Characterization of the unique organization and co-regulation of a gene cluster required for phenol and benzene catabolism in Pseudomonas sp. M1

This work describes a new genetic organization and co-regulation of a cluster of genes involved in the first steps of phenol and benzene catabolic pathways in Pseudomonas sp. M1, different from the established models for Pseudomonas upper pathway. Pseudomonas sp. M1 was isolated by others from the sediments of the Rhine River and exhibits an exceptional biodegradation ability towards a wide range of toxic and/or recalcitrant compounds. Although the taxonomic classification of strain M1 could not be determined, we found in a previous study that Pseudomonas citronellolis is the closest species. The genetic organization characterized in this study, the phc (phenol catabolism) genes, includes eight clustered genes, encoding a catechol 1,2-dioxygenase (phcA), a multicomponent phenol hydroxylase (phcKLMNOP) and the transcriptional regulator PhcR (phcR). PhcR controls the transcription of the referred seven clustered genes from two catabolic promoters: Pa (for phcA) and Pk (for phcKLMNOP). In agreement with in silico prediction, the activity of Pa and Pk promoters was proved to depend on the presence of σ54. Both promoters are phenol and benzene inducible and evidence supporting the unique σ54-dependent co-regulation of the phenol/benzene inducible genes phcA and phcKLMNOP, mediated by PhcR, was obtained.