#1043 Annot. to GO:0010421 hydrogen peroxide-mediated programmed

[Paola Roncaglia]

Hello,

Stemming from the apoptosis project, some edits have been done in the more general 'programmed cell death' node as well.
In particular, I'm looking at GO:0010421 hydrogen peroxide-mediated programmed cell death.
A new is_a parent term has just been created and added to it ('programmed cell death in response to reactive oxygen species'), and also an is_a link to existing 'cellular response to hydrogen peroxide'.
Now looking at the manual annotations, one from UniProt looks incorrect:

F2JXJ3 based on PMID:18502869:
this is a bacterial protein and the paper abstract reads:
'The marine bacterium Pseudoalteromonas tunicata produces an antibacterial and autolytic protein, AlpP, which causes death of a subpopulation of cells during biofilm formation...'.
Therefore this process shouldn't be annotated to a type of (programmed) cell death, but rather to 'killing of cells of other organism' or similar, I think.

Many thanks,
Paola

[rach_huntley]

Hi Paola,

I'm looking into this and it looks like the cell death is from the same organism, not a second organism;
"LodA, in M. mediterranea has a similar ecological function to AlpP during biofilm development. LodA production leads to cell death of a subpopulation of cells within microcolonies of M. mediterranea biofilms".

There is another annotation from this paper to "negative regulation of single-species biofilm formation", confirming it's one species involved. Does this still look incorrect to you?

If you don't consider it programmed cell death, I could always add an extension to the other annotation to say dependent_on: hydrogen peroxide?

Thanks,
Rachael.

[Paola Roncaglia]

Hi Rachael,

Thanks for looking into this. This one is a bit tricky. If cell death occurs in the same species that produces the annotated protein, but not the same individual organism producing the protein, is it cell death or cell killing?

'cell death' is_a 'single-organism cellular process' (= Any process that is carried out at the cellular level, occurring within a single organism.)

'cell killing' is_a generic 'biological process' and is defined as "Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions."

I suspect that if the protein-producing bacterium is part of a colony, the hydrogen peroxide will have effect on the protein-producing bacterium as well as on other individuals nearby. This sounds like both cell death and cell killing to me, but looking at it from the bacterial/biological point of view, maybe we should consider it as a form of programmed cell death. Then the current annotation would be correct. But it might be good to hear the opinion of a microbiologist...

Let me know what you think.
Thanks,
Paola

[Paola Roncaglia]

Thinking again, if the protein leads to death of other cells, we can't really annotate it to a single-organism cellular process... or not to that alone... or we need to change the way we look at programmed cell death.

[rach_huntley]

Ah, OK. I see the distinction - I was thinking of other organism as other species - the only way I have used these terms before is when two species are involved. I will go with your original suggestion and change the term to killing of cells of other organism.

Thanks!
Rachael.