priority papers for causal modelling

pombase / curation

PomBase curation

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priority papers for causal modelling #3165

Open ValWood opened 2 years ago

ValWood commented 2 years ago

https://www.pombase.org/reference/PMID:23813957 Any1 Ub ligase adaptor->Aat1 amino acid transporter

ValWood commented 2 years ago

PMID:16252005 (possibly other papers)

The cul4 Ub ligase containing Cdt2 needs some work to capture substrates:

(Li-Lin) Cdt2 is a subunit of a PCNA-dependent E3 ubiquitin ligase composed of Rbx1/Roc1, Cul4, Ddb1, and Cdt2. The known substrates of this E3 ubiquitin ligase in S. pombe include Cdt1, Spd1, and Pxd1.

Cdt2-mediated ubiquitination happens during S phase and after DNA damage treatment. Thus, Cdt2 can be considered a factor involved in cell cycle regulation and DNA damage response, but I do not think Cdt2 is considered to be involved in G2/M checkpoint, at least not in the checkpoint signaling process.

ValWood commented 2 years ago

PMID: 23213482 tor2-> substrate Maf1 from https://github.com/pombase/curation/issues/3122

ValWood commented 2 years ago

PMID:24055157 protein kinases, Hhp1 and Hhp2 (CK1) phosphoproteomics screen substrates should includes imp1 (not sure where I read this)

ValWood commented 2 years ago

PMID: 2170029 seems to be missing the phenotypes: exhibiting strikingly different cell cycle phenotypes: cold-sensitive mutations in the same amino acid lesion of PP1 and PP2A produce chromosome nondisjunction and premature mitosis, respectively.

ValWood commented 2 years ago

PMID:11369198 Mutants in dis1 lack the chromosome alignment phase in metaphase and arrest with elongated spindles and segregated but unseparated chromosome pairs seems like should have complete but unequal mitotic sister chromatid segregation with unseparated chromosomes (FYPO:0005739)

ValWood commented 2 years ago

from https://github.com/pombase/curation/issues/857

The Yamano lab has also used Ubc4 for in vitro ubiquitination assays with APC/C: 2009 JBC Ors Yamano PMID: 19584054 2011 MBC Kimata Yamano PMID: 21389117

[ ] ubc4 is the E2 for the Slp1-APC for degradation of cut2(securin) and cdc13 at metaphase /anaphase PMID:23442800
[ ] ubc11 is the E2 for the Srw1-APC for degradation of slp1 at mitotic exit (cessation of checkpoint) PMID:23442800
- [ ] ubc11 and ubc4 are both E2's for srw1-APC degradation of cdc13 in G1 (PMID:12724408)
- [ ] ubc11 is required also at G2 (not completely sure which E3 this is, but the pathway is chk1 dependent?) PMID:9154838
[ ] PMID:9154838 also reports the ubc11 has a role in metaphase/anaphase transition, but only cyclin degradation is mentioned. If securin degradation is the defining event of the metaphase/anaphase transition does this mean that ubc11 also acts as a E2 for Slp1-APC in securin degradation?