Function and Molecular Ecology Significance of Two Catechol-Degrading Gene Clusters in Pseudomonas putida ND6

Many bacteria metabolize aromatic compounds via catechol as a catabolic intermediate, and possess multiple genes or clusters encoding catechol-cleavage enzymes. The presence of multiple isozyme-encoding genes is a widespread phenomenon that seems to give the carrying strains a selective advantage in the natural environment over those with only a single copy. In the naphthalene-degrading strain Pseudomonas putida ND6, catechol can be converted into intermediates of the tricarboxylic acid cycle via either the ortho- or meta-cleavage pathways. In this study, we demonstrated that the catechol ortho-cleavage pathway genes (catB(I)C(I)A(I) and catB(II)C(II)A(II)) on the chromosome play an important role. The cat(I) and cat(II) operons are co-transcribed, whereas catA(I) and catA(II) are under independent transcriptional regulation. We examined the binding of regulatory proteins to promoters. In the presence of cis-cis-muconate, a well-studied inducer of the cat gene cluster, CatR(I) and CatR(II) occupy an additional downstream site, designated as the activation binding site. Notably, CatR(I) binds to both the cat(I) and cat(II) promoters with high affinity, while CatR(II) binds weakly. This is likely caused by a T to G mutation in the G/T-N(11)-A motif. Specifically, we found that CatR(I) and CatR(II) regulate catB(I)C(I)A(I) and catB(II)C(II)A(II) in a cooperative manner, which provides new insights into naphthalene degradation.