# HISTORY 08 May 2016: Updated by: TOUCHUP-v1.19 27 Mar 2016: Updated by: TOUCHUP-v1.15 18 Mar 2016: Updated by: TOUCHUP-v1.14 07 May 2016: Updated by: TOUCHUP-v1.18 # molecular_function 20150216: Deuterostomia_PTN000664982 has function histamine receptor activity (GO:0004969) 20150213: Bilateria_PTN001207082 has function G-protein coupled acetylcholine receptor activity (GO:0016907) 20150216: Eumetazoa_PTN001205456 has function dopamine binding (GO:0035240) 20150216: Eumetazoa_PTN001205456 has function dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588) 20150213: Deuterostomia_PTN000665047 has function trace-amine receptor activity (GO:0001594) 20150216: Mammalia_PTN000665160 has function 2-phenylethylamine receptor activity (GO:1990080) 20150216: Eumetazoa_PTN001545996 has function G-protein coupled serotonin receptor activity (GO:0004993) 20150216: Arthropoda_PTN001206597 has function octopamine receptor activity (GO:0004989) # cellular_component 20150213: Bilateria_PTN001207082 is found in synapse (GO:0045202) # biological_process 20150219: Deuterostomia_PTN000664982 participates in immune response (GO:0006955) 20150219: Deuterostomia_PTN001545719 participates in regulation of vasoconstriction (GO:0019229) 20150216: Deuterostomia_PTN001545719 participates in modulation of synaptic transmission (GO:0050804) 20150216: Deuterostomia_PTN001545719 participates in phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200) 20150216: Deuterostomia_PTN001545719 participates in inflammatory response (GO:0006954) 20150219: Bilateria_PTN001205349 participates in synaptic transmission, cholinergic (GO:0007271) 20150219: Bilateria_PTN001205349 participates in G-protein coupled acetylcholine receptor signaling pathway (GO:0007213) 20150219: Bilateria_PTN001207082 participates in phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207) 20150216: Bilateria_PTN001207082 participates in adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway (GO:0007197) 20150216: Bilateria_PTN001207082 participates in synaptic transmission, cholinergic (GO:0007271) 20150219: Euteleostomi_PTN000665558 participates in regulation of heart contraction (GO:0008016) 20150219: Euteleostomi_PTN000665558 participates in regulation of smooth muscle contraction (GO:0006940) 20150216: Mammalia_PTN000665502 participates in inflammatory response (GO:0006954) 20150216: Mammalia_PTN000665519 participates in regulation of norepinephrine secretion (GO:0014061) 20150216: Mammalia_PTN000665519 participates in negative regulation of serotonin secretion (GO:0014063) 20150216: Mammalia_PTN000665519 participates in negative regulation of glutamate secretion (GO:0014050) 20150216: Mammalia_PTN000665519 participates in cognition (GO:0050890) 20150219: Euteleostomi_PTN000665645 participates in regulation of vascular smooth muscle contraction (GO:0003056) 20150217: Eumetazoa_PTN001205456 participates in synaptic transmission, dopaminergic (GO:0001963) 20150217: Bilateria_PTN000665343 participates in phospholipase C-activating dopamine receptor signaling pathway (GO:0060158) 20150219: Bilateria_PTN000665343 participates in learning (GO:0007612) 20150216: Bilateria_PTN000665343 participates in adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191) 20150213: Mammalia_PTN000665160 participates in behavioral fear response (GO:0001662) 20150219: Mammalia_PTN000665160 participates in chemosensory behavior (GO:0007635) 20150216: Eumetazoa_PTN001545996 participates in serotonin receptor signaling pathway (GO:0007210) 20150216: Euteleostomi_PTN000665293 participates in gamma-aminobutyric acid signaling pathway (GO:0007214) 20150216: Ecdysozoa_PTN000757308 participates in octopamine or tyramine signaling pathway (GO:0007211) # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES 06 May 2016: Diptera_PTN001956164 has been pruned from tree Annotated PG 2015-02-18 Reviewed PG & MAF 2015-08-19 KRC - 2016-05-05 - reannotated PTN001205456 and below due to MGI user email that DRD4 is incorrectly annotated to GO:0001588 ("coupled via Gs") ======================================================================== KRC notes on reannotation of PTN001205456 and below - Passage from Yamamoto & Verner 2011 (below) suggests that "dopamine binding" evolved independently in each of the two classes of dopamine receptor, so I have removed both of these two terms from a node that is ancestral to both classes of dopamine receptors in this tree. From the notes file before I made changes, these are the annotations I removed: -- # molecular_function -- 20150216: Eumetazoa_PTN001205456 has function dopamine binding (GO:0035240) -- 20150216: Eumetazoa_PTN001205456 has function dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588) - The literature I have seen is consistent in indicating the the Gs coupled receptors are involved in activating adenylate cyclase. However, while it is clear that dopamine receptors activate additional receptors, I haven't seen anything suggesting that activating phospholipase C is universal in this group, so I am going to remove this previous propagation: -- 20150217: Bilateria_PTN000665343 participates in phospholipase C-activating dopamine receptor signaling pathway (GO:0060158) - Mustard et al. 2005 suggests that invertebrate dopamine receptors also share the D1 D2 split, but are more diverged from the vertebrate receptors. - The tree structure does not seem to reflect the thinking in the field (all three references listed below) that the primary split is between D1 (via Gs) versus D2 (via Gi/Go) types. Thus, I am going to annotate each of the 9BILA nodes separately based on evidence within each branch. ------------------------------------------------------------------------------------------------------------ Relevant Tree Structure below PTN001205456 ------------------ - PTN001205456 -- 9ZZZZ:PTN001956100 (dup node): with MANY NEMVE sequences -- 9ZZZZ:PTN001545971 (dup node) --- 9BILA:PTN000664816 ---- PTN001205373 - vertebrate Drd4 & Drd3 [IDA/IMP via Gi/Go] ---- PTN001956115 - insect TyrR & TyrRII --- 9BILA:PTN001545876 - Dmel Dop2R [IDA via Gi/Go] --- 9BILA:PTN001206555 - Dmel Dop1R1 [IDA/IMP via Gs], Cel dop-1 --- 9BILA:PTN000665343 [<= IBD adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191) ---- 9ZZZZ:PTN001956128 (dup node) ----- PTN001206415 - vert GPR21 & GPR52 [TAS annots from sequence data only papers (PINC)] ----- PTN001545930 ------ 9CHOR:PTN000664818 - vert DRD1 & DRD5 [IDA/IMP via Gs] ------ 9ZZZZ:PTN001545908 (dup node): a bunch of STRPU seqs ---- PTN000665440 - Dmel 5-HT2B [IDA GPC-serotonin-R; PRUNED], Dop1R [IDA via Gs]; Cel tyra-2, dop-4 [IDA gen], tyra-3 ---- 9ZZZZ:PTN001206613 - several GO:0004952SCHMA seqs ------------------------------------------------------------------------------------------------------------ REFERENCES * Yamamoto K, Vernier P. The evolution of dopamine systems in chordates. Front Neuroanat. 2011 Mar 29;5:21. (PMID:21483723): QUOTE: "The dopamine receptors are divided into two classes of GPCR, D1- and D2-class receptors (reviewed in Missale et al., 1998; Callier et al., 2003). Members of the D1 receptor class are structurally characterized by a short third cytoplasmic loop and a very long C-terminal tail. They are coupled to the Gs/Golf class of G proteins and accordingly they activate adenylyl cyclase. In contrast, receptors of the D2 class are coupled to Gi/Go proteins and they display a long third cytoplasmic loop and a short cytoplasmic C-terminal end. D2 receptors have been initially described as mediating adenylyl cyclase inhibition, but their major cellular effects in adult vertebrates are the modulation of neuronal excitability through inhibition of voltage-sensitive Ca++ and activation of K+ channels. D2-like receptors are able to regulate other signaling pathways related to changes of cell shape or mitosis (Missale et al., 1998; O’Keeffe et al., 2009). --The nomenclature of DA receptors is quite confusing. Originally one excitatory and one inhibitory DA subtype were found, and they are named to be D1 and D2. Molecular cloning techniques led finding of additional subtypes, and they were named D3, D4, and D5, however, later characterization of the subtypes defined that D5 is rather close to D1 (D1-class) and D3 and D4 are close to D2 (D2-class). D1 and D5 are often called D1A and D1B respectively in non-human, and especially in non-mammalian vertebrate species, according findings of additional D1-class receptors; D1C (Xenopus; Sugamori et al., 1994), D1D (chicken; Demchyshyn et al., 1995), and D1X (carp; Hirano et al., 1998). --Molecular phylogenies are the best way to classify the DA receptors, especially when analyzed together with other classes of monoamine receptors; the adrenergic (α1, α2, β), serotoninergic (5HT1, 5HT2, 5HT4, 5HT5, 5HT6, and 5HT7), or trace amine receptors. A first important observation made by such a molecular analysis is that the different receptor classes binding the same neurotransmitter (D1 and D2 receptors for example) are not more related to each other than to other classes of monoamine receptors (Figure 2B). This observation implicates that DA receptors have acquired independently (by convergence) the ability to bind DA, as it was also the case for the other classes of monoamine GPCR." ---- * Yamamoto K, Fontaine R, Pasqualini C, Vernier P. Classification of Dopamine Receptor Genes in Vertebrates: Nine Subtypes in Osteichthyes. Brain Behav Evol. 2015;86(3-4):164-75. (PMID:26613258) ---- * Mustard JA, Beggs KT, Mercer AR. Molecular biology of the invertebrate dopamine receptors. Arch Insect Biochem Physiol. 2005 Jul;59(3):103-17. Review. (PMID:15986382) - Phylogenetic tree in Figure 1 shows Dm_5-HT2B as distantly related to the D2 class, so I think it does not belong in a duplication node with Dm Dop1R2 and I have pruned the node 9DIPT:PTN001956164 # REFERENCE Annotation inferences using phylogenetic trees The goal of the GO Reference Genome Project, described in PMID 19578431, is to provide accurate, complete and consistent GO annotations for all genes in twelve model organism genomes. To this end, GO curators are annotating evolutionary trees from the PANTHER database with GO terms describing molecular function, biological process and cellular component. GO terms based on experimental data from the scientific literature are used to annotate ancestral genes in the phylogenetic tree by sequence similarity (ISS), and unannotated descendants of these ancestral genes are inferred to have inherited these same GO annotations by descent. The annotations are done using a tool called PAINT (Phylogenetic Annotation and INference Tool).