Catabolic Linear Plasmids

Abstract

Catabolic gene clusters localized on invertron-type linear plasmids significantly contribute to the ability of actinobacteria to degrade a wide range of organic compounds. Especially in Rhodococcus spp., several large linear plasmids have been identified which are involved in alkane oxidation, or in the degradation of aromatic compounds like fluorene, dibenzofuran, naphthalene, biphenyl, or alkylbenzenes and other monocyclic aromatic compounds. Rhodococci often contain multiple copies of key catabolic genes, which is thought to be an important factor for their catabolic efficiency and versatility. Other actinobacteria with catabolic linear plasmids include Terrabacter sp. DBF63 containing the pDBF1 plasmid that codes for the degradation of fluorene, and Arthrobacter nitroguajacolicus Ru61a harboring pAL1 encoding 2-methylquinoline conversion. Remarkably, linear replicons carrying genes for the degradation of short-chain alkenes and chloroalkenes via the coenzyme M pathway were identified not only in Gram-positive bacteria, such as Mycobacterium sp. strains, Gordonia rubripertincta B-276, and Nocardioides sp. JS614, but also in the Gram-negative strains Xanthobacter sp. Py2, Pseudomonas putida AJ, and Ochrobactrum sp. TD. In Xanthobacter autotrophicus GJ10, genes encoding 1,2-dichloroethane degradation are segregated between the chromosome and the linear plasmid pXAU1. The presence of highly homologous gene clusters on catabolic plasmids of phylogenetically different bacteria and the genetic organization of some linear plasmids sequenced as yet suggest that horizontal transfer of mobile genetic elements and genomic rearrangements significantly contribute to the evolution of catabolic diversity.