NTR: regulation term GO:0031122 cytoplasmic microtubule organization

[ValWood]

regulation of cytoplasmic microtubule organization

PMID:38442865

Title | The fission yeast NDR kinase Orb6 and its signalling pathway MOR regulate cytoplasmic microtubule organization during the cell cycle.

CC @PCarme

[ValWood]

Actually, I think here we can use regulation of microtubule cytoskeleton organization (during mitotic interphase) (occurs in cytoplasm) (since the cytoplasmic cytoskeleton is only in interpahse).

I remembered that we no longer use components in BP terms unless necessary

[ValWood]

We need to revisit this.

i) MOR negatively regulates non-centrosomal MTOCs, by phosphorylation of Mto2, to ensure proper organization of cytoplasmic microtubules during polarized growth in interphase.

I can make the annotations like

instead of regulation of cytoplasmic microtubule organization as suggested.

BUT we have lots of other terms that do reference cytoplasmic microtubules which will result in inconsistency

GO:0031122    cytoplasmic microtubule organization 62,239 annotations GO:0010938    cytoplasmic microtubule depolymerization 53 annotations GO:1905755    protein localization to cytoplasmic microtubule 108 annotations GO:0010937    regulation of cytoplasmic microtubule depolymerization GO:1904518    protein localization to cytoplasmic microtubule plus-end (and also cytoplasmic microtubule in CC)

(also need a negative regulation term for GO:0070507 regulation of microtubule cytoskeleton organization)

[pgaudet]

What would be helpful here is to have a clearer definition of cytoplasmic microtubule organization, right now we have quite a generic one: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures formed of microtubules and associated proteins in the cytoplasm of a cell."

If you could describe at least some important parts of the process, so that it's a coordinated process, and not just a bag of MFs that may help microtubule organization, it would be easier to decide which terms to keep and maybe if there are multiple pathways that lead to microtubule organization.

[ValWood]

This process (cytosolic microtubule cytoskeleton) is referring to the non-spindle associated microtubule cytoskeleton (and also excludes specific structures like cilia and flagella); it is generally referred to as either the “cytoplasmic cytoskeleton” or the Interphase cytoskeleton. Interphase cytoskeleton seems to be more popular:

https://pubmed.ncbi.nlm.nih.gov/?term=%22interphase++microtubule+cytoskeleton%22&sort=date&size=50 (11) Pubmed https://europepmc.org/search?query=%22interphase%20microtubule%20cytoskeleton%22 (80) EPMC https://pubmed.ncbi.nlm.nih.gov/?term=%22cytoplasmic+microtubule+cytoskeleton%22&sort=date&size=50 (4) PubMed https://europepmc.org/search?query=%22cytoplasmic%20microtubule%20cytoskeleton%22 (24) EPMC

A review https://europepmc.org/article/MED/29858272 The interphase array of microtubules (usually dynamic, sometimes stabilized) helps to determine cell shape and organization and acts as a substrate for motor-driven intracellular transport.

I’m not sure how this is best defined. In pombe, it emanates from “interphase microtubule organizing centres”, so perhaps this feature can be used as a differentia? (it's a non SBB/Centrosome derived cytoskeleton) The review says “ In many cell types, ranging from vertebrate fibroblasts to Dictyostelium amoebas, the interphase microtubule cytoskeleton is a radially organized structure that emanates from a centrally located microtubule-organizing center (MTOC; see below) (Fig. 1A)”

Also CCing @manulera Manu, is this suggestion too simplistic or will it work across species?

@pgaudet the review above will also be useful to define missing microtubule cytoskeleton-associated activities(provides a list).

[ValWood]

@PCarme for now I have put this session through with the less specific "regulation of microtubule cytoskeleton organization" so keep an eye open for this ticket closing to revise the annotation. tks val

[manulera]

Hi @ValWood not sure I have a great answer. I think most people will distinguish the three structures you have defined as distinct parts of the microtubule cytoskeletton:

• Spindle-related -> present only during mitosis / meiosis
• Specialised structures like flagella
• "The rest" typicially cells will have some internal network of microtubules that organises the position of organelles, gives some mechanical property, or is used for vesicular transport etc.

I think there is a clear-cut between the spindle-related and the rest, because as far as I know most dividing cells lose the rest of microtubule organisation when they divide. For instance, cells with flagella will round up and lose them during mitosis, pombe will lose the cytoplasmic arrays, etc. In the end, spindle microtubule cytoskeleton has a very clear role, so conceptually it makes sense to have a term for non-spindle microtubule structures, although not sure that is very GO-style.

There is not so much clear-cut between the specialised structures and "the rest". Not sure if the microtubule cytoskeleton in an axon in neurons would be considered a specialised structure or not. Flagella typically have unusual microtubules (different number of protofilaments, and organised in a very clear way, or assembled not as a cylinder, a bit like in the centriole).

Sadly, I think "a bag of MFs" is probably what most people have in mind when they speak about microtubule organisation in papers, and I think the only differentiation applying to all eukaryotes you can make is between spindle-related and non-spindle related.

[ValWood]

So that is the question, what label to give to the non-spindle microtubule cytoskeleton? In fission yeast I have seen it referred to as "interphase cytoskeleton" and "cytoplasmic cytoskeleton" and these labels does seem to be used a bit outside fungi (although not so much).

"interphase microtubule cytoskeleton" at least clearly excludes the spindle...

[manulera]

I think interphase cytoskeleton makes more sense, also because most "higher" eukaryotes disassemble their nucleus during mitosis, and never have microtubules inside their nucleus as far as I know.

[ValWood]

Of course! that makes sense!