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Source ontology files for the Gene Ontology
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NTR: response to cell envelope stress #10671

Closed gocentral closed 8 years ago

gocentral commented 10 years ago

As a child of GO:0006590. Proposed definition: "A process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in the cell envelope, e.g. a disruption of the cell membrane. "

Reported by: imk07

Original Ticket: geneontology/ontology-requests/10478

gocentral commented 10 years ago

Original comment by: rebeccafoulger

gocentral commented 10 years ago

Hi Ingrid,

Do you have a paper I could look at/reference for the definition, please?

thanks, Becky

Original comment by: rebeccafoulger

gocentral commented 10 years ago

Hi Becky,

A reference! I knew this wouldn't be so easy... ;-) Anyway, I searched PubMed with "envelope stress" to get reviews; e.g. I picked this older one:

16: Raivio TL. Envelope stress responses and Gram-negative bacterial pathogenesis. Mol Microbiol. 2005 Jun;56(5):1119-28. Review. PubMed PMID: 15882407. or the one from Carol Gross's lab: 18: Alba BM, Gross CA. Regulation of the Escherichia coli sigma-dependent envelope stress response. Mol Microbiol. 2004 May;52(3):613-9. Review. PubMed PMID: 15101969.

It's a bit difficult to come up with a straightforward definition. In a way, it is more a "stress acting at a given location" than "stress by a given agent" type thing, because there are many ways to disrupt the cell envelope. Can that be turned into a GO term?

This review actually says "membrane damage": 2: Poole K. Bacterial stress responses as determinants of antimicrobial resistance. J Antimicrob Chemother. 2012 Sep;67(9):2069-89. doi: 10.1093/jac/dks196. Epub 2012 May 22. Review. PubMed PMID: 22618862.

Does this help?

-Ingrid

Original comment by: imk07

gocentral commented 10 years ago

Mostly for go eds:

We have a small ontology of environmental conditions (oxidative stress etc) we use for making logical definitions of these terms. Time to add to production?

We already have a precedent for stress:

id: GO:0034976
name: response to endoplasmic reticulum stress
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating endoplasmic reticulum (ER) stress. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen." [GOC:mah]
synonym: "ER stress response" EXACT []
synonym: "response to ER stress" EXACT []
is_a: GO:0033554  ! cellular response to stress

I'm not really fond of the weasel-word "indicating" in this definition. I prefer the pattern Ingrid suggests of acting-at-a-location, or of specifically disrupting a cell component. Shall we adopt this as a general pattern?

Original comment by: cmungall

gocentral commented 10 years ago

Hi Chris, I've put it on Thursday's agenda for the editors call:http://gocwiki.geneontology.org/index.php/Ontology_meeting_2013-11-07

Where's the environmental conditions ontology stored at the moment?

Thanks for the extra info Ingrid!

Original comment by: rebeccafoulger

gocentral commented 10 years ago

Original comment by: rebeccafoulger

gocentral commented 10 years ago

Sorry for the delay Ingrid. Here's your new term: cellular response to cell envelope stress ; GO:0036460

Also reworded definition of 'GO:0034976 ! response to endoplasmic reticulum stress' to stress acting at the ER.

And created a JIRA issue as a holding place for the XP plan.

Thanks, Becky

Original comment by: rebeccafoulger