CopR (PA2809) is the cytoplasmic response regulator of the copper-responsive CopR-CopS two-component system of Pseudomonas aeruginosa. It is a 226-residue OmpR/PhoB-family protein with a receiver domain phosphorylated by the periplasmic-sensing kinase CopS (PA2810) and a winged-helix domain that binds promoter DNA; CopS also dephosphorylates CopR when copper is absent, which keeps the regulon off. CopR drives the transcriptional response to copper and is required for copper tolerance. Beyond the copper regulon it connects metal and antibiotic resistance - it activates the czcR-czcS operon and the czcCBA zinc efflux pump and represses the porin gene oprD, so increased CopR lowers OprD in the outer membrane and raises resistance to imipenem. CopR is closely related to the zinc-responsive regulator CzcR (55% identity), and the two systems overlap on these targets.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000156 phosphorelay response regulator activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the ten-seed GO:0000156 IBD at PTN000724188, the OmpR/PhoB response-regulator node, seeded by characterised E. coli regulators (ArcA, OmpR, CpxR) and by PAO1 ParR. CopR has the receiver domain, its cognate kinase CopS is encoded next to it, and the regulon is constitutively on in a copS deletion, which is what a phosphorelay regulator with a dephosphorylating partner predicts. Reason: Sound node-level inference, corroborated in this organism by the copS-dependent behaviour of the CopR regulon. Supporting Evidence: PMID:33361129 However, in the absence of Cu, CopS shuts down the transcriptional response to Cu+, likely dephosphorylating CopR. |
| GO:0000160 phosphorelay signal transduction system | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO from the receiver and winged-helix signatures. CopR-CopS is a genuine two-component system responding to periplasmic copper. Reason: Correct and informative; the copper response is lost in a copR mutant and constitutive in a copS mutant. Supporting Evidence: PMID:33361129 In contrast, the ΞcopS mutant strain showed a constitutive activation of all the genes of the CopRS regulon, even in the absence of the Cu2+ stimulus. |
| GO:0000976 transcription cis-regulatory region binding | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the twelve-seed IBD at the same node, seeded by response regulators with demonstrated promoter binding. CopR has the winged-helix output domain, and its P. syringae orthologue binds a defined cop box; binding by the P. aeruginosa protein is expected but was explicitly left as an inference in PMID:17449606. Reason: Well-seeded family-level claim, consistent with the organism's own transcriptional data; the inherited term is the right level given that no footprint has been published for CopR itself. Supporting Evidence: PMID:17449606 It is therefore very likely that the P. aeruginosa CopR regulator binds to this cop box |
| GO:0000976 transcription cis-regulatory region binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO from the OmpR/PhoB-type DNA-binding domain; agrees with the IBA row on the same term. Reason: Consistent electronic assertion of the same claim. |
| GO:0003677 DNA binding | IEA GO_REF:0000120 | TOO GENERAL | Summary: Generic DNA binding from the winged-helix signature, the CopR/CusR-type signature and a UniRule. Entailed by the accepted GO:0000976. Reason: Uninformative given the more specific cis-regulatory region binding term asserted in this review. |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: Four-seed IBD at the same node. CopR is the soluble half of the pair - CopS senses copper in the periplasm and CopR acts on chromosomal promoters - so the cytosol is where its activity takes place. Reason: Sound for a soluble DNA-binding response regulator. |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the 33-seed GO:0006355 IBD at this node, which this gene's own PseudoCAP IDA row helped to seed - an expected self-appearance in WITH/FROM, not circularity. The general claim is directly borne out here - CopR lowers oprD transcription and raises czcR-czcS and czcC transcription. The more specific signed terms (GO:0045892 accepted below, GO:0045893 proposed) are what this gene does; the generic parent is the right level for a node whose members regulate in both directions. Reason: Correct at the node and true of the gene. Not marked too general - this gene both activates and represses, and the two signed descendants together are what the parent summarises. Supporting Evidence: PMID:17449606 Altogether these results show that the CopR regulator, like CzcR, negatively regulates oprD and positively regulates the czcCBA operon |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO assertion of the same process claim as the IBA row above. Reason: Consistent with the accepted IBA row and with the organism's own data. |
| GO:0032993 protein-DNA complex | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Seven-seed IBD at the same node, restating promoter binding as a complex. Not wrong for a DNA-binding response regulator, but it adds nothing beyond GO:0000976, and no CopR-DNA complex has been shown directly. Reason: As precise as the evidence allows but peripheral; the informative claims are the DNA binding and the signed regulation terms. |
| GO:0045892 negative regulation of DNA-templated transcription | IDA PMID:17449606 A copper-activated two-component system interacts with zinc ... | ACCEPT | Summary: PseudoCAP row and a seed of the GO:0006355 IBD at PTN000724188. Full text read - inducing CopR from a plasmid lowers oprD mRNA by qRT-PCR and abolishes OprD protein by western blot, in the wild type and in a czcRS deletion background, so the repression is attributable to CopR and not to CzcR. Whether CopR represses oprD by binding that promoter itself is not settled in the paper, but the annotated term claims regulation, not binding, and CopR is the regulator performing it. Reason: Direct, in-organism evidence for a signed transcriptional role; the right term and an appropriate evidence code, and a sound seed for the generic node term. Supporting Evidence: PMID:17449606 This study shows that CopR is a new negative regulator of OprD porin and that it links Zn, Cu, and imipenem resistances by interacting with the CzcRS TCS. PMID:17449606 Altogether these results show that the CopR regulator, like CzcR, negatively regulates oprD and positively regulates the czcCBA operon |
| GO:0045893 positive regulation of DNA-templated transcription | IDA PMID:17449606 A copper-activated two-component system interacts with zinc ... | NEW | Summary: Proposed row. The same qRT-PCR experiments that established the oprD repression also show that CopR overproduction raises czcC and czcR-czcS transcription, in the wild type and in the czcRS deletion strain, and the later CopRS study shows the whole CopRS regulon being switched on in response to copper. CopR is the transcription factor doing the activating, so this is participation rather than a downstream consequence. Reason: The activating half of CopR's transcriptional role is missing from GOA although it rests on the same experiments, in the same paper, as the accepted GO:0045892 row. Proposed conservatively and signed, with no new claim about mechanism. Supporting Evidence: PMID:17449606 Altogether these results show that the CopR regulator, like CzcR, negatively regulates oprD and positively regulates the czcCBA operon PMID:33361129 In contrast, the ΞcopS mutant strain showed a constitutive activation of all the genes of the CopRS regulon, even in the absence of the Cu2+ stimulus. |
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Download this section (compressed HTML)Q: Does phospho-CopR bind the oprD promoter directly, or is the repression relayed through another regulator? The 2007 work inferred cop-box binding from the Pseudomonas syringae orthologue rather than demonstrating it.
Q: CopR and CzcR share 55% identity and overlapping targets. Do they bind the same sites, and does cross-phosphorylation between the two systems occur in vivo?
Experiment: Define the CopR regulon and its binding sites directly - ChIP-seq or ChIP-exo on epitope-tagged CopR after copper exposure, with EMSA and footprinting of purified phospho-CopR on the oprD, czcR and copA1 promoters, run alongside CzcR to test site overlap.
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