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Journal of Bacteriology, January 2007, p. 464-472, Vol. 189, No. 2
0021-9193/07/$08.00+0     doi:10.1128/JB.01310-06

Complete and Integrated Pyrene Degradation Pathway in Mycobacterium vanbaalenii PYR-1 Based on Systems Biology ^,

Seong-Jae Kim,^1, Ohgew Kweon,^1, Richard C. Jones,^2, James P. Freeman,³ Ricky D. Edmondson,² and Carl E. Cerniglia^1*

Division of Microbiology,¹ Division of Systems Toxicology,² Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079³

Received 17 August 2006/ Accepted 23 October 2006

Mycobacterium vanbaalenii PYR-1 was the first bacterium isolated by virtue of its ability to metabolize the high-molecular-weight polycyclic aromatic hydrocarbon (PAH) pyrene. We used metabolic, genomic, and proteomic approaches in this investigation to construct a complete and integrated pyrene degradation pathway for M. vanbaalenii PYR-1. Genome sequence analyses identified genes involved in the pyrene degradation pathway that we have proposed for this bacterium. To identify proteins involved in the degradation, we conducted a proteome analysis of cells exposed to pyrene using one-dimensional gel electrophoresis in combination with liquid chromatography-tandem mass spectrometry. Database searching performed with the M. vanbaalenii PYR-1 genome resulted in identification of 1,028 proteins with a protein false discovery rate of <1%. Based on both genomic and proteomic data, we identified 27 enzymes necessary for constructing a complete pathway for pyrene degradation. Our analyses indicate that this bacterium degrades pyrene to central intermediates through o-phthalate and the ß-ketoadipate pathway. Proteomic analysis also revealed that 18 enzymes in the pathway were upregulated more than twofold, as indicated by peptide counting when the organism was grown with pyrene; three copies of the terminal subunits of ring-hydroxylating oxygenase (NidAB2, MvanDraft_0817/0818, and PhtAaAb), dihydrodiol dehydrogenase (MvanDraft_0815), and ring cleavage dioxygenase (MvanDraft_3242) were detected only in pyrene-grown cells. The results presented here provide a comprehensive picture of pyrene metabolism in M. vanbaalenii PYR-1 and a useful framework for understanding cellular processes involved in PAH degradation.

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* Corresponding author. Mailing address: Division of Microbiology, NCTR/US FDA, 3900 NCTR Road, Jefferson, AR 72079. Phone: (870) 543-7341. Fax: (870) 543-7307. E-mail: Carl.Cerniglia{at}fda.hhs.gov.

Published ahead of print on 3 November 2006.

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

S.-J.K., O.K., and R.C.J. contributed equally to this work.

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Journal of Bacteriology, January 2007, p. 464-472, Vol. 189, No. 2
0021-9193/07/$08.00+0     doi:10.1128/JB.01310-06

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