The phn genes of Burkholderia sp. strain RP007 constitute a divergent genecluster for polycyclic aromatic hydrocarbon catabolism

Cloning and molecular ecological studies have underestimated the diversity of polycyclic aromatic hydrocarbon (PAH) catabolic genes by emphasizing cla ssical nah-like (nah, ndo, pah, and dox) sequences. Here we report the desc ription of a divergent set of PAH catabolic genes, the phn genes, which alt hough isofunctional to the classical nah-like genes, show very low homology , This phn locus, which contains nine open reading frames (ORFs), was isola ted on an 11.5-kb HindIII fragment from phenanthrene-degrading Burkholderia sp. strain RP007, The phn genes are significantly different in sequence an d gene order from previously characterized genes for PAH degradation. They are transcribed by RP007 when grown at the expense of either naphthalene or phenanthrene, while in Escherichia coli the recombinant phn enzymes have b een shown to be capable of oxidizing both naphthalene and phenanthrene to p redicted metabolites. The locus encodes iron sulfur protein a and beta subu nits of a PAH initial dioxygenase but lacks the ferredoxin and reductase co mponents. The dihydrodiol dehydrogenase of the RP007 pathway, PhnB, shows g reater similarity to analogous dehydrogenases from described biphenyl pathw ays than to those characterized from naphthalene/phenanthrene pathways. An unusual extradiol dioxygenase, PhnC, shows no similarity to other extradiol dioxygenases for naphthalene or biphenyl oxidation but is the first member of the recently proposed class III extradiol dioxygenases that is specific for polycyclic arene diols, Upstream of the phn catabolic genes are two pu tative regulatory genes, phnR and phnS, Sequence homology suggests that phn S is a LysR-type transcriptional activator and that phnR, which is divergen tly transcribed with respect to phnSFECDAcAdB, is a member of the sigma(54) -dependent family of positive transcriptional regulators. Reverse transcrip tase PCR experiments suggest that this gene cluster is coordinately express ed and is under regulatory control which may involve PhnR and PhnS.