Question about GO:0097199 cysteine-type endopeptidase activity involved in apoptotic signaling pathway

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Hello,

What is this term supposed to represent ? "GO:0097199 cysteine-type endopeptidase activity involved in apoptotic signaling pathway" ? Activator caspases ?

Note that there are no annotations.

Thanks,

Pascale

Reported by: pgaudet

Original Ticket: geneontology/ontology-requests/10645

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• assigned_to: David Osumi-Sutherland

Original comment by: dosumis

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my interpretation is yes, activator caspases Ruth

Original comment by: RLovering

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• labels: --> Apoptosis, Other term-related request
• assigned_to: David Osumi-Sutherland --> Paola Roncaglia

Original comment by: paolaroncaglia

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Hi Pascale (and Ruth),

Yes, these are activator caspases. The term already has synonyms for 'initiator caspase activity' and 'apical caspase activity', but I'm happy to add 'activator' too - will do tomorrow.

The background behind this term, and its sibling GO:0097200 'cysteine-type endopeptidase activity involved in execution phase of apoptosis', is as follows - taken from an old presentation of mine:

(...) GO:0030693 caspase activity was obsoleted because it represents gene product(s) the distinction from other types of proteases is outside the scope of GO

However, we still had several terms referring explicitly to “caspase activity” in GO, e.g. GO:0043281 regulation of caspase activity.

We might be doing the community a disservice in not referring to caspases at all in GO.

Therefore, based on consensus among experts and editors: caspase activity => cysteine-type endopeptidase activity involved in apoptosis

Experts would like to have terms for activities of commonly called “initiator caspases” and “effector caspases”, and to distinguish between the two of them, but without using the word “caspase”. We did it as follows:

cysteine-type endopeptidase activity involved in apoptotic signaling pathway; GO:0097199 [NEW] Synonyms: initiator caspase activity, apical caspase activity

cysteine-type endopeptidase activity involved in execution phase of apoptosis; GO:0097200 [NEW]
Synonyms: effector caspase activity, executioner caspase activity (...)

I hope this helps clarify. Tomorrow I'll look into adding PMID references/annotations (the term has, of course, an internal reference for GOC:mtg_apoptosis, as often happens when many new terms come out of a content meeting, but I appreciate that the more information, the merrier...). And I'll possibly expand on the definition or add a definition comment.

Thanks, Paola.

Original comment by: paolaroncaglia

[gocentral]

Hi Pascale,

Following up on my comment above, I've done the following edits:

GO:0097199 cysteine-type endopeptidase activity involved in apoptotic signaling pathway: added dbxrefs: PMID: 11717445, http://en.wikipedia.org/wiki/Caspase; added 'activator caspase activity' as a narrow synonym; added def. comment: Examples of gene products that may be annotated to this term include CASP2, CASP8, CASP9, and CASP10, also called initiator (or apical, or activator) caspases.

GO:0097200 cysteine-type endopeptidase activity involved in execution phase of apoptosis: added dbxref http://en.wikipedia.org/wiki/Caspase; added def. comment: Examples of gene products that may be annotated to this term include CASP3, CASP6 and CASP7, also called effector (or executioner) caspases.

As for adding annotations to GO:0097199: 1) There are some manual experimental annotations for caspases 2 and 8 to GO:0097153 'cysteine-type endopeptidase activity involved in apoptotic process' (parent of GO:0097199). I'm emailing MGI to see if they can be moved to GO:0097199. 2) PMID: 11717445 describes the role of human caspase 10 as an initiator caspase. I'm emailing Rachael to ask if this paper may be annotated to GO:0097199.

Closing this ticket now, but feel free to re-open if you have any comment. Thanks, Paola

Original comment by: paolaroncaglia

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• status: open --> closed-accepted

Original comment by: paolaroncaglia

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Great, Thanks for all this Paola !

-Pascale

Original comment by: pgaudet