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Journal of Bacteriology, March 1999, p. 1585-1602, Vol. 181, No. 5
0021-9193/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.

Complete Sequence of a 184-Kilobase Catabolic Plasmid from Sphingomonas aromaticivorans F199

Margaret F. Romine,^1,* Lisa C. Stillwell,¹ Kwong-Kwok Wong,¹ Sarah J. Thurston,¹ Ellen C. Sisk,^1, Christoph Sensen,² Terry Gaasterland,^3,4,§ Jim K. Fredrickson,¹ and Jeffrey D. Saffer¹

Pacific Northwest National Laboratory, Richland, Washington 99352¹; National Research Council of Canada, Institute for Marine Biosciences, Halifax, Nova Scotia B3H 3Z1, Canada²; Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois 60439³; and Department of Computer Science, University of Chicago, Chicago, Illinois 60637⁴

Received 10 July 1998/Accepted 16 November 1998

The complete 184,457-bp sequence of the aromatic catabolic plasmid, pNL1, from Sphingomonas aromaticivorans F199 has been determined. A total of 186 open reading frames (ORFs) are predicted to encode proteins, of which 79 are likely directly associated with catabolism or transport of aromatic compounds. Genes that encode enzymes associated with the degradation of biphenyl, naphthalene, m-xylene, and p-cresol are predicted to be distributed among 15 gene clusters. The unusual coclustering of genes associated with different pathways appears to have evolved in response to similarities in biochemical mechanisms required for the degradation of intermediates in different pathways. A putative efflux pump and several hypothetical membrane-associated proteins were identified and predicted to be involved in the transport of aromatic compounds and/or intermediates in catabolism across the cell wall. Several genes associated with integration and recombination, including two group II intron-associated maturases, were identified in the replication region, suggesting that pNL1 is able to undergo integration and excision events with the chromosome and/or other portions of the plasmid. Conjugative transfer of pNL1 to another Sphingomonas sp. was demonstrated, and genes associated with this function were found in two large clusters. Approximately one-third of the ORFs (59 of them) have no obvious homology to known genes.

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^* Corresponding author. Mailing address: Pacific Northwest National Laboratory, Environmental Microbiology Group, 902 Battelle Blvd., MS P7-50, Richland, WA 99352. Phone: (509) 376-8287. Fax: (509) 376-1321. E-mail: Margie.Romine{at}pnl.gov.

NRCC publication 42280.

Present address: Seattle Biomedical Research Institute, Seattle, WA 98109-1651.

^§ Present address: The Rockefeller University, New York, NY 10021-6399.

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Journal of Bacteriology, March 1999, p. 1585-1602, Vol. 181, No. 5
0021-9193/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.

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