated in the control of growth of osteoblast progenitors (Teplyuk et al. 2009). RUNX2 promotes chondrocyte maturation by stimulating transcription of the IHH gene, encoding Indian hedgehog (Takeda et al. 2001, Yoshida et al. 2004). Germline loss-of-function mutations of the RUNX2 gene are associated with cleidocranial dysplasia syndrome (CCD), an autosomal skeletal disorder (reviewed in Jaruga et al. 2016). The function of RUNX2 is frequently disrupted in osteosarcoma (reviewed in Mortus et al. 2014). Vitamin D3 is implicated in regulation of transcriptional activity of the RUNX2:CBFB complex (Underwood et al. 2012).
RUNX2 expression is regulated by estrogen signaling, and RUNX2 is implicated in breast cancer development and metastasis (reviewed in Wysokinski et al. 2014). Besides estrogen receptor alpha (ESR1) and estrogen-related receptor alpha (ERRA) (Kammerer et al. 2013), RUNX2 transcription is also regulated by TWIST1 (Yang, Yang et al. 2011), glucocorticoid receptor (NR3C1) (Zhang et al. 2012), NKX3-2 (BAPX1) (Tribioli and Lufkin 1999, Lengner et al. 2005), DLX5 (Robledo et al. 2002, Lee et al. 2005) and MSX2 (Lee et al. 2005). RUNX2 can autoregulate, by directly inhibiting its own transcription (Drissi et al. 2000). Several E3 ubiquitin ligases target RUNX2 for proteasome-mediated degradation: STUB1 (CHIP) (Li et al. 2008), SMURF1 (Zhao et al. 2003, Yang et al. 2014), WWP1 (Jones et al. 2006), and SKP2 (Thacker et al. 2016). Besides formation of RUNX2:CBFB heterodimers, transcriptional activity of RUNX2 is regulated by binding to a number of other transcription factors, for example SOX9 (Zhou et al. 2006, TWIST1 (Bialek et al. 2004) and RB1 (Thomas et al. 2001).
RUNX2 regulates expression of several genes implicated in cell migration during normal development and bone metastasis of breast cancer cells. RUNX2 stimulates transcription of the ITGA5 gene, encoding Integrin alpha 5 (Li et al. 2016) and the ITGBL1 gene, encoding Integrin beta like protein 1 (Li et al. 2015). RUNX2 mediated transcription of the MMP13 gene, encoding Colagenase 3 (Matrix metalloproteinase 13), is stimulated by AKT mediated phosphorylation of RUNX2 (Pande et al. 2013). RUNX2 is implicated in positive regulation of AKT signaling by stimulating expression of AKT-activating TORC2 complex components MTOR and RICTOR, which may contribute to survival of breast cancer cells (Tandon et al. 2014).
RUNX2 inhibits CDKN1A transcription, thus preventing CDKN1A-induced cell cycle arrest. Phosphorylation of RUNX2 by CDK4 in response to high glucose enhances RUNX2-mediated repression of the CDKN1A gene in endothelial cells (Pierce et al. 2012). In mice, Runx2-mediated repression of Cdkn1a may contribute to the development of acute myeloid leukemia (AML) (Kuo et al. 2009). RUNX2 can stimulate transcription of the LGALS3 gene, encoding Galectin-3 (Vladimirova et al. 2008, Zhang et al. 2009). Galectin 3 is expressed in myeloid progenitors and its levels increase during the maturation process (Le Marer 2000).
For a review of RUNX2 function, please refer to Long 2012 and Ito et al. 2015.
R-HSA-8878159 Transcriptional regulation by RUNX3 The transcription factor RUNX3 is a RUNX family member. All RUNX family members, RUNX1, RUNX2 and RUNX3, possess a highly conserved Runt domain, involved in DNA binding. For a more detailed description of the structure of RUNX proteins, please refer to the pathway 'Transcriptional regulation by RUNX1'. Similar to RUNX1 and RUNX2, RUNX3 forms a transcriptionally active heterodimer with CBFB (CBF-beta). Studies in mice have shown that RUNX3 plays a role in neurogenesis and development of T lymphocytes. RUNX3 is implicated as a tumor suppressor gene in various human malignancies.
During nervous system formation, the Cbfb:Runx3 complex is involved in development of mouse proprioceptive dorsal root ganglion neurons by regulating expression of Ntrk3 (Neurotrophic tyrosine kinase receptor type 3) and possibly other genes (Inoue et al. 2002, Kramer et al. 2006, Nakamura et al. 2008, Dykes et al. 2011, Ogihara et al. 2016). It is not yet known whether RUNX3 is involved in human neuronal development and neuronal disorders.
RUNX3 plays a major role in immune response. RUNX3 regulates development of T lymphocytes. In mouse hematopoietic stem cells, expression of Runx3 is regulated by the transcription factor TAL1 (Landry et al. 2008). RUNX3 promotes the CD8+ lineage fate in developing thymocytes. In the CD4+ thymocyte lineage in mice, the transcription factor ThPOK induces transcription of SOCS family members, which repress Runx3 expression (Luckey et al. 2014). RUNX3, along with RUNX1 and ETS1, is implicated in regulation of transcription of the CD6 gene, encoding a lymphocyte surface receptor expressed on developing and mature T cells (Arman et al. 2009). RUNX3 and ThPOK regulate intestinal CD4+ T cell immunity in a TGF-beta and retinoic acid-dependent manner, which is important for cellular defense against intestinal pathogens (Reis et al. 2013). Besides T lymphocytes, RUNX3 is a key transcription factor in the commitment of innate lymphoid cells ILC1 and ILC3 (Ebihara et al. 2015). RUNX3 regulates expression of CD11A and CD49D integrin genes, involved in immune and inflammatory responses (Dominguez-Soto et al. 2005). RUNX3 is involved in mouse TGF-beta-mediated dendritic cell function and its deficiency is linked to airway inflammation (Fainaru et al. 2004).
In addition to its developmental role, RUNX3 is implicated as a tumor suppressor. The loss of RUNX3 expression and function was first causally linked to the genesis and progression of human gastric cancer (Li et al. 2002). Expression of RUNX3 increases in human pancreatic islet of Langerhans cells but not in pancreatic adenocarcinoma cells in response to differentiation stimulus (serum withdrawal) (Levkovitz et al. 2010). Hypermethylation of the RUNX3 gene is associated with an increased risk for progression of Barrett's esophagus to esophageal adenocarcinoma (Schulmann et al. 2005). Hypermethylation-mediated silencing of the RUNX3 gene expression is also frequent in granulosa cell tumors (Dhillon et al. 2004) and has also been reported in colon cancer (Weisenberger et al. 2006), breast cancer (Lau et al. 2006, Huang et al. 2012), bladder cancer (Wolff et al. 2008) and gastric cancer (Li et al. 2002). In colorectal cancer, RUNX3 is one of the five markers in a gene panel used to classify CpG island methylator phenotype (CIMP+) (Weisenberger et al. 2006).
RUNX3 and CBFB are frequently downregulated in gastric cancer. RUNX3 cooperates with TGF-beta to maintain homeostasis in the stomach and is involved in TGF-beta-induced cell cycle arrest of stomach epithelial cells. Runx3 knockout mice exhibit decreased sensitivity to TGF-beta and develop gastric epithelial hyperplasia (Li et al. 2002, Chi et al. 2005). RUNX3-mediated inhibition of binding of TEADs:YAP1 complexes to target promoters is also implicated in gastric cancer suppression (Qiao et al. 2016).
RUNX3 is a negative regulator of NOTCH signaling and RUNX3-mediated inhibition of NOTCH activity may play a tumor suppressor role in hepatocellular carcinoma (Gao et al. 2010, Nishina et al. 2011).
In addition to RUNX3 silencing through promoter hypermethylation in breast cancer (Lau et al. 2006), Runx3+/- mice are predisposed to breast cancer development. RUNX3 downregulates estrogen receptor alpha (ESR1) protein levels in a proteasome-dependent manner (Huang et al. 2012).
Besides its tumor suppressor role, mainly manifested through its negative effect on cell proliferation, RUNX3 can promote cancer cell invasion by stimulating expression of genes involved in metastasis, such as osteopontin (SPP1) (Whittle et al. 2015).
R-HSA-5578749 Transcriptional regulation by small RNAs Recent evidence indicates that small RNAs participate in transcriptional regulation in addition to post-transcriptional silencing. Components of the RNAi machinery (ARGONAUTE1 (AGO1, EIF2C1), AGO2 (EIF2C2), AGO3 (EIF2C3), AGO4 (EIF2C4), TNRC6A, and DICER) are observed associated with microRNAs (miRNAs) in both the cytosol and the nucleus (Robb et al. 2005, Weinmann et al. 2009, Doyle et al. 2013, Nishi et al. 2013, Gagnon et al. 2014). The AGO:miRNA complexes are imported into the nucleus by IMPORTIN-8 (IPO8, IMP8, RANBP8) and also by an unknown importin while associated with the nuclear shuttling protein TNRC6A (reviewed in Schraivogel and Meister 2014).
Within the nucleus, AGO2, TNRC6A, and DICER may associate in a complex (Gagnon et al. 2014). Nuclear AGO1 and AGO2 in complexes with small RNAs are observed to activate transcription (RNA activation, RNAa) or repress transcription (Transcriptional Gene Silencing, TGS) of genes that contain sequences matching the small RNAs (reviewed in Malecova and Morris 2010, Huang and Li 2012, Gagnon and Corey 2012, Huang and Li 2014, Salmanidis et al. 2014, Stroynowska-Czerwinska et al. 2014). TGS is associated with methylation of cytosine in DNA and methylation of histone H3 at lysine-9 and lysine-27 (Castanotto et al. 2005, Suzuki et al. 2005, Kim et al. 2006, Weinberg et al. 2006, Kim et al. 2008, reviewed in Malecova and Morris 2010, Li et al. 2014); RNAa is associated with methylation of histone H3 at lysine-4 (Huang et al. 2012, reviewed in Li et al. 2014). Small RNAs in the nucleus have also been shown to play roles in alternative splicing (Liu et al., 2012, Ameyar-Zazoua et al., 2012) and DNA damage repair (Wei et al., 2012; Francia et al., 2012). Nevertheless, elucidation of the detailed mechanisms of small RNA action requires further research.
R-HSA-8864260 Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors The AP-2 (TFAP2) family of transcription factors includes five proteins in mammals: TFAP2A (AP-2 alpha), TFAP2B (AP-2 beta), TFAP2C (AP-2 gamma), TFAP2D (AP-2 delta) and TFAP2E (AP-2 epsilon). The AP-2 family transcription factors are evolutionarily conserved in metazoans and are characterized by a helix-span-helix motif at the C-terminus, a central basic region, and the transactivation domain at the N-terminus. The helix-span-helix motif and the basic region enable dimerization and DNA binding (Eckert et al. 2005).
AP-2 dimers bind palindromic GC-rich DNA response elements that match the consensus sequence 5'-GCCNNNGGC-3' (Williams and Tjian 1991a, Williams and Tjian 1991b). Transcriptional co-factors from the CITED family interact with the helix-span-helix (HSH) domain of TFAP2 (AP-2) family of transcription factors and recruit transcription co-activators EP300 (p300) and CREBBP (CBP) to TFAP2-bound DNA elements. CITED2 shows the highest affinity for TFAP2 proteins, followed by CITED4, while CITED1 interacts with TFAP2s with a very low affinity. Mouse embryos defective for CITED2 exhibit neural crest defects, cardiac malformations and adrenal agenesis, which can at least in part be attributed to a defective Tfap2 transactivation (Bamforth et al. 2001, Braganca et al. 2002, Braganca et al. 2003). Transcriptional activity of AP-2 dimers in inhibited by binding of KCTD1 or KCTD15 to the AP-2 transactivation domain (Ding et al. 2009, Zarelli and Dawid 2013). Transcriptional activity of TFAP2A, TFAP2B and TFAP2C is negatively regulated by SUMOylation mediated by UBE2I (UBC9) (Eloranta and Hurst 2002, Berlato et al. 2011, Impens et al. 2014, Bogachek et al. 2014).
During embryonic development, AP-2 transcription factors stimulate proliferation and suppress terminal differentiation in a cell-type specific manner (Eckert et al. 2005).
TFAP2A and TFAP2C directly stimulate transcription of the estrogen receptor ESR1 gene (McPherson and Weigel 1999). TFAP2A expression correlates with ESR1 expression in breast cancer, and TFAP2C is frequently overexpressed in estrogen-positive breast cancer and endometrial cancer (deConinck et al. 1995, Turner et al. 1998). TFAP2A, TFAP2C, as well as TFAP2B can directly stimulate the expression of ERBB2, another important breast cancer gene (Bosher et al. 1996). Association of TFAP2A with the YY1 transcription factor significantly increases the ERBB2 transcription rate (Begon et al. 2005). In addition to ERBB2, the expression of another receptor tyrosine kinase, KIT, is also stimulated by TFAP2A and TFAP2B (Huang et al. 1998), while the expression of the VEGF receptor tyrosine kinase ligand VEGFA is repressed by TFAP2A (Ruiz et al. 2004, Li et al. 2012). TFAP2A stimulates transcription of the transforming growth factor alpha (TGFA) gene (Wang et al. 1997). TFAP2C regulates EGFR in luminal breast cancer (De Andrade et al. 2016).
TFAP2C plays a critical role in maintaining the luminal phenotype in human breast cancer and in influencing the luminal cell phenotype during normal mammary development (Cyr et al. 2015).
In placenta, TFAP2A and TFAP2C directly stimulate transcription of both subunits of the human chorionic gonadotropin, CGA and CGB (Johnson et al. 1997, LiCalsi et al. 2000).
TFAP2A and/or TFAP2C, in complex with CITED2, stimulate transcription of the PITX2 gene, involved in left-right patterning and heart development (Bamforth et al. 2004, Li et al. 2012).
TFAP2A and TFAP2C play opposing roles in transcriptional regulation of the CDKN1A (p21) gene locus. While TFAP2A stimulates transcription of the CDKN1A cyclin-dependent kinase inhibitor (Zeng et al. 1997, Williams et al. 2009, Scibetta et al. 2010), TFAP2C represses CDKN1A transcription (Williams et al. 2009, Scibetta et al. 2010, Wong et al. 2012). Transcription of the TFAP2A gene may be inhibited by CREB and E2F1 (Melnikova et al. 2010).
For review of the AP-2 family of transcription factors, please refer to Eckert et al. 2005.
R-HSA-9843743 Transcriptional regulation of brown and beige adipocyte differentiation Brown and beige adipocytes convert chemical energy produced by the oxidation of fatty acids and glucose into heat, which is important for thermoregulation and control of body weight. Brown and beige adipocytes largely share the transcription program involved in adaptive non-shivering thermogenesis but develop from different lineages (reviewed in Wang and Seale 2016, Ghaben and Scherer 2019). Brown adipocytes share their precursor cells with skeletal muscle cells and develop in discrete, homogeneous brown adipose tissue depots. Beige adipocytes share their precursor cells with white adipocytes and develop in white adipose tissue in response to environmental stimuli, mainly exposure to cold, with an ability to revert to a white adipocyte-like phenotype. Development of beige adipocytes in white adipose tissue is known as white adipose tissue browning (reviewed in Wang and Seale 2016).
Brown and beige adipocytes have been characterized in most detail in rodents. In humans, brown adipose tissue was thought to regress after infancy, but was shown by multiple studies published after 2007 to persist in substantial deposits into adulthood adulthood (reviewed in Bartlet and Heeren 2014, Wang and Seale 2016, Ghaben and Scherer 2019, and Cannon et al. 2020). Molecular profiles that correspond to both brown and beige rodent adipocytes have been identified in human brown-designated adipose tissue, and therefore both brown and beige adipocytes are now thought to be conserved in humans (Nedergaard et al. 2007; Virtanen et al. 2009; Cypess et al. 2009; Sharp et al. 2012; Wu et al. 2012; Nedergaard and Cannon 2013; de Jong et al. 2019; reviewed in Bartlet and Heereb 2014, Wang and Seale 2016, and Cannon et al. 2020).
The major protein marker of brown and beige adipocytes is Uncoupling protein 1 (UCP1). UCP1 resides at the inner mitochondrial membrane where it translocates protons (H+) from the intermembrane space into the mitochondrial matrix. UCP1 thus dissipates the proton-motive force to be used by ATP synthase, converting the energy released by the respiratory chain into heat (reviewed in Bartlet and Heereb 2014, Wang and Seale 2016). Brown adipose tissue is innervated by the sympathetic nervous system. Noradrenaline is secreted by sympathetic neurons when the central nervous system senses cold. Brown adipocytes possess adrenergic receptors on their surface that are activated by noradrenaline. Activated adrenergic receptors trigger a signaling cascade that induces lipolysis and activates UCP1 (reviewed in Wang and Seale 2016).
Multiple transcription factors that regulate the thermogenic molecular signature are shared between brown and beige adipocytes, such as EBF2, PRDM16, ZNF516, and PPARGC1A. Master regulators of adipogenesis, such as PPARG and CEBPB, are shared between white, brown, and beige adipocytes (reviewed in Wang and Seale 2016).
Besides its role in thermoregulation, white adipose tissue browning is implicated in cancer-associated cachexia, a complex tissue-wasting syndrome characterized by inflammation, hypermetabolism, increased energy expenditure, and anorexia (reviewed in Weber et al. 2022).
For review, please refer to Bartelt and Heeren 2014, Wang and Seale 2016, Ghaben and Scherer 2019, Cannon et al. 2020, Weber et al. 2022.
R-HSA-9844594 Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 EBF2 (Early B-cell factor 2) is a transcription factor that marks committed brown and beige preadipocytes. EBF2 cooperates with PPARG, a master regulator of adipogenesis, to activate the brown/beige adipocyte thermogenic program (inferred from mouse homologs in Rajakumari et al. 2013). In white adipocytes, the activity of EBF2 is negatively regulated by binding of the transcription factor ZNF423, a key transcription factor for white adipocyte differentiation. In brown/beige fate-committed cells, the interaction between ZNF423 and EBF2 is impeded by BMP7, which acts as a positive regulator of brown/beige adipogenesis (inferred from mouse homologs in Shao et al. 2016; Shao et al. 2021). Direct transcriptional targets of EBF2 include PRDM16, UCP1, and PPARA genes. Other marker genes of brown/beige adipocytes, such as CIDEA, PPARGC1A, COX7A, and DIO2 are positively regulated by EBF2 and probably also direct targets of EBF2 (inferred from mouse homologs in Rajakumari et al. 2013; Wang et al. 2014; Stine et al. 2016; Shapira et al. 2017; Lai et al. 2017; Angueira et al. 2020). Based on mouse studies, EBF1 may function partially redundantly with EBF2 in regulation of thermogenesis genes (Angueira et al. 2020). Transcriptional activity of EBF2 is positively regulated by binding of the long noncoding RNA (lncRNA) Blnc1 (inferred from mouse homologs in Zhao et al. 2014; Mi et al. 2017). Based on mouse studies, EBF2 was reported to recruit the BAF chromatin remodeling complex to activate the transcription of target genes (Shapira et al. 2017; Liu et al. 2020). In addition to PPARG, based on mouse studies, EBF2 was reported to cooperate with other transcription factors such as SIX1 during brown/beige adipogenesis (Brunmeir et al. 2016). Besides ZNF423, based on mouse studies, other transcription factors, such as ID1 (Patil et al. 2017) and TLE3 (Pearson et al. 2019), have been reported to act as inhibitors of EBF2-mediated transcription. The transcription factor GATA6 was reported to directly stimulate EBF2 transcription during mouse beige/brown thermogenesis (Jun et al. 2023). Besides BPM7, BPM9-mediated upregulation of FGFR3 (Yamamoto et al. 2022), and FGF11 (Jiang et al. 2023) have been reported as indirect activators of EBF2 transcriptional activity in mouse and goat, respectively. ZAG (Zinc-alpha2-glycoprotein), a tumor secretory factor, has been reported to stimulate EBF2 expression, which contributes to white adipose tissue browning and energy wasting in cancer-related cachexia (Elattar et al. 2018). In the single cell atlas of human white adipose tissue (Emont et al. 2022) it was reported that the EBF2-positive hAd6 white adipocyte subpopulation with UCP1 expression, consistent with the beige profile, shows an association with increased BMI and visceral adiposity. For review, please refer to Wang and Seale 2016.
R-HSA-9616222 Transcriptional regulation of granulopoiesis Neutrophilic granulocytes (hereafter called granulocytes) are distinguished by multilobulated nuclei and presence of cytoplasmic granules containing antipathogenic proteins (reviewed in Cowland and Borregaard 2016, Yin and Heit 2018). Granulocytes comprise eosinophils, basophils, mast cells, and neutrophils, all of which are ultimately derived from hemopoietic stem cells (HSCs), a self-renewing population of stem cells located in the bone marrow. A portion of HSCs exit self-renewing proliferation and differentiate to form multipotent progenitors (MPPs). MPPs then differentiate to form common myeloid progenitors (CMPs) as well as the erythrocyte lineage. CMPs further differentiate into granulocyte-monocyte progenitors (GMPs) which can then differentiate into monocytes or any of the types of granulocytes (reviewed in Fiedler and Brunner 2012). granulocytes are the most abundant leukocytes in peripheral blood.
For early granulopoiesis the CEBPA, SPI1 (PU.1), RAR, CBF, and MYB transcription factors are essential. CEBPE, SPI1, SP1, CDP, and HOXA10 transcription factors initiate terminal neutrophil differentiation.
Initially, RUNX1 activates SPI1 (PU.1), which is believed to be the key transcription factor driving the formation of MPPs and CMPs (reviewed in Friedman 2007, Fiedler and Brunner 2012). SPI1, in turn, activates expression of CEBPA, an indispensable transcription factor for granulopoiesis especially important in the transition from CMP to GMP (inferred from mouse homologs in Wilson et al. 2010, Guo et al. 2012, Guo et al. 2014, Cooper et al. 2015). CEBPA, in turn, activates the expression of several transcription factors and receptors characteristic of granulocytes, including CEBPA (autoregulation), CEBPE (Loke et al. 2018, and inferred from mouse homologs in Wang and Friedman 2002, Friedman et al. 2003), GFI1 (inferred from mouse homologs in Lidonnici et al. 2010), KLF5 (Federzoni et al. 2014), IL6R (inferred from mouse homologs in Zhang et al. 1998), and CSF3R (Smith et al. 1996). Importantly, CEBPA dimers repress transcription of MYC (c-Myc) (Johansen et al. 2001, and inferred from mouse homologs in Slomiany et al. 2000, Porse et al. 2001). CEBPA binds CDK2 and CDK4 (Wang et al. 2001) which inhibits their kinase activity by disrupting their association with cyclins thereby limiting proliferation and favoring differentiation of granulocyte progenitors during regular ("steady-state") granulopoiesis (reviewed in Friedman 2015). The transcription factor GFI1 regulates G-CSF signaling and neutrophil development through the Ras activator RasGRP1 (de la Luz Sierra et al. 2010).
Inhibitors of DNA binding (ID) proteins ID1 and ID2 regulate granulopoiesis and eosinophil production such that ID1 induces neutrophil development and inhibits eosinophil differentiation, whereas ID2 induces both eosinophil and neutrophil development (Buitenhuis et al. 2005, Skokowa et al. 2009).
Major infection activates emergency granulopoiesis (reviewed in Manz and Boettcher 2014, Hirai et al. 2015), the production of large numbers of granulocytes in a relatively short period of time. Emergency granulopoiesis is activated by cytokines, CSF2 (GM-CSF) and especially CSF3 (G-CSF, reviewed in Panopoulos and Watowich 2008, Liongue et al. 2009) which bind receptors, CSF2R and CSF3R, respectively, resulting in expression of CEBPB, which interferes with repression of MYC by CEBPA (inferred from mouse homologs in Zhang et al. 2010) and represses MYC less than CEBPA does (Hirai et al. 2006), leading to proliferation of granulocyte progenitors prior to final differentiation.Both, emergency and steady-state granulopoiesis are regulated by direct interaction of CEBPA (steady-state) or CEBPB (emergency) proteins with NAD+-dependent protein deacetylases, SIRT1 and SIRT2 (Skokowa et al. 2009). G-CSF induces the NAD+-generating enzyme, Nicotinamide phosphoribosyltransferase (NAMPT, or PBEF), that in turn activates sirtuins (Skokowa et al. 2009).
GADD45A and GADD45B proteins are essential for stress-induced granulopoiesis and granulocyte chemotaxis by activation of p38 kinase (Gupta et al. 2006, Salerno et al. 2012). SHP2 is required for induction of CEBPA expression and granulopoiesis in response to CSF3 (G-CSF) or other cytokines independent of SHP2-mediated ERK activation (Zhang et al. 2011).
Transcription of neutrophil granule proteins (e.g. ELANE, MPO, AZU1, DEFA4), that play an essential role in bacterial killing are regulated by CEBPE and SPI1 (PU.1) transcription factors (Gombart et al. 2003, Nakajima et al. 2006). RUNX1 and LEF1 also regulate ELANE (ELA2) mRNA expression by binding to its promoter (Li et al. 2003).
R-HSA-452723 Transcriptional regulation of pluripotent stem cells Pluripotent stem cells are undifferentiated cells posessing an abbreviated cell cycle (reviewed in Stein et al. 2012), a characteristic profile of gene expression (Rao et al. 2004, Kim et al. 2006, Player et al. 2006, Wang et al 2006 using mouse, International Stem Cell Initiative 2007, Assou et al. 2007, Assou et al. 2009, Ding et al. 2012 using mouse), and the ability to self-renew and generate all cell types of the body except extraembryonic lineages (Marti et al. 2013, reviewed in Romeo et al. 2012). They are a major cell type in the inner cell mass of the early embryo in vivo, and cells with the same properties, induced pluripotent stem cells, can be generated in vitro from differentiated adult cells by overexpression of a set of transcription factor genes (Takahashi and Yamanaka 2006, Takahashi et al. 2007, Yu et al. 2007, Jaenisch and Young 2008, Stein et al. 2012, reviewed in Dejosez and Zwaka 2012).
Pluripotency is maintained by a self-reinforcing loop of transcription factors (Boyer et al. 2005, Rao et al. 2006, Matoba et al. 2006, Player et al. 2006, Babaie et al. 2007, Sun et al. 2008, Assou et al. 2009, reviewed in Kashyap et al. 2009, reviewed in Dejosez and Zwaka 2012). In vivo, initiation of pluripotency may depend on maternal factors transmitted through the oocyte (Assou et al. 2009) and on DNA demethylation in the zygote (recently reviewed in Seisenberger et al. 2013) and hypoxia experienced by the blastocyst in the reproductive tract before implantation (Forristal et al. 2010, reviewed in Mohyeldin et al. 2010). In vitro, induced pluripotency may initiate with demethylation and activation of the promoters of POU5F1 (OCT4) and NANOG (Bhutani et al. 2010). Hypoxia also significantly enhances conversion to pluripotent stem cells (Yoshida et al. 2009). POU5F1 and NANOG, together with SOX2, encode central factors in pluripotency and activate their own transcription (Boyer et al 2005, Babaie et al. 2007, Yu et al. 2007, Takahashi et al. 2007). The autoactivation loop maintains expression of POU5F1, NANOG, and SOX2 at high levels in stem cells and, in turn, complexes containing various combinations of these factors (Remenyi et al. 2003, Lam et al. 2012) activate the expression of a group of genes whose products are associated with rapid cell proliferation and repress the expression of a group of genes whose products are associated with cell differentiation (Boyer et al. 2005, Matoba et al. 2006, Babaie et al. 2007, Chavez et al. 2009, Forristal et al. 2010, Guenther 2011).
Comparisons between human and mouse embryonic stem cells must be made with caution and for this reason inferences from mouse have been used sparingly in this module. Human ESCs more closely resemble mouse epiblast stem cells in having inactivated X chromosomes, flattened morphology, and intolerance to passaging as single cells (Hanna et al. 2010). Molecularly, human ESCs differ from mouse ESCs in being maintained by FGF and Activin/Nodal/TGFbeta signaling rather than by LIF and canonical Wnt signaling (Greber et al. 2010, reviewed in Katoh 2011). In human ESCs POU5F1 binds and directly activates the FGF2 gene, however Pou5f1 does not activate Fgf2 in mouse ESCs (reviewed in De Los Angeles et al. 2012). Differences in expression patterns of KLF2, KLF4, KLF5, ESRRB, FOXD3, SOCS3, LIN28, NODAL were observed between human and mouse ESCs (Cai et al. 2010) as were differences in expression of EOMES, ARNT and several other genes (Ginis et al.2004).
R-HSA-9690406 Transcriptional regulation of testis differentiation In humans, primordial germ cells (PGCs) are specified about 2 weeks after fertilization, a time before gastrulation (reviewed in Svingen and Koopman 2013, Mäkelä et al. 2019). PGCs are initially located extraembryonically and then migrate to colonize the gonadal ridges (genital ridges) of the embryo during the fifth week after fertilization. At this time, either ovaries and testes can originate from the gonadal ridges. That is, the cells of the gonadal ridges are initially bipotential and remain bipotential until about 42 days after conception, when transient expression of the SRY gene located on the Y chromosome in male embryos is initiated in some somatic cells of the gonadal primordium (reviewed in Sekido and Lovell-Badge 2013, Barrionuevo et al. 2013, Svingen et al. 2013, Mäkelä et al. 2019).
The transcription factors WT1, GATA4, ZFPM2 (FOG2), and the nuclear receptor NR5A1 (SF1) activate transcription of SRY (Shimamura et al. 1997, Hossain and Saunders 2001, De Santa Barbara et al. 2001, Miyamoto et al. 2008, and inferred from mouse homologs). SRY and NR5A1 then activate transcription of SOX9, one of the master regulators of testis development and maintenance (Knower et al. 2011, Croft et al. 2018, inferred from mouse homologs, reviewed in Gonen and Lovell-Badge 2019). Regulation of genes by SRY and then, when expression of SRY decreases, by SOX9 causes the specification of Sertoli cells that further organize formation of the testis by encasing the primordial germ cells in protocords, which then form fully developed testis cords.
SOX9 directly activates its own promoter to maintain SOX9 expression through development and into adulthood (Croft et al. 2018, and inferred from mouse homologs). SOX9 and GATA4 directly activate DMRT1 (inferred from mouse homologs), which maintains testis specification by maintaining expression of SOX9 and other testis-related genes. DMRT1 also acts to suppress ovarian specification by binding and repressing FOXL2 and WNT4 genes (inferred from mouse homologs). SOX9 directly activates FGF9 (inferred from mouse homologs), which acts via FGFR2 to maintain SOX9 expression, and PTGDS (inferred from mouse homologs), which converts Prostaglandin H2 to Prostaglandin D2, a critical hormone-like lipid that recruits supporting cells to Sertoli cells and acts indirectly to maintain SOX9 expression. SOX9, NR5A1, and GATA4 directly activate AMH (De Santa Barbara et al. 1998, and inferred from mouse homologs), an extracellular signaling molecule which causes regression of the Muellerian duct of the female reproductive system. SOX9 also directly activates many other genes, including DHH (Rahmoun et al. 2017, and inferred from mouse homologs), an intercellular signaling molecule required for testis formation.
R-HSA-381340 Transcriptional regulation of white adipocyte differentiation Adipogenesis is the process of cell differentiation by which preadipocytes become adipocytes. During this process the preadipocytes cease to proliferate, begin to accumulate lipid droplets and develop morphologic and biochemical characteristics of mature adipocytes such as hormone responsive lipogenenic and lipolytic programs. The most intensively studied model system for adipogenesis is differentiation of the mouse 3T3-L1 preadipocyte cell line by an induction cocktail of containing mitogens (insulin/IGF1), glucocorticoid (dexamethasone), an inducer of cAMP (IBMX), and fetal serum (Cao et al. 1991, reviewed in Farmer 2006). More recently additional cellular models have become available to study adipogenesis that involve almost all stages of development (reviewed in Rosen and MacDougald 2006). In vivo knockout mice lacking putative adipogenic factors have also been extensively studied. Human pathways are traditionally inferred from those discovered in mouse but are now beginning to be validated in cellular models derived from human adipose progenitors (Fischer-Posovszky et al. 2008, Wdziekonski et al. 2011).
Adipogenesis is controlled by a cascade of transcription factors (Yeh et al. 1995, reviewed in Farmer 2006, Gesta et al. 2007). One of the first observable events during adipocyte differentiation is a transient increase in expression of the CEBPB (CCAAT/Enhancer Binding Protein Beta, C/EBPB) and CEBPD (C/EBPD) transcription factors (Cao et al. 1991, reviewed in Lane et al. 1999). This occurs prior to the accumulation of lipid droplets. However, it is the subsequent inductions of CEBPA and PPARG that are critical for morphological, biochemical and functional adipocytes.
Ectopic expression of CEBPB alone is capable of inducing substantial adipocyte differentiation in fibroblasts while CEBPD has a minimal effect. CEBPB is upregulated in response to intracellular cAMP (possibly via pCREB) and serum mitogens (possibly via Krox20). CEBPD is upregulated in response to glucocorticoids. The exact mechanisms that upregulate the CEBPs are not fully known.
CEBPB and CEBPD act directly on the Peroxisome Proliferator-activated Receptor Gamma (PPARG) gene by binding its promoter and activating transcription. CEBPB and CEBPD also directly activate the EBF1 gene (and possibly other EBFs) and KLF5 (Jimenez et al. 2007, Oishi 2005). The EBF1 and KLF5 proteins, in turn bind, and activate the PPARG promoter. Other hormones, such as insulin, affect PPARG expression and other transcription factors, such as ADD1/SREBP1c, bind the PPARG promoter. This is an area of ongoing research.
During adipogenesis the PPARG gene is transcribed to yield 2 variants. The adipogenic variant 2 mRNA encodes 30 additional amino acids at the N-terminus compared to the widely expressed variant 1 mRNA.
PPARG encodes a type II nuclear hormone receptor (remains in the nucleus in the absence of ligand) that forms a heterodimer with the Retinoid X Receptor Alpha (RXRA). The heterodimer was initially identified as a complex regulating the aP2/FABP4 gene and named ARF6 (Tontonoz et al. 1994).
The PPARG:RXRA heterodimer binds a recognition sequence that consists of two hexanucleotide motifs (DR1 motifs) separated by 1 nucleotide. Binding occurs even in the absence of ligands, such as fatty acids, that activate PPARG. In the absence of activating ligands, the PPARG:RXRA complex recruits repressors of transcription such as SMRT/NCoR2, NCoR1, and HDAC3 (Tontonoz and Spiegelman 2008).
Each molecule of PPARG can bind 2 molecules of activating ligands. Although, the identity of the endogenous ligands of PPARG is unknown, exogenous activators include fatty acids and the thiazolidinedione class of antidiabetic drugs (reviewed in Berger et al. 2005, Heikkinen et al. 2007, Lemberger et al. 1996). The most potent activators of PPARG in vitro are oxidized derivatives of unsaturated fatty acids.. Upon binding activating ligands PPARG causes a rearrangement of adjacent factors: Corepressors such as SMRT/NCoR2 are lost and coactivators such as TIF2, PRIP, CBP, and p300 are recruited (Tontonoz and Spiegelman). PPARG also binds directly to the TRAP220 subunit of the TRAP/Mediator complex that recruits RNA polymerase II. Thus binding of activating ligand by PPARG causes transcription of PPARG target genes.
Targets of PPARG include genes involved in differentiation (PGAR/HFARP, Perilipin, aP2/FABP4, CEBPA), fatty acid transport (LPL, FAT/CD36), carbohydrate metabolism (PEPCK-C, AQP7, GK, GLUT4 (SLC2A4)), and energy homeostasis (LEPTIN and ADIPONECTIN) (Perera et al. 2006).
Within 10 days of differentiation CEBPB and CEBPD are no longer located at the PPARG promoter. Instead CEBPA is present. EBF1 and PPARG bind the CEBPA promoter and activate transcription of CEBPA, one of the key transcription factors in adipogenesis. A current hypothesis posits a self-reinforcing loop that maintains PPARG expression and the differentiated state: PPARG activates CEBPA and CEBPA activates PPARG. Additionally EBF1 (and possibly other EBFs) activates CEBPA, CEBPA activates EBF1, and EBF1 activates PPARG.
R-HSA-166020 Transfer of LPS from LBP carrier to CD14 LBP delivers LPS from bacteria (or bacterial membrane fragments) to CD14 on the surfaces of phagocytes, where it is recognised by the MD2:TLR4 complex . Thus, LBP is an opsonin and CD14 is an opsonic receptor for complexes of LPS (or LPS-containing particles such as bacteria) and LBP. CD14 exists as two isoforms. CD14 can be either secreted into the extracellular compartment, or it can be anchored to the plasma membrane via its GPI module.
R-HSA-917977 Transferrin endocytosis and recycling Endocytosis of iron loaded transferrin/receptor complex leads, after acidification of the endosome, to the separation of iron and its diffusion out of the vesicle. The endosome is not fused with a lysosome but recycles its content back to the cell surface where soon transferrin dissociates from its receptor (Dautry-Varsat, 1986).
R-HSA-72766 Translation Protein synthesis is accomplished through the process of translation of an mRNA sequence into a polypeptide chain. This process can be divided into three distinct stages: initiation, elongation and termination. During the initiation phase, the two subunits of the ribosome are brought together to the translation start site on the mRNA where the polypeptide chain is to begin. Extension of the polypeptide chain occurs when a specific aminoacyl-tRNA, as determined by the template mRNA, binds an elongating ribosome. The protein chain is released from the ribosome when any one of three stop codons in the relevant reading frame on the mRNA is reached. Individual reactions at each one of these stages are catalyzed by a number of initiation, elongation and release factors, respectively.
Proteins destined for the endoplasmic reticulum (ER) contain a short sequence of hydrophobic amino acid residues (approximately 20 residues) at their N-termini. Upon protrusion of the signal sequence from the translating ribosome, the signal sequence is bound by the cytosolic signal recognition particle (SRP), translation is temporarily halted, and the SRP:nascent peptide:ribosome complex then docks with a SRP receptor complex on the ER membrane. There the nascent peptide:ribosome complex is transferred from the SRP complex to a translocon complex embedded in the ER membrane and reoriented so that the nascent polypeptide protrudes through a pore in the translocon into the ER lumen. Translation now resumes, the signal peptide is cleaved from the polypeptide by signal peptidase as the signal peptide emerges into the ER, and elongation proceeds with the growing polypeptide oriented into the ER lumen.
The 13 proteins encoded by the mitochondrial genome are translated within the mitochondrion by mitochondrial ribosomes (mitoribosomes) at the matrix face of the inner mitochondrial membrane. Mitochondrial translation reflects both the bacterial origin of the organelle and subsequent divergent evolution during symbiosis. Mitoribosomes have shorter rRNAs, mitochondria-specific proteins, and rearranged protein positions. Mitochondrial mRNAs have either no untranslated leaders or very short untranslated leaders of 1-3 nucleotides. Translation begins with N-formylmethionine, as in bacteria, and continues with cycles of aminoacyl-tRNA:TUFM:GTP binding, GTP hydrolysis and dissociation of TUFM:GDP. All 13 proteins encoded by the mitochondrial genome are hydrophobic inner membrane proteins which are inserted cotranslationally into the membrane by an interaction with OXA1L. Translation is terminated when MTRF1L:GTP recognizes a UAA or UAG codon at the A-site of the mitoribosome. The translated polypeptide is released and MRRF and GFM2:GTP act to dissociate the 55S ribosome into 28S and 39S subunits.
R-HSA-72649 Translation initiation complex formation The translation initiation complex forms when the 43S complex binds the mRNA that is associated with eIF4F, eIF4B and eIF4H. eIF4G in the eIF4F complex can directly contact eIF3 in the 43S complex. eIF1A is necessary for the formation of this complex.
R-HSA-9727281 Translation of Accessory Proteins Accessory proteins are encoded after the polymerase/replicase genes by mRNA6 (protein 6), mRNA7 (protein 7a), mRNA8 (protein 8), and bicistronic mRNA9b (protein 9b). These proteins are not essential for viral replication and assembly in vitro, but likely influence the pathogenesis of the SARS-CoV-2, like the accessory ORFs of other coronaviruses (Frieman et al, 2006; Narayanan et al, 2008).
R-HSA-9679504 Translation of Replicase and Assembly of the Replication Transcription Complex After entry and uncoating, the SARS-CoV-1 genomic RNA serves as a transcript to allow cap dependent translation of ORF1a to produce polyprotein pp1a. A slippery sequence and an RNA pseudoknot near the end of ORF1a enable 25 - 30% of the ribosomes to undergo -1 frameshifting, to continue translation of ORF1b to produce a longer polyprotein pp1ab. The autoproteolytic cleavage of pp1a and pp1ab generates 15-16 nonstructural proteins (nsps) with various functions. The RNA dependent RNA polymerase (RdRP) activity is encoded in nsp12, and papain like protease (PLPro) and main protease (Mpro) activities are encoded in nsp3 and nsp5, respectively. nsp3, 4, and 6 induce rearrangement of the cellular membrane to form double membrane vesicles (DMVs) where the coronavirus replication transcription complex (RTC) is assembled and anchored.
Programmed ribosomal frameshifting (PRF) may be regulated by viral or host factors in addition to viral RNA secondary structures. For example, PRF in the related arterivirus porcine reproductive and respiratory syndrome virus (PRRSV) is transactivated by the viral protein nsp1, which interacts with the PRF signal via a putative RNA binding motif. A host RNA-binding protein called annexin A2 (ANXA2) binds the pseudoknot structure in the IBV genome. Host factors in the early secretory pathway appear to be involved in DMV formation and RTC assembly: Golgi specific brefeldin A resistance guanine nucleotide exchange factor 1 (GBF1) and its effector ADP ribosylation factor 1 (ARF1) are both required for normal DMV formation and efficient RNA replication of mouse hepatitis virus (MHV), a prototypic betacoronavirus that infects mice (Fung & Liu 2019).
R-HSA-9694676 Translation of Replicase and Assembly of the Replication Transcription Complex This COVID-19 pathway has been created by a combination of computational inference from SARS-CoV-1 data (https://reactome.org/documentation/inferred-events) and manual curation, as described in the summation for the overall SARS-CoV-2 infection pathway.
After entry and uncoating, the genomic RNA serves as a transcript to allow cap dependent translation of ORF1a to produce polyprotein pp1a. A slippery sequence and an RNA pseudoknot near the end of ORF1a enable 25 - 30% of ribosomes to undergo -1 frameshifting, to continue translation of ORF1b to produce a longer polyprotein pp1ab. Autoproteolytic cleavage of pp1a and pp1ab generates 15-16 nonstructural proteins (nsps) with various functions. RNA dependent RNA polymerase (RdRP) activity is encoded in nsp12, and papain like protease (PLPro) and main protease (Mpro) activities are encoded in nsp3 and nsp5, respectively. nsp3, 4, and 6 induce rearrangement of the cellular membrane to form double membrane vesicles (DMVs) where the coronavirus replication transcription complex (RTC) is assembled and anchored.
Programmed ribosomal frameshifting (PRF) may be regulated by viral or host factors in addition to viral RNA secondary structures. For example, PRF in the related arterivirus porcine reproductive and respiratory syndrome virus (PRRSV) is transactivated by the viral protein nsp1, which interacts with the PRF signal via a putative RNA binding motif. A host RNA-binding protein called annexin A2 (ANXA2) binds the pseudoknot structure in the IBV genome. Host factors in the early secretory pathway appear to be involved in DMV formation and RTC assembly: Golgi specific brefeldin A resistance guanine nucleotide exchange factor 1 (GBF1) and its effector ADP ribosylation factor 1 (ARF1) are both required for normal DMV formation and efficient RNA replication of mouse hepatitis virus (MHV), a prototypic betacoronavirus that infects mice (Fung & Liu 2019).
R-HSA-9683701 Translation of Structural Proteins SARS-CoV-1 mRNA is translated according to the ribosomal scanning model. Virus mRNA is capped and polyadenylated, with regions of nontranslated sequences on both the 5' and 3' ends. Structural proteins are encoded after the polymerase/replicase genes by mRNAs 2 (Spike protein), 3, 4 (Envelope protein), 5 (Membrane protein), and 9. mRNA 3 and 9 are bicistronic, the proteins 3a and 9a (Nucleocapsid protein) having functions in virus assembly and structure. Translation happens in the ER with the exception of 9a which is translated by cytosolic free ribosomes (Fung and Liu, 2019).
R-HSA-9694635 Translation of Structural Proteins This COVID-19 pathway has been created by a combination of computational inference from SARS-CoV-1 data (https://reactome.org/documentation/inferred-events) and manual curation, as described in the summation for the overall SARS-CoV-2 infection pathway.
Virus mRNA is translated according to the ribosomal scanning model. It is capped and polyadenylated, with regions of nontranslated sequences on both the 5' and 3' ends. Structural proteins are encoded after the polymerase/replicase genes by mRNAs 2 (Spike protein), 3, 4 (Envelope protein), 5 (Membrane protein), and 9. mRNA 3 and 9 are bicistronic, the proteins 3a and 9a (Nucleocapsid protein) having functions in virus assembly and structure. Translation happens in the ER with the exception of 9a which is translated by cytosolic free ribosomes (Fung and Liu, 2019).
R-HSA-9828721 Translation of respiratory syncytial virus mRNAs The 10 subgenomic mRNAs of human respiratory syncytial virus A (hRSV A) are translated into 11 proteins. Except for the M2 mRNA, each mRNA encodes one distinct protein. The two overlapping open reading frames (ORFs) of the M2 mRNA encode proteins M2-1 and M2-2. The M2-1 product of the M2 gene is a transcription processivity factor, while the M2-2 product of the M2 gene is a nonstructural protein that regulates the switch between transcription and genome replication. The N mRNA encodes the nucleoprotein, which forms decameric and hendecameric rings around which viral genomic RNA is packaged. The L and P mRNAs encode the large polymerase subunit and the phosphoprotein polymerase cofactor subunit, respectively, of the RNA-dependent RNA polymerase complex (RdRP). The SH, G, and F mRNAs encode three proteins that are embedded in the viral envelope: small hydrophobic protein, attachment protein, and fusion protein, respectively. The secreted isoform of G protein (sG), involved in mediation of immune evasion, and the truncated form of SH (SHt), are translated from G mRNA and SH mRNA, respectively, through the usage of an alternative start codon. The NS1 and NS2 genes encode nonstructural proteins that function together to inhibit apoptosis and interferon response in infected cells. For review, please refer to Battles and McLellan 2019.
R-HSA-110320 Translesion Synthesis by POLH DNA polymerase eta (POLH) consists of 713 amino acids and can bypass thymidine-thymidine dimers, correctly adding two dAMPs opposite to the lesion. Mutations in the POLH gene result in the loss of this bypass activity and account for the XP variant phenotype (XPV) in human xeroderma pigmentosum disorder patients. POLH can carry out TLS past various UV and chemically induced lesions via two steps: (a) preferential incorporation of correct bases opposite to the lesion (b) conditional elongation only at the sites where such correct bases are inserted (Masutani et al. 1999, Masutani et al. 2000).
R-HSA-5656121 Translesion synthesis by POLI DNA polymerase iota (POLI) is a Y family DNA polymerase with an active site that favours Hoogsteen base pairing instead of Watson-Crick base pairing. POLI-mediated Hoogsteen base pairing and rotation of template purines from anti to syn conformation serves as a mechanism to displace adducts on template G or template A that interfere with DNA replication, or to allow base pairing of damaged purines with a disrupted Watson-Crick edge but an intact Hoogsteen edge (Nair et al. 2004, Nair et al. 2006).
POLI is recruited to DNA damage sites through its interaction with PCNA and REV1. POLI contains a PIP box and two UBMs (ubiquitin binding motifs) that are responsible for POLI binding to monoubiquitinated PCNA (MonoUb:K164-PCNA) (Bienko et al. 2005, Haracska et al. 2005, Bomar et al. 2010). The interaction between POLI and the C-terminus of REV1 is evolutionarily conserved (Kosarek et al. 2003, Guo et al. 2003, Ohashi et al. 2004).
After it incorporates a dNMP opposite to damaged template base, POLI is unable to efficiently elongate the DNA strand further. The elongation step is performed by the polymerase zeta complex (POLZ), composed of REV3L and MAD2L2 subunits (Johnson et al. 2000). The involvement of REV1 and POLZ in POLI-mediated translesion DNA synthesis (TLS) suggests that POLI forms a quaternary complex with REV1 and POLZ, as shown for POLK and proposed for other Y family DNA polymerases (Xie et al. 2012).
R-HSA-5655862 Translesion synthesis by POLK DNA polymerase kappa (POLK) is a Y family DNA polymerase that is most efficient in translesion DNA synthesis (TLS) across oxidation derivatives of DNA bases, such as thymine glycol (Tg) and 8-oxoguanine (OGUA), as well as bulky DNA adducts, such as benzo(a)pyrene diol epoxide guanine adduct (BPDE-G) (Zhang et al. 2000, Fischhaber et al.2002, Avkin et al. 2004, Vasquez-Del Carpio et al. 2009, Yoon et al. 2010, Lior-Hoffmann et al. 2012, Christov et al. 2012, Yoon et al. 2014). POLK carries out TLS by forming a quaternary complex with REV1 and POLZ (REV3L:MAD2L2) at DNA damage sites, where POLK simultaneously binds REV1 and monoubiquitinated PCNA (Ohashi et al. 2009, Haracska, Unk et al. 2002, Bi et al. 2006). POLK and POLZ cooperate in the elongation of nucleotides inserted opposite to lesioned bases by POLK. Similarly to POLZ, POLK has low processivity and is error-prone (Ohashi et al. 2000, Haracska, Prakash et al. 2002, Yoon et al. 2010).
R-HSA-110312 Translesion synthesis by REV1 REV1 (hREV1) encodes a template-dependent dCMP transferase that can insert a C residue opposite an abasic site (Lin et al. 1999, Gibbs et al. 2000). Interaction with monoubiquitinated PCNA at a DNA damage site enhances REV1-mediated translesion synthesis (TLS) (Garg and Burgers 2005, Wood et al. 2007). After REV1 incorporates dCMP opposite to the apurinic/apyrimidinic (AP) template site, TLS is continued by the DNA polymerase zeta complex (POLZ). POLZ consists of the catalytic subunit REV3L and the accessory subunit MAD2L2 (REV7). MAD2L2 binds REV1, thus recruiting POLZ to DNA damage site (Hara et al. 2010, Kikuchi et al. 2010, Xie et al. 1012). POLZ is error-prone and contributes to TLS-related mutagenesis (Shachar et al. 2009, Lee et al. 2014). POLZ has a low processivity and dissociates from the DNA template after incorporating less than 30 nucleotides (Nelson et al. 1996, Lee et al. 2014).
R-HSA-110313 Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template Ubiquitous environmental and endogenous genotoxic agents cause DNA lesions that can interfere with normal DNA metabolism including DNA replication, eventually resulting in mutations that lead to carcinogenesis and/or cell death. Cells possess repair mechanisms like nucleotide excision and base excision repair pathways to maintain the integrity of the genome. However, some types of lesions are repaired very inefficiently and others may not be recognized and repaired before the lesion-containing DNA undergoes DNA replication. To prevent acute cell death through arrested DNA replication at unrepaired lesions, cells have a mechanism, referred to as translesion synthesis (TLS), which allows DNA synthesis to proceed past lesions. TLS depends on the Y family of DNA polymerases (Lindahl and Wood 1999, Masutani et al. 2000, Yang 2014).
R-HSA-1445148 Translocation of SLC2A4 (GLUT4) to the plasma membrane In adipocytes and myocytes insulin signaling causes intracellular vesicles carrying the GLUT4 (SLC2A4) glucose transporter to translocate to the plasma membrane, allowing the cells to take up glucose from the bloodstream (reviewed in Zaid et al. 2008, Leney and Tavare 2009, Bogan and Kandror 2010, Foley et al. 2011, Hoffman and Elmendorf 2011, Kandror and Pilch 2011, Jaldin-Fincati et al. 2017). In myocytes muscle contraction alone can also cause translocation of GLUT4.
Though the entire pathway leading to GLUT4 translocation has not been elucidated, several steps are known. Insulin activates the kinases AKT1 and AKT2. Muscle contraction activates the kinase AMPK-alpha2 and possibly also AKT. AKT2 and, to a lesser extent, AKT1 phosphorylate the RAB GTPase activators TBC1D1 and TBC1D4, causing them to bind 14-3-3 proteins and lose GTPase activation activity. As a result RAB proteins (probably RAB8A, RAB10, RAB14 and possibly RAB13) accumulate GTP. The connection between RAB:GTP and vesicle translocation is unknown but may involve recruitment and activation of myosins.
Myosins 1C, 2A, 2B, 5A, 5B have all been shown to play a role in translocating GLUT4 vesicles near the periphery of the cell. Following docking at the plasma membrane the vesicles fuse with the plasma membrane in a process that depends on interaction between VAMP2 on the vesicle and SNAP23 and SYNTAXIN-4 at the plasma membrane.
R-HSA-202430 Translocation of ZAP-70 to Immunological synapse The dual phosphorylated ITAMs recruit SYK kinase ZAP70 via their tandem SH2 domains (step 8). ZAP70 subsequently undergoes phosphorylation on multiple tyrosine residues for further activation. ZAP70 includes both positive and negative regulatory sites. Tyrosine 493 is a conserved regulatory site found within the activation loop of the kinase domain. This site has shown to be a positive regulatory site required for ZAP70 kinase activity and is phosphorylated by LCK (step 9). This phosphorylation contributes to the active conformation of the catalytic domain. Later ZAP70 undergoes trans-autophosphorylation at Y315 and Y319 (step 10). These sites appear to be positive regulatory sites. ZAP70 achieves its full activation after the trans-autophosphorylation. Activated ZAP70 along with LCK phosphorylates the multiple tyrosine residues in the adaptor protein LAT (step 11). PTPN22 can dephosphorylate and inhibit ZAP70 activity to downregulate TCR signaling (step 12).
R-HSA-112315 Transmission across Chemical Synapses Chemical synapses are specialized junctions that are used for communication between neurons, neurons and muscle or gland cells. The synapse involves a presynaptic neuron and a postsynaptic neuron, muscle cell or glad cell. The pre and the postsynaptic cell are separated by a gap (space) of 20 to 40 nm called the synaptic cleft. The signals pass in a single direction from the presynaptic to postsynaptic neuron (cell). The presynaptic neuron communicates via the release of neurotransmitter which bind the receptors on the postsynaptic cell. The process is initiated when an action potential invades the terminal membrane of the presynaptic neuron.
Action potentials occur in electrically excitable cells such as neurons and muscles and endocrine cells. They are initiated by the transient opening of voltage dependent sodium channels, causing a rapid, large depolarization of membrane potentials that spread along the axon membrane.
When action potentials arrive at the synaptic terminals, depolarization in membrane potential leads to the opening of voltage gated calcium channels located on the presynaptic membrane. The external Ca2+ concentration is approximately 10-3 M while the internal Ca2+ concentration is approximately 10-7 M. Opening of calcium channels causes a rapid influx of Ca2+ into the presynaptic terminal. The elevated presynaptic Ca2+ concentration allows synaptic vesicles to fuse with the plasma membrane of the presynaptic neuron and release their contents, neurotransmitters, into the synaptic cleft. These diffuse across the synaptic cleft and bind to specific receptors on the membrane of the postsynaptic cells. Activation of postsynaptic receptors upon neurotransmitter binding can lead to a multitude of effects in the postsynaptic cell, such as changing the membrane potential and excitability, and triggering intracellular signaling cascades.
R-HSA-112307 Transmission across Electrical Synapses Electrical transmission across nerve cells is accomplished when the current generated in the upstream neuron spreads to the downstream neuron through a path of low electrical resistance. In neurons this is accomplished at gap junctions. Electrical synapses are found in neuronal tissue where the activity of neurons must be highly synchronized. The neurons responsible for hormone secretion from the mammalian hypothalamus are a class of highly synchronized electric neurons. Gap junctions connecting the presynaptic cell with the postsynaptic cell allow current generated in the presynaptic cell to flow directly into the postsynaptic cell. Transmission speed is dramatically increased in such a system. The junction itself is composed of two hemichannels, one each on the pre- and postsysnaptic cells. These channels are composed of members of the connexin family of proteins.
R-HSA-174362 Transport and synthesis of PAPS PAPS (3'-phosphoadenosine-5'-phosphosulfate), which functions as a sulfate donor in the cell, is synthesized from sulfate and two molecules of ATP in a two-step process (Robbins & Lipmann 1958) catalyzed in vertebrates by a bifunctional enzyme (Venkatachalam et al. 1998). PAPS synthesis takes place in the cytosol, and it is either consumed there in the sulfonation of a variety of hormones and xenobiotics, or it is transported to the Golgi apparatus and consumed in the synthesis of proteoglycans like chondroitin sulfate. Two isoforms of the human bifunctional enzyme are known, mutations in one of which are associated with defects in proteoglycan biosynthesis (Girard et al. 1998, ul Haque et al. 1998).
R-HSA-168874 Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus Processed viral proteins are transported from the endoplasmic reticulum to the Golgi apparatus.
R-HSA-72202 Transport of Mature Transcript to Cytoplasm Transport of mRNA through the Nuclear Pore Complex (NPC) is a dynamic process involving distinct machinery and receptor subsets. The separation of the two compartments and the regulation of this transport provide spatial and temporal control over mRNA expression and ultimately control over translation. It should be noted that mRNA export does not rely on a specific motif in the mRNA molecule, but rather transport appears to be coupled to processing and regulation. The specific proteins that are bound to the mRNA determine when it will be transported to the cytoplasm. This limitation insures that transport overwhelmingly favors transport of fully processed mRNA molecules.
R-HSA-159231 Transport of Mature mRNA Derived from an Intronless Transcript Transport of mRNA from the nucleus to the cytoplasm, where it is translated into protein, is highly selective and closely coupled to correct RNA processing.
R-HSA-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript Transport of mRNA from the nucleus to the cytoplasm, where it is translated into protein, is highly selective and closely coupled to correct RNA processing. This coupling is achieved by the nuclear pore complex, which recognizes and transports only completed mRNAs.
R-HSA-159234 Transport of Mature mRNAs Derived from Intronless Transcripts Transport of mature mRNAs derived from intronless transcripts require some of the same protein complexes as mRNAs derived from intron containing complexes, including TAP and Aly/Ref. However a number of the splicing related factors are lacking from the intronless derived mRNAs, as they required no splicing.
R-HSA-9758890 Transport of RCbl within the body The steps of transport of cobalamins (RCbl) from the enterocyte to the cells in which it will function as a cofactor, together with its reuptake in the renal tubule, are annotated here. While methylcobalamin is the predominant cobalamin in the blood (Chu et al. 1993), other cobalamins including cyanocobalamin and adenosylcobalamin are also present and the proteins involved in these processes accommodate all of them (Banerjee et al. 2021; Nielsen et al. 2012; Quadros 2010). This broad specificity is indicated by annotating R-cob(III)alamin (RCbl - CHEBI:140785) as the cargo in all of these processes.
R-HSA-168271 Transport of Ribonucleoproteins into the Host Nucleus An unusual characteristic of the influenza virus life cycle is its dependence on the nucleus. Trafficking of the viral genome into and out of the nucleus is a tightly regulated process with all viral RNA synthesis occurring in the nucleus. The eight influenza virus genome segments never exist as naked RNA but are associated with four viral proteins to form viral ribonucleoprotein complexes (vRNPs). The major viral protein in the RNP complex is the nucleocapsid protein (NP), which coats the RNA. The remaining proteins PB1, PB2 and PA bind to the partially complementary ends of the viral RNA, creating the distinctive panhandle structure. These RNPs (10-20nm wide) are too large to passively diffuse into the nucleus and therefore, once released from an incoming particle must rely on the active import mechanism of the host cell nuclear pore complex. All proteins in the RNP complex can independently localize to the nucleus due to the presence of nuclear localization signals (NLSs) which mediate their interaction with the nuclear import machinery, including the RanGTPase (Fodor, 2004; Deng et al., 2006). However the signals on NP have been shown to be both sufficient and necessary for the import of viral RNA.
R-HSA-425366 Transport of bile salts and organic acids, metal ions and amine compounds SLC transporters described in this section transport bile salts, organic acids, metal ions and amine compounds.
Myo-Inositol is a neutral cyclic polyol, abundant in mammalian tissues. It is a precursor to phosphatidylinositols (PtdIns) and to the inositol phosphates (IP), which serve as second messengers and also act as key regulators of many cell functions. Three members of the glucose transporter gene family encode inositol transporters (SLC2A13, SLC5A3 and SLC5A11) (Schneider 2015).
Five human SLC13 genes encode sodium-coupled sulphate, di- and tri-carboxylate transporters typically located on the plasma membrane of mammalian cells (Pajor 2006).
The SLC16A gene family encode proton-linked monocarboxylate transporters (MCT) which mediate the transport of monocarboxylates such as lactate and pyruvate, major energy sources for all cells in the body so their transport in and out of cells is crucial for cellular function (Morris & Felmlee 2008).
The transport of essential metals and other nutrients across tight membrane barriers such as the gastrointestinal tract and blood-brain barrier is mediated by metal-transporting proteins (encoded by SLC11, SLC30, SLC31, SLC39, SLC40 and SLC41). They can also regulate metals by efflux out of cells and cellular compartments to avoid toxic build-up (Bressler et al. 2007).
The SLC6 gene family encodes proteins that mediate neurotransmitter uptake in the central nervous system (CSN) and peripheral nervous system (PNS), thus terminating a synaptic signal. The proteins mediate transport of GABA (gamma-aminobutyric acid), norepinephrine, dopamine, serotonin, glycine, taurine, L-proline, creatine and betaine (Chen et al. 2004).
Carrier-mediated urea transport allows rapid urea movement across the cell membrane, which is particularly important in the process of urinary concentration and for rapid urea equilibrium in non-renal tissues. Two carriers exist in humans, encoded by SLC14A1 and ALC14A2 (Olives et al. 1994).
Choline uptake is the rate-limiting step in the synthesis of the neurotransmitter acetylcholine. SLC genes SLC5A7 and the SLC44 family encode choline transporters ((Okuda & Haga 2000, Traiffort et al. 2005).
The SLC22 gene family of solute carriers function as organic cation transporters (OCTs), cation/zwitterion transporters (OCTNs) and organic anion transporters (OATs). Most of this family are polyspecific transporters. Since many of these transporters are expressed in the liver, kidney and intestine, they play an important role in drug absorption and excretion. Substrates include xenobiotics, drugs, and endogenous amine compounds (Koepsell & Endou 2004).
R-HSA-190827 Transport of connexins along the secretory pathway Connexins follow the classical secretory transport route from the ER to the plasma membrane: ER -> ERGIC -> Golgi -> TGN (Trans Golgi Network) -> PM (Plasma Membrane). All connexins assemble or oligomerize into hexameric connexons. The site of assembly varies and depends on Cx isoform, or cell type (see Koval et al., 2006).
Oligomerization of connexins has been observed during ER membrane insertion (Cx32), just after exit from the ER, in the ER-Golgi-intermediate compartment (Cx26) and inside the Trans-Golgi Network (Cx43) (Falk et al. 1997; Ahmad et al. 1999; Musil and Goodenough 1993; Diez et al. 1999).
R-HSA-190872 Transport of connexons to the plasma membrane Following connexon oligomerization, the hemichannels must be transported to the plasma membrane. This has been shown to occur in transport vesicles called "cargo containers". Most of post-Golgi cargo containers have a diameter of of 50- 200 nm (Lauf et al., 2002). Recently direct transport of connexins to GJ assembly sides has been described (Shaw et al., 2007). Besides microtuble-dependent trafficking, a microtubule-independent delivery pathway may exist as concluded from studies using the secretory transport inhibitor, Brefeldin A (Musil and Goodenough 1993; De Sousa et al. 1993; Laird et al. 1995).
R-HSA-804914 Transport of fatty acids Long chain fatty acids (LCFAs) are involved in many cellular functions. They can be used as an important source of energy by skeletal muscle and heart tissues. Also, they are used in the production of hormones which can regulate inflammation, blood pressure, the clotting process, blood lipid levels and the immune response. Fatty acid transporter proteins (FATPs) are a family of proteins which mediate fatty acid uptake into cells when overexpressed. FATPs also possess enzymatic activity, the details of which are captured elsewhere. There are 6 human genes of the SLC27A family which encode for FATP1-6 (Stahl A, 2004; Gimeno RE, 2007). To date, only FATP1, 4 and 6 have demonstrable transporter function. Fatty acids with carbon chain lengths of more than 10 are the most likely substrates for these transporters.
R-HSA-159763 Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus Gamma-carboxylated proteins are moved by anterograde transport from the endoplasmic reticulum to the Golgi apparatus (Kirchhausen 2000).
R-HSA-432030 Transport of glycerol from adipocytes to the liver by Aquaporins Triglycerides stored in adipocytes are hydrolyzed to yield fatty acids and glycerol. The glycerol is passively transported out of the adipocyte and into the bloodstream by Aquaporin-7 (AQP7) located in the plasma membrane of adipocytes. Glycerol in the bloodstream is passively transported into liver cells by AQP9 located in the plasma membrane of hepatocytes. Once inside the liver cell the glycerol is a substrate for gluconeogenesis.
R-HSA-425393 Transport of inorganic cations/anions and amino acids/oligopeptides Teleologically, one might argue that inorganic cation and anion transport would be evolutionarily among the oldest transport functions. Eight families comprise the group that transports exclusively inorganic cations and anions across membranes : SLC4 plays a pivotal role in mediating Na+ - and/or Cl- -dependent transport of basic anions [e.g. HCO3-, (CO3)2-] in various tissues and cell types (in addition to pH regulation, specific members of this family also contribute to vectorial trans-epithelial base transport in several organ systems including the kidney, pancreas, and eye) (Pushkin A and Kurtz I, 2006); SLC8 is a group of Na+/Ca2+ exchangers (SLC8A1 is involved in cardiac contractility) (Quednau BD et al, 2004); SLC24 is a group of Na+/Ca2+ or Na+/K+ exchangers (Altimimi HF and Schnetkamp PP, 2007); SLC9 comprises Na+/H+ exchanger proteins involved in the electroneutral exchange of sodium ion and protons (Orlowski J and Grinstein S, 2004); SLC12 functions as Na+, K+ and Cl- ion electroneutral symporters (Hebert SC et al, 2004); SLC26 is the trans-epithelial multifunctional anion (e.g. sulfate, oxalate, HCO-, Cl-) exchanger family, important in cartilage development, production of thyroid hormone, sound amplification in the cochlea etc (Sindic A et al, 2007; Dorwart MR et al, 2008; Ashmore J, 2008). SLC34 is an important Type II Na+/(HPO4)2- symporter (Forster IC et al, 2006; Virkki LV et al, 2007); SLC20 was originally identified as a viral receptor, and functions as a Type III Na+/(H2PO4)- symporter (Collins JF et al, 2004; Virkki LV et al, 2007). Eight SLC gene families are involved in the transport of amino acids and oligopeptides.
R-HSA-83936 Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane Two families of transport proteins mediate the movement of nucleosides and free purine and pyrimidine bases across the plasma membrane. Equilibrative nucleoside transporters allow the movement of these molecules along concentration gradients into or out of cells (Baldwin et al. 2003); concentrative nucleoside transporters actively transport nucleosides into cells by coupling their transport to the inward movement of sodium ions (Gray et al. 2003).
Of the four human equilibrative nucleoside transporters, two are well characterized. SLC29A1 (solute carrier family 29 (nucleoside transporters), member 1) mediates the transport of nucleosides across the plasma membrane. SLC29A2 (solute carrier family 29 (nucleoside transporters), member 2) mediates the transport of both nucleosides and free bases. Transporter specificities were determined by expressing cloned human genes in Xenopus oocytes or in mammalian cultured cell lines whose own nucleotide transporters had been disrupted by mutation. These studies establish that the transport processes are specific and saturable, and that the multiple nucleotides and bases compete for a single binding site on each transporter. Some features of SLC29A2 specificity are complex. For example, in the Xenopus oocyte system, radiolabeled uracil and adenine are taken up, and an excess of either molecule inhibits uptake of radiolabeled hypoxanthine, while in the cultured mammalian cell system, neither adenine nor uracil can inhibit uptake of radiolabeled uridine. If these results reflect ENT2 function in vivo, they indicate that the net movement of a nucleoside or base across the cell membrane is determined not only by its own concentrations in the extracellular space and the cytosol, but also by the concentrations of the other nucleosides and bases competing for access to the transporter.
The human genome encodes three concentrative transporters, SLC28A1, 2, and 3 (solute carrier family 28 (sodium-coupled nucleoside transporter), member 1, 2, and 3). All three genes have been cloned, and expression of the human proteins in Xenopus oocytes has allowed their transport properties to be determined. SLC28A1 mediates the uptake of pyrimidine nucleosides and adenosine (Ritzel et al. 1997); SLC28A2 the uptake of purine nucleosides and uridine (Wang et al. 1997); and SLC28A3 the uptake of purine and pyrimidine nucleosides (Ritzel et al. 2001). Amino acid sequence motifs that determine the specificities of these transporters have been identified in studies of chimeric and mutant proteins (Loewen et al. 1999). SLC28A3 protein co-transports two sodium ions per nucleoside; SLC28A1 and 2 transport one sodium per nucleoside (Ritzel et al. 2001).
Physiological roles for nucleoside and base transport include provision of nucleosides to cells with little capacity to synthesize these molecules de novo, and regulation of extracellular levels of adenosine, which is released from muscle during intense exercise and has signaling properties. In kidney and intestinal epithelia, the combination of apically localized CNT transporters and basolaterally localized ENT transporters provides a mechanism for net transport of nucleosides (Mangravite et al. 2003). These transporters also mediate the uptake of nucleoside analogs used clinically as anti-viral and anti-tumor drugs.
Orthologs of human concentrative and equilibrative transporter proteins have been identified in many eukaryotes, but functional studies of transporters even from organisms closely related to humans (e.g. rat, Gerstin et al. 2002) have revealed differences in substrate specificities. Prediction of drug uptake and other functions of these molecules by human - model organism orthology is thus risky.
R-HSA-727802 Transport of nucleotide sugars Nucleotide sugars are used as sugar donors by glycosyltransferases to create the sugar chains for glycoconjugates such as glycoproteins, polysaccharides and glycolipids. Glycosyltransferases reside mainly in the lumen of the Golgi apparatus and endoplasmic reticulum (ER) whereas nucleotide sugars are synthesized in the cytosol. The human solute carrier family SLC35 encode nucleotide sugar transporters (NSTs) which can mediate the antiport of nucleotide sugars in exchange for the corresponding nucleoside monophosphates (eg. UMP for UDP-sugars). Owing to their function, NSTs are primarily located on Golgi and ER membranes (He L et al, 2009; Handford M et al, 2006; Ishida N and Kawakita M, 2004).
R-HSA-879518 Transport of organic anions Organic anion transporting polypeptides (OATPs) are membrane transport proteins that mediate the sodium-independent transport of a wide range of amphipathic organic compounds including bile salts, steroid conjugates, thyroid hormones, anionic oligopeptides and numerous drugs (Hagenbuch B and Meier PJ, 2004).
R-HSA-382551 Transport of small molecules By definition cells have a critical separation between inner (cytoplasmic) and outer (extracellular) compartments. This separation provides for protection, gradient assembly, and environmental control but at the same time isolates the interior compartments of the cell from energy resources, oxygen, and raw materials. Cells have evolved a myriad of mechanisms to regulate, and enable transportation of small molecules ascross plasma membranes and between cellular organelle compartments within cells.
R-HSA-159230 Transport of the SLBP Dependant Mature mRNA Transport of U7 snRNP and stem-loop binding protein (SLBP) processed mRNA.
R-HSA-159227 Transport of the SLBP independent Mature mRNA Transport of the SLBP independent Mature mRNA through the nuclear pore.
R-HSA-425397 Transport of vitamins, nucleosides, and related molecules This section groups the processes mediated by SLC transporters, by which vitamins and cofactors, as well as nucleosides, nucleotides, nucleobases, and related molecules cross lipid bilayer membranes (He et al. 2009).
The human SLC5A6 encodes the Na+-dependent multivitamin transporter SMVT (Prasad et al. 1999). SMVT co-transports biotin (vitamin B7), D-Pantothoate (vitamin B5) and lipoic acid into cells with Na+ ions electrogenically.
Four SLC gene families encode transporters that mediate the movement of nucleosides and free purine and pyrimidine bases across the plasma membrane. These transporters play key roles in nucleoside and nucleobase uptake for salvage pathways of nucleotide synthesis, and in the cellular uptake of nucleoside analogues used in the treatment of cancers and viral diseases (He et al. 2009).
The human gene SLC33A1 encodes acetyl-CoA transporter AT1 (Kanamori et al. 1997). Acetyl-CoA is transported to the lumen of the Golgi apparatus, where it serves as the substrate of acetyltransferases that O-acetylates sialyl residues of gangliosides and glycoproteins.
Nucleotide sugars are used as sugar donors by glycosyltransferases to create the sugar chains for glycoconjugates such as glycoproteins, polysaccharides and glycolipids. Glycosyltransferases reside mainly in the lumen of the Golgi apparatus and endoplasmic reticulum (ER) whereas nucleotide sugars are synthesized in the cytosol. The human solute carrier family SLC35 encode nucleotide sugar transporters (NSTs), localised on Golgi and ER membranes, which can mediate the antiport of nucleotide sugars in exchange for the corresponding nucleoside monophosphates (eg. UMP for UDP-sugars) (Handford et al. 2006).
Long chain fatty acids (LCFAs) can be used for energy sources and steroid hormone synthesis and regulate many cellular processes such as inflammation, blood pressure, the clotting process, blood lipid levels and the immune response. The SLC27A family encode fatty acid transporter proteins (FATPs) (Stahl 2004).
The SLC gene family members SLCO1 SLCO2 and SLCO3 encode organic anion transporting polypeptides (OATPs). OATPs are membrane transport proteins that mediate the sodium-independent transport of a wide range of amphipathic organic compounds including bile salts, steroid conjugates, thyroid hormones, anionic oligopeptides and numerous drugs (Hagenbuch & Meier 2004).
R-HSA-948021 Transport to the Golgi and subsequent modification At least two mechanisms of transport of proteins from the ER to the Golgi have been described. One is a general flow requiring no export signals (Wieland et al, 1987; Martinez-Menarguez et al, 1999). The other is mediated by LMAN1/MCFD2, mannose-binding lectins that recognize a glycan signal (Zhang B et al, 2003).
R-HSA-75109 Triglyceride biosynthesis The overall process of triglyceride (triacylglycerol) biosynthesis consists of four biochemical pathways: fatty acyl-CoA biosynthesis, conversion of fatty acyl-CoA to phosphatidic acid, conversion of phosphatidic acid to diacylglycerol, and conversion of diacylglycerol to triacylglycerol.
R-HSA-163560 Triglyceride catabolism Triacylglycerol is a major energy store in the body and its hydrolysis to yield fatty acids and glycerol is a tightly regulated part of energy metabolism. A central part in this regulation is played by hormone-sensitive lipase (HSL), a neutral lipase abundant in adipocytes and skeletal and cardiac muscle, but also abundant in ovarian and adrenal tissue, where it mediates cholesterol ester hydrolysis, yielding cholesterol for steroid biosynthesis. The hormones to which it is sensitive include catecholamines (e.g., epinephrine), ACTH, and glucagon, all of which trigger signaling cascades that lead to its phosphorylation and activation, and insulin, which sets off events leading to its dephosphorylation and inactivation (Holm et al. 2000; Kraemer and Shen 2002).
The processes of triacylglycerol and cholesterol ester hydrolysis are also regulated by subcellular compartmentalization: these lipids are packaged in cytosolic particles and the enzymes responsible for their hydrolysis, and perhaps for additional steps in their metabolism, are organized at the surfaces of these particles (e.g., Brasaemle et al. 2004). This organization is dynamic: the inactive form of HSL is not associated with the particles, but is translocated there after being phosphorylated. Conversely, perilipin, a major constituent of the particle surface, appears to block access of enzymes to the lipids within the particle; its phosphorylation allows greater access.
Here, HSL-mediated triacylglycerol hydrolysis is described as a pathway containing twelve reactions. The first six of these involve activation: phosphorylation of HSL, dimerization of HSL, disruption of CGI-58:perilipin complexes at the surfaces of cytosolic lipid particles, phosphorylation of perilipin, association of phosphorylated HSL with FABP, and translocation of HSL from the cytosol to the surfaces of lipid particles. The next four reactions are the hydrolysis reactions themselves: the hydrolysis of cholesterol esters, and the successive removal of three fatty acids from triacylglycerol. The last two reactions, dephosphorylation of perilipin and HSL, negatively regulate the pathway. These events are outlined in the figure below. Inputs (substrates) and outputs (products) of individual reactions are connected by black arrows; blue lines connect output activated enzymes to the other reactions that they catalyze.
Despite the undoubted importance of these reactions in normal human energy metabolism and in the pathology of diseases such as type II diabetes, they have been studied only to a limited extent in human cells and tissues. Most experimental data are derived instead from two rodent model systems: primary adipocytes from rats, and mouse 3T3-L1 cells induced to differentiate into adipocytes.
R-HSA-8979227 Triglyceride metabolism Fatty acids derived from the diet and synthesized de novo in the liver are assembled into triglycerides (triacylglycerols) for transport and storage. Synthesis proceeds in steps of conversion of fatty acyl-CoA to phosphatidic acid, conversion of phosphatidic acid to diacylglycerol, and conversion of diacylglycerol to triacylglycerol (Takeuchi & Reue 2009).
Hydrolysis of triacylglycerol to yield fatty acids and glycerol is a tightly regulated part of energy metabolism. A central part in this regulation is played by hormone-sensitive lipase (HSL), a neutral lipase abundant in adipocytes and skeletal and cardiac muscle, but also abundant in ovarian and adrenal tissue, where it mediates cholesterol ester hydrolysis, yielding cholesterol for steroid biosynthesis. The hormones to which it is sensitive include catecholamines (e.g., epinephrine), ACTH, and glucagon, all of which trigger signaling cascades that lead to its phosphorylation and activation, and insulin, which sets off events leading to its dephosphorylation and inactivation (Kraemer & Shen 2002).
The processes of triacylglycerol and cholesterol ester hydrolysis are also regulated by subcellular compartmentalization: these lipids are packaged in cytosolic particles and the enzymes responsible for their hydrolysis, and perhaps for additional steps in their metabolism, are organized at the surfaces of these particles (e.g., Brasaemle et al. 2004).
R-HSA-450513 Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA Tristetraproline (TTP) binds RNAs that contain AU-rich elements and recruits enzymes that degrade RNA. TTP interacts with the exosome (3' to 5' exonuclease), XRN1 (5' to 3' exonuclease), and the decapping enzymes DCP1 and DCP2a.
The activity of TTP is regulated by phosphorylation. MK2 phosphorylates TTP, which then binds 14-3-3.The interaction with 14-3-3 prevents phosphorylated TTP from entering stress granules and stabilizes mRNA bound by phosphorylated TTP. Tristetraproline is known to bind AU-rich elements in the following mRNAs: Tumor necrosis factor alpha (TNFA), Granulocyte-macrophage colony stimulating factor (CSF2, GM-CSF), Interleukin-2 (IL-2), and Proto-oncogene C-FOS (FOS, c-fos). Mice deficient in TTP exhibit arthritis, weight loss, skin lesions, autoimmunity, and myeloid hyperplasia.
R-HSA-5467348 Truncations of AMER1 destabilize the destruction complex AMER1/WTX is a known component of the destruction complex and interacts directly with beta-catenin through the C-terminal half (Major et al, 2007). siRNA depletion of AMER1 in mammalian cells stabilizes cellular beta-catenin levels and increases the expression of a beta-catenin-dependent reporter gene, suggesting that AMER1 is a tumor suppressor gene (Major et al, 2007; reviewed in Huff, 2011). Consistent with this, nonsense and missense mutations that truncate AMER1 and result in loss of the beta-catenin binding region have been identified in Wilms tumor, a pediatric kidney cancer (Ruteshouser et al, 2008; Wegert et al, 2009).
R-HSA-71240 Tryptophan catabolism Tryptophan is catabolized in seven steps to yield aminomuconate. Intermediates in this process are also used in the synthesis of serotonin and kynurenine (Peters 1991).
R-HSA-9860927 Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells Both turbulent (disturbed) flow and low laminar flow across epithelial cells initiate an inflammatory response that causes atherosclerosis (reviewed in Rahaman et al. 2023, Tamargo et al. 2023, Wang et al. 2023). In vivo, this process makes curved and branched regions of arteries especially prone to atherosclerosis.
In endothelial cells, fluid flow is sensed by mechanoresponsive membrane-localized PIEZO1 channels, which open and cause an influx of cations including calcium ions (Ca2+) (inferred from the mouse homolog in Conte et al. 2010). Intracellular Ca2+ activates the protease complex Calpain2, which cleaves Vinculin (VCL), a component of the peripheral cytoskeleton located between integrins and actin fibers (Miyazaki et al. 2007, 2010). Turbulent flow across endothelial cells also causes release of ATP by an uncharacterized mechanism (Albarrán-Juárez et al. 2018).
Through an uncharacterized PIEZO1-dependent mechanism, the phosphatase PTPN1 (PTP1B) is activated to dephosphorylate Annexin-2 (ANXA2), which relocalizes with integrins (ITGA5:ITGB1) to lipid rafts in the cell membrane (Zhang et al. 2020). The integrins recruit the phosphodiesterase PDE4D5 and the phosphatase PP2A, which activates PDE4D5 by dephosphorylating serine-715 and activates YAP1 by dephosphorylating serine-127 (inferred from mouse homologs in Yun et al. 2016). Activated PDE4D5 hydrolyzes cAMP and thereby increases inflammation. YAP1 is phosphorylated by ABL1 on tyrosine-407 and transits to the nucleus to activate pro-inflammatory genes (Li et al. 2019).
The kinase PTK2 (focal adhesion kinase, FAK) is phosphorylated, likely through autophosphorylation, and then activates pro-inflammatory NF-κB signaling through phosphorylation of CHUK (IKKA) (Dwyer et al. 2015) and RELA (Albarrán-Juárez et al. 2018). IKBKE is phosphorylated by an uncharacterized mechanism and phosphorylates STAT1, which dimerizes and transits to the nucleus to activate pro-inflammatory genes such as NLRP3 (Lv et al. 2024).
R-HSA-446107 Type I hemidesmosome assembly Hemidesmosomes (HDs) are specialized multiprotein junctional complexes that connect the keratin cytoskeleton of epithelial cells to the extracellular matrix and play a critical role in the maintenance of tissue structure and integrity (reviewed in Litjens et al., 2006). HDs mediate adhesion of epithelial cells to the underlying basement membrane in stratified squamous, transitional and pseudostratified epithelia (Jones et al., 1994 ; Borradori and Sonnenberg, 1996). Classical Type I HDs are found in stratified and pseudo-stratified epithelia, such as the skin, and contain a6b4, plectin, tetraspanin CD151 and the bullous pemphigoid (BP) antigens BP180 and BP230 (reviewed in Litjens et al., 2006). While HDs function in promoting stable adhesion, they are highly dynamic structures that are able to disassemble quickly, for example, during cell division, differentiation, or migration (see Margadant et al, 2008).
R-HSA-427589 Type II Na+/Pi cotransporters The SLC34 family of type II Na+/Pi cotransporters consist of three members; NaPi-IIa (SLC34A1), NaPi-IIb (SLC34A2) and NaPi-IIc (SLC34A3) (Murer H et al, 2004). They are expressed mainly in the kidney and small intestine, located at the apical sites of epithelial cells although other areas of the body express them to a lesser extent. NaPi-IIa and b cotransports divalent Pi (HPO4[2-]) with three Na+ ions (electrogenic transport) whereas NaPi-IIc cotransports divalent Pi with two Na+ ions (electroneutral transport).
R-HSA-8963684 Tyrosine catabolism Cytosolic tyrosine is transaminated to form 3-(4-hydroxyphenyl)pyruvate which in four further reactions is converted to fumarate and acetoacetate. Tyrosine is thus both a glucogenic (fumarate) and a ketogenic (acetoacetate) amino acid. Defects in any of the steps lead to metabolic diseases with accumulation of tyrosine (tyrosinemia) (Mitchell et al. 2001; Held, 2006).
R-HSA-5689603 UCH proteinases DUBs of the Ub C-terminal Hydrolase (UCH) family are thiol proteases that have an N-terminal catalytic domain sometimes followed by C-terminal extensions that mediate protein-protein interactions. Humans have four UCH DUBs (UCH-L1, UCH-L3, UCH37/UCH-L5, and BAP1) that can be divided into the smaller UCH DUBs (UCH-L1 and UCH-L3), which cleave small leaving groups from the C-terminus of ubiquitin (Larsen et al. 1998), and the larger UCH DUBs (UCH37 and BAP1), which can disassemble poly-Ub chains (Misaghi et al. 2009, Lam et al. 1997).
R-HSA-5602415 UNC93B1 deficiency - HSE UNC93B1 is an endoplasmic reticulum protein with 12 membrane-spanning domains. Signaling cascades of nucleotide-sensing endosomal toll like receptors (TLR3 and TLR7-9) depends on functional UNC93B1, which is thought to deliver these TLRs from the ER to the endosome where they recognize specific pathogenic patterns and initiate host immune responses.
UNC93B deficiency has been implicated in the increased susceptibility to herpes simplex virus type 1 (HSV1) encephalitis (HSE), a rare complication during HSV-1 infection of the central nervous system (CNS) (Casrouge A et al. 2006). Patients-derived UNC96B1-deficient fibroblasts showed an impaired production of IFN-beta and -gamma following stimulation with TLR3 agonist poly(I:C) (Casrouge A et al. 2006). These cells were also more susceptible to HSV1 infection, showing rapid viral replication together with high mortality rates. Furthermore, pluripotent stem cells (iPSC) derived from HSE patient dermal fibroblasts were differentiated into populations of neural stem cells (NSC), neurons, astrocytes and oligodendrocytes (Lafaille FG et al. 2012). The impaired induction of IFN beta and gamma was observed in all tested CNS cells upon stimulation with poly(I:C). However, HSV1 infection selectively affected type I and III IFN production in UNC93B1-deficient neurons and oligodendrocytes (Lafaille FG et al. 2012). Thus, impaired TLR3-mediated UNC93B-dependent type I and III IFN production in respose to HSV1 infection in CNS, in neurons and oligodendrocytes in particular, may underline the pathogenesis of HSE in patients with UNC93B1 deficiency (Casrouge A et al. 2006; Lafaille FG et al. 2012).
Defective UNC93B1 also impairs the TLR7, TLR8 and TLR9 signaling pathways. Peripheral blood mononuclear cells (PBMCs) from UNC93B-deficient patients did not respond to the stimulation of TLR7, TLR8, or TLR9, in terms of the production of type I and III interferons, and other cytokines tested (Casrouge A et al. 2006). Moreover, no inducible CD62L shedding on granulocytes was detected after stimulation of whole blood cells derived from UNC93B-deficients patients with R-848 (agonist of TLR7 and TLR8) (von Bernuth H. et al. 2008). However, no clinical condition has been so far associated with impaired TLR7, TLR8, TLR9 due to UNC93B1 deficiency so this defect is not annotated here.
R-HSA-5689880 Ub-specific processing proteases Ub-specific processing proteases (USPs) are the largest of the DUB families with more than 50 members in humans. The USP catalytic domain varies considerably in size and consists of six conserved motifs with N- or C-terminal extensions and insertions occurring between the conserved motifs (Ye et al. 2009). Two highly conserved regions comprise the catalytic triad, the Cys-box (Cys) and His-box (His and Asp/Asn) (Nijman et al. 2005, Ye et al. 2009, Reyes-Turcu & Wilkinson 2009). They recognize their substrates by interactions of the variable regions with the substrate protein directly, or via scaffolds or adapters in multiprotein complexes.
R-HSA-2142789 Ubiquinol biosynthesis The length of the polyisoprenoid chain of ubiquinone, aka coenzyme Q (CoQ), varies depending on the species involved: it is 6 in budding yeast, Saccharomyces cerevisiae, (CoQ6) and 10 in humans (CoQ10). Most ubiquinone is naturally reduced to ubiquinol (CoQ10H2 in humans), and this form dominates in human tissues. It functions as a ubiquitous coenzyme in redox reactions, and has a central role in the electron transport chain of the inner mitochondrial membrane.to shuttle electrons from complexes I and II to complex III. It also acts as a cofactor for biosynthetic and catabolic reactions, detoxifies damaging lipid species, and engages in cellular signaling and oxygen sensing. In eukaryotes, ubiquinones/ubiquinols are also found in other membranes such as the endoplasmic reticulum, Golgi vesicles, lysosomes, peroxisomes and the plasma membrane (reviewed in Guerra & Pagliarini, 2023).
Ubiquinol/ubiquinone is synthesized in the following way. Initially, mitochondrial 4-hydroxyphenylpyruvate dioxygenase-like protein (HPDL) processes 4-hydroxphenylpyruvate (HPP, HPPA) to (S)-4-hydroxymandelate (4-HMA). HPDL defects lead to CoQ10 deficiency. The HPDL product 4-HMA is a precursor for the synthesis of 4-hydroxybenzoate (PHB), from which the CoQ10 head group is derived (Banh et al., 2021). Because HPDL is a mitochondrial protein, cytosolic HPP from tyrosine catabolism must either be imported by a yet unknown transport mechanism or mitochondrial HPP could be the product of an unknown mitochondrial reaction (Husain et al., 2020; reviewed in Staiano et al., 2023). A polyprenyl diphosphate synthase (PDSS1-2) assembles the polyisoprenoid tail. Next, 4-hydroxybenzoate polyprenyltransferase (COQ2) catalyzes the formation of the covalent linkage between PHB and the polyisoprenoid tail to produce 4-hydroxy-3-polyprenyl benzoic acid intermediate (DHB, 3-decaprenyl-4-hydroxybenzoic acid in humans). Modifications of the aromatic ring follow and involve an oxidative decarboxylation, two hydroxylations, two O-methylations, one C-methylation. This series of reactions, which precise order is not fully established, especially regarding the oxidative decarboxylation step (Pelosi et al., 2024; Nicoll et al., 2024), yield the fully substituted hydroquinone, ubiquinol (reviewed in Guerra & Pagliarini, 2023).
Homologs of the core enzymes COQ3, COQ4, COQ5, COQ6, COQ7, and COQ9 have been shown to form a membrane-localized multienzyme complex ("COQ synthome") in yeast (He et al., 2014). There is some evidence of such a complex, called complex Q, in humans (Floyd et al., 2016). A complex was reconstituted in vitro with ancestral versions of COQ3-7 and COQ9, and was able to convert a short chain analog of DHB (4-Hydroxy-3-(3-methylbut-2-en-1-yl)benzoic acid) into CoQ1 (Nicoll et al., 2024). COQ8A and COQ8B proteins may contribute to the formation and functionality of this complex, as they can bind to most core enzymes (Floyd et al., 2016), and as COQ8B increased the in vitro activity of COQ6 via phosphorylation of COQ3 (Nicoll et al., 2024)..
Parts of CoQ10 synthesis may also occur in the Golgi and endoplasmic reticulum membranes, adding to the cellular membrane CoQ10 pool. The relevance of such processes seems minor (Kalén et al., 1990; Staiano et al., 2023).The precise function of two other genes, COQ10A and COQ10B, which appear to be quinone-binding proteins, is still under investigation. Most of the time, CoQ10 is transported out of the mitochondrion and to the plasma membrane by isoforms of the STARD7 lipid carrier (reviewed in Guile et al., 2023).
CoQ10 deficiency, which can result from reduced activity of any biosynthesis core enzymes or the COQ8A, and COQ8B proteins, has significant implications. It is associated with several inherited metabolic disorders, the phenotypes of which are extremely heterogeneous. These disorders range from fatal neonatal presentations with multisystem involvement to adult-onset isolated myopathy. However, in many cases, the symptoms can be ameliorated by nutritional supplementation with CoQ10 (reviewed in Quinzii et al., 2017; Staiano et al., 2023).
R-HSA-69601 Ubiquitin Mediated Degradation of Phosphorylated Cdc25A cdc25A protein is degraded by the ubiquitin-proteasome machinery in both terminally differentiating and cycling cells (Bernardi et al. 2000).
R-HSA-75815 Ubiquitin-dependent degradation of Cyclin D Cyclin D turnover is regulated by ubiquitination and proteasomal degradation which are positively regulated by cyclin D phosphorylation on threonine-286 (Diehl et al., 1997).
After the Cyclin D serves the role of mediating reactions by Cdk4 and Cdk6, it is shuttled to the cytoplasm and degraded in a ubiquitin-dependent manner. Whether Cdk4 and Cdk6 are truly redundant is a topic still under investigation, although both the kinases are required for normal cell cycle progression.
Destruction of the D type cyclins accompanies the end of the G1 phase, and the E type cyclins are involved in transition of the cell from G1 to S phase.
R-HSA-438066 Unblocking of NMDA receptors, glutamate binding and activation At resting membrane potential, the NMDA receptor ion channel is blocked by extracellular Mg2+ ions and is unable to mediate ion permeation upon binding of ligands (glutamate, glycine, D-serine, NMDA). The voltage block is removed upon depolarization of the post-synaptic cell membrane and Mg2+ is expelled from the NMDA receptor pore (channel), resulting in activated ligand-bound NMDA receptors. The depolarization of the membrane may happen in response to activation of Ca2+ impermeable AMPA receptors, which facilitates Na+ influx, contributing to the unblocking of NMDA receptors. For review, please refer to Traynelis et al. 2010, Paoletti et al. 2013, and Iacobucci and Popescu 2017.
R-HSA-162585 Uncoating of the HIV Virion HIV-1 uncoating is a poorly understood process. It likely involves a progressive and partial dissembly of matrix and capsid layers. While viral proteins like MA and Nef are thought to be involved, the primary cause seems to be the cytosolic pH and a simple dilution effect. Successful uncoating generates the viral reverse transcription complex, which comprises the diploid viral RNA genome, tRNALys primer, RT, IN, MA, nucleocapsid (NC), viral protein R (Vpr) and various host proteins; the reverse-transcription complex is thus liberated from the plasma membrane. It is believed that the transiting viral nucleoprotein complex associates with the elements of cytoskeleton like actin microfilaments.
R-HSA-168336 Uncoating of the Influenza Virion The precise timing and location of uncoating (early vs. late endosomes) depends on the pH-mediated transition of the specific viral hemagglutinin (HA) molecule involved. The uncoating of influenza viruses in endosomes is blocked by changes in pH caused by weak bases (e.g. ammonium chloride and chloroquine) or ionophores (e.g. monensin). Effective uncoating is also dependent on the presence of the viral M2 ion channel protein. Early on it was recognized that amantadine and rimantadine inhibit replication immediately following virus infection. Later it was found that the virus-associated M2 protein allows the influx of H+ ions into the virion, which disrupts protein-protein interactions, resulting in the release of viral RNP free of the viral matrix (M1) protein. Amantadine and rimantadine have been shown to block the ion channel activity of the M2 protein and thus uncoating. The HA mediated fusion of the viral membrane with the endosomal membrane and the M2-mediated release of the RNP results in the appearance of free RNP complexes in the cytosol. This completes the uncoating process. The time frame for the uncoating process has been examined by inhibiting virus penetration with ammonium chloride. Typically, virus particles show a penetration half time of about 25 minutes after viral adsorption. Ten minutes later (half time of 34 minutes after adsorption) RNP complexes are found in the nucleus. Uptake of RNP molecules through nuclear pores is an active process, involving the nucleo-cytoplasmic trafficking machinery of the host cell.
R-HSA-381119 Unfolded Protein Response (UPR) The Unfolded Protein Response (UPR) is a regulatory system that protects the Endoplasmic Reticulum (ER) from overload. The UPR is provoked by the accumulation of improperly folded protein in the ER during times of unusually high secretion activity. Analysis of mutants with altered UPR, however, shows that the UPR is also required for normal development and function of secretory cells.
One level at which the URP operates is transcriptional and translational regulation: mobilization of ATF6, ATF6B, CREB3 factors and IRE1 leads to increased transcription of genes encoding chaperones, while mobilization of PERK (pancreatic eIF2alpha kinase, EIF2AK3) leads to phosphorylation of the translation initiation factor eIF2alpha and global down-regulation of protein synthesis.
ATF6, ATF6B, and CREB3 factors (CREB3 (LUMAN), CREB3L1 (OASIS), CREB3L2 (BBF2H7, Tisp40), CREB3L3 (CREB-H), and CREB3L4 (CREB4)) are membrane-bound transcription activators that respond to ER stress by transiting from the ER membrane to the Golgi membrane where their transmembrane domains are cleaved, releasing their cytosolic domains to transit to the nucleus and activate transcription of target genes. IRE1, also a resident of the ER membrane, dimerizes and autophosphorylates in response to ER stress. The activated IRE1 then catalyzes unconventional splicing of XBP1 mRNA to yield an XBP1 isoform that is targeted to the nucleus and activates chaperone genes.
R-HSA-176974 Unwinding of DNA DNA Replication is regulated accurately and precisely by various protein complexes. Many members of the MCM protein family are assembled into the pre-Replication Complexes (pre-RC) at the end of M phase of the cell cycle. DNA helicase activity of some of the MCM family proteins are important for the unwinding of DNA and initiation of replication processes. This section contains four events which have been proved in different eukaryotic experimental systems to involve various proteins for this essential step during DNA Replication.
R-HSA-5339562 Uptake and actions of bacterial toxins The toxic effects of many bacteria on their human hosts are mediated by proteins released from the bacteria that enter human cells and disrupt critical cellular functions (Henkel et al. 2010). All of the ones annotated here share a bipartiite mechanism of host intoxication: one moiety binds target cells and mediates the delivery of the other part to the intracellular compartment where it can function as an enzyme to degrade or derivatize and inactivate critical target cell proteins or to activate constitutive synthesis of high levels of cAMP.
R-HSA-5210891 Uptake and function of anthrax toxins Bacillus anthracis bacteria target cells in an infected human through the action of three secreted bacterial proteins, lef (also known as LF, lethal factor), cya (also known as EF, edema factor), and pagA (also known as PA, protective antigen) (Turk 2007; Young and Collier 2007). lef is a protease that cleaves and inactivates many MAP2K (MAP kinase kinase, MEK) proteins (Duesbery et al. 1998; Vitale et al. 2000), disrupting MAP kinase signaling pathways. cya is an adenylate cyclase that mediates the constitutive production of cAMP (Leppla 1982), a molecule normally generated transiently in tightly regulated amounts in response to extracellular signals. Both lef and cya depend on pagA to enter their target cells, a strategy characteristic of bacterial binary toxins (Barth et al. 2004). pagA binds to the target cell receptors, is cleaved by furin or other cellular proteases, and thereupon forms an oligomer that exposes binding sites for lef and cya molecules (Young and Collier 2007). This complex is taken into the target cell by clathrin mediated endocytosis and delivered to endosomes. The low pH of the endosome causes the bacterial toxin complex to rearrange: the pagA oligomer forms a pore in the endosome membrane through which lef and cya molecules enter the target cell cytosol.
R-HSA-5336415 Uptake and function of diphtheria toxin Diphtheria is a serious, often fatal human disease associated with damage to many tissues. Bacteria in infected individuals, however, are typically confined to the lining of the throat or to a skin lesion; systemic effects are due to the secretion of an exotoxin encoded by a lysogenic bacteriophage. The toxin is encoded as a single polypeptide but is cleaved by host furin-like proteases to yield an aminoterminal fragment A and a carboxyterminal fragment B, linked by a disulfide bond. Toxin cleavage can occur when it first contacts the target cell surface, as annotated here, or as late as the point at which fragment A is released into the cytosol. Fragment B mediates toxin uptake into target cell endocytic vesicles, where acidification promotes a conformational change enabling fragment B to form a channel in the vesicle membrane through which fragment A is extruded into the target cell cytosol. Cleavage of the inter-fragment disulfide bond frees DT fragment A, which catalyzes ADP ribosylation of the translation elongation factor 2 (EEF2) in a target cell, thereby blocking protein synthesis. Neither fragment is toxic to human cells by itself (Collier 1975; Pappenheim 1977; Murphy 2011).
R-HSA-9758881 Uptake of dietary cobalamins into enterocytes The steps of transport of dietary cobalamins through the digestive tract to the distal ileum, leading to its endocytosis are annotated here. The proteins involved in these processes accommodate cobalamins including cyanocobalamin, methylcobalamin, and adenosylcobalamin. (Banerjee et al. 2021; Nielsen et al. 2012; Quadros 2010). This broad specificity is indicated by annotating R-cob(III)alamin (RCbl - CHEBI:140785) as the cargo in all of these processes.
R-HSA-70635 Urea cycle The urea cycle yields urea, the major form in which excess nitrogen is excreted from the human body, and the amino acid arginine (Brusilow and Horwich 2001). It consists of four reactions: that of ornithine and carbamoyl phosphate to form citrulline, of citrulline and aspartate to form argininosuccinate, the cleavage of argininosuccinate to yield fumarate and arginine, and the cleavage of arginine to yield urea and re-form ornithine. The carbamoyl phosphate consumed in this cycle is synthesized in the mitochondria from bicarbonate and ammonia, and this synthesis in turn is dependent on the presence of N-acetylglutamate, which allosterically activates carbamoyl synthetase I enzyme. The synthesis of N-acetylglutamate is stimulated by high levels of arginine. Increased levels of free amino acids, indicated by elevated arginine levels, thus stimulate urea synthesis.
Two enzymes catalyze the hydrolysis of arginine to yield ornithine and urea. Cytosolic ARG1 is the canonical urea cycle enzyme. Mitochondrial ARG2 likewise catalyzes urea production from arginine and may have a substantial sparing effect in patients lacking ARG1 enzyme, so its reaction is annotated here although the role of ARG2 under normal physiological conditions remains unclear.
R-HSA-77108 Utilization of Ketone Bodies The levels of acetone in ketone bodies are much lower than those of acetoacetic acid and beta-hydroxybutyric acid. Acetone cannot be converted back to acetyl-CoA, and is excreted in urine, or breathed out through the lungs. Extrahepatic tissues utilize ketone bodies by converting the beta-hydroxybutyrate successively to acetoacetate, acetoacetatyl-CoA, finally to acetyl-CoA (Sass 2011).
R-HSA-195399 VEGF binds to VEGFR leading to receptor dimerization The binding of VEGF ligands to VEGFR receptors in the cell membrane induces dimerization and activation of the latter, initiating intracellular signaling cascades that result in proliferation, survival, migration and increased permeability of vascular endothelial cells (Matsumoto and Mugishima, 2006). The receptors predominantly form homodimers but heterodimers between VEGFR-1 and -2 have been observed. Although both VEGFR-1 and -2 are expressed in the vascular endothelium, the angiogenic activities of VEGFs are transduced mainly through VEGFR-2 in vivo.
R-HSA-194313 VEGF ligand-receptor interactions The VEGF family is encoded by seven genes (VEGF-A, B, C, D, E: PLGF (Placenta Growth Factor)-1, 2). Six isoforms of VEGF-A protein, containing 121, 145, 165, 183, 189, and 206 amino acid residues, and two isoforms of VEGF-B (167 and 186 residues) are specified by alternatively spliced mRNAs. The active form of each of these proteins is a homodimer.
The specificities of the three VEGF tyrosine kinase receptors, VEGFR-1, VEGFR-2 and VEGFR-3, for these ligands are shown in the figure (Hicklin and Ellis 2005). All VEGF-A isoforms bind both VEGFR-1 and VEGFR-2; PLGF-1 and -2, and VEGF-B isoforms bind only VEGFR-1; VEGF-E binds VEGFR-2; and VEGF-C and -D bind both VEGFR-2 and -3. VEGF-D undergoes a complex series of post-translational modifications that results in secreted forms with increased activity toward VEGFR-3 and VEGFR-2.
Two co-receptor proteins in the cell membrane, neuropilin (NRP)-1 and NRP-2, interact with VEGFR proteins to increase the affinity of the latter for their ligands (Neufeld et al.,2002). They differ from VEGFR proteins in not having intracellular signaling domains.
R-HSA-4420097 VEGFA-VEGFR2 Pathway Angiogenesis is the formation of new blood vessels from preexisting vasculature. One of the most important proangiogenic factors is vascular endothelial growth factor (VEGF). VEGF exerts its biologic effect through interaction with transmembrane tyrosine kinase receptors VEGFR, selectively expressed on vascular endothelial cells. VEGFA signaling through VEGFR2 is the major pathway that activates angiogenesis by inducing the proliferation, survival, sprouting and migration of endothelial cells (ECs), and also by increasing endothelial permeability (Lohela et al. 2009, Shibuya & Claesson-Welsh 2006, Claesson-Welsh & Welsh, 2013). The critical role of VEGFR2 in vascular development is highlighted by the fact that VEGFR2-/- mice die at E8.5-9.5 due to defective development of blood islands, endothelial cells and haematopoietic cells (Shalaby et al. 1995).
R-HSA-5218921 VEGFR2 mediated cell proliferation VEGFR2 stimulates ERK not via GRB2-SOS-RAS, but via pY1175-dependent phosphorylation of PLC gamma and subsequent activation of PKCs. PKC plays an important mediatory role in the proliferative Ras/Raf/MEK/ERK pathway. PKC alpha can intersect the Ras/Raf/MEK/ERK cascade at the level of Ras (Clark et al. 2004) or downstream of Ras through direct phosphorylation of Raf (Kolch et al. 1993). VEGF stimulation leads to Ras activation in a Ras-guanine nucleotide exchange factor (GEF) independent mechanism. It rather relies on modulating the regulation of Ras-GTPase activating protein (GAP) than regulation of Ras-GEFS (Wu et al. 2003).
R-HSA-5218920 VEGFR2 mediated vascular permeability The free radical nitric oxide (NO), produced by endothelial NO synthase (eNOS), is an important vasoactive substance in normal vascular biology and pathophysiology. It plays an important role in vascular functions such as vascular dilation and angiogenesis (Murohara et al. 1998, Ziche at al. 1997). NO has been reported to be a downstream mediator in the angiogenic response mediated by VEGF, but the mechanism by which NO promotes neovessel formation is not clear (Babaei & Stewart 2002). Persistent vasodilation and increase in vascular permeability in the existing vasculature is observed during the early steps of angiogenesis, suggesting that these hemodynamic changes are indispensable during an angiogenic processes. NO production by VEGF can occur either through the activation of PI3K or through a PLC-gamma dependent manner. Once activated both pathways converge on AKT phosphorylation of eNOS, releasing NO (Lin & Sessa 2006). VEGF also regulates vascular permeability by promoting VE-cadherin endocytosis at the cell surface through a VEGFR-2-Src-Vav2-Rac-PAK signalling axis.
R-HSA-8866423 VLDL assembly Very low-density lipoprotein (VLDL) is synthesised in the liver in two steps. First, apolipoprotein B-100 (APOB-100) is co- and post-translationally lipidated in the rough ER lumen. After transfer to the smooth ER lumen, lipidated APOB-100 acquires lipids to become bona fide VLDL. Lipid composition of VLDL - triglycerides (50-60%), cholesterol (10-12%), cholesterol esters (4-6%), phospholipids (18-20%), and apolipoprotein B (8-12%). When VLDL assembly is complete, it travels along the Golgi apparatus to be eventually secreted from the liver into general circulation. In circulation, VLDL can acquire more lipoproteins. At least two other apolipoproteins are constituents; apolipoprotein C-I (APOC1, around 20%) and apolipoprotein C4 (APOC4, minor amount) (Gibbons et al. 2004; Olofsson et al. 2000).
R-HSA-8964046 VLDL clearance Very-low-density lipoprotein (VLDL) is a lipoprotein made by the liver and mediates the export of triglycerides from the liver to the rest of the body (Gibbons et al. 2004). VLDL particles are bound by cell surface receptors and internalized in reactions annotated here.
R-HSA-8866427 VLDLR internalisation and degradation The steps involved in proprotein convertase PCSK9-induced degradation of VLDLR are described here (Poirier et al. 2008). The rate of this catabolic process plays a clinically significant role in determining the efficiency of lipoprotein clearance from the blood.
R-HSA-5619094 Variant SLC6A14 may confer susceptibility towards obesity SLC6A14 mediates the uptake of multiple basic and nonpolar amino acids as well as beta-alanine across the plasma membrane. Uptake of one amino acid molecule is accompanied by uptake of two sodium ions and a chloride ion (Broer & Gether 2012, Schweikhard & Ziegler 2012). As assessed by Northern blotting, SLC6A14 is expressed at high levels in lung but only at low levels, if at all, in intestine or kidney. Variations in SLC6A14 may be associated with obesity (BMIQ11; MIM:300306) in some populations. SLC6A14 is an interesting candidate for obesity because it may potentially regulate tryptophan availability for serotonin synthesis and thus could affect appetite control (Suviolahti et al. 2003, Durand et al. 2004).
R-HSA-5619101 Variant SLC6A20 contributes towards hyperglycinuria (HG) and iminoglycinuria (IG) SLC6A20 encodes the sodium- and chloride-dependent transporter SIT1 and mediates the sodium-dependent uptake of imino acids such as L-proline, N-methyl-L-proline and pipecolate as well as N-methylated amino acids and glycine (Broer & Gether 2012, Schweikhard & Ziegler 2012). The human protein is expressed in the intestine and kidney. A common SNP in the SLC6A20 gene, a 596C-T transition that results in a thr199-to-met (T199M) substitution can contribute towards iminoglycinuria (IG; MIM:242600) or hyperglycinuria (HG; MIM:138500) (Broer et al. 2008). Overall, mutations in SLC36A2 together with polymorphisms in the modifiers SLC6A20, SLC6A18, and SLC6A19 constitute the genetic basis for these phenotypes.
R-HSA-5660686 Variant SLC6A20 contributes towards hyperglycinuria (HG) and iminoglycinuria (IG) SLC6A20 encodes the sodium- and chloride-dependent transporter SIT1 and mediates the sodium-dependent uptake of imino acids such as L-proline, N-methyl-L-proline and pipecolate as well as N-methylated amino acids and glycine (Broer & Gether 2012, Schweikhard & Ziegler 2012). The human protein is expressed in the intestine and kidney. A common SNP in the SLC6A20 gene, a 596C-T transition that results in a thr199-to-met (T199M) substitution can contribute towards iminoglycinuria (IG; MIM:242600) or hyperglycinuria (HG; MIM:138500) (Broer et al. 2008). Overall, mutations in SLC36A2 together with polymorphisms in the modifiers SLC6A20, SLC6A18, and SLC6A19 constitute the genetic basis for these phenotypes.
R-HSA-432040 Vasopressin regulates renal water homeostasis via Aquaporins In the kidney water and solutes are passed out of the bloodstream and into the proximal tubule via the slit-like structure formed by nephrin in the glomerulus. Water is reabsorbed from the filtrate during its transit through the proximal tubule, the descending loop of Henle, the distal convoluted tubule, and the collecting duct.
Aquaporin-1 (AQP1) in the proximal tubule and the descending thin limb of Henle is responsible for about 90% of reabsorption (as estimated from mouse knockouts of AQP1). AQP1 is located on both the apical and basolateral surface of epithelial cells and thus transports water through the epithelium and back into the bloodstream.
In the collecting duct epithelial cells have AQP2 on their apical surface and AQP3 and AQP4 on their basolateral surface to transport water across the epithelium. The permeability of the epithelium is regulated by vasopressin, which activates the phosphorylation and subsequent translocation of AQP2 from intracellular vesicles to the plasma membrane.
R-HSA-388479 Vasopressin-like receptors The vasopressins are peptide hormones consisting of nine amino acids (nonapeptides). They include arginine vasopressin (AVP; anti-diuretic hormone, ADH) and oxytocin. They are synthesized in the hypothalamus from a precursor and released from stores in the posterior pituitary into the blood stream. One of the most important roles of vasopressins is the regulation of water retention in the body. Oxytocin is important in uterine contraction during birth. The vasopressins act via AVP and oxytocin receptors. These are connected to G proteins which act as second messengers and convey the signal inside the cell.
R-HSA-5653656 Vesicle-mediated transport The transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The transport process begins with the formation of the vesicle itself, often triggered by the interaction of the cargo with the vesicle formation machinery. Vesicular transport pathways can include vesicle formation, coating, budding, uncoating and target membrane fusion depending upon the function of the pathway described. Vesicle-mediated transport occurs from within cell via ER and Golgi transport, as well as functioning in the endocytosis of material taken into the cell via scavenger receptors.
R-HSA-180585 Vif-mediated degradation of APOBEC3G The HIV-1 accessory protein Vif (Viral infectivity factor) is required for the efficient infection of primary cell populations (e.g., lymphocytes and macrophages) and 'non-permissive' cell lines. Vif neutralises the host DNA editing enzyme, APOBEC3G, in the producer cell. Indeed, in the absence of a functional Vif, APOBEC3G is selectively incorporated into the budding virions and in the next cycle of infection leads to the deamination of deoxycytidines (dC) within the minus-strand cDNA during reverse transcription (Sheehy et al 2003; Li et al., 2005 ; Stopak et al. 2003).
Deamination changes cytidine to uracil and thus results in G to A transitions and stop codons in the provirus. The aberrant cDNAs produced in the infected cell can either be integrated in form of non-functional proviruses or degraded. Vif counteracts the antiviral activity of APOBEC3G by associating directly with it and promoting its polyubiquitination and degradation by the 26S proteasome.
Vif binds APOBEC3G and recruits it into an E3 ubiquitin-enzyme complex composed by the cytoplasmic proteins Cullin5, Rbx, ElonginC and ElonginB (Yu et al., 2003) . Thus, in the presence of Vif, APOBEC3G incorporation into the virion is minimal.
R-HSA-9824446 Viral Infection Pathways Viral infection pathways aim to capture molecular mechanisms of human viral diseases related to viral adhesion and penetration of human host cells, viral genome replication and synthesis of viral proteins, interaction of viral proteins with the proteins of the human host, and evasion of the host's immune defense.
Viral infection pathways currently include the life cycles of SARS-CoV viruses, influenza virus, HIV (human immunodeficiency virus), and human cytomegalovirus (HCMV).
Newly discovered coronaviruses SARS-CoV-1 and SARS-CoV-2 cause severe acute respiratory syndrome (SARS). These viruses belong to the family Coronaviridae, characterized by the presence of lipid envelope and genome in the form of single-stranded, linear, nonsegmented, positive-sense RNA.
Influenza viruses, the causative agents of flu, belong to the family Orthomyxoviridae, characterized by the presence of lipid envelope and genome in the form of single-stranded, segmented, negative-sense RNA.
Human immunodeficiency viruses (HIV), the causative agents of acquired immunodeficiency syndrome (AIDS), belong to the genus Lentivirus, family Retroviridae, characterized by the presence of lipid envelope and genome in the form of single-stranded, nonsegmented, linear, diploid, positive-sense RNA that produces a DNA intermediate during viral replication. Namely, retroviral RNA-directed DNA polymerase (reverse transcriptase) transcribes genomic RNA into viral DNA that integrates into host cell's DNA as a provirus.
Human cytomegalovirus (HCMV), one of the causative agents of infectious mononucleosis and pneumonia, belongs to the the family of herpesviruses (Herpesviridae), characterized by their large size, presence of lipid envelope, and genome in the form of linear double-stranded DNA that encodes more than a hundred different proteins.
R-HSA-168325 Viral Messenger RNA Synthesis Like the mRNAs of the host cell, influenza virus mRNAs are capped and polyadenylated (reviewed in Neumann, 2004). The methylated caps, however, are scavenged from host cell mRNAs and serve as primers for viral RNA synthesis, a process termed 'cap-snatching' (Krug, 1981; Hagen, 1994). The PB2 polymerase protein binds the cap, activating endonucleolytic cleavage of the host mRNA by PB1. The 3' poly-A tracts on viral messages are generated by polymerase stuttering on poly-U tracts near the 5' end of the template vRNA (Robertson, 1981; Zheng, 1999). The second process allows polyadenylation of viral mRNAs when the host cell polyadenylation process has been inhibited (Engelhardt, 2006; Amorim, 2006). Notably, early transcripts (including NP and NS1) accumulate in the cytoplasm before late transcripts (M1, HA, and NS2), and in varying abundances, suggesting additional control mechanisms regulating viral gene expression (Shapiro, 1987; Hatada, 1989; Amorim, 2006).
R-HSA-168330 Viral RNP Complexes in the Host Cell Nucleus Viral RNP is assembled in the host cell nucleus through the interaction of full-length negative strand viral RNA (vRNA) and the viral nucleocapsid (NP) and matrix (M1) proteins. Studies of interactions of the purified components in vitro and of tissue culture model systems expressing various combinations of the components have established roles for both NP and M1 proteins in the assembly of a complex that has the physical properties of vRNP purified from virions and that can be exported from the host cell nucleus (Whittaker, 1996; Huang, 2001; Baudin, 2001). Viral RNP complexes have been found in the nucleoplasm, and also in the nuclear periphery, associated with the nuclear matrix or chromatin, particularly for vRNA-containing complexes and M1 protein (Elton, 2005; Garcia-Robles, 2005; Takizawa et al., 2006).
R-HSA-192823 Viral mRNA Translation Spliced and unspliced viral mRNA in the cytoplasm are translated by host cell ribosomal translation machinery (reviewed in Kash, 2006). At least ten viral proteins are synthesized: HA, NA, PB1, PB2, PA, NP, NS1, NEP/NS2, M1, and M2. Viral mRNA translation is believed to be enhanced by conserved 5'UTR sequences that interact with the ribosomal machinery and at least one cellular RNA-binding protein, G-rich sequence factor 1 (GRSF-1), has been found to specifically interact with the viral 5' UTRs. (Park, 1995; Park, 1999). The viral NS1 protein and the cellular protein P58(IPK) enhance viral translation indirectly by preventing the activation of the translational inhibitor PKR (Salvatore, 2002; Goodman, 2006). The viral NS1 protein has also been proposed to specifically enhance translation through interaction with host poly(A)-binding protein 1 (PABP1) (Burgui, 2003). Simultaneously, host cell protein synthesis is downregulated in influenza virus infection through still uncharacterized mechanisms (Katze, 1986; Garfinkel, 1992; Kash, 2006). In most human influenza A strains (such as PR8), the PB1 mRNA segment is capable of producing a second protein, PB1-F2, from a short +1 open reading frame initiating downstream of the PB1 ORF initiation codon (Chen, 2001).
R-HSA-9694322 Virion Assembly and Release This COVID-19 pathway has been created by a combination of computational inference from SARS-CoV-1 data (https://reactome.org/documentation/inferred-events) and manual curation, as described in the summation for the overall SARS-CoV-2 infection pathway.
The structures of complete SARS-CoV-2 virions, as well as their assembly stages, have been elucidated in great detail by cryo-electron microscopy methods. In particular, the Spike trimer is localized to ERGIC or Golgi compartments upon coexpression of E or M, which prevents syncytia formation (Boson et al, 2020). It is then transported via small transport vesicles to assembly sites (Klein et al, 2020; Mendonça et al, 2021; reviewed by Hardenbrook and Zhang, 2021). Based on work done in related coronaviruses, viral assembly is expected to occur at the ERGIC membrane (reviewed in Masters, 2006; Fehr and Perlman, 2015; Fung and Liu, 2019). Membrane protein components of the virus concentrate at the ERGIC membrane but are also found throughout the secretory system including at the plasma membrane. Accumulation at the site of viral assembly has been shown to depend on interaction between retrieval signals in the cytoplasmic tails of viral proteins and host factors such as the COPI coat, and likely involves repeated rounds of anterograde and retrograde traffic (McBride et al, 2007; Ujike et al, 2016; Tan et al, 2004; Tan et al, 2005; reviewed in McBride and Fielding, 2012; Chang et al, 2014).
Viral assembly is initiated by homotypic interactions of M protein (Tseng et al, 2010; Siu et al, 2008). This forms an M-lattice that contributes to the induction of membrane curvature and additionally acts as a scaffold for the recruitment of the other structural components of the virus (Voss et al, 2009). M protein makes interactions with each of the main components of the mature virus, including E, S and N (He et al, 2004; Luo et al, 2006; Siu et al, 2008; reviewed in Masters, 2006). Electron micrographic studies suggest the final size of the mature virus is ~100 nm. The ribonuclear particle is predominantly helical and is packaged with an outer diamter of ~ 16 nm (Neuman et al, 2006; Neuman et al, 2011; reviewed in Chang et al, 2014). These physical constraints suggest a final stoichiometry in the mature virion of 75 S trimers:1200 M proteins:300 N:1 RNA genome (Neuman et al, 2011; reviewed in Chang et al, 2014). Minor amounts of other viral proteins, including proteins E, 3a and 7a may also be components of the mature virus, although their functions are not well established (reviewed in Schoeman and Fielding, 2019; Liu et al, 2014).
R-HSA-9679509 Virion Assembly and Release SARS viral assembly occurs at the ERGIC membrane (reviewed in Masters, 2006; Fehr and Perlman, 2015; Fung and Liu, 2019). Membrane protein components of the virus concentrate at the ERGIC membrane but are also found throughout the secretory system including at the plasma membrane. Accumulation at the site of viral assembly has been shown to depend on interaction between retrieval signals in the cytoplasmic tails of viral proteins and host factors such as the COPI coat, and likely involves repeated rounds of anterograde and retrograde traffic (McBride et al, 2007; Ujike et al, 2016; Tan et al, 2004; Tan et al, 2005; reviewed in McBride and Fielding, 2012; Chang et al, 2014).
Viral assembly is intitiated by homotypic interactions of M protein (Tseng et al, 2010; Siu et al, 2008). This forms an M-lattice that contributes to the induction of membrane curvature and additionally acts as a scaffold for the recruitment of the other structural components of the virus (Voss et al, 2009). M protein makes interactions with each of the main components of the mature virus, including E, S and N (He et al, 2004; Luo et al, 2006; Siu et al, 2008; reviewed in Masters, 2006). Electron micrographic studies suggest the final size of the mature virus is ~100 nm. The ribonuclear particle is predominantly helical and is packaged with an outer diamter of ~ 16 nm (Neuman et al, 2006; Neuman et al, 2011; reviewed in Chang et al, 2014). These physical constraints suggest a final stoichiometry in the mature virion of 75 S trimers:1200 M proteins:300 N:1 RNA genome (Neuman et al, 2011; reviewed in Chang et al, 2014). Minor amounts of other viral proteins, including proteins E, 3a and 7a may also be components of the mature virus, although their functions are not well established (reviewed in Schoeman and Fielding, 2019; Liu et al, 2014).
R-HSA-168268 Virus Assembly and Release Influenza viruses assemble and bud from the apical plasma membrane of polarized cells e.g. lung epithelial cells of the infected host. This asymmetrical process (i.e. apical [Influenza virus] or basolateral [Marburg virus]) is thought to have an important role in viral pathogenesis and tissue tropism. In most cases the individual viral envelope proteins are seen to accumulate at the same polar surface from which virus budding occurs, suggesting that they determine the maturation site
R-HSA-2187338 Visual phototransduction Visual phototransduction is the process by which photon absorption by visual pigment molecules in photoreceptor cells is converted to an electrical cellular response. The events in this process are photochemical, biochemical and electrophysiological and are highly conserved across many species. This process occurs in two types of photoreceptors in the retina, rods and cones. Each type consists of two parts, the outer segment which detects a photon signal and the inner segment which contains the necessary machinery for cell metabolism. Each type of cell functions differently. Rods are very light sensitive but their flash response is slow so they work best in twilight conditions but are not good at detecting objects moving quickly. Cones are less light-sensitive and have a fast flash response so they work best in daylight conditions and are better at detecting fast moving objects than rods.
The visual pigment consists of a chromophore (11-cis-retinal, 11cRAL, A1) covalently attached to a GPCR opsin family member. The linkage is via a Schiff base forming retinylidene protein. Upon photon absorption, 11cRAL isomerises to all-trans retinal (atRAL), changing the conformation of opsin to an activated form which can activate the regulatory G protein transducin (Gt). The alpha subunit of Gt activates phosphodiesterase which hydrolyses cGMP to 5'-GMP. As high level of cGMP keep cGMP-gated sodium channels open, the lowering of cGMP levels closes these channels which causes hyperpolarization of the cell and subsequently, closure of voltage-gated calcium channels. As calcium levels drop, the level of the neurotransmitter glutamate also drops causing depolarization of the cell. This effectively relays the light signal to postsynaptic neurons as electrical signal (Burns & Pugh 2010, Korenbrot 2012, Pugh & Lamb 1993).
11cRAL cannot be synthesised in vertebrates. Vitamin A from many dietary sources is the precursor for 11cRAL. It is taken from food in the form of esters such as retinyl acetate or palmitate or one of four caretenoids (alpha-carotene, beta-carotene, gamma-carotene and beta-cryptoxanthin). Retinoids are transported from the gut to be stored in liver, until required by target organs such as the eye (Harrison & Hussain 2001, Harrison 2005). In the eye, in the form 11cRAL, it is used in the retinoid (visual) cycle to initiate phototransduction and for visual pigment regeneration to ready the photoreceptor for the next phototransduction event (von Lintig 2012, Blomhoff & Blomhoff 2006, von Lintig et al. 2010, D'Ambrosio et al. 2011, Wang & Kefalov 2011, Kefalov 2012, Wolf 2004).
R-HSA-196819 Vitamin B1 (thiamin) metabolism Vitamin B1 (thiamin) is found naturally in certain foodstuffs such as green peas, spinach, liver, bananas, whole grains and legumes. Human diseases associated with thiamin deficiency include beriberi, due to a thiamin-deficient diet, TMRA, due to defects in the SLC19A2 transport protein, and Wernicke-Korsakoff Syndrome, associated with thiamin deficiency in alcoholism (Haas 1988). Thiamin is water-soluble so is not stored in the body. When pyrophosphorylated, thiamin is converted into the coenzyme thiamin pyrophosphate (ThPP, codecarboxylase) which plays an essential role in oxidative decarboxylation and group transfer reactions.
R-HSA-196843 Vitamin B2 (riboflavin) metabolism Riboflavin (vitamin B2, E101) is an essential component for the cofactors FAD (flavin-adenine dinucleotide) and FMN (flavin mononucleotide). Together with NAD+ and NADP+, FAD and FMN are important hydrogen carriers and take part in more than 100 redox reactions involved in energy metabolism. Riboflavin is present in many vegetables and meat and during digestion, various flavoproteins from food are degraded and riboflavin is resorbed. The major degradation and excretion product in humans is riboflavin (Rivlin 1970).
R-HSA-199220 Vitamin B5 (pantothenate) metabolism Vitamin B5 ((R)-pantothenate, PanK), is an essential precursor for the synthesis of the metabolic cofactor Coenzyme A (CoA-SH) (Robishaw and Neely 1985) and is the prosthetic group of acyl carrier protein (ACP) (Joshi et al. 2003). The name pantothenate is from the Greek “pantothen”, "from everywhere". Both pantothenate and CoA-SH are found in nearly every foodstuff and in the gut microbiome. CoA-SH itself is readily degraded in the gut and in extracellular fluids within the body. No processes are known to transport it across plasma membranes. Instead, individual cells take up PanK, which is stable in the extracellular environment, to synthesize CoA-SH for their own use. Within a cell, distinct groups of CoA-SH-requiring reactions occur in the cytosol, mitochondrial matrix, and peroxisomes, and controlling CoA pool size in each location plays a major role in regulating and integrating cellular metabolic processes. Control is achieved by selective degradation, synthesis, and transport of CoA within a cell (Cavestro et al. 2023, Naquet et al. 2020). The reactions annotated here provide an incomplete description of these processes, as key steps remain incompletely understood.
R-HSA-964975 Vitamin B6 activation to pyridoxal phosphate Animals cannot synthesize pyridoxal 5'-phosphate (PLP) which is a ligand in aminotransferases and other enzymes. PLP's accessible derivatives pyridoxine, pyridoxal, and pyridoxamine are traditionally called vitamins B6. They are taken up nutritionally from bacteria and plants, but also created from PLP in the body. The pathways used to recycle PLP from these three compounds can therefore be called vitamin B6 activation as well as PLP salvage. Because of the close similarity of the molecules, only two enzymes are needed for the task (McCormick & Chen, 1999).
R-HSA-196836 Vitamin C (ascorbate) metabolism Vitamin C (ascorbate) is an antioxidant and a cofactor in reactions catalyzed by Cu+-dependent monooxygenases and Fe++-dependent dioxygenases. Many mammals can synthesize ascorbate de novo; humans and other primates cannot due to an evolutionarily recent mutation in the gene catalyzing the last step of the biosynthetic pathway. Reactions annotated here mediate the uptake of ascorbate and its fully oxidized form, dehydroascorbate (DHA) by cells, and the reduction of DHA and monodehydroascorbate to regenerate ascorbate (Linster and Van Schaftingen 2007).
R-HSA-196791 Vitamin D (calciferol) metabolism Vitamin D3 (VD3, cholecalciferol) is a steroid hormone that principally plays roles in regulating intestinal calcium absorption and in bone metabolism. It is obtained from the diet and produced in the skin by photolysis of 7-dehydrocholesterol and released into the bloodstream. Very few foods (eg. oily fish, mushrooms exposed to sunlight and cod liver oil) are natural sources of vitamin D. A small number of countries in the world artificially fortify a few foods with vitamin D. The metabolites of vitamin D are carried in the circulation bound to a plasma protein called vitamin D binding protein (GC) (for review see Delanghe et al. 2015, Chun 2012). Vitamin D undergoes two subsequent hydroxylations to form the active form of the vitamin, 1-alpha, 25-dihydroxyvitamin D (1,25(OH)2D). The first hydroxylation takes place in the liver followed by subsequent transport to the kidney where the second hydroxylation takes place. 1,25(OH)2D acts by binding to nuclear vitamin D receptors (Neme et al. 2017) and it has been estimated that upwards of 2000 genes are directly or indirectly regulated which are involved in calcium homeostasis, immune responses, cellular growth, differentiation and apoptosis (Hossein-nezhad et al. 2013, Hossein-nezhad & Holick 2013). Inactivation of 1,25(OH)2D occurs via C23/C24 oxidation catalysed by cytochrome CYP24A1 enzyme (Christakos et al. 2016).
R-HSA-8877627 Vitamin E Vitamins A, D, E and K are lipophilic compounds, the so-called fat-soluble vitamins. Because of their lipophilicity, fat-soluble vitamins are solubilised and transported by intracellular carrier proteins to exert their actions. Alpha-tocopherol, the main form of vitamin E found in the body, is transported by alpha-tocopherol transfer protein (TTPA) in hepatic cells (Kono & Arai 2015, Schmolz et al. 2016).
R-HSA-211916 Vitamins A number of CYPs can act upon vitamins.
R-HSA-1296072 Voltage gated Potassium channels Voltage-gated K+ channels (Kv) determine the excitability of heart, brain and skeletal muscle cells. Kv form octameric channel with alpha subunits that forms the pore of the channel and associated beta subunits. The alpha subunits associate with beta subunits with a stoichiometry of alpha4beta4.The alpha subunits have been classified into 12 families, 1-12 with several representatives from each family. Members of Kv 1-4 form both homotetramers and heterotetramers, however, members of Kv 5-12 form functional heterotetramers. Kv's are expressed in the axon, at axon nodes, somatodendritic sites and axon termini.
R-HSA-180897 Vpr-mediated induction of apoptosis by mitochondrial outer membrane permeabilization In one model of Vpr mediated induction of apoptosis, Vpr acts directly on the mitochondrial permeability transition pore complex through its interaction with adenine nucleotide translocator (ANT). This interaction promotes the permeabiliztion of the mitochondrial membranes resulting in the release of cytochrome c and apoptosis-inducing factors.
R-HSA-180910 Vpr-mediated nuclear import of PICs Vpr appears to function in anchoring the PIC to the nuclear envelope. This anchoring likely involves interactions between Vpr and host nucleoporins.
R-HSA-180534 Vpu mediated degradation of CD4 The HIV-1 Vpu protein promotes the degradation of the CD4 receptor by recruiting an SCF like ubiquitination complex that promotes CD4 degradation. Vpu links beta-TrCP to CD4 at the ER membrane through interactions with beta-TrCP and the cytoplasmic tail of CD4. The SKP1 component of the SCF complex is then recruited to the Vpu:beta-TrCP:CD4 promoting ubiquitination and subsequent proteasome-mediated degradation of CD4 (reviewed in Li et al., 2005). Vpu has also been shown to also increases progeny virus secretion from infected cells. Although the precise role of Vpu in this process is not yet known, it may affect ion conductive membrane pore formation and/or interference with TASK-1, an acid-sensitive K+ channel that inhibits virion release in some cells (see references in Li et al., 2005).
R-HSA-5620916 VxPx cargo-targeting to cilium A number of membrane proteins destined for the ciliary membrane are recognized by ARF4 in the trans-Golgi network, initiating the formation of a ciliary targeting complex that directs the passage of these cargo to the cilium (Mazelova et al, 2009; Geng et al, 2006; Jenkins et al, 2006; Ward et al, 2011; reviewed in Deretic, 2013). Although there is some support for the presence of a VxPx or related motif in the C-terminal tail of cargo destined for ARF4-mediated transport to the cilium, the details of this have not been definitively established and other ciliary targeting sequences have also been identified (reviewed in Deretic, 2013; Bhogaraju et al, 2013).
R-HSA-3238698 WNT ligand biogenesis and trafficking 19 WNT proteins have been identified in human cells. The WNTs are members of a conserved metazoan family of secreted morphogens that activate several signaling pathways in the responding cell: the canonical (beta-catenin) WNT signaling cascade and several non-canonical pathways, including the planar cell polarity (PCP), the regulation of intracellular calcium signaling and activation of JNK kinases. WNT proteins exist in a gradient outside the secreting cell and are able to act over both short and long ranges to promote proliferation, changes in cell migration and polarity and tissue homeostasis, among others (reviewed in Saito-Diaz et al, 2012; Willert and Nusse, 2012).
The WNTs are ~40kDa proteins with 23 conserved cysteine residues in the N-terminal that may form intramolecular disulphide bonds. They also contain an N-terminal signal sequence and a number of N-linked glycosylation sites (Janda et al, 2012). In addition to being glycosylated, WNTs are also lipid-modified in the endoplasmic reticulum by a WNT-specific O-acyl-transferase, Porcupine (PORCN), contributing to their characteristic hydrophobicity. PORCN-dependent palmitoylation is required for the secretion of WNT as well as its signaling activity, as either depletion of PORCN or mutation of the conserved serine acylation site results in the intracellular accumulation of WNT ligand (Takada et al, 2006; Barrott et al, 2011; Biechele et al, 2011; reviewed in Willert and Nusse, 2012).
Secretion of WNT requires a number of other dedicated factors including the sorting receptor Wntless (WLS) (also knownas Evi, Sprinter, and GPR177), which binds WNT and escorts it to the cell surface (Banziger et al, 2006; Bartscherer et al, 2006; Goodman et al, 2006). A WNT-specific retromer containing SNX3 is subsequently required for the recycling of WLS back to the Golgi (reviewed in Herr et al, 2012; Johannes and Wunder, 2011). Once at the cell surface, WNT makes extensive contacts with components of the extracellular matrix such as heparan sulphate proteoglycans (HSPGs) and may be bound by any of a number of regulatory proteins, including WIFs and SFRPs. The diffusion of the WNT ligand may be aided by its packing either into WNT multimers, exosomes or onto lipoprotein particles to shield the hydrophobic lipid adducts from the aqueous extracellular environment (Gross et al, 2012; Luga et al, 2012, Korkut et al, 2009; reviewed in Willert and Nusse, 2012).
R-HSA-201688 WNT mediated activation of DVL The three human Dishevelled (DVL) proteins play a central and overlapping role in the transduction of the WNT signaling cascade (Lee et al, 2008; reviewed in Gao and Chen 2010). DVL activity is regulated by phosphorylation, although the details are not completely worked out. DVL likely exists as a phosphoprotein even in the absence of WNT stimulation, and is further phosphorylated upon ligand binding. Casein kinase 1epsilon (CSNK1E), casein kinase 2 (CSNK2) and PAR1 have all been reported to phosphorylate DVL (Willert et al, 1997; Sun et al, 2001; Cong et al, 2004; Ossipova et al, 2005). Upon pathway activation, phosphorylated DVL translocates to the plasma membrane through an interaction between the DVL PDZ domain and the FZD KTxxxW motif (Wong et al, 2003; Umbhauer et al, 2000; Kikuchi et al, 2011). At the plasma membrane, DVL is believed to oligomerize through its DIX domain, providing a platform for AXIN recruitment; recruitment of AXIN is also facilitated by interaction with LRP (Schwarz-Romond et al, 2007; Mao et al, 2001). DVL interacts with phosphatidylinositol-4-kinase type II (PI4KII) and phophatidylinositol-4-phosphate 5-kinase type I (PIP5KI) to promote formation of phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) in the membrane, which is required for the clustering and phosphorylation of LRP6 and the recruitment of AXIN (Pan et al, 2008; Qin et al, 2009).
R-HSA-9673324 WNT5:FZD7-mediated leishmania damping Wnt-5a (WNT5) is known for being a highly specific regulated gene in response to microbial infection (Blumenthal et al. 2006, Pereira et al. 2008 & Ljungberg et al. 2019) including leishmaniasis (Chakraborty et al. 2017), where it seems to be involve in mechanisms that dampen the parasite load within main host macrophages (Chakraborty et al. 2017). In addition, WNT5 is a highly responsive gene in human macrophages present in chronic diseases such as rheumatoid arthritis (Sen et al. 2000), cancer (Pukrop et al. 2006), atherosclerosis (Christman et al. 2008) and obesity (Ouchi et al. 2010 & Ljungberg et al. 2019).
Frizzled-7 (FZD7) acts as a receptor of WNT5 which, upon binding, is implicated in the initiation of the non-canonical WNT pathway that ends up in the re-accommodation of the cytoskeleton to allow a process called planar cell polarity (PCP) (Ljungberg et al. 2019). The activation of the WNT5:FZD7 non-canonical signalling cascade that drives PCP is being studied for its involvement in inflammatory responses (Shao et al. 2016). Treatment of RAW264.7 macrophages with recombinant Wnt5a induced NADPH oxidase-mediated ROS production, which has been suggested to contribute to the macrophage control of L. donovani. Consequently, detailed understanding of how WNT signaling network defines host responses to infection could be important to identify potential targets (Ljungberg et al. 2019).
R-HSA-5140745 WNT5A-dependent internalization of FZD2, FZD5 and ROR2 Internalization of FZD2, FZD5 and ROR2 after WNT5A binding is thought to occur in a clathrin-dependent manner and is required for the activation of RAC signaling (Kurayoshi et al, 2007; Sato et al, 2010; Hanaki et al, 2012; Yamamoto et al, 2009).
R-HSA-5099900 WNT5A-dependent internalization of FZD4 WNT5A induces internalization of FZD4 in a manner that depends upon PKC-mediated phosphorylation of DVL2. Uptake of FZD4 appears to occur in a clathrin, AP-2 and ARBB2-dependent mannner (Chen et al, 2003; Yu et al, 2007; Yu et al, 2010).
R-HSA-8848584 Wax and plasmalogen biosynthesis Waxes are esters of long chain fatty acids and long chain fatty alcohols that play an important role in protecting the skin surface from drying and abrasion (Cheng & Russell 2004a,b). Plasmalogens are an abundant subclass of phospholipids. While their functions are not well understood, defects in their metabolism are associated with serious human disease (de Vet et al. 1999; Nagan and Zoeller 2001). The biosynthesis of these two classes of molecules both start with the reduction of palmitoyl-CoA (PALM-CoA) to hexadecan-1-ol (HXOL) so it is convenient to group them here.
R-HSA-9640463 Wax biosynthesis Waxes are esters of long chain fatty acids and long chain fatty alcohols that play an important role in protecting the skin surface from drying and abrasion. Enzymes that catalyze two reactions of wax biosynthesis have been characterized in humans. FAR1 and FAR2 catalyze the reduction of fatty acids to fatty alcohols in the peroxisome and AWAT1 and AWAT2 catalyze the reaction of fatty alcohols and acyl-CoA in the cytosol to form wax esters. The existence of a transport process, otherwise uncharacterized, to move fatty alcohols from the peroxisome to the cytosol is inferred from the observation that cultured cells that do not normally synthesize waxes can be induced to do so by co-transfection with DNA constructs encoding FAR and AWAT enzymes (Cheng & Russell 2004a,b).
R-HSA-5545619 XAV939 stabilizes AXIN XAV939 binds to the catalytic sites of tankyrase 1 and 2 and inhibits the ADP-ribosylation of AXIN1 and 2. Treatment of cells with XAV939 significantly increases the protein, but not the mRNA levels of AXIN1 and 2 and supports a strong increase in the level of GSK3beta-AXIN complexes. These cells also show increased phosphorylation of beta-catenin, decreased beta-catenin protein levels and a corresponding decrease in beta-catenin dependent transcription. Treatment of DLD-1 cells with XAV939 has also been shown to inhibit proliferation (Huang et al, 2009). XAV939 has not been tested in a clinical setting.
R-HSA-381038 XBP1(S) activates chaperone genes Xbp-1 (S) binds the sequence CCACG in ER Stress Responsive Elements (ERSE, consensus sequence CCAAT (N)9 CCACG) located upstream from many genes. The ubiquitous transcription factor NF-Y, a heterotrimer, binds the CCAAT portion of the ERSE and together the IRE1-alpha: NF-Y complex activates transcription of a set of chaperone genes including DNAJB9, EDEM, RAMP4, p58IPK, and others. This results in an increase in protein folding activity in the ER.
R-HSA-211981 Xenobiotics Of the 50 microsomal CYPs, 15 act on xenobiotics. They all possess wide substrate specificity to cater for most foreign compounds that find their way into the body.
R-HSA-2032785 YAP1- and WWTR1 (TAZ)-stimulated gene expression YAP1 and WWTR1 (TAZ) are transcriptional co-activators, both homologues of the Drosophila Yorkie protein. They both interact with members of the TEAD family of transcription factors, and WWTR1 interacts as well with TBX5 and RUNX2, to promote gene expression. Their transcriptional targets include genes critical to regulation of cell proliferation and apoptosis. Their subcellular location is regulated by the Hippo signaling cascade: phosphorylation mediated by this cascade leads to the cytosolic sequestration of both proteins (Murakami et al. 2005; Oh and Irvine 2010).
R-HSA-9820865 Z-decay: degradation of maternal mRNAs by zygotically expressed factors Maternal transcripts accumulate in the oocyte during oogenesis. Subsets of maternal transcripts are degraded during later development of the unfertilized oocyte and after fertilization of the oocyte. Zygotic decay (Z-decay) refers to the degradation of maternal transcripts by factors expressed by the zygotic genome after fertilization. In the zygote the YAP1:TEAD4 complex activates expression of TUT4 and TUT7 which then uridylate the 3' ends of specific, partially deadenylated maternal transcripts (inferred from mouse zygotes in Sha et al. 2020). The terminal uridylate residues recruit PABPN1 which recruits the 3'-5' ribonuclease DIS3L2 to degrade the mRNA (inferred from mouse homologs in Zhao et al. 2022). Absence of TUT4, TUT7, or PABPN1 results in altered mRNA abundances (inferred from mouse zygotes in Morgan et al. 2017, Sha et al. 2020, Zhao et al. 2022) and infertility (Morgan et al. 2017, Zhao et al. 2022). BTG4 expressed in oocytes and present in zygotes also plays a role in Z-decay possibly by recruiting the CCR4-NOT complex to deadenylate mRNAs prior to uridylation (inferred from mouse zygotes in Sha et al. 2020). Similar patterns of expression and mRNA decay are observed in human and mouse zygotes (Sha et al. 2020).
R-HSA-1606322 ZBP1(DAI) mediated induction of type I IFNs Z-DNA-binding protein-1 (ZBP1), also known as, DNA-dependent activator of IFN-regulatory factors (DAI) was reported to initiate innate immune responses in murine L929 cells upon stimulation by multiple types of exogenously added DNA (Takaoka A et al 2007). Human cytomegalovirus (HCMV) was shown to stimulate ZBP1-mediated induction of IRF3 in human foreskin (DeFilippis VR et al 2010). ZBP1 was also implicated in activation of NF-kappaB pathways in human embryonic kidney HEK293T cells (Kaiser WJ et al 2008, Rebsamen M et al 2009). However, the role and importance ofZBP1 as dsDNA sensor remain controversial, since knocking down ZBP1 expression in other human or murine cell types by siRNA had very little effect on cellular responses to cytosolic DNA, suggesting the presence of alternative pathway (Wang ZC et al 2008, Lippmann J et al 2008). Tissue-specific expression of human ZBP1 also suggests that ZBP1 may function in cell-type specific way (Rothenburg S et al 2002).
R-HSA-435368 Zinc efflux and compartmentalization by the SLC30 family The human SLC30 gene family of solute carriers is thought to participate in the homeostasis of zinc ions and facilitate zinc transport into specialized compartments of the cell such as endosomes, golgi network and synaptic vesicles. There are 10 members of this family, named ZnT1-10. ZnT4, ZnT9 and ZnT10 have no function determined as of yet (Palmiter RD and Huang L, 2004).
R-HSA-442380 Zinc influx into cells by the SLC39 gene family The SLC39 gene family encode zinc transporters belonging to the ZIP (Zrt-, Irt-like proteins) family of metal ion transporters. All ZIPs transport metal ions into the cytoplasm of cells, be it across cellular membranes or from intracellular compartments. To date, there are 14 human SLC39 genes that encode the zinc transporters hZIP1-14. There are 9 members which belong to a subfamily of the ZIPs called the LZTs (LIV-1 subfamily of ZIP zinc transporters) (Taylor KM and Nicholson RI, 2003). Of these 14 proteins, four (hZIP9, 11, 12 and 13) have no function determined yet (Eide DJ, 2004).
R-HSA-435354 Zinc transporters Zinc is an essential element for all organisms because it serves as a catalytic or structural cofactor for many different proteins. Cellular zinc homoeostasis is co-ordinated through Zn2+-specific transporters which are members of two distinct gene families. Members of the SLC39 gene family (ZRTL-like import proteins1-14, ZIP1-14) are responsible for Zn2+ import into the cytoplasm, either across the plasma membrane or out of intracellular organelles. In contrast, members of the SLC30 gene family (zinc transporters 1-10, ZnT1-10) export Zn2+ from the cytoplasm, either across the plasma membrane into the extracellular space or into intracellular organelles (Murakami M and Hirano T, 2008; Devirgiliis C et al, 2007; Eide DJ, 2006).
R-HSA-9819196 Zygotic genome activation (ZGA) After fertilization the maternal and paternal pronuclei undergo major changes in epigenetic modifications, including demethylation of DNA and changes in methylation and acetylation of histones. At this 1-cell stage in mouse zygotes and possibly in human zygotes (Asami et al. 2022), a minor wave of expression from both the female and male genomes occurs, the minor zygotic genome activation (ZGA, also known as embryonic genome activation, EGA) (reviewed in Eckersley-Maslin et al. 2018, Schulz and Harrison 2019, Wu and Vastenhouw 2020, Aoki 2022).
Among the first loci to be transcribed is the DUX4 array of double-homeobox transcription factors. (DUX4 appears to be homologous in structure and function with Dux of mice.) DUX4 binds the promoters of ZGA-expressed genes such as ZSCAN4, DUXA, DUXB, LEUTX, and KDM4E and interacts with the Mediator complex to activate transcription (Vuoristo et al. 2022, reviewed in Kobayashi and Tachibana 2021).
DUX4 also binds long terminal repeats (LTRs) of thousands of endogenous retroelements, notably the HERVL family of retroelements, and activates bidirectional transcription that can initiate expression of adjacent genes (reviewed in Fu et al. 2019, Low et al. 2021). Interestingly, this transcription of endogenous retroviruses evidently results in production of retrovirus-like particles in the plasma and tissues of human embryos (Mondal and Hofschneider 1982).
DUX4 binds HSATII pericentric satellite repeats (Young et al. 2013, Hendrickson et al. 2017) and initiates bidirectional transcription (Hendrickson et al. 2017, Shadle et al. 2019). The transcripts appear to be required for subsequent formation of chromocenters, large multichromosome conglomerations of heterochromatin (Probst et al. 2010).
The minor ZGA is followed by the major ZGA at the 2-cell stage in mice and the 8-cell stage in humans. During the major ZGA, chromatin reverts to a more usual configuration, with broad regions of histone H3 trimethyllysine-4 across genes converted to narrow peaks near transcription start sites (reviewed in Eckersley-Maslin et al. 2018, Schulz and Harrison 2019, Wu and Vastenhouw 2020, Aoki 2022). Histones H3.1 and H3.2 are also added at this time (Ishiuchi et al. 2021).
R-HSA-450302 activated TAK1 mediates p38 MAPK activation p38 mitogen-activated protein kinase (MAPK) belongs to a highly conserved family of serine/threonine protein kinases.
The p38 MAPK-dependent signaling cascade is activated by pro-inflammatory or stressful stimuli such as ultraviolet radiation, oxidative injury, heat shock, cytokines, and other pro-inflammatory stimuli. p38 MAPK exists as four isoforms (alpha, beta, gamma, and delta). Of these, p38alpha and p38beta are ubiquitously expressed while p38gamma and p38delta are differentially expressed depending on tissue type. Each isoform is activated by upstream kinases including MAP kinase kinases (MKK) 3, 4, and 6, which in turn are phosphorylated by activated TAK1 at the typical Ser-Xaa-Ala-Xaa-Thr motif in their activation loops.
Once p38 MAPK is phosphorylated it activates numerous downstream substrates, including MAPK-activated protein kinase-2 and 3 (MAPKAPK-2 or 3) and mitogen and stress-activated kinase-1/2 (MSK1/2). MAPKAPK-2/3 and MSK1/2 function to phosphorylate heat shock protein 27 (HSP27) and cAMP-response element binding protein transcriptional factor, respectively. Other transcription factors, including activating transcription factor 2, Elk, CHOP/GADD153, and myocyte enhancer factor 2, are known to be regulated by these kinases.
R-HSA-9717316 alectinib-resistant ALK mutants Alectinib is a second generation tyrosine kinase inhibitor that is approved for use in ALK positive non-small cell lung cancers (NSCLCs). Alectinib is effective against a number of ALK mutants that arise after treatment with crizotinib, however resistance to alectinib has also been reported. This pathway describes ALK mutants that are resistant to inhibition with alectinib (reviewed in Lovly and Pao, 2012; Lin et al, 2017; Della Corte et al, 2018; Hallberg and Palmer, 2016).
R-HSA-2046104 alpha-linolenic (omega3) and linoleic (omega6) acid metabolism There are two major classes of polyunsaturated fatty acids (PUFAs): the omega-3 (n-3) and the omega-6 (n-6) fatty acids, where the number corresponds to the position of the first double bond proximate to the methyl end of the fatty acid. Omega-3 and omega-6 fatty acids are considered essential fatty acids. Humans cannot synthesize them, instead they are supplied through diet. Linoleic acid (LA, 18:2(n-6)), a major component of omega-6 fatty acids and alpha-linolenic acid (ALA, 18:2(n-3)) a major component of omega-3 fatty acids are the two main dietary essential fatty acids (EFAs) in humans. ALA and LA obtained from diet are converted in the body into their longer chain and more unsaturated omega-3 and omega-6 products by a series of desaturation and elongation steps. Metabolism of ALA and LA to their corresponding products is mediated via common enzyme systems. In humans ALA is finally converted to docosahexaenoic acid (DHA, C22:6(n-3)), and LA is converted to docosapentaenoic acid (DPA, C22:5(n-6)). The intermediary omega-3 and omega-6 series fatty acids play a significant role in health and disease by generating potent modulatory molecules for inflammatory responses, including eicosanoids (prostaglandins, and leukotrienes), and cytokines (interleukins) and affecting the gene expression of various bioactive molecules (Kapoor & Huang 2006, Sprecher 2002, Burdge 2006).
R-HSA-2046106 alpha-linolenic acid (ALA) metabolism Alpha-linolenic acid (ALA, 18:3(n-3)) is an omega-3 fatty acid, supplied through diet as it cannot be synthesized by humans. ALA has an important role in human health. It is converted to long chain more unsaturated n-3 fatty acids by a series of alternating desaturation and elongation reactions. Omega-3 products of ALA such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) reduce inflammation and may help lower risk of chronic diseases, such as heart disease and arthritis. All the desaturation and elongation steps occur in the endoplasmic reticulum (ER) except for the final step which requires translocation to peroxisomes for partial beta-oxidation.
The alpha-linolenic acid pathway involves the following steps: 18:3(n-3)--> 18:4(n-3)-->20:4(n-3)-->20:5(n-3)-->22:5(n-3)-->24:5(n-3)-->24:6(n-3)-->22:6(n-3). Two desaturation enzymes are involved in this process: delta-6 desaturase that converts 18:3(n-3) to 18:4(n-3) and 24:5(n-3) to 24:6(n-3) respectively, delta-5 desaturase 20:4(n-3) to 20:5(n-3). (Sprecher 2002).
R-HSA-1307965 betaKlotho-mediated ligand binding FGF21 and FGF19 require betaKlotho for efficient signaling through FGFR1c and FGFR3c. betaKlotho does not interact with 'b' receptor isoforms, and only weakly with FGFR2c. In addition, FGF19, but not FGF21, signals through FGFR4 in a betaKlotho-dependent fashion
R-HSA-9717319 brigatinib-resistant ALK mutants Brigatinib is a second generation tyrosine kinase inhibitor with activity against ALK. This pathway describes ALK mutants that are resistant to inhibition by brigatinib (reviewed in Della Corte et al, 2018; Roskoski, 2013; Lin and Pao, 2017; Hallberg and Palmer, 2013).
R-HSA-418457 cGMP effects Cyclic guanosine monophosphate (cGMP) is an important secondary messenger synthesized by guanylate cyclases. cGMP has effects on phosphodiesterases (PDE), ion-gated channels, and the cGMP-dependent protein kinases (cGK, Protein Kinase G or PKG). It is involved in regulation of several physiological functions including vasodilation, platelet aggregation and neurotransmission. Elevation of intracellular cGMP activates PKG (Haslam et al. 1999) which regulates several intracellular molecules and pathways including the vasodilator-stimulated phosphoprotein (VASP) (Halbrugge et al. 1990) and the ERK pathway (Hood and Granger 1998, Li et al. 2001). cGMP mediates nitric oxide (NO)-induced vascular smooth muscle relaxation (Furchgott and Vanhoutte 1989). Phosphodiesterase 5 (PDE5) hydrolyzes cGMP; the PDE5 inhibitor sildenafil (Viagra) increases intracellular cGMP and thereby can be used as a treatment for erectile dysfunction (Corbin and Francis 1999). The role of the cGMP and PKG in platelet activation was controversial as increases in platelet cGMP levels were observed in response to both platelet agonists (thrombin, ADP or collagen) and inhibitors (NO donors such as sodium nitroprusside), but it is currently accepted that PKG inhibits platelet activation (Haslam et al. 1999). Consistent with this, nitric oxide (NO) donors that inhibit platelet activation enhance intracellular cGMP (Haslam et al. 1999). cGMP also plays an important stimulatory role in GPIb-IX-mediated platelet activation. Platelet responses to cGMP have been proposed to be biphasic, consisting of an early stimulatory response that promotes platelet activation followed by a delayed platelet inhibition that serves to limit the size of platelet aggregates (Li et al 2003).
R-HSA-192869 cRNA Synthesis Synthesis of full length complementary viral RNA (cRNA) requires that vRNA transcription initiates without the help of a host cell methyl RNA cap as a primer (Crow, 2004; Vreede, 2004; Deng, 2006), and that it proceeds to the 5' end of the vRNA template without stuttering on the sub-terminal poly-U sequence. Free viral NP protein appears to play a central role in enabling both of these features of cRNA synthesis, although the molecular details of its role remain unclear (Shapiro, 1988; Medcalf, 1999; Mullin, 2004).
R-HSA-9717323 ceritinib-resistant ALK mutants Ceritinib is a type I TKI that is effective against ALK driven cancers and is approved for treatment of NSCLC. Ceritinib is a second-generation TKI that shows activity against a number of crizotinib-resistant ALK alleles, however, resistance to ceritinib has also been documented. This pathway describes ALK mutants that are resistant to inhibition with ceritinib (reviewed in Lovly and Pao, 2012; Lin et al, 2017; Della Corte et al, 2018).
R-HSA-9702581 crenolanib-resistant FLT3 mutants Crenolanib is a second-generation type I tyrosine kinase inhibitor with activity against FLT3 (reviewed in Daver et al, 2019; Staudt et al, 2018; Larrosa-Garcia and Bauer, 2017). This pathway describes FLT3 mutants that are resistant to crenolanib-mediated inhibition.
R-HSA-9717326 crizotinib-resistant ALK mutants Crizotinib is a type I tyrosine kinase inhibitor that is approved for treatment of ALK-positive non-small cell lung cancer. Crizotinib is also effective against ALCL and IMTs. Development of resistance to crizotinib is not uncommon, however, with patients acquiring secondary mutations or amplifications of the ALK gene that limit the effectiveness of the drug. This pathway describes ALK mutants that are resistant to crizotinib-mediated inhibition (reviewed in Roskoski, 2013; Lin et al, 2017; Della Corte et al, 2018).
R-HSA-203615 eNOS activation eNOS activity is regulated by numerous post-translational modifications including phosphorylation and acylation, which also modulate its interactions with other proteins and its subcellular localization.
In general, following myristoylation and palmitoylation, eNOS localizes to caveolae in the plasma membrane, where in resting cells, it is bound to caveolin and remains inactive. Several agonists that raise intracellular calcium concentrations promote calmodulin binding to eNOS and the dissociation of caveolin from the enzyme, leading to an activated eNOS-calmodulin complex.
Phosphorylation plays a significant role in regulating eNOS activity, especially the phosphorylation of Ser1177, located within the reductase domain, which increases enzyme activity by enhancing reductase activity and calcium sensitivity. In unstimulated, cultured endothelial cells, Ser1177 is rapidly phosphorylated following a variety of stimuli: fluid shear stress, insulin, estrogen, VEGF, or bradykinin. The kinases involved in this process depend upon the stimuli applied. For instance, shear stress phosphorylates Ser1177 by activating Akt and PKA; insulin activates both Akt and the AMP-activated protein kinase (AMPK); estrogen and VEGF mainly phosphorylate eNOS via Akt; whereas the bradykinin-induced phosphorylation of Ser1177 is mediated by CaMKII. When Ser1177 is phosphorylated, NO production is increased several-fold above basal levels.
The phosphorylation of a threonine residue (Thr 495), located in the CaM binding domain, is associated with a decrease in eNOS activity. When this residue is dephosphorylated, substantially more CaM binds to eNOS and elevates enzyme activity. Stimuli associated with dephosphorylation of Thr495 (e.g., bradykinin, histamine, and Ca2+ ionophores) also increase Ca2+ levels resulting in the phosphorylation of Ser1177.
Additional phosphorylation sites, such as Ser114 and Ser633, and tyrosine phosphorylation have all been detected, but their functional relevance remains unclear. It is speculated that the tyrosine phosphorylation of eNOS is unlikely to affect enzyme activity directly, but more likely to impact the protein-protein interactions with associated scaffolding and regulatory proteins. R-HSA-9702590 gilteritinib-resistant FLT3 mutants Gilteritinib is a second-generation type I tyrosine kinase inhibitor with activity against FLT3 (reviewed in Daver et al, 2019; Hassanein et l, 2016; Lim et al, 2017; Luxkin et al, 2017). This pathway describes FLT3 mutants that are resistant to inhibition by gilteritinib. R-HSA-9702596 lestaurtinib-resistant FLT3 mutants Lestaurtinib is a first-generation, type I tyrosine kinase inhibitor with activity against a range of receptor tyrosine kinases including FLT3 (reviewed in Larrosa-Garcia and Baer, 2017; Staudt et al, 2018; Daver et al, 2019). This pathway describes FLT3 mutants that are resistant to lestaurtinib-mediated inhibition. R-HSA-9702998 linifanib-resistant FLT3 mutants Linifanib is a type I tyrosine kinase inhibitor with activity against a broad range of receptor tyrosine kinases including FLT3. This pathway describes FLT3 mutants that are resistant to inhibition by linifanib (Hernandez-Davies et al, 2011; Nguyen et al, 2017). R-HSA-9717329 lorlatinib-resistant ALK mutants Lorlatinib is a third generation tyrosine kinase inhibitor with effectiveness against ALK and ROS rearranged cancers. This pathway describes ALK mutants that are resistant to inhibition by lorlatinib (Yoda et al, 2018; Takahashi et al, 2020; reviewed in Della Corte et al, 2018; Lin et al, 2017; Facchinietti et al, 2016). R-HSA-72187 mRNA 3'-end processing The 3' ends of eukaryotic mRNAs are generated by posttranscriptional processing of an extended primary transcript. For almost all RNAs, 3'-end processing consists of two steps: (i) the mRNA is first cleaved at a particular phosphodiester bond downstream of the coding sequence, (ii) the upstream fragment then receives a poly(A) tail of approximately 250 adenylate residues, whereas the downstream fragment is degraded. The two partial reactions are coupled so that reaction intermediates are usually undetectable. While 3' processing can be studied as an isolated event in vitro, it appears to be connected to transcription, splicing, and transcription termination in vivo.
The only known exception to the rule of cleavage followed by polyadenylation are the major histone mRNAs, which are cleaved but not polyadenylated.
R-HSA-72086 mRNA Capping The 5'-ends of all eukaryotic pre-mRNAs studied thus far are converted to cap structures. The cap is thought to influence splicing of the first intron, and is bound by 'cap-binding' proteins, CBP80 and CBP20, in the nucleus. The cap is important for translation initiation, and it also interacts with the poly(A)terminus, via proteins, resulting in circularization of the mRNA to facilitate multiple rounds of translation. The cap is also important for mRNA stability, protecting it from 5' to 3' nucleases, and is required for mRNA export to the cytoplasm.
The capping reaction usually occurs very rapidly on nascent transcripts; after the synthesis of only a few nucleotides by RNA polymerase II. The capping reaction involves the conversion of the 5'-end of the nascent transcript from a triphosphate to a diphosphate by a RNA 5'-triphosphatase, followed by the addition of a guanosine monophosphate by the mRNA guanylyltransferase, to form a 5'-5'-triphosphate linkage. This cap is then methylated by 2'-O-methyltransferases.
R-HSA-75072 mRNA Editing After transcription, some RNA molecules are altered to contain bases not encoded in the genome. Most often this involves the editing or modification of one base to another, but in some organisms can involve the insertion or deletion of a base. Such editing events alter the coding properties of mRNA.
RNA editing can be generally defined as the co- or post transcriptional modification of the primary sequence of RNA from that encoded in the genome through nucleotide deletion, insertion, or base modification mechanisms.
There are two pathways of RNA editing: the substitution/conversion pathway and the insertion/deletion pathway. The insertion/deletion editing occurs in protozoans like Trypanosoma, Leishmania; in slime molds like Physarum spp., and in some viral categories like paramyxoviruses, Ebola virus etc. To date, the substitution/conversion pathway has been observed in human along with other mammals, Drosophila, and some plants. The RNA editing processes are known to create diversity in proteins involved in various pathways like lipid transport, metabolism etc. and may act as potential targets for therapeutic intervention (Smith et al., 1997).
The reaction mechanisms of cytidine and adenosine deaminases is represented below. In both these reactions, NH3 is presumed to be released:
R-HSA-75064 mRNA Editing: A to I Conversion In humans the deamination of adenosines to inosines is the most common editing event. It is particularly prevalent in the brain, where it leads to amino acid changes that affect the conductance of several ion channels. Inosines are recognized by the translation machinery as if they were guanosines.
ADARs (Adenosine Deaminases Acting on RNA) modify pre-mRNA, acting as single peptides and recognize structural determinants in the RNA. To date 3 members of this deaminase family are known: ADAR 1, ADAR 2, and ADAR 3 that share a common modular domain structure. ADAR 1 and 2 contain a catalytic deaminase domain, a double-stranded RNA binding domain and exhibit RNA editing activity. ADAR1 activity is found in various mammalian tissues with the highest concentration in brain.
An increasing number of mammalian genes have been found to undergo deamination by ADARs. Deamination by editing in pre-mRNAs encoding subunits of ionotropic glutamate receptors (GluRs) is another well studied example. An editing event at the Q/R site of the GluR2 (GluRB) subunit of AMPA receptors converts a Gln codon CAG to an Arg codon CIG rendering the heteromeric receptor impermeable to Ca 2+ ions. Another example is the editing of 5-HT2C subtype serotonin receptor mRNA resulting in receptor isoforms with reduced G-protein coupling efficiency (reviewed by Gerber and Keller, 2001).
In mice, the editosomes with ADAR proteins require some cis-acting elements like an intronic 'editing-site complementary sequence (ECS)'. Although evolutionarily conserved, the actual role of ECS is not yet elucidated in humans. The editing complex can be generally represented as:
R-HSA-72200 mRNA Editing: C to U Conversion The best characterized case of C to U editing is in the intestinal apolipoprotein B transcript, where the editing event creates a premature translation stop codon and consequently leads to a shorter form of the protein. In the liver, C to U editing is important in the expression of specific isoforms of the apolipoprotein B enzyme. ApoB mRNA editing is a posttranscriptional, nuclear process that can be initiated after splicing, at the time of polyadenylation and is completed by the time pre-mRNA matures fully (reviewed by Blanc and Davidson, 2003).
This editing event is a simple hydrolytic cytidine deamination to uridine, and is carried out by the Apobec-1 enzyme, along with the Apobec-1 complementing factor, ACF. The editing of apo-B mRNA involves the site-specific deamination of (C6666 to U), which converts codon 2153 from a glutamine codon, CAA, to a premature stop codon, UAA. As ACF is distributed in a variety of tissues, and these genes contain multiple family members, it is possible that editing events in additional targets will be found.
The cis-acting regulatory elements for C to U editing include: 22 nt editing site within ApoB mRNA, 5' tripartite motif with an enhancer element adjacent to the target cytidine, a spacer element and mooring sequence both 3' to the cytidine (reviewed by Smith et al., 1997).
R-HSA-72172 mRNA Splicing The process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing. Most of the mRNA is spliced by the major pathway, involving the U1, U2, U4, U5 and U6 snRNPs. A minor fraction, about 1 %, of the mRNAs are spliced via the U12 dependent pathway.
R-HSA-72163 mRNA Splicing - Major Pathway Eukaryotic genes are transcribed to yield pre-mRNAs that are processed to add methyl guanosine cap structures and polyadenylate tails and to splice together segments of a pre-mRNA termed exons, thereby removing segments termed introns. More than 90% of human genes contain introns, with an average of 4.0 introns per gene and 3413 nucleotides per intron compared with 5.0 exons per gene and 50.9 nucleotides per exon (Deutsch and Long 1999). (Notable exceptions are the histone genes, which are intronless.)
Pre-mRNA splicing is performed by a large ribonucleoprotein complex, the spliceosome, which contains 5 small nuclear RNAs (snRNAs) and more than 150 proteins (reviewed in Will and Luhrmann 2011, Kastner et al. 2019, Yan et al. 2019, Fica et al. 2020, Wan et al. 2020, Wilkinson et al. 2020). The catalyst in the spliceosome comprises magnesium ions coordinated by the U6 snRNA that catalyze transesterification reactions between hydroxyl groups and phosphate groups from the pre-mRNA. The role of the U6 snRNA demonstrates that the spliceosome is a ribozyme hints at the origin of the spliceosome as a self-splicing group II intron.
The spliceosome is initially assembled cotranscriptionally on the pre-mRNA as the Spliceosomal E (Early) complex and then remodelled sequentially by association and dissociation of proteins and snRNAs to catalyze of the two reactions of splicing. First, a nucleophilic attack by the 2' hydroxyl group of a conserved adenine residue, the branch point, within the intron on the phosphate group of the 5' residue of the intron yields a lariat (looped) structure in the intron joined to the downstream (3') exon and a free upstream exon with a 3' hydroxyl group. Second, a nucleophilic attack by the 3' hydroxyl group of the upstream exon on the phosphate of the 5' residue of the downstream exon yields a spliced mRNA containing the upstream exon ligated to the downstream exon and a free intron containing a lariat structure.
The Spliceosomal E complex contains the U1 snRNP bound to the 5' splice site, SF1 bound to the branch point, and the U2AF complex bound to the polypyrimidine tract of the intron and the 3' splice site of the pre-mRNA (Zhuang and Weiner 1986, Hong et al. 1997, Das et al. 2000, Hartmuth et al. 2002, Rappsilber et al. 2002, Hegele et al. 2012, Makarov et al. 2012, Crisci et al. 2015, Kondo et al. 2015, Tan et al. 2016). SF1 and U2AF are displaced on the pre-mRNA and the U2 snRNP binds the branch region to yield the Spliceosomal A complex (Wu and Manley 1989, Fleckner et al. 1997, Neubauer et al. 1998, Hartmuth et al. 2002, Rappsilber et al. 2002, Xu et al. 2004, Behzadnia et al. 2007, Shen et al. 2008, Chen et al. 2017, Zhang et al. 2020). The U4/U6.U5 tri-snRNP, containing the U4 snRNA base-paired with the U6 snRNA plus the U5 snRNP and accessory proteins, binds the Spliceosomal A complex to form the Spliceosomal Pre-B complex (Hausner et al. 1990, Kataoka and Dreyfuss 2004, Chi et al. 2013, Mohlmann et al. 2014, Boesler et al. 2016, Zhan et al. 2018, Charenton et al. 2019, Kastner et al. 2019, Townsend et al. 2020). The U1 snRNP is replaced at the 5' splice site by the U6 snRNA and the spliceosome is remodelled to yield the Spliceosomal B complex (Ismaïli et al. 2001, Deckert et al. 2006, Bessonov et al. 2008, Wolf et al. 2009, Bessonov et al. 2010, Schmidt et al. 2014, Boesler et al. 2016, Bertram et al. 2017, Zhang et al. 2018, Kastner et al. 2019). The Spliceosomal B complex is activated to form the Spliceosomal Bact complex by dissociation of the U4 snRNP and Lsm proteins from the U6 snRNA, freeing the U6 snRNA to form the active site of the spliceosome (Lamond et al. 1988, Laggerbauer et al. 1998, Ajuh et al. 2000, Bessonov et al. 2010, Agafonov et al. 2011, Haselbach et al. 2018, Zhang et al. 2018, Kastner et al. 2019, Busetto et al. 2020). Dissociation of the SF3A and SF3B subcomplexes of the U2 snRNP allows the intron branch point to dock near the 5' splice site, forming the B* Spliceosomal complex. Reaction of the branch point at the 5' splice site, yields the Spliceosomal C complex (Jurica et al. 2002, Makarov et al. 2002, Rappsilber et al. 2002, Reichert et al. 2002, Kataoka and Dreyfuss 2004, Bessonov et al. 2010, Gencheva et al. 2010, Agafonov et al. 2011, Alexandrov et al. 2012, Barbosa et al. 2012, Steckelberg et al. 2012, Schmidt et al. 2014, Zhan et al. 2018, Kastner et al. 2019, Busetto et al. 2020). The branch point is rotated to allow the 3' splice site to enter the active site, yielding the Spliceosomal C* complex (Ortlepp et al. 1998, Zhou and Reed 1998, Jurica et al. 2002, Makarov et al. 2002, Rappsilber et al. 2002, Ilagan et al. 2013, Bertram et al. 2017, Zhang et al. 2017, Kastner et al. 2019). Reaction of the 3' hydroxyl group of the upstream exon at the 3' splice site yields the Spliceosomal P (postcatalytic) complex (Zhou et al. 2000, Kataoka and Dreyfuss 2004, Tange et al. 2005, Zhang and Krainer 2007, Chi et al. 2013, Ilagan et al. 2013, Bertram et al. 2017, Zhang et al. 2017, Fica et al. 2019, Zhang et al. 2019). The Spliceosomal P complex then dissociates to yield an mRNP containing the spliced mRNA and associated proteins, including the exon junction complex (EJC) (Ohno and Shimura 1996, Merz et al. 2007, Yoshimoto et al. 2009, Zanini et al. 2017, Felisberto-Rodrigues et al. 2019, Zhang et al. 2019, EJC reviewed in Schlautmann and Gehring 2020), and the Intron Lariat Spliceosome (ILS), which contains the intron lariat. The ILS is then disassembled to free its components for further splicing reactions and the intron lariat is degraded (Wen et al. 2008, Yoshimoto et al. 2009, Yoshimoto et al. 2014, Zhang et al. 2019, Studer et al. 2020).
R-HSA-72165 mRNA Splicing - Minor Pathway The splicing of a subset of pre-mRNA introns occurs by a second pathway, designated the AT-AC or U12-dependent splicing pathway. AT-AC introns have highly conserved, non-canonical splice sites that are removed by the AT-AC spliceosome, which contains distinct snRNAs (U11, U12, U4atac, U6atac) that are structurally and functionally analogous to the major spliceosome. U5 snRNA as well as many of the protein factors appear to be conserved between the two spliceosomes.
R-HSA-429958 mRNA decay by 3' to 5' exoribonuclease The degradation of mRNA from 3' to 5' occurs in two steps. First, the exosome exoribonuclease complex binds the 3' end of the oligoadenylated mRNA and hydrolyzes it from 3' to 5', yielding ribonucleotides having 5'-monophosphates, until a capped oligoribonucleotide remains. Second, the scavenging decapping enzyme DCPS hydrolyzes the 7-methylguanosine cap.
R-HSA-430039 mRNA decay by 5' to 3' exoribonuclease Degradation of mRNA from 5' to 3' occurs in three steps. First, the mRNA is bound at its 3' end by the Lsm1-7 complex. The bound Lsm1-7 may prevent nucleases from accessing the 3' end. Second, the 7-methylguanosine cap of the mRNA is hydrolyzed by the DCP1-DCP2 complex. Third, the 5' end of the decapped mRNA is attacked by the XRN1 exoribonuclease which digests the remainder of the mRNA from 5' to 3'. These processes may be physically connected by PATL1, the homolog of yeast Pat1, which stably binds the Lsm1-7 complex and interacts with the DCP1-DCP2 decapping complex and the Ccr4-NOT deadenylation complex (Ozgur et al. 2010).
R-HSA-166208 mTORC1-mediated signalling mTORC1 integrates four major signals – growth factors, energy status, oxygen and amino acids – to regulate many processes that are involved in the promotion of cell growth. Growth factors stimulate mTORC1 through the activation of the canonical insulin and Ras signaling pathways. The energy status of the cell is signaled to mTORC1 through AMP-activated protein kinase (AMPK), a key sensor of intracellular energy status (Hardie 2007). Energy depletion (low ATP:ADP ratio) activates AMPK which phosphorylates TSC2, increasing its GAP activity towards Rheb which reduces mTORC1 activation (Inoki et al. 2003). AMPK can reduce mTORC1 activity by directly phosphorylating Raptor (Gwinn et al. 2008). Amino acids positively regulate mTORC1 (reviewed by Guertin & Sabatini 2007). In the presence of amino acids, Rag proteins bind Raptor to promote the relocalization of mTORC1 from the cytoplasm to lysosomal membranes (Puertollano 2014) where it is activated by Rheb (Saucedo et al. 2003, Stocker et al. 2003). Translocation of mTOR to the lysosome requires active Rag GTPases and a complex known as Ragulator, a pentameric protein complex that anchors the Rag GTPases to lysosomes (Sancak et al. 2008, 2010, Bar-Peled et al. 2012). Rag proteins function as heterodimers, consisting of GTP-bound RagA or RagB complexed with GDP-bound RagC or RagD. Amino acids may trigger the GTP loading of RagA/B, thereby promoting binding to raptor and assembly of an activated mTORC1 complex, though a recent study suggested that the activation of mTORC1 is not dependent on Rag GTP charging (Oshiro et al. 2014). The activity of Rheb is regulated by a complex consisting of tuberous sclerosis complex 1 (TSC1), TSC2, and TBC1 domain family member 7 (TBC1D7) (Huang et al. 2008, Dibble et al. 2012). This complex localizes to lysosomes and functions as a GTPase-activating protein (GAP) that inhibits the activity of Rheb (Menon et al. 2014, Demetriades et al. 2014). In the presence of growth factors or insulin, TSC releases its inhibitory activity on Rheb, thus allowing the activation of mTORC1.
R-HSA-9702600 midostaurin-resistant FLT3 mutants Midostaurin, also known as PKC412, is a type I tyrosine kinase inhibitor with activity against FLT3 (reviewed in Kazi and Roonstrand, 2019; Luskin and DeAngelo, 2017). This pathway describes FTL3 mutants that are resistant to inhibition by midostaurin.
R-HSA-77286 mitochondrial fatty acid beta-oxidation of saturated fatty acids Once fatty acids have been imported into the mitochondrial matrix by the carnitine acyltransferases, the beta-oxidation spiral begins. Each turn of this spiral concludes with the repetitive removal of two carbon units from the fatty acyl chain. beta-oxidation of saturated fatty acids (fatty acids with even numbered carbon chains and no double bonds) involves four different enzymatic steps: oxidation, hydration, a second oxidation, and a concluding thiolysis step, resulting in the two-carbon acetyl-CoA and a newly CoA primed acyl-CoA for the next turn of the spiral.
R-HSA-77288 mitochondrial fatty acid beta-oxidation of unsaturated fatty acids The complete beta-oxidation spiral produces and consumes intermediates with a trans configuration. Mitochondrial beta-oxidation of unsaturated fatty acids leads to intermediates not compatible with the four enzymatic steps responsible for the beta-oxidation of saturated fatty acids. Unsaturated fatty acids that have bonds in the cis configuration require three separate enzymatic steps to prepare these molecules for the beta-oxidation pathway. The further processing of these intermediates requires additional enzymes, depending on the position of the double bonds in the original fatty acids. Described here is the beta-oxidation of linoleoyl-CoA.
R-HSA-372708 p130Cas linkage to MAPK signaling for integrins Integrin signaling is linked to the MAP kinase pathway by recruiting p130cas and Crk to the FAK/Src activation complex.
R-HSA-171007 p38MAPK events NGF induces sustained activation of p38, a member of the MAPK family (Morooka T, Nishida E, 1998). Both p38 and the ERKs appear to be involved in neurite outgrowth and differentiation caused by NGF in PC12 cells. As a matter of fact, PC12 cell differentiation appears to involve activation of both ERK/MAPK and p38. Both ERK/MAPK and p38 pathways contribute to the phosphorylation of the transcription factor CREB and the activation of immediate-early genes (Xing J, 1998). p38 activation by NGF may occur by at least two mechanisms, involving SRC or MEK kinases.
R-HSA-69563 p53-Dependent G1 DNA Damage Response Most of the damage-induced modifications of p53 are dependent on the ATM kinase. The first link between ATM and p53 was predicted based on the earlier studies that showed that AT cells exhibit a reduced and delayed induction of p53 following exposure to IR (Kastan et al, 1992 and Khanna and Lavin, 1993).
Under normal conditions, p53 is a short-lived protein. The MDM2 protein, usually interacts with p53 (Haupt et al, 1997 and Kubbutat et al, 1997), and by virtue of its E3 ubiquitin ligase activity, shuttles p53 to the cytoplasm and mediates its degradation by the ubiquitin-proteasome machinery. Upon detection of DNA damage, the ATM kinase mediates the phosphorylation of the Mdm2 protein to block its interaction with p53. Also, phosphorylation of p53 at multiple loci, by the ATM kinase and by other kinases activated by the ATM kinase, stabilizes and activates the p53 protein.
The p53 protein activates the transcription of cyclin-dependent kinase inhibitor, p21. p21 inactivates the CyclinE:Cdk2 complexes, and prevent entry of the cell into S phase, leading to G1 arrest. Under severe conditions, the cell may undergo apoptosis. R-HSA-69580 p53-Dependent G1/S DNA damage checkpoint The arrest at G1/S checkpoint is mediated by the action of a widely known tumor suppressor protein, p53. Loss of p53 functions, as a result of mutations in cancer prevent the G1/S checkpoint (Kuerbitz et al, 1992). P53 is rapidly induced in response to damaged DNA. A number of kinases, phosphatases, histone acetylases and ubiquitin-conjugating enzymes regulate the stability as well as transcriptional activity of p53 after DNA damage. R-HSA-69610 p53-Independent DNA Damage Response In response to DNA damage due to exposure to ultraviolet light or to ionizing radiation, Cdc25A is phosphorylated by Chk1 or Chk2. The phosphorylation of Cdc25A at ser-123, in response to DNA damage from ionizing radiation is a signal for ubiquitination and subsequent degradation of Cdc25A. The destruction of Cdc25A prevents the normal G1/S transition. Cdc25A is required for the activation of the Cyclin E:Cdk2 complexes via dephosphorylation.
Chk1 is activated in response to DNA damage due to uv light. However, the phosphorylation occurs at a different site. R-HSA-69613 p53-Independent G1/S DNA damage checkpoint The G1 arrest induced by DNA damage has been ascribed to the transcription factor and tumor suppressor protein p53. To be effective within minutes after DNA damage, induction of the G1 block should exploit transcription and protein synthesis independent mechanisms.
Upon exposure to ultraviolet light (UV) or ionizing radiation (IR), the abundance and activity of a protein, Cdc25A, rapidly decreases; this DNA damage response is not dependent on p53. The rapid destruction of Cdc25A phosphatase prevents entry of a cell into S-phase, by maintaining the CyclinE:Cdk2 complexes in their T14Y15 phosphorylated form.
R-HSA-193704 p75 NTR receptor-mediated signalling Besides signalling through the tyrosine kinase receptors TRK A, B, and C, the mature neurotrophins NGF, BDNF, and NT3/4 signal through their common receptor p75NTR. NGF binding to p75NTR activates a number of downstream signalling events controlling survival, death, proliferation, and axonogenesis, according to the cellular context. p75NTR is devoid of enzymatic activity, and signals by recruiting other proteins to its own intracellular domain. p75 interacting proteins include NRIF, TRAF2, 4, and 6, NRAGE, necdin, SC1, NADE, RhoA, Rac, ARMS, RIP2, FAP and PLAIDD. Here we annotate only the proteins for which a clear involvement in p75NTR signalling was demonstrated.
A peculiarity of p75NTR is the ability to bind the pro-neurotrophins proNGF and proBDNF. Proneurotrophins do not associate with TRK receptors, whereas they efficiently signal cell death by apoptosis through p75NTR. The biological action of neurotrophins is thus regulated by proteolytic cleavage, with proforms preferentially activating p75NTR, mediating apoptosis, and mature forms activating TRK receptors, to promote survival. Moreover, the two receptors are utilised to differentially modulate neuronal plasticity. For instance, proBDNF-p75NTR signalling facilitates LTD, long term depression, in the hippocampus (Woo NH, et al, 2005), while BDNF-TRKB signalling promotes LTP (long term potentiation). Many biological observations indicate a functional interaction between p75NTR and TRKA signaling pathways.
R-HSA-193670 p75NTR negatively regulates cell cycle via SC1 SC1 (Schwann Cell factor 1; also called PR domain zinc finger protein 4, PRDM4) interacts with an NGF:p75NTR complex and signals cell cycle arrest by regulating the levels of cyclin E.
R-HSA-209543 p75NTR recruits signalling complexes NF-kB activation involves recruitment at the cell membrane of several proteins such as RIP2, MYD88, IRAK1, TRAF6, p62 and atypical PKC by the NGF:p75NTR complex.
R-HSA-193697 p75NTR regulates axonogenesis p75NTR modulates axonal growth by regulating the activity of small GTPases like RHOA and RHOB, that control the state of actin polymerization. The best studied is RHOA. In its active, GTP-bound form, RHOA rigidifies the actin cytoskeleton, thereby inhibiting axonal elongation and causing growth cone collapse. Depending on the ligand that binds to it, p75NTR can either promote or inhibit axonal growth, Neurotrophin binding leads to inhibition of RHOA activity and axonal growth. Axonal growth inhibition is caused by myelin molecules named MDGIs (myelin-derived growth inhibitors), such as NOGO, MAG, OMGP. MDGIs bind to a complex made up of p75NTR and the NOGO receptor, causing RHOA activation and axonal growth inhibition.
R-HSA-193639 p75NTR signals via NF-kB The NF-kB pathway is an important pro-survival signalling pathway activated by mature NGF, but not BDNF or NT-3, through p75NTR. It is unclear whether TRKA activity also affects NF-kB activation.
R-HSA-9702605 pexidartinib-resistant FLT3 mutants Pexidartinib is a type II tyrosine kinase inhibitor that is active against FLT3, including the quizartinib-resistant gatekeeper mutation F691L. Activating mutations at TKD aspartic acid residue 835 are resistant to pexidartinib-mediated inhibition, however (Smith et al, 2015a, b).
R-HSA-111995 phospho-PLA2 pathway Phospholipase A2 (PLA2) enzymes hydrolyze arachidonic acid (AA) from the sn-2 position of phospholipids. AA is a precursor of eicosanoids, lipid mediators involved in inflammtory responses. PLA2 enzymes function as regulators of phospholipid acyl turnover, either as housekeepers for membrane repair or for the production of imflammatory lipid mediators. There are diverse forms of PLA2 enyzmes including secretory (sPLA2), calcium-independent and cytosolic (cPLA2). The cPLA2 form which mediates arachidonic acid release is annotated here.
R-HSA-9702614 ponatinib-resistant FLT3 mutants Ponatinib is a first generation tyrosine kinase inhibitor with activity against a broad range of receptor tyrosine kinases, including FLT3 (reviewed Pemmeraju et al, 2014; Kazi and Roonstrand, 2019). This pathway describes FLT3 mutants that are resistant to inhibition by ponatinib.
R-HSA-9702620 quizartinib-resistant FLT3 mutants Quizartinib is a type II tyrosine kinase inhibitor that is in phase III clinical trials for treatment of acute myeloid leukemias with FLT3 internal tandem duplications (ITDs). This pathway describes FLT3 mutants that display resistance to quizartinib (reviewed in Kazi and Roonstrand, 2019; Daver et al, 2019).
R-HSA-6793080 rRNA modification in the mitochondrion Five modified nucleotides have been detected in the 12S rRNA: 5-methylcytidine-841 catalyzed by NSUN4, 6-dimethyladenosine-936 catalyzed by TFB1M, 6-dimethyladenosine-937 catalyzed by TFB1M, 5-methyluridine-429, and 4-methylcytidine-839 (reviewed in Van Haute et al. 2015). Four modified nucleotides have been detected in 16S rRNA: 2'-O-methylguanosine-1145 catalyzed by MRM1, 2'-O-methylguanosine-1370 catalyzed by RNMTL1 (MRM3), 2'-O-methyluridine-1369 catalyzed by FTSJ2 (MRM2), and pseudouridine-1397. 2'-O-methyluridine-1369 and 2'-O-methylguanosone-1370 occur in the A-loop of rRNA which is located at the peptidyl transferase center of the large subunit. Here the modified residues play a role in interaction with the aminoacyl site of tRNA. Knockouts of TFB1M and NSUN4 are lethal in mice and mutations in TFB1M may be related to aminoglycoside-induced deafness (reviewed in Van Haute et al. 2015).
R-HSA-6790901 rRNA modification in the nucleus and cytosol Human ribosomal RNAs (rRNAs) contain about 200 residues that are enzymatically modified after transcription in the nucleolus (Maden and Khan 1977, Maden 1988, Maden and Hughes 1997, reviewed in Hernandez-Verdun et al. 2010, Boschi-Muller and Motorin 2013). The modified residues occur in regions of the rRNAs that are located in functionally important parts of the ribosome, notably in the A and P peptidyl transfer sites, the polypeptide exit tunnel, and intersubunit contacts (Polikanov et al. 2015, reviewed in Decatur and Fournier 2002, Chow et al. 2007, Sharma and Lafontaine 2015). The two most common modifications are pseudouridines and 2'-O-methylribonucleotides. Formation of pseudouridine from encoded uridine is catalyzed by box H/ACA small nucleolar ribonucleoprotein (snoRNP) complexes (reviewed in Hamma and Ferre-D'Amare 2010, Watkins and Bohnsack 2011, Ge and Yu 2013, Kierzek et al. 2014, Yu and Meier 2014) and methylation of the hydroxyl group of the 2' carbon is catalyzed by box C/D snoRNPs (Kiss-Laszlo et al. 1996, Lapinaite et al. 2013, reviewed in Watkins and Bohnsack 2011). The snoRNP complexes contain common sets of protein subunits and unique snoRNAs that guide each complex to its target nucleotide of the rRNA by base-pairing between the snoRNA and the rRNA (reviewed in Henras et al. 2004, Watkins and Bohnsack 2011). Other modifications of rRNA include 5-methylcytidine (reviewed in Squires and Preiss 2010), 1-methylpseudouridine, 7-methylguanosine, 6-dimethyladenosine, and 4-acetylcytidine (reviewed in Sharma and Lafontaine 2015). In yeast most modifications are introduced co-transcriptionally (Kos and Tollervey 2010, reviewed in Turowski and Tollervey 2015), however the order of modification events and pre-rRNA cleavage events is not well characterized.
R-HSA-72312 rRNA processing Each eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 28S rRNA are produced by endonucleolytic and exonucleolytic processing of a single 47S precursor (pre-rRNA) (reviewed in Henras et al. 2015). Transcription of ribosomal RNA genes, processing of pre-rRNA, and assembly of precursor 60S and 40S subunits occur in the nucleolus (reviewed in Hernandez-Verdun et al. 2010), with a few late reactions occurring in the cytosol. Within the nucleolus non-transcribed DNA and inactive polymerase complexes are located in the fibrillar center, active DNA polymerase I transcription occurs at the interface between the fibrillar center and the dense fibrillar component, early processing of pre-rRNA occurs in the dense fibrillar component, and late processing of pre-rRNA occurs in the granular component (Stanek et al. 2001).
Processed ribosomal RNA contains many modified nucleotides which are generated by enzymes acting on encoded nucleotides contained in the precursor rRNA (reviewed in Boschi-Muller and Motorin 2013). The most numerous modifications are pseudouridine residues and 2'-O-methylribonucleotides. Pseudouridylation is guided by base pairing between the precursor rRNA and a small nucleolar RNA (snoRNA) in a Box C/D snoRNP (reviewed in Henras et al 2004, Yu and Meier 2014). Similarly, 2'-O-methylation is guided by base pairing between the precursor rRNA and a snoRNA in a Box H/ACA snoRNP (reviewed in Henras et al. 2004, Hamma and Ferre-D'Amare 2010). Other modifications include N(1)-methylpseudouridine, 5-methylcytosine, 7-methylguanosine, 6-dimethyladenosine, and 4-acetylcytidine. Modification of nucleotides occur as the pre-rRNA is being cleaved. However, the order of cleavage and modification steps is not clear so these two processes are presented separately here. Defects in ribosome biogenesis factors can cause disease (reviewed in Freed et al. 2010).
Mitochondrial ribosomes are completely distinct from cytoplasmic ribosomes, having different protein subunits and 12S rRNA and 16S rRNA. The mitochondrial rRNAs are encoded in the mitochondrial genome and are produced by processing of a long H strand transcript. Specific residues in the rRNAs are modified by enzymes to yield 5 different types of modified nucleotides:
R-HSA-8868766 rRNA processing in the mitochondrion Mitochondrial ribosomes contain 16S rRNA (large subunit) and 12S rRNA (small subunit) that are encoded in the mitochondrial genome and produced by processing of a long H strand transcript (reviewed in Van Haute et al. 2015). Enzymes encoded in the nucleus and acting in the mitochondrial matrix modify 5 nucleotides in the 12S RNA and 4 nucleotides in the 16S rRNA (reviewed in Van Haute et al. 2015).
R-HSA-8868773 rRNA processing in the nucleus and cytosol Each eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 28S rRNA are produced by endonucleolytic and exonucleolytic processing of a single 47S precursor (pre-rRNA) (reviewed in Henras et al. 2015). Transcription of ribosomal RNA genes, processing of pre-rRNA, modification of nucleotide residues within the rRNA, and assembly of precursor 60S and 40S subunits occur predominantly in the nucleolus (reviewed in Hernandez-Verdun et al. 2010, Boschi-Muller and Motorin 2013), with a few late reactions occurring in the cytosol.
R-HSA-9702577 semaxanib-resistant FLT3 mutants Semaxanib, also known as SU5614, is an investigational type I tyrosine kinase inhibitor with activity against a wide range of receptor tyrosine kinases. It is not currently approved for clinical use. This pathway describes FLT3 mutants that show resistance to semaxanib-mediated inhibition (Yee et al, 2002; Spiekermann et al, 2003).
R-HSA-191859 snRNP Assembly Small nuclear ribonucleoproteins (snRNPs) are crucial for pre-mRNA processing to mRNAs. Each snRNP contains a small nuclear RNA (snRNA) and an extremely stable core of seven Sm proteins. The U6 snRNA differs from the other snRNAs; it binds seven Sm-like proteins and its assembly does not involve a cytoplasmic phase. The snRNP biogenesis pathway for all of the other snRNAs is complex, involving nuclear export of snRNA, Sm-core assembly in the cytoplasm and re-import of the mature snRNP. The assembly of the snRNA:Sm-core is carried out by the survival of motor neurons (SMN) complex. The SMN complex stringently scrutinizes RNAs for specific features that define them as snRNAs and binds the RNA-binding Sm proteins.
R-HSA-9702624 sorafenib-resistant FLT3 mutants Sorafenib is a first generation type II tyrosine kinase inhibitor with broad specificity for receptor tyrosine kinases including FLT3. This pathway describes FLT3 mutants that are resistant to sorafenib-mediated inhibition (Nguyen et al 2017; Linblad et al, 2017;reviewed in Kazi and Roonstrand, 2019).
R-HSA-9702632 sunitinib-resistant FLT3 mutants Sunitinib is a first generation type II tyrosine kinase inhibitor with broad specifity for receptor tyrosine kinases, including FLT3. This pathway describes FLT3 mutants that show resistance to sunitinib-mediated inhibition (reviewed in Kazi and Roonstrand, 2019).
R-HSA-2033515 t(4;14) translocations of FGFR3 Translocations which put the FGFR3 gene under the control of the strong IGH promoter have been identified in 15% of multiple myelomas (Avet-Loiseau, 1998; Chesi, 1997; Chesi, 2001). This translocation, which occurs 70kb upstream of the FGFR3 gene, also involves the nearby multiple myeloma SET-domain containing (MMSET) gene (Lauring, 2008), and although the contribution of each of these genes to the development of cancer has not been fully elucidated, several studies have shown that t(4:14) myeloma cell lines are sensitive to FGFR3 inhibitors (Trudel, 2006; Qing, 2009). In ~5% of cases, the translocation is accompanied by activating mutations of FGFR3 (Onwuazor, 2003; Ronchetti, 2001). The t(4;14) translocation results in overexpression of FGFR3 and subsequent ligand independent or anomalous ligand-dependent signaling (Otsuki, 1999).
R-HSA-379724 tRNA Aminoacylation tRNA synthetases catalyze the ligation of tRNAs to their cognate amino acids in an ATP-dependent manner. The reaction proceeds in two steps. First, amino acid and ATP form an aminoacyl adenylate molecule, releasing pyrophosphate. The aminoacyl adenylate remains associated with the synthetase enzyme where, in the second step it reacts with tRNA to form aminoacyl tRNA and AMP. The rapid hydrolysis of pyrophosphate makes these reactions essentially irreversible under physiological conditions (Fersht and Kaethner 1976a). Specificity of the tRNA charging reactions is achieved both by specific recognition of amino acid and tRNA substrates by the synthetase, and by an editing process in which incorrect aminoacyl adenylate molecules (e.g., valyl adenylate associated with isoleucyl tRNA synthetase) are hydrolyzed rather than conjugated to tRNAs in the second step of the reaction (Baldwin and Berg 1966a,b; Fersht and Kaethner 1976b). The tRNA synthetases can be divided into two structural classes based on conserved amino acid sequence features (Burnbaum and Schimmel 1991).
A single synthetase mediates the charging of all of the tRNA species specific for any one amino acid but, with three exceptions, glycine, lysine, and glutamine, the synthetase that catalyzes aminoacylation of mitochondrial tRNAs is encoded by a different gene than the one that acts on mitochondrial tRNAs. Both mitochondrial and cytosolic tRNA synthetase enzymes are encoded by genes in the nuclear genome.
A number of tRNA synthetases are known to have functions distinct from tRNA charging (reviewed by Park et al. 2005). Additionally, mutations in several of the tRNA synthetases, often affecting protein domains that are dispensable in vitro for aminoacyl tRNA synthesis, are associated with a diverse array of neurological and other diseases (Antonellis and Green 2008; Park et al. 2008). These findings raise interest into the role of these enzymes in human development and disease.
R-HSA-6787450 tRNA modification in the mitochondrion The 22 tRNAs encoded by the mitochondrial genome are modified in the mitochondrial matrix by enzymes encoded in the nucleus and imported into mitochondria (reviewed in Suzuki et al. 2011, Salinas-Giege et al. 2015). Some enzymes such as PUS1 and TRIT1 are located in more than one compartment and modify both mitochondrial tRNAs and cytosolic tRNAs. Other enzymes such as MTO1, TRMU, and TRMT61B are exclusively mitochondrial.
Modifications near the anticodon and near the 3' end of tRNAs tend to affect interaction of the tRNA with mRNA within ribosomes and with tRNA synthetases, respectively. Modifications in other regions, typically in the "core" of the tRNA tend to affect folding and stability of the tRNA (reviewed in Hou et al. 2015). The unusual modification 5-taurinomethyl-2-thiouridine-34 in the anticodon of at least 3 tRNAs is found only in mammalian mitochondria and mutations that affect the responsible biosynthetic enzymes (GTPBP3, MTO1, TRMU) cause mitochondrial dysfunction and disease (reviewed in Torres et al. 2014).
R-HSA-6782315 tRNA modification in the nucleus and cytosol At least 92 distinct tRNA nucleotide base modifications have been found. The modifications are made post-transcriptionally by a large group of disparate enzymes located in the nucleus, cytosol, and mitochondria (reviewed in Boschi-Muller and Motorin 2013, Jackman and Alfonzo 2013, Gu et al. 2014, Helm and Alfonzo 2014, Li and Mason 2014). Modifications near the anticodon and near the 3' end affect interaction of the tRNA with ribosomes and tRNA synthetases, respectively, while modifications in other regions of the tRNA affect folding and stability of the tRNA (reviewed in Hou et al. 2015). Mutations in tRNA modification enzymes are associated with human diseases (reviewed in Sarin and Leidel 2014, Torres et al. 2014).
R-HSA-72306 tRNA processing Genes encoding transfer RNAs (tRNAs) are transcribed by RNA polymerase III in the nucleus and by mitochondrial RNA polymerase in the mitochondrion.
In the nucleus transcription reactions produce precursor tRNAs (pre-tRNAs) that have extra 5' leaders, 3' trailers, and, in some cases, introns which are removed by enzymes and enzyme complexes: RNase P cleaves the 5' leader, RNase Z cleaves the 3' trailer, TRNT1 polymerizes CCA onto the resulting 3' end, the TSEN complex cleaves at each end of the intron, and the tRNA ligase complex ligates the resulting exons (reviewed in Rossmanith et al. 1995, Phizicky and Hopper 2010, Suzuki et al. 2011, Abbott et al. 2014, Li and Mason 2014). The nucleotides within tRNAs undergo further chemical modifications such as methylation and deamination by a diverse set of enzymes (reviewed in Helm and Alfonzo 2014, Boschi-Muller and Motorin 2013). The order of events for each tRNA is not fully known and the understanding of the overall process is complicated by the retrograde (cytosol to nucleus) transport of tRNAs.
In the mitochondrial matrix transcription produces long precursor RNAs, H strand transcripts and an L strand transcript, that are cleaved by mitochondrial RNase P (an entirely proteinaceous complex), ELAC2, and other nucleases to yield 12S rRNA, 16S rRNA, mRNAs, and pre-tRNAs lacking 3' CCA sequences (reviewed in Van Haute et al. 2015). TRNT1 polymerizes an untemplated CCA sequence onto the 3' ends of the pre-tRNAs and chemical modifications are made to several nucleotides in the tRNAs.
R-HSA-6785470 tRNA processing in the mitochondrion Each strand of the circular mitochondrial genome is transcribed to yield long polycistronic transcripts, the heavy strand transcript and the light strand transcript, which are then cleaved to yield tRNAs, rRNAs, and mRNAs (Mercer et al. 2011, reviewed in Suzuki et al. 2011, Rossmanith 2012, Powell et al. 2015). Mitochondrial RNase P, which is completely distinct from nuclear RNase P in having different protein subunits and no RNA component, cleaves at the 5' ends of tRNAs. RNase Z, an isoform of ELAC2 in mitochondria, cleaves at the 3' ends of tRNAs. (A different isoform of ELAC2 serves as RNase Z in the nucleus.) Unknown nucleases make additional cleavages near the 5' end of MT-CO3, the 5' end of CO1, the 5' end of CYB, and the 3' end of ND6. TRNT1 (CCA-adding enzyme) then post-transcriptionally polymerizes the universal acceptor sequence CCA onto the 3' ends of the cleaved tRNAs. In yeast, plants, and protozoa additional tRNAs encoded in the nucleus are imported into mitochondria from the cytosol (reviewed in Schneider 2011), however human mitochondria encode a complete complement of 22 tRNAs required for translation and tRNA import has not been observed in mammals. Mutations that affect mitochondrial tRNA processing cause human diseases that are generally characterized by abnormalities in energy-requiring tissues such as brain and muscle (reviewed in Suzuki et al. 2011, Sarin and Leidel 2014).
R-HSA-6784531 tRNA processing in the nucleus Genes encoding transfer RNAs are transcribed in the nucleus by RNA polymerase III. (Distinct processes of transcription and processing also occur in mitochondria.) The initial transcripts, pre-tRNAs, contain extra nucleotides at the 5' end and 3' end. 6.3% (32 of 509) of human tRNAs also contain introns, which are located in the anticodon loop, 3' to the anticodon. The additional nucleotides are removed and a non-templated CCA sequence is added to the resulting 3' terminus by processing reactions in the nucleus and cytosol (reviewed in Nakanishi and Nureki 2005, Phizicky and Hopper 2010).
The order of processing and nucleotide modification events may be different for different tRNAs and its analysis is complicated by a retrograde transport mechanism that can import tRNAs from the cytosol back to the nucleus (retrograde movement, Shaheen and Hopper 2005, reviewed in Phizicky 2005). Generally, the 5' leader of the pre-tRNA is removed first by endonucleolytic cleavage by the RNase P ribonucleoprotein complex, which contains a catalytic RNA (RNA H1 in humans) and at least 10 protein subunits (reviewed in Jarrous 2002, Xiao et al. 2002, Jarrous and Gopalan 2010).
The 3' trailer is then removed by RNase Z activity, a single protein in humans (reviewed in Maraia and Lamichhane 2011). ELAC2 is a RNase Z found in both nucleus and mitochondria. ELAC1 is found in the cytosol and may also act as an RNase Z. Human tRNA genes do not encode the universal acceptor 3' terminus CCA, instead it is added post-transcriptionally by TRNT1, an unusual polymerase that requires no nucleic acid template (reviewed in Xiong and Steitz 2006, Hou 2010, Tomita and Yamashita 2014).
In humans introns are spliced from intron-containing tRNAs in the nucleus by a two step mechanism that is distinct from mRNA splicing (reviewed in Popow et al. 2012, Lopes et al. 2015). The TSEN complex first cleaves 5' and 3' to the intron, generating a 2'3' cyclic phosphate on the 5' exon and a 5' hydroxyl group on the 3' exon. These two ends are ligated by a complex containing at least 6 proteins in a single reaction that both hydrolyzes the 2' phosphate bond and joins the 3' phosphate to the 5' hydroxyl. (In yeast the ligation and the hydrolysis of the 2' phosphate are separate reactions. The splicing reactions in yeast occur in the cytosol at the mitochondrial outer membrane.)
Mature transfer RNAs contain a large number of modified nucleotide residues that are produced by post-transcriptional modification reactions (reviewed in Li and Mason 2014). Depending on the specific tRNA these reactions may occur before or after splicing and before or after export from the nucleus to the cytosol.
R-HSA-9708296 tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis Defined fragments of tRNAs, termed tRNA‑derived small RNAs (tsRNAs), have been observed in particular cell types and in response to biological conditions such as exposure to sex hormone or stresses such as hypoxia, starvation, oxidative stress, and virus infection (reviewed in Keam and Hutvagner 2015, Kumar et al. 2016, Oberbauer and Schaefer 2018, Park et al. 2020, Su et al. 2020, Xie et al. 2020, Zhu et al. 2020). Rather than being the random products of tRNA degradation, tsRNAs appear to be the specific products of ribonucleases. Two categories of tRNA‑derived small RNAs (tsRNAs) have been described: (1) longer (31‑40nt) tsRNAs known as tRNA halves or stress‑induced tsRNAs (tiRNAs) that are produced by single cleavage of tRNAs within or near the anticodon and (2) shorter (15‑30 nt) tsRNAs termed tRNA-related fragments (tRFs) that result from cleavage closer to the 5' or 3' end of the tRNA. tRF-3s are derived from the 3' region of the tRNA, approximately the region from the T loop to the 3' terminus. tRF-5s are derived from the 5' region of the tRNA, approximately the region from the D loop to the 5' terminus. tRF2‑type tRFs (also called internal tRFs) are derived from the central region of the tRNA, approximately the region between the D loop and the T loop and containing the anticodon. tRF-1s, also known as Type II tRFs or 3’U tRFs, are the 3' trailers of particular tRNAs that persist after processing.
In most cases the enzymes responsible for the cleavages are not yet known, however several ribonucleases involved in cleavage of tRNA have been identified: the secreted and endocytosed ribonuclease A family members angiogenin (ANG) and RNase 1; the interferon-induced ribonucleases RNase L, Schlafen 11 (SLFN11) and Schlafen13 (SLFN13 or RNase S13); the cytosolic ribonuclease III‑like (double strand RNA‑specific) enzyme DICER1; and the RNA processing enzyme ELAC2. ANG is secreted, binds receptors on cell membranes, is endocytosed, and translocates to the nucleus. ANG cleaves within the anticodon loop to produce tRNA halves and the cleavage is thought to occur while ANG is transiently located in the cytosol (Lee and Vallee 1989, Saxena et al. 1992, Fu et al. 2009, Yamasaki et al. 2009, Emara et al. 2010, Ivanov et al. 2011). Cleavage by ANG is observed in response to cellular stresses such as starvation (Fu et al. 2009, Yamasaki et al. 2009, Emara et al. 2010, Ivanov et al. 2011). However, ANG knockout cells continue to produce stress-induced tRNA halves, suggesting that other enzymes are also involved in producing the halves (Su et al. 2019). Similar to ANG as an RNase A member, the secreted endoribonuclease RNase 1 cleaves tRNAs at the anticodon loop in the extracellular space (Nechooshtan et al. 2020).
Interferon-induced RNases can also cleave tRNAs. RNase L is responsive to double stranded RNAs and cleaves at the tRNA anticodon loop (Donovan et al. 2017). Schlafen family members SLFN11 and SLFN13 can also cleave tRNAs (Li et al. 2018, Yang et al. 2018).
DICER1 cleaves double‑stranded regions of tRNAs near the 5' terminus or 3' terminus to produce short tRFs (Cole et al. 2009, Yeung et al. 2009, Maute et al. 2013, Hasler et al. 2016). The mechanism that dissociates the double‑stranded products of DICER1 to yield single‑stranded tRFs may be the same as that for miRNAs, but this has not yet been demonstrated. Furthermore, the bulk of the short tRFs is still detected in DICER1-null cells (Kumar 2014, Kuscu & Kumar et al. 2018), suggesting other unknown factors are involved in their biogenesis. ELAC2 in the cytosol cleaves the 3' trailers of precursors of tRNA Ser TGA, tRNA Ser GTC, and tRNA Asp GTC, and tRNA Asp GTC (Lee et al. 2009). The trailers (also called tRF-1s) then persist in the cytosol (Kumar et al. 2014).
R-HSA-9703009 tamatinib-resistant FLT3 mutants Tamatinib is a type I tyrosine kinase inhibitor with activity against FLT3. This pathway describes FLT3 mutants that are resistant to inhibition by tamatinib (Nguyen et al, 2017).
R-HSA-9702636 tandutinib-resistant FLT3 mutants Tandutinib, also known as MLN519, is a type II tyrosine kinase inhibitor with activity against FLT3 (Clark et al, 2004; reviewed in Staudt et al, 2018; Daver et al, 2019). This pathway describes FLT3 mutants that are resistant to tandutinib-mediated inhibition.
R-HSA-199992 trans-Golgi Network Vesicle Budding After passing through the Golgi complex, secretory cargo is packaged into post-Golgi transport intermediates (post-Golgi), which translocate plus-end directed along microtubules to the plasma membrane. There at least two classes of clathrin coated vesicles in cells, one predominantly Golgi-associated, involved in budding from the trans-Golgi network and the other at the plasma membrane. Here the clathrin-coated vesicles emerging from the Golgi apparatus are triggered by the heterotetrameric adaptor protein complex, AP-1 at the trans-Golgi network membrane. The cargo can be transmembrane, membrane associated or golgi luminal proteins. Each step in the vesicle sculpting pathway, gathers cargo and clathrin triskeletons, until a complete vesicular sphere is formed. With the scission of the membrane the vesicle is released and eventually losses its clathrin coat.
R-HSA-192814 vRNA Synthesis The synthesis of full-length negative strand viral RNA from a cRNA template is believed to follow the same principles as the synthesis of cRNA from a vRNA template. The cRNA, complexed with viral nucleocapsid (NP) protein, is used as template by the trimeric viral polymerase (Pritlove, 1995; Vreede, 2004; Crow, 2004), and newly synthesized vRNA molecules are immediately packaged with NP molecules to form ribonucleoprotein complexes (Vreede, 2004). There is some evidence that the production of vRNA-containing vRNP occurs in the nuclear matrix as well as the nucleoplasm (Takizawa, 2006).
R-HSA-192905 vRNP Assembly For each of eight gene segments, a viral ribonucleoprotein (vRNP), containing a viral negative-sense RNA (vRNA) segment complexed with nucleoprotein (NP) and the trimeric influenza polymerase (PB1, PB2, and PA), is assembled in the nucleus (Braam, 1983; Jones, 1986; Cros, 2003; reviewed in Buolo, 2006). The vRNP functions in three modes (reviewed in Mikulasova, 2000; Neumann, 2004): (1) transcription, which synthesizes viral messenger RNA from the vRNA template using as primers 5' ends of cellular mRNAs containing the cap; (2) replication, which produces positive-sense complementary RNA (cRNA) and subsequently vRNA, both complexed with NP and the trimeric polymerase; or (3), the vRNP is exported from the nucleus into the cytoplasm and is incorporated into assembling virions at the plasma membrane.