# HISTORY 07 May 2016: Updated by: TOUCHUP-v1.18 16 Mar 2016: Updated by: TOUCHUP-v1.14 26 Mar 2016: Updated by: TOUCHUP-v1.15 # molecular_function 20130227: Euteleostomi_PTN000422281 has function antigen binding (GO:0003823) 20130227: Amniota_PTN000422284 has function exogenous lipid antigen binding (GO:0030884) 20130227: Amniota_PTN000422284 has function lipopeptide binding (GO:0071723) 20130227: Amniota_PTN000422284 has function beta-2-microglobulin binding (GO:0030881) 20130227: Amniota_PTN000422284 has function endogenous lipid antigen binding (GO:0030883) 20130906: Boreoeutheria_PTN000422361 has function receptor binding (GO:0005102) 20130227: Boreoeutheria_PTN000422454 has function natural killer cell lectin-like receptor binding (GO:0046703) 20130227: Boreoeutheria_PTN000422535 has function natural killer cell lectin-like receptor binding (GO:0046703) 20130906: Boreoeutheria_PTN000422481 has function natural killer cell lectin-like receptor binding (GO:0046703) 20130227: Theria _PTN000422410 has function beta-2-microglobulin binding (GO:0030881) 20130227: Theria _PTN000422410 has function IgG receptor activity (GO:0019770) 20130906: Theria _PTN000422452 has function receptor binding (GO:0005102) 20130227: Theria _PTN000422452 has function peptide antigen binding (GO:0042605) # cellular_component 20130227: Euteleostomi_PTN000422281 is found in plasma membrane (GO:0005886) 20130906: Theria _PTN000422425 is found in extracellular space (GO:0005615) # biological_process 20130227: Euteleostomi_PTN000422281 participates in antigen processing and presentation (GO:0019882) 20130227: Amniota_PTN000422284 participates in antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007) 20130906: Boreoeutheria_PTN000422361 participates in iron ion import into cell (GO:0097459) 20130906: Boreoeutheria_PTN000422454 participates in natural killer cell mediated cytotoxicity (GO:0042267) 20130906: Boreoeutheria_PTN000422454 participates in T cell mediated cytotoxicity (GO:0001913) 20130906: Boreoeutheria_PTN000422535 participates in T cell mediated cytotoxicity (GO:0001913) 20130906: Boreoeutheria_PTN000422535 participates in natural killer cell mediated cytotoxicity (GO:0042267) 20130906: Boreoeutheria_PTN000422481 participates in natural killer cell mediated cytotoxicity (GO:0042267) 20130906: Theria _PTN000422452 participates in antigen processing and presentation of peptide antigen via MHC class I (GO:0002474) # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES PTHR16675 MHC class I http://en.wikipedia.org/wiki/MHC_class_I What is tricky here in regards to PAINT is the fact that the MHC molecules are closely related and extremely polymorphic and subject to rapid change during evolution. The classical class I proteins (HLA-A, B, and C in human, and H2-K, H2-L, and H2-D in mouse, for instance) all bind peptides as do HLA-E, F, and G. However, one needs to be a bit careful as some MHC Class Ib proteins bind lipids and others don't bind either peptide or lipids. PMID:21570669 Structural diversity of class I MHC-like molecules and its implications in binding specificities. 1 Amniota_PTN000422284 MF: exogenous lipid antigen binding GO:0030883 endogenous lipid antigen binding GO:0030883 beta-2-microglobulin binding GO:0030881 lipopeptide binding GO:0071723 PMID:14722359 the assembly of CD1 molecules with PI in the endoplasmic reticulum is evolutionarily conserved. These findings suggest that PI plays a chaperone-like role in CD1 assembly, possibly to preserve the integrity of the antigen-binding groove until CD1 binds antigenic lipids in the endocytic pathway BP: antigen processing and presentation, exogenous lipid antigen via MHC class Ib GO:0048007 2 Theria_ PTN000422410 MF: IgG binding or IgG receptor activity?? beta-2-microglobulin binding GO:0030881 PMID:7964511 shows FCFRT binds IgG preferentially at low pH, which may imply that IgG binds FCGRT in an acidic intracellular compartment during transport across the placenta. Most of those are actually citations from rat system. receptor activity has_part binding BP Add human annotation to FCGRT, then propagate: IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor GO:0002416 PMID:7964511 3. Theria_ PTN000422425 MF: PMID:10206894 Instead of a peptide, the ZAG groove contains an as yet unidentified ligand that cocrystallizes with the protein CC: extracellular space GO:0005615 4 PTN000422535 PTN000422454 MF: natural killer cell lectin-like receptor binding GO:0046703 Not beta-2-microglobulin binding GO:0030881 BP: PMID: 10894171 Add annotation to mouse Raet1d natural killer cell mediated cytotoxicity GO:0042267 PMID:11567106 Add annotation to mouse Raet1e T cell mediated cytotoxicity GO:0001913 PMID:18209064 Add annotation to mouse H60c and H60b natural killer cell mediated cytotoxicity GO:0042267 PMID:10426993 Add annotation to Human MICA natural killer cell mediated cytotoxicity GO:0042267 T cell mediated cytotoxicity GO:0001913 Add annotation above and propagate: T cell mediated cytotoxicity GO:0001913 Natural killer cell mediated cytotoxicity 5 Eutheria_PTN000422481 mini review: NKG2D and its Ligands : MICA/MICB; ULBPs; Rae-1 and H-60 http://www.rndsystems.com/mini_review_detail_objectname_MR02_NKG2D.aspx MF: GO:0046703 natural killer cell lectin-like receptor binding BP: natural killer cell mediated cytotoxicity GO:0042267 Can?t propagate at the moment, since none of the members has any annotation to that term or it?s child Ask GOA (mostly human genes) to update their manual annotation to members of this sub-family, and eventually PAINT? PMID:15240696 (used for human Raet1g) PMID:11239445 (Only used as NAS annotation for Human ULBP1-3) Both need to update annotations to at least: GO:0046703 natural killer cell lectin-like receptor binding GO:0046703 natural killer cell mediated cytotoxicity GO:0042267 Question about the tree: Is it possible to reconsider the tree structure to somehow put the two subfamilies at one place? Eutheria_PTN000422481 and Root_PTN001047449 6 Eutheria_PTN000422361 For annotation below, put a not at murinae_PTN000422650 Update annotations first then propagate: MF: receptor binding activity BP: iron ion import into cell GO:0097459 According to PMID: 10638746 change human protein binding annotation for gene HFE to receptor binding According to PMID: 10085150, add BP annotation to human HFE: iron ion import into cell GO:0097459 PMID: 10077651 Mouse add annotation ?iron ion import into cell GO:0097459? 7. Theria_PTN000422452 MF: peptide antigen binding ; GO:0042605 BP: antigen processing and presentation of peptide antigen via MHC class I GO:0002474 Annotation mistake: All annotations of human HLA-A; HLA-B; HLA-C; HLA-E; HLA-F; HLA-G etc to 'MHC class I receptor activity ; GO:0032393' are wrong, these proteins are the MHC class I molecules themselves. These annotations should be removed, as they are in contradiction to the definition of the term. The comment of term GO:0032393 specifically warns annotators not to use this term and similar MHC receptor activity terms for annotation of MHC proteins. 8. Theria_PTN000422452 MF: receptor binding GO:0005102 although the major function of these MHC class I protein complexes is to bind potentially antigenic peptides and display them on the cell surface. HLA-A and HLA_B do binding to immunoglobulin-like receptor. Request new term: immunoglobulin-like receptor binding? 9. To root OSteichthyes_PTN000422281 plasma membrane GO:0005886 antigen processing and presentation GO:0019882 antigen binding GO:0003823 # 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).