1887

Abstract

Dichloromethane dehalogenase/glutathione transferase allows methylotrophic bacteria to grow with dichloromethane (DCM), a predominantly man-made compound. Bacteria growing with DCM by virtue of this enzyme have been readily isolated in the past. So far, the sequence of the gene encoding DCM dehalogenase has been determined for DM4 and sp. DM11. DCM dehalogenase genes closely related to that of strain DM4 were amplified by PCR and cloned from total DNA from 14 different DCM-degrading strains, enrichment cultures and sludge samples from wastewater treatment plants. In total, eight different sequences encoding seven different protein sequences were obtained. Sequences of different origin were identical in several instances. Sequence variation was limited to base substitutions; strikingly, 16 of the 19 substitutions in the gene itself encoded amino acids that were different from those of the DM4 sequence. The kinetic parameters and , the pH optimum and the stability of representative DCM dehalogenase variants were investigated, revealing minor differences between the properties of DCM dehalogenases related to that from strain DM4.

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2001-03-01
2021-10-25
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References

  1. van Agteren M. H. Keuning S., Janssen D. B. 1998 In Handbook on Biodegradation and Biological Treatment of Hazardous Organic Compounds , chapter 3 pp 79–91 Dordrecht: Kluwer;
    [Google Scholar]
  2. Akashi H., Eyre-Walker A. 1998; Translational selection and molecular evolution. Curr Opin Genet Dev 8:688–693 [CrossRef]
    [Google Scholar]
  3. Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. 1987–2000 Current Protocols in Molecular Biology New York: Wiley-Interscience;
    [Google Scholar]
  4. Bader R., Leisinger T. 1994; Isolation and characterization of the Methylophilus sp. strain DM11 gene encoding dichloromethane dehalogenase/glutathione S -transferase. J Bacteriol 176:3466–3473
    [Google Scholar]
  5. Berthelet M., Whyte L. G., Greer C. W. 1996; Rapid, direct extraction of DNA from soils for PCR analysis using polyvinylpolypyrrolidone spin columns. FEMS Microbiol Lett 138:17–22 [CrossRef]
    [Google Scholar]
  6. De Souza M. L., Seffernick J., Martinez B., Sadowsky M. J., Wackett L. P. 1998; The atrazine catabolism genes atzABC are widespread and highly conserved. J Bacteriol 180:1951–1954
    [Google Scholar]
  7. Doronina N. V., Braus-Stromeyer S. A., Leisinger T., Trotsenko Y. A. 1995; Isolation and characterization of a new facultatively methylotrophic bacterium: description of Methylorhabdus multivorans , gen. nov., sp. nov. Syst Appl Microbiol 18:92–98 [CrossRef]
    [Google Scholar]
  8. Doronina N. V., Trotsenko Y. A., Tourova T. P., Kuznetzov B. B., Leisinger T. 2000; Methylophila helvetica sp. nov. and Methylobacterium dichloromethanicum sp. nov. – novel aerobic facultatively methylotrophic bacteria utilizing dichloromethane. Syst Appl Microbiol 23:210–218 [CrossRef]
    [Google Scholar]
  9. Eulberg D., Kourbatova E. M., Golovleva L. A., Schlömann M. 1998; Evolutionary relationship between chlorocatechol catabolic enzymes from Rhodococcus opacus 1CP and their counterparts in proteobacteria: sequence divergence and functional convergence. J Bacteriol 180:1082–1094
    [Google Scholar]
  10. Felsenstein J. 1993 phylip (phylogeny inference package) version 3.5c Department of Genetics, University of Washington; Seattle, USA:
    [Google Scholar]
  11. Fersht A. R. 1999 Structure and Mechanism in Protein Science New York: W. H. Freeman;
    [Google Scholar]
  12. Gillespie J. H. 1991 The Causes of Molecular Evolution Oxford: Oxford University Press;
    [Google Scholar]
  13. Gisi D., Willi L., Traber H., Leisinger T., Vuilleumier S. 1998; Effects of bacterial host and dichloromethane dehalogenase on the competitiveness of methylotrophic bacteria growing with dichloromethane. Appl Environ Microbiol 64:1194–1202
    [Google Scholar]
  14. Goodwin K. D., Schaefer J. K., Oremland R. S. 1998; Bacterial oxidation of dibromomethane and methyl bromide in natural waters and enrichment cultures. Appl Environ Microbiol 64:4629–4636
    [Google Scholar]
  15. Green T. 1997; Methylene chloride induced mouse liver and lung tumours: an overview of the role of mechanistic studies in human safety assessment. Hum Exp Toxicol 16:3–13 [CrossRef]
    [Google Scholar]
  16. Hill K. E., Marchesi J. R., Weightman A. J. 1999; Investigation of two evolutionarily unrelated halocarboxylic acid dehalogenase gene families. J Bacteriol 181:2535–2547
    [Google Scholar]
  17. Holben W. E., Jansson J. K., Chelm B. K., Tiedje J. M. 1988; DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl Environ Microbiol 54:703–711
    [Google Scholar]
  18. Janssen D. B., Oldenhuis R, van den Wijngaard A. J., van der Waarde J. J. 1991; Biochemistry and kinetics of aerobic degradation of chlorinated aliphatic hydrocarbons. In On-site Bioreclamation pp 92–112 Edited by Hinchee R. E., Olfenbuttel R. F. Boston, MA: Butterworth-Heinemann;
    [Google Scholar]
  19. Josephy P. D. 1997 Molecular Toxicology Oxford: Oxford University Press;
    [Google Scholar]
  20. Keith L. H., Telliard W. A. 1979; Priority pollutants I – a perspective view. Environ Sci Technol 13:416–423 [CrossRef]
    [Google Scholar]
  21. Kohler-Staub D., Leisinger T. 1985; Dichloromethane dehalogenase of Hyphomicrobium sp. strain DM2. J Bacteriol 162:676–681
    [Google Scholar]
  22. Kohler-Staub D., Hartmans S., Suter F., Leisinger T, Gälli R. 1986; Evidence for identical dichloromethane dehalogenases in different methylotrophic bacteria. J Gen Microbiol 132:2837–2844
    [Google Scholar]
  23. La Roche S. D., Leisinger T. 1990; Sequence analysis and expression of the bacterial dichloromethane dehalogenase structural gene, a member of the glutathione S -transferase supergene family. J Bacteriol 172:164–171
    [Google Scholar]
  24. Lewontin R. C. 1989; Inferring the number of evolutionary events from DNA coding sequence differences. Mol Biol Evol 6:15–32
    [Google Scholar]
  25. Mckay D., Shiu W. Y., Ma K. C. 1993 In Volatile Organic Chemicals vol. 3 pp 400–406 Boca Raton, FL: Lewis;
    [Google Scholar]
  26. Myazaki K., Arnold F. H. 1999; Exploring nonnatural evolutionary pathways by saturation mutagenesis: rapid improvement of protein function. J Mol Evol 49:716–720 [CrossRef]
    [Google Scholar]
  27. Newman J., Peat T. S., Richard R., Kan L., Swanson P. E., Affholter J. A., Holmes I. H., Schindler J. F., Unkefer C. J., Terwilliger T. C. 1999; Haloalkane dehalogenases: structure of a Rhodococcus enzyme. Biochemistry 38:16105–16114 [CrossRef]
    [Google Scholar]
  28. Ottengraf S. P. P., Meesters J. J. P., Rozema H. R, van den Oever A. H. C. 1986; Biological elimination of volatile xenobiotic compounds in biofilters. Bioprocess Eng 1:61–69 [CrossRef]
    [Google Scholar]
  29. Perrière G. Gouy M. 1996; WWW-Query: an on-line retrieval system for biological sequence banks. Biochimie 78:364–369 [CrossRef]
    [Google Scholar]
  30. Poelarends G. J., Kulakov L. A., Larkin M. J., Vlieg J., Janssen D. B. 2000; Roles of horizontal gene transfer and gene integration in evolution of 1,3-dichloropropene- and 1,2-dibromoethane-degradative pathways. J Bacteriol 182:2191–2199 [CrossRef]
    [Google Scholar]
  31. Pohl T. M., Maier E. 1995; Sequencing 500 kb of yeast DNA using a GATC 1500 direct blotting electrophoresis system. Biotechniques 19:482–486
    [Google Scholar]
  32. Pries F., Bos R., Pentenga M., Janssen D. B, van der Wijngaard A. J. 1994; The role of spontaneous cap domain mutations in haloalkane dehalogenase specifity and evolution. J Biol Chem 26:17490–17494
    [Google Scholar]
  33. Rozen S., Skaletsky H. J. 1998; Primer3. Code available at http://www-genome.wi.mit.edu/genome-software/other/primer3.html
  34. Schmid-Appert M., Zoller K., Traber H., Vuilleumier S., Leisinger T. 1997; Association of newly discovered IS elements with the dichloromethane utilization genes of methylotrophic bacteria. Microbiology 143:2557–2567 [CrossRef]
    [Google Scholar]
  35. Scholtz R., Wackett L. P., Egli C., Cook A. M., Leisinger T. 1988; Dichloromethane dehalogenase with improved catalytic activity isolated from a fast-growing dichloromethane-utilizing bacterium. J Bacteriol 170:5698–5704
    [Google Scholar]
  36. Stucki G., Ebersold H. R., Leisinger T, Gälli R. 1981; Dehalogenation of dichloromethane by cell extracts of Hyphomicrobium DM2. Arch Microbiol 130:366–371 [CrossRef]
    [Google Scholar]
  37. Sutherland J. D. 2000; Evolutionary optimisation of enzymes. Curr Opin Chem Biol 4:263–269 [CrossRef]
    [Google Scholar]
  38. Vuilleumier S. 1997; Bacterial glutathione S-transferases: what are they good for?. J Bacteriol 179:1431–1441
    [Google Scholar]
  39. Vuilleumier S. 2001; Coping with a halogenated one-carbon diet: aerobic dichloromethane-mineralising bacteria. In Biotechnology for the Environment, Focus on Biotechnology Series vol. 3 Edited by Hofman M., Agathos S. Dordrecht: Kluwer; in press
    [Google Scholar]
  40. Vuilleumier S., Leisinger T. 1996; Protein engineering studies of dichloromethane dehalogenase/glutathione S -transferase from Methylophilus sp. strain DM11. Ser12 but not Tyr6 is required for enzyme activity. Eur J Biochem 239:410–417 [CrossRef]
    [Google Scholar]
  41. Vuilleumier S., Sorribas H., Leisinger T. 1997; Identification of a novel determinant of glutathione affinity in dichloromethane dehalogenase/glutathione S-transferases. Biochem Biophys Res Commun 238:452–456 [CrossRef]
    [Google Scholar]
  42. van den Wijngaard A. J., van der Kamp K. W. H. J., van der Ploeg J. Pries F., Kazemier B., Janssen D. B. 1992; Degradation of 1,2-dichloroethane by Ancylobacter aquaticus and other facultative methylotrophs. Appl Environ Microbiol 58:976–983
    [Google Scholar]
  43. Zuber L. 1995 Trickling filter and three-phase airlift bioreactor for the removal of dichloromethane from air PhD thesis ETH Zürich; Switzerland:
    [Google Scholar]
  44. Zuber L., Dunn I. J., Deshusses M. A. 1997; Comparative scale-up and cost estimation of a biological trickling filter and a three-phase airlift bioreactor for the removal of methylene chloride from polluted air. J Air Waste Manag Assoc 47:969–975 [CrossRef]
    [Google Scholar]
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