Proposal for "amino acid starvation" and "nitrogen starvation"

[ValWood]

I would like to understand the difference between this term: GO:1990928 response to amino acid starvation/ cellular response to amino acid starvation Definition Any 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 deprivation of amino acids. [PMID:7765311]()

and nitrogen starvation. The paper used in the reference [PMID:7765311 which describes "amino acid starvation" seems to be describing total removal of nitrogen, so I don't see a difference between these term and

GO:0006995 cellular response to nitrogen starvation

Does anyone know? should main acid starvation be a child of nitrogen starvation?

users @ValWood pombase Uniprot @Antonialock FlyBase @hattrill and others. I will check my annotations...

I am aware of a "response" called "amino acid stress" where one or more amino acids are removed from the food. But that does not seem to be what is described here.

[ValWood]

I just spotted the children like

"cellular response to leucine starvation" which is the removal of one amino acid. So this seems to be describing a mixture of "amino acid stress" and nitrogen starvation"

If others agree with this , suggest 1) change the reference to one which represents "specific amino acid removal" 2) add synonym "amino acid stress" 4) refine the definition.

[ValWood]

I also just noticed that the "nitrogen starvation" terms refer specifically to inorganic nitrogen. These terms are used all the time for yeast. There are annotations from all yeast (pombe, cerevisiae, candida) and PomBase use them in 1000s of extensions). We don't differentiate between organic and inorganic nitrogen source when we use these terms (and neither do the authors). Usually they are referring to amino acid supply. Does "response to nitrogen starvation" term need to refer to inorganic nitrogen? We even have specific terms hardwired underneath here.

[Antonialock]

Hmm, can an organism truly starve of a specific amino acid if it has the capability to synthesise it?

In my understanding TOR senses nitrogen levels. When levels are low, autophagy is upregulated, protein synthesis is down and amino acid import is up. So "amino acid management" is a consequence of nitrogen starvation?

Different sources of nitrogen can be used: inorganic or amino acids like leucine, proline, gutamine. Some amino acids make for poor nitrogen sources (eg leucine) and some for good nitrogen sources.

Jurg might be a good person to ask to clarify?

[ValWood]

I'm in a conversation with Janni Petersen, who is the expert here. This is the next part of the conversation.

nitrogen starvation: Current definition: 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 deprivation of nitrogen.

Revise to:
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 the depravation of nitrogen to a level below that 
required to sustain  cell division.

Add Comment:
In yeast nitrogen starvation results in a reversible arrest of 
proliferation (i.e. cell cycle exit).

Request new term

nitrogen stress:  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 the reduction in bioavailable 
nitrogen.

Add Comment
This can include reduction in bioavailable nitrogen by changing diet to 
a poor nitrogen source.  In yeast reduced available nitrogen 
concentration resets the cell sizer and results in earlier mitotic entry 
and division at reduced size.

Reference PMID:33823663 + others?

This is from PMID:33823663. I think "amino acid stress" is equivalent to "nitrogen stress" that I describe above. This is what I was trying to establish. The distinction between 'stress' and 'starvation' is really important because it has opposite effects.

[ValWood]

I'm also trying to make the terms generic. Starvation (complete deprivation) for some organisms would result in cell death, but some can go into quiescence or differentiate and survive.

[ValWood]

This is the final proposal after consulation with Janni:

Nitrogen starvation and nitrogen stress and amino acid starvation and amino acid stress terms are used differently in the community. The difference is important because for those studying TOR signalling these stresses have different responses (but use the same pathway).

Having these terms correctly defined is important to create GO-CAM models for these pathways. because the same signalling pathways have different outcomes in response to starvation vs limitation. It is more than just semantics.

Proposal below involves descendants of the term:

GO:0043562 cellular response to nitrogen levels Definition 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 reflecting the presence, absence, or concentration of inorganic nitrogen.

1. nitrogen starvation: Current definition: 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 deprivation of nitrogen. Revise to: 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 the deprivation of nitrogen to a level below that required to sustain cell division. Add Comment: In yeast nitrogen starvation results in a reversible arrest of proliferation (i.e. cell cycle exit). Reference PMID:33823663

Rationale. The wikepedia definition of https://en.wikipedia.org/wiki/Starvation “starvation” Is below the level required to maintain an organism's life (extreme malnutrition), and this is really how it is used in biology. Howe er, to allow for organisms that can enter quiescence in response to nitrogen starvation the definition for G is altered a little.

New term request nitrogen stress: 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 the reduction in bioavailable nitrogen.

Add Comment
This can include reduction in bioavailable nitrogen by changing diet to 
a poor nitrogen source.  In yeast reduced available nitrogen 
concentration resets the cell sizer and results in earlier mitotic entry 
and division at reduced size.

References This is the seminal paper for this PMID: 872891 P Fantes, P Nurse Control of cell size at division in fission yeast by a growth-modulated size control over nuclear division also add for more recent TOR and endosulphine pathway papers PMID:17952063 PMID:33823663 PMID: 26776736 Add synonym “nitrogen limitation” Add related synonym “poor nitrogen course” Add exact synonym “amin acid stress”

GO:1990928 response to amino acid starvation Please add the parent “response to nitrogen starvation” This is a type of nitrogen starvation. In higher eukaryotes it refers to the removal of protein from food (i.e the complete nitrogen sources), and in yeast it refers also to nitrogen starvation.