Review annotations to GO:0019835 cytolysis and regulation children

[pgaudet]

Tge proposal has been made to obsolete GO:0019835 ‘cytolysis’ and its regulation children, see 'https://github.com/geneontology/go-ontology/issues/13041'

There are 10 annotations remaining: https://docs.google.com/spreadsheets/d/1_A0Pzar4fu1y-jnVwRj85dH5gxjac52OwpUbeBAAw6g/edit#gid=0

• 2 ARUK @RLovering - done
• 3 CACAO @dsiegele
• 1 dictyBase
• 2 PseudoCAP
• 3 UniProt (from Sylvain)

Please correct your annotations - suggestions have been made.

Thanks, Pascale

[pfey03]

@pgaudet the best term to use for our annotation would be: GO:0140367 antibacterial innate immune response This is not taxon restricted for Dicty, but the second part of def is a problem: "An defense response against a bacteria mediated through an innate immune response. An innate immune response is mediated by germline encoded components that directly recognize components of potential pathogens"

Dicty has certain immune responses but a primordial immunity. However, the term itself describes what the authors intend quite well, as 'bacteriolytic activity' which they use often is not a GO term. They show that this gene is responsible for this activity in the phagosome.

[pgaudet]

Hi @pfey03 Innate immune response is not appropriate for unicellular organisms, without large changes to the ontology. How about if we created 'killing of bacteria ingested by phagocytosis' as a child of 'killing of cells of another organism' ? (I cannot find how this is represented for macrophages in GO, but that would be general enough to cover that as well, or we could add a child if needed)

What do you think ?

[pfey03]

Hi @pgaudet maybe it could be 'killing of phagocytosed bacteria' Not sure if the verb is very common but it's correct. Maybe your term is better, can you add a synonym such as: 'bacteriolysis after phagocytosis' or something along these lines?

Many thanks, this would be a good term to add instead!!

[pfey03]

I will wait then until the new term is available in P2GO to update this annotation.

@pgaudet are you adding the term above? Thanks!

[sylvainpoux]

Hi Pascale,

I had a look to these annotations and they are 'correct' in the sense that these proteins really mediate cell lysis (in a context of programmed cell death)

For example, Ninjurin promotes plasma membrane rupture. Which term would you propose then? If we just delete this term, we will lose valuable information

Thanks

Sylvain

[sylvainpoux]

Hi @pgaudet

I really think that it is an error to remove cytolysis. term. A bunch of human proteins mediate this process in the context of programmed cell death (see NINJ1 for axample) or innate immunity (see PMID:34022140 for a case of cytolysis in another organism GO:0051715 mediated by GSDMB)

Deleting this term would remove some valuable annotation and knowledge. Controlled cell membrane rupture and cytolysis is an emerging field and deleting these term would be an error in my opinion, since recent publications in Cell or Nature describe this process.

Sylvain

[sylvainpoux]

After discussion with @pgaudet , I found alternative terms and changed my annotations to remove cytolysis annotations Thanks Sylvain

[pgaudet]

@glwinsor can you please review the Pseudocap annotations ?