The plasmid-borne pheBA operon of Pseudomonas putida strain PaW85 allows growth of the host cells on
phenol. The promoter of this operon is activated by the chromosomally encoded LysR-type regulator CatR, in the presence of the inducer
cis,cis-muconate.
cis,cis-muconate is an intermediate of
catechol degradation by the chromosomally encoded ortho or
beta-ketoadipate pathway. The catBC operon encodes two
enzymes of the
beta-ketoadipate pathway and also requires CatR and
cis,cis-muconate for its expression. The promoters of the pheBA and catBC operons are highly homologous, and since both respond to CatR, it is likely that the pheBA promoter was recruited from the ancestral catBC promoter. Gel shift assays and
DNase I footprinting have shown that the pheBA promoter has a higher binding affinity for CatR than the catBC promoter. Like the catBC promoter, the pheBA promoter forms two complexes (C1 and C2) with CatR in the absence of
cis,cis-muconate, but only forms a single complex (C2) in the presence of
cis,cis-muconate. Like the catBC promoter CatR repression binding site (RBS) and activation binding site (ABS) arrangement, the pheBA promoter demonstrates the presence of a 26 bp segment highly homologous to the RBS that is protected by CatR from
DNase I digestion in the absence of the inducer. An additional 16 bp sequence, similar to the catBC promoter ABS, is protected only when the inducer
cis-cis-muconate is present. The binding of CatR in absence of
cis,cis-muconate bends the catBC and pheBA promoter regions to significantly different degrees, but CatR binding in the presence of
cis,cis-muconate results in a similar degree of
DNA bending. The evolutionary implications of the interactions of CatR with these two promoters are discussed.