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#1056 abnormal contractile ring organization / uncoupled cytokinetic rings
Based on this paper I don't think "actomyosin contractile ring" can be synonymous to "cytokinetic ring" (there appears to be more than one ring one consisting of actomyosin and one of other proteins. They appear to be coordinated but can be uncoupled in different mutatns). See the section headed "the absence of gef2 or nod1 reveals that node proteins can be recruited separately and form independent rings"
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3547912/
based on this can we have the terms:
abnormal contractile ring organization
and the child:
uncoupled cytokinetic rings
also need to add to the def of actomyosin contractile ring splitting
that this term refers to the actomyosin contractile ring
won't get to this today ... but looks like GO needs a bit of work too, because this synonym scope looks inconsistent with that paper:
id: GO:0005826
name: actomyosin contractile ring
[snip]
synonym: "cytokinetic ring" NARROW []
can you put in a GO ticket? ta,
m
yep, will do now
also I would like to request
"abolished cytokinetic ring assembly" (not actomyosin ring only)
and then a child term:
"formation of medial cortical node fragments"
with a definition along the lines of "a cell phenotype where medial cortical nodes form fragments, but do not form into a ring"
I have asked for author input on this so might come back with another comment..
Last edit: Antonia Lock 2013-09-05
are you sure that you "other ring" isn't the medial node.
http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0071341
I don't think we should alter the fact that everyone uses cytokinetic ring to refer to the actomyosin contractile ring, and we shouldn't refer to every ring which forms at the cell division site as a "cytokinetic ring" even if they have done so in this paper.
what are the components of the ring they are referring to?
Do they call it anything else other than a "cytokinetic ring"?
val
or this
http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0036391#term=info
yes well. The paper is about the medial cortical node proteins.
From the paper (paraphrasing different bits): These form a belt of cortical dots in interphase, but during cytokinesis the nodes seem to fuse and form a ring that is separate from the actomyosin ring. This second ring seems to form and constrict simultaneously with the actomyosin ring. Absence of the proteins that are part of the ring leads to increased G2 duration and an offset division plane (there is a genetic interaction with the plo1 pathway).
They say in the discussion that they believe that there are several rings that are intertwined (= one cytokinetic ring)
I asked the author, this was her reply:
No, I do not know what my rings are (maybe scaffolds or links between the plasma membrane and the actomyosin ring) and I don't have a name for them. I just know that they are not part of the actomyosin ring, nor the septum. My former boss, Takashi Toda, used to call them "rainbows", but I doubt this poetic wording could work as a Go term! For info, Mercè Guzman-Vendrell, MCB 2013 saw a similar stack of rings (Mercè Guzman-Vendrell, MCB 2013 , somewhere in the supp material).
ok....we can avoid it altogether if you are not convinced
name: accumulation of medial cortical node fragments in mitosis
"a cell phenotype where upon mitotic entry, medial cortical nodes fuse to form short or long fragments, but do not form a complete ring-like structure"
and make it a child of something else?
ps. no it is not the septum, they look at calcofluor stainging and it is separate
I think I would wait. Do you see this ring splitting in WT cells or only on mutants? The ring which is called the "cytokinetic ring" should be the contractile ring which contains the motor proteins "actin and myosin".....for the time being.
If more papers support this change we should do it later when some nomenclature is established. i think is we try to do it now it will probably be wrong.
Might be worth talking to people work more on cytokinesis too...I will ask next time I speak to somebody....otherwise we could end up with a proliferation of terms which don't work for all organisms.
This paper has a good composite EM of a contractile ring
http://www.sciencedirect.com/science/article/pii/S0966842X09002352
...this would include actin, myosin, cdc8 etc.
I think other rings if they are separate should not be described as the "cytokinetic ring"
...I guess it is possible they become part of the actomyosin ring.....
Ok...should I not include any of these phenotypes then?
I still think that this looks like the correct term....it is already used for some of these proteins?
http://www.pombase.org/spombe/related/GO:0071341
you could ask Isabelle
no I annotated the genes in this paper to that term. But look at the section headed "the absence of gef2 or nod1 reveals that node proteins can be recruited separately and form independent rings" and fig4
Well, I'm glad I didn't try to do anything on this yesterday!
At present, some 'actomyosin contractile ring' terms have strings with 'cytokinetic ring' as related synonyms. I think that's correct, and would advise GO to do the same, based on all the comments here, plus the meaning implied by words in the phrase 'cytokinetic ring' itself. In other words, I won't make 'cytokinetic ring' terms exact synonyms for 'actomyosin contractile ring' terms, because the meanings really aren't exactly the same (for example, bacterial FtsZ forms a ring that isn't actomyosin, may or may not be contractile, but certainly is "cytokinetic" in that it forms during, and is required for, cytokinesis).
I can add a term for the medial cortical node fragments. Beyond that, I can look at the paper after I do some other stuff if there's anything else outstanding.
The nodes form first and are involved in ring positioning...they coalesce and this eventually form the actin ring, when the contractile proteins are added (this is the ring also called the cytokinetic ring)
absence of gef2 or nod1 reveals that node proteins can be recruited separately and form independent rings" and fig4
(this is a mutant though? you don't see the "ring splitting" or independent assembly in in WT cells, because this cortical band is the point of eventual contractile ring assembly?)
All I'm saying is there is only one contractile ring/cytokentic ring/actomyosin ring in
WT cells, although there are precursors to the contractile ring (so we shouldn't change GO to call all rings at the division plane "cytokinetic rings"), or to represent non-WT observations.
We should still represent these phenotypes.
Let me know if this doesn't make sense.
val
We should look at these phenotypes
FYPO:0000161
abnormal actomyosin contractile ring assembly
and is "uncoupled cytokinetic rings"
the same as
FYPO:0000232
actomyosin contractile ring splitting
?
or your suggestion
accumulation of medial cortical node fragments in mitosis
It seems like there's a lot still up in the air for this ticket, but a couple of things look doable. First, there's no problem with this suggestion:
... because the term name and xp are already specific for the actomyosin ring.
It also sounds like it won't be too controversial to capture one of the phenotypes. If I understand earlier comments correctly, in the mutant of interest, medial cortical nodes (GO:0071341) form, but don't go on to coalesce into the medial cortex (GO:0031097).
I do have a couple of follow-up questions, though (of which the first is the most important):
Are there more nodes in the mutant than in wt, or is it just that the nodes stay separate?
Should there be a GO BP term for the nodes coalescing to form the cortex (e.g. 'medial cortex assembly')? It might make an xp for the phenotype term simpler.
Is the 'medial cortical node part_of medial cortex' link in GO really accurate, or are the nodes precursors of the cortex? I'm not sure it's worth changing in GO at the moment, but if they ever adopt the develops_from relation, that might capture the biology better.
Re:
and
-Is the 'medial cortical node part_of medial cortex' link in GO really accurate, or are the nodes precursors of the cortex? I'm not sure it's worth changing in GO at the moment, but if they ever adopt the develops_from relation, that might capture the biology better.
From my understanding the medial cortical nodes are part of the medial cortex
cortex = "The region of a cell that lies just beneath the plasma membrane"
So maybe the wording of the medial cortex term def is a bit weird. if the medial cortex was defined without using the word "band" it would probably be fine. People have referred to this as medial ring, and medial band, but I think they could just be referring to the "nodes" when they use these phrases.
So should medial cortex just be "the part of the cell cortex at the midpoint of the cell"? Or does it have other distinguishing features, e.g. composition?
When people talk about the medial cortex, do they mean a set of (still discrete) nodes, or have the nodes merged into something contiguous at that point?
For this
So should medial cortex just be "the part of the cell cortex at the midpoint of the cell"?
I think definitly yes
It has synonym "medial ring" which shuld be related, or deleted. it could refer to the septin band child, or i think people used to refer to the cortical nodes as a medial 'band', although they are discrete.....
Antonia does this make sense to you?
No! - I don't know enough....I'm happy to go with whatever you think is correct :)
Or,
we should have
medial cortex
-- medial ring (new)
-- medial nodes
-- medial spetin ring
if the medial ring is a "thing" and not just the coalesence of the nodes into the eventual actinomyosin ring...
....mid1 and mid2 are described as "medial ring proteins"
(all I am saying is medial ring shouldn't be equivalent to medial cortex, medial cortex is a 'region')