cell cycle arrest in response to nitrogen starvation

[gocentral]

Hi,

I wonder if :

GO:0071849 G1 cell cycle arrest in response to nitrogen starvation (The process in which the cell cycle is halted during G1 phase, as a result of deprivation of nitrogen.)

applies to any other organisms than yeast? I know that nitrogen starvation results in autophagy in other organisms, but not if this occurs in a specific part of the cell cycle, and I have a feeling some might go into a short bout of quiescence before cell death.

In fission yeast, nitrogen starvation results in G1 arrest followed by quiescence (ref PMID: 19366728) it would be nice to capture this with one term, ideas? Can GO:0071849 be part_of GO:0070315 G1 to G0 transition involved in cell differentiation (A cell cycle arrest process that results in arrest during G1 phase, whereupon the cell enters G0 phase, in the context of cell differentiation.)

Reported by: antonialock

Original Ticket: geneontology/ontology-requests/9392

[gocentral]

• assigned_to: nobody --> paolaroncaglia

Original comment by: paolaroncaglia

[gocentral]

Hi Antonia,

It seems that the effects of nitrogen starvation have been studied, other than in fission and buddying yeasts, in plants (Arabidopsis, coffee plant), in algae (Chlamidomonas), and more. However, I cannot easily tell if nitrogen starvation results in G1 cell cycle arrest in species other than yeasts, and GO:0071849 has no current annotations to help answer the question. I'd be reluctant to add a taxon constraint to GO:0071849 unless we know for sure that this is the case. I can ask some of the plant curators if they have any comments on this.

As for the second part of your request, I'm not entirely sure, based on PMID: 19366728, that the same gene products involved in G1 cell cycle arrest in response to nitrogen starvation are also implicated in the entry into quiescence, which is likely to be controlled by multiple factors I think. Therefore, it may not be 100% appropriate to try to represent both processes with the same term to use in annotations. GO:0071849 could have a part_of relationship to GO:0070315 only if we had evidence that GO:0071849 is necessarily (always) part of GO:0070315 (i.e., wherever GO:0071849 exists, it is as part of GO:0070315, and the presence of the GO:0071849 implies the presence of GO:0070315). Currently, the only manual annotation to GO:0070315 is to a mouse protein, so I'd be reluctant to create that link due to the lack of further knowledge. I'll link this SF request to the wiki that Becky has set up for Cell Cycle (http://wiki.geneontology.org/index.php/Cell\_Cycle).

In the short term, I'll leave this item open to see if plant curators wish to add any comment, but if not, I'll close this item. You may re-open it at any time if you find references to support changes for GO:0071849.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

• labels: 397373 --> cell cycle

Original comment by: paolaroncaglia

[gocentral]

Ok, thank you Paola!

Original comment by: antonialock

[gocentral]

Antonia and Paola,

According to http://genomebiology.com/2010/11/2/R17, this phenomenon also occurs in algae: "Nitrogen starvation in diatoms generally leads to a G1-phase arrest". I was not able to find literature on whether this occurs in Arabidopsis or not. Currently no Arabidopsis genes annotated to GO:0030996 (cell cycle arrest in response to nitrogen starvation).

Donghui TAIR

Original comment by: donghui

[gocentral]

Thanks Donghui.

Definitely no taxon constraint for GO:0071849 then. As for the second part of Antonia's request, it may be some time before consistent efforts can be devoted to the cell cycle ontology revision, but this SF item is now linked to the relevant wiki, so this issue won't be forgotten.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

• status: open --> closed-works-for-me

Original comment by: paolaroncaglia