Tuning biphenyl dioxygenase for extended substrate specificity

Biotechnology and Bioengineering

Volumn 63, Issue 5, 1999, Pages 544-551

  Brühlmann, Fredi ^a   Chen, Wilfred ^a  

^a University of California Riverside   (United States)

Author keywords

Biphenyl dioxygenase; DNA shuffling; Polychlorinated biphenyls (PCBs); Random mutagenesis; Staggered extension process

Indexed keywords

BIODEGRADATION; DNA; GENES; GENETIC ENGINEERING; MUTAGENESIS; POLYCHLORINATED BIPHENYLS;

BIPHENYL DIOXYGENASE; DNA SHUFFLING; STAGGERED EXTENSION PROCESSES;

ENZYMES;

ALANINE; BACTERIAL ENZYME; BIPHENYL DIOXYGENASE; ISOLEUCINE; OXYGENASE; PHENYLALANINE; POLYCHLORINATED BIPHENYL; THREONINE; UNCLASSIFIED DRUG;

AMINO ACID SUBSTITUTION; ARTICLE; BURKHOLDERIA CEPACIA; CONTROLLED STUDY; DEGRADATION; DIRECTED MOLECULAR EVOLUTION; ENZYME MECHANISM; ENZYME MODIFICATION; ENZYME SPECIFICITY; NONHUMAN; PROTEIN DOMAIN; PSEUDOMONAS PSEUDOALCALIGENES; SEQUENCE ANALYSIS; STRUCTURE ACTIVITY RELATION;

AMINO ACID SEQUENCE; BASE SEQUENCE; BIODEGRADATION, ENVIRONMENTAL; CLONING, MOLECULAR; DNA PRIMERS; ESCHERICHIA COLI; MUTAGENESIS; OXYGENASES; POLYCHLORINATED BIPHENYLS; SEQUENCE HOMOLOGY, AMINO ACID; SUBSTRATE SPECIFICITY;

BACTERIA (MICROORGANISMS); BURKHOLDERIA; BURKHOLDERIA CEPACIA; NEGIBACTERIA; PSEUDOMONAS; PSEUDOMONAS PSEUDOALCALIGENES;

EID: 0040684812     PISSN: 00063592     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0290(19990605)63:5<544::AID-BIT4>3.0.CO;2-6     Document Type: Article

References (23)

1. Bedard DL, Unterman R, Bopp LH, Brennan MJ, Haberl ML, Johnson C. 1986. Rapid assay for screening and characterizing microorganisms for the ability to degrade polychlorinated biphenyls. Appl Environ Microbiol 51:761-768.
2. Bopp LH. 1986. Degradation of highly chlorinated PCBs by Pseudomonas strain LB400. J Ind Microbiol 1:23-29.
3. Cadwell RC, Joyce GF. 1992. Randomization of genes by PCR mutagenesis. PCR Meth Appl 2:28-33.
4. Crameri A, Whitehorn EA, Tate E, Stemmer WPC. 1996. Improved green fluorescent protein by molecular evolution using DNA shuffling. Nature Biotechnol 14:315-319.
5. Erickson BD, Mondello FJ. 1992. Nucleotide sequencing and transcriptional mapping of the genes encoding biphenyl dioxygenase, a multicomponent polychlorinated-biphenyl-degrading enzyme in Pseudomonas strain LB400. J Bacteriol 174:2903-2912.
6. Erickson BD, Mondello FJ. 1993. Enhanced biodegradation of polychlorinated biphenyls after site-directed mutagenesis of a biphenyl dioxygenase gene. Appl Environ Microbiol 59:3858-3862.
7. Furukawa K, Hirose J, Suyama A, Zaiki T, Hayashida S. 1993. Gene components responsible for discrete substrate specificity in the metabolism of biphenyl (bph operon) and toluene (tod operon). J Bacteriol 175:5224-5232.
8. Gibson DT, Cruden DL, Haddock JD, Zylstra GJ, Brand JM. 1993. Oxidation of polychlorinated biphenyls by Pseudomonas sp. strain LB400 and Pseudomonas pseudoalcaligenes KF707. J Bacteriol 175: 4561-1564.
9. Haddock JD, Nadim LM, Gibson DT. 1993. Oxidation of biphenyl by a multicomponent enzyme system from Pseudomonas sp. strain LB400. J Bacteriol 175:395-400.
10. Hirose J, Suyama A, Hayashida S, Furukada K. 1994. Construction of hybrid biphenyl (bph) and toluene (tod) genes for functional analysis of aromatic ring dioxygenases. Gene 138:27-33.
11. Jobling MC, Holmes RK. 1990. Construction of vectors with the p15a replicon, kanamycin resistance, inducible lacZα and pUC19 or pUC19 multiple cloning sites. Nucl Acids Res 18:5315-5316.
12. Kauppi B, Lee K, Carredano E, Parales RE, Gibson DT, Eklund H, Ramaswamy S. 1998. Structure of an aromatic-ring-hydroxylating dioxygenase - naphthalene 1,2-dioxygenase. Structure 6:571-586.
13. Kimura N, Nishi A, Goto M, Furukawa K. 1997. Functional analysis of a variety of chimeric dioxygenases constructed from two biphenyl dioxygenases that are similar structurally but different functionally. J Bacteriol 179:3996-3943.
14. Kumamaru T, Suenaga H, Mitsuoka M, Watanabe M, Furukawa K. 1998. Enhanced degradation of polychlorinated biphenyls by directed evolution of biphenyl dioxygenase. Nature Biotechnol 16:663-666.
15. Leung DW, Chen E, Goeddel DV. 1989. A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction. Technique 1:11-15.
16. Minshull J. 1995. Cleaning up our own backyard: Developing new catabolic pathways to degrade pollutants. Chem Biol 2:775-780.
17. Mondello FJ, Turcich MP, Lobos JH, Erickson BD. 1997. Identification and modification of biphenyl dioxygenase sequences that determine the specificity of polychlorinated biphenyl degradation. Appl Environ Microbiol 63:3096-3103.
18. Safe S. 1992. Toxicology, structure-function relationship, and human and environmental health impacts of polychlorinated biphenyls: Progress and problems. Environ Health Perspect 100:259-268.
19. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: A laboratory manual, 2nd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
20. Stemmer WPC. 1994. DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution. Proc Natl Acad Sci USA 91:10747-10751.
21. Sylvestre M, Sirois M, Hurtubise Y, Bergeron J, Ahmad D, Shareck F, Barriault D, Guillemette I, Juteau JM. 1996. Sequencing of Comamonas testosteroni strain B-356-biphenyl/chlorobiphenyl dioxygenase genes: Evolutionary relationships among Gram-negative bacterial biphenyl dioxygenases. Gene 174:195-202.
22. Yanisch-Perron C, Vieira J, Messing J. 1985. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103-109.
23. Zhao H, Giver L, Shao Z, Affholter JA, Arnold F. 1998. Molecular evolution by staggered extension process (StEP) in vitro recombination. Nature Biotechnol 16:258-261.