PTN000459161 SAGA complex

[PCarme]

PTHR ID & PTN node:
GO:0000124 | SAGA complex | IBA with PTN000459161

Sequences with problematic annotation (ID + gene/protein name):
PomBase=SPBC15D4.14 ; taf51 https://www.pombase.org/gene/SPBC15D4.14

Type of Issue: Erroneous source or erroneous propagation, or other issue
Taf51 is not part of the SAGA complex in yeast [PMID:31969704 ; PMID:31969703]

[ValWood]

Note, there is no S. cerevisiae ortholog of Taf51, but there is a human ortholog.

https://www.uniprot.org/uniprotkb/O75529/entry

This has a note
Functions as a component of the PCAF complex. The PCAF complex is capable of efficiently acetylating histones in a nucleosomal context. The PCAF complex could be considered as the human version of the yeast SAGA complex (Probable).

and an annotation to SAGA from this paper:
Human STAGA complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo.

https://pubmed.ncbi.nlm.nih.gov/11564863/

so I think this annotation is incorrect, the paper isn't describing SAGA but a SAGA like complex?
(STAGA contains most subunits of SAGA), but TAF5L is not one of them (all 19 subunits are conserved)

Systematic ID	Gene name	Product description	Human orthologs
SPBC25H2.11c	spt7	SAGA complex bromodomain subunit Spt7	SUPT7L
SPAC57A10.14	sgf11	SAGA complex deubiquitinating submodule subunit Sgf11	ATXN7L3
SPCC126.04c	sgf73	SAGA complex deubiquitinating submodule subunit Sgf73	ATXN7,ATXN7L1,ATXN7L2
SPBC6B1.12c	sus1	SAGA complex deubiquitinating submodule subunit, TREX complex subunit Sus1	ENY2
SPAC1952.05	gcn5	SAGA complex histone acetyltransferase catalytic subunit Gcn5	KAT2A,KAT2B
SPCC24B10.08c	ada2	SAGA complex subunit Ada2	TADA2A,TADA2B
SPBC887.18c	hfi1	SAGA complex subunit Hfi1/Ada1	TADA1
SPBC28F2.10c	ngg1	SAGA complex subunit Ngg1/Ada3	TADA3
SPBC1921.07c	sgf29	SAGA complex subunit Sgf29	SGF29
SPAC4D7.10c	spt20	SAGA complex subunit Spt20	SUPT20H,​SUPT20HL1,​SUPT20HL2
SPCC61.02	spt3	SAGA complex subunit Spt3	SUPT3H
SPAC13A11.04c	ubp8	SAGA complex ubiquitin C-terminal hydrolase Ubp8	USP22,USP51
SPBC14C8.17c	spt8	SAGA complex WD repeat subunit Spt8	WDR38
SPBP16F5.03c	tra1	SAGA complex, phosphatidylinositol pseudokinase subunit Tra1	TRRAP
SPCC5E4.03c	taf5	SAGA complex/TATA-binding protein associated factor/transcription factor TFIID complex WD repeat subunit Taf5	TAF5
SPCC16C4.18c	taf6	SAGA complex/transcription factor TFIID complex histone H4-like subunit Taf6	TAF6,TAF6L
SPAC15A10.02	taf12	SAGA complex/transcription factor TFIID complex subunit A Taf12	TAF12
SPBC21H7.02	taf10	SAGA complex/transcription factor TFIID complex subunit Taf10	TAF10
SPAC12G12.05c	taf9	SAGA complex/transcription factor TFIID complex subunit Taf9	TAF9,TAF9B

@PCarme do you agree, if so I'll dispute that one in Protein2GO

[PCarme]

So basically in yeasts Taf5 is a structural component of both SAGA and TFIID. In human, there is two paralogs, TAF5 which is TFIID-specific, and TAF5L (the ortholog of Taf51 in S. pombe) which is SAGA-specific. As you said, there is no ortholog of Taf51 in S. cerevisiae. I have never seen Taf51 detected in any purifications or structures of neither SAGA nor TFIID in yeast.

In metazoans several SAGA-like complexes have been characterised through the years, which are absent from yeast (there is only SAGA). Humans used to have the TFTC, the PCAF and the STAGA complexes, but it is now generally assumed that these were probably different conformations of the human SAGA (PMID: 32673655).

Also, there is not a perfect conservation of the structure and subunits composition of SAGA from yeast to human: the human SAGA lacks an ortholog of the yeast Spt8 subunit, and contains two spliceosome-related subunits which are absent from the yeast SAGA (PMID: 34811519).

So, while the human ortholog of Taf51, TAF5L, is a subunit of the human SAGA, there is no evidence of the presence of Taf51 in S. pombe SAGA (and more than 20 years of genetic and biochemical evidence supporting the presence of Taf5 instead).

[marcfeuermann]

The erroneous annotation is partly due to the topology of the tree in which S. pombe taf5 and taf51 cluster together. I've blocked the SAGA annotation for taf51.

[ValWood]

Thanks @PCarme and @marcfeuermann !