algB (PA5483, P23747) review notes
Literature summary
- AlgB is an NtrC-subclass regulator that controls algD expression and alginate output [PMID:1738315 "regulates the expression of the alginate biosynthetic gene, algD, thereby resulting in increased expression of alginate in mucoid P. aeruginosa"; "The predicted amino acid sequence of AlgB revealed a high degree of similarity to the regulatory proteins in the NtrC subclass"].
- AlgB is needed for algD transcription PMID:1899859 and binds PalgD directly PMID:17981963, activating a sigma-22 promoter PMID:17981963.
- The algD role is phosphorylation-independent PMID:9473053; KinB is the cognate kinase PMID:9473053.
- In a kinB background, phosphorylated AlgB represses acute virulence PMID:23024348; deleting algB restores pyocyanin/elastase PMID:23024348 and complementation restores the reduced motility PMID:23024348.
- algB is needed for AlgW-dependent MucA degradation in a kinB mutant PMID:19168621; that paper does not mention biofilm.
Literature search (2026-11-05): PubMed MCP and NCBI E-utilities failed all session; Europe PMC title search found
the AlgB papers. Full text read for PMID:23024348 and PMID:19168621 (the two multi-phenotype PseudoCAP sources);
PMID:1738315, 1899859, 17981963, 9473053 are abstract-only in cache.
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? |
| PTN000787214 |
GO:0045893 positive regulation of DNA-templated transcription |
10 |
214 (28 taxa) |
GO:0045893, IMP, PMID:1738315 |
SOUND |
AlgB activates algD transcription (algB mutant loses algD expression; AlgB binds PalgD by ChIP/EMSA/SELEX). |
E. coli GlrR, PspF, RtcR, PrpR, AtoC (EcoCyc IDA/IMP); FhlA/NorR via other node terms; FleQ, CbrB, Vibrio/Xanthomonas/Geobacter EBPs (CollecTF) |
Yes; many EcoCyc IDA seeds |
Node-level assessment for PTN000787214 is recorded once on fleQ (genes/PSEAE/fleQ/fleQ-notes.md), the gene with the
most direct evidence in this batch. The node is a sigma-54 enhancer-binding-protein clade (PTHR32071); its four IBD
terms (GO:0000987, GO:0001216, GO:0032993, GO:0045893) each rest on several independent experimental seeds and suit
the clade, so no GO_CENTRAL defect is filed. AlgB's own PseudoCAP IMP appearing in the WITH/FROM is expected.
Source defects (non-seed PseudoCAP rows)
These rows are not IBD seeds; they are PseudoCAP annotations on algB from two multi-phenotype papers whose full text
was read:
- GO:0042121 alginic acid biosynthetic process (IMP, PMID:1738315, and the UniPathway IEA): AlgB is a regulator of
algD, not an alginate enzyme. MODIFY to GO:0032885; PSEUDOCAP WRONG_TERM, CONFIRMED. A positive-regulation-of-alginate
term is proposed.
- GO:1900378 positive regulation of secondary metabolite biosynthesis (IMP, PMID:23024348): sign inverted (AlgB
represses pyocyanin in the kinB background). MODIFY to GO:1900377; PSEUDOCAP WRONG_TERM, CONFIRMED.
- GO:2000147 positive regulation of cell motility (IMP, PMID:23024348): sign inverted. MODIFY to GO:2000146;
PSEUDOCAP WRONG_TERM, CONFIRMED.
- GO:0045862 positive regulation of proteolysis (IMP, PMID:23024348): the cited paper has no proteolysis assay;
MARK_AS_OVER_ANNOTATED with a PSEUDOCAP WRONG_REFERENCE/CHECK defect (the MucA-proteolysis result is in PMID:19168621).
- GO:1900232 negative regulation of biofilm formation (IMP, PMID:19168621): the cited paper does not mention biofilm;
UNDECIDED with a PSEUDOCAP WRONG_REFERENCE/CHECK defect.
Action summary
15 rows. ACCEPT 4; MODIFY 4 (GO:0042121 x2, GO:1900378, GO:2000147); KEEP_AS_NON_CORE 3 (GO:0032993, GO:0000160,
GO:0005524); TOO_GENERAL 2 (GO:0006355, GO:0043565); MARK_AS_OVER_ANNOTATED 1 (GO:0045862); UNDECIDED 1 (GO:1900232).