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Applied and Environmental Microbiology, April 2005, p. 1754-1764, Vol. 71, No. 4
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.4.1754-1764.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Web-Type Evolution of Rhodococcus Gene Clusters Associated with Utilization of Naphthalene

Leonid A. Kulakov,* Shenchang Chen, Christopher C. R. Allen, and Michael J. Larkin

The Questor Centre and School of Biology and Biochemistry, Medical Biology Centre, The Queen's University of Belfast, Belfast, United Kingdom

Received 18 August 2004/ Accepted 22 October 2004

Clusters of genes which include determinants for the catalytic subunits of naphthalene dioxygenase (narAa and narAb) were analyzed in naphthalene-degrading Rhodococcus strains. We demonstrated (i) that in the region analyzed homologous gene clusters are separated from each other by nonhomologous DNA, (ii) that there are various degrees of homology between related genes, and (iii) that nar genes are located on plasmids in strains NCIMB12038 and P400 and on a chromosome in P200. These observations suggest that genetic exchange and reshuffling of genetic modules, as well as vertical descent of the genetic information, were the main routes in the evolution of naphthalene degradation in Rhodococcus. These conclusions were supported by studies of transcription patterns in the region analyzed. It was found that the nar region is not organized into a single operon but there are several transcription units which differ in the strains investigated. The narA and narB genes were found to be transcribed as a single unit in all strains analyzed, and their transcription was induced by naphthalene. The putative aldolase gene (narC) was found on the same transcript only in strains P200 and P400. In NCIMB12038 transcription of two more gene clusters was induced by growth on naphthalene. Transcription start sites for narA and narB were found to be different in all of the strains studied. Putative regulatory genes (narR1 and narR2) were transcribed as a single mRNA in naphthalene-induced cells. At the same time, a number of the genes known to be essential for naphthalene catabolism in gram-negative bacteria were not found in the region analyzed.

* Corresponding author. Mailing address: The Questor Centre, David Keir Building, The Queen's University of Belfast, Belfast BT9 5AG, United Kingdom. Phone: 44 (0)28 90 274218. Fax: 44 (0)28 90 661462. E-mail: L.Kulakov{at}qub.ac.uk.

Applied and Environmental Microbiology, April 2005, p. 1754-1764, Vol. 71, No. 4
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.4.1754-1764.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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