Obsoletion Term merge: RNA polymerase I core factor complex (GO:0070860), RNA polymerase transcription factor SL1 complex (GO:0005668)

[ValWood]

Yeast has RNA polymerase I core factor complex (GO:0070860) A RNA polymerase I-specific transcription factor complex that is required for the transcription of rDNA by RNA polymerase I. In yeast the complex consists of Rrn6p, Rrn7p, and Rrn11p. [PMID:8702872] Rrn6 = ? Rrrn7 = TAF1B Rrn11 = ?

Human has RNA polymerase transcription factor SL1 complex (GO:0005668) A RNA polymerase I-specific transcription factor complex that contains the TATA-box-binding protein (TBP) and at least three TBP-associated factors including proteins known in mammals as TAFI110, TAFI63 and TAFI48. [PMID:15691654] TAFI110 TAF1C ?? Looks like rrn6 (AlphaFold) TAFI63 TAF1B TAFI48 TAF1A ?? Looks like rrn11. (AlphaFold)

• Reference(s)

Googling "TAF1C and rrn6" found https://pubmed.ncbi.nlm.nih.gov/28340337/ Which confirms these orthologies.

• Any other information

I mailed Pfam to

https://pfam.xfam.org/family/PF10214 To include the human members in https://www.ebi.ac.uk/interpro/entry/panther/PTHR15319/

And https://pfam.xfam.org/family/PF04090 https://pfam.xfam.org/family/PF14929

[ValWood]

spotted via a PAINT Mapping for pombe to RNA polymerase transcription factor SL1 complex (GO:0005668) for rrn6

[ValWood]

RNA polymerase transcription factor SL1 complex (GO:0005668) has ony 8 EXP. @pgaudet do you agree to obsolete and merge into GO:0070860 JSON RNA polymerase I core factor complex

[ValWood]

can I obsolete RNA polymerase transcription factor SL1 complex (GO:0005668) replace by RNA polymerase I core factor complex add exact synonym?

[ValWood]

in yeast core factor is composed of Core Factor (CF) composed of subunits Rrn6, Rrn7, and Rrn11 The CF subunits assemble through an interconnected network of interactions between five structural domains that are conserved in orthologous subunits of the human Pol I factor SL1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4219626/

It seems the names are not shared at all, but we could make RNA polymerase I core factor/SL1 complex as a portmanteau term to group these orthologous, functionally equivalent complexes?

[pgaudet]

I see EXP annotations by FlyBase and MGI; maybe @hattrill and @LiNiMGI have feedback? https://amigo.geneontology.org/amigo/term/GO:0005668

[hattrill]

I am fine with this proposal. Agree that modifying name to reflect those in use is a good idea.

[LiNiMGI]

@krchristie Would you please take a quick look of this one? Thanks!

[ValWood]

Actually looking back to the beginning of this ticket, the ortholog is unconfirmed. I meant to ask Pfam to see if these families should extend/merge. I'll do this first. There is quite a bit of literature saying the complexes are functionally equivalent, but it would make more sense if the ortholog was confirmed first.

[ValWood]

I see I have already mailed Pfam, will check for response.

[ValWood]

This is a summary of the connections

I will also submit to Panther:

yeast rrn6 = human TAF1C

InterPro/Pfam

The domain IPR049087 TAF1C, beta-propeller domain (PF20641) https://www.ebi.ac.uk/interpro/entry/InterPro/IPR049087/

Is https://www.ebi.ac.uk/interpro/entry/InterPro/IPR048535/ IPR048535 RRN6, beta-propeller PF10214

And the domain TAF1C, helical bundle domain (PF20642) https://www.ebi.ac.uk/interpro/entry/InterPro/IPR049090/

Is https://www.ebi.ac.uk/interpro/entry/InterPro/IPR048536/ IPR048536 RRN6, K-rich C-terminal domain (PF20639)

PANTHER Yeast https://www.pantherdb.org/panther/family.do?clsAccession=PTHR28221 Is Metazoan https://www.pantherdb.org/panther/family.do?clsAccession=PTHR15319

The connection is documented in the literature but isn't captured by any ortholog predictor or family database

======

Yeast Rrn11 = humans TAF1A https://www.ebi.ac.uk/interpro/entry/InterPro/IPR039495/

IPR039495 TATA box-binding protein-associated factor RNA polymerase I subunit A (PF14929) https://www.ebi.ac.uk/interpro/entry/InterPro/IPR039495/

PANTHER

Yeast https://www.pantherdb.org/panther/family.do?clsAccession=PTHR28244 Is Metazoan https://www.pantherdb.org/panther/family.do?clsAccession=PTHR32122

[krchristie]

Based on the reference that @ValWood found via Googling "TAF1C and rrn6" (citation and relevant quote below), I agree that having one term to represent the complexes currently represented by the two separate terms "RNA polymerase I core factor complex (GO:0070860)" & "RNA polymerase transcription factor SL1 complex (GO:0005668)".

Engel C, Gubbey T, Neyer S, Sainsbury S, Oberthuer C, Baejen C, Bernecky C, Cramer P. Structural Basis of RNA Polymerase I Transcription Initiation. Cell. 2017 Mar 23;169(1):120-131.e22. doi: 10.1016/j.cell.2017.03.003. PMID:28340337.

The human counterpart of CF, selectivity factor (SL) 1 (Comai et al., 1992; Learned et al., 1985), comprises homologs to Rrn6 (TAF1C), Rrn7 (TAF1B), Rrn11 (TAF1A) (Russell and Zomerdijk, 2006), and the additional subunits TAF1D and TAF12

To summarize the above sentence diagrammatically, you get this:

Scer = human Rrn6 = TAF1C Rrrn7 = TAF1B Rrn11 = TAF1A none = TAF1D none = TAF12

[ValWood]

I can't detect TAF1D outside chordata, it's low complexity and has no identifiable domains. TAF12 = yeast Taf12. This is a member of SAGA /TFIID (may or may not be a bona fida member of SL1).

I feel comfortable representing RNA polymerase I core factor/SL1 complex as a single complex. Will go ahead.