{"action":"created","issue":{"url":"https://api.github.com/repos/geneontology/go-ontology/issues/12574","repository_url":"https://api.github.com/repos/geneontology/go-ontology","labels_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12574/labels{/name}","comments_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12574/comments","events_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12574/events","html_url":"https://github.com/geneontology/go-ontology/issues/12574","id":169892019,"number":12574,"title":"exosome complexes, their relationships and functions","user":{"login":"bmeldal","id":10517124,"avatar_url":"https://avatars.githubusercontent.com/u/10517124?v=3","gravatar_id":"","url":"https://api.github.com/users/bmeldal","html_url":"https://github.com/bmeldal","followers_url":"https://api.github.com/users/bmeldal/followers","following_url":"https://api.github.com/users/bmeldal/following{/other_user}","gists_url":"https://api.github.com/users/bmeldal/gists{/gist_id}","starred_url":"https://api.github.com/users/bmeldal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bmeldal/subscriptions","organizations_url":"https://api.github.com/users/bmeldal/orgs","repos_url":"https://api.github.com/users/bmeldal/repos","events_url":"https://api.github.com/users/bmeldal/events{/privacy}","received_events_url":"https://api.github.com/users/bmeldal/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/geneontology/go-ontology/labels/protein%20complex","name":"protein complex","color":"ededed"}],"state":"open","locked":false,"assignee":{"login":"mcourtot","id":2214135,"avatar_url":"https://avatars.githubusercontent.com/u/2214135?v=3","gravatar_id":"","url":"https://api.github.com/users/mcourtot","html_url":"https://github.com/mcourtot","followers_url":"https://api.github.com/users/mcourtot/followers","following_url":"https://api.github.com/users/mcourtot/following{/other_user}","gists_url":"https://api.github.com/users/mcourtot/gists{/gist_id}","starred_url":"https://api.github.com/users/mcourtot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mcourtot/subscriptions","organizations_url":"https://api.github.com/users/mcourtot/orgs","repos_url":"https://api.github.com/users/mcourtot/repos","events_url":"https://api.github.com/users/mcourtot/events{/privacy}","received_events_url":"https://api.github.com/users/mcourtot/received_events","type":"User","site_admin":false},"assignees":[{"login":"mcourtot","id":2214135,"avatar_url":"https://avatars.githubusercontent.com/u/2214135?v=3","gravatar_id":"","url":"https://api.github.com/users/mcourtot","html_url":"https://github.com/mcourtot","followers_url":"https://api.github.com/users/mcourtot/followers","following_url":"https://api.github.com/users/mcourtot/following{/other_user}","gists_url":"https://api.github.com/users/mcourtot/gists{/gist_id}","starred_url":"https://api.github.com/users/mcourtot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mcourtot/subscriptions","organizations_url":"https://api.github.com/users/mcourtot/orgs","repos_url":"https://api.github.com/users/mcourtot/repos","events_url":"https://api.github.com/users/mcourtot/events{/privacy}","received_events_url":"https://api.github.com/users/mcourtot/received_events","type":"User","site_admin":false}],"milestone":null,"comments":35,"created_at":"2016-08-08T10:33:54Z","updated_at":"2016-08-26T08:18:29Z","closed_at":null,"body":"There are three eukaryotic exosomes, the cytoplasmic, nuclear and nucleolar exosomes. \r\n\r\nGO currently has the following terms:\r\nGO:0000178 exosome (RNase complex)\r\nDef: Complex of 3'-5' exoribonucleases.\r\nwith 2 children:\r\nGO:0000177 cytoplasmic exosome (RNase complex)\r\nDef: Complex of 3'-5' exoribonucleases found in the cytoplasm.\r\nand\r\nGO:0000176 nuclear exosome (RNase complex)\r\nDef: Complex of 3'-5' exoribonucleases found in the nucleus.\r\nalso:\r\nGO:1902555 endoribonuclease complex\r\nDef: A protein complex which is capable of endoribonuclease activity. \r\nis_a GO:0032991 macromolecular complex\r\ncapable_of GO:0004521 endoribonuclease activity\r\n\r\nbut that's not the whole story!\r\nRead on, the changes are smaller than the ticket, I just want to give you all the background info!\r\n\r\nAll three complexes have the same core nonamer complex (Exo-9) which is then complimented with one or two of three enzymes to give the holocomplex its catalytic activities:\r\nDIS3/RRP44 has endoribonuclease & processive hydrolytic exoribonuclease activity (GO:0016891 / EC:3.1.26.-, GO:0000175 / EC:3.1.13.-)\r\nDIS3L has only processive hydrolytic exoribonuclease activity (EC:3.1.13) (this isoform is not present in yeast)\r\nEXOSC10/RRP6 has only distributive hydrolytic exoribonuclease activity (EC:3.1.13)\r\n[NB: the human Exo-9 has weak constitutional phosphorolytic activity as well but it might not be physiological. Phosphorolytic activity is, however, commonly found in the prokaryotic exosome]\r\n\r\nThe composition of the catalytically active complexes is as follows:\r\na) 10-subunit cytoplasmic exosome:\r\nCore +\r\nQ8TF46\t(DI3L1_HUMAN) = DIS3L = DIS3L1 (restricted to cytoplasm, PMID:26726035, Uniprot has refs for nuclear/nucleolar location but may not be physiological)\r\n\r\n[May contain small fraction of Exo-11 (composition below) with either DIS3 (Q9Y2L1) or DIS3L but DIS3 is primarily nuclear and is missing from nucleolus, PMID:20531386]\r\n\r\nb) 11-subunit nuclear exosome:\r\nCore +\r\nQ9Y2L1\t(RRP44_HUMAN) = DIS3 (primarily nuclear isoform, PMID:20531386)\r\nQ01780\t(EXOSX_HUMAN) = EXOSC10 = RRP6 (missing in small fraction of nuclear exosomes, PMID:26726035)\r\n\r\nc) 10-subunit nucleolar exosome:\r\nCore +\r\nQ01780\t(EXOSX_HUMAN) = EXOSC10 = RRP6\r\n(plus DIS3 (Q08162) in yeast, PMID:26726035)\r\n\r\nI propose the following changes:\r\n1) GO:0000178 exosome (RNase complex)\r\n-Def: Complex of 3'-5' exoribonucleases.\r\n+Def: A ribonuclease complex that has 3-prime to 5-prime exoribonuclease activity and possibly endoribonuclease activity, producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured.\r\nReferences: PMID:17174896, PMID:20531386, PMID:26726035 \r\n+is_a GO:1905354 (NEW in TG) exoribonuclease complex\r\n+capable_of GO:0000175 3'-5'-exoribonuclease activity\r\n \r\n2) GO:0000177 cytoplasmic exosome (RNase complex)\r\n-Def: Complex of 3'-5' exoribonucleases found in the cytoplasm.\r\n+Def: A ribonuclease complex that has 3-prime to 5-prime processive hydrolytic exoribonuclease activity producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured.\r\nReferences: PMID:17174896, PMID:20531386, PMID:26726035 \r\nis_a GO:0000178 exosome (RNase complex) [currently there]\r\n+is_a GO:1905354 (NEW in TG) exoribonuclease complex (should get relationship via parent though)\r\n+capable_of GO:0000175 3'-5'-exoribonuclease activity (should get relationship via parent though)\r\n\r\n3) GO:0000176 nuclear exosome (RNase complex)\r\n-Def: Complex of 3'-5' exoribonucleases found in the nucleus.\r\n+Def: A ribonuclease complex that has 3-prime to 5-prime processive and distributive hydrolytic exoribonuclease activity and endoribonuclease activity, producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured.\r\nReferences: PMID:17174896, PMID:20531386, PMID:26726035 \r\nis_a GO:0000178 exosome (RNase complex) [currently there]\r\n+is_a GO:1905354 (NEW in TG) exoribonuclease complex (should get relationship via parent though)\r\n+is_a GO:1902555 endoribonuclease complex\r\n+capable_of GO:0000175 3'-5'-exoribonuclease activity (should get relationship via parent though)\r\n+capable_of GO:0016891 endoribonuclease activity, producing 5'-phosphomonoesters\r\n\r\n4) GO:NEW nucleolar exosome (RNase complex)\r\nDef: A ribonuclease complex that has 3-prime to 5-prime distributive hydrolytic exoribonuclease activity and in some taxa (e.g. yeast) endoribonuclease activity, producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured.\r\nReferences: PMID:17174896, PMID:20531386, PMID:26726035\r\n+is_a GO:0000178 exosome (RNase complex)\r\n+is_a GO:1905354 (NEW in TG) exoribonuclease complex (should get relationship via parent though)\r\n+capable_of GO:0000175 3'-5'-exoribonuclease activity (should get relationship via parent though)\r\n\r\nRelevant references (incl reviews):\r\n26726035 - Review: structure, function\r\n23352926 - Review: structure, function (evolutionary aspects)\r\n23910895 - Review: more emphasis on RNA threading\r\n17174896 - crystal structure of human Exo-9 (2nn6), human & yeast function\r\n20531386 - DIS3(L) isoforms: complex evidence by CoIP+MS, cellular locations by cell fractionation + colocolisation, substrate selectivity\r\n\r\nYeast crystals:\r\n23376952 (Makino et al, 2013) - 4ifd - Exo-11 + RNA\r\n25043052 (Wasmuth et al, 2014) - 4oo1 - Exo-10 (RRP6) + RNA\r\n27345150 (Kowalinski et al, 2016) - 5jea - Exo-10 (RRP44) + SKI7 (co-factor) + RNA by xray\r\n27174052 (Lui et al, 2016) - 5g06 (EM-3366) - Exo-10 (RRP44) + SKI7 (co-factor) by EM\r\n\r\nThanks,\r\nBirgit"},"comment":{"url":"https://api.github.com/repos/geneontology/go-ontology/issues/comments/242663130","html_url":"https://github.com/geneontology/go-ontology/issues/12574#issuecomment-242663130","issue_url":"https://api.github.com/repos/geneontology/go-ontology/issues/12574","id":242663130,"user":{"login":"dosumis","id":112839,"avatar_url":"https://avatars.githubusercontent.com/u/112839?v=3","gravatar_id":"","url":"https://api.github.com/users/dosumis","html_url":"https://github.com/dosumis","followers_url":"https://api.github.com/users/dosumis/followers","following_url":"https://api.github.com/users/dosumis/following{/other_user}","gists_url":"https://api.github.com/users/dosumis/gists{/gist_id}","starred_url":"https://api.github.com/users/dosumis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dosumis/subscriptions","organizations_url":"https://api.github.com/users/dosumis/orgs","repos_url":"https://api.github.com/users/dosumis/repos","events_url":"https://api.github.com/users/dosumis/events{/privacy}","received_events_url":"https://api.github.com/users/dosumis/received_events","type":"User","site_admin":false},"created_at":"2016-08-26T08:18:29Z","updated_at":"2016-08-26T08:18:29Z","body":"> OK, for now we'll have to move this entire branch under macromolecular complex.\r\n> And then sort out the more general issue in the new ticket.\r\n\r\n+1"}}
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