ptxR (PA2258, P72131) review notes

Review session 2026-11-05 (PseudoCAP IBA-seed protocol, tier 2)

Fetched with just fetch-gene PSEAE P72131 --alias ptxR; accession matches the worklist.
No deep-research provider was used; PubMed esearch unavailable (NCBI SOLR errors), Europe PMC
used. Cached: PMID:22844393 (full text read), PMID:8843437 and PMID:16803594 (abstract only).

Literature

PMID:8843437 (Hamood et al. 1996): ptxR found as a gene raising exotoxin A production;
PMID:8843437; ptxR mutants have less exotoxin A
activity; PMID:8843437.
PMID:22844393 (Daddaoua et al. 2012, full text): DNaseI footprint and ITC of PtxR on PtoxA
(palindrome CGCCGCCGCG overlapping -35) and Pkgu/Pgad; PMID:22844393; PtxS binds PtxR.
PMID:16803594 (Carty et al. 2006): PMID:16803594; PtxR reduces phzA1-G1 and pqsABCDE expression; ptxR mutation lowers lasB.

Annotation decisions

GO:0045893 (IDA, seed), GO:0001216 (IPI), GO:0000976 (IBA, IPI): ACCEPT.
GO:0006355 (IBA, IEA), GO:0003700 (IEA): TOO_GENERAL.
GO:0032993 (IPI): KEEP_AS_NON_CORE.
GO:0003950 NAD+ poly-ADP-ribosyltransferase activity (IMP, PMID:8843437): REMOVE; it is the
activity of the target toxin ToxA. PSEUDOCAP WRONG_TERM defect, CONFIRMED (the abstract states
PtxR is a LysR regulator and the readout was exotoxin A activity).
GO:0045862 positive regulation of proteolysis (IMP): MARK_AS_OVER_ANNOTATED (lasB expression,
probably via QS; abstract only).
GO:1900377 (IMP): MODIFY to GO:1900981 negative regulation of phenazine biosynthetic process.
Action counts: ACCEPT 4, TOO_GENERAL 3, KEEP_AS_NON_CORE 1, REMOVE 1, MARK_AS_OVER_ANNOTATED 1,
MODIFY 1.

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?
PTN001248394	GO:0006355 regulation of DNA-templated transcription	7	202 (30 taxa)	GO:0045893, IDA, PMID:22844393 (PseudoCAP)	SOUND	Full text read: PtxR footprints a -35 palindrome at PtoxA (and Pkgu, Pgad) and toxA expression falls three-fold in the deletion. Generic term suits a LysR clade.	E. coli MetR, YjiE, AaeR, YhaJ; P. aeruginosa CysB (G3XCU6) and Q9I1R1	Yes

Consistent with the cysB review (genes/PSEAE/cysB/cysB-notes.md), which also judged this node
SOUND. No GO_CENTRAL defect. The PSEUDOCAP defect on GO:0003950 concerns a non-seed row.