Biotechnology and Bioprocess Engineering:BBE

  • 제9권5호
  • /
  • Pages.393-399
  • /
  • 2004
  • /
  • 1226-8372(pISSN)
  • /
  • 1976-3816(eISSN)
한국생물공학회 (The Korean Society for Biotechnology and Bioengineering)
권호 표지

Identification of the bphC Gene for meta-Cleavage of Aromatic Pollutants from a Metagenomic Library Derived from Lake Waters

  • Moon Mi-Sook (Department of Microbiology and Biotechnology, and Biotechnology Research Institute, Chungbuk National University) ;
  • Lee Dong-Hun (Department of Microbiology and Biotechnology, and Biotechnology Research Institute, Chungbuk National University) ;
  • Kim Chi-Kyung (Department of Microbiology and Biotechnology, and Biotechnology Research Institute, Chungbuk National University)
  • 발행 : 2004.10.01
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

Useful genes can be Screened from various environments by construction of metagenomic DNA libraries. In this study, water samples were collected from several lakes in mid Korea, and analyzed by T-RFLP to examine diversities of the microbial communities. The crude DNAs r were extracted by the SDS-based freezing-thawing method, and then further purified using an $UltraClean^{TM}$ kit (MoBio, USA). The metagenomic libraries were constructed with the DNAs partially digested with EcoR I, BamH I, and Sac II in Escherichia coli DH 10B using the pBACe3.6 vector. About 44.0 Mb of metagenomic libraries were obtained with average inserts 13-15 kb in size. The bphC genes responsible for degradation of aromatic hydrocarbons via mets-cleavage were identified from the metagenomic libraries by colony hybridization using the bphC specific sequence as a probe. The 2,3-dihydroxybiphenyl (2, 3-DHBP) dioxygenase gene (bphC ), capable of degradation of 2,3-DHBP, was cloned and its nucleotide Sequences analyzed. The genes consisted of 966 and 897 base pairs with an ATG initiation codon and a TGA termination codon. The activity of the 2,3-DHBP dioxygenase was highly expressed to 2,3-DHBP and Showed a broad substrate range to 2,3-DHBP, catechol, 3-methylcatechol and 4-methylcatechol. These results in-dicated that the bphC gene identified from the metagenomes derived from lake water might be useful in the development of a potent strain for degradation of aromatic pollutants.

키워드

참고문헌

  1. Whitman, W. B., D. C. Coleman, and W. J. Wiebe (1998) Prokaryotes: the unseen majority. Proc. Natl. Acad. Sci. USA 95: 6578-6583 https://doi.org/10.1073/pnas.95.12.6578
  2. Hugenholtz, P. and N. R. Pace (1996) Identifying microbial diversity in the natural environment: a molecular phylogenetic approach. Trends Biotechnol. 14: 190-197 https://doi.org/10.1016/0167-7799(96)10025-1
  3. Hugenholtz, P., B. M. Goebel, and N. R. Pace (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180: 4765-4774
  4. Ferguson, R. L., E. N. Buckley, and A. V. Palumbo (1984) Response of marine bacterioplankton to differential filtration and confinement. Appl. Environ. Microbiol. 47: 49-55
  5. Kogure, K., U. Simidu, and N. Taga (1979) A tentative direct microscopic method for counting living marine bacteria. Can. J. Microbiol. 25: 415-420 https://doi.org/10.1139/m79-063
  6. Kogure, K., U. Simidu, and N. Taga (1980) Distribution of viable marine bacteria in neritic seawater around Japan. Can. J. Microbiol. 26: 318-323 https://doi.org/10.1139/m80-052
  7. Jones, J. G. (1977) The effect of environmental factors on estimated viable and total populations of planktonic bacteria in lakes and experimental enclosures. Freshwater Biol. 7: 67-91 https://doi.org/10.1111/j.1365-2427.1977.tb01659.x
  8. Staley, J. T. and A. Konopka (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu. Rev. Microbiol. 39: 321-346 https://doi.org/10.1146/annurev.mi.39.100185.001541
  9. Wagner, M., R. Amann, H. Lemmer, and K. H. Schleifer (1993) Probing activated sludge with proteobacteriaspecific oligonucleotides: inadequacy of culture-dependent methods for describing microbial community structure. Appl. Environ. Microbiol. 59: 1520- 1525
  10. Wagner, M., R. Erhart, W Manz, R. Amann, H. Lemmer, D. Wedi, and K. H. Schleifer (1994) Development of an rRNA-targeted oligonucleotide probe specific for the genus Acinetobacter and its application for in situ monitoring in activated sludge. Appl. Environ. Microbiol. 60: 792-800
  11. Tosvik, V., J. Goksoyr, and F. L. Daae (1990) High diversity of DNA of soil bacteria. Appl. Environ. Microbiol. 56: 782-787
  12. Amann, R. I., W Ludwig, and K.-H. Schleifer (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143-169 https://doi.org/10.1103/PhysRev.59.143
  13. Gillespie, D. E., S. F. Brady, A. D. Bettermann, N. P. Cianciotto, M. R. Liles, M. R. Rondon, J. Clardy, R. M. Goodman, and J. Handelsman (2002) Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Appl. Environ. Micobiol. 68: 4301-4306 https://doi.org/10.1128/AEM.68.9.4301-4306.2002
  14. Rondon, M. R., P. R. August, A. D. Bettermann, S. F. Brady, T. H. Grossman, M. R. Liles, K. A. Loiacono, B. A. Lynch, I. A. MacNeil, C. Minor, C. L. Tiong, M. Gilman, M. S. Osburne, J. Clardy, J. Handelsman, and R. M. Goodman (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Micobiol. 66: 2541-2547 https://doi.org/10.1128/AEM.66.6.2541-2547.2000
  15. Boyle, A. W, C. J. Silvin, J. P. Hassett, J. P. Nakas, and S. W. Tanenbaum (1992) Bacterial PCB biodegradation. Biodegradation 3: 285-298 https://doi.org/10.1007/BF00129089
  16. Lee, M. S., H. W Chang, H. Y. Kahng, J. S. So, and K. H. Oh (2002) Biological removal of explosive 2,4,6-trini trotoluene by Stenotrophomonas sp. OK-5 in bench-scale bioreactors. Biotechnol. Bioprocess Eng. 7: 98-105
  17. Kim, J. H., W. H. Jeong, T. B. Karegoudar, and C. K. Kim (2002) Stable degradation of benzoate by Klebsiella oxytoea C302 immobilized in alginate and polyurethane. Biotechnol. Bioprocess. Eng. 7: 347- 351 https://doi.org/10.1007/BF02933519
  18. Kimbara, K., T. Hashimoto, M. Fukuda, T. Koana, M. Takagi, M. Oishi, and K. Yano (1989) Cloning and sequencing of two tandem genes involved in degradation of 2,3-dihydroxybiphenyl to benzoic acid in the polychlorinated iphenyl-degrading soil bacterium Pseudomonas sp. strain KKS102. J. acteriol. 171: 2740-2747 https://doi.org/10.1128/jb.171.5.2740-2747.1989
  19. Kim, E., Y. Kim, and C. K. Kim (1996) Genetic structures of the genes encoding 2,3-dihydroxybiphenyl 1,2-dioxygenase and 2-hydroxy-6-oxo-6 phenylhexa-2,4-dienoic acid hydrolase from biphenyl- and 4 chlorobiphenyl-degrading Pseudomonas sp. Strain DJ-12. Appl. Environ. Micobioi. 62: 262-265
  20. Park, S. H., K Lee, J. C. Chae, and C. K. Kim (2004) Construction of transformant reporters carrying fused genes using pcbC promoter of Pseudomonas sp. DJ -12 for detection of aromatic pollutants. Environ. Manit. Assess. 92: 241-251 https://doi.org/10.1023/B:EMAS.0000014513.00754.95
  21. Kim, C. K, E. Kim, J. C. Chae, and Y. Kim (1996) Structure of the pcbC gene encoding 2,3-dihydroxybiphenyl dioxygenase of Pseudomonas sp. P20. Biochem. Biophys. Res. Commun. 226: 15-20 https://doi.org/10.1006/bbrc.1996.1304
  22. Lim, J. C., J. Lee, J. D. Jang, J. Y. Lim, K R. Min, C. K. Kim, and Y. Kim (2000) Characterization of the pcbE gene encoding 2-hydroxypenta-2,4-dienoate hydratase in Pseudomonas sp. DJ-12.Arch. Pharm. Res. 23: 187-95 https://doi.org/10.1007/BF02975512
  23. Mondello, F. J. (1989) Cloning and expression in Escherichia coli of Pseudomonas strain LB400 genes encoding polychlorinated biphenyl degradation. J. Bacterial. 171: 1725-1732 https://doi.org/10.1128/jb.171.3.1725-1732.1989
  24. On, H. Y., N. R. Lee, Y. C. Kim, C. K. Kim, Y. S. Kim, Y. K. Park, J. O. Ka, K. S. Lee, and K. H. Min (1998) Extradiol cleavage of two-ring structure of biphenyl and indole oxidation by biphenyl dioxygenase in Comamonas acidovorans. J. Microbial. Biotechnol. 8: 264-269 https://doi.org/10.1038/nbt0390-264
  25. Rhocelle, P. A., J. C. Fry, R. J. Parkes, and A. J. Weightman (1992) DNA extraction for 16S rRNA gene analysis to determine genetic diversity in deep sediment communities. FEMS. Microbial. Lett. 79: 59-65 https://doi.org/10.1103/PhysRevLett.79.59
  26. Lee, D. H., S. A. Noh, and C. K. Kim (2000) Development of molecular biological methods to analyze bacterial species diversity in freshwater and soil ecosystems. J. Microbial. 38: 11-17
  27. Sambrook, J., E. Fritsch, and T. Maniatis (1989) Molecular Cloning: A Laboratory Manual. 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA
  28. Wagner, M. and A. Loy (2002) Bacterial community composition and function in sewage treatment systems. Curr. Opin. Biotechnol. 13: 218-227 https://doi.org/10.1016/S0958-1669(02)00315-4
  29. Furukawa, K. and N. Arimura (1987) Purification and properties of 2,3 -dihydroxybiphenyl dioxygenase from polychlorinated biphenyl-degrading Pseudomonas pseudoalcaligenes and Pseudomonas aeruginosa carrying the cloned bphc gene. J. Bacteriol. 169: 924-927 https://doi.org/10.1128/jb.169.2.924-927.1987
  30. McKay, D. B., M. Prucha, W. Reineke, K. N. Timmis, and D. H. Pieper (2003) Substrate specificity and expression of three 2,3-dihydroxybiphenyl 1,2-dioxygenases from Rhodococcus globerulus Strain P6. J. Bacteriol. 185: 2944-295l https://doi.org/10.1128/JB.185.9.2944-2951.2003
  31. Candidus, S., H. H. vanPee, and F. Lingens (1994) The catechol 2,3-dioxygenase gene of Rhodococcus rhodochrous CTM: nucleotide sequence, comparison with isofunctional dioxygenases and evidence for an active-site histidine. Microbiology 140: 321-30 https://doi.org/10.1099/13500872-140-2-321