Term issue: Phosphosites for alp7 (TACC protein alp7)

manulera commented 2 years ago

Gene name in pombe: alp7 Uniprot id: Q9URY2

All phosphorylations added by cdc2 (CDK in pombe) during mitosis: S50,S51,T100,T116,T131

https://www.pombase.org/reference/PMID:24790093

cc @ValWood

nataled commented 2 years ago

Hi Manuel, Your term is given (in OBO format) below. Please note that--though the term page will be immediately active--the term will not appear in the full PRO download until the next release (scheduled for August).

One question: what would be an appropriate evidence code for the experiment showing the phosphorylation? For the moment I put ECO:000006 'Experimental' but I'm sure something better can be used.

PR:000050595 = alp7/(Phos):Ser50/Ser51/Thr100/Thr116/Thr131

[Term] id: PR:000050595 name: microtubule protein alp7 phosphorylated 2 (Schizosaccharomyces pombe) def: "A microtubule protein alp7 (Schizosaccharomyces pombe) that has been phosphorylated at positions equivalent to Ser-50, Ser-51, Thr-100, Thr-116, and Thr-131 of the amino acid sequence represented by UniProtKB:Q9URY2. Example: UniProtKB:Q9URY2, Ser-50/Ser-51, MOD:00046|Thr-100/Thr-116/Thr-131, MOD:00047." [PRO:DAN, PomBase:MLR, PMID:24790093] comment: Category=organism-modification. Requested by=PomBase. Kinase=("cdc2"; PR:000036301; Ser-50/Ser-51/Thr-100/Thr-116/Thr-131). Evidence=(ECO:0000006, based on PMID:24790093). synonym: "Spom-alp7/Phos:2" EXACT PRO-short-label [PRO:DAN] synonym: "UniProtKB:Q9URY2, Ser-50/Ser-51, MOD:00046|Thr-100/Thr-116/Thr-131, MOD:00047" NARROW PRO-proteoform-std [PRO:DAN] is_a: PR:000050514 ! microtubule protein alp7 (Schizosaccharomyces pombe) relationship: has_part MOD:00046 ! O-phospho-L-serine relationship: has_part MOD:00047 ! O-phospho-L-threonine relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

manulera commented 2 years ago

Hi, @nataled sorry for the late reply, I was on leave.

The important evidence comes from Fig. 5 (below) in https://www.molbiolcell.org/doi/10.1091/mbc.e13-11-0679

They use a construct where they substitute the 5 mentioned residues by Alanin. They show in the figure that:

No radioactive phosphate is incorporated into the protein in an in vitro kinase assay when the residues are replaced by alanin (panel C)
In vivo, no shift of the band is observed for the alanin version of the protein in synchronised cells (panel D, 17 degrees in the western blot)

PROconsortium / PRoteinOntology

Term issue: Phosphosites for alp7 (TACC protein alp7) #277