A genetic system for the rapid isolation of aromatic-ring-hydroxylating dioxygenase activities

Microbiology

Volumn 149, Issue 6, 2003, Pages 1475-1481

  Kahl, Silke ^a   Hofer, Bernd ^a  

^a HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC COMPOUND; AROMATIC RING HYDROXYLATING DIOXYGENASE; BACTERIAL ENZYME; UNCLASSIFIED DRUG;

ALPHA CHAIN; AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIAL METABOLISM; BACTERIUM ISOLATE; BURKHOLDERIA; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CHIMERA; CONSENSUS SEQUENCE; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME ISOLATION; ENZYME SUBUNIT; GENE AMPLIFICATION; GENE CLUSTER; GENE FUNCTION; GENE IDENTIFICATION; GENE INSERTION; GENE INSERTION SEQUENCE; GENETIC CODE; GENETIC PROCEDURES; GENETIC VARIABILITY; HETEROLOGOUS EXPRESSION; HYBRID GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; VALIDATION PROCESS;

BACTERIA (MICROORGANISMS); BURKHOLDERIA; BURKHOLDERIA SP.;

EID: 0037804252     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.25976-0     Document Type: Article

References (36)

1. Amann, R. I., Ludwig, W. & Schleifer, K. H. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59, 143-169.
2. Asturias, J. A., Moore, E., Yakimov, M. M., Klatte, S. & Timmis, K. N. (1994). Reclassification of the polychlorinated biphenyl-degraders Acinetobacter sp. strain P6 and Corynebacterium sp. strain MB1 as Rhodococcus globerulus. Syst Appl Microbiol 17, 226-231.
3. Asturias, J. A., Diaz, E. & Timmis, K. N. (1995). The evolutionary relationship of biphenyl dioxygenase from Gram-positive Rhodococcus globerulus P6 to multicomponent dioxygenases from Gram-negative bacteria. Gene 156, 11-18.
4. Bartels, F., Backhaus, S., Moore, E. R. B., Timmis, K. N. & Hofer, B. (1999). Occurrence and expression of glutathione-S-transferase-encoding bphK genes in Burkholderia sp. strain LB400 and other biphenyl-utilizing bacteria. Microbiology 145, 2821-2834.
5. Bedard, D. L., Haberl, M. L., May, R. J. & Brennan, M. J. (1987). Evidence for novel mechanisms of polychlorinated biphenyl metabolism in Alcaligenes eutrophus H850. Appl Environ Microbiol 53, 1103-1112.
6. Beil, S., Mason, J. R., Timmis, K. N. & Pieper, D. H. (1998). Identification of chlorobenzene dioxygenase sequence elements involved in dechlorination of 1,2,4,5-tetrachlorobenzene. J Bacteriol 180, 5520-5528.
7. Bopp, L. H. (1986). Degradation of highly chlorinated PCBs by Pseudomonas strain LB400. J Ind Microbiol 1, 23-29.
8. Bopp, L. H., Chakrabarty, A. M. & Ehrlich, H. L. (1983). Chromate resistance plasmid in Pseudomonas fluorescens. J Bacteriol 155, 1105-1109.
9. Boyd, D. R. & Sheldrake, G. N. (1998). The dioxygenase-catalyzed formation of vicinal cis-diols. Nat Prod Rep 15, 309-325.
10. Butler, C. S. & Mason, J. R. (1997). Structure-function analysis of the bacterial aromatic ring hydroxylating dioxygenases. Adv Microb Physiol 38, 47-84.
11. Carredano, E., Karlsson, A., Kauppi, B. & 7 other authors (2000). Substrate binding site of naphthalene 1,2-dioxygenase: functional implications of indole binding. J Mol Biol 296, 701-712.
12. Erickson, B. D. & Mondello, F. J. (1993). Enhanced biodegradation of polychlorinated biphenyls after site-directed mutagenesis of a biphenyl dioxygenase gene. Appl Environ Microbiol 59, 3858-3862.
13. Fain, M. G. & Haddock, J. D. (2001). Phenotypic and phylogenetic characterization of Burkholderia (Pseudomonas) sp. strain LB400. Curr Microbiol 42, 269-75.
14. Furukawa, K., Matsumura, F. & Tonomura, K. (1978). Alcaligenes and Acinetobacter strains capable of degrading polychlorinated biphenyls. Agric Biol Chem 42, 543-548.
15. Furukawa, K., Simon, J. R. & Chakrabarty, A. M. (1983). Common induction and regulation of biphenyl, xylene/toluene and salicylate catabolism in Pseudomonas paucimobilis Q1. J Bacteriol 154, 1356-1362.
16. Furukawa, K., Hirose, J., Hayashida, S. & Nakamura, K. (1994). Efficient degradation of trichloroethylene by a hybrid aromatic ring dioxygenase. J Bacteriol 176, 2121-2123.
17. Grant, S. G. N., Jessee, J., Bloom, F. R. & Hanahan, D. (1990). Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. Proc Natl Acad Sci U S A 87, 4645-4649.
18. Higuchi, R., Krummel, B. & Saiki, R. K. (1988). A general method of in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions. Nucleic Acids Res 16, 7351-7367.
19. Hofer, B., Eltis, L. D., Dowling, D. N. & Timmis, K. N. (1993). Genetic analysis of a Pseudomonas locus encoding a pathway for biphenyl/polychlorinated biphenyl (PCB) degradation. Gene 130, 47-55.
20. Hurtubise, Y., Barriault, D. & Sylvestre, M. (1998). Involvement of the terminal oxygenase beta subunit in the biphenyl dioxygenase reactivity pattern toward chlorobiphenyls. J Bacteriol 180, 5828-5835.
21. Kim, E. & Zylstra, G. J. (1999). Functional analysis of genes involved in biphenyl, naphthalene, phenanthrene, and m-xylene degradation by Sphingomonas yanoikuyae B1. J Ind Microbiol Biotechnol 23, 294-302.
22. Kimura, N., Nishi, A., Goto, M. & 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.
23. Kitagawa, W., Suzuki, A., Hoaki, T., Masai, E. & Fukuda, M. (2001). Multiplicity of aromatic ring hydroxylation dioxygenase genes in a strong PCB degrader, Rhodococcus sp. strain RHA1 demonstrated by denaturing gradient gel electrophoresis. Biosci Biotechnol Biochem 65, 1907-1911.
24. Mondello, F. J., Turcich, M. P., Lobos, J. H. & Erickson, B. D. (1997). Identification and modification of biphenyl dioxygenase sequences that determine the specificity of polychlorinated biphenyl degradation. Appl Environ Microbiol 63, 3096-3103.
25. Mullis, K. B. & Faloona, F. (1987). Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol 155, 335-350.
26. Resnick, S. M., Lee, K. & Gibson, D. T. (1996). Diverse reactions catalyzed by naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816. J Ind Microbiol 17, 438-457.
27. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
28. Seeger, M., Timmis, K. N. & Hofer, B. (1997). Bacterial pathways for degradation of polychlorinated biphenyls. Mar Chem 58, 327-333.
29. Studier, F. W. (1991). Use of bacteriophage T7 lyzozyme to improve an inducible T7 expression system. J Mol Biol 219, 37-44.
30. Tabor, S. & Richardson, C. C. (1985). A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes. Proc Natl Acad Sci U S A 82, 1074-1078.
31. Taira, K., Hayase, N., Arimura, N., Yamashita, S., Miyazaki, T. & Furukawa, K. (1988). Cloning and nucleotide sequence of the 2,3-dihydroxybiphenyl dioxygenase gene from the PCB-degrading strain of Pseudomonas paucimobilis Q1. Biochemistry 27, 3990-3996.
32. Wackett, L. P. & Gibson, D. T. (1988). Degradation of trichloroethylene by toluene dioxygenase in whole-cell studies with Pseudomonas putida F1. Appl Environ Microbiol 54, 1703-1708.
33. Wagner-Döbler, I., Bennasar, A., Vancanneyt, M., Strömpl, C., Brümmer, I., Eichner, C., Grammel, I. & Moore, E. R. B. (1998). Microcosm enrichment of biphenyl-degrading microbial communities from soils and sediments. Appl Environ Microbiol 64, 3014-3022.
34. Wang, Y. & Lau, P. C. (1996). Sequence and expression of an isocitrate dehydrogenase-encoding gene from a polycyclic aromatic hydrocarbon oxidizer, Sphingomonas yanoikuyae B1. Gene 168, 15-21.
35. Williams, W. A., Lobos, J. H. & Cheetham, W. E. (1997). A phylogenetic analysis of aerobic polychlorinated biphenyl-degrading bacteria. Int J Syst Bacteriol 47, 207-210.
36. Zielinski, M., Backhaus, S. & Hofer, B. (2002). The principal determinants for the structure of the substrate-binding pocket are located within a central core of a biphenyl dioxygenase α subunit. Microbiology 148, 2439-2448.