#113 cleavage products of pombe sre2

[Valerie Wood]

Sre2 is proteolytically cleaved for activation (release from the ER membrane, its a memebrane bound transcription factor) to give 2 cleavage products
Sre2P and sre2N
Unfortunately we don't know the exact cleavage site
PMID: 23729666 gives a prediction

UniProt ID is O43019

Can we do a generic thing (we have done this for modified forms in the past, but I'm not sure if we can do it for claved forms......)

[Valerie Wood]

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711301/figure/F3/

The N-terminal portion is the TF

[Valerie Wood]

Actually Sre2P is the full length (Sre2-precursor)
The N-term (cleaved portion) refers to the active form

[Darren Natale]

We can definitely do a generic thing. I have made terms corresponding to all products of the sre2 gene in S. pombe, the Sre2P form, and the Sre2N form. Let me know if you need a term for the C-terminal part as well (if so, the identifier will be the same PRO ID incremented by one).

[Term]
id: PR:000046670
name: transcription factor sre2 (Schizosaccharomyces pombe)
def: "A protein that is a translation product of the Schizosaccharomyces pombe sre2 gene." [PRO:DAN]
comment: Category=organism-gene. Requested by=PomBase.
synonym: "Spom-sre2" EXACT PRO-short-label [PRO:DAN]
synonym: "sterol regulatory element-binding protein 2 (Schizosaccharomyces pombe)" EXACT [UniProtKB:O43019]
intersection_of: PR:000000001 ! protein
intersection_of: has_gene_template PomBase:SPBC354.05c ! sre2 (Schizosaccharomyces pombe)
intersection_of: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000046671
name: transcription factor sre2, Sre2P form (Schizosaccharomyces pombe)
def: "A transcription factor sre2 (Schizosaccharomyces pombe) that has not been processed by proteolytic cleavage." [PRO:DAN, PomBase:VW, PMID:23729666]
comment: Category=organism-modification. Requested by=PomBase.
synonym: "Spom-sre2/Sre2P" EXACT PRO-short-label [PRO:DAN]
synonym: "sre2 precursor (Schizosaccharomyces pombe)" EXACT []
is_a: PR:000046670 ! transcription factor sre2 (Schizosaccharomyces pombe)

[Term]
id: PR:000046672
name: transcription factor sre2, Sre2N form (Schizosaccharomyces pombe)
def: "The N-terminal portion of transcription factor sre2 (Schizosaccharomyces pombe) that remains after proteolytic cleavage. This portion represents the functionally active part." [PRO:DAN, PomBase:VW, PMID:23729666]
comment: Category=organism-modification. Requested by=PomBase.
synonym: "Spom-sre2/Sre2N" EXACT PRO-short-label [PRO:DAN]
synonym: "sre2 nuclear (Schizosaccharomyces pombe)" EXACT []
is_a: PR:000046670 ! transcription factor sre2 (Schizosaccharomyces pombe)

Note: I decided to name these in a rather neutral way (as opposed to 'active', for example), since it is possible that there are some other modifications needed to make Sre2N active. I note that there are a few possible phosphorylation sites, and the true active form might require one or more of these.

Best regards,
Darren

[Valerie Wood]

Perfect.

I have a question too.

We have been using the
name: transcription factor sre2, Sre2P form (Schizosaccharomyces pombe)
on our gene pages for display.

I'd like to use the name the community uses (Sre2N in this case),
I see:
synonym: "Spom-sre2/Sre2N" EXACT PRO-short-label [PRO:DAN]
we don't need to say Spom-sre2

So I was wondering if all of the short labels are formatted in this way (so we could use the portion after the "/")

Thanks,

Val

[Darren Natale]

The PRO-short-label does indeed follow a standard that we use. In general it is composed of some organism indicator, the gene label, isoform label, and modification type or product (with incremental numbering), as necessary. This format is not really intended for anything other than display when using Cytoscape (the long names quickly make things messy. So, yes, you can use the community standard. In fact, I changed the name in PRO to that standard :)

[Valerie Wood]

fab, thanks.