RocA1 (PA3948) is a NarL/FixJ-family two-component response regulator of Pseudomonas aeruginosa, with an N-terminal receiver domain and a C-terminal LuxR-type helix-turn-helix DNA-binding domain. It is the output regulator of the RocS1-RocR-RocA1 (SadARS) system: the hybrid sensor kinase RocS1 activates RocA1 by phosphorelay, and the EAL-domain protein RocR antagonises it. RocA1 activates transcription of the cupB and cupC chaperone-usher fimbrial gene clusters that contribute to biofilm formation.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000160 phosphorelay signal transduction system | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the response-regulator receiver domain. Reason: RocA1 is the phosphorelay output of RocS1, as stated in the abstract. Supporting Evidence: PMID:15659157 the sensor kinase activates its cognate response regulator through a phosphorelay pathway |
| GO:0000976 transcription cis-regulatory region binding | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN008449896 (seeds E. coli NarL and P. aeruginosa NarL). Reason: RocA1 has the LuxR-type HTH DNA-binding domain of the clade and is described as a DNA-binding activator of cup genes. No operator has been mapped, so the generic term is as precise as the evidence allows. Supporting Evidence: PMID:15659157 RocS1 is a sensor kinase, RocA1 is a DNA binding response regulator that activates cup genes, and RocR is an antagonist of RocA1 activity |
| GO:0000976 transcription cis-regulatory region binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO (WalR-like) mapping. Reason: Consistent with the IBA row and the LuxR-type DNA-binding domain. Supporting Evidence: file:PSEAE/rocA1/rocA1-uniprot.txt PF00196; GerE |
| GO:0003677 DNA binding | IEA GO_REF:0000120 | TOO GENERAL | Summary: InterPro/UniRule mapping to DNA binding. Reason: True, but GO:0000976 transcription cis-regulatory region binding, accepted in this review, is_a GO:0003677. Supporting Evidence: file:PSEAE/rocA1/rocA1-uniprot.txt PF00196; GerE |
| GO:0003700 DNA-binding transcription factor activity | IBA GO_REF:0000033 | MODIFY | Summary: IBA from PTN008449896 (seeds E. coli NarL, RcsB, BglJ and P. aeruginosa NarL). Reason: Correct and right for the node, but RocA1 is described as an activator of cup genes, which supports GO:0001216 DNA-binding transcription activator activity for this gene. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN008449896 · PTN008449896 SUPPORTS TRANSFER NarL/FixJ (LuxR-type HTH) response-regulator node (167 leaf IBAs, 26 taxa). Its GO:0003700 IBD rests on E. coli NarL, RcsB and BglJ and P. aeruginosa NarL, all characterised DNA-binding transcription factors; it does not depend on PseudoCAP. Node-level verdict in the notes. Proposed replacements: DNA-binding transcription activator activity Supporting Evidence: PMID:15659157 RocS1 is a sensor kinase, RocA1 is a DNA binding response regulator that activates cup genes, and RocR is an antagonist of RocA1 activity |
| GO:0006351 DNA-templated transcription | IEA GO_REF:0000104 | MARK AS OVER ANNOTATED | Summary: UniRule keyword-based IEA. Reason: RocA1 regulates transcription; it is not part of the transcription machinery. The regulatory role is captured by GO:0045893. Supporting Evidence: PMID:15659157 RocS1 is a sensor kinase, RocA1 is a DNA binding response regulator that activates cup genes, and RocR is an antagonist of RocA1 activity |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBA from the PTN008449896 GO:0006355 IBD (9 seeds). rocA1 is one of them, which is expected, not circular; the IBD stands on the seven characterised E. coli, B. subtilis and P. aeruginosa regulators as well. Reason: True, but GO:0045893 positive regulation of DNA-templated transcription, accepted in this review from the gene's own evidence, is_a GO:0006355. Supporting Evidence: PMID:15659157 RocS1 is a sensor kinase, RocA1 is a DNA binding response regulator that activates cup genes, and RocR is an antagonist of RocA1 activity |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000120 | TOO GENERAL | Summary: InterPro/UniRule mapping. Reason: GO:0045893, accepted in this review, is_a GO:0006355. Supporting Evidence: PMID:15659157 RocS1 is a sensor kinase, RocA1 is a DNA binding response regulator that activates cup genes, and RocR is an antagonist of RocA1 activity |
| GO:0045893 positive regulation of DNA-templated transcription | IMP PMID:15659157 A novel two-component system controls the expression of Pseu... | ACCEPT | Summary: PseudoCAP IMP and one of the nine seeds of the PTN008449896 GO:0006355 IBD. RocA1 was identified in a screen for regulators of cupB/cupC transcription and activates the cup genes. Seed verdict SOUND. Reason: Core BP; RocA1 is the DNA-binding activator of cup fimbrial gene transcription. Supporting Evidence: PMID:15659157 RocS1 is a sensor kinase, RocA1 is a DNA binding response regulator that activates cup genes, and RocR is an antagonist of RocA1 activity |
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Download this section (compressed HTML)Q: Does RocA1 bind the cupB and cupC promoters directly, and what operator sequence does it recognise?
Experiment: EMSA and DNase I footprinting of purified, phosphorylated RocA1 on the cupB and cupC promoters, with ChIP-seq of RocA1 in a rocR mutant background.
Type: EMSA / ChIP-seq
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