Curation Information

Transcriptional repression mediated by LysR-type regulator CatR bound at multiple binding sites.;Chugani SA, Parsek MR, Chakrabarty AM;Journal of bacteriology 1998 May; 180(9):2367-72 [9573187]
CatR [F8G324, view regulon]
Reported TF sp.
Pseudomonas putida PRS2000
Reported site sp.
Pseudomonas putida PRS2000
Created by
Matthew Coveyou
Curation notes

Experimental Process

Visual inspection of the catB gene of Pseudomonas putida revealed a site similar to the catR binding consensus sequence. Beta-gal initially indicated this internal binding site (IBS) acted as a repression site for the catBCA operon. Site-directed mutagenesis was used to investigate key nucleotides; the mutant containing the T-N11-A motif showed increased binding over the wild type, while mutations deviating from the catR consensus reduced binding. Beta-gal and gel shift assays were used to visualize the effects of the mutations against the wild type. DNase I protection identified the precise location of the IBS, and the protection pattern was not altered by the presence of the catR inducer (CCM). Assays of nucleotide fragments containing intact RBS, activation binding site (ABS), and IBS demonstrated a 10-fold increase in catR binding affinity for the IBS, suggesting binding is cooperative.

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
... ... PPS_3181 PPS_3180 PPS_3179 PPS_3182
Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) - Experimental technique details Visual sequence inspection (nan) - repressor not specified