The Naphthalene Catabolic (nag) Genes of Polaromonas naphthalenivorans CJ2: Evolutionary Implications for Two Gene Clusters and Novel Regulatory Control

다국어 초록 (Multilingual Abstract)

<B>ABSTRACT</B><P><I>Polaromonas naphthalenivorans</I> CJ2, found to be responsible for the degradation of naphthalene in situ at a coal tar waste-contaminated site (C.-O. Jeon et al., Proc. Natl. Acad. Sci. USA 100:13591-13596, 2003), is able to grow on mineral salts agar media with naphthalene as the sole carbon source. Beginning from a 484-bp <I>nagAc</I>-like region, we used a genome walking strategy to sequence genes encoding the entire naphthalene degradation pathway andadditional flanking regions. We found that the naphthalene catabolic genes in <I>P. naphthalenivorans</I> CJ2 were divided into one large and one small gene cluster, separated by an unknown distance. The large gene cluster (<I>nagRAaGHAbAcAdBFCQEDJI′ORF1tnpA</I>) is bounded by a LysR-type regulator (<I>nagR</I>). The small cluster (<I>nagR2ORF2I'KL</I>) is bounded by a MarR-type regulator (<I>nagR2</I>). The catabolic genes of <I>P. naphthalenivorans</I> CJ2 were homologous to many of those of <I>Ralstonia</I> U2, which uses the gentisate pathway to convert naphthalene to central metabolites. However, three open reading frames (<I>nagY</I>, <I>nagM</I>, and <I>nagN</I>), present in <I>Ralstonia</I> U2, were absent. Also, <I>P. naphthalenivorans</I> carries two copies of gentisate dioxygenase (<I>nagI</I>) with 77.4% DNA sequence identity to one another and 82% amino acid identity to their homologue in <I>Ralstonia</I> sp. strain U2. Investigation of the operons using reverse transcription PCR showed that each cluster was controlled independently by its respective promoter. Insertional inactivation and lacZ reporter assays showed that <I>nagR2</I> is a negative regulator and that expression of the small cluster is not induced by naphthalene, salicylate, or gentisate. Association of two putative <I>Azoarcus</I>-related transposases with the large cluster and one <I>Azoarcus</I>-related putative salicylate 5-hydroxylase gene (<I>ORF2</I>) in the small cluster suggests that mobile genetic elements were likely involved in creating the novel arrangement of catabolic and regulatory genes in <I>P. naphthalenivorans</I>.</P>