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ThecatBCA operon ofPseudomonas putida encodes enzymes involved in the catabolism of benzoate. Transcription of this operon requires the LysR-type transcriptional regulator CatR and an inducer molecule,cis ,cis -muconate. Previous gel shift assays and DNase I footprinting have demonstrated that CatR occupies two adjacent sites proximal to thecatBCA promoter in the presence of the inducer. We report the presence of an additional binding site for CatR downstream of thecatBCA promoter within thecatB structural gene. This site, called the internal binding site (IBS), extends from +162 to +193 with respect to thecatB transcriptional start site and lies within thecatB open reading frame. Gel shift analysis and DNase I footprinting determined that CatR binds to this site with low affinity. CatR binds cooperatively with higher affinity to the IBS in the presence of the two upstream binding sites. Parallel in vivo and in vitro studies were conducted to determine the role of the internal binding site. We measured β-galactosidase activity ofcatB-lacZ transcriptional fusions in vivo. Our results suggest a probablecis -acting repressor function for the internal binding site. Site-directed mutagenesis of the IBS verified this finding. The location of the IBS within thecatB structural gene, the cooperativity observed in footprinting studies, and phasing studies suggest that the IBS likely participates in the interaction of CatR with the upstream binding sites by looping out the intervening DNA.

Transcriptional Repression Mediated by LysR-Type Regulator CatR Bound at Multiple Binding Sites