Journal of Microbiology and Biotechnology

  • 제17권10호
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  • Pages.1655-1660
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  • 2007
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  • 1017-7825(pISSN)
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  • 1738-8872(eISSN)
한국미생물·생명공학회 (The Korean Society for Microbiology and Biotechnology)
권호 표지

Selection and Characterization of Forest Soil Metagenome Genes Encoding Lipolytic Enzymes

  • Hong, Kyung-Sik (Bio-Organic Science Division, Korea Research Institute of Chemical Technology) ;
  • Lim, He-Kyoung (Bio-Organic Science Division, Korea Research Institute of Chemical Technology) ;
  • Chung, Eu-Jin (Division of Applied Biology, College of Natural Resources and Life Science, Dong-A University) ;
  • Park, Eun-Jin (Division of Applied Biology, College of Natural Resources and Life Science, Dong-A University) ;
  • Lee, Myung-Hwan (Division of Applied Biology, College of Natural Resources and Life Science, Dong-A University) ;
  • Kim, Jin-Cheol (Bio-Organic Science Division, Korea Research Institute of Chemical Technology) ;
  • Cho, Gyung-Ja (Bio-Organic Science Division, Korea Research Institute of Chemical Technology) ;
  • Cho, Kwang-Yun (Bio-Organic Science Division, Korea Research Institute of Chemical Technology) ;
  • Lee, Seon-Woo (Division of Applied Biology, College of Natural Resources and Life Science, Dong-A University)
  • 발행 : 2007.10.30
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초록

A metagenome is a unique resource to search for novel microbial enzymes from the unculturable microorganisms in soil. A forest soil metagenomic library using a fosmid and soil microbial DNA from Gwangneung forest, Korea, was constructed in Escherichia coli and screened to select lipolytic genes. A total of seven unique lipolytic clones were selected by screening of the 31,000-member forest soil metagenome library based on tributyrin hydrolysis. The ORFs for lipolytic activity were subcloned in a high copy number plasmid by screening the secondary shortgun libraries from the seven clones. Since the lipolytic enzymes were well secreted in E. coli into the culture broth, the lipolytic activity of the subclones was confirmed by the hydrolysis of p-nitrophenyl butyrate using culture supernatant. Deduced amino acid sequence analysis of the identified ORFs for lipolytic activity revealed that 4 genes encode hormone-sensitive lipase (HSL) in lipase family IV. Phylogenetic analysis indicated that 4 proteins were clustered with HSL in the database and other metagenomic HSLs. The other 2 genes and 1 gene encode non-heme peroxidase-like enzymes of lipase family V and a GDSL family esterase/lipase in family II, respectively. The gene for the GDSL enzyme is the first description of the enzyme from metagenomic screening.

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참고문헌

  1. Akoh, C. C., G. C. Lee, Y. C. Liaw, T. H. Huang, and J. F. Shaw. 2004. GDSL family of serine esterases/lipases. Prog. Lipid Res. 43: 534-552 https://doi.org/10.1016/j.plipres.2004.09.002
  2. 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
  3. Arpigny, J. L. and K. H. Jaeger. 1999. Bacterial lipolytic enzymes: Classification and properties. Biochem. J. 343: 177-183 https://doi.org/10.1042/0264-6021:3430177
  4. Beja, O., M. T. Suzuki, E. V. Koonin, L. Aravind, A. Hadd, L. P. Nguyen, R. Villacorta, M. Amjadi, C. Garrigues, S. B. Jovanovich, R. A. Feldman, and E. F. DeLong. 2000. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ. Microbiol. 2: 516-529 https://doi.org/10.1046/j.1462-2920.2000.00133.x
  5. Eom, G. T., J. S. Rhee, and J. K. Song. 2006. An efficient secretion of type I secretion pathway-dependent lipase, TliA, in Escherichia coli: Effect of relative expression levels and timing of passenger protein and ABC transporter. J. Microbiol. Biotechnol. 16: 1422-1428
  6. Fenster, K. M., K. L. Parkin, and J. L. Steele. 2000. Characterization of an arylesterase from Lactobacillus helveticus CNRZ32. J. Appl. Microbiol. 88: 572-583 https://doi.org/10.1046/j.1365-2672.2000.00993.x
  7. Handelsman, J. 2004. Metagenomics: Application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68: 669-685 https://doi.org/10.1128/MMBR.68.4.669-685.2004
  8. Henne, A., R. A. Schmitz, M. Bomeke, G. Gottschalk, and R. Daniel. 2000. Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity of Escherichia coli. Appl. Environ. Microbiol. 66: 3113-3116 https://doi.org/10.1128/AEM.66.7.3113-3116.2000
  9. 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
  10. Jaeger, K. E., S. Ransac, B. W. Dijkstra, C. Colson, M. van Heuvel, and O. Misset. 1994. Bacterial lipases. FEMS Microbiol. Rev. 15: 29-63 https://doi.org/10.1111/j.1574-6976.1994.tb00121.x
  11. Jaeger, K. E. and T. Eggert. 2002. Lipases for biotechnology. Curr. Opin. Biotechnol. 13: 390-397 https://doi.org/10.1016/S0958-1669(02)00341-5
  12. Ji, S. C., D. Kim, J.-H. Yoon, T.-K. Oh, and C.-H. Lee. 2006. Sequence-based screening for putative polyketide synthase gene-harboring clones from soil metagenomic library. J. Microbiol. Biotechnol. 16: 153-157
  13. Karasawa, K., K. Yokoyama, M. Setaka, and S. Nojima. 1999. The Escherichia coli pldC gene encoding lysophospholipase L(1) is identical to the apeA and tesA genes encoding protease I and thioesterase I, respectively. J. Biochem. 126: 445-448 https://doi.org/10.1093/oxfordjournals.jbchem.a022470
  14. Kim, J.-N., M. J. Seo, E. A. Cho, S. J. Lee, S.-B. Kim, C.-I. Cheigh, and Y.-R. Pyun. 2005. Screening and characterization of an esterase from a metagenomic library. J. Microbiol. Biotechnol. 15: 1067-1072
  15. Kim, U. J., H. Shizuya, P. J. De Jong, B. Birren, and M. I. Simon. 1992. Stable propagation of cosmid-sized human DNA inserts in an F factor based vector. Nucleic Acids Res. 20: 1083-1085 https://doi.org/10.1093/nar/20.5.1083
  16. Kiyasu, T., Y. Nagahashi, and T. Hoshino. 2001. Cloning and characterization of biotin biosynthetic genes of Kurthia sp. Gene 265: 103-113 https://doi.org/10.1016/S0378-1119(01)00354-7
  17. Lee, S. W., K. Won, H. K. Lim, J. C. Kim, G. J. Choi, and K. Y. Cho. 2004. Screening for novel lipolytic enzymes from uncultured soil microorganisms. Appl. Microbiol. Biotechnol. 65: 720-726 https://doi.org/10.1007/s00253-004-1722-3
  18. Lim, H. K., E. J. Chung, J. C. Kim, G. J. Choi, G. S. Jang, Y. R. Chung, K. Y. Cho, and S.-W. Lee. 2005. Characterization of a forest soil metagenome clone that confers indirubin and indigo production on Escherichia coli. Appl. Environ. Microbiol. 71: 7768-7777 https://doi.org/10.1128/AEM.71.12.7768-7777.2005
  19. Lorenz, P. and C. Schleper. 2002. Metagenome - a challenging source of enzyme discovery. J. Mol. Catal. B Enzym. 19-20: 13-19
  20. Nolling, J., G. Breton, M. V. Omelchenko, K. S. Makarova, O. Zeng, R. Gibson, H. M. Lee, J. Dubois, D. Qiu, J. Hitti, Y. I. Wolf, R. L. Tatusov, F. Sabathe, L. Doucette-Stamm, P. Soucaille, M. J. Daly, G. N. Bennett, E. V. Koonin, and D. R. Smith. 2001. Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J. Bacteriol. 183: 4823-4838 https://doi.org/10.1128/JB.183.16.4823-4838.2001
  21. Rondon, M. R., P. R. August, A. D. Bettermann, S. F. Brady, T. H. Grossman, and M. R. Liles. 2000. Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66: 2541-2547 https://doi.org/10.1128/AEM.66.6.2541-2547.2000
  22. Saitou, N. and M. Nei. 1987. The neighbor-joining method: A new method for constructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425
  23. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular Cloning: A Laboratory Manual, 2nd Ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
  24. Tasaki, Y., H. Yoshikawa, and H. Tamura. 2006. Isolation and characterization of an alcohol dehydrogenase gene from the octylphenol polyethoxylate degrader Pseudomonas putida S-5. Biosci. Biotechnol. Biochem. 70: 1855-1863 https://doi.org/10.1271/bbb.60009
  25. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680 https://doi.org/10.1093/nar/22.22.4673
  26. Torsvik, V., F. L. Daae, R. A. Sandaa, and L. Ovreas. 1998. Novel techniques for analyzing microbial diversity in natural and perturbed environments. J. Biotechnol. 64: 53-62 https://doi.org/10.1016/S0168-1656(98)00103-5
  27. Ueda, K., A. Yamashita, J. Ishikawa, T. O. Watsuji, H. Ikeda, M. Hattori, and T. Beppu. 2004. Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalisms. Nucleic Acids Res. 32: 4937-4944 https://doi.org/10.1093/nar/gkh830
  28. Wei, Y., J. A. Contreras, P. Sheffield, T. Osterlund, U. Derewenda, and R. E. Kneusel. 1999. Crystal structure of brefeldin A esterase, a bacterial homolog of the mammalian hormone-sensitive lipase. Nat. Struct. Biol. 6: 340-345 https://doi.org/10.1038/7576
  29. Zhou, J., M. A. Bruns, and J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62: 316-322