cifR (PA2931, Q9HZR6) notes

Identity

CifR, 196 aa TetR-family (TFR) transcriptional repressor, divergently
transcribed from the morB-cfrX-cif operon. UniProt TrEMBL entry
(Q9HZR6_PSEAE, SubName "CifR"), PE 1 (evidence at protein level) on the
strength of three crystal structures (PDB 6NSM, 6NSN, 6NSR).
Domains: HTH tetR-type 9..69 with the H-T-H motif at 32..51
(PROSITE PS50977, PRU00335); TetR_N (PF00440) plus TetR_C_13 (PF16925)
ligand-binding domain. PANTHER PTHR47506 / PTHR47506:SF1.
UniProt records Cys107 modified as cysteine sulfenic and sulfinic acid from
the 6NSN structure (ECO:0007829), matching the epoxide/oxidant-sensing
cysteine of the 2024 study.

Function

CifR was identified as the repressor of cif, the secreted epoxide hydrolase
virulence factor that reduces apical CFTR
PMID:18458065
and the DNA complex is released by the epoxide epibromohydrin
PMID:18458065
Two operators in the cifR-morB intergenic region, mapped by EMSA and
chromosomal mutagenesis, controlling both divergent transcripts
PMID:22843844
PMID:22843844
So CifR represses its own gene as well as the cif operon
PMID:22843844
Structures of CifR alone and bound to operator DNA, with Cys107 as the
epoxide-sensing residue
PMID:39413156
PMID:39413156
PMID:39413156
PMID:39413156
CifR is described as the first epoxide-sensing bacterial transcription factor
PMID:39413156
See genes/PSEAE/cif (reviewed separately) for the regulated target.

PAINT node PTN002934616

PTHR47506 ("transcriptional regulatory protein"; subfamily SF1 "HTH-type
transcriptional regulator YjdC"). The repository family folder has no
PAINT file, so the node content was read from QuickGO: 25 leaf IBAs of
GO:0045892 in 9 taxa (E. coli yjdC, Shewanella mexR and SO_1578/SO_3393,
Bradyrhizobium bll/blr genes, Streptomyces SCO genes, Vibrio VC_A genes,
Xanthomonas XCC0044, Gloeobacter gll1420, Rhodopirellula RB genes, and
P. aeruginosa cifR and PA2484).
The only IBD at the node is GO:0045892, and cifR is the sole seed. The
supporting annotations are all experimental and all on CifR itself:
CollecTF EXP and IEP from PMID:22843844 and PseudoCAP IMP from
PMID:18458065. Only the IMP is a PseudoCAP row.
The leaves are TetR/MarR-type HTH regulators, for which repression is the
usual mode; the term is a cautious, aspect-appropriate family-level claim,
not a transfer of the epoxide-sensing specialisation. CollecTF's finer MF/CC
rows (GO:0001217, GO:0000976, GO:0032993) were not propagated, which is the
right choice since operator identity is gene-specific.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN002934616	GO:0045892 negative regulation of DNA-templated transcription	1 (sole seed)	25 (9 taxa)	GO:0045892, IMP, PMID:18458065 (PseudoCAP); same term EXP and IEP, PMID:22843844 (CollecTF)	SOUND	The seed is the gene's own direct activity, not a downstream phenotype: purified CifR binds two mapped operators in the cifR-morB intergenic region, chromosomal operator mutations raise cif and cifR transcription, and the epoxide EBH releases CifR from DNA; the 2024 structures show a CifR dimer on its operator. A sole seed is not weak support (the IBD rests on a well-characterised repressor), and cifR appearing in its own With/From marks the experimental grounding on the target. The node term is a broad, sign-correct generalisation for a clade of TetR/MarR-type HTH repressors, and the gene-specific operator and epoxide-sensing claims were correctly not propagated.

The other PseudoCAP row types for this gene: there is only one PseudoCAP
annotation in the GOA file (the GO:0045892 IMP above). PA2931 has no other
PseudoCAP seeding, so no further seeds need assessment.

Decisions summary

ACCEPT: negative regulation of DNA-templated transcription (IMP, EXP, IEP,
IBA), DNA-binding transcription repressor activity, transcription
cis-regulatory region binding, protein-DNA complex.
MODIFY: DNA binding (IEA) -> transcription cis-regulatory region binding;
regulation of DNA-templated transcription (ARBA IEA) -> negative regulation
of DNA-templated transcription.
No REMOVE; no source defects found.