Curation Information

Nucleotide sequence and initial functional characterization of the clcR gene encoding a LysR family activator of the clcABD chlorocatechol operon in Pseudomonas putida.;Coco WM, Rothmel RK, Henikoff S, Chakrabarty AM;Journal of bacteriology 1993 Jan; 175(2):417-27 [8419291]
ClcR [A0A024HKB0, view regulon]
Reported TF sp.
Pseudomonas putida PRS2000
Reported site sp.
Pseudomonas putida PRS2000
Created by
Matthew Coveyou
Curation notes
ClcR and clcABD are borne on the Pseudomonas putida plasmid pAC27, which has no RefSeq equivalent. Bordetella petrii DSM 12804 (NC_010170.1) has a clcR gene (YP_001630141) which has been used as a placeholder.

Experimental Process

Beta-gal assay of both the clcA and clcR genes demonstrated activation and autoregulation by clcR, respectively. EMSA confirmed specific binding of clcR to the clcA-clcR promoter region. Comparison of the promoter region with a proposed LysR family consensus binding site identified a putative binding site for clcR.

Transcription Factor Binding Sites


Gene Regulation

Regulated genes for each binding site are displayed below. Gene regulation diagrams show binding sites, positively-regulated genes, negatively-regulated genes, both positively and negatively regulated genes, genes with unspecified type of regulation. For each indvidual site, experimental techniques used to determine the site are also given.

Site sequence Regulated genes Gene diagram Experimental techniques TF function TF type
... ... clcR clcA catB2 bug36 Bpet1537 Bpet1538 Bpet1539
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details EMSA (ECO:0001807) - repressor not specified