Biochemical and molecular characterization of a tetrachloroethylene (PCE) dechlorinating Clostridium bifermentans DPH-1

  • Chang, Young-Cheol (Department of Applied Chemistry, Muroran Institute of Technology) ;
  • Toyama, Tadashi (Department of Applied Chemistry, Muroran Institute of Technology) ;
  • Kikuchi, Shintaro (Department of Applied Chemistry, Muroran Institute of Technology)
  • Published : 2008.06.30

Abstract

The tetrachloroethylene (PCE) dehalogenase of Clostridium bifermentans DPH-1 (a halorespiring organism) was purified, cloned, and sequenced. This enzyme is a homodimer with a molecular mass of ca. 70 kDa and exhibits dehalogenation of dichloroethylene isomers along with PCE and trichloroethylene (TCE). Broad range of substrate specificity for chlorinated aliphatic compounds (PCE, TCE, cis-1,2-dichloroethylene, trans-1,2-dichloroethylene, 1,1-dichloroethylene, 1,2-dichloropropene, and 1,1,2-trichloroethane) for this enzyme was also observed. A mixture of propyl iodide and titanium citrate caused a light-reversible inhibition of enzymatic activity suggesting the involvement of a corrinoid cofactor. A partial sequence (81 bp) of the encoding gene for PCE dehalogenase was amplified and sequenced with degenerateprimers designed from the N-terminal sequence (27 amino acid residues). Southern analysis of C. bifermentans genomic DNA using the polymerase chain reaction product as a probe revealed restriction fragment bands. A 5.0 kb ClaI fragment, harboring the relevant gene (designated pceC) was cloned (pDEHAL5) and the complete nucleotide sequence of pceC was determined. The gene showed homology mainly with microbial membrane proteins and no homology with any known dehalogenase, suggesting a distinct PCE dehalogenase. So, C. bifermentans could play some important role in the initial breakdown of PCE and other chlorinated aliphatic compounds in sites contaminated with mixtures of halogenated substances.

Keywords

References

  1. Ryoo, D., Shim, H., Canada, K., Barbieri, P., and Wood, T. K.: Aerobic degradation of tetrachloroethylene by toluene-o-xylene monooxygenase of Pseudomonas stutzeri OX1. Nat. Biotechnol., 18: 775-778, 2000 https://doi.org/10.1038/77344
  2. Ensley, B. D.: Biochemical diversity of trichloroethylene metabolism. Annu. Rev. Microbiol., 45: 283-299, 1991 https://doi.org/10.1146/annurev.mi.45.100191.001435
  3. Lovley, D. R., Phillips, E. J. P.,and Lonergan, D. J.: Hydrogen and formate oxidation coupled to dissimilatory reduction of iron or manganese by Alteromonas putrefaciens. Appl. Environ. Microbiol., 55: 700-706, 1989
  4. Loffler, F. E., Tiedje, J. M., and Sanford, R. A.:Fraction of electrons consumed in electron acceptor reduction and hydrogen thresholds as indicators of halorespiratory physiology. Appl. Environ. Microbiol., 65: 4049-4056, 1999
  5. Lampron, K. J., Chiu, P. C., and Cha, D. K.: Reductive dehalogenation of chlorinated ethenes with elemental iron: the role of microorganisms. Water Res., 13: 3077-3084, 2001
  6. Chang, Y. C., Hatsu, M., Jung, K., Yoo, Y. S., and Takamizawa, K.: Isolation and characterization of a tetrachloroethylene dechlorinating bacterium, Clostridium bifermentans DPH-1. J. Biosci. Bioeng., 89: 489-491, 2000 https://doi.org/10.1016/S1389-1723(00)89102-1
  7. Brunsbach, F. R. and Reineke, W.: Degradation of mixture of chloroaromatics compounds in soil slurry by mixed cultures of specialized organism. Appl. Microbiol. Biotechnol., 43: 529-533, 1995 https://doi.org/10.1007/BF00218461
  8. Harkness, M. R., Bracco, A. A., Brennan, M. J. J., Deweerd, K. A., and Spivack,J. L.: Use of bioaugmentation to stimulate complete reductive dechlorination of trichloroethene in Dover soil columns. Environ. Sci. Technol., 33: 1100-1109, 1999 https://doi.org/10.1021/es9807690
  9. Holliger, C., Schraa, G., Stams, A. J. M., and Zehnder. A. J. B.: A highly purified enrichment culture couples the reductive dechlorination of tetrachloroethene to growth. Appl. Environ. Microbiol., 59: 2991-2997, 1993
  10. Scholz-Muramatsu, H., Neumann, A., MeBmer, M., Moore, E., Diekert,G.: Isolation and characterization of Dehalospirillum multivorans gen. nov., a tetrachloroethene-utilizing, strictly anaerobic bacterium. Arch. Microbiol., 163: 48-56, 1995 https://doi.org/10.1007/BF00262203
  11. Suyama, A., Iwakiri, R., Kai, K., Tokunaga, T., Sera, N., and Furukawa, K.: Isolation and characterization of Desulfitobacteriumsp. strain Y51 capable of efficient dechlorination of tetrachloroethene and polychloroethanes. Biosci. Biotechnol. Biochem., 65: 1474-1481, 2001 https://doi.org/10.1271/bbb.65.1474
  12. Gerritse, J., Renard, V., Pedro Gomes, T. M., Lawson, P. A., Collins, M. D.,and Gottschal, J. C.: Desulfitobacteriumsp. strain PCE1, an anaerobic bacterium that can grow by reductive dechlorination of tetrachloroethylene or ortho-chlorinated phenols. Arch. Microbiol., 165: 132-140, 1996 https://doi.org/10.1007/s002030050308
  13. Miller, E., Wohlfarth, G., and Diekert, G.: Studies on tetrachloroethene respiration in Dehalospirillum multivorans. Arch. Microbiol., 166: 379-387, 1996 https://doi.org/10.1007/BF01682983
  14. Maymo-Gatell, X., Tandoi, V., Gossett, J. M., and Zinder, S. H.: Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethane. Science, 276: 1568-1571, 1997 https://doi.org/10.1126/science.276.5318.1568
  15. Adrian, L., Szewzyk, U., Wecke, J., and Gorisch, H.: Bacterial dehalorespiration with chlorinated benzenes. Nature, 408: 580-583, 2000 https://doi.org/10.1038/35046063
  16. Sung, Y., Ritalahti, K. M., Sanford, R. A., Urbance, J. W., Flynn, S. J., Tiedje, J. M., and Loffler, F. E.: Characterization of two tetrachloroethene (PCE)-reducing, acetate-oxidizing anaerobic bacteria, and their description as Desulfuromonas michiganensis sp. nov. Appl. Environ. Microbiol., 69: 2964-2974, 2003 https://doi.org/10.1128/AEM.69.5.2964-2974.2003
  17. He, J., Sung, Y., Dollhopf, M. E., Fathepure, B. Z., Tiedje, Z. M., and Loffler, F. E.: Acetate versus hydrogen as direct electron donors to stimulate the microbial reductive dechlorination process at chloroethene-contaminated sites. Environ. Sci. Technol., 36: 3945-3952, 2002 https://doi.org/10.1021/es025528d
  18. Magnuson, J. K., Romine, M. F., Burris, D. R., and Kingsley, M. T.: Trichloroethene reductive dehalogenase from Dehalococcoides ethenogenes: sequence of tceA and substrate range characterization. Appl. Environ. Microbiol., 66: 5141-5147, 2000 https://doi.org/10.1128/AEM.66.12.5141-5147.2000
  19. Magnuson, J. K., Stern, R. V., Gossett, J. M., Zinder, S. H., and Burris, D. R.: Reductive dechlorination of tetrachloroethene to ethene by a two-component enzyme pathway. Appl. Environ. Microbiol., 64: 1270-1275, 1998
  20. Maillard, J., Schumacher, W., Vazquez, F., Regeard, C., Hagen, W. R., and Holliger, C.: Characterization of the corrinoid iron-sulfur protein tetrachloroethene reductive dehalogenase of Dehalobacter restrictus. Appl. Environ. Microbiol., 69: 4628-4638, 2003 https://doi.org/10.1128/AEM.69.8.4628-4638.2003
  21. Neumann, A., Scholz-Muramatsu, H., Diekert, G.: Tetrachloroethene metabolism of Dehalospirillum multivorans. Arch. Microbiol., 162: 295-301, 1994 https://doi.org/10.1007/BF00301854
  22. Okeke, B. C., Chang, Y. C., Hatsu, M., Suzuki, T., and Takamizawa, K.: Purification, cloning, and sequencing of an enzyme mediating the reductive dechlorination of tetrachloroethylene (PCE) from Clostridium bifermentans DPH-1. Can. J. Microbiol., 47: 448- 456, 2001 https://doi.org/10.1139/cjm-47-5-448
  23. Schumacher, W., Holliger, C., Zehnder, A. J. B., and Hagen, W. R.: Redox chemistry of cobalamin and iron-sulfur cofactors in the tetrachloroethene reductase of Dehalobacter restrictus. FEBS Lett., 409: 421-425, 1997 https://doi.org/10.1016/S0014-5793(97)00520-6
  24. Suyama, A., Yamashita, M., Yoshino, S., and Furukawa, K.: Molecular characterization of the PceA reductive dehalogenase of Desulfitobacterium sp. strain Y51. J. Bacteriol., 184: 3419- 3425, 2002 https://doi.org/10.1128/JB.184.13.3419-3425.2002
  25. Neumann, A., Wohlfarth, G., and Diekert, G.: Tetrachloroethene dehalogenase from Dehalospirillum multivorans: cloning, sequencing of the encoding genes, and expression of the pceA gene in Escherichia coli. J. Bacteriol., 180: 4140- 4145, 1998
  26. Smidt, H., van Leest, M., van Der Oost, J., and de Vos, W. M.: Transcriptional regulation of the cpr gene cluster in ortho-chlorophenol-respiring Bacteriol., 182: 5683-5691, 2000 https://doi.org/10.1128/JB.182.20.5683-5691.2000
  27. Van de Pas, B. A., Smidt, H., Hagen, W. R., van der Oost, J., Schraa, G., Stams, A. J. M., and deVos, W. M.: Purification and molecular characterization of ortho- chlorophenol reductive dehalogenase, a key enzyme of halorespiration in Desulfitobacterium dehalogenans. J. Biol. Chem., 274: 20287-20292, 1999 https://doi.org/10.1074/jbc.274.29.20287
  28. Malachowski, K. J., Phelps, T. J., Teboli, A. B., Minnikin, D. E., and White, D. C.: Aerobic mineralization of trichloroethylene, vinyl chloride, and aromatic compounds by Rhodococcus species. Appl. Environ. Microbiol., 60: 542-548, 1994
  29. Vannelli, T., Logan, M., Arciero, D. M., and Hooper, A. B.:Degradation of halogenated aliphatic compounds by the ammonia-oxidizing bacterium Nitrosomonas europaea. Appl. Environ. Microbiol., 56: 1169-1171, 1990
  30. Gali, R. and McCarty, P. L.: Biotransformation of 1,1,1-trichloroethane, trichloromethane, and tetrachloromethane by a clostridium sp. Appl. Environ. Mictrobiol., 55: 837-844, 1989
  31. Chang, Y. C., Hatsu, M., Jung, K., Yoo, Y. S., and Takamizawa, K.: In vitro dehalogenation of tetrachloroethylene (PCE) by cell-free extracts of Clostridium bifermentans DPH-1. Bioresour. Technol., 78: 141-147, 2001 https://doi.org/10.1016/S0960-8524(01)00005-0
  32. Cole, J. R., Fathepure, B. Z., and Tiedje, J. M.: Tetrachloroethene and 3-chlorobenzoate dechlorination activities are co-induced in Desulfomonile tiedjei DCB-1. Biodegradation, 6: 167-172, 1995 https://doi.org/10.1007/BF00695347
  33. Fathepure, B. Z. and Boyd, S. A.:Reductive dechlorination of perchloroethylene and the role of methanogens. FEMS Microbiol. Lett., 49: 149-156 (1988) https://doi.org/10.1111/j.1574-6968.1988.tb02706.x
  34. Sharma, P. K. and McCarty, P. L.: Isolation and characterization of a facultative aerobic bacterium that reductively dehalogenates tetrachloroethene to cis-1,2-dichloroethene. Appl. Environ. Microbiol., 62: 761-765, 1996
  35. Miller, E., Wohlfarth, G., and Diekert, G.: Purification and characterization of tetrachloroethene reductive dehalogenase of strain PCE-S. Arch. Microbiol., 169: 497-502, 1998 https://doi.org/10.1007/s002030050602
  36. Neumann, A., Wohlfarth, G. and Diekert, G.:Properties of tetrachloroethene dehalogenase of Dehalospirillum multivorans. Arch. Microbiol., 163: 76-281, 1995 https://doi.org/10.1007/BF00262207
  37. Neumann, A., Wohlfarth, G., and Diekert, G.: Purification and characterization of tetrachloroethene reductive dehalogenase from Dehalospirillum multivorans. J. Biol. Chem., 271: 16515-16519, 1996 https://doi.org/10.1074/jbc.271.28.16515
  38. Van de Pas, B., Gerritse, J., de Vos, W. M., Schraa, G., and Stams, A. J. M.:Two distinct enzyme systems are responsible for tetrachloroethene and reductive dehalogenation in Desulfitobacterium strain PCE1. Arch. Microbiol., 176: 165-169, 2001 https://doi.org/10.1007/s002030100316
  39. Christiansen, N., Ahring, B. K., Wohlfarth, G., and Diekert, G.: Purification and characterization of the 3-chloro-4- hydroxy-phenylacetate reductive dehalogenase of Desulfitobacterium hafniense. FEBS Lett., 436: 159-162, 1998 https://doi.org/10.1016/S0014-5793(98)01114-4
  40. Krasotkina, J., Walters, T., Maruya, K. A., and Ragsdale, S. W.: Characterization of the $B_{12}$- and iron-sulfur-containing reductive dehalogenase from Desulfitobacterium chlororespirans. J. Biol. Chem., 276: 40991-40997, 2001 https://doi.org/10.1074/jbc.M106217200
  41. Boyer, A., Page-Belanger, R., Saucier, M., Villemur, R., Lepine, F., Juteau, P., and Beaudet, R.: Purification, cloning and sequencing of an enzyme mediating the reductive dechlorination of 2,4,6-trichlorophenol from Desulfitobacterium frappieri PCP-1. Biochem. J., 373: 297-303, 2003 https://doi.org/10.1042/BJ20021837
  42. Ni, S., Fredrickson, J. K., and Xun, L.:Purification and characterization of a novel 3-chlorobenzoate-reductive dehalogenase from the cytoplasmic membrane of Desulfomonile tiedjei DCB-1. J. Bacteriol., 177: 5135-5139, 1995 https://doi.org/10.1128/jb.177.17.5135-5139.1995
  43. Neumann, A., Siebert, A., Trescher, T., Reinhardt, S., Wohlfarth, G., and Diekert, G.: Tetrachloroethene reductive dehalogenase of Dehalospirillum multivorans: substrate specificity of the native enzyme and its corrinoid cofactor. Arch. Microbiol., 177: 420-426, 2002 https://doi.org/10.1007/s00203-002-0409-3
  44. Gantzer, C. J. and Wackett, L. P.:Reductive dechlorination by bacterial transition- metal coenzymes. Environ. Sci. Technol., 25: 715-722, 1991 https://doi.org/10.1021/es00016a017
  45. Fetzner, S. and Lingens, F.: Bacterial dehalogenases: biochemistry, genetics, and biotechnological applications. Microbiol. Rev., 58: 641-685, 1994
  46. Holliger, C., Wohlfarth, G., and Diekert, G.:Reductive dechlorination in the energy metabolism of anaerobic bacteria. FEMS Microbiol. Rev., 22: 383-398, 1999 https://doi.org/10.1111/j.1574-6976.1998.tb00377.x
  47. De Bruin, W. P., Kotterman, M. J. J., Posthumus, M. A., Schraa, G., and Zehnder, A. J. B.: Complete biological reductive transformation of tetrachloroethene to ethane. Appl. Environ. Microbiol., 58: 1996-2000, 1992
  48. Koziollek, P., Bryniok, D., Knackmuss, H. J.: Ethene as an auxiliary substrate for the cooxidation of cis-1,2-dichloroethene and vinyl chloride. Arch. Microbiol., 172: 240-246, 1999 https://doi.org/10.1007/s002030050766
  49. Miller, E., Wohlfarth, G., and Diekert, G.: Studies on tetrachloroethene respiration in Dehalospirillum multivorans. Arch. Microbiol., 166: 379-387, 1997 https://doi.org/10.1007/s002030050399
  50. Villemur, R., Saucier, M., Gauthier, A., and Beaudet, R.: Occurrence of several genes encoding putative reductive dehalogenases in Desulfitobacterium hafniense/frappieri and Dehalococcoides ethenogenes. Can. J. Microbiol., 48: 697-706, 2002 https://doi.org/10.1139/w02-057
  51. Seshadri, R., Adrian, L., Fouts, D. E., Eisen, J. A., Phillippy, A. M., Methe, B. A., Ward, N. L., Nelson, W. C., Deboy, R. T., Khouri, H. M., Kolonay, J. F., Dodson, R. J., Daugherty, S. C., Brinkac, L. M., Sullivan, S. A., Madupu, R., Nelson, K. E., Kang, K. H., Impraim, M., Tran, K., Robinson, J. M., Forberger, H. A., Fraser, C. M., Zinder, S. H., and Heidelberg, J. F.: Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science, 307: 105-108, 2005 https://doi.org/10.1126/science.1102226
  52. Fung, J. M., Morris, R. M., Adrian, L., and Zinder, S. H.: Expression of reductive dehalogenase genes in Dehalococcoides ethenogenes strain 195 growing on tetrachloroethene, trichloroethene, or 2,3-dichlorophenol. Appl. Environ. Microbiol., 73: 4439-4445, 2007 https://doi.org/10.1128/AEM.00215-07
  53. Nonaka, H., Keresztes, G., Shinoda, Y., Ikenaga, Y., Abe, M., Naito, K., Inatomi, K., Furukawa, K., Inui M., and Yukawa, H.: Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195. J. Bacteriol., 188: 2262-2274, 2006 https://doi.org/10.1128/JB.188.6.2262-2274.2006