Catabolic Linear Plasmids

Susanne Fetzner (K) • Stephan Kolkenbrock • Katja Parschat

Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149 Münster, Germany [email protected]

1 Introduction 64

2 Linear Plasmids Involved in the Degradation of Halogenated Alkenes and Alkanes 65

2.1 Degradation of Short-Chain Alkenes and Chloroalkenes via the Coenzyme M Pathway of Epoxide Metabolism is Encoded on Linear Plasmids in Phylogenetically Different Bacteria 65

2.2 Genes Encoding 1,2-Dichloroethane Degradation by Xanthobacter autotrophicus GJ10 Are Segregated Between the Chromosome and pXAUl 73

3 Rhodococcus spp.: Linear Plasmids and Other Genetic Determinants of Their Catabolic Versatility 74

3.1 Alkane Oxidation Genes Located on pRELl of Rhodococcus erythropolis PR4 75

3.2 Linear Plasmids Involved in the Degradation of Biphenyl and Monocyclic Aromatic Compounds by Rhodococcus sp. Strains 76

3.2.1 Catabolic Gene Clusters of Rhodococcus sp. RHA1 Are Distributed on Several Replicons 76

3.2.2 Megaplasmids pDK2 and pRHL2, as well as pDK3 and pRHL1,

Share Almost Identical Catabolic Gene Clusters 79

3.2.3 Multiple Extradiol Dioxygenase Genes Are Distributed on the Genomes of the Biphenyl Degrading Strains Rhodococcus erythropolis TA421

and Rhodococcus globerulus P6 81

3.2.4 Alkylbenzene Degradation and Co-oxidation of Trichloroethene by Rhodococcus erythropolis BD2 is Encoded on pBD2 81

3.2.5 Plasmid p1CP of Rhodococcus opacus 1CP Codes for Two Distinct Chlorocatechol Pathways 82

3.3 Linear Plasmids Involved in the Degradation of Polycyclic Aromatic Compounds by Rhodococcus sp. Strains 84

3.3.1 Modular Organization and Different Genomic Localization of Naphthalene Degradation Genes in Strains I24, P200, P400, NCIMB12038, CIR2, TKN14, R7, and SAO101 84

4 Terrabacter sp 87

4.1 Dibenzofuran and Fluorene Oxidation via Angular Dioxygenation as well as the Protocatechuate Pathway are Encoded on pDBF1

of Terrabacter sp. DBF63 87

5 Arthrobacter sp 90

5.1 Linear Plasmid pAL1 of Arthrobacter nitroguajacolicus Ru61a Codes for Degradation of 2-Methylquinoline 90

6 Concluding Remarks 92

References 92

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 pDBFl 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 pXAUl. 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.

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