Term issue: Term issue: rpb1 Phos:CTD-T4 (P36594)

[ValWood]

rpb1 Phos:CTD-T4 (P36594)

https://www.pombase.org/reference/PMID:31276588 The S. pombe Pol2 CTD consists of tandem repeats of a heptapeptide Y1S2P3T4S5P6S7. CTD mutations S7A and S5A that prevent installation of the Ser7-PO4 or Ser5-PO4 marks de-repress pho1 and pho84 in phosphate-replete cells (7,8,10,13). By contrast, prevention of the Thr4-PO4 mark by T4A hyper-represses pho1 and pho84 under phosphate-rich conditions (7,13). Because such CTD mutations do not affect the activity of the lncRNA or mRNA gene promoters per se (8,10), it is proposed that CTD status affects Pol2 termination during lncRNA synthesis (Figure 1A). Specifically, it is hypothesized that loss of the Ser7-PO4 or Ser5-PO4 marks leads to precocious termination of prt lncRNA transcription prior to the pho1 promoter and loss of the Thr4-PO4 mark reduces termination and hence increases transcription across the pho1 promoter (8)

I'm not sure which kinase yet... I't might also be worth to add also independent S7 and S5

[nataled]

Shall we close this one too?

[ValWood]

I'd still like this one so that I have a couple of curated exampes.

[nataled]

Okay, I will make this.

I notice that this one references a phosphorylation on the fourth position. Currently, the 'phosphorylated at the CTD' term, PR:000050494, does not include this, but probably it should. Do you agree? The definition of that term is "A DNA-directed RNA polymerase II subunit rpb1 (Schizosaccharomyces pombe) that has been phosphorylated at either the second, fifth, or seventh positions of one or more of the C-terminal heptad repeats (YSPTSPS)."

[ValWood]

I guess so if it is "OR"

This is the best overview I could find but it's 2016 https://www.nature.com/articles/nsmb.3285/figures/3

An older paper by the same authors has a bit more information about which combinations co-occur

https://www.semanticscholar.org/paper/Cracking-the-RNA-polymerase-II-CTD-code.-Egloff-Murphy/cc57d273d95c13959222178206e5d98a468be7a7/figure/3

and what they recruit

My aim is to get the versions which are known to recruit specific protein partners, but there isn't a great deal of evidence for fission yeast.

[nataled]

Hi Val,

The pT4 term has been created (see below). I also found that we already have the following:

pS2 - PR:000044738 DNA-directed RNA polymerase II subunit rpb1 phosphorylated 5 (Schizosaccharomyces pombe) pS5 - PR:000044737 DNA-directed RNA polymerase II subunit rpb1 phosphorylated 3 (Schizosaccharomyces pombe) pS7 - PR:000044739 DNA-directed RNA polymerase II subunit rpb1 phosphorylated 6 (Schizosaccharomyces pombe)

[Term] id: PR:000064868 name: DNA-directed RNA polymerase II subunit rpb1 phosphorylated 7 (Schizosaccharomyces pombe) def: "A DNA-directed RNA polymerase II subunit rpb1 CTD-phosphorylated form (Schizosaccharomyces pombe) that has been post-translationally modified to include phosphothreonine at the fourth position of one or more of the C-terminal heptad repeats (YSPTSPS)." [PRO:DAN, PomBase:VW, PMID:31276588] comment: Category=organism-modification. Requested by=PomBase. synonym: "Spom-rpb1/Phos:7" EXACT PRO-short-label [PRO:DAN] synonym: "T4P-Pol II (Schizosaccharomyces pombe)" EXACT [PRO:DAN] is_a: PR:000050494 ! DNA-directed RNA polymerase II subunit rpb1 CTD-phosphorylated form (Schizosaccharomyces pombe) relationship: has_part MOD:00047 ! O-phospho-L-threonine relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[ValWood]

Thanks! I used these now, but do you know why I cant find them when I search using P36594? v

P36594

[nataled]

Technically all PomBase requests are made to the species level, not strain (as used in UniProtKB). Most of the time, when making proteoform terms, I can use the strain numbering as an example, and in such cases I'd reference the UniProtKB accession. However, once in a while a term is created where there is no single proteoform described, as is the case here. When that happens, it creates a situation where specifying a single example would be very misleading, and so we avoid doing so.

The relevant terms can be found using this link:

https://lod.proconsortium.org/yasgui.html#query=PREFIX rdfs:http://www.w3.org/2000/01/rdf-schema#PREFIX owl:http://www.w3.org/2002/07/owl#PREFIX PomBase:http://www.pombase.org/spombe/result/PREFIX has_gene_template:http://purl.obolibrary.org/obo/pr#has_gene_templatePREFIX oboInOwl:http://www.geneontology.org/formats/oboInOwl#PREFIX pr:http://purl.obolibrary.org/obo/pr#SELECT DISTINCT?PRO_term?Label FROMhttp://purl.obolibrary.org/obo/prWHERE{VALUES?gn_id{PomBase:SPBC28F2.12}?PRO_term rdfs:subClassOf%2B?r.?r owl:onProperty has_gene_template:.?r owl:someValuesFrom?gn_id.?PRO_term rdfs:label?_Label.OPTIONAL{?gn_id rdfs:label?g}.bind(str(?_Label) as?Label)}ORDER BY ASC(?_PRO_short_label)%0A&endpoint=https://sparql.proconsortium.org/virtuoso/sparql&requestMethod=POST&tabTitle=Query&contentTypeConstruct=text/turtle,*/*;q=0.9&contentTypeSelect=application/sparql-results%2Bjson,*/*;q=0.9&outputFormat=table

Right around the middle of all this you'll see "{PomBase:SPBC28F2.12}". You can enter any PomBase gene accession in its place to see the relevant terms for that gene.

[ValWood]

I see this, but I don't see where to access the results?

[nataled]

Ugh, I forgot that github will change things that are pasted unless I 'quote' it. Try this instead:

https://lod.proconsortium.org/yasgui.html#query=PREFIX rdf%3A %3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E%0APREFIX rdfs%3A %3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0APREFIX owl%3A %3Chttp%3A%2F%2Fwww.w3.org%2F2002%2F07%2Fowl%23%3E  %0APREFIX PomBase%3A %3Chttp%3A%2F%2Fwww.pombase.org%2Fspombe%2Fresult%2F%3E%0APREFIX has_gene_template%3A %3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fpr%23has_gene_template%3E%0APREFIX oboInOwl%3A %3Chttp%3A%2F%2Fwww.geneontology.org%2Fformats%2FoboInOwl%23%3E%0ASELECT DISTINCT %3FPRO_term %3FLabel%0AFROM %3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fpr%3E%0AWHERE%0A%7B%0A   VALUES %3Fgn_id %7B PomBase%3ASPBC28F2.12 %7D%0A   %3FPRO_term rdfs%3AsubClassOf%2B %3Fr . %0A   %3Fr owl%3AonProperty has_gene_template%3A . %0A   %3Fr owl%3AsomeValuesFrom %3Fgn_id . %0A   %3FPRO_term rdfs%3Alabel %3F_Label .%0A   OPTIONAL %7B%0A     %3Fgn_id rdfs%3Alabel %3Fg%0A   %7D .%0A   bind(str(%3F_Label) as %3FLabel)%0A%7D%0AORDER BY ASC(%3F_PRO_short_label)%0A&endpoint=https%3A%2F%2Fsparql.proconsortium.org%2Fvirtuoso%2Fsparql&requestMethod=POST&tabTitle=Query&headers=%7B%7D&contentTypeConstruct=text%2Fturtle%2C*%2F*&contentTypeSelect=application%2Fsparql-results%2Bjson%2C*%2F*&q%3D0.9&q%3D0.9&outputFormat=table

[ValWood]

thanks!