sigX (PA1776, Q9I2W5) review notes
Reviewer: claude-code, 2026-11-05. PseudoCAP tier-2 IBA-seed batch (ECF sigma factors).
Literature
- SigX was identified upstream of oprF. Its disruption reduces OprF expression, and
primer extension maps a SigX-dependent ECF-type oprF promoter PMID:10438740.
The mutant phenotypes include slow growth in rich medium and imipenem sensitivity.
Abstract only: PMC93957 returned no body text from PubMed MCP or Europe PMC (2026-11-05).
- oprF transcription depends mainly on SigX PMID:22685281.
- ChIP-seq and RNA-seq define the SigX regulon (fatty acid biosynthesis, T3SS, swarming,
c-di-GMP) and its DNA motif [PMID:24187091, full text].
- The review groups SigX with AlgU and SbrI as cell-wall-stress ECF sigmas PMID:29729420.
Decisions
- Sigma factor activity (IBA, IDA seed): ACCEPT. On the IDA there is a PSEUDOCAP
WRONG_EVIDENCE_CODE defect (SUSPECTED, CHECK): the abstract describes only mutant-based
evidence.
- GO:0030307 positive regulation of cell growth (IMP): MARK_AS_OVER_ANNOTATED. The
phenotype is a pleiotropic growth-rate defect, and GO cell growth means an increase in
cell size. PSEUDOCAP WRONG_TERM defect, PROBABLE, CHECK.
- GO:0006355: MODIFY to GO:2000142. GO:0003700: TOO_GENERAL.
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:10438740 (PseudoCAP) |
SOUND |
The abstract supports the term (SigX-dependent ECF-type promoter mapped by mutant/WT primer extension), and later ChIP-seq (PMID:24187091) confirms it. The evidence code looks like IMP rather than IDA (SUSPECTED, abstract only); this does not affect the IBD. |
15 others (FecI, Mtb SigD/SigE/SigL, Sco SigR, 10 PAO1 ECF sigmas incl. PvdS and AlgU with in vitro transcription) |
Yes |
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).