Location and sequence analysis of a 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase-encoding gene (bpdF) of the biphenyl/ polychlorinated biphenyl degradation pathway in Rhodococcus sp. M5

Gene

Volumn 171, Issue 1, 1996, Pages 53-57

  Lau, Peter C K ^a   Garnon, James ^a   Labbé, Diane ^a   Wang, Ying ^a  

^a NATIONAL RESEARCH COUNCIL CANADA   (Canada)

Author keywords

Aromatic metabolism; Biodegradation; Gram+ bacteria; Nocardioform actinomycete; PCB; Primordial serine codon; Pseudomonads; Serine hydrolase; hydrolase fold

Indexed keywords

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; RHODOCOCCUS SP.; UNCULTURED ACTINOMYCETE;

BACTERIAL ENZYME; BIPHENYL DERIVATIVE; HYDROLASE;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; BIODEGRADATION; CODON USAGE; ENZYME STRUCTURE; ESCHERICHIA COLI; GENE LOCATION; GENE SEQUENCE; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; RHODOCOCCUS;

AMINO ACID SEQUENCE; BASE SEQUENCE; BIODEGRADATION, ENVIRONMENTAL; CLONING, MOLECULAR; CODON; CONSERVED SEQUENCE; FATTY ACIDS, UNSATURATED; GENES, BACTERIAL; HYDROLASES; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; POLYCHLORINATED BIPHENYLS; RESTRICTION MAPPING; RHODOCOCCUS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; SERINE; SUBSTRATE SPECIFICITY;

EID: 0029928993     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/0378-1119(96)00025-X     Document Type: Article

References (23)

1. 112 in catalytic activity. Gene 156 (1995) 69-74.
2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J.: Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410.
3. Asturias, J.A., Diaz, E. and Timmis, K.N.: The evolutionary relationship of biphenyl dioxygenase from Gram-positive Rhodococcus globerulus P6 to multicomponent dioxygenases from Gram-negative bacteria. Gene 156 (1995) 11-18.
4. Corpet, F.: Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16 (1988) 10881-10890.
5. Diaz, E. and Timmis, K.N.: Identification of functional residues in a 2-hydroxymuconic semialdehyde hydrolase: a new member of the α/β hydrolase-fold family of enzymes which cleaves carbon-carbon bonds. J. Biol. Chem. 270 (1995) 6403-6411.
6. Diaz-Lazcoz, Y., Hénaut, A., Vigier, Ph. and Risler, J.-L.: Differential codon usage for conserved amino acids: evidence that the serine codons TCN were primordial. J. Mol. Biol. 250 (1995) 123-127.
7. Furukawa, K., Hirose, J., Suyama, A., Zaiki, T. and Hayashida, S.: Gene components responsible for discrete substrate specificity in the metabolism of biphenyl (bph operon) and toluene (tod operon). J. Bacteriol. 175 (1993) 5224-5232.
8. Hayase, N., Taira, K. and Furukawa, K.: Pseudomonas putida KF715 bphABCD operon encoding biphenyl and polychlorinated biphenyl degradation: cloning, analysis, and expression in soil bacteria. J. Bacteriol. 172 (1990) 1160-1164.
9. Hofer, B., Eltis, L.D., Dowling, D.N. and Timmis, K.N.: Genetic analysis of a Pseudomonas locus encoding a pathway for biphenyl/polychlorinated biphenyl degradation. Gene 130 (1993) 47-55.
10. Horn, J.M., Harayama, S. and Timmis, K.N.: DNA sequence determination of the TOL plasmid (pWWO) xylGFJ genes of Pseudomonas putida: implications for the evolution of aromatic evolution. Mol. Microbiol. 5 (1991) 2459-2474.
11. Kimbara, K., Hashimoto, T., Fukuda, M., Koan, T., Takagi, M., Oishi, M. and Yano, K.: Cloning and sequencing of two tandem genes involved in degradation of 2,3-dihydroxybiphenyl to benzoic acid in the polychlorinated biphenyl-degrading soil bacterium Pseudomonas sp. strain KKS102. J. Bacteriol. 171 (1989) 2740-2747.
12. Layton, A.C., Lajoie, C.A., Easter, J.P., Jernigan, R., Sanseverino, J. and Sayler, G.S.: Molecular diagnostics and chemical analysis for assessing biodegradation of polychlorinated biphenyls in contaminated soils. J. Ind. Microbiol. 13 (1994) 392-401.
13. Masai, E., Yamada, A., Healy, J.M., Hatta, T., Kimbara, K., Fukuda, M. and Yano, K.: Characterization of biphenyl catabolic genes of Gram-positive polychlorinated biphenyl degrader Rhodococcus sp. RHA1. Appl. Environ. Microbiol. 61 (1995) 2079-2085.
14. Menn, F.-M., Zylstra, G.J. and Gibson, D.T.: Location and sequence of the todF gene encoding 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase in Pseudomonas putida F1. Gene 104 (1991) 91-94.
15. Mueller, J.G., Chapman, P.J., Blattmann, B.O. and Pritchard, P.H.: Isolation and characterization of a fluoranthene-utilizing strain Pseudomonas paucimobilis. Appl. Environ. Microbiol. 56 (1990) 1079-1086.
16. Norlund, I. and Shingler, V.: Nucleotide sequences of the meta-cleavage pathway enzymes 2-hydroxymuconic semialdehyde dehydrogenase and 2-hydroxymuconic semialdehyde hydrolase. Biochim. Biophys. Acta 1049 (1990) 227-230.
17. Pries, F., Van der Ploeg, J.R., Dolfing, J. and Janssen, D.B.: Degradation of halogenated aliphatic compounds: the role of adaptation. FEMS Microbiol. Rev. 15 (1994) 279-295.
18. Puente, X.S. and Lopez-Otin, C.: Cloning and expression analysis of a novel human serine hydrolase with sequence similarity to prokaryotic enzymes involved in the degradation of aromatic compounds. J. Biol. Chem. 270 (1995) 12926-12932.
19. Sambrook, J., Fritsch, E.F. and Maniatis, T.: Molecular Cloning. A Laboratory Manual, 2nd ed. CSHL Press, Cold Spring Harbor, NY, 1989.
20. Tabor, S.: Expression using the T7 RNA polymerase/promoter system. In: Ausubel, F.A., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A. and Struhl, K. (Eds.), Current Protocols in Molecular Biology. Greene Publishing/Wiley-Interscience, New York, 1990, pp. 16.2.1-16.2.11.
21. Timmis, K.N., Steffan, R.J. and Unterman, R.: Designing microorganisms for the treatment of toxic wastes. Annu. Rev. Microbiol. 48 (1994) 525-557.
22. Wang, Y., Garnon, J., Labbé, D., Bergeron, H. and Lau, P.C.K.: Sequence and expression of the bpdC1C2BADE genes involved in the initial steps of biphenyl/chlorobiphenyl degradation by Rhodocccus sp. M5. Gene 164 (1995) 117-122.
23. Yanisch-Perron, C., Vieira, J. and Messing, J.: Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33 (1985) 103-119.