question NMS complex interaction involved in chromosome segregation (and descendants)

[gocentral]

I just spotted a weird process term(s)

GO:0044768
"NMS complex interaction" involved in chromosome segregation (and descendants)

The interaction and association of NMS complexes required for kinetochore-spindle binding and chromosome segregation to occur. (which seems to be describing a specific binding interaction involved in a process rather than a process)

How does this differ from the existing process: GO:0051315 attachment of mitotic spindle microtubules to kinetochore The cell cycle process in which spindle microtubules become physically associated with the proteins making up the kinetochore complex during mitosis. During mitosis, the kinetochores of sister chromosomes are situated facing opposite spindle poles and bipolar attachment of the sister chromosomes to the spindle occurs.

(currently it does not have any annotations)

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/11370

[gocentral]

The term was added by Jane in Dec. 2012. I can't find a relevant SF item. Will assign to Jane to see if this jogs her memory.

Original comment by: tberardini

[gocentral]

It's definitely from a ticket but it must predate the SF transition so you can't search for it unfortunately.

The reference on the term is this one:

http://europepmc.org/articles/PMC3438452

which is S. cerevisae so we might check with SGD, but looks like they never annotated to it.

Original comment by: jl242

[gocentral]

OK, mailed SGD

Happy New Year!

Val

Original comment by: ValWood

[gocentral]

Happy Birthday :-)

Original comment by: jl242

[gocentral]

Hi,

How about we change 'interaction' to 'assembly' in the term name to read 'NMS complex assembly involved in chromosome segregation'? The word interaction is misleading. CNN1 is annotated to this term.

Rama (Belated Birthday wishes Val!)

Original comment by: rbalakri

[gocentral]

This raises a bunch of issues.

So NMS complex is part of the kinetochore. Therefore NMS complex assembly is part of kinetochore assembly.

Now "kinetochore assembly" The aggregation, arrangement and bonding together of a set of components to form the kinetochore, a multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.

isn't part of chromosome segregation.

This is because "chromosome segregation" is defined "begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles"

and I think the kinetochore is assembled onto the uncondensed chromosomes?

There is a similar issue for "spindle assembly" it is not defined or positioned as being part of chromosome segregation. So currently the assembly of these complexes are processes which occur "upstream" of chromosome segregation, (although they are required to occur for effective chromosome segregation to happen). I do not know if it should be like this, but based on the current definitions of starts and ends, and would require quite a bit of work.

either NMS complex assembly involved in chromosome segregation or NMS complex interaction involved in chromosome segregation

are inconsistent with the way these processes are currently modelled.

Thanks for the SF birthday wishes...

Original comment by: ValWood

[gocentral]

Val,

Kinetochore is assembled on condensed chromosomes (check the definition of kinetochore binding- http://amigo.geneontology.org/amigo/term/GO:0043515).

R

Original comment by: rbalakri

[gocentral]

Of course. So it seems that kinetochore assembly and children could be descendants of chromosome segregation terms. I will check if Midori can remember another reason why not.

Original comment by: ValWood

[gocentral]

Midori doesn't remember. v

Original comment by: ValWood

[gocentral]

• assigned_to: Jane Lomax --> David Hill
• Group: None --> PomBase

Original comment by: jl242

[ukemi]

Hi Val and Rama,

Kinetochore assembly is now part of nuclear chromosome segregation, so that part of this issue is solved. For the term in question, looking at the paper I propose this: NMS complex interaction involved in kinetochore assembly-->NMS complex assembly involved in kinetochore assembly

def:The formation of a supercomplex by the association of two subcomplexes (known as MIND and Ndc80 in Schizosaccharomyces) that is required for kinetochore assembly.

[ValWood]

Yep, sounds perfect to me....

[ValWood]

Oh, except.... I think the jury is still out as to whether "kinetochore assembly" is part of "chromosome segregation", or precedes it?

"kinetochore assembly" is excluded from the current definition of chromosome segregation: "begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles"

...... I think the kinetochore is assembled onto the uncondensed chromosomes? Or maybe some of the kinetochore is assembled onto incomplete chromosomes, I am not sure of the exact timing of inner vs outer...

So, I have never figured out fully if it should be like this and I keep meaning to ask chromosome segregation experts. I could go either way...

Maybe Rama @rbalakri knows?

[ukemi]

Last week I made kinetochore assembly part_of nuclear chromosome segregation based on another ticket where I moved a bunch of terms. According to an earlier comment in this ticket, the kinetochore assembles on a condensed chromosome. Should I remove that part_of relation?

[rbalakri]

hmm..I am not sure of the exact timing either. I suggest we leave it like this and remove the relation later.

Rama

[ValWood]

Adding this link has other knock on effects. Currently mitotic spindle organization is also not part of mit. chromosome segregation. If kinetochore assembly is part of chromosome segregations, then the some aspects of spindle/centromere organization should be too?

Before adding these parents, we should figure out the historical reason for the way chromosome segregation in the existing term definitions. If kinetochore assembly and aspects of spindle assembly are considered to be part of this process, and these parents are added, the chromosome segregation definitions should also be revised accordingly.

This question has been on my list of "things to look at eventually" for a long while. It would be better to make any large changes here in consultation with experts.

[ukemi]

So what I am hearing is that I should remove the new part_of link?

-D

[ValWood]

Yeah, and make the question a "long term project" ;) We can have a look when the rest of cell cycle is done. Chromosome segregation is my big annotation project so that's what I'll be working on when I get the chance ...

[ukemi]

OK. Edited existing term as above and removed the part of relation between kinetochore assembly and nuclear chromosome segregation.