Multiplicity of genes for aromatic ring-hydroxylating dioxygenases in Mycobacterium isolate KMS and their regulation

Abstract

Mycobacterium sp. strain KMS has bioremediation potential for polycyclic aromatic hydrocarbons (PAHs), such as pyrene, and smaller ring aromatics, such as benzoate. Degradation of these aromatics involves oxidation catalyzed by aromatic ring-hydroxylating dioxygenases. Multiple genes encoding dioxygenases exist in KMS: ten genes encode large-subunits with homology to phenylpropionate dioxygenase genes, sixteen pairs of adjacent genes encode alpha- and beta-subunits of dioxygenase and two genes encode beta-subunits. These genes include orthologs of nid genes essential for degradation of multi-ring PAHs in M. vanbaalenii isolate PYR-1. The multiplicity of genes in part is explained by block duplication that results in two or three copies of certain genes on the chromosome, a linear plasmid, and a circular plasmid within the KMS genome. Quantitative real-time PCR showed that four dioxygenase beta-subunit nid genes from operons with almost identical promoter sequences otherwise unique in the genome were induced by pyrene to similar extents. No induction occurred with benzoate. Unlike isolate PYR-1, isolate KMS has an operon specifying benzoate catabolism and the expression of the alpha-subunit dioxygenase gene was activated by benzoate but not pyrene. These studies showed that isolate KMS had a genome well adapted to utilization of different aromatic compounds.