pvdS (PA2426, G3XCV1) review notes

Reviewer: claude-code, 2026-11-05. PseudoCAP tier-2 IBA-seed batch (ECF sigma factors).

Literature

pvdS is required for pyoverdine promoter expression and activates them in E. coli
PMID:7751284. A null mutant makes no pyoverdine
PMID:7651323. pvdA transcription needs PvdS PMID:8636031.
Biochemistry: purified PvdS directs core RNAP to pvd promoters and transcribes them in
vitro PMID:10873648. It forms 1:1 complexes with core RNAP
PMID:10692351.
The IS box is the PvdS -35 recognition element PMID:11222621.
PvdS also drives toxA, regA and ptxR PMID:18048935. Membrane retention of part of the
PvdS pool is relieved by pyoverdine signalling PMID:18047579. pvdS is a Fur target
PMID:8633080.

Decisions

Sigma factor activity rows (IBA, IEA, 2 IDA): ACCEPT.
GO:0006355 (IBA, IEA, IMP seed): MODIFY to GO:2000142.
GO:1900378 (6 rows): MODIFY to GO:1900706 positive regulation of siderophore
biosynthetic process. The VqsR paper (PMID:15073293) does not mention pvdS in its
abstract: PSEUDOCAP WRONG_REFERENCE defect, SUSPECTED, CHECK.
CollecTF rows: GO:0000976 MODIFY to GO:0001046; GO:0001216 MODIFY to GO:0016987;
GO:0032993 KEEP_AS_NON_CORE; GO:0045893 MODIFY to GO:2000144.
GO:0071281 cellular response to iron ion (EXP): KEEP_AS_NON_CORE. This is Fur acting on
the pvdS promoter.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN002455017	GO:0016987 sigma factor activity	16	250 (29 taxa)	GO:0016987, IDA, PMID:10692351 and PMID:10873648 (PseudoCAP)	SOUND	The abstracts state core-RNAP binding, holoenzyme promoter binding and in vitro transcription: direct evidence (CONFIRMED from abstract text).	15 others (FecI, Mtb SigD/SigE/SigL, Sco SigR, 10 PAO1 ECF sigmas incl. PvdS and AlgU with in vitro transcription)	Yes
PTN002455017	GO:0006355 regulation of DNA-templated transcription	8	250 (29 taxa)	GO:0006355, IMP, PMID:7751284 (PseudoCAP)	SOUND	The abstract states loss- and gain-of-function control of pvd promoter expression. The term is general but correct; the gene-level row is refined to GO:2000142 without affecting the IBD.	7 others (E. coli and V. cholerae RpoE, Mtb SigC/SigH/SigL/SigM, plus AlgU or PvdS)	Yes; this batch owns the node (no parallel-agent gene seeds it). No GO_CENTRAL defect.

Node PTN002455017 (shared by the whole ECF sigma batch)

PTN002455017 is the ECF sigma factor clade of PANTHER PTHR43133 (250 leaf IBAs, 29
taxa). It carries two IBDs (.cache/paint/IBD.gaf):

GO:0016987 sigma factor activity, 16 seeds: E. coli FecI (P23484), M. tuberculosis
SigE (P9WGG7), SigL (P9WGH5) and SigD (P9WGG9), S. coelicolor SigR (Q7AKG9), and 11
P. aeruginosa ECF sigmas: PA2093 (Q9I222), foxI (Q9I114), PA2050 (Q9I265), PA0149
(Q9I6Y3), PA0472 (Q9I646), PA4896 (Q9HUR7), vreI (Q9I5P9), sigX (Q9I2W5), fpvI
(Q9I193), algU (Q06198), pvdS (G3XCV1). Accessions were resolved against UniProt REST.
GO:0006355 regulation of DNA-templated transcription, 8 seeds: M. tuberculosis SigC
(P9WGH1), SigL (P9WGH5), SigH (P9WGH9) and SigM (O53590), V. cholerae RpoE (Q9KPA6),
E. coli RpoE (P0AGB6), algU (Q06198), pvdS (G3XCV1).

Both node terms suit a clade made up entirely of ECF sigma-70 family proteins. The
GO:0016987 IBD has direct biochemical seeds: PvdS (PMID:10873648, in vitro transcription)
and AlgU (PMID:7644517, in vitro transcription). It also has well-characterised
non-Pseudomonas seeds. It stands without any single seed. The GO:0016987 node is also
seeded by PA2093, foxI, PA2050, PA0149 and PA0472, which the parallel agent is reviewing,
and any node-level GO_CENTRAL defect for it is recorded there. I found none to record.
None of those five genes seeds the GO:0006355 IBD, so its node assessment belongs to
this batch (pvdS, algU). It is sound, and no GO_CENTRAL defect is needed.

Cross-reference: the same node is assessed in the reviews of PA4896, vreI, pvdS, sigX, fpvI and algU (this batch) and of PA2093, foxI, PA2050, PA0149 and PA0472 (parallel agent).