pgaudet
commented
6 years ago Proposal with @thomaspd
- Obsolete
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GO:0051715 cytolysis in other organism: 43 EXP
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GO:0051801 cytolysis in other organism involved in symbiotic interaction
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regulation of these terms
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Rehouse annotations under either
- GO:0051838 cytolysis by host of symbiont cells
- GO:0001897 cytolysis by symbiont of host cells
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Keep GO:0019835 cytolysis as a grouping term (+ tag 'do not annotate').
Thanks,
Pascale
ValWood
RLovering
Stemming from https://github.com/geneontology/go-ontology/issues/12343.
The ‘cytolysis’ node needs work to clarify the meaning of the term (phenotype vs. active process), decide on its fate (in scope for GO vs. not) and on rehousing/deleting its annotations if necessary. Currently:
[Term] id: GO:0019835 name: cytolysis namespace: biological_process def: "The rupture of cell membranes and the loss of cytoplasm." [UniProtKB-KW:KW-0204] subset: goslim_chembl subset: gosubset_prok synonym: "autolysin activity" RELATED [] synonym: "bacteriocin activity" RELATED [] synonym: "bacteriolytic toxin activity" RELATED [] synonym: "holin" RELATED [] synonym: "lysin activity" RELATED [] synonym: "lysis" BROAD [] synonym: "necrosis" RELATED [] xref: Wikipedia:Cytolysis is_a: GO:0009987 ! cellular process
Children of ’cytolysis’: (is_a) cytolysis in other organism plus ‘regulation of cytolysis’ triad. Importantly, ‘cytolysis in other organism’ is explicitly defined and placed in the ‘cell killing’ branch:
[Term] id: GO:0051715 name: cytolysis in other organism namespace: biological_process alt_id: GO:0001901 def: "The killing by an organism of a cell in another organism by means of the rupture of cell membranes and the loss of cytoplasm." [GOC:ai] subset: gosubset_prok synonym: "cytolysis of cells of another organism" EXACT [GOC:bf] synonym: "cytolysis of cells of another, non-host, organism" NARROW [] synonym: "cytolysis of cells of competing organism" NARROW [] is_a: GO:0019835 ! cytolysis is_a: GO:0031640 ! killing of cells of other organism
So then what does the GO term ‘cytolysis’ stands for?
1) If it stands for the explosion of a cell as an uncontrollable reaction to osmotic stress (https://en.wikipedia.org/wiki/Cytolysis), then it’s a phenotype rather than a process, and it shouldn’t be in GO. However,
2) It it stands for a form of cell killing, then it’s a process and we can have it in GO. (The UniProt keyword used as a dbxref also suggests cell killing, see http://www.uniprot.org/keywords/KW-0204.) Attention should be paid as to whether there is an appropriate term in GO already: 2a) Does it stand for cell killing directed towards the same cell that does the killing? Then it’s programmed cell death. More specifically, it could be ‘autolysis’ (“A programmed cell death process observed in bacteria and filamentous fungi and leading to spontaneous death by lysis. Examples are lysis of the mother cell during sporulation of Bacillus subtilis and self-degradation of fungal cells in Aspergillus nidulans. Autolysis is also involved in bacterial biofilm formation.”; never_in_taxon Metazoa). 2b) Does it stand for cell killing directed towards cells in the same organism? Then it’s a form of cell killing. The existing term ‘cell killing’ could be used, or its child ‘complement-dependent cytotoxicity’ or a newly created child of ‘cell killing’. Also see https://github.com/geneontology/go-ontology/issues/12343#issuecomment-196421409, https://github.com/geneontology/go-ontology/issues/12343#issuecomment-196430345, https://github.com/geneontology/go-ontology/issues/12343#issuecomment-196436655. 2c) Does it stand for cell killing directed towards cells in other organisms? Then it’s a form of ’killing of cells of other organism’; precisely, it’s the existing ‘cytolysis in other organism’, which should be renamed ‘killing of cells of other organism by cytolysis’ or similar. 2d) Does it stand for cell killing directed towards unicellular cells in the same species, but different from self? E.g. in a colony of bacteria. Still a form of ‘cell killing’ I’d say, also see below.
In all cases above, the direct manual annotations to ‘cytolysis’ and its regulation terms would need to be examined. (There are 67 direct manual experimental annotations to ‘cytolysis’ alone.) The necessity of revising annotations to ‘cytolysis’ is confirmed when I look at the first of the supporting papers in QuickGO, http://europepmc.org/abstract/MED/25876762, describing features of antimicrobial peptides in fish - it’s the fish peptides that are annotated to cytolysis, so in this case I’d lean towards ‘killing of cells of other organism by cytolysis’ = existing ‘cytolysis in other organism’. However, 3 E. coli annotations to ‘cytolysis’ seem to refer to self-lysis = autolysis, or perhaps to cell killing directed towards cells of the same species but not the same organism.