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Journal of Bacteriology, November 2004, p. 7783-7795, Vol. 186, No. 22
0021-9193/04/$08.00+0     DOI: 10.1128/JB.186.22.7783-7795.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Functional Characterization of a Catabolic Plasmid from Polychlorinated- Biphenyl-Degrading Rhodococcus sp. Strain RHA1{dagger} ,{ddagger}

René Warren,1 William W. L. Hsiao,2 Hisashi Kudo,3 Matt Myhre,4 Manisha Dosanjh,4 Anca Petrescu,1 Hiroyuki Kobayashi,3 Satoru Shimizu,3 Keisuke Miyauchi,3 Eiji Masai,3 George Yang,1 Jeff M. Stott,1 Jacquie E. Schein,1 Heesun Shin,1 Jaswinder Khattra,1 Duane Smailus,1 Yaron S. Butterfield,1 Asim Siddiqui,1 Robert Holt,1 Marco A. Marra,1 Steven J. M. Jones,1 William W. Mohn,4 Fiona S. L. Brinkman,2 Masao Fukuda,3 Julian Davies,4 and Lindsay D. Eltis4*

Genome Sciences Centre,1 Department of Microbiology and Immunology, University of British Columbia, Vancouver,4 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada,2 Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan3

Received 31 December 2003/ Accepted 5 June 2004

Rhodococcus sp. strain RHA1, a potent polychlorinated-biphenyl (PCB)-degrading strain, contains three linear plasmids ranging in size from 330 to 1,100 kb. As part of a genome sequencing project, we report here the complete sequence and characterization of the smallest and least-well-characterized of the RHA1 plasmids, pRHL3. The plasmid is an actinomycete invertron, containing large terminal inverted repeats with a tightly associated protein and a predicted open reading frame (ORF) that is similar to that of a mycobacterial rep gene. The pRHL3 plasmid has 300 putative genes, almost 21% of which are predicted to have a catabolic function. Most of these are organized into three clusters. One of the catabolic clusters was predicted to include limonene degradation genes. Consistent with this prediction, RHA1 grew on limonene, carveol, or carvone as the sole carbon source. The plasmid carries three cytochrome P450-encoding (CYP) genes, a finding consistent with the high number of CYP genes found in other actinomycetes. Two of the CYP genes appear to belong to novel families; the third belongs to CYP family 116 but appears to belong to a novel class based on the predicted domain structure of its reductase. Analyses indicate that pRHL3 also contains four putative "genomic islands" (likely to have been acquired by horizontal transfer), insertion sequence elements, 19 transposase genes, and a duplication that spans two ORFs. One of the genomic islands appears to encode resistance to heavy metals. The plasmid does not appear to contain any housekeeping genes. However, each of the three catabolic clusters contains related genes that appear to be involved in glucose metabolism.

* Corresponding author. Mailing address: Department of Microbiology and Immunology, University of British Columbia, #300-6174 University Blvd., Vancouver, BC V6T 1Z3, Canada. Phone: (604) 822-0042. Fax: (604) 822-6041. E-mail: leltis{at}interchange.ubc.ca.

{dagger} Supplemental material for this article may be found at http://jb.asm.org/.

{ddagger} Presented in part at the 11th International Conference on Microbial Genomes, Durham, N.C., 28 September to 2 October 2003.

Journal of Bacteriology, November 2004, p. 7783-7795, Vol. 186, No. 22
0021-9193/04/$08.00+0     DOI: 10.1128/JB.186.22.7783-7795.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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