Further Insights into the Architecture of the Promoter That Controls the Expression of the Genes in

The anaerobic degradation of benzoate in bacteria involves the benzoyl-CoA central pathway. strains are a major group of anaerobic benzoate degraders, and the transcriptional regulation of the genes was extensively studied in sp. CIB. In this work, we show that the regulatory gene and the promoter can also be identified upstream of the catabolic operon in all benzoate-degrader strains whose genome sequences are currently available. All the promoters from strains described here show a conserved architecture including three operator regions (ORs), i.e., OR1 to OR3, for binding to the BzdR transcriptional repressor. Here, we demonstrate that, whereas OR1 is sufficient for the BzdR-mediated repression of the promoter, the presence of OR2 and OR3 is required for de-repression promoted by the benzoyl-CoA inducer molecule. Our results reveal that BzdR binds to the promoter in the form of four dimers, two of them binding to OR1. The BzdR/ complex formed induces a DNA loop that wraps around the BzdR dimers and generates a superstructure that was observed by atomic force microscopy. This work provides further insights into the existence of a conserved BzdR-dependent mechanism to control the expression of the genes in strains.