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  • Research Article
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Enhanced degradation of polychlorinated biphenyls by directed evolution of biphenyl dioxygenase

Abstract

Biphenyl dioxygenases (BP Dox) from different organisms, which are involved in the initial oxygenation and subsequent degradation of polychlorinated biphenyls (PCB), are similar in structure but have different functions. The large subunit of BP Dox, encoded by the bphA1 gene, is crucial for substrate selectivity. Using the process of DMA shuffling, we randomly recombined the bphA1 genes of Pseudomonas pseudoalcaligenes KF707 and Burkholderia cepacia LB400 and selected for genes that expressed proteins with altered function. Upon expression in Escherichia coli, some of these evolved genes exhibited enhanced degradation capacity, not only for PCB and related biphenyl compounds, but for single aromatic hydrocarbons such as benzene and toluene, which are poor substrates for the original BP Dox.

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References

  1. van der Meer, J.R., de Vos, W.M., Harayama, S., and Zehnder, A.J.B. 1992. Molecular mechanisms of genetic adaptation to xenobiotic compounds. Microbiol Rev. 56: 677–694.

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Chung, S.-Y., Maeda, M., Song, E., Honkoshi, K., and Kudo, T. 1994. A gram-positive polychlonnated biphenyl-degrading bacterium Rhodococcus erythropolis strain TA421, isolated from a termite ecosystem. Biosa Biatech Biochem. 58: 2111–2113.

    Article  CAS  Google Scholar 

  3. Kimura, K., Kato, H., Nishi, A., and Furukawa, K. 1996. Analysis of substrate range of biphenyl-catabolic enzymes. Biosci. Biotech. Biochem. 60: 220–223.

    Article  CAS  Google Scholar 

  4. Furukawa, K. 1982. Microbial degradation of polychlonnated biphenyls, pp. 33–57 in Biodegradation and detoxification of environmental pollutants. Chakrabarty, A.M. (ed.). CRC Press, Boca Raton, FL

    Google Scholar 

  5. Bedard, D.L., Unterman, R., Bopp, L.H., Brennan, M.J., Haberl, M.L., and Johnson, C. 1986. Rapid assay for screening and characterizing microorganisms for the ability to degrade polychlonnated biphenyls. Appl Environ Microbiol. 51: 761–768.

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Abramowicz, D.A. 1990. Aerobic and anaerobic biodegradation of RGBs a review. Cnt Rev Biotechnol. 10: 241–251.

    Article  CAS  Google Scholar 

  7. Bedard, D.L. and Haberl, M.L. 1990. Influence of chlonne substitution pattern on the degradation of polychlonnated biphenyls by eight bacterial strains. Microb Ecol. 20: 87–102.

    Article  CAS  Google Scholar 

  8. Furukawa, K. 1994. Molecular genetics and evolutionary relationship of RGB-degrading bacteria. Biodegradation 5: 289–300.

    Article  CAS  Google Scholar 

  9. Unterman, R. 1996. A history of RGB biodegradation, pp. 209–253 in Bioremediation. R.L Crawford and D.L Crawford (eds.). Cambridge University Press, New York.

    Chapter  Google Scholar 

  10. Erickson, B.D. and Mondello, F.J. 1993. Enhanced biodegradation of polychlorinated biphenyls after site-directed mutagenesis of a biphenyl dioxygenase gene. Appl. Environ. Microbiol. 59: 3858–3862.

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Gibson, D.T., Cruden, D.L., Haddock, J.D., Zylstra, G.J., and Brand, J.M. 1993. Oxidation of polychlorinated biphenyls by Pseudomonas sp. strain LB400 and Pseudomonas pseudoalcaligenes KF707. J. Bacteriol. 175: 4561–1564.

    Article  CAS  Google Scholar 

  12. Haddock, J.D., Horton, J.R., and Gibson, D.T. 1995. Dihydroxylation and dechlorination of chlorinated biphenyls by purified biphenyl 2,3-dioxygenase from Pseudomonas sp. strain LB400. J. Bacteriol. 177: 20–26.

    Article  CAS  Google Scholar 

  13. Taira, K., Hirose, J., Hayashida, S., and Furukawa, K. 1992.Analysis of bph operon from the polychlorinated biphenyl-degrading strain of Pseudomonas pseudoalcaligenes KF707. J. Biol. Chem. 267: 4844–4853.

    CAS  PubMed  Google Scholar 

  14. Erickson, B.D. and Mondello, F.J. 1992. Nucleotide sequencing and transcriptional mapping of genes encoding biphenyl dioxygenase, a multicomponent polychlorinat-ed-biphenyl-degrading enzyme in Pseudomonas strain LB400. J. Bacteriol. 174: 2903–2912.

    Article  CAS  Google Scholar 

  15. Mason, J.R. and Cammack, R. 1992. The electron-transport proteins of hydroxylat-ing bacterial dioxygenases. Annu. Rev. Microbiol. 46: 277–305.

    Article  CAS  Google Scholar 

  16. Jiang, H., Parales, R.E., Lynch, N.A., and Gibson, D.T. 1996. Site-directed mutagenesis of conserved amino acids in the alpha subunit of toluene dioxygenase: potential mononuclear non-heme iron coordination sites. J. Bacteriol. 178: 3133–3139.

    Article  CAS  Google Scholar 

  17. Hirose, J., Suyama, A., Hayashida, S., and Furukawa, K. 1994. Construction of hybrid biphenyl (bph) and toluene (tod) genes for functional analysis of aromatic ring dioxygenase. Gene 138 27–33.

    Article  CAS  Google Scholar 

  18. Suyama, A., Iwakiri, R., Kimura, N., Nishi, A., Nakamura, K., and Furukawa, K. 1996. Engineering hybrid pseudomonads capable of utilizing a wide range of aromatic hydrocarbons and of efficient degradation of trichloroethylene. J. Bacteriol. 178: 4039–4046.

    Article  CAS  Google Scholar 

  19. Kimura, N., Nishi, A., Goto, M., and Furukawa, K. 1997. Functional analyses of a variety of chimeric dioxygenases constructed from two biphenyl dioxygenases that are similar structurally but different functionally. J. Bacteriol. 179: 3936–3943.

    Article  CAS  Google Scholar 

  20. Zhao, H. and Arnold, F.H. 1997. Optimization of DNA shuffling for high fidelity recombination. Nucleic Acids Res. 25: 1307–1308.

    Article  CAS  Google Scholar 

  21. Furukawa, K. and Miyazaki, T. 1986. Cloning of gene cluster encoding biphenyl degradation in Pseudomonaspseudoalcaligenes. J. Bacteriol. 166: 392–398.

    Article  CAS  Google Scholar 

  22. Ensley, B.D., Ratzkin, B.J., Ossulund, T.D., Simon, M.J., Wackett, L.P., and Gibson, D.T. 1983. Expression of naphthalene oxidation genes in Escherichia coli results in the biosynthesis of indigo. Science 22: 167–169.

    Article  Google Scholar 

  23. Hart, S., Koch, K.R., and Woods, D.R. 1992. Identification of indigo related pigments produced by Escherichia coli containing a cloned Rhodococcus gene. J. Gen. Microbiol. 138: 211–216.

    Article  CAS  Google Scholar 

  24. Murdock, D., Ensley, B.D., Serdar, C., and Thalen, M. 1993. Construction of metabolic operons catalyzing the de novo synthesis of indigo in Escherichia coli . Bio/Technology 11: 381–386.

    Article  CAS  Google Scholar 

  25. Eaton, R.W. and Chapman, P.J. 1995. Formation of indigo and related compounds from indolecarboxylic acids by aromatic acid-degrading bacteria: chromogenic reactions for cloning genes encoding dioxygenases that act on aromatic acids. J. Bacteriol. 177: 6983–6988.

    Article  CAS  Google Scholar 

  26. O'Connor, K.E., Dobson, A.D.W., and Hartmans, S. 1997. Indigo formation by microorganisms expressing styrene monooxygenase activity. Appl. Environ. Microbiol. 63: 4287–4291.

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Mondello, F., Turcich, M.P., Lobos, J.H., and Erickson, B.D 1997. Identification and modification of biphenyl dioxygenase sequences that determine the specificity of polychlorinated biphenyl degradation. Appl. Environ. Microbiol. 63: 3039–3103.

    Google Scholar 

  28. Atkins, W.M. and Sligar, S.G. 1988. The roles of active site hydrogen bonding in cytochrome P-450cam as revealed by site directed mutagenesis. J. Biol. Chem. 263: 18842–18849.

    CAS  PubMed  Google Scholar 

  29. Loida, P.J. and Sligar, S.G. 1993. Engineering cytochrome P-450cam to increase stereospecificity and coupling of aliphatic hydroxylations. Protein Eng. 6: 207–212.

    Article  CAS  Google Scholar 

  30. Pikus, J.D., Studts, J.M., McClay, K., Steffan, R.J., and Fox, B.C. 1997. Changes in the regiospecificity of aromatic hydroxylation produced by active site engineering in the diiron enzyme toluene 4-monooxygenase. Biochemistry 36: 9283–9289.

    Article  CAS  Google Scholar 

  31. Bopp, L.H. 1986. Degradation of highly chlorinated RGBs by Pseudomonas strain LB400. J. Ind. Microbiol. 1: 23–29.

    Article  CAS  Google Scholar 

  32. Bullock, W.O., Fernandez, J.M., and Short, J.M. 1987. XL-1-Blue: a high efficiency plasmid transforming recA Escherichia coli strain with p-galactosidase selection. BioTechniques 5: 376–378.

    CAS  Google Scholar 

  33. Vanish-Perron, C., Vieira, J., and Messing, J. 1985. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33: 103–119.

    Article  Google Scholar 

  34. Hirose, J., Auyama, A., Hayashida, S., and Furukawa, K. 1994. Construction of hybrid biphenyl (Ibph) and toluene (tod) genes for functional analysis of aromatic ring dioxygenases. Gene 138: 27–33.

    Article  CAS  Google Scholar 

  35. Stemmer, W.P.C. 1994. Rapid evolution of a protein in vitro by DNA shuffling. Nature 370: 389–391.

    Article  CAS  Google Scholar 

  36. Stemmer, W.P.C. 1994. DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc. Watt Acad. Sci. USA 91: 10747–10751.

    Article  CAS  Google Scholar 

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Kumamaru, T., Suenaga, H., Mitsuoka, M. et al. Enhanced degradation of polychlorinated biphenyls by directed evolution of biphenyl dioxygenase. Nat Biotechnol 16, 663–666 (1998). https://doi.org/10.1038/nbt0798-663

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  • DOI: https://doi.org/10.1038/nbt0798-663

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