Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Characterization of Two Metagenome-Derived Esterases That Reactivate Chloramphenicol by Counteracting Chloramphenicol Acetyltransferase

  • Received : 2011.07.18
  • Accepted : 2011.08.30
  • Published : 2011.12.28
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Abstract

Function-driven metagenomic analysis is a powerful approach to screening for novel biocatalysts. In this study, we investigated lipolytic enzymes selected from an alluvial soil metagenomic library, and identified two novel esterases, EstDL26 and EstDL136. EstDL26 and EstDL136 reactivated chloramphenicol from its acetyl derivates by counteracting the chloramphenicol acetyltransferase (CAT) activity in Escherichia coli. These two enzymes showed only 27% identity in amino acid sequence to each other; however both preferentially hydrolyzed short-chain p-nitrophenyl esters (${\leq}C_5$) and showed mesophilic properties. In vitro, EstDL136 catalyzed the deacetylation of 1- and 3-acetyl and 1,3-diacetyl derivates; in contrast, EstDL26 was not capable of the deacetylation at $C_1$, indicating a potential regioselectivity. EstDL26 and EstDL136 were similar to microbial hormone-sensitive lipase (HSL), and since chloramphenicol acetate esterase (CAE) activity was detected from two other soil esterases in the HSL family, this suggests a distribution of CAE among the soil microorganisms. The isolation and characterization of EstDL26 and EstDL136 in this study may be helpful in understanding the diversity of CAE enzymes and their potential role in releasing active chloramphenicol in the producing bacteria.

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References

  1. Alexander, N. J., S. P. McCormick, C. Waalwijk, T. van der Lee, and R. H. Proctor. 2011. The genetic basis for 3-ADON and 15-ADON trichothecene chemotypes in Fusarium. Fungal Genet. Biol. 48: 485-495. https://doi.org/10.1016/j.fgb.2011.01.003
  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. E. Jaeger. 1999. Bacterial lipolytic/enzymes: Classification and properties. Biochem. J. 343: 177-183. https://doi.org/10.1042/0264-6021:3430177
  4. Bornscheuer, U. T. 2002. Microbial carboxyl esterases: Classification, properties and application in biocatalysis. FEMS. Microbiol. Rev. 26: 73-81. https://doi.org/10.1111/j.1574-6976.2002.tb00599.x
  5. Cundliffe, E. 1989. How antibiotic-producing organisms avoid suicide. Annu. Rev. Microbiol. 43: 207-233. https://doi.org/10.1146/annurev.mi.43.100189.001231
  6. Gross, F., E. A. Lewis, M. Piraee, K. H. Van Pee, L. C. Vining, and R. L. White. 2002. Isolation of 3'-O-acetylchloramphenicol: A possible intermediate in chloramphenicol biosynthesis. Bioorg. Med. Chem. Lett. 12: 283-286. https://doi.org/10.1016/S0960-894X(01)00739-9
  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. He, J., N. Magarvey, M. Piraee, and L. C. Vining. 2001. The gene cluster for chloramphenicol biosynthesis in Streptomyces venezuelae ISP5230 includes novel Shikimate pathway homologues and a monomodular nonribosomal peptide synthetase gene. Microbiology 147: 2817-2829.
  9. 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 on Escherichia coli. Appl. Environ. Microbiol. 66: 3113-3116. https://doi.org/10.1128/AEM.66.7.3113-3116.2000
  10. Hong, K. S., H. K. Lim, E. J. Chung, E. J. Park, M. H. Lee, J. C. Kim, G. J. Choi, K. Y. Cho, and S. W. Lee. 2007. Selection and characterization of forest soil metagenome genes encoding lipolytic enzymes. J. Microbiol. Biotechnol. 17: 1655-1660.
  11. Hu, Y., G. Zhang, A. Li, J. Chen, and L. Ma. 2008. Cloning and enzymatic characterization of a xylanase gene from a soilmetagenomic library with an efficient approach. Appl. Microbiol. Biotechnol. 80: 823-830. https://doi.org/10.1007/s00253-008-1636-6
  12. Jaeger, K. E., B. W. Dijkstra, and M. T. Reetz. 1999. Bacterial biocatalysts: Molecular biology, three-dimensional structures, and biotechnological applications of lipases. Annu. Rev. Microbiol. 53: 315-351. https://doi.org/10.1146/annurev.micro.53.1.315
  13. Jeanmougin, F., J. D. Thompson, M. Gouy, D. G. Higgins, and T. J. Gibson. 1998. Multiple sequence alignment with Clustal X. Trends Biochem. Sci. 23: 403-405. https://doi.org/10.1016/S0968-0004(98)01285-7
  14. Jeon, J. H., J. T. Kim, S. G. Kang, J. H. Lee, and S. J. Kim. 2009. Characterization and its potential application of two esterases derived from the arctic sediment metagenome. Mar. Biotechnol. (NY) 11: 307-316. https://doi.org/10.1007/s10126-008-9145-2
  15. Kim, Y. J., G. S. Choi, S. B. Kim, G. S. Yoon, Y. S. Kim, and Y. W. Ryu. 2006. Screening and characterization of a novel esterase from a metagenomic library. Protein Expr. Purif. 45: 315-323. https://doi.org/10.1016/j.pep.2005.06.008
  16. Kimura, M., I. Kaneko, M. Komiyama, A. Takatsuki, H. Koshino, K. Yoneyama, and I. Yamaguchi. 1998. Trichothecene 3-O-acetyltransferase protects both the producing organism and transformed yeast from related mycotoxins. Cloning and characterization of Tri101. J. Biol. Chem. 273: 1654-1661. https://doi.org/10.1074/jbc.273.3.1654
  17. Kneusel, R. E., E. Schiltz, and U. Matern. 1994. Molecular characterization and cloning of an esterase which inactivates the macrolide toxin brefeldin A. J. Biol. Chem. 269: 3449-3456.
  18. Lee, M. H., K. S. Hong, S. Malhotra, J. H. Park, E. C. Hwang, H. K. Choi, Y. S. Kim, W. Tao, and S. W. Lee. 2010. A new esterase EstD2 isolated from plant rhizosphere soil metagenome. Appl. Microbiol. Biotechnol. 88: 1125-1134. https://doi.org/10.1007/s00253-010-2729-6
  19. Lee, S. W., L. 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
  20. Lewis, E. A., T. L. Adamek, L. C. Vining, and R. L. White. 2003. Metabolites of a blocked chloramphenicol producer. J. Nat. Prod. 66: 62-66. https://doi.org/10.1021/np020306e
  21. Lim, H. K., E. J. Chung, J. C. Kim, G. J. Choi, K. 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
  22. Mandrich, L., V. Menchise, V. Alterio, G. D. Simone, C. Pedone, M. Rossi, and G. Manco. 2008. Functional and structural features of the oxyanion hole in a thermophilic esterase from Alicyclobacillus acidocaldarius. Proteins 71: 1721-1731.
  23. McCormick, S. P. and N. J. Alexander. 2002. Fusarium Tri8 encodes a trichothecene C-3 esterase. Appl. Environ. Microbiol. 68: 2959-2964. https://doi.org/10.1128/AEM.68.6.2959-2964.2002
  24. Nakagawa, Y., Y. Nitahara, and S. Miyamura. 1979. Kinetic studies on enzymatic acetylation of chloramphenicol in Streptococcus faecalis. Antimicrob. Agents Chemother. 16: 719-723. https://doi.org/10.1128/AAC.16.6.719
  25. Nakano, H., Y. Matsuhashi, T. Takeuchi, and H. Umezawa. 1977. Distribution of chloramphenicol acetyltransferase and chloramphenicol-3-acetate esterase among Streptomyces and Corynebacterium. J. Antibiot. (Tokyo) 30: 76-82. https://doi.org/10.7164/antibiotics.30.76
  26. Ping, L., R. Buchler, A. Mithofer, A. Svatos, D. Spiteller, K. Dettner, et al. 2007. A novel Dps-type protein from insect gut bacteria catalyses hydrolysis and synthesis of N-acyl amino acids. Environ. Microbiol. 9: 1572-1583. https://doi.org/10.1111/j.1462-2920.2007.01279.x
  27. Pongs, O. 1979. Chloramphenicol. pp. 26-42. In F. E. Hahn (ed.). Antibiotics: Mechanism of Action of Antibacterial Agents. Springer-Verlag, Berlin.
  28. Rhee, J. K., D. G. Ahn, Y. G. Kim, and J. W. Oh. 2005. New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library. Appl. Environ. Microbiol. 71: 817-825. https://doi.org/10.1128/AEM.71.2.817-825.2005
  29. Riaz, K., C. Elmerich, D. Moreira, A. Raffoux, Y. Dessaux, and D. Faure. 2008. A metagenomic analysis of soil bacteria extends the diversity of quorum-quenching lactonases. Environ. Microbiol. 10: 560-570. https://doi.org/10.1111/j.1462-2920.2007.01475.x
  30. Shaw, W. V. 1983. Chloramphenicol acetyltransferase: Enzymology and molecular biology. Crit. Rev. Biochem. 14: 1-46. https://doi.org/10.3109/10409238309102789
  31. Sohaskey, C. D. 2004. Enzymatic inactivation and reactivation of chloramphenicol by Mycobacterium tuberculosis and Mycobacterium bovis. FEMS. Microbiol. Lett. 240: 187-192. https://doi.org/10.1016/j.femsle.2004.09.028
  32. Sohaskey, C. D. and A. G. Barbour. 1999. Esterases in serumcontaining growth media counteract chloramphenicol acetyltransferase activity in vitro. Antimicrob. Agents Chemother. 43: 655-660.
  33. Sohaskey, C. D. and A. G. Barbour. 2000. Spirochaeta aurantia has diacetyl chloramphenicol esterase activity. J. Bacteriol. 182: 1930-1934. https://doi.org/10.1128/JB.182.7.1930-1934.2000
  34. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24: 1596-1599. https://doi.org/10.1093/molbev/msm092
  35. Zhou, J., M. A. Bruns, and J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62: 316-322.

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