title: Complete and integrated pyrene degradation pathway in Mycobacterium vanbaalenii PYR-1 based on systems biology.
abstract: 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 beta-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.
authors.affiliation: Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
authors.forename: Seong-Jae
authors.initials: SJ
authors.lastname: Kim
authors.forename: Ohgew
authors.initials: O
authors.lastname: Kweon
authors.forename: Richard C
authors.initials: RC
authors.lastname: Jones
authors.forename: James P
authors.initials: JP
authors.lastname: Freeman
authors.forename: Ricky D
authors.initials: RD
authors.lastname: Edmondson
authors.forename: Carl E
authors.initials: CE
authors.lastname: Cerniglia
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D008401:Gas Chromatography-Mass Spectrometry; D023061:Gene Order; D005798:Genes, Bacterial / Q000235:genetics; D023281:Genomics / Q000379:methods; D053858:Metabolic Networks and Pathways; D015394:Molecular Structure; D005810:Multigene Family; D009161:Mycobacterium / Q000235:genetics / Q000378:metabolism*; D040901:Proteomics / Q000379:methods; D011721:Pyrenes / Q000737:chemistry / Q000378:metabolism*; D049490:Systems Biology / Q000379:methods*
chemical_list: D001426:Bacterial Proteins; D011721:Pyrenes; C030984:pyrene