1887

Abstract

Methyl -butyl ether (MTBE) is a persistent pollutant of surface and groundwater, and the reasons for its low biodegradability are poorly documented. Using one of the rare bacterial strains able to grow in the presence of MTBE, IFP 2012, the protein profiles of crude extracts after growth in the presence of MTBE and glucose were compared by SDS-PAGE. Ten proteins with molecular masses of 67, 64, 63, 55, 50, 27, 24, 17, 14 and 11 kDa were induced after growth in the presence of MTBE. Partial amino acid sequences of N-terminal and internal peptide fragments of the 64 kDa protein were used to design degenerate oligonucleotide primers to amplify total DNA by PCR, yielding a DNA fragment that was used as a probe for cloning. A two-step cloning procedure was performed to obtain a 10 327 bp genomic DNA fragment containing seven ORFs, including a putative regulator, , and four genes, , , and , in the same cluster. The MpdB protein (64 kDa) was related to a flavoprotein of the glucose–methanol–choline oxidoreductase family, and the MpdC protein (55 kDa) showed a high similarity with NAD(P) aldehyde dehydrogenases. Heterologous expression of these gene products was performed in mc2 155. The recombinant strain was able to degrade an intermediate of MTBE biodegradation, 2-methyl 1,2-propanediol, to hydroxyisobutyric acid. This is believed to be the first report of the cloning and characterization of a cluster of genes specifically involved in the MTBE biodegradation pathway of IFP 2012.

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2006-05-01
2019-11-22
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References

  1. Alix, J. H. ( 2004; ). The work of chaperone. In Protein Synthesis and Ribosome Structure, vol. 1, pp. 529–553. Edited by K. H. Nierhaus & D. N. Wilson. Weinheim: Wiley-VCH.
  2. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, Z. J., Zhang Miller, W. & Lipman, D. J. ( 1997; ). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.[CrossRef]
    [Google Scholar]
  3. Austin, S. & Dixon, R. ( 1992; ). The prokaryotic enhancer binding protein NTRC has an ATPase activity which is phosphorylation and DNA dependent. EMBO J 11, 2219–2228.
    [Google Scholar]
  4. Austin, S., Kundrot, C. & Dixon, R. ( 1991; ). Influence of a mutation in the putative nucleotide binding site of the nitrogen regulatory protein NTRC on its positive control function. Nucleic Acids Res 19, 2281–2287.[CrossRef]
    [Google Scholar]
  5. Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A. & Struhl, K. ( 1990; ). Current Protocols in Molecular Biology. New York: Greene Publishing and Wiley Interscience.
  6. Bateman, A., Birney, E. & 8 other authors ( 2002; ). The Pfam protein families database. Nucleic Acids Res 30, 276–280.[CrossRef]
    [Google Scholar]
  7. Boncompagni, E., Østerås, M., Poggi, M. C. & Le Rudulier, D. ( 1999; ). Occurrence of choline and glycine betaine uptake and metabolism in the family Rhizobiaceae and their roles in osmoprotection. Appl Environ Microbiol 65, 2072–2077.
    [Google Scholar]
  8. Buck, M., Gallegos, M. T., Studholme, D. J., Guo, Y. & Gralla, J. D. ( 2000; ). The bacterial enhancer-dependent σ 54 (σ N) transcription factor. J Bacteriol 182, 4129–4136.[CrossRef]
    [Google Scholar]
  9. Burgess, R. R., Travers, A. A., Dunn, J. J. & Bautz, E. K. ( 1969; ). Factor stimulating transcription by RNA polymerase. Nature 221, 43–46.[CrossRef]
    [Google Scholar]
  10. Bystrykh, L. V., Vonck, J., van Bruggen, E. F., van Beeumen, J., Samyn, B., Govorukhina, N. I., Arfman, N., Duine, J. A. & Dijkhuizen, L. ( 1993; ). Electron microscopic analysis and structural characterization of novel NADP(H)-containing methanol: N,N′-dimethyl-4-nitrosoaniline oxidoreductases from the Gram-positive methylotrophic bacteria Amycolatopsis methanolica and Mycobacterium gastri MB19. J Bacteriol 175, 1814–1822.
    [Google Scholar]
  11. Cavener, D. R. ( 1992; ). GMC oxidoreductases: a newly defined family of homologous proteins with diverse catalytic activities. J Mol Biol 223, 811–814.[CrossRef]
    [Google Scholar]
  12. Csonka, L. N. & Epstein, W. ( 1996; ). Osmoregulation. In Escherichia and Salmonella: Cellular and Molecular Biology, 2nd edn, pp. 1210–1223. Edited by F. C. Neidhardt, R. Curtiss, J. L. Ingraham, E. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter & H. E. Umbarger. Washington, DC: American Society for Microbiology.
  13. Deeb, R. A., Hu, H.-Y., Hanson, J. R., Scow, K. M. & Alvarez-Cohen, L. ( 2001; ). Substrate interactions in BTEX and MTBE mixtures by an MTBE-degrading isolate. Environ Sci Technol 35, 312–317.[CrossRef]
    [Google Scholar]
  14. Draper, D. E. ( 1996; ). Translational initiation. In Escherichia and Salmonella: Cellular and Molecular Biology, 2nd edn, pp. 902–908. Edited by F. C. Neidhardt, R. Curtiss, J. L. Ingraham, E. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter & H. E. Umbarger. Washington, DC: American Society for Microbiology.
  15. Fayolle, F. & Monot, F. ( 2005; ). Biodegradation of fuel ethers. In Petroleum Microbiology, pp. 301–316. Edited by M. Magot & B. Ollivier. Washington, DC: American Society for Microbiology.
  16. Fayolle, F., Francois, A., Garnier, L., Godefroy, D., Mathis, H., Piveteau, P. & Monot, F. ( 2003; ). Limitations in MTBE biodegradation. Oil Gas Sci Technol 58, 497–504.[CrossRef]
    [Google Scholar]
  17. Fortin, N. Y., Morales, M., Nakagawa, Y., Focht, D. D. & Deshusses, M. A. ( 2001; ). Methyl tert-butyl ether (MTBE) degradation by a microbial consortium. Environ Microbiol 3, 407–416.[CrossRef]
    [Google Scholar]
  18. François, A. ( 2002; ). Biodegradation of a recalcitrant xenobiotic compound: metabolism of methyl tert-butyl ether (MTBE) by Mycobacterium austroafricanum IFP 2012. PhD thesis, Institut National Agronomique de Paris-Grignon, Paris.
  19. François, A., Mathis, H., Godefroy, D., Piveteau, P., Fayolle, F. & Monot, F. ( 2002; ). Biodegradation of methyl tert-butyl ether and other fuel oxygenates by a new strain, Mycobacterium austroafricanum IFP 2012. Appl Environ Microbiol 68, 2754–2762.[CrossRef]
    [Google Scholar]
  20. François, A., Garnier, L., Mathis, H., Fayolle, F. & Monot, F. ( 2003; ). Roles of tert-butyl formate, tert-butyl alcohol and acetone in the regulation of methyl tert-butyl ether degradation by Mycobacterium austroafricanum IFP 2012. Appl Microbiol Biotechnol 62, 256–262.[CrossRef]
    [Google Scholar]
  21. Garnier, P. M., Auria, R., Augur, C. & Revah, S. ( 1999; ). Cometabolic biodegradation of methyl t-butyl ether by Pseudomonas aeruginosa grown on pentane. Appl Microbiol Biotechnol 51, 498–503.[CrossRef]
    [Google Scholar]
  22. Giegel, D. A., Williams, C. H., Jr & Massey, V. ( 1990; ). l-Lactate 2-monooxygenase from Mycobacterium smegmatis. Cloning, nucleotide sequence, and primary structure homology within an enzyme family. J Biol Chem 265, 6626–6632.
    [Google Scholar]
  23. Grant, S. G., Jessee, J., Bloom, F. R. & Hanahan, D. ( 1990; ). Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. Proc Natl Acad Sci U S A 87, 4645–4649.[CrossRef]
    [Google Scholar]
  24. Hanahan, D., Jesse, J. & Bloom, F. R. ( 1991; ). Plasmid transformation of Escherichia coli and other bacteria. Methods Enzymol 204, 63–113.
    [Google Scholar]
  25. Hanson, J. R., Ackerman, C. E. & Scow, K. M. ( 1999; ). Biodegradation of methyl tert-butyl ether by a bacterial pure culture. Appl Environ Microbiol 65, 4788–4792.
    [Google Scholar]
  26. Hatzinger, P. B., Mac Clay, K., Vainberg, S., Tugusheva, M., Condee, C. W. & Steffan, R. J. ( 2001; ). Biodegradation of methyl tert-butyl ether by a pure bacterial culture. Appl Environ Microbiol 67, 5601–5607.[CrossRef]
    [Google Scholar]
  27. Hellman, U., Wernstedt, C., Góñez, J. & Heldin, C.-H. ( 1995; ). Improvement of an ‘In Gel’ digestion procedure for the micropreparation of internal protein fragments for amino acid sequencing. Anal Biochem 224, 451–455.[CrossRef]
    [Google Scholar]
  28. Hewick, R. M., Hunkaliller, M. W., Hood, L. E. & Dreyer, W. J. ( 1981; ). A gas-liquid solid phase peptide and protein sequenator. J Biol Chem 256, 7990–7997.
    [Google Scholar]
  29. Hu, Y. & Coates, A. R. ( 1999; ). Transcription of two sigma 70 homologue genes, sigA and sigB, in stationary-phase Mycobacterium tuberculosis. J Bacteriol 181, 469–476.
    [Google Scholar]
  30. Jenö, P., Mini, T., Moes, S., Hintermann, E. & Horst, M. ( 1995; ). Internal sequences from proteins digested in polyacrylamide gels. Anal Biochem 224, 75–82.[CrossRef]
    [Google Scholar]
  31. Johansson, K., El-Ahmad, M., Ramaswamy, S., Hjelmqvist, L., Jornvall, H. & Eklund, H. ( 1998; ). Structure of betaine aldehyde dehydrogenase at 2·1 Å resolution. Protein Sci 10, 2106–2117.
    [Google Scholar]
  32. Johnson, R., Pankow, J., Bender, D., Price, C. & Zogorsky, J. ( 2000; ). MTBE. To what extent will past releases contaminate community water supply wells? Environ Sci Technol 34, 210A–217A.[CrossRef]
    [Google Scholar]
  33. Kamalakannan, V., Ramachandran, G., Narayanan, S., Vasan, S. K. & Narayanan, P. R. ( 2002; ). Identification of a novel mycobacterial transcriptional regulator and its involvement in growth rate dependence and stringent control. FEMS Microbiol Lett 209, 261–266.[CrossRef]
    [Google Scholar]
  34. Khan, A. A., Wang, R. F., Cao, W.-W., Doerge, D. R., Wennerstrom, D. & Cerniglia, C. E. ( 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.[CrossRef]
    [Google Scholar]
  35. Kiess, M., Hecht, H. J. & Kalisz, H. M. ( 1998; ). Glucose oxidase from Penicillium amagasakiense. Primary structure and comparison with other glucose–methanol–choline (GMC) oxidoreductases. Eur J Biochem 252, 90–99.[CrossRef]
    [Google Scholar]
  36. Laemmli, U. K. ( 1970; ). Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680–685.[CrossRef]
    [Google Scholar]
  37. Lamark, T., Kaasen, I., Eshoo, M. W., Falkenberg, P., McDougall, J. & Strom, A. R. ( 1991; ). DNA sequence and analysis of the bet genes encoding the osmoregulatory choline–glycine betaine pathway of Escherichia coli. Mol Microbiol 5, 1049–1064.[CrossRef]
    [Google Scholar]
  38. Landfald, B. & Strom, A. R. ( 1986; ). Choline–glycine betaine pathway confers a high level of osmotic tolerance in Escherichia coli. J Bacteriol 65, 849–855.
    [Google Scholar]
  39. Lopes Ferreira, N. & Alix, J.-H. ( 2002; ). The DnaK chaperone is necessary for α-complementation of β-galactosidase in Escherichia coli. J Bacteriol 184, 7047–7054.[CrossRef]
    [Google Scholar]
  40. Lopes Ferreira, N., Maciel, H., Mathis, H., Monot, F., Fayolle-Guichard, F. & Greer, C. W. ( 2005; ). Isolation and characterization of a new Mycobacterium austroafricanum strain, IFP 2015, growing on MTBE. Appl Microbiol Biotechnol (in press). doi:0.1007/s00253-005-0074-y
    [Google Scholar]
  41. Ma, J., Campbell, A. & Karlin, S. ( 2002; ). Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures. J Bacteriol 184, 5733–5745.[CrossRef]
    [Google Scholar]
  42. McGuffin, L. J., Bryson, K. & Jones, D. T. ( 2000; ). The psipred protein structure prediction server. Bioinformatics 16, 404–405.[CrossRef]
    [Google Scholar]
  43. Misra, N., Habib, S., Ranjan, A., Hasnain, S. E. & Nath, I. ( 1996; ). Expression and functional characterisation of the clpC gene of Mycobacterium leprae: ClpC protein elicits human antibody response. Gene 172, 99–104.[CrossRef]
    [Google Scholar]
  44. Morett, E. & Segovia, L. ( 1993; ). The sigma 54 bacterial enhancer-binding protein family: mechanism of action and phylogenetic relationship of their functional domains. J Bacteriol 175, 6067–6074.
    [Google Scholar]
  45. Parish, T. & Stoker, N. G. ( 1998; ). Electroporation of Mycobacteria. In Mycobacteria Protocols: Methods in Molecular Biology, vol. 101, pp. 129–144. Edited by T. Parish & N. G. Stoker. Totowa, NJ: Humana Press.
  46. Park, S. W., Hwang, E. H. & 8 other authors ( 2003; ). Growth of mycobacteria on carbon monoxide and methanol. J Bacteriol 185, 142–147.[CrossRef]
    [Google Scholar]
  47. Picardeau, M., Le Dantec, C. & Vincent, V. ( 2000; ). Analysis of the internal replication region of a mycobacterial linear plasmid. Microbiology 146, 305–313.
    [Google Scholar]
  48. Piveteau, P., Fayolle, F., Vandecasteele, J.-P. & Monot, F. ( 2001; ). Biodegradation of tert-butyl alcohol and related xenobiotics by a methylotrophic bacterial isolate. Appl Microbiol Biotechnol. 55, 369–373.[CrossRef]
    [Google Scholar]
  49. Pocard, J. A., Vincent, N., Boncompagni, E., Smith, L. T., Poggi, M. C. & Le Rudulier, D. ( 1997; ). Molecular characterization of the bet genes encoding glycine betaine synthesis in Sinorhizobium meliloti 102F34. Microbiology 143, 1369–1379.[CrossRef]
    [Google Scholar]
  50. Pollastri, G., Przybylski, D., Rost, B. & Baldi, P. ( 2002; ). Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 47, 228–235.[CrossRef]
    [Google Scholar]
  51. Pospiech, A. & Neumann, B. ( 1995; ). A versatile quick-prep of genomic DNA from Gram-positive bacteria. Trends Genet 6, 217–218.
    [Google Scholar]
  52. Pruden, A. & Suidan, M. ( 2004; ). Effect of benzene, toluene, ethylbenzene and p-xylene (BTEX) mixture on biodegradation of methyl tert-butyl ether (MTBE) and tert-butyl alcohol by pure culture UC1. Biodegradation 15, 213–227.[CrossRef]
    [Google Scholar]
  53. Revel-Viravau, V., Truong, Q. C., Moreau, N., Jarlier, V. & Sougakoff, W. ( 1996; ). Sequence analysis, purification, and study of inhibition by 4-quinolones of the DNA gyrase from Mycobacterium smegmatis. Antimicrob Agents Chemother 40, 2054–2061.
    [Google Scholar]
  54. Rohwerder, T., Cenini, V., Held, C., Martienessen, M., Lechner, U. & Müller, R. H. ( 2004; ). Novel MTBE-degrading bacterial isolate from Leuna groundwater (Germany): characterization of the degradation pathway with focus on HIBA oxidase. In Proceedings of the Second European Conference on MTBE. Edited by D. Barcelo & M. Petrovic. Barcelona: Consejo Superior de Investigaciones Científicas.
  55. Røkenes, T. P., Lamark, T. & Strom, A. R. ( 1996; ). DNA-binding properties of the BetI repressor protein of Escherichia coli: the inducer choline stimulates BetI-DNA complex formation. J Bacteriol 178, 1663–1670.
    [Google Scholar]
  56. Rost, B. & Eyrich, V. A. ( 2001; ). EVA: large-scale analysis of secondary structure prediction. Proteins 45, 192–199.[CrossRef]
    [Google Scholar]
  57. Salanitro, J. P. ( 1995; ). Understanding the limitations of microbial metabolism of ethers used as fuel octane enhancers. Curr Opin Biotechnol 6, 337–340.[CrossRef]
    [Google Scholar]
  58. Sambrook, J. & Russell, D. W. ( 2001; ). Molecular Cloning: a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  59. Smith, C. A. & Hyman, M. R. ( 2004; ). Oxidation of methyl tert-butyl ether by propane-grown Pseudomonas putida GPo1. Appl Environ Microbiol 70, 4544–4550.[CrossRef]
    [Google Scholar]
  60. Smith, C. A., O'Reilly, K. T. & Hyman, M. R. ( 2003; ). Characterization of the initial reactions during the cometabolic oxidation of methyl tert-butyl ether by propane-grown Mycobacterium vaccae JOB5. Appl Environ Microbiol 69, 796–804.[CrossRef]
    [Google Scholar]
  61. Snapper, S. B., Melton, R. E., Mustafa, S., Keiser, T. & Jacobs, W. R., Jr ( 1990; ). Isolation and characterization of efficient plasmid transformation mutants of Mycobacterium smegmatis. Mol Microbiol 4, 1911–1919.[CrossRef]
    [Google Scholar]
  62. Steffan, R. J., McClay, K., Vainberg, S., Condee, C. W. & Zhang, D. ( 1997; ). Biodegradation of the gasoline oxygenates methyl tert-butyl ether, ethyl tert-butyl ether, and tert-amyl methyl ether by propane-oxidizing bacteria. Appl Environ Microbiol 63, 4216–4222.
    [Google Scholar]
  63. Tatusov, R. L., Koonin, E. V. & Lipman, D. J. ( 1997; ). A genomic perspective on protein families. Science 278, 631–637.[CrossRef]
    [Google Scholar]
  64. Thompson, J. D., Higgins, D. G. & Gibson, T. J. ( 1994; ). clustalw: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.[CrossRef]
    [Google Scholar]
  65. United States Environmental Protection Agency ( 1997; ). Drinking Water Advisory: Consumer Acceptability Advice and Health Effects Analysis on Methyl Tertiary Butyl Ether (MtBE). EPA/822/F-97/008, December 1997. Washington, DC: Office of Water.
  66. United States Environmental Protection Agency ( 1999; ). Achieving Clean Air and Clean Water: the Report of the Blue Ribbon Panel on Oxygenates in Gasoline. EPA 420-R-99–021, 15 September, 1999. Washington, DC: Office of Water.
  67. VanBriesen, J. M. ( 2001; ). Thermodynamic yield predictions for biodegradation through oxygenase activation reactions. Biodegradation 12, 265–281.
    [Google Scholar]
  68. Wierenga, R. K., De Maeyer, M. C. H. & Hol, W. J. G. ( 1985; ). Interaction of pyrophosphate moieties with alpha-helixes in dinucleotide binding proteins. Biochemistry 24, 1346–1357.[CrossRef]
    [Google Scholar]
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