Cloning and characterization of the genes involved in the degradation of dibenzofuran by Terrabacter sp. strain DBF63

Journal of Fermentation and Bioengineering

Volumn 84, Issue 5, 1997, Pages 387-399

  Kasuga, Kano ^a   Nojiri, Hideaki ^a   Yamane, Hisakazu ^a   Kodama, Tohru ^a,b   Omori, Toshio ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b SHINSHU UNIVERSITY   (Japan)

Author keywords

Dibenzofuran degradation; Dioxin degradation; Extradiol dioxygenase gene; Terrabacter species

Indexed keywords

BIPHENYL DERIVATIVE; CATECHOL DERIVATIVE; DIBENZOFURAN DERIVATIVE; DIOXIN; DNA FRAGMENT; GENE PRODUCT; HYDROLASE; OXYGENASE; POLYCHLORINATED DIBENZODIOXIN; RIBOSOME RNA; DIBENZOFURAN;

ARTICLE; BACTERIUM CULTURE; BURKHOLDERIA CEPACIA; DEGRADATION; ESCHERICHIA COLI; GENE LOCATION; GENETIC ANALYSIS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; RESTRICTION MAPPING; SEQUENCE ANALYSIS; STAPHYLOCOCCUS; TERRABACTER; BACTERIUM; BACTERIUM MUTANT; BIODEGRADATION; BIOTRANSFORMATION; ENZYME ACTIVITY; ENZYME SPECIFICITY; GENE INSERTION SEQUENCE; PLASMID; STRAIN DIFFERENCE;

BACTERIA; BIODEGRADATION; CATALYSIS; DNA SEQUENCES; ENZYMES; GENES; ORGANIC COMPOUNDS; OXIDATION;

DIBENZOFURAN; DIOXIN; EXTRADIOL DIOXYGENASE GENE; TERRABACTER;

CLONING;

EID: 0031284266     PISSN: 0922338X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0922-338X(97)81997-6     Document Type: Article

References (38)

1. Firestone, D.: The 2,3,7,8-tetrachlorodibenzo-para-dioxin problem: a review. Ecol. Bull. (Stockholm), 27, 39-52 (1978).
2. Hansen, D. J.: Dioxin toxicity: new studies prompt debate, regulatory action. Chem. Eng. News, 69, 7-14 (1991).
3. Fortnagel. P., Harms, H., Wittich, R.-M., Francke, W., Krohn, S., and Meyer, H.: Cleavage of dibenzofuran and dibenzodioxin ring systems by a Pseudomonas bacterium. Naturwissenschaften, 76, 222-223 (1989).
4. Harms, H., Wittich, R.-M., Sinwell, V., Meyer, H., Fortnagel, P., and Francke, W.: Transformation of dibenzo-p-dioxin by Pseudomonas sp. strain HH69. Appl. Environ. Microbiol., 56, 1157-1159(1990).
5. Wittich, R.-M., Wilkes, H., Sinnwell, V., Francke, W., and Fortnagel, P.: Metabolism of dibenzo-p-dioxin by Sphingomonas sp. strain RW1. Appl. Environ. Microbiol., 58, 1005-1010 (1992).
6. Monna, L., Omori, T., and Kodama, T.: Microbial degradation of dibenzofuran, fluorene, dibenzo-p-dioxin by Staphylococcus auriculans DBF63. Appl. Environ. Microbiol., 59, 285-289 (1993).
7. Bünz, P.V. and Cook, A.M.: Dibenzofuran 4,4a-dioxygenase from Sphingomonas sp. strain RW1: angular dioxygenation by a three-component enzyme system. J. Bacteriol., 175, 64676475 (1993).
8. Batie, C. J., Ballou, D.P., and Correll, C. J.: Phthalate dioxygenase reductase and related flavin-iron-sulfur containing electron transferases, p. 543-556. In Müller, F. (ed.), Chemistry and biochemistry of flavoenzymes, CRC Press, Boca Raton, Fla (1992).
9. Mason, J. R. and Cammack, R.: The electron-transport proteins of hydroxylating bacterial dioxygenases. Annu. Rev. Microbiol., 46, 277-305 (1992).
10. Sato, S., Nam, J.-W., Kasuga, K., Nojiri, H., Yamane, H., and Omori, T.: Identification and characterization of genes encoding carbazole 1,9a-dioxygenase in Pseudomonas sp. strain CA10. J. Bacteriol., 179, 4850-4858 (1997).
11. Happe, B., Eltis, L. D., Poth, H., Hedderich, R., and Timmis, K. N.: Characterization of 2,2′,3-trihydroxybiphenyl dioxygenase, an extradiol dioxygenase from the dibenzofuran- and dibenzo-p-dioxin-degrading bacterium Sphingomonas sp. strain RW1. J. Bacteriol., 175, 7313-7320 (1993).
12. Schmid, A., Rothe, B., Altenbuchner, J., Ludwig, W., and Engesser, K.-H.: Characterization of three distinct extradiol dioxygenases involved in mineralization of dibenzofuran by Terrabacter sp. strain DPO360. J. Bacteriol., 179, 53-62 (1997).
13. Sambrook, J., Fritsch, E. F., and Maniatis, T.: Molecular cloning, 2nd ed: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989).
14. Ausubel, F.M., Brent, R., Kington, E., Moore, D.D., Seidman, J. D., Smith, J. A., and Struhl, K.: Current protocols in molecular biology. Greene Publishing Associates Inc. and John Wiley & Sons Inc., N.Y. (1987).
15. Birnboim, H. C.: A rapid alkaline extraction for the isolation of plasmid DNA. Methods Enzymol., 100, 243-255 (1983).
16. Hanahan, D.: Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol., 166, 557-580 (1983).
17. Anzai, Y., Kudo, Y., and Oyaizu, H.: The phytogeny of the genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera. Int. J. System. Bacteriol., 47, 249-251 (1997).
18. Veieira, J. and Messing, J.: Production of single-stranded plasmid DNA. Methods Enzymol., 153, 3-11 (1987).
19. Saito, I. and Stark, G. R.: Charomids: cosmid vectors for efficient cloning and mapping of large or small restriction enzymes. Proc. Natl. Acad. Sci. USA, 83, 8664-8668 (1986).
20. Laemmli, U. K.: Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature (London), 227, 680-685 (1970).
21. Suzuki, M., Hayakawa, T., Shaw, J. P., Rekik, M., and Harayama, S.: Primary structure of xylene monooxygenase: similarities to and differences from the alkane hydroxylation system. J. Bacteriol., 173, 1690-1695 (1991).
22. Higgins, D. G., Bleasby, A. L., and Fuchs, R.: Clustal V: improved software for multiple sequence alignment. Comput. Appl. Biosci., 8, 189-191 (1992).
23. Thompson, J. D., Higgins, D. G., and Gibson, T. J.: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucl. Acids Res., 22, 4673-4680 (1994).
24. Felsenstein, J.: Confidence limits on phytogenies: an approach using the bootstrap. Evolution, 39, 783-791 (1985).
25. Saitou, N. an Nei, M.: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425 (1987).
26. Collins, M. D., Dorsch, M., and Stackebrandt, E.: Transfer of Pimelobacter tumescens to Terrabacter gen. nov. as Terrabacter tumescens comb. nov. and of Pimelobacter jensenii to Nocardioides as Nocardioides jensenii comb. nov. Int. J. Sys. Bacteriol., 39, 1-6 (1989).
27. Holt, J.G., Krieg, N. R., Sneath, P. H. A., Staley, J.T., and Williams, S. T.: Bergey's manual of determinative bacteriology, 9th ed. Williams & Wilkins, Baltimore, Md. (1994).
28. Harayama, S. and Rekik, M.: Bacterial aromatic ring-cleavage enzymes are classified into two different gene families. J. Biol. Chem., 264, 15328-15333 (1989).
29. Shine, J. and Dalgarno, L.: Determinant of cistron specificity in bacterial ribosome. Nature (London), 254, 34-38 (1975).
30. Senda, T., Sugiyama, K., Narita, H., Yamamoto, T., Kimbara, K., Fukuda, M., Sato, M., Yano, K., and Mitsui, Y.: Three-dimensional structures of free form and two substrate complexes of an extradiol ring-cleavage type dioxygenase, the BphC enzyme from Pseudomonas sp. strain KKS102. J. Mol. Biol., 255, 735-752 (1996).
31. Ollis, D. L., Cheah, E., Cygler, M., Dijkstra, B., Frolow, F., Franken, S. M., Harel, M., Remington, S. J., Silman, I., Schrag, J., Sussman, J. L., Verschueren, K. H. G., and Goldman, A.: The α/β hydrolase fold. Protein Eng., 5, 197-211 (1992).
32. Díaz, E. and Timmis, K. N.: Identification of functional residues in a 2-hydroxymuconic acid semialdehyde hydrolase. A new member of the α/β hydrolase-fold family of enzymes which cleaves carbon-carbon bonds. J. Biol. Chem., 270, 6403-6411 (1995).
33. Wierenga, R. K., Terpstra, P., and Hol, G. J.: Prediction of the occurrence of the ADP-binding bab-fold in proteins, using an amino acid sequence fingerprint. J. Mol. Biol., 187, 101107 (1986).
34. Eggink, G., Engel, H., Vriend, G., Terpstra, P., and Witholt, B.: Rubredoxin reductase of Pseudomonas oleovolans. Structural relationship to other flavoprotein oxidoreductases based on one NAD and two FAD fingerprints. J. Mol. Biol., 212, 135142 (1990).
35. Perkins, E. J., Gordon, M. P., Caceres, O., and Lurquin, P.P.: Organization and sequence analysis of the 2,4-dichlorophenol hydroxylase and dichlorocatechol oxidative operons of plasmid pJP4. J. Bacteriol., 172, 2351-2359 (1990).
36. Nurk, A., Kasak, L., and Kivisaar, M.: Sequence of the gene (pheA) encoding phenol monooxygenase from Pseudomonas sp. EST1001: expression in Escherichia coli and Pseudomonas putida. Gene, 102, 13-18 (1991).
37. Shen, B. S. and Hutchinson, C. R.: Triple hydroxylation of tertacenomycin A2 to tetracenomycin C in Streptomyces glaunoscens. J. Biol. Chem., 269, 30726-30333 (1994).
38. Byrne, A. M. and Lessie, T. G.: Characteristics of IS401, a new member of the IS3 family implicated in plasmid rearrangements in Pseudomonas cepacia. Plasmid, 31, 138-147 (1994).