apoptotic process

[ValWood]

Please remove from the fission yeast slim set and add the taxon restriction 'never in S.pombe' See https://github.com/geneontology/go-annotation/issues/3474 for more detail.

[cmungall]

The linked paper (really interesting) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6069115/ suggests never-in Fungi

The paper also cites https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5864239/ "Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018" which may be informative for synonyms in this part of the ontology

UPDATE I see we use this PMID:18846107 for many def xrefs so we have used this, I would have expected attribution on syns too, but not so important

[pgaudet]

For 'apoptotic process ' and children, there are 52 EXP annotations to fungal proteins.

Example papers:

• PMID:16436509 "Yeast AMID homologue Ndi1p displays respiration-restricted apoptotic activity and is involved in chronological aging. " cerevisiae @srengel
• PMID:18047809 "Ectopic expression of mitochondria endonuclease Pnu1p from Schizosaccharomyces pombe induces cell death of the yeast."

Looks like this is related to apoptosis but different ?

Thanks, Pascale

[ValWood]

I only put "never in fission yeast"

There are papers which refer to apoptosis,. The general feeling in the pombe community is that people originally wanted to label this 'apoptosis' but it is not really apoptosis. It is also difficult to separate cause and effects here. Certainly when cells age proteostasis breaks down (more ER overload, more ERAD etc) proteases get released and things get degraded. The whole 'apoptosis' thing is part of the history of yeast researchers trying to make yeast relevant as a human model. Usually it is- but here it is still up for debate.

Current evidence it seems that there not enough to label these processes as apoptosis without any real positive evidence that this is really regulated phenomena. At present we just don't have any such evidence for 'apoptosis' in fission yeast despite many people looking a lot for a long time.

The S. cerevisiae community may feel differently.

I removed the PMID:18047809 "Ectopic expression of mitochondria endonuclease Pnu1p from Schizosaccharomyces pombe induces cell death of the yeast." annotation yesterday.

The researchers removed the mitochondrial signal sequence to ectopically express a non-specific mitochondrial nuclease in the cytosol/nucleus. Unsurprisingly nuclear DNA was fragmented. I should not have annotated this to apoptosis. I now has only a phenotype annotation.

[srengel]

please do not add this constraint for all yeasts. we need these terms for the S.cerevisiae community.

[pgaudet]

I've added Never in NCBITaxon:2 Bacteria

I think that's all we can assert confidently.

[pgaudet]

https://github.com/geneontology/go-ontology/pull/20312