Advertisement

Archives of Microbiology

, Volume 183, Issue 2, pp 95–106 | Cite as

Physiological and molecular genetic analyses of vinyl chloride and ethene biodegradation in Nocardioides sp. strain JS614

  • Timothy E. Mattes
  • Nicholas V. Coleman
  • Jim C. Spain
  • James M. Gossett
Original Paper

Abstract

Nocardioides sp. strain JS614 utilizes vinyl chloride and ethene as carbon and energy sources. JS614 could be influential in natural attenuation and biogeochemical ethene cycling, and useful for bioremediation, biocatalysis and metabolic engineering, but a fundamental understanding of the physiological and genetic basis of vinyl chloride and ethene assimilation in strain JS614 is required. Alkene monooxygenase (AkMO) activity was demonstrated in whole-cell assays and epoxyalkane:coenzyme M transferase (EaCoMT) activity was detected in JS614 cell-free extracts. Pulsed-field gel electrophoresis revealed a 290-kb plasmid (pNoc614) in JS614. Curing experiments and PCR indicated that pNoc614 encodes vinyl chloride/ethene-degradation genes. JS614 vinyl chloride/ethene catabolic genes and flanking DNA (34.8 kb) were retrieved from a fosmid clone. AkMO and EaCoMT genes were found in a putative operon that included CoA transferase, acyl-CoA synthetase, dehydrogenase, and reductase genes. Adjacent to this gene cluster was a divergently transcribed gene cluster that encoded possible coenzyme M biosynthesis enzymes. Reverse transcription-PCR demonstrated the vinyl chloride- and ethene-inducible nature of several genes. Genes encoding possible plasmid conjugation, integration, and partitioning functions were also discovered on the fosmid clone.

Keywords

Linear plasmid Alkene oxidation Bioremediation Vinyl chloride 

Notes

Acknowledgements

We thank Anthony Hay, Ruth Richardson, and Steve Zinder for use of their laboratories and for technical advice. We thank Michelle Detwiler at RPCI for her DNA sequencing expertise and persistence in attempts to sequence the hairpin loop. We also thank Juli Rubin, Brian Weisenstein, and Linda Rankin for technical assistance. The US Strategic Environmental Research and Development Program funded this work.

References

  1. Allen JR, Ensign SA (1999) Two short-chain dehydrogenases confer stereoselectivity for enantiomers of epoxypropane in the multiprotein epoxide carboxylating systems of Xanthobacter strain Py2 and Nocardia corallina B276. Biochemistry 38:247–256PubMedGoogle Scholar
  2. Arenghi FLG, Pinti M, Galli E, Barbieri P (1999) Identification of the Pseudomonas stutzeri OX1 toluene-o-xylene monooxygenase regulatory gene (touR) and of its cognate promoter. Appl Environ Microbiol 65:4057–4063PubMedGoogle Scholar
  3. Bont JAM de, Harder W (1978) Metabolism of ethylene by Mycobacterium E 20. FEMS Microbiol Lett 3:89–93CrossRefGoogle Scholar
  4. Broker D, Arenskotter M, Legatzki A, Nies DH, Steinbuchel A (2004) Characterization of the 101-kilobase-pair megaplasmid pKB1, isolated from the rubber-degrading bacterium Gordonia westfalica Kb1. J Bacteriol 186:212–225PubMedGoogle Scholar
  5. Bucher JR, Cooper G, Haseman JK, Jameson CW, Longnecker M, Kamel F, Maronpot R, Matthews HB, Melnick R, Newbold R, Tennant RW, Thompson C, Waalkes M (2001) Ninth report on carcinogens. In: US Department of Health and Human Services, National Toxicology Program. Available via http://ehis.niehs.nih.gov/roc/ninth/known/vinylchloride.pdf.
  6. Byrne A, Olsen R (1996) Cascade regulation of the toluene-3-monooxygenase operon (tbuA1UBVA2C) of Burkholderia pickettii PKO1: role of the tbuA1 promoter (PtbuA1) in the expression of its cognate activator, TbuT. J Bacteriol 178:6327–6337PubMedGoogle Scholar
  7. Cardy DL, Laidler V, Salmond GP, Murrell JC (1991) Molecular analysis of the methane monooxygenase (MMO) gene cluster of Methylosinus trichosporium OB3b. Mol Microbiol 5:335–342PubMedGoogle Scholar
  8. Clark DD, Allen JR, Ensign SA (2000) Characterization of five catalytic activities associated with the NADPH:2-ketopropyl-coenzyme M [2-(2-ketopropylthio)ethanesulfonate] oxidoreductase/carboxylase of the Xanthobacter strain Py2 epoxide carboxylase system. Biochemistry 39:1294–1304PubMedGoogle Scholar
  9. Coleman NV, Spain JC (2003a) Distribution of the coenzyme M pathway of epoxide metabolism among ethene- and vinyl chloride-degrading Mycobacterium strains. Appl Environ Microbiol 69:6041–6046PubMedGoogle Scholar
  10. Coleman NV, Spain JC (2003b) Epoxyalkane: coenzyme M transferase in the ethene and vinyl chloride biodegradation pathways of Mycobacterium strain JS60. J Bacteriol 185:5536–5545PubMedGoogle Scholar
  11. Coleman NV, Mattes TE, Gossett JM, Spain JC (2002) Phylogenetic and kinetic diversity of aerobic vinyl chloride-assimilating bacteria from contaminated sites. Appl Environ Microbiol 68:6162–6171PubMedGoogle Scholar
  12. Cook DM, Farrand SK (1992) The oriT region of the Agrobacterium tumefaciens Ti plasmid pTiC58 shares DNA sequence identity with the transfer origins of RSF1010 and RK2/RP4 and with T-region borders. J Bacteriol 174:6238–6246PubMedGoogle Scholar
  13. Danko AS, Luo M, Bagwell CE, Brigmon RL, Freedman DL (2004) Involvement of linear plasmids in aerobic biodegradation of vinyl chloride. Appl Environ Microbiol 70:6092–6097PubMedGoogle Scholar
  14. delCardayre SB, Davies JE (1998) Staphylococcus aureus coenzyme A disulfide reductase, a new subfamily of pyridine nucleotide-disulfide oxidoreductase. J Biol Chem 273:5752–5757PubMedGoogle Scholar
  15. Graham DE, Xu H, White RH (2002) Identification of coenzyme M biosynthetic phosphosulfolactate synthase. J Biol Chem 277:13421–13429CrossRefPubMedGoogle Scholar
  16. Hartmans S, de Bont JAM (1992) Aerobic vinyl chloride metabolism in Mycobacterium aurum L1. Appl Environ Microbiol 58:1220–1226PubMedGoogle Scholar
  17. Hylckama Vlieg JE van, Leemhuis H, Spelberg JHL, Janssen DB (2000) Characterization of the gene cluster involved in isoprene metabolism in Rhodococcus sp. strain AD45. J Bacteriol 182:1956–1963PubMedGoogle Scholar
  18. Klee HJ, Hayford MB, Kretzmer KA, Barry GF, Kishore GM (1991) Control of ethylene synthesis by expression of a bacterial enzyme in transgenic tomato plants. Plant Cell 3:1187–1193PubMedGoogle Scholar
  19. Kotani T, Yamamoto T, Yurimoto H, Sakai Y, Kato N (2003) Propane monooxygenase and NAD+-dependent secondary alcohol dehydrogenase in propane metabolism by Gordonia sp. strain TY-5. J Bacteriol 185:7120–7128PubMedGoogle Scholar
  20. Krum JG, Ensign SA (2001) Evidence that a linear megaplasmid encodes enzymes of aliphatic alkene and epoxide metabolism and coenzyme M (2-mercaptoethanesulfonate) biosynthesis in Xanthobacter strain Py2. J Bacteriol 183:2172–2177PubMedGoogle Scholar
  21. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackbrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 177–203Google Scholar
  22. Leahy JG, Batchelor PJ, Morcomb SM (2003) Evolution of the soluble diiron monooxygenases. FEMS Microbiol Rev 27:449–479Google Scholar
  23. Nocek B, Jang SB, Jeong MS, Clark DD, Ensign SA, Peters JW (2002) Structural basis for CO2 fixation by a novel member of the disulfide oxidoreductase family of enzymes, 2-ketopropyl-coenzyme M oxidoreductase/carboxylase. Biochemistry 41:12907–12913PubMedGoogle Scholar
  24. Nunes-Duby S, Kwon H, Tirumalai R, Ellenberger T, Landy A (1998) Similarities and differences among 105 members of the Int family of site-specific recombinases. Nucleic Acids Res 26:391–406CrossRefPubMedGoogle Scholar
  25. Saeki H, Furuhashi K (1994) Cloning and characterization of a Nocardia corallina B-276 gene cluster encoding alkene monooxygenase. J Ferment Bioeng 78:399–406Google Scholar
  26. Saeki H, Akira M, Furuhashi K, Averhoff B, Gottschalk G (1999) Degradation of trichloroethene by a linear-plasmid-encoded alkene monooxygenase in Rhodococcus corallinus (Nocardia corallina) B-276. Microbiology 145:1721–1730PubMedGoogle Scholar
  27. Sajjaphan K, Shapir N, Wackett LP, Palmer M, Blackmon B, Tomkins J, Sadowsky MJ (2004) Arthrobacter aurescens TC1 atrazine catabolism genes trzN, atzB, and atzC are linked on a 160-kilobase region and are functional in Escherichia coli. Appl Environ Microbiol 70:4402–4407PubMedGoogle Scholar
  28. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring HarborGoogle Scholar
  29. Sanchez LB, Galperin MY, Muller M (2000) Acetyl-CoA synthetase from the Amitochondriate eukaryote Giardia lamblia belongs to the newly recognized superfamily of acyl-CoA synthetases (nucleoside diphosphate-forming). J Biol Chem 275:5794–5803CrossRefPubMedGoogle Scholar
  30. Sluis MK, Sayavedra-Soto LA, Arp DJ (2002) Molecular analysis of the soluble butane monooxygenase from ‘Pseudomonas butanovora’. Microbiology 148:3617–3629PubMedGoogle Scholar
  31. Squillace PJ, Moran MJ, Lapham WW, Price CV, Clawges RM, Zogorski JS (1999) Volatile organic compounds in untreated ambient groundwater of the United States, 1985–1995. Environ Sci Technol 33:4176–4187Google Scholar
  32. Takai S, Hines SA, Sekizaki T, Nicholson VM, Alperin DA, Osaki M, Takamatsu D, Nakamura M, Suzuki K, Ogino N, Kakuda T, Dan H, Prescott JF (2000) DNA Sequence and Comparison of Virulence Plasmids from Rhodococcus equi ATCC 33701 and 103. Infect Immun 68:6840–6847PubMedGoogle Scholar
  33. Van Hellemond JJ, Opperdoes FR, Tielens AGM (1998) Trypanosomatidae produce acetate via a mitochondrial acetate:succinate CoA transferase. Proc Natl Acad Sci USA 95:3036–3041PubMedGoogle Scholar
  34. Verce MF, Ulrich RL, Freedman DL (2000) Characterization of an isolate that uses vinyl chloride as a growth substrate under aerobic conditions. Appl Environ Microbiol 66:3535–3542PubMedGoogle Scholar
  35. Yanisch-Perron C, Vieira J, Messing J (1985) Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103–119CrossRefPubMedGoogle Scholar
  36. Zhou NY, Chion CK, Leak DJ (1996) Cloning and expression of the genes encoding the propene monooxygenase from Xanthobacter Py2. Appl Microbiol Biotechnol 44:582–588Google Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Timothy E. Mattes
    • 1
  • Nicholas V. Coleman
    • 2
  • Jim C. Spain
    • 3
  • James M. Gossett
    • 4
  1. 1.Department of Civil and Environmental Engineering, 4105 Seamans CenterThe University of IowaIowa CityUSA
  2. 2.School of Molecular and Microbial BiosciencesUniversity of SydneyAustralia
  3. 3.AFRL-MLQL, Tyndall AFBUSA
  4. 4.School of Civil and Environmental Engineering, Hollister HallCornell UniversityNYUSA

Personalised recommendations