Transcriptional activation of the catechol and chlorocatechol operons: variations on a theme

The ortho-cleavage pathways of catechol and 3-chlorocatechol are central catabolic pathways of Pseudomonas putida that convert aromatic and chloroaromatic compounds to tricarboxylic acid (TCA)-cycle intermediates. They are encoded by the evolutionarily related catBCA and clcABD operons, respectively. Expression of the cat and clc operons requires the LysR-type transcriptional activators CatR and ClcR, and the inducer molecules cis,cis-muconate and 2-chloro-cis,cis-muconate. In addition to sequence similarities, CatR and ClcR share functional similarities which allow catR to complement clcR mutants. DNase-I footprinting, DNA bending and in vitro transcription analyses with RNA polymerase mutants indicate that CatR and ClcR activate transcription via a similar mechanism which involves interaction with the C-terminal domain of the alpha-subunit (alpha-CTD) of RNA polymerase. In vitro transcription assays with different regions of the clc promoter indicate that the ClcR dimer bound to the promoter proximal site (the activation binding site) interacts with the alpha-CTD. Gel shift assays and DNase-I footprinting have demonstrated that CatR occupies two adjacent sites proximal to the catBCA promoter in the presence of inducer and an additional binding site within the catB structural gene called the internal binding site (IBS). CatR binds the IBS with low intrinsic affinity that is increased by cooperativity in presence of the two promoter binding sites. Site-directed mutations in the IBS indicate a probable cis-acting repressor function for the IBS. The location of the IBS within the catB structural gene, the cooperativity observed in footprinting studies and phasing studies suggest that the IBS participates in the interaction of CatR with the upstream binding sites by looping out the intervening DNA. Although the core transcriptional activation mechanisms of CatR and ClcR have been conserved, nature has provided some flexibility to respond to different environmental signals in addition to the presence of inducer. Transcriptional fusion studies demonstrate that the expression from the clc promoter is repressed when the cells are grown on succinate, citrate or fumarate and that this repression is ClcR-dependent and occurs at the transcriptional level. The presence of these organic acids did not affect the expression from the cat promoter. In vitro transcription assays demonstrate that the TCA-cycle intermediate, fumarate, directly and specifically inhibits the formation of the clcA transcript. No such inhibition was observed when CatR was used as activator on either the cat or clc template. Since both the catechol and the chlorocatechol pathways feed into the TCA cycle, but only the chlorocatechol pathway is inhibited by fumarate, there is a subtle difference in the regulation of these two pathways where intracellular sensing of a TCA-cycle intermediate leads to a reduction of chloroaromatic degradation.