AlgB (PA5483) is an NtrC-family response regulator of the AlgB/KinB two-component system. It has an N-terminal receiver domain (phosphorylation site Asp59), a central sigma-54 activation (AAA+) domain and a C-terminal Fis-type helix-turn-helix DNA-binding domain. In mucoid P. aeruginosa AlgB is needed for high-level alginate production: it binds the algD promoter in vivo and in vitro and activates transcription of the algD alginate biosynthetic operon from the sigma-22 (AlgU)-dependent promoter. Unusually, this role does not need its phosphorylation or its receiver domain. The sensor KinB phosphorylates AlgB but mainly acts as an AlgB phosphatase; in kinB mutants phosphorylated AlgB raises algU expression, which promotes alginate production and represses acute-virulence traits such as pyocyanin, elastase and motility.
Definition: Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of alginic acid.
Justification: Alginate regulators such as AlgB (and AlgR, AmrZ) act on transcription of the alginate operon, not on the chemistry, and are currently annotated to the biosynthetic process itself because no regulation term exists.
Parent term: regulation of polysaccharide biosynthetic process
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000160 phosphorelay signal transduction system | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO from the receiver domain. KinB phosphorylates AlgB on Asp59 and dephosphorylates it, so AlgB is a phosphorelay response regulator, though its alginate role does not need phosphorylation. Reason: True for the KinB-AlgB system (which controls virulence traits); peripheral to the phosphorylation-independent algD activation. Supporting Evidence: PMID:9473053 kinB was identified downstream of algB and was shown to encode the cognate histidine protein kinase that efficiently phosphorylates AlgB PMID:23024348 These data suggest that in the absence of KinB, AlgB must be phosphorylated in order to repress virulence. |
| GO:0000987 cis-regulatory region sequence-specific DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN000787214 (seeded by E. coli GlrR, FhlA, NorR IDA and FleQ IDA). AlgB binds a defined 50-bp site upstream of PalgD. Reason: Direct binding evidence for AlgB itself. Supporting Evidence: PMID:17981963 Chromosome immunoprecipitation revealed that AlgB bound in vivo to PalgD but did not bind when AlgB had an R442E substitution that disrupted the DNA binding domain. |
| GO:0001216 DNA-binding transcription activator activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the PTN000787214 IBD (seeded by FleQ, CbrB and Vibrio, Xanthomonas and Geobacter orthologues; node assessment in genes/PSEAE/fleQ/fleQ-notes.md). AlgB binds PalgD and activates algD transcription. Reason: Supported for AlgB by ChIP, EMSA and SELEX binding to PalgD and by loss of algD transcription in algB mutants. Supporting Evidence: PMID:17981963 Chromosome immunoprecipitation revealed that AlgB bound in vivo to PalgD but did not bind when AlgB had an R442E substitution that disrupted the DNA binding domain. PMID:17981963 in this case to stimulate transcription from the sigma(22)-dependent PalgD promoter PMID:1899859 AlgB was shown to be involved in the transcription of algD |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO from the sigma-54 interaction domain, which carries Walker motifs. No ATP binding or ATPase assay has been reported for AlgB, and it activates a sigma-22 promoter. Reason: Domain-based and plausible; whether ATP hydrolysis is used at PalgD is unknown. Supporting Evidence: PMID:1738315 The predicted amino acid sequence of AlgB revealed a high degree of similarity to the regulatory proteins in the NtrC subclass |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | TOO GENERAL | Summary: Regulation of transcription. Correct; GO:0045893 is accepted. Reason: Entailed by GO:0045893 (is_a GO:0006355), accepted elsewhere. Supporting Evidence: PMID:1899859 AlgB was shown to be involved in the transcription of algD |
| GO:0032993 protein-DNA complex | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA from PTN000787214. AlgB binds the algD promoter in vivo (ChIP). Reason: True, but restates DNA binding; kept non-core as on fleQ. Supporting Evidence: PMID:17981963 Chromosome immunoprecipitation revealed that AlgB bound in vivo to PalgD but did not bind when AlgB had an R442E substitution that disrupted the DNA binding domain. |
| GO:0042121 alginic acid biosynthetic process | IEA GO_REF:0000041 | MODIFY | Summary: UniPathway mapping of the record's PATHWAY line, which reads alginate biosynthesis [regulation]; the regulation qualifier was lost in the mapping. Reason: AlgB is a transcriptional regulator of the algD operon, not an enzyme of alginate synthesis, so it does not take part in the biosynthetic process itself. GO has no regulation-of-alginate term; the nearest existing term is GO:0032885 regulation of polysaccharide biosynthetic process (a positive-regulation child is proposed as a new term). Proposed replacements: regulation of polysaccharide biosynthetic process Supporting Evidence: PMID:1738315 regulates the expression of the alginate biosynthetic gene, algD, thereby resulting in increased expression of alginate in mucoid P. aeruginosa PMID:1899859 AlgB was shown to be involved in the transcription of algD |
| GO:0042121 alginic acid biosynthetic process | IMP PMID:1738315 Pseudomonas aeruginosa AlgB, which modulates the expression ... | MODIFY | Summary: PseudoCAP IMP to the alginate biosynthetic process for a regulator. The abstract shows algB regulating algD expression, which is regulation of the process. Reason: AlgB is a transcriptional regulator of the algD operon, not an enzyme of alginate synthesis, so it does not take part in the biosynthetic process itself. GO has no regulation-of-alginate term; the nearest existing term is GO:0032885 regulation of polysaccharide biosynthetic process (a positive-regulation child is proposed as a new term). Proposed replacements: regulation of polysaccharide biosynthetic process Supporting Evidence: PMID:1738315 regulates the expression of the alginate biosynthetic gene, algD, thereby resulting in increased expression of alginate in mucoid P. aeruginosa PMID:1899859 AlgB was shown to be involved in the transcription of algD |
| GO:0043565 sequence-specific DNA binding | IEA GO_REF:0000002 | TOO GENERAL | Summary: Sequence-specific DNA binding from the HTH signature. Correct; GO:0000987 is accepted. Reason: Entailed by GO:0000987 (is_a GO:0043565). Supporting Evidence: PMID:17981963 Chromosome immunoprecipitation revealed that AlgB bound in vivo to PalgD but did not bind when AlgB had an R442E substitution that disrupted the DNA binding domain. |
| GO:0045862 positive regulation of proteolysis | IMP PMID:23024348 The two-component sensor KinB acts as a phosphatase to regul... | MARK AS OVER ANNOTATED | Summary: PseudoCAP IMP to positive regulation of proteolysis. The cited paper (full text read) has no proteolysis assay. Its only protease readout is elastase, which phosphorylated AlgB represses in a kinB background. The related paper PMID:19168621 shows that algB is needed for AlgW-dependent MucA degradation in a kinB mutant, an indirect, background-specific effect. Reason: Not supported by the cited paper. The nearest support (PMID:19168621) is an indirect requirement in a kinB mutant, not a general role of AlgB in proteolysis. Supporting Evidence: PMID:19168621 Our results also indicate that AlgW-mediated MucA degradation required algB and rpoN in the kinB mutant. PMID:23024348 Similarly, algB deletion in PA14Ξ kinB also restores wild-type levels of pyocyanin and elastase |
| GO:0045893 positive regulation of DNA-templated transcription | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN000787214, of which AlgB's own PseudoCAP IMP is one of ten seeds. AlgB in its own WITH/FROM is expected, not circular. Reason: AlgB activates algD transcription; the IBD also stands on nine other experimental seeds. Supporting Evidence: PMID:1899859 AlgB was shown to be involved in the transcription of algD PMID:17981963 in this case to stimulate transcription from the sigma(22)-dependent PalgD promoter |
| GO:0045893 positive regulation of DNA-templated transcription | IMP PMID:1738315 Pseudomonas aeruginosa AlgB, which modulates the expression ... | ACCEPT | Summary: PseudoCAP IMP and one of the ten seeds of the PTN000787214 IBD. The abstract states that algB regulates algD expression and increases alginate output. Later work showed that AlgB binds PalgD directly and activates its transcription. Reason: Sound seed. Loss of algD expression in the algB mutant, with direct promoter binding shown later, supports positive regulation of transcription. Supporting Evidence: PMID:1738315 regulates the expression of the alginate biosynthetic gene, algD, thereby resulting in increased expression of alginate in mucoid P. aeruginosa PMID:1899859 AlgB was shown to be involved in the transcription of algD PMID:17981963 Chromosome immunoprecipitation revealed that AlgB bound in vivo to PalgD but did not bind when AlgB had an R442E substitution that disrupted the DNA binding domain. |
| GO:1900232 negative regulation of single-species biofilm formation on inanimate substrate | IMP PMID:19168621 The Pseudomonas aeruginosa sensor kinase KinB negatively con... | UNDECIDED | Summary: PseudoCAP IMP to negative regulation of biofilm formation on inanimate substrate. The cited paper (full text read) does not mention biofilms; it concerns alginate overproduction and MucA proteolysis in kinB mutants. The source of the claim cannot be identified. Reason: The cited paper does not support the row and no other source for it was found. Supplementary material or a mis-keyed reference could explain it, so the call is left to the curators. Supporting Evidence: PMID:19168621 Our results also indicate that AlgW-mediated MucA degradation required algB and rpoN in the kinB mutant. |
| GO:1900378 positive regulation of secondary metabolite biosynthetic process | IMP PMID:23024348 The two-component sensor KinB acts as a phosphatase to regul... | MODIFY | Summary: PseudoCAP IMP to positive regulation of secondary metabolite biosynthesis (pyocyanin). In the full text, deleting algB in a kinB background restores wild-type pyocyanin, and phosphorylatable AlgB is needed to repress it; AlgB therefore lowers pyocyanin, indirectly through AlgU. Reason: Sign inverted. The evidence supports negative regulation, indirect and limited to the kinB background, so it is non-core. Proposed replacements: negative regulation of secondary metabolite biosynthetic process Supporting Evidence: PMID:23024348 Similarly, algB deletion in PA14Ξ kinB also restores wild-type levels of pyocyanin and elastase PMID:23024348 These data suggest that in the absence of KinB, AlgB must be phosphorylated in order to repress virulence. |
| GO:2000147 positive regulation of cell motility | IMP PMID:23024348 The two-component sensor KinB acts as a phosphatase to regul... | MODIFY | Summary: PseudoCAP IMP to positive regulation of cell motility. In the full text, AlgB is needed for the reduced motility of the kinB mutant (complementation restores the reduced motility), so AlgB lowers motility. Reason: Sign inverted; negative regulation, indirect via AlgU and seen only in the kinB background. Proposed replacements: negative regulation of cell motility Supporting Evidence: PMID:23024348 Episomal complementation of the algB deletion in the PA14Ξ algB Ξ kinB strain restores the reduced pyocyanin, elastase, and motility phenotypes of the PA14Ξ kinB strain PMID:23024348 These data suggest that in the absence of KinB, AlgB must be phosphorylated in order to repress virulence. |
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