Obsoletion: abortive mitotic cell cycle GO:0033277

ValWood commented 3 years ago

Please taxon restrict abortive mitotic cell cycle GO:0033277

There are only 2 EXP annotation based on:

http://europepmc.org/article/MED/23509158 entitled "Megakaryocyte-specific deletion of the protein-tyrosine phosphatases Shp1 and Shp2 causes abnormal megakaryocyte development, platelet production, and function."

so this might even be a phenotype?

pgaudet commented 3 years ago

@hdrabkin those are mouse annotations; would you please check that they are valid?

hdrabkin commented 3 years ago

Are you saying it does not occur in mammals? Can you point me to a reference?

ValWood commented 3 years ago

Hi Harold,

My original request was to make a taxon restriction never in fungi for 'abortive mitotic cell cycle' as it is never normal for fungi to do this- unless a gene was deleted which compromised completion of a cell cycle.

The title of the paper seems to imply that this is not normal in mammalian cells either: "Megakaryocyte-specific deletion of the protein-tyrosine phosphatases Shp1 and Shp2 causes abnormal megakaryocyte development, platelet production, and function."

of course, if you delete cell cycle components the cell cycle will abort, because it can't complete (even if the checkpoints are activated), if a required component is missing, aborting (i.e. a non-resolvable cell -cycle block) is the only option.

In this paper, where the title specifies "abnormal" (because the abortive cell cycle is inflicted by a deleterious mutation), this presumably isn't a normal process.

Presumably what would happen in a 'normal ' context if the cell cycle cannot continue (i.e in ageing cells or otherwise defective cells), if the cell cycle checkpoints can't deal with the problem then the outcome would usually enter senescence or apoptotic pathways. But I'm pretty sure "abortive mitotic cell cycle" is describing a phenotype that is observed. It might be better as a 'related' synonym of some other process(s). Although I'm not sure that this paper would be annotated to any of those terms.

All you can get from this paper is "mitotic cell cycle" although they do say "The cause of the block in ploidy in Shp1-deficient megakaryocytes remains undefined but suggests a defect in the formation of the cleavage furrow and/or cytokinesis at the 2N/4N transition during the endomitotic process". I did not read in detail do I don't know if it is possible to annotate to a more specific cell cycle term.

To have the term "abortive cell cycle" in GO we need a term to support its existence as a biological process (as opposed to a phenotype as in this instance) , rather than a term to disprove its existence. It might exist (I don't know multicellular biology well enough), but this annotation/publication isn't an example.

ValWood commented 3 years ago

Hang on, I see the term comment

"Note that this term should be used only for abortive mitotic events that occur normally, e.g. during megakaryocyte differentiation; it should not be used for incomplete mitosis resulting from mutation or other abnormal occurrences. Note that this term should not be confused with 'endomitotic cell cycle ; GO:0007113', which describes a process in which no mitotic spindle forms."

but maybe this is a terminology issue.

If I search PubMed for "megakaryocyte" and "abortive cell cycle" I get no results. but if I search "megakaryocyte" and "endomitotic cell cycle" I get 20 results. Including:

Endomitosis in megakaryocytes....PMID: 18677109
MK achieve polyploidy by switching from a normal to an endomitotic cell cycle. PMID: 16258287
endomitosis of megakaryocytes...PMID: 19339696 etc.

So I'm not sure that the comment is correct? particularly "Note that this term should not be confused with 'endomitotic cell cycle ; GO:0007113', which describes a process in which no mitotic spindle forms." which is true, but it sounds like this term is meant to represent "endomitotic cell cycle"?

GO:0007113 endomitotic cell cycle A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell. Comments Note that this term should not be confused with 'abortive mitotic cell cycle ; GO:0033277'. Although abortive mitosis is sometimes called endomitosis, GO:0033277 refers to a process in which a mitotic spindle forms and chromosome separation begins.

We need to look into this more- but it seems that"

"abortive mitotic cell cycle" probably isn't needed (It seems to refer to "endomitotic cell cycle")
"endomitotic cell cycle" is badly defined (this definition sound like it could be based on the cytological markers of a fission yeast endomitotic cell cycle which occurs in some mutants, which fits with the date and the fact that the cell cycle workshop had mainly fission yeast cell-cycle experts)