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Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1

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Abstract

Mycobacterium vanbaalenii PYR-1 is well known for its ability to degrade a wide range of high-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs). The genome of this bacterium has recently been sequenced, allowing us to gain insights into the molecular basis for the degradation of PAHs. The 6.5 Mb genome of PYR-1 contains 194 chromosomally encoded genes likely associated with degradation of aromatic compounds. The most distinctive feature of the genome is the presence of a 150 kb major catabolic region at positions 494 ~ 643 kb (region A), with an additional 31 kb region at positions 4,711 ~ 4,741 kb (region B), which is predicted to encode most enzymes for the degradation of PAHs. Region A has an atypical mosaic structure made of several gene clusters in which the genes for PAH degradation are complexly arranged and scattered around the clusters. Significant differences in the gene structure and organization as compared to other well-known aromatic hydrocarbon degraders including Pseudomonas and Burkholderia were revealed. Many identified genes were enriched with multiple paralogs showing a remarkable range of diversity, which could contribute to the wide variety of PAHs degraded by M. vanbaalenii PYR-1. The PYR-1 genome also revealed the presence of 28 genes involved in the TCA cycle. Based on the results, we proposed a pathway in which HMW PAHs are degraded into the β-ketoadipate pathway through protocatechuate and then mineralized to CO2 via TCA cycle. We also identified 67 and 23 genes involved in PAH degradation and TCA cycle pathways, respectively, to be expressed as proteins.

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Abbreviations

CYPs:

Cytochrome P450 monooxygenases

HMW:

High-molecular-weight

JGI:

Joint Genome Institute

KEGG:

Kyoto Encyclopedia of Genes and Genomes

ORFs:

Open reading frames

PAHs:

Polycyclic aromatic hydrocarbons

RHOs:

Ring-hydroxylating oxygenases

References

  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

  • Barbe V, Vallenet D, Fonknechten N, Kreimeyer A, Oztas S, Labarre L, Cruveiller S, Robert C, Duprat S, Wincker P, Ornston LN, Weissenbach J, Marliere P, Cohen GN, Medigue C (2004) Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium. Nucleic Acids Res 32:5766–5779

    Article  PubMed  CAS  Google Scholar 

  • Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O’Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141–147

    Article  PubMed  Google Scholar 

  • Boldrin B, Tiehm A, Fritzsche C (1993) Degradation of phenanthrene, fluorene, fluoranthene, and pyrene by a Mycobacterium sp. Appl Environ Microbiol 59:1927–1930

    PubMed  CAS  Google Scholar 

  • Bolton JL, Trush MA, Penning TM, Dryhurst G, Monks TJ (2000) Role of quinones in toxicology. Chem Res Toxicol 13:135–160

    Article  PubMed  CAS  Google Scholar 

  • Brezna B, Khan AA, Cerniglia CE (2003) Molecular characterization of dioxygenases from polycyclic aromatic hydrocarbon-degrading Mycobacterium spp. FEMS Microbiol Lett 223:177–183

    Article  PubMed  CAS  Google Scholar 

  • Brezna B, Kweon O, Stingley RL, Freeman JP, Khan AA, Polek B, Jones RC, Cerniglia CE (2006) Molecular characterization of cytochrome P450 genes in the polycyclic aromatic hydrocarbon degrading Mycobacterium vanbaalenii PYR-1. Appl Microbiol Biotechnol 71:522–532

    Article  PubMed  CAS  Google Scholar 

  • Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J (2005) ACT: the Artemis Comparison Tool. Bioinformatics 21:3422–3423

    Article  PubMed  CAS  Google Scholar 

  • Chain PS, Denef VJ, Konstantinidis KT, Vergez LM, Agullo L, Reyes VL, Hauser L, Cordova M, Gomez L, Gonzalez M, Land M, Lao V, Larimer F, LiPuma JJ, Mahenthiralingam E, Malfatti SA, Marx CJ, Parnell JJ, Ramette A, Richardson P, Seeger M, Smith D, Spilker T, Sul WJ, Tsoi TV, Ulrich LE, Zhulin IB, Tiedje JM (2006) Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc Natl Acad Sci USA 103:15280–15287

    Article  PubMed  Google Scholar 

  • Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE 3rd, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jagels K, Krogh A, McLean J, Moule S, Murphy L, Oliver K, Osborne J, Quail MA, Rajandream MA, Rogers J, Rutter S, Seeger K, Skelton J, Squares R, Squares S, Sulston JE, Taylor K, Whitehead S, Barrell BG (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537–544

    Article  PubMed  CAS  Google Scholar 

  • Dos Santos VA, Heim S, Moore ER, Stratz M, Timmis KN (2004) Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. Environ Microbiol 6:1264–1286

    Article  PubMed  CAS  Google Scholar 

  • Eulberg D, Lakner S, Golovleva LA, Schlömann M (1998) Characterization of a protocatechuate catabolic gene cluster from Rhodococcus opacus 1CP: evidence for a merged enzyme with 4-carboxymuconolactone-decarboxylating and 3-oxoadipate enol-lactone-hydrolyzing activity. J Bacteriol 180:1072–1081

    PubMed  CAS  Google Scholar 

  • Fiorenza S, Ward CH (1997) Microbial adaptation to hydrogen peroxide and biodegradation of aromatic hydrocarbons. J Ind Microbiol Biotechnol 18:140–151

    Article  PubMed  CAS  Google Scholar 

  • Gescher J, Ismail W, Olgeschlager E, Eisenreich W, Worth J, Fuchs G (2006) Aerobic benzoyl-coenzyme A (CoA) catabolic pathway in Azoarcus evansii: conversion of ring cleavage product by 3, 4-dehydroadipyl-CoA semialdehyde dehydrogenase. J Bacteriol 188:2919–2927

    Article  PubMed  CAS  Google Scholar 

  • Gibson DT, Parales RE (2000) Aromatic hydrocarbon dioxygenases in environmental biotechnology. Curr Opin Biotechnol 11:236–243

    Article  PubMed  CAS  Google Scholar 

  • Gilmartin N, Ryan D, Sherlock O, Dowling D (2003) BphK shows dechlorination activity against 4-chlorobenzoate, an end product of bph-promoted degradation of PCBs. FEMS Microbiol Lett 222:251–255

    Article  PubMed  CAS  Google Scholar 

  • Gonçalves ER, Hara H, Miyazawa D, Davies JE, Eltis LD, Mohn WW (2006) Transcriptomic assessment of isozymes in the biphenyl pathway of Rhodococcus sp. strain RHA1. Appl Environ Microbiol 72:6183–6193

    Article  PubMed  CAS  Google Scholar 

  • Grosser RJ, Warshawsky D, Vestal JR (1991) Indigenous and enhanced mineralization of pyrene, benzo[a]pyrene, and carbazole in soils. Appl Environ Microbiol 57:3462–3469

    PubMed  CAS  Google Scholar 

  • Guengerich FP, Wu ZL, Bartleson CJ (2005) Function of human cytochrome P450 s: characterization of the orphans. Biochem Biophys Res Commun 338:465–469

    Article  PubMed  CAS  Google Scholar 

  • Habe H, Chung JS, Ishida A, Kasuga K, Ide K, Takemura T, Nojiri H, Yamane H, Omori T (2005) The fluorene catabolic linear plasmid in Terrabacter sp. strain DBF63 carries the ß-ketoadipate pathway genes, pcaRHGBDCFIJ, also found in proteobacteria. Microbiology 151:3713–3722

    Article  PubMed  CAS  Google Scholar 

  • Habe H, Omori T (2003) Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria. Biosci Biotechnol Biochem 67:225–243

    Article  PubMed  CAS  Google Scholar 

  • Haggblom MM, Nohynek LJ, Salkinoja-Salonen MS (1988) Degradation and O-methylation of chlorinated phenolic compounds by Rhodococcus and Mycobacterium strains. Appl Environ Microbiol 54:3043–3052

    PubMed  CAS  Google Scholar 

  • Hall K, Miller CD, Sorensen DL, Anderson AJ, Sims RC (2005) Development of a catabolically significant genetic probe for polycyclic aromatic hydrocarbon-degrading mycobacteria in soil. Biodegradation 16:475–484

    Article  PubMed  CAS  Google Scholar 

  • Hamann C, Hegemann J, Hildebrandt A (1999) Detection of polycyclic aromatic hydrocarbon degradation genes in different soil bacteria by polymerase chain reaction and DNA hybridization. FEMS Microbiol Lett 173:255–263

    Article  PubMed  CAS  Google Scholar 

  • Harayama S, Rekik M, Wasserfallen A, Bairoch A (1987) Evolutionary relationships between catabolic pathways for aromatics: conservation of gene order and nucleotide sequences of catechol oxidation genes of pWW0 and NAH7 plasmids. Mol Gen Genet 210:241–247

    Article  PubMed  CAS  Google Scholar 

  • Harwood CS, Parales RE (1996) The ß-ketoadipate pathway and the biology of self-identity. Annu Rev Microbiol 50:553–590

    Article  PubMed  CAS  Google Scholar 

  • Hearn EM, Dennis JJ, Gray MR, Foght JM (2003) Identification and characterization of the emhABC efflux system for polycyclic aromatic hydrocarbons in Pseudomonas fluorescens cLP6a. J Bacteriol 185:6233–6240

    Article  PubMed  CAS  Google Scholar 

  • Heitkamp MA, Cerniglia CE (1988) Mineralization of polycyclic aromatic hydrocarbons by a bacterium isolated from sediment below an oil field. Appl Environ Microbiol 54:1612–1614

    PubMed  CAS  Google Scholar 

  • Heitkamp MA, Cerniglia CE (1989) Polycyclic aromatic hydrocarbon degradation by a Mycobacterium sp. in microcosms containing sediment and water from a pristine ecosystem. Appl Environ Microbiol 55:1968–1973

    PubMed  CAS  Google Scholar 

  • Heitkamp MA, Freeman JP, Miller DW, Cerniglia CE (1988) Pyrene degradation by a Mycobacterium sp.; identification of ring oxidation and ring fission products. Appl Environ Microbiol 54:2556–2565

    PubMed  CAS  Google Scholar 

  • IARC (1983) Monograph on the evaluation of carcinogenic risk of chemicals to man: polynuclear aromatic compounds. Part 1: chemical, environmental and experimental data, vol. 32, World Health Organization. Lyon, France

  • Jimenez JI, Minambres B, Garcia JL, Diaz E (2002) Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ Microbiol 4:824–841

    Article  PubMed  CAS  Google Scholar 

  • Jouanneau Y, Meyer C, Jakoncic J, Stojanoff V, Gaillard J (2006) Characterization of a naphthalene dioxygenase endowed with an exceptionally broad substrate specificity toward polycyclic aromatic hydrocarbons. Biochemistry 45:12380–12391

    Article  PubMed  CAS  Google Scholar 

  • Kanaly RA, Harayama S (2000) Biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons by bacteria. J Bacteriol 182:2059–2067

    Article  PubMed  CAS  Google Scholar 

  • Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34:D354–D357

    Article  PubMed  CAS  Google Scholar 

  • Karlson U, Dwyer DF, Hooper SW, Moore ER, Timmis KN, Eltis LD (1993) Two independently regulated cytochromes P-450 in a Rhodococcus rhodochrous strain that degrades 2-ethoxyphenol and 4-methoxybenzoate. J Bacteriol 175:1467–1474

    PubMed  CAS  Google Scholar 

  • Kelley I, Cerniglia CE (1995) Degradation of a mixture of high-molecular-weight polycyclic aromatic hydrocarbons by a Mycobacterium strain, PYR-1. J Soil Contam 4:77–91

    CAS  Google Scholar 

  • Kelley I, Freeman JP, Cerniglia CE (1990) Identification of metabolites from degradation of naphthalene by a Mycobacterium sp. Biodegradation 1:283–290

    Article  PubMed  CAS  Google Scholar 

  • Kelley I, Freeman JP, Evans FE, Cerniglia CE (1991) Identification of a carboxylic acid metabolite from the catabolism of fluoranthene by a Mycobacterium sp. Appl Environ Microbiol 57:636–641

    PubMed  CAS  Google Scholar 

  • Kelley I, Freeman JP, Evans FE, Cerniglia CE (1993) Identification of metabolites from the degradation of fluoranthene by Mycobacterium sp. strain PYR-1. Appl Environ Microbiol 59:800–806

    PubMed  CAS  Google Scholar 

  • Khan AA, Wang RF, Cao WW, Doerge DR, Wennerstrom D, Cerniglia CE (2001) Molecular cloning, nucleotide sequence, and expression of genes encoding a polycyclic aromatic ring dioxygenase from Mycobacterium sp. strain PYR-1. Appl Environ Microbiol 67:3577–3585

    Article  PubMed  CAS  Google Scholar 

  • Khan AA, Kim SJ, Paine DD, Cerniglia CE (2002) Classification of a polycyclic aromatic hydrocarbon-metabolizing bacterium, Mycobacterium sp. strain PYR-1, as Mycobacterium vanbaalenii sp. nov. Int J Syst Evol Microbiol 52:1997–2002

    Article  PubMed  CAS  Google Scholar 

  • Kim YH, Engesser KH, Cerniglia CE (2003) Two polycyclic aromatic hydrocarbon o-quinone reductases from a pyrene-degrading Mycobacterium. Arch Biochem Biophys 416:209–217

    Article  PubMed  CAS  Google Scholar 

  • Kim SJ, Jones RC, Cha CJ, Kweon O, Edmondson RD, Cerniglia CE (2004a) Identification of proteins induced by polycyclic aromatic hydrocarbon in Mycobacterium vanbaalenii PYR-1 using two-dimensional polyacrylamide gel electrophoresis and de novo sequencing methods. Proteomics 4:3899–3908

    Article  PubMed  CAS  Google Scholar 

  • Kim YH, Moody JD, Freeman JP, Engesser KH, Cerniglia CE (2004b) Evidence for the existence of PAH-quinone reductase and catechol-O-methyltransferase in Mycobacterium vanbaalenii PYR-1. J Ind Microbiol Biotechnol 31:507–516

    Article  PubMed  CAS  Google Scholar 

  • Kim YH, Engesser KH, Cerniglia CE (2005a) Numerical and genetic analysis of polycyclic aromatic hydrocarbon-degrading mycobacteria. Microbial Ecol 50:110–119

    Article  CAS  Google Scholar 

  • Kim YH, Freeman JP, Moody JD, Engesser KH, Cerniglia CE (2005b) Effects of pH on the degradation of phenanthrene and pyrene by Mycobacterium vanbaalenii PYR-1. Appl Microbiol Biotechnol 67:275–285

    Article  PubMed  CAS  Google Scholar 

  • Kim SJ, Kweon O, Freeman JP, Jones RC, Adjei MD, Jhoo JW, Edmondson RD, Cerniglia CE (2006) Molecular cloning and expression of genes encoding a novel dioxygenase involved in low- and high-molecular-weight polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. Appl Environ Microbiol 72:1045–1054

    Article  PubMed  CAS  Google Scholar 

  • Kim SJ, Kweon O, Jones RC, Freeman JP, Edmondson RD, Cerniglia CE (2007) Complete and integrated pyrene degradation pathway in Mycobacterium vanbaalenii PYR-1 based on systems biology. J Bacteriol 189:464–472

    Article  PubMed  CAS  Google Scholar 

  • Kurbatov L, Albrecht D, Herrmann H, Petruschka L (2006) Analysis of the proteome of Pseudomonas putida KT2440 grown on different sources of carbon and energy. Environ Microbiol 8:466–478

    Article  PubMed  CAS  Google Scholar 

  • Kweon O, Kim SJ, Jones RC, Freeman JP, Adjei MD, Edmondson RD, Cerniglia CE (2007) A polyomic approach to elucidate the fluoranthene degradative pathway in Mycobacterium vanbaalenii PYR-1. J Bacteriol 189:4635–4647

    Article  PubMed  CAS  Google Scholar 

  • Lamb DC, Ikeda H, Nelson DR, Ishikawa J, Skaug T, Jackson C, Omura S, Waterman MR, Kelly SL (2003) Cytochrome P450 complement (CYPome) of the avermectin-producer Streptomyces avermitilis and comparison to that of Streptomyces coelicolor A3(2). Biochem Biophys Res Commun 307:610–619

    Article  PubMed  CAS  Google Scholar 

  • Larkin MJ, Allen CC, Kulakov LA, Lipscomb DA (1999) Purification and characterization of a novel naphthalene dioxygenase from Rhodococcus sp. strain NCIMB12038. J Bacteriol 181:6200–6204

    PubMed  CAS  Google Scholar 

  • Lloyd-Jones G, Lau PC (1997) Glutathione S-transferase-encoding gene as a potential probe for environmental bacterial isolates capable of degrading polycyclic aromatic hydrocarbons. Appl Environ Microbiol 63:3286–3290

    PubMed  CAS  Google Scholar 

  • López Z, Vila J, Grifoll M (2005) Metabolism of fluoranthene by mycobacterial strains isolated by their ability to grow in fluoranthene or pyrene. J Ind Microbiol Biotechnol 32:455–464

    Article  PubMed  CAS  Google Scholar 

  • MacLeod CT, Daugulis AJ (2003) Biodegradation of polycyclic aromatic hydrocarbons in a two-phase partitioning bioreactor in the presence of a bioavailable solvent. Appl Microbiol Biotechnol 62:291–296

    Article  PubMed  CAS  Google Scholar 

  • Mason JR, Cammack R (1992) The electron-transport proteins of hydroxylating bacterial dioxygenases. Annu Rev Microbiol 46:277–305

    Article  PubMed  CAS  Google Scholar 

  • McLellan SL, Warshawsky D, Shann JR (2002) The effect of polycyclic aromatic hydrocarbons on the degradation of benzo[a]pyrene by Mycobacterium sp. strain RJGII-135. Environ Toxicol Chem 21:253–259

    Article  PubMed  CAS  Google Scholar 

  • McLeod MP, Warren RL, Hsiao WW, Araki N, Myhre M, Fernandes C, Miyazawa D, Wong W, Lillquist AL, Wang D, Dosanjh M, Hara H, Petrescu A, Morin RD, Yang G, Stott JM, Schein JE, Shin H, Smailus D, Siddiqui AS, Marra MA, Jones SJ, Holt R, Brinkman FS, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis LD (2006) The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci USA 103:15582–15587

    Article  PubMed  Google Scholar 

  • Moody JD, Freeman JP, Doerge DR, Cerniglia CE (2001) Degradation of phenanthrene and anthracene by cell suspensions of Mycobacterium sp. strain PYR-1. Appl Environ Microbiol 67:1476–1483

    Article  PubMed  CAS  Google Scholar 

  • Moody JD, Fu PP, Freeman JP, Cerniglia CE (2003) Regio- and stereoselective metabolism of 7, 12-dimethylbenz[a]anthracene by Mycobacterium vanbaalenii PYR-1. Appl Environ Microbiol 69:3924–3931

    Article  PubMed  CAS  Google Scholar 

  • Moody JD, Freeman JP, Fu PP, Cerniglia CE (2004) Degradation of benzo[a]pyrene by Mycobacterium vanbaalenii PYR-1. Appl Environ Microbiol 70:340–345

    Article  PubMed  CAS  Google Scholar 

  • Moody JD, Freeman JP, Cerniglia CE (2005) Degradation of benz[a]anthracene by Mycobacterium vanbaalenii strain PYR-1. Biodegradation 16:513–526

    Article  PubMed  CAS  Google Scholar 

  • Mukerjee-Dhar G, Shimura M, Miyazawa D, Kimbara K, Hatta T (2005) bph Genes of the thermophilic PCB degrader, Bacillus sp. JF8: characterization of the divergent ring-hydroxylating dioxygenase and hydrolase genes upstream of the Mn-dependent BphC. Microbiology 151:4139–4151

    Article  PubMed  CAS  Google Scholar 

  • Page RD (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358

    PubMed  CAS  Google Scholar 

  • Patrauchan MA, Florizone C, Dosanjh M, Mohn WW, Davies J, Eltis LD (2005) Catabolism of benzoate and phthalate in Rhodococcus sp. strain RHA1: redundancies and convergence. J Bacteriol 187:4050–4063

    Article  PubMed  CAS  Google Scholar 

  • Penning TM, Burczynski ME, Hung CF, McCoull KD, Palackal NT, Tsuruda LS (1999) Dihydrodiol dehydrogenases and polycyclic aromatic hydrocarbon activation: generation of reactive and redox active o-quinones. Chem Res Toxicol 12:1–18

    Article  PubMed  CAS  Google Scholar 

  • Pinyakong O, Habe H, Yoshida T, Nojiri H, Omori T (2003) Identification of three novel salicylate 1-hydroxylases involved in the phenanthrene degradation of Sphingobium sp. strain P2. Biochem Biophys Res Commun 301:350–357

    Article  PubMed  CAS  Google Scholar 

  • Ramirez N, Cutright T, Ju LK (2001) Pyrene biodegradation in aqueous solutions and soil slurries by Mycobacterium PYR-1 and enriched consortium. Chemosphere 44:1079–1086

    Article  PubMed  CAS  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    PubMed  CAS  Google Scholar 

  • Sakai M, Masai E, Asami H, Sugiyama K, Kimbara K, Fukuda M (2002) Diversity of 2, 3-dihydroxybiphenyl dioxygenase genes in a strong PCB degrader, Rhodococcus sp. strain RHA1. J Biosci Bioeng 93:421–427

    PubMed  CAS  Google Scholar 

  • Schneider J, Grosser R, Jayasimhulu K, Xue W, Warshawsky D (1996) Degradation of pyrene, benz[a]anthracene, and benzo[a]pyrene by Mycobacterium sp. strain RJGII-135, isolated from a former coal gasification site. Appl Environ Microbiol 62:13–19

    PubMed  CAS  Google Scholar 

  • Seah SY, Labbe G, Nerdinger S, Johnson MR, Snieckus V, Eltis LD (2000) Identification of a serine hydrolase as a key determinant in the microbial degradation of polychlorinated biphenyls. J Biol Chem 275:15701–15708

    Article  PubMed  CAS  Google Scholar 

  • Stingley RL, Khan AA, Cerniglia CE (2004) Molecular characterization of a phenanthrene degradation pathway in Mycobacterium vanbaalenii PYR-1. Biochem Biophys Res Commun 322:133–146

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  PubMed  CAS  Google Scholar 

  • Vila J, Lopez Z, Sabate J, Minguillon C, Solanas AM, Grifoll M (2001) Identification of a novel metabolite in the degradation of pyrene by Mycobacterium sp. strain AP1: actions of the isolate on two- and three-ring polycyclic aromatic hydrocarbons. Appl Environ Microbiol 67:5497–5505

    Article  PubMed  CAS  Google Scholar 

  • Vuilleumier S, Pagni M (2002) The elusive roles of bacterial glutathione S-transferases: new lessons from genomes. Appl Microbiol Biotechnol 58:138–146

    Article  PubMed  CAS  Google Scholar 

  • Wang RF, Wennerstrom D, Cao WW, Khan AA, Cerniglia CE (2000) Cloning, expression, and characterization of the katG gene, encoding catalase-peroxidase, from the polycyclic aromatic hydrocarbon-degrading bacterium Mycobacterium sp. strain PYR-1. Appl Environ Microbiol 66:4300–4304

    Article  PubMed  CAS  Google Scholar 

  • Zhou HW, Guo CL, Wong YS, Tam NF (2006) Genetic diversity of dioxygenase genes in polycyclic aromatic hydrocarbon-degrading bacteria isolated from mangrove sediments. FEMS Microbiol Lett 262:148–157

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

We thank Robin L. Stingley and Ashraf A. Khan for critical review of the manuscript and Thomas D. Yun for graphical assistance. The authors acknowledge Charles D. Miller and Ronald C. Sims at the Utah State University and the staff of the Joint Genome Institute for their efforts with the genome sequencing of M. vanbaalenii PYR-1. This work was supported by an appointment to the Postgraduate Research Program at the National Center for Toxicological Research administered by the Oak Ridge Institute for Science and Education through an interagency agreement between the U. S. Department of Energy and the U. S. Food and Drug Administration.

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Author notes

  1. Richard C. Jones

    Present address: NextGen/PRS, Ann Arbor, MI, 48108, USA

  2. Ricky D. Edmondson

    Present address: Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72305, USA

Authors and Affiliations

  1. Division of Microbiology, National Center for Toxicological Research/U.S. FDA, Jefferson, AR, 72079, USA

    Seong-Jae Kim, Ohgew Kweon & Carl E. Cerniglia

  2. Division of Systems Toxicology, National Center for Toxicological Research/U.S. FDA, Jefferson, AR, 72079, USA

    Richard C. Jones & Ricky D. Edmondson

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  1. Seong-Jae Kim
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Correspondence to Carl E. Cerniglia.

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The views presented in this article do not necessarily reflect those of the Food and Drug Administration.

S.-J. Kim and O. Kweon contributed equally to this work.

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Kim, SJ., Kweon, O., Jones, R.C. et al. Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. Biodegradation 19, 859–881 (2008). https://doi.org/10.1007/s10532-008-9189-z

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