The phn Genes of Burkholderia sp. Strain RP007 Constitute a Divergent Gene Cluster for Polycyclic Aromatic Hydrocarbon Catabolism

Abstract

Cloning and molecular ecological studies have underestimated the diversity of polycyclic aromatic hydrocarbon (PAH) catabolic genes by emphasizing classical nah-like (nah,ndo, pah, and dox) sequences. Here we report the description of a divergent set of PAH catabolic genes, the phn genes, which although isofunctional to the classical nah-like genes, show very low homology. Thisphn locus, which contains nine open reading frames (ORFs), was isolated on an 11.5-kb HindIII fragment from phenanthrene-degrading Burkholderia sp. strain RP007. The phn genes are significantly different in sequence and 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 been shown to be capable of oxidizing both naphthalene and phenanthrene to predicted metabolites. The locus encodes iron sulfur protein α and β subunits of a PAH initial dioxygenase but lacks the ferredoxin and reductase components. The dihydrodiol dehydrogenase of the RP007 pathway, PhnB, shows greater similarity to analogous dehydrogenases from described biphenyl pathways 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 putative regulatory genes, phnR andphnS. Sequence homology suggests that phnS is a LysR-type transcriptional activator and that phnR, which is divergently transcribed with respect to phnSFECDAcAdB, is a member of the ς54-dependent family of positive transcriptional regulators. Reverse transcriptase PCR experiments suggest that this gene cluster is coordinately expressed and is under regulatory control which may involve PhnR and PhnS.

Occurrence and diversity of naphthalene dioxygenase genes in soil microbial communities from the Maritime Antarctic

“…The closest relatives to these nahAc genotypes are genes encoding proteins described in Pseudomonas species originating from both mesophilic and Antarctic environments ( Table 2). As mentioned before, the ndo primers used in this study were designed to detect a wide range of ndo genes of environmental importance, including the divergent phnAc genes (Laurie and Lloyd-Jones, 1999). In this regard, it was not possible to target the less related ndo alleles, such as narA-like gene present in Rhodococcus strains or the nidA/pdoA1-like genes from Mycobacterium, among others (Habe and Omori, 2003).…”

A novel, inducible, citral lyase purified from spores of Penicillium digitatum

“…Furthermore, trans-2-carboxybenzalpyruvate hydratase/aldolase [32] (Fig. 1B3) and 6-hydroxy-2-keto-5-methyl-3,5-heptadienoic acid hydratase/aldolase [33] (Fig. 1C) have been reported in literature.…”

“…The pH dependence of the conversion was determined by varying the pH form 5.66-10.19 (by adding 0.8 mL of 0.1 M buffer to 0.2 mL of purified enzyme). The exact pH during [29]; (B3) trans-2-carboxybenzalpyruvate hydratase/aldolase [32]; (C) 6-hydroxy-2-keto-5-methyl-3,5-heptadienoic acid hydratase/ aldolase [33].…”

Analysis of catabolic genes for naphthalene and phenanthrene degradation in contaminated New Zealand soils

“…The phn genes were isolated from Burkholderia sp. RP007 and show only 24^73% amino acid sequence homology with the corresponding nah-like sequences [18].…”

“…Two of the primer pairs target genes that encode the iron^sulfur protein (K-subunits) of two divergent initial dioxygenases which are integral components of the ¢rst enzyme of bacterial oxidative attack on PAHs [16,17]. One primer pair speci¢cally targets the nah-like genes [1^6], the other the disparate phn-type phenanthrene-catabolic genes [18]. The phn genes were isolated from Burkholderia sp.…”