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Source ontology files for the Gene Ontology
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Ntr: SIP (SIN Inhibitory Phosphatase complex) #10078

Closed gocentral closed 9 years ago

gocentral commented 11 years ago

One of our community has requested a new complex term: SIP (SIN Inhibitory Phosphatase complex) s a PP2A-striatin complex (analogous to STRIPAK) that regulates the SIN

I wonder if it is exactly analogous to STRIPAK ( in which case maybe this should be called STRIPAK/SIP complex?)

STRIPAK signalling complex Definition A core protein complex containing the catalytic subunit PP2Acat, its scaffolding subunit PP2AA, members of the striatin family of regulatory subunits, the striatin interactor Mob3, STRIP1, members of the germinal center kinase III (GCKIII) group (STK24, STK25, and MST4), and the small molecular weight protein CCM3. Additional proteins can associate with this core STRIPAK complex in a mutually exclusive manner.

I'm trying to check, but I have no idea which organism these gene names refer to..... val

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/9875

gocentral commented 11 years ago

Also STRIPAK has related synonym "FAR complex" which I think is the S. cerevisiae name for the SIP complex... so perhaps STRIPAK/FAR/SIP complex

I'm struggling to find which organism STRIPAK is defined using, as it has no annotations yet. I can only find Mob3 in drosophila but I can't find STRIP1 or CCM3 in any organism, and STK24 appears to be mouse/human/rat...

Val

Original comment by: ValWood

gocentral commented 11 years ago

Original comment by: ValWood

gocentral commented 11 years ago

Oh crap, I found it (thought it all sounded familiar) https://sourceforge.net/tracker/index.php?func=detail&aid=3561051&group\_id=36855&atid=440764

Can we change the name, and make the def a bit more generic...assigning back to Tanya;)

Thanks Val

Original comment by: ValWood

gocentral commented 11 years ago

Original comment by: ValWood

gocentral commented 11 years ago

pombe SIP S.c FAR ppg1 protein phosphatase type 2A Ppg1 ? paa1 protein phosphatase regulatory subunit Paa1 ? far8 striatin homolog Far8 FAR8 far11 conserved eukaryotic protein Far11 FAR11 far10 FHA domain protein Far10 FAR10 /FAR9 (FHA domain picks up pombe FAR10 with PSI blast) SPAC2C4.10c sequence orphan FAR3 or 7 possibly both small, not conserved?

Far complex is described as a conserved PPA2 regulator complex , but I don't know which phosphatase (it isn't the one called PPA2, as this is something else...so I think it is probably PPG1/TPD3? can't find any reference to this though....will try to find out

So I think we can assume that SIN and FAR are analogous.

Should be defined as a "phosphatase complex" child of protein phosphatase type 2A complex (although the definition for this complex is very odd, ...I would happily obsolete these grouping term which attempt to describe a complex based on a family membership like phosphatase type 2 A, they are a bit meaningless, as there are so many).

Perhaps FAR/SIN complex A conserved protein phosphatase type 2A complex which contains a protein phosphatase type 2A, a protein phosphatase regulatory subunit, a striatin, an FHA domain protein and other subunits (at least six proteins). In fission yeast this complex negatively regulate the septation iniitiation network at the spinlde pole body.

Then decide whether this should be extended to include STIPAK (this looks similar but different complex (as it contains kinases), but it would fit the definition above....

Original comment by: ValWood

gocentral commented 11 years ago

sorry my formatting didn't work, this was supposed to be pombe/cerevisiae (2 columns)

Original comment by: ValWood

gocentral commented 11 years ago

The paper you provided for the initial term request was this one:

http://www.ncbi.nlm.nih.gov/pubmed?term=21561862

I've kind of lost track of the exact request of this issue:

1) rename GO:0090443, STRIPAK signalling complex and broaden definition

2) create new term for FAR/SIN complex

3) relate two terms to each other

All of these or just 2 and 3?

Thanks,

Tanya

Original comment by: tberardini

gocentral commented 11 years ago

After completing the new paper PMID:22119525, and remembering the original paper and a comment from one of the authors of which I had overlooked "based on its presence in the SIP which is conserved in humans (STRIPAK, see Frost et al. Cell 149(6), 8 June 2012, Pages 1339–1352)".

I think the complex should be renamed:

FAR/SIN/STRIPAK complex A conserved protein phosphatase type 2A complex which contains a protein phosphatase type 2A, a protein phosphatase regulatory subunit, a striatin, an FHA domain protein and other subunits (at least six proteins). In fission yeast this complex negatively regulate the septation iniitiation network at the spinlde pole body.

This should work for all organisms based on what is known !

Val

Original comment by: ValWood

gocentral commented 11 years ago

Name modified and definition updated as requested in the final comment.

Original comment by: tberardini

gocentral commented 11 years ago

Original comment by: tberardini