NMS complex and Ndc80 complex

[ValWood]

NMS complex (GO:0031617)

Definition	Parents

A supercomplex formed by the association of two subcomplexes (known as MIND and Ndc80 in Schizosaccharomyces) with additional proteins at the kinetochores of condensed nuclear chromosomes. [PMID:16079914]

I don't think we need this complex, it's a bit abstract, and complicates the ontology because it is a connection between inner and outer kinetochore components.

Also, it isn't a "DNA packaging complex" as suggested by the parents.

I suggest to obsolete.

The child term Ndc80 complex (GO:0031262)

Definition	Parents

An outer kinetochore protein complex that is part of the KMN kinetochore network (also known as the NMS complex) providing the platform with which the plus ends of spindle microtubules directly interact to form stable kinetochore-microtubule attachments.

should be rehoused under "outer kinetochore" GO:0000940

I think you can also edit the definition of Ndc80 complex (GO:0031262) to An essential outer kinetochore complex involved in the attachment of microtubule ends to the chromosomes during mitosis. adapted from PMID: 28502666 and PMID:34810257

[raymond91125]

GO:0031617 NMS complex 10 experimental annotations from PomBase, all of the gene names contain "NMS complex". There are other NMS complex terms GO:0044768 NMS complex assembly 0 annotations GO:1901719 regulation of NMS complex assembly GO:1901721 positive regulation of NMS complex assembly GO:1901720 negative regulation of NMS complex assembly (1 IMP annotation from SGD)

[ValWood]

OK, don't worry. Its a bit odd because it is really a "network" and consists of components of the outer and inner kinetochore:

Some members are not Ndc80 or MIND so we could keep the complex term.

I'm not so sure about the complex assembly terms though (I would such processes to annotate to inner or outer kinetochore assembly if warranted , and this would be orthogonal). The single annotation is part of the inner kinetochore which forms a platform for the assembly of the kinetchore. I would not annotate to NMS complex assembly though...

[ValWood]

Here is another schematic https://www.nature.com/scitable/content/the-centromere-kinetochore-region-43815/

Although Ndc and MIND do interact physically and genetically, the complex grouping is a bit odd. I think on balance we don't need NMS, and it could merge into outer kinetochore (which is really what it represented historically).

and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5371998/ The core of the outer kinetochore is a 10-subunit protein assembly known as KMN (for Knl1 complex, Mis12 complex, Ndc80 complex, described in Figure 2)

I don't think we need this extra level if we have outer kinetochore and the sub-complexes. It adds an extra complication.

[raymond91125]

@ValWood Could you advise what needs to be done still? Thanks.

[ValWood]

I still think we should remove NMS complex. It isn't a complex as such and was defined based on other. characteristics. PMID: 17035632 " We found that the 22 mitotic proteins can be classified into three groups: the Mis6-like group, the NMS (Ndc80-Mis12-Spc7) group, and the DASH group, based on their meiotic behavior." I t is sometimes also called "NMS network".

The Ndc80 and MIND complexes (and others) are sufficient and enable us to organize the terms more cleanly.

1. Merge NMS complex into "kinetochore" (unnecessary grouping term)
2. Ensure that the existing parent "DNA packaging complex is not transferred) (this is incorrect)
3. Make Ndc80 complex (GO:0031262) part of GO:0000940 | outer kinetochore (to match existing definition)
4. Edit the definition of Ndc80 complex (GO:0031262) to An essential outer kinetochore complex involved in the attachment of microtubule ends to the chromosomes during mitosis. adapted from PMID: 28502666 and PMID:34810257
5. Make GO:0000444 | MIS12/MIND type complex part of inner kinetochore complex (to match existing definition)
6. Merge GO:0044768 NMS complex assembly 0 annotations GO:1901719 regulation of NMS complex assembly GO:1901721 positive regulation of NMS complex assembly GO:1901720 negative regulation of NMS complex assembly (1 IMP annotation from SGD) into the equivalent kinetochore assembly terms
7. add Mcm21 complex as a synonym of "Mis6-Sim4 complex".

[raymond91125]

Thanks.

[ValWood]

Thanks @raymond91125 This will be cleaner and reflects the biology better.

[Antonialock]

5. Make GO:0000444 | MIS12/MIND type complex part of inner kinetochore complex (to match existing definition)

Val, why is MIS12/MIND inner kinetochore? in the figure above it is annotated as an outer component? is that a typo?

other papers also describe MIS12?MIND as outer "The outer kinetochore contains the microtubule-binding activity and consists of the essential subcomplexes Mtw1/Mis12/MIND, Spc105/Knl-1/Blinkin, Ndc80, Dam1/DASH/DDD, as well as nonessential proteins such as motors and checkpoint components (Table 1)" PMC3730914

eg

[ValWood]

hmm some pubs call it inner https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063780/ All of the hMis12 complex proteins localized to kinetochores at constant levels throughout mitosis, which is consistent with this complex being a stable component of the mitotic inner kinetochore....

[ValWood]

mis12 is at the junction between inner and outer. If the distinction is that inner is assembled during interphase and outer during mitosis, then it is probably better classified as "inner"

The schematic is not to realistic. Consider

[ValWood]

Perhaps it should not be described as 'inner" or "outer" and is more of a linkler between the 2? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6781445/

The inner kinetochore, composed of the 16-subunit constitutive centromere-associated network (CCAN), is assembled on centromeric nucleosomes and persists throughout the cell cycle. The outer kinetochore contains the 10-subunit Knl1–Mis12–Ndc80 (KMN) network, which links the inner kinetochore to microtubules. In higher eukaryotes, the four-subunit Mis12 complex (Mis12C; Mis12, Dsn1, Nsl1, and Pmf1) serves as a hub for outer kinetochore assembly by interacting with both CENP-C and CENP-T at the inner kinetochore (Gascoigne et al., 2011; Przewloka et al., 2011; Screpanti et al., 2011; Rago et al., 2015; Huis In ’t Veld et al., 2016; Hara et al., 2018) and the Ndc80 complex and Knl1 at the outer kinetochore (Cheerambathur and Desai, 2014)

Regulation of outer kinetochore Ndc80 complex-based microtubule attachments by the central kinetochore Mis12/MIND complex. Kudalkar EM, Scarborough EA, Umbreit NT, Zelter A, Gestaut DR, Riffle M, Johnson RS, MacCoss MJ, Asbury CL, Davis TN. Proc Natl Acad Sci U S A. 2015 Oct 13;112(41):E5583-9. doi: 10.1073/pnas.1513882112. Epub 2015 Oct 1. PMID: 26430240

[Antonialock]

I think the text suggests that MIS12 is the part of the outer kinetochore that contacts the inner kinetochore

it looks like inner kinetochore is synonymous with CCAN / Mis6-Sim4 complex

outer kinetochore consists of MIS12 subcomplex, NDC80 subcomplex, and some other proteins e.g. KNL1

[Antonialock]

NMS complex / KMN network synonymous with outer kinetochore?

Structure of the MIS12 Complex and Molecular Basis of Its Interaction with CENP-C at Human Kinetochores pmid 27881301 Kinetochores, multisubunit protein assemblies, connect chromosomes to spindle microtubules to promote chromosome segregation. The 10-subunit KMN assembly (comprising KNL1, MIS12, and NDC80 complexes, designated KNL1C, MIS12C, and NDC80C) binds microtubules and regulates mitotic checkpoint function through NDC80C and KNL1C, respectively. MIS12C, on the other hand, connects the KMN to the chromosome-proximal domain of the kinetochore through a direct interaction with CENP-C. The structural basis for this crucial bridging function of MIS12C is unknown. Here, we report crystal structures of human MIS12C associated with a fragment of CENP-C and unveil the role of Aurora B kinase in the regulation of this interaction. The structure of MIS12:CENP-C complements previously determined high-resolution structures of functional regions of NDC80C and KNL1C and allows us to build a near-complete structural model of the KMN assembly. Our work illuminates the structural organization of essential chromosome segregation machinery that is conserved in most eukaryotes

[ValWood]

I still think if it is a permanent part of the kinetochore , it would be inner. Hopefully somebody will reply to my question.

• [ ] Also it seems GO:0061838 CENP-T-W-S-X complex should be part_of inner rather than " GO:0034080 CENP-A containing chromatin assembly

[ValWood]

it looks like inner kinetochore is synonymous with CCAN / Mis6-Sim4 complex

• Mis6-sim4 is narrower than inner kinetochore. Other proteins like Aurora, shugoshin, bub1 alsolocalize to the inner kinetochore, but are not Mis6-Sim4 complex

• [ ] CCAN = constitutive centromere associated network. This is CENP-A containing chromatin, plus inner kinetochore. I think it is useful to keep these separate since they have different assembly pathways. I can add as a broad synonym of both.

Since https://www.cell.com/molecular-cell/fulltext/S1097-2765(22)00390-2?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1097276522003902%3Fshowall%3Dtrue is a structure, and recent and excludes mis12 it seems that this is not a constitutive component after all.

• [ ] I will switch from inner to outer!

[ValWood]

PomBAse user says:

I think the pombe Mis12 complex is rightly assigned to the "inner kinetochore" category. However, in vertebrates it is considered to be an outer kinetochore component because it localizes to centromeres only during mitosis. This categorization breaks down in budding yeast!

It may be time for the field to abandon this description entirely. It derives from the trilaminar appearance of metazoan and fission yeast kinetochores in serial section EM; this appearance itself is thought to be an artifact of sample preparation.

-

So I think what I will do here for now is to make Mis6-sim4 a child of kinetochore only . Human can co-annotate to "outer", and fission yeast can co-annotate to "inner"

OK?

[ValWood]

A different opinion:

Mis12 is generally considered part of the outer kinetochore. eg see this budding yeast diagram from Sue Biggins
and this in fission yeast

(Diagrams below)

In mammalian cells etc, some proteins are present at the centromere all through the cell cycle (CENP-A, CENP-C etc), and other (outer kinetochore) proteins join in Mitosis (such at Ndc80).

But in pombe, almost all proteins stay at the centromere all through the cell cycle, including Mis12, so this isn’t a good way to determine whether they are inner or outer kinetochore.

(Some pombe proteins, including HJURP/Scm3 and Mis18 actually leave the centromere during part of mitosis.)

Hope that helps.

[ValWood]

The papers Alison refers to budding yeast https://elifesciences.org/articles/37819

fission yeast https://cshperspectives.cshlp.org/content/7/7/a018770

~but look at the fission yeast subunits of Mis12 complex, they are split between inner and outer ?~

[Antonialock]

but look at the fission yeast subunits of Mis12 complex, they are split between inner and outer ?

I don't understand what you mean - in this image the fission yeast MIS12 complex are all annotated as outer components (mis12, nsl1, dsn1, nnf1? - they just use higher eukaryote gene names?)

"Outside of CCAN, we find the “outer kinetochore” KMN complex, which is made up of another conserved network of proteins including the Ndc80 and Mis12 protein subcomplexes and Spc7"

[ValWood]

so they are

[Antonialock]

is KMN / NMS network / "super complex" more modern nomenclature than "outer kinetochore"? (it's a bit annoying that the names don't match even if the components seem to match evolutionary?) (not sure if that is what the comment by Ajit Joglekar was referring to?)

[ValWood]

KMN/NMS nomenclature has been around for a long time.

The network originally referred to a genetic network the organization was fully known. That's why we obsoleted NMS complex, it was difficult to accommodate all of the different nomenclatures.

https://pubmed.ncbi.nlm.nih.gov/17035632/

But I can add "NMS complex" back as related to "outer kinetochore"

[Antonialock]

Ok - maybe - I don't know much about this field! But I started looking at it since I was annotating the hsp90-sugt1 complex which helps assemble the MIS12 complex (which I am only doing because of Alaynes request of annotating the plant sugt1 protein....1 paper projects have a tendency to grow!!).....these kinetochore components were annotated a bit inconcistently e.g. mis12 complex in human, but uniprot had "Component of the NMS super complex...." for pombe mis12

[ValWood]

So far:

• [ ] It makes sense the Mis12 complex moves to outer kinetochore.
• [x] I don't think we need a specific NMS term (it would be an unnecessary intermediate, and didn't originally represent a specific component) but I will move the synonym from "kinetochore" to be a "narrow synonym" of "outer kinetochore (which will be OK if Mis12 is relocated) (this is why I originally thought we should remove it).
• [ ] Add CCAN = constitutive centromere associated network. This is CENP-A containing chromatin, plus inner kinetochore. It is probably useful to keep these separate since they have different assembly pathways. I can add as a broad synonym of both terms.
• [ ] GO:0061838 CENP-T-W-S-X complex should be part_of "inner kinetochore" rather than part_of "GO:0034080 CENP-A containing chromatin assembly"

In summary there are organismal differences between when some components localize (interphase or mitosis), and so this isn't a useful way to classify inner/outer kinetochore.

[Antonialock]

thanks, don't worry about broad synonym for CCAN for me - it was weird not seeing it in go when I searched but I'm sure it would have made sense if I had looked in to it in more detail)

[ValWood]

I think it is good to add based on feedback received. Some people use KLM/CCAN in preference to inner/outer, but we need to be aware that the "constitutive" part can be misleading

[ValWood]

hmm, that makes me think that git7, hsp90 are unlikely to be directly involved in adenylate cyclase-activating glucose-activated G protein-coupled receptor signaling pathway

;) causally upstream?

[Antonialock]

I haven't got to that yet. currently looking at how hsp90-sgt1 stabilises mis12 - but there are other functions to look into (the adenylate cyclase things, innate immunity....maybe it has separate functions - i'll let you know if something looks odd when I get to it.

[ValWood]

Takashi wisdom:

One review paper (attached) said this complex locates between inner (CCAN) and outer kinetochores (Knl1 and Noc80C) and is assigned as central. As Mis12C is part of KNM and it dissociates from the kinetochore during meiotic prophase together with Ndc80C (pdf attached also), I think that Mis12C is not inner and would be classified as outer, but you could assign it as central. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6756984/

The consensus is definitely outer.

[Antonialock]

looks like a term for knl1 complex part of the outer kinetochore is missing

note from vw: see https://github.com/geneontology/go-ontology/issues/25544

[ValWood]

I can add that, it used to be covered by NMS

knl1 complex So this would be Knl-1 and zwint. synonym spc105c complex https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6756984/

note from vw: see https://github.com/geneontology/go-ontology/issues/25544

[ValWood]

edited previous comment