add parent negative regulation of translation in response to nitrogen starvation

[ValWood]

negative regulation of translation in response to nitrogen starvation

• synonym negative regulation of translation in response to amino acid starvation

could this have the parent " cellular response to amino acid starvation GO:0034198"

[pgaudet]

Isn't that some pathway that is not well defined by just being put under 'regulation of transcription'?

[ValWood]

translation....

It is a signalling pathway really https://www.pombase.org/term/GO:0043555 (downstream of TOR signalling)

but I have never seen it called anything except 'negative regulation of translation in response to nitrogen starvation/amino acid starvation.

This is just an attempt to group these, since they both exist. I think we could do a better job of this longer term.

[pgaudet]

@ValWood There are only 2 annotations to this term (negative regulation of translation in response to nitrogen starvation), both from pombase, both from the same paper: PMID:10725227.

You annotated the B-type cyclins Cig2 and Cdc13, that are regulated by the Ded1/Sum3 translation initiation factor - they are the target of the negative regulation of translation - they should anyway not be annotated to this term, should they ?

It seems 'cellular response to amino acid starvation' is a perfectly good term to annotate Cig2 and Cdc13 - in which case 'negative regulation of translation in response to nitrogen starvation' would not be needed anymore.

What do you think ?

Thanks, Pascale

[ValWood]

yes that annotation is incorrect. I removed it.

I only read the abstract but it seems. that Ded1/Sum3 is receiving a signal and "negative regulation of translation in response to nitrogen starvation" would be required to annotate this pathway.

However, for others we have done precomposition with the stress term

negative regulation of cytoplasmic translational initiation in response to stress   | gcn2 during cellular response to nitrogen starvation

So this still leaves the issue what is the difference between 'cellular response to amino acid starvation' and  cellular response to nitrogen starvation

which is what I was trying to establish, but by going around the houses!

[ValWood]

AND if we get rid of the term, we should also 'decompose' these (which look over-composed)

GOID	Term label
GO:1905287	positive regulation of G2/M transition of mitotic cell cycle involved in cellular response to nitrogen starvation
GO:0036278	positive regulation of transcription from RNA polymerase II promoter in response to nitrogen starvation
GO:0070321	regulation of translation in response to nitrogen starvation
GO:1901482	L-lysine import into vacuole involved in cellular response to nitrogen starvation
GO:0031142	induction of conjugation upon nitrogen starvation
GO:0010516	negative regulation of cellular response to nitrogen starvation
GO:1901481	L-glutamate import involved in cellular response to nitrogen starvation

[pgaudet]

For now I'll obsolete

• GO:0070321 regulation of translation in response to nitrogen starvation
• GO:0070322 negative regulation of translation in response to nitrogen starvation
• GO:0070323 positive regulation of translation in response to nitrogen starvation

OK ?

[ValWood]

OK!

[pgaudet]

Dear all,

The proposal has been made to obsolete

• GO:0070321 regulation of translation in response to nitrogen starvation
• GO:0070322 negative regulation of translation in response to nitrogen starvation
• GO:0070323 positive regulation of translation in response to nitrogen starvation

The reason for obsoletion is that these terms represent 'GO:0034198' cellular response to amino acid starvation'. There were 2 annotations to these terms (by PomBase) that have now been removed (see https://github.com/geneontology/go-ontology/issues/19092#issuecomment-600508114).

There are no mappings; this term is not present in any subset.

You can comment in the ticket: https://github.com/geneontology/go-ontology/issues/19092

We are opening a comment period for this proposed obsoletion. We’d like to proceed with the obsoletion this term on March 21st, 2020. Unless objections are received by March 21st, 2020, we will assume that you agree to this change.

Thanks, Pascale

[tberardini]

@ukemi pointed out this paper, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586203/, which shows that in Arabidopsis, at least one miRNA family is involved in regulating the translation of target mRNAs in response to nitrogen starvation. Perhaps these terms should be retained. We have not (yet) annotated the miRNAs but would use at least one of the terms slated for obsoletion.

[ValWood]

I had a use for them - but I now post-composed using "cellular response to nitrogen starvation"

happy to do it either way (although now I have changed) My only requirement is that nitrogen starvation/amino acid starvation. are linked in some way.

[pgaudet]

at least one miRNA family is involved in regulating the translation of target mRNAs in response to nitrogen starvation.

Shouldn't we post-compose it as: "negative regulation of translation - has_target xx" part of "cellular response to nitrogen starvation"?