copR (PA2809) review notes

UniProt: Q9I034 (unreviewed, 226 aa), "Two-component response regulator, CopR".
Locus PA2809; cognate sensor kinase CopS is PA2810.

What is established

CopR is the response regulator of the copper-responsive CopR-CopS
two-component system, and it is a new negative regulator of the porin gene
oprD, linking copper, zinc and imipenem resistance
PMID:17449606.
Overproduction of CopR in PAO1-derived PT5 and in a czcRS deletion strain
lowers oprD mRNA, abolishes OprD protein, and raises czcC and czcR-czcS
transcription
PMID:17449606.
So the same paper supports both a negative and a positive transcriptional role.
Direct promoter binding was not demonstrated in that work; it is inferred
from the P. syringae CopR cop box
PMID:17449606.
Later work confirms a CopRS regulon that is induced by external Cu2+ and that
is constitutively on when CopS is absent, consistent with CopS controlling the
phosphorylation state of CopR
PMID:33361129, PMID:33361129.
CopR is 55% identical to CzcR, the zinc-responsive regulator
PMID:17449606.

Literature search

Europe PMC, 2026-11-05: aeruginosa AND CopR AND copper AND regulon. Cached and
used: PMID:17449606 (full text), PMID:33361129 (full text). Also returned:
PMID:28760827 and PMID:38861577 (copper homeostasis network reviews), not needed
for the annotation calls.

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?
PTN000724188	GO:0006355 regulation of DNA-templated transcription	33	475 (45 taxa)	GO:0045892 negative regulation of DNA-templated transcription, IDA, PMID:17449606 (PseudoCAP)	SOUND	Full text read. CopR overproduction drops 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 itself and is measured in the organism. The one caveat is that the paper does not show CopR at the oprD promoter, so whether repression is direct is not settled; this does not affect the annotated term, which is regulation rather than promoter binding, nor the IBD, whose node term is the generic parent GO:0006355.	32 further seeds, including E. coli ArcA (P0A9Q1), OmpR (P0AA16), PhoB (P0AFJ5), CpxR (P0AE88), six M. tuberculosis regulators, Vibrio and plant/cyanobacterial regulators, and the PAO1 genes Q9I034 (this gene) and Q9I0I1	Yes - overwhelmingly. The node term rests on dozens of characterised response regulators. No `GO_CENTRAL` defect.

Node-level judgement for PTN000724188 (recorded here for the batch)

This node is the OmpR/PhoB winged-helix response-regulator node. It carries five
IBDs: GO:0000156 (10 seeds), GO:0006355 (33), GO:0000976 (12), GO:0032993 (7) and
GO:0005829 (4). Each term is at the family level and each is seeded by
experimentally characterised bacterial response regulators, mostly from E. coli.
The terms suit a clade of this size and breadth: every member has a receiver
domain plus a DNA-binding output domain, and the node makes no claim about which
regulon or which direction of regulation. No GO_CENTRAL defect is filed, and
the same judgement is applied to genes/PSEAE/parR (ParR, Q9I2U3), the other
leaf of this node in this batch, whose notes cross-reference this table.

PseudoCAP defects from this gene: none. The seed row is sound and, unusually for
this project, rests on data in the organism rather than on a mutant phenotype.
One NEW row is proposed from the same paper: GO:0045893 positive regulation of
DNA-templated transcription, for the CopR-dependent increase in czcR-czcS and
czcC transcription measured in the same qRT-PCR experiments.