# HISTORY 07 May 2016: Updated by: TOUCHUP-v1.18 24 Mar 2016: Updated by: TOUCHUP-v1.15 14 Mar 2016: Updated by: TOUCHUP-v1.14 07 May 2016: Updated by: TOUCHUP-v1.18 # molecular_function 20110214: Eukaryota_PTN000091699 has function actin filament binding (GO:0051015) # cellular_component 20110215: Eukaryota_PTN000091699 is found in actin cytoskeleton (GO:0015629) 20110215: Ascomycota_PTN000091920 is found in actin cortical patch (GO:0030479) 20110215: Ascomycota_PTN000091920 is found in actomyosin contractile ring (GO:0005826) 20110215: Ascomycota_PTN000091920 is found in Arp2/3 protein complex (GO:0005885) 20110215: Mammalia_PTN000091755 is found in transcriptional repressor complex (GO:0017053) 20110215: Amoebozoa_PTN000091929 is found in phagocytic cup (GO:0001891) 20110215: Theria _PTN000091711 is found in Golgi apparatus (GO:0005794) # biological_process 20110215: Eukaryota_PTN000091699 participates in actin cytoskeleton organization (GO:0030036) 20110215: Ascomycota_PTN000091920 participates in negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316) 20110215: Ascomycota_PTN000091920 participates in actin cortical patch localization (GO:0051666) # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES Fast-pass curation of the PTHR10856 family of Coronins, actin- and microtubule-binding proteins involved in phagocytosis (cf. Wikipedia). Description of phylogeny The root is trifurcated with 3 proteins in outgroups which we will ignore. Consider AN1 to be the root. This leaves the family with successive dicty (An231) and fungal (AN222) outgroups. AN3 contains 3 paralogous clades spanning the metazoa. AN4 contains the vertebrate Coro7 clade and worm/fly pod1 outgroup. AN47 contains the paralogous vertebrate CORO2A and -B clades. AN108 contains a vertebrate trifurcation at AN111 leading to AN112 (CORO6), AN141 (CORO1A), and AN166. There is a duplication at AN170 that formed a mammalian CORO1B clade paralogous to mammalian CORO1C. Most of the annotations are limited to the fungal, dicty, and CORO1A clades. This makes it difficult to know when to propagate annotations widely. MF -Widespread annotations to "actin filament binding" in almost every clade and in the AN231 outgroup. Propagate to AN1. -Wikipedia: "Mammalian Coronin-7 does not interact with actin nor does it execute any actin mediated processes, but rather participates in Golgi trafficking." Agrees with UniProt note on mouse Coro7: "Detected on vesicle-like cytoplasmic structures and on the cis-Golgi. Not associated with actin filaments [PMID 15327992]." Similar note for human (PMID 16905771). Block/IRD "actin filament binding" to mammalian Coro7 clade (AN13). CC Actin: -Based on 6 annotations to "actin cytoskeleton" or its children, including several in the fungal and dicty clades, and in accordance with the MF annotations above, propagate "actin cytoskeleton" to AN1 and block/IRD to AN13. -Propagate "Golgi" to AN13. -Propagate GO:0005885 "Arp2/3 protein complex" to fungal clade. Would prefer a "colocalizes with" qualifier, but PAINT beta 36 does not support that. -Propagate GO:0017053 "transcriptional repressor complex" to mammalian CORO2A clade, but no farther for now. Cortex: -There are multiple annotations to GO:0005938 "cell cortex" and its children, but mostly in the fungal and dicty outgroups. There is one in the CORO1A clade, to GO:0030864 "cortical actin cytoskeleton." Propagate 30864 to AN141 and AN231. Propagate GO:0005826 "actomyosin contractile ring" and GO:0030479 "actin cortical patch" to the fungal clade. Phagocytosis-related: -There's only 1 LTP annotation to GO:0045335 "phagocytic vesicle," in human CORO1A. Propagate to AN141. -Propagate GO:0001891 "phagocytic cup" and GO:0045335 "phagocytic vesicle" to AN141 and AN231. -Propagate GO:0030027 "lamellipodium" to AN141. BP -Other than the worm-specific annotations on pod-1, all annotations are limited to the CORO1A clade, its worm/fly outgroup, and the dicty and fungal clades Actin: -Based on annotation in the CORO1A clade and the yeast and dicty outgroups, plus the MF annotation to "actin filament binding," propagate GO:0030036 "actin cytoskeleton organization" to AN1 and block/IRD it to AN13. -To AN141 (the CORO1A clade): GO:0051126 "negative regulation of actin nucleation" GO:0008064 "regulation of actin polymerization or depolymerization" -Some of these and other terms within dicty and fungal clades. -Propagate GO:0006909 "phagocytosis" and GO:0001845 "phagolysosome assembly" to the CORO1A clade. Can't justify expanding beyond there. Movement and shape: -To AN141: GO:0016477 "cell migration" GO:0050918 "positive chemotaxis" GO:0030595 "leukocyte chemotaxis" GO:0032796 "uropod organization" GO:0008360 "regulation of cell shape" =Questions for MOD curators= ==Cellular Component== ===Human=== * '''Critical''': Human CORO1A is annotated to GO:0031941 "filamentous actin," where the comment states, "Note that this term refers only to the actin portion of a microfilament, and does not encompass associated proteins." **'''Curator answer: '''Changed this annotation to GO:0005884 actin filament. =Questions for ontology curators= ==Biological Process== *'''Question: '''Problem with definition of GO:0050918 "positive chemotaxis": "The directed movement of a motile cell or organism, or the directed growth of a cell guided by a higher concentration, in a concentration gradient of a specific chemical." This should specify "toward higher concentration" as mentioned in the definition of the parent term "chemotaxis." (SF# 3220790) **'''Curator answer: '''I've changed the definitions to: **#positive chemotaxis ; GO:0050918 **#*The directed movement of a motile cell or organism towards a higher concentration of a chemical. **#negative chemotaxis ; GO:0050919 **#*The directed movement of a motile cell or organism towards a lower concentration of a chemical. ***A lot of the child terms have this wording already. MSL 15 Feb 2011 Updated with answers from wiki 23 Mar 2011, MSL # 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).