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
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.
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.
Kimura, K., Kato, H., Nishi, A., and Furukawa, K. 1996. Analysis of substrate range of biphenyl-catabolic enzymes. Biosci. Biotech. Biochem. 60: 220–223.
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
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.
Abramowicz, D.A. 1990. Aerobic and anaerobic biodegradation of RGBs a review. Cnt Rev Biotechnol. 10: 241–251.
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.
Furukawa, K. 1994. Molecular genetics and evolutionary relationship of RGB-degrading bacteria. Biodegradation 5: 289–300.
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.
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.
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.
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.
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.
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.
Mason, J.R. and Cammack, R. 1992. The electron-transport proteins of hydroxylat-ing bacterial dioxygenases. Annu. Rev. Microbiol. 46: 277–305.
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.
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.
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.
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.
Zhao, H. and Arnold, F.H. 1997. Optimization of DNA shuffling for high fidelity recombination. Nucleic Acids Res. 25: 1307–1308.
Furukawa, K. and Miyazaki, T. 1986. Cloning of gene cluster encoding biphenyl degradation in Pseudomonaspseudoalcaligenes. J. Bacteriol. 166: 392–398.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Bopp, L.H. 1986. Degradation of highly chlorinated RGBs by Pseudomonas strain LB400. J. Ind. Microbiol. 1: 23–29.
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.
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.
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.
Stemmer, W.P.C. 1994. Rapid evolution of a protein in vitro by DNA shuffling. Nature 370: 389–391.
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.
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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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