A Cold-Adapted Epoxide Hydrolase from a Strict Marine Bacterium, Sphingophyxis alaskensis

  • Kang, Ji-Hyun (Marine Biotechnology Research Centre, Korea Ocean Research and Development Institute) ;
  • Woo, Jung-Hee (Marine Biotechnology Research Centre, Korea Ocean Research and Development Institute) ;
  • Kang, Sung-Gyun (Marine Biotechnology Research Centre, Korea Ocean Research and Development Institute) ;
  • Hwang, Young-Ok (Marine Biotechnology Research Centre, Korea Ocean Research and Development Institute) ;
  • Kim, Sang-Jin (Marine Biotechnology Research Centre, Korea Ocean Research and Development Institute)
  • Published : 2008.08.31

Abstract

An open reading frame (ORF) encoding a putative epoxide hydrolase (EHase) was identified by analyzing the genome sequence of Sphingophyxis alaskensis. The EHase gene (seh) was cloned and expressed in E. coli. To facilitate purification, the gene was fused in-frame to 6$\times$ histidine at the C-terminus. The recombinant EHase (rSEH) was highly soluble and could be purified to apparent homogeneity by one step of metal affinity chromatography. The purified SEH displayed hydrolyzing activities toward various epoxides such as styrene oxide, glycidyl phenyl ether, epoxyhexane, epoxybutane, epichlorohydrin, and epifluorohydrin. The optimum activity toward styrene oxide was observed at pH 6.5 and $35^{\circ}C$. The purified SEH showed a cold-adapted property, displaying more than 40% of activity at low temperature of $10^{\circ}C$ compared with the optimum activity. Despite the catalytic efficiency, the purified SEH did not hydrolyze various epoxides enantioselectively. $K_m$ and $k_{cat}$ of SEH toward (R)-styrene oxide were calculated as 4$\pm$0.3 mM and 7.42$s^{-1}$ respectively, whereas $K_m$ and $k_{cat}$ of SEH toward (S)-styrene oxide were 5.25$\pm$0.3 mM and 10.08$s^{-1}$ respectively.

Keywords

References

  1. Arahira, M., V. H. Nong, K. Udaka, and C. Fukazawa. 2000. Purification, molecular cloning and ethylene-inducible expression of a soluble-type epoxide hydrolase from soybean (Glycine max [L.] Merr.). Eur. J. Biochem. 267: 2649-2657 https://doi.org/10.1046/j.1432-1327.2000.01276.x
  2. Arand, M., H. Hemmer, H. Durk, J. Baratti, A. Archelas, R. Furstoss, and F. Oesch. 1999. Cloning and molecular characterization of a soluble epoxide hydrolase from Aspergillus niger that is related to mammalian microsomal epoxide hydrolase. Biochem. J. 344: 273-280 https://doi.org/10.1042/0264-6021:3440273
  3. Arand, M., H. Wagner, and F. Oesch. 1996. Asp333, Asp495, and His523 form the catalytic triad of rat soluble epoxide hydrolase. J. Biol. Chem. 271: 4223-4229 https://doi.org/10.1074/jbc.271.8.4223
  4. Archelas, A. and R. Furstoss. 1997. Synthesis of enantiopure epoxides through biocatalytic approaches. Annu. Rev. Microbiol. 51: 491-525 https://doi.org/10.1146/annurev.micro.51.1.491
  5. Archelas, A. and R. Furstoss. 2001. Synthetic applications of epoxide hydrolases. Curr. Opin. Chem. Biol. 5: 112-119 https://doi.org/10.1016/S1367-5931(00)00179-4
  6. Bhatnagar, T., K. M. Manoj, and J. C. Baratti. 2001. A spectrophotometric method to assay epoxide hydrolase activity. J. Biochem. Biophys. Methods 50: 1-13 https://doi.org/10.1016/S0165-022X(01)00162-2
  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 https://doi.org/10.1016/0003-2697(76)90527-3
  8. Falany, C. N., P. McQuiddy, and C. B. Kasper. 1987. Structure and organization of the microsomal xenobiotic epoxide hydrolase gene. J. Biol. Chem. 262: 5924-5930
  9. Giovannoni, S. J. and U. Stingl. 2005. Molecular diversity and ecology of microbial plankton. Nature 437: 343-348 https://doi.org/10.1038/nature04158
  10. Hwang, S. H., H. J. Hyun, B. J. Lee, Y. S. Park, C. Y. Choi, J. Han, and H. Joo. 2006. Screening from the genome database: Novel epoxide hydrolase from Caulobacter crescentus. J. Microbiol. Biotechnol. 16: 32-36
  11. Hwang, Y.-O., S. G. Kang, J.-H. Woo, K. K. Kwon, T. Sato, E. Y. Lee, M. S. Han, and S.-J. Kim. 2008. Screening enantioselective epoxide hydrolase activities from marine microorganisms: Detection of activities in Erythrobacter spp. Marine Biotechnol. (in press)
  12. Janssen, D. B., F. Pries, J. van der Ploeg, B. Kazemier, P. Terpstra, and B. Witholt. 1989. Cloning of 1,2-dichloroethane degradation genes of Xanthobacter autotrophicus GJ10 and expression and sequencing of the dhlA gene. J. Bacteriol. 171: 6791-6799 https://doi.org/10.1128/jb.171.12.6791-6799.1989
  13. Kim, J.-T., S. G. Kang, J.-H. Woo, J.-H. Lee, B. C. Jeong, and S.-J. Kim. 2007. Screening and its potential application of lipolytic activity from a marine environment: Characterization of a novel esterase from Yarrowia lipolytica CL180. Appl. Microbiol. Biotechnol. 74: 820-828 https://doi.org/10.1007/s00253-006-0727-5
  14. Kim, Y. J., H. S. Lee, S. S. Bae, J. H. Jeon, J. K. Lim, Y. Cho, et al. 2007. Cloning, purification, and characterization of a new DNA polymerase from a hyperthermophilic archaeon, Thermococcus sp. NA1. J. Microbiol. Biotechnol. 17: 1090-1097
  15. Knehr, M., H. Thomas, M. Arand, T. Gebel, H. D. Zeller, and F. Oesch. 1993. Isolation and characterization of a cDNA encoding rat liver cytosolic epoxide hydrolase and its functional expression in Escherichia coli. J. Biol. Chem. 268: 17623-17627
  16. Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5: 150-163 https://doi.org/10.1093/bib/5.2.150
  17. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680-685 https://doi.org/10.1038/227680a0
  18. Lim, J. K., H. S. Lee, Y. J. Kim, S. S. Bae, J. H. Jeon, S. G. Kang, and J.-H. Lee. 2007. Critical factors to high thermostability of an alpha-amylase from hyperthermophilic archaeon Thermococcus onnurineus NA1. J. Microbiol. Biotechnol. 17: 1242-1248
  19. Misawa, E., C. K. Chion, I. V. Archer, M. P. Woodland, N. Y. Zhou, S. F. Carter, D. A. Widdowson, and D. J. Leak. 1998. Characterisation of a catabolic epoxide hydrolase from a Corynebacterium sp. Eur. J. Biochem. 253: 173-183 https://doi.org/10.1046/j.1432-1327.1998.2530173.x
  20. Nardini, M. and B. W. Dijkstra. 1999. $\alpha$/$\beta$ hydrolase fold enzymes: The family keeps growing. Curr. Opin. Struct. Biol. 9: 732-737 https://doi.org/10.1016/S0959-440X(99)00037-8
  21. Ollis, D. L., E. Cheah, M. Cygler, B. Dijkstra, F. Frolow, S. M. Franken, et al. 1992. The $\alpha$/$\beta$ hydrolase fold. Protein Eng. 5: 197-211 https://doi.org/10.1093/protein/5.3.197
  22. Oppenheimer, C. H. and C. E. ZoBell. 1952. The growth and viability of sixty-three species of marine bacteria as influenced by hydrostatic pressure. J. Mar. Res. 11: 10-18
  23. Park, S.-Y., J.-T. Kim, S. G. Kang, J.-H. Woo, J.-H. Lee, H.-T. Choi, and S.-J. Kim. 2007. A new esterase showing similarity to putative dienelactone hydrolase from a strict marine bacterium, Vibrio sp. GMD509. Appl. Microbiol. Biotechnol. 77: 107-115 https://doi.org/10.1007/s00253-007-1134-2
  24. Rink, R., M. Fennema, M. Smids, U. Dehmel, and D. B. Janssen. 1997. Primary structure and catalytic mechanism of the epoxide hydrolase from Agrobacterium radiobacter AD1. J. Biol. Chem. 272: 14650-14657 https://doi.org/10.1074/jbc.272.23.14650
  25. Rink, R., J. H. L. Spelberg, R. J. Pieters, J. Kingma, M. Nardini, R. M. Kellogg, B. W. Dijkstra, and D. B. Janssen. 1999. Mutation of tyrosine residues involved in the alkylation half reaction of epoxide hydrolase from Agrobacterium radiobacter AD1 results in improved enantioselectivity. J. Am. Chem. Soc. 121: 7417-7418 https://doi.org/10.1021/ja990501o
  26. Rink, R., J. Kingma, J. H. Spelberg, and D. B. Janssen. 2000. Tyrosine residues serve as proton donor in the catalytic mechanism of epoxide hydrolase from Agrobacterium radiobacter. Biochemistry 39: 5600-5613 https://doi.org/10.1021/bi9922392
  27. Sambrook, J. and D. W. Russell. 2001. Molecular Cloning: A Laboratory Manual, 3rd Ed. Vol 2, pp. 8.65-8.71. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
  28. Stapleton, A., J. K. Beetham, F. Pinot, J. E. Garbarino, D. R. Rockhold, M. Friedman, B. D. Hammock, and W. R. Belknap. 1994. Cloning and expression of soluble epoxide hydrolase from potato. Plant J. 6: 251-258 https://doi.org/10.1046/j.1365-313X.1994.6020251.x
  29. Straathof, A. J. J. and J. A. Jongejan. 1997. The enantiomeric ratio: Origin, determination and prediction. Enzyme Microb. Tech. 21: 559-571 https://doi.org/10.1016/S0141-0229(97)00066-5
  30. Strausberg, R. L., E. A. Feingold, L. H. Grouse, J. G. Derge, R. D. Klausner, F. S. Collins, et al. 2002. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc. Natl. Acad. Sci. USA 99: 16899-16903
  31. Thompson, J. D., D. G. Higgin, and T. J. Gibson. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680 https://doi.org/10.1093/nar/22.22.4673
  32. Tokunaga, M., J. F. Larrow, F. Kakiuchi, and E. N. Jacobsen. 1997. Asymmetric catalysis with water: Efficient kinetic resolution of terminal epoxides by means of catalytic hydrolysis. Science 277: 936-938 https://doi.org/10.1126/science.277.5328.936
  33. van Loo, B., J. Kingma, M. Arand, M. G. Wubbolts, and D. B. Janssen. 2006. Diversity and biocatalytic potential of epoxide hydrolases identified by genome analysis. Appl. Environ. Microbiol. 72: 2905-2917 https://doi.org/10.1128/AEM.72.4.2905-2917.2006
  34. van Loo, B., J. H. L. Spelberg, J. Kingma, T. Sonke, M. G. Wubbolts, and D. B. Janssen. 2004. Directed evolution of epoxide hydrolase from A. radiobacter toward higher enantioselectivity by error-prone PCR and DNA shuffling. Chem. Biol. 11: 981-990 https://doi.org/10.1016/j.chembiol.2004.04.019
  35. Venter, J. C., K. Remington, J. F. Heidelberg, A. L. Halpern, D. Rusch, J. A. Eisen, et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74 https://doi.org/10.1126/science.1093857
  36. Visser, H., J. A. M. de Bont, and J. C. Verdoes. 1999. Isolation and characterization of the epoxide hydrolase-encoding gene from Xanthophyllomyces dendrorhous. Appl. Environ. Microbiol. 65: 5459-5463
  37. Visser, H., S. Vreugdenhil, J. A. M. de Bont, and J. C. Verdoes. 2000. Cloning and characterization of an epoxide hydrolaseencoding gene from Rhodotorula glutinis. Appl. Microbiol. Biotechnol. 53: 415-419 https://doi.org/10.1007/s002530051635
  38. Weijers, C. A. G. M. and J. A. M. de Bont. 1999. Epoxide hydrolases from yeasts and other sources: Versatile tools in biocatalysis. J. Mol. Catal. B Enzym. 6: 199-214 https://doi.org/10.1016/S1381-1177(98)00123-4
  39. Woo, J.-H., O.-K. Hwang, S. G. Kang, H. S. Lee, J. Cho, and S.-J. Kim. 2007. Cloning and characterization of three novel epoxide hydrolases from a marine bacterium, Erythrobacter litoralis HTCC2594. Appl. Microbiol. Biotechnol. 76: 365-375 https://doi.org/10.1007/s00253-007-1011-z
  40. Yamada, T., C. Morisseau, J. E. Maxwell, M. A. Argiriadi, D. W. Christianson, and B. D. Hammock. 2000. Biochemical evidence for the involvement of tyrosine in epoxide activation during the catalytic cycle of epoxide hydrolase. J. Biol. Chem. 275: 23082-23088 https://doi.org/10.1074/jbc.M001464200
  41. Zou, J., B. M. Hallberg, T. Bergfors, F. Oesch, M. Arand, S. L. Mowbray, and T. A. Jones. 2000. Structure of Aspergillus niger epoxide hydrolase at 1.8 A resolution: Implications for the structure and function of the mammalian microsomal class of epoxide hydrolases. Structure 15: 111-122