#108 cleavage products of pombe cut1 (separase) and rad21(cohesin, kleisin subunti)

[Valerie Wood]

I'm not sure what onfo you require for this one (I'm trying to capture a phanotype with increased level of the cleavage product(s))

The cleavage sites of Rad21 are at R179 and R231 from, PMID:15329725 the paper I cam curating

I'll track down the cut1 cleavage sites elsewhere (I hope) and updat the ticket shortly.

Thanks,

Val

[Valerie Wood]

Ignore the 2nd part of the request. Upon checking again I only need the rad21 cleavage products (describing increased level of cleavage product in specific rad21 and cut2 mutants. I don't know where I got cut1 from.....)

[Darren Natale]

Hi Val,

From what I can tell from the paper, the two sites you refer to are the ones that are cleaved after irradiation. The text mentions one bit of information that I'd like clarification on:

"Hyper-modified Rad21 produced upon irradiation might be the target of separase." If that's always the case, then the longer cleaved product (based on R231) should be phosphorylated (at S219). Based on the information presented in this paper, I'm inclined to be agnostic about other modifications. However, If you have any information indicating otherwise, let me know and I'll revise the term.

For now, here are the terms (I included a generic class as a parent).

[Term]
id: PR:000037020
name: cohesin subunit rad21 (Schizosaccharomyces pombe)
def: "A double-strand-break repair protein rad21 that is encoded in the genome of Schizosaccharomyces pombe." [PRO:DAN]
comment: Category=organism-gene. Requested by=PomBase.
synonym: "Spom-RAD21" EXACT PRO-short-label [PRO:DAN]
synonym: "double-strand-break repair protein rad21 (Schizosaccharomyces pombe)" EXACT [UniProtKB:P30776]
synonym: "SCC1 homolog (Schizosaccharomyces pombe)" EXACT [UniProtKB:P30776]
intersection_of: PR:000013667 ! double-strand-break repair protein rad21
intersection_of: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe
relationship: has_gene_template PomBase:SPCC338.17c ! rad21 (Schizosaccharomyces pombe)

[Term]
id: PR:000037021
name: cohesin subunit rad21 Arg-179 cleavage product (Schizosaccharomyces pombe)
def: "A cohesin subunit rad21 (Schizosaccharomyces pombe) that has been cleaved after Arg-179 by separase. Example: UniProtKB:P30776-1, 1-179." [PRO:DAN, PMID:15329725]
comment: Category=organism-gene. Requested by=PomBase.
synonym: "Spom-RAD21/Clv:179" EXACT PRO-short-label [PRO:DAN]
is_a: PR:000037020 ! cohesin subunit rad21 (Schizosaccharomyces pombe)
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000037022
name: cohesin subunit rad21 Arg-231 cleavage product (Schizosaccharomyces pombe)
def: "A cohesin subunit rad21 (Schizosaccharomyces pombe) that has been cleaved after Arg-231 by separase. Example: UniProtKB:P30776-1, 1-231." [PRO:DAN, PMID:15329725]
comment: Category=organism-gene. Requested by=PomBase.
synonym: "Spom-RAD21/Clv:231" EXACT PRO-short-label [PRO:DAN]
is_a: PR:000037020 ! cohesin subunit rad21 (Schizosaccharomyces pombe)
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Valerie Wood]

Hi Darren,

Thanks for your rapid reponse.

It ended up that I did not need the PRO term, as I described the phenotype in terms of increased proteolysis of the protein, rather than increased level of the cleavage product, consistently with similar phenotypes in PomBase.
https://github.com/pombase/fypo/issues/2677

We will probably later use the cleavage product in othe situations though, so hopefully this will not be wasted effort.

Val