Characterization and expression of the plasmid-borne bedD gene from Pseudomonas putida ML2, which codes for a NAD+-dependent cis-benzene dihydrodiol dehydrogenase

Journal of Bacteriology

Volumn 178, Issue 19, 1996, Pages 5592-5601

  Fong, Karen P Y ^a   Goh, Christopher B H ^a   Tan, Hai Meng ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT;

AFFINITY CHROMATOGRAPHY; AMINO ACID SEQUENCE; ARTICLE; CATABOLISM; GENE CLUSTER; GENE EXPRESSION; GENE INSERTION; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PLASMID; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PSEUDOMONAS PUTIDA; RNA TRANSLATION; SEQUENCE ANALYSIS;

EID: 0029824723     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.178.19.5592-5601.1996     Document Type: Article

References (59)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Axcell, B. C., and P. J. Geary. 1973. Metabolism of benzene by bacteria-purification and some properties of the enzyme cis-1,2-dihydroxy-cyclohexa-3,5-diene (nicotinamide adenine dinucleotide) oxidoreductase (cis-benzene glycol dehydrogenase). Biochem. J. 136:927-934.
3. Axcell, B. C., and P. J. Geary. 1975. Purification and some properties of a soluble benzene-oxidizing system from a strain of Pseudomonas. Biochem. J. 146:173-183.
4. Balroch, A. 1991. PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Res. 19:2241-2245.
5. Bertani, G. 1951. Studies of lysogenesis. I. The mode of phage liberation of lysogenic Escherichia coli. J. Bacteriol. 62:293-300.
6. Blattner, F. R., V. Burland III, G. Plunket, H. J. Sofia, and D. L. Daniels. 1993. Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res. 21:5408-5417.
7. Bradford, M. M. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72:248-254.
8. Dagley, S. 1986. Biochemistry of aromatic hydrocarbon degradation in Pseudomonads, p. 527-555. In J. R. Sokatch (ed.), The bacteria, vol. X. Academic Press, London.
9. Daniel, R., K. Stuertz, and G. Gottschalk. 1995. Biochemical and molecular characterization of the oxidative branch of glycerol utilization by Citrobacter freundii. J. Bacteriol. 177:4392-4401.
10. Davison, J., M. Heusterspreute, N. Chevalier, H. T. Vuhn, and F. Brunel. 1987. Vectors with restriction site banks. V. pJRD215, a wide-host-range cosmid vector with multiple cloning sites. Gene 51:275-280.
11. DiMarco, A. A., and L. N. Ornston. 1994. Regulation of the p-hydroxybenzoate hydroxylase synthesis by PobR bound to an operator in Acinetobacter calcoaceticus, J. Bacteriol. 176:4277-4284.
12. Ditta, G., S. Stanfield, D. Corbin, and D. R. Helsinki. 1980. Broad host range DNA cloning system for Gram-negative bacteria: construction of a gene bank of Rhizobium meliloti. Proc. Natl. Acad. Sci. USA 77:7347-7351.
13. Ensley, B. D., and D. T. Gibson. 1983. Naphthalene dioxygenase, purification, and properties of a terminal oxygenase component. J. Bacteriol. 155:505-511.
14. +-dependent 15-hydroxyprostaglandin dehydrogenase yields a catalytically inactive enzyme. Biochem. Biophys. Res. Commun. 176:840-845.
15. Fong, K. P. Y., and H. M. Tan. Unpublished data.
16. Furukawa, K., and T. Miyazaki. 1986. Cloning of a gene cluster encoding biphenyl and chlorobiphenyl degradation in Pseudomonas pseudoalcaligenes, J. Bacteriol. 166:392-398.
17. Gibson, D. T., M. Hensley, H. Yoshioka, and T. J. Mabry. 1970. Formation of (+) cis-2,3-dihydroxy-1-methylcyclohexa-4,6-diene from toluene by Pseudomonas putida. Biochemistry 9:1626-1630.
18. Gibson, D. T., and V. Subramanian. 1984. Microbial degradation of aromatic hydrocarbons, p. 181-252. In D. T. Gibson (ed.), Microbial degradation of organic compounds. Marcel Dekker, New York.
19. Goyal, A. K., and G. J. Zylstra. 1996. Molecular cloning of novel genes for polycyclic aromatic hydrocarbon degradation from Comamonas testostroni GZ39. Appl. Environ. Microbiol, 62:230-236.
20. Harayama, S., M. Rekik, A. Wasserfallen, and A. Bairoch. 1987. Evolutionary relationships between catabolic pathways for aromatics: conservation of gene order and nucleotide sequences of catechol oxidation genes of pWWO and NAH7 plasmids. Mol. Gen. Genet. 210:241-247.
21. Hawley, D. K., and W. R. McClure. 1983. Compilation and analysis of Escherichia coli promoter DNA sequence. Nucleic Acids Res. 11:2237-2255,
22. Herraro, M., V. de Lorenzo, and K. N. Timmis. 1990. Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria. J. Bacteriol. 172:6557-6567.
23. Holloway, B. W., S. Dharmsthiti, V. Krishapillai, A. Morgan, V. Obeyesekere, E. Ratnaningsih, M. Sinclair, D. Strom, and C. Zhang. 1990. Patterns of gene linkage in Pseudomonas species, p. 97-105, In K. Drlica and M. Riley (ed.), The bacterial chromosome. American Society for Microbiology, Washington, D.C.
24. Ismaiel, A. A., C.-X. Zhu, G. D. Colby, and J.-S. Chen. 1993. Purification and characterization of primary-secondary alcohol dehydrogenase from two strains of Clostridium beijerinckii. J. Bacteriol. 175:5097-5105.
25. Kaniga, K., I. Delor, and G. R. Cornelis. 1991. A wide-host-range suicide vector for improving reverse genetics in Gram-negative bacteria: inactivation of the blaA gene of Yersinia enterocolitica. Gene 109:137-141.
26. Kikuchi, Y., Y. Nagata, M. Hinata, K. Kimbara, M. Fukuda, K. Yano, and M. Takagi. 1944. Identification of the bphA4 gene encoding ferredoxin reductase involved in biphenyl and polychlorinated biphenyl degradation in Pseudomonas sp, strain KKS102. J. Bacteriol. 176:1689-1694.
27. Kurkela, S., H. Lehvaslaiho, E. T. Palva, and T. H. Teeri. 1988. Cloning, nucleotide sequence and characterization of genes encoding naphthalene dioxygenase of Pseudomonas putida strain NCIB 9816. Gene 73:355-362.
28. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature (London) 227:680-685.
29. Masal, E., A. Yamada, J. M. Healy, T. Hatta, K. Kimbara, M. Fukuda, and K. Yano. 1995. Characterization of biphenyl catabolic genus of gram-positive polychlorinated biphenyl degrader Rhodococcus sp. strain RHA1. Appl. Environ. Microbiol. 61:2079-2085.
30. Mallinder, P. R., A. Pritchard, and A. Moir. 1992. Cloning and characterization of a gene from Bacillus stearothemophilus var. non-diastaticus encoding a glycerol dehydrogenase. Gene 110:9-16,
31. Menn, F. M., G. J. Zylstra, and D. T. Gibson. 1991. Location and sequence of the todF gene encoding 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase in Pseudomonas putida F1. Gene 104:91-94.
32. Mollet, B., S. Iida, J. Shepherd, and W. Arber. 1981. Nucleotide sequence of 1526, a new prokaryotic mobile genetic element. Nucleic Acids Res, 11:6319-6330.
33. Neidle, E. L., C. Hartnett, L. N. Ornston, A. Balroch, M. Rekik, and S. Harayama. 1992. Cis-diol dehydrogenases encoded by the TOL pWWO plasmid xylL gene and the Acinetobacter calcaaceticus chromosomal bedD gene are members of the short-chain alcohol dehydrogenase superfamily. Eur. J. Biochem. 204:113-120.
34. Oesch, F., and J. W. Daly. 1972. Conversion of naphthalene to trans-naphthalene dihydrodiol: evidence for the presence of a coupled aryl monooxygenase-epoxide hydrase system in hepatic microsomes. Biochem. Biophys. Res. Commun. 46:1713-1720.
35. Patel, T. R., and D. T. Gibson. 1974. Purification and properties of (-) cis-naphthalene dihydrodiol dehydrogenase of Pseudomonas putida. J. Bacteriol. 119:879-888.
36. Patel, T. R., and D. T. Gibson. 1976. Bacterial cis-dihydrodiol dchydrogenase: comparison of physicochemical and immunological properties. J. Bacteriol. 128:842-850.
37. Persson, B., M. Krook, and H. Jurnvail. 1991. Characteristics of short-chain alcohol dehydrogenases and related enzymes. Eur. J. Biochem. 200:537-543.
38. +) oxidoreductase (decarboxylating). J. Biol. Chem. 247:4960-4965.
39. Rhoades, D. D., and D. J. Roufa. 1991. The SeqAid II programme. Kansas State University, Manhattan. Kans,
40. Rogers, J. E., and D. T. Gibson. 1977. Purification and properties of astoluene dihydrodiol dehydrogenase from Pseudomonas putida. J. Bacteriol. 130:1117-1124.
41. Sambrook, J., E. F. Fritich, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
42. Sanger, F., S. Nicklen, and A. R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74:5463-5467,
43. Shine, J., and L. Dalgarno. 1975. Determinant of cistron specificity in bacterial ribosomes. Nature (London) 254:34-37.
44. Simon, M. J., T. D. Osslund, R. Saunders, B. D. Ensley, S. Suggs, A. Harcourt, W. C. Suen, D. L. Cruden, D. T. Gibson, and G. J. Zylstra. 1993. Sequences of genes encoding naphthalene dioxygenase in Pseudomonas putida strains G7 and NCIB 9816-4. Gene 127:31-37.
45. Subramanian, V., T. N. Liu, W. K. Yen, and D. T. Gibson. 1979. Toluene dioxygenase: purification of an iron-sulfur protein by affinity chromatography. Biochem. Biophys. Res. Commun. 91:1131-1139.
46. Sueoka, N. 1964. Composition variation and heterogeneity of nucleic acid and protein in bacteria, p. 419-443. In I. C. Gunsalus and R. Y. Stanier (ed.), The bacteria, vol. V. Academic Press, New York.
47. Tan, H. M., and C. M. Cheong. 1994. Substitution of the ISP α subunit of biphenyl dioxygenase from Pseudomonas results in a modification of the enzyme activity. Biochem. Biophys. Res. Commun. 204:912-917.
48. Tan, H. M., and K. P. Y. Fong. 1993. Molecular analysis of the plasmid-borne bed gene cluster from Pseudomonas putida ML2 and cloning of the risbenzene dihydrodiol dehydrogenase gene. Can. J. Microbiol. 39:357-362.
49. Tan, H. M., C. B. H. Goh, and K. P. Y. Fong. 1995. Nucleotide sequence and biochemical properties of a nicotinamide adenine dinucleotide-linked dehydrogenase associated with benzene dioxygenase in Pseudomonas putida ML2. J. Cell. Biochem. 21A(Suppl.):52,
50. BED overexpression on benzene dioxygenase activity in Pseudomonas putida ML2. J. Bacteriol. 176:2507-2512.
51. Tan, H. M., and J. R. Mason. 1990. Cloning and expression of the plasmidencoded benzene dioxygenase genes from Pseudomonas putida ML2. FEMS Microbiol. Lett. 72:259-264.
52. Tan, H. M., H. Y. Tang, C. L. Joannou, N. H. Abdel-Wahab, and J. R. Mason. 1943. The Pseudomonas putida ML2 plusmid-encoded genes for benzene dioxygenase are unusual in codon usage and low in G+C content. Gene 130:32-39.
53. Tang, C. T., F. E. Ruch, Jr., and E. C. C. Lin. 1979. Purification and properties of a nicotinamide adenine dinucleotide-linked dehydrogenase that serves an Escherichia cali mutant for glycerol catabolism. J. Bacteriol. 140:182-187.
54. van der Meer, J. R., A. J. B. Zehnder, and W. M. de Vos. 1991. Identification of a novel composite transposuble clement, Tn5280, carrying chlorobenzene dioxygenase genes of Pseudomonas sp. strain P51. J. Bacteriol. 173:7077-7083.
55. Vieira, J., and J. Messing. 1982. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene 19:259-268.
56. Yanisch-Perron, C., J. Vielra, and J. Messing. 1985. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13 mp18 and pUC19 vectors. Gene 33:103-119.
57. Yen, K. M., and I. C. Gunsalus. 1982. Plasmid gene organization: naphthalene/salicylate oxidation. Proc. Natl. Acad. Sci. USA 79:874-878.
58. Zamanian, M., and J. R. Mason. 1987. Benzene dioxygenase in Pseudomonas putida. Biochem. J. 244:611-616.
59. Zylstra, G. J., and D. T. Gibson. 1989. Toluene degradation by Pseudomonas putida F1. J. Biol. Chem. 264:14940-14946.