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The search for the ideal biocatalyst

Abstract

While the use of enzymes as biocatalysts to assist in the industrial manufacture of fine chemicals and pharmaceuticals has enormous potential, application is frequently limited by evolution-led catalyst traits. The advent of designer biocatalysts, produced by informed selection and mutation through recombinant DNA technology, enables production of process-compatible enzymes. However, to fully realize the potential of designer enzymes in industrial applications, it will be necessary to tailor catalyst properties so that they are optimal not only for a given reaction but also in the context of the industrial process in which the enzyme is applied.

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Figure 1: The paradigm shift?

© Bob Crimi

Figure 2: Contributions to the design of the ideal biotransformation process.

© Bob Crimi

Figure 3: Temperature/activity profiles for caseinolytic activities of extracellular proteases from different thermal sources.
Figure 4: Moving around in sequence space.

© Bob Crimi

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Elizabeth L. Bell, William Finnigan, … Sabine L. Flitsch

References

  1. Halling, P.J. Biocatalysis in low-water media: understanding effects of reaction conditions. Curr. Opin. Chem. Biol. 4, 74–80 (2000).

    CAS  PubMed  Google Scholar 

  2. Wangikar, P.P, Michels, Clark, D.S. & Dordick, J.S. Structure and function of subtilisin BPN solubilized in organic solvents. J. Am. Chem. Soc. 119, 70–76 (1997).

    CAS  Google Scholar 

  3. Kazlauskas, R.J. Molecular modelling and biocatalysis: explanations, predictions, limitations and opportunities. Curr. Opin. Chem. Biol. 4, 81–88 (2000).

    CAS  PubMed  Google Scholar 

  4. Selleck, G.A. & Chaudhuri, J. B. Biocatalysis in organic media using enzymes from extremophiles. Enzyme Microb. Technol. 25, 471–482 (1999).

    Google Scholar 

  5. Schmitke, J.L., Stern, L.J. & Klibanov, A.M. The crystal structure of subtilisin Carlsberg in anhydrous dioxane and its comparison with those in water and acetonitrile. Proc. Natl. Acad. Sci. USA 94, 4250–4255 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Aguilar, C.F. et al. Crystal structure of the β-galactosidase from the hyperthermophilic archaeon Sulfolobus solfaricus: resilience as a key factor in thermostability. J. Mol. Biol. 271, 789–802 (1997).

    CAS  PubMed  Google Scholar 

  7. Villeret, V. et al. The crystal structure of Pyrococcus furiosus ornithine carbamoyltransferase reveals a key role for oligomerisation in enzyme stability at extremely high temperatures. Proc. Natl. Acad. Sci. USA 95, 2801–2806 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Martin A.B. & Schulze, P.G. Opportunities at the interface of chemistry and biology. Trends Biochem. Sci.. 24, M24–M28 (1999).

    Google Scholar 

  9. Arnold, F.H. & Volkov, A.A. Directed evolution of biocatalysts. Curr. Opin. Chem. Biol. 3, 54–59 (1999).

    CAS  PubMed  Google Scholar 

  10. Arnold, F.H. Design by directed evolution. Acc. Chem Res. 31, 125–131 (1998).

    CAS  Google Scholar 

  11. Affholter, J. & Arnold, F.H. Engineering a revolution. ChemTech. 26, 34–39 (1999).

    Google Scholar 

  12. Tapolczay, D.J., Kobylecki, R.J., Payne, L.J. & Hall, B. Extracting order from chaos. Chem. Ind. 19, 772–775 (1998).

    Google Scholar 

  13. Woodley, J.M. & Lilly, M.D. Process engineering of two-liquid phase biocatalysis. Prog. Biotechnol. 8, 147–154 (1992).

    CAS  Google Scholar 

  14. Wandrey, C., Liese, A. & Kihumbu, D. Industrial biocatalysis: past, present and future. Org. Process Res. Dev. 4, 286–290 (2000).

    CAS  Google Scholar 

  15. Flitsch, S.L., Aitken, S.J., Cho, C.S.Y., Grogan, G. & Staines, A. Biohydroxylation reactions catalysed by enzymes and whole-cell systems. Bioorg. Chem. 27, 81–90 (1999).

    CAS  Google Scholar 

  16. Sette, L., Lanzarini, G. & Pifferi, P.G. Whole cell biocataysis for an oil desulphurization process. Fuel Process. Technol. 52, 145–153 (1997).

    Google Scholar 

  17. Woodley, J.M. & Lilly, M.D. Biotransformation reactor selection and operation. In Applied biocatalysis. (eds Cabral, J.M.S., Best, D., Boross L. & Tramper J.) 371–393 (Harwood Academic, London; 1994).

    Google Scholar 

  18. Chauhan, R.P. & Woodley, J.M. Increasing the productivity of bioconversion processes. ChemTech 27, 26–30 (1997)

    CAS  Google Scholar 

  19. Shanklin, J. Exploring the possibilities presented by protein engineering. Curr. Opin. Plant Biol. 3, 243–248 (2000)

    CAS  PubMed  Google Scholar 

  20. Tischer, W. & Kasche, V. Immobilised enzymes: crystals or carriers? Trends Biotechnol. 17, 326–335 (1999).

    CAS  PubMed  Google Scholar 

  21. Adlercreutz, P. On the importance of the support material for enzymatic synthesis in organic media—support effects at controlled water activity. Eur. J. Biochem. 199, 609–614 (1991).

    CAS  PubMed  Google Scholar 

  22. Kim, J. & Dordick, J.S. Unusual salt and solvent tolerance of a protease from an extreme halophile. Biotechnol. Bioeng. 55, 471–479 (1997).

    CAS  PubMed  Google Scholar 

  23. Toba, S. & Mez, K.M. The concept of solvent compatibility and its impact on protein stability and activity enhancement in non-aqueous solvents. J. Am. Chem. Soc. 119, 9939–9948 (1997).

    CAS  Google Scholar 

  24. Jaeger, K.-E. & Reetz, M.T. Directed evolution of enantioselective enzymes for organic chemistry. Curr. Opin. Chem. Biol. 4, 68–73 (2000).

    CAS  PubMed  Google Scholar 

  25. Altamirano, M.M., Blackburn, J.M., Aguayo, C. & Fersht, AR. Directed evolution of a new catalytic activity using alpha/beta barrel scaffold. Nature 403, 617–622 (2000).

    CAS  PubMed  Google Scholar 

  26. May, O., Nguyen, P.T., & Arnold, F.H. Inverting enantioselectivity and increasing total activity of a key enzyme in a multi-enzyme synthesis creates a viable process for production of l-methionine. Nat. Biotechnol. 18, 317–320 (2000).

    CAS  PubMed  Google Scholar 

  27. Kumamaru, T., Suenaga, H., Watanabe, T. & Furukawa, K. Enhanced degradation of polychlorinated biphenyls by directed evolution of biphenyl dioxygenase. Nat. Biotechnol. 16, 663–666 (1998).

    CAS  PubMed  Google Scholar 

  28. Hough, D. & Danson, M.J. Extremozymes. Curr. Opin. Chem. Biol. 3, 39–36 (1999).

    CAS  PubMed  Google Scholar 

  29. Daniel, R.M. & Cowan, D.A. Biomolecular stability and life at high temperatures. Cell. Mol. Life Sci. 57, 250–264 (2000)

    CAS  PubMed  Google Scholar 

  30. Jaenicke, R. & Bohm, G. The stability of proteins in extreme environments. Curr. Opin. Struct. Biol. 8, 738–748 (1998).

    CAS  PubMed  Google Scholar 

  31. Lee, B. & Vasmatzis, G. Stabilization of protein structures. Curr. Opin. Biotechnol.. 8, 423–428 (1999).

    Google Scholar 

  32. Kuchner, O. & Arnold, F.H. Directed evolution of enzyme catalysts. Trends Biotechnol. 15, 523–530 (1997).

    CAS  PubMed  Google Scholar 

  33. Giver, L., Gershenson, A, Freskard, P.O. & Arnold, F.H. Directed evolution of a thermostable esterase. Proc. Natl. Acad. Sci. USA 95, 12809–12813 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Van den Burg, B., Vriend, G., Venema, O.R. & Eijsink, V.G. Engineering an enzyme to resist boiling. Proc. Natl. Acad. Sci. USA 95, 2056–2060 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Daniel, R.M., Cowan, D.A., Curran, M. & Morgan, H.W. A correlation between protein thermostability and susceptibility to proteolysis. Biochem. J. 207, 641–644 (1982).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Owusu, R.K. & Cowan, D.A. A correlation between microbial protein thermostability and resistance to denaturation in aqueous–organic solvent two-phase systems. Enz. Microb. Technol. 11, 568–574 (1989).

    CAS  Google Scholar 

  37. Richins, R.D., Kaneva, I., Mulchandari, A., & Chen, W. Biodegradation of organophosphorus pesticides by surface-expressed organophosphorus hydrolase. Nat. Biotechnol. 15, 984–987 (1997).

    CAS  PubMed  Google Scholar 

  38. Jung, H.C., Lebeault, J.M. & Pan, J.G. Surface display of Zymomonas mobilis levansucrase by using ice-nucleation protein of Pseudomonas syringae. Nat. Biotechnol. 16, 576–580 (1998).

    CAS  PubMed  Google Scholar 

  39. Blanco, R.M. &, Guisan, J.M. Stabilization of enzymes by multipoint covalent attachment to agarose aldehyde gels—borohydride reduction of trypsin agarose derivatives. Enz. Microb. Technol. 11, 360–366 (1989).

    CAS  Google Scholar 

  40. Häring, D. & Schreier, P. Cross-linked enzyme crystals. Curr. Opin. Chem. Biol. 3, 35–38 (1999).

    PubMed  Google Scholar 

  41. Stemmer, W.P.C. Searching sequence space—using recombination to search more efficiently and thoroughly instead of making bigger combinatorial libraries. Bio/Technol. 13, 549–553 (1995).

    CAS  Google Scholar 

  42. Amann, R.I., Ludwig, W. & Schleiffer K.H. Phylogenetic identification and in-situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143–169 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Cottrell, M.T., Moore, J.A. & Kirchman, D.L. Chitinases from uncultured marine microorganisms. Appl. Environ. Microbiol. 65, 2553–2557 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Cowan, D.A. Microbial genomes-the untapped resource. Trends Biotechnol. 18, 14–16 (2000).

    CAS  PubMed  Google Scholar 

  45. Henne, A., Schmitz, R.A., Bömeke, M., Gottschalk, G. & Daniel, R. Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli. Appl. Environ. Microbiol. 66, 3113–3116 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Rondon, M.R. et al. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66, 2541–2547 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Petrounia, I.P. & Arnold, F.H. Designed evolution of enzymatic properties. Curr. Opin. Biotechnol. 11, 325–330 (2000).

    CAS  PubMed  Google Scholar 

  48. Jaenicke, R. & Bohm, G. The stability of proteins in extreme environments. Curr. Opin. Struct. Biol. 8, 738–748 (1998).

    CAS  PubMed  Google Scholar 

  49. Malakauskas, S.M. & Mayo, S.L. Design, structure and stability of a hyperthermophilic protein variant. Nat. Struct. Biol. 5, 470–475 (1998).

    CAS  PubMed  Google Scholar 

  50. Chen K. & Arnold, F. Tuning the activity of an enzyme for unusual environments: sequential random mutagenesis of subtilisin E for catalysis in dimethylformamide. Proc. Natl. Acad. Sci. USA 90, 5618–5622 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Wehtje, E. & Adlercreutz, P. Water activity and substrate concentration effects on lipase activity. Biotechnol. Bioeng. 55, 798–806 (1997).

    CAS  PubMed  Google Scholar 

  52. Burton, S.G., Duncan, J.R., Kaye P.T. & Rose P.D. Activity of mushroom polyphenol oxidase in organic medium. Biotechnol. Bioeng. 42, 938–946 (1994).

    Google Scholar 

  53. Reimann, A., Robb, D.A. & Halling, P.J. Solvation of CBZ–amino acid nitrophenyl esters in organic media and the kinetics of their transesterification by subtilisin. Biotechnol. Bioeng. 43, 1081–1086 (1994).

    CAS  PubMed  Google Scholar 

  54. Khemelnitsky, Y.L., Welch, S.H., Clark, D.S & Dordick, D.S. Salts dramatically enhance activity of enzymes suspended in organic solvents. J. Am. Chem. Soc. 116, 2647–2648 (1994).

    Google Scholar 

  55. Ru, M.T., Dordick, J.S., Reimer, J.A. & Clark, D.S. Optimising the salt-induced activation of enzymes in organic solvents: effects of lyophilisation time and water content. Biotechnol. Bioeng. 63, 233–241 (1999).

    CAS  PubMed  Google Scholar 

  56. Schmid, A., Dordick, J.S., Haven, B., Wubbolts, M. & Witholt, B. Industrial biocatalysis today and tomorrow. Nature 409, 258–268 (2001).

    CAS  PubMed  Google Scholar 

  57. Liese, A., Seelbach, K. & Wandrey, C. Industrial biotransformations. (Wiley-VCH, Weinheim, Germany; 2000).

    Google Scholar 

  58. Wang, P., Sergeeva, M.V., Lim, L. & Dordick J.S. Biocatalyst plastics as active and stable materials for biotransformations. Nat. Biotechnol. 15, 789–793 (1997).

    CAS  PubMed  Google Scholar 

  59. Partridge, J., Halling, P.J. & Moore, B.D. Practical route to high activity enzyme preparations for synthesis in organic media. Chem. Commun. 7, 841–842 (1998).

    Google Scholar 

  60. Rich, J.O. & Dordick, J.S. Controlling subtilisin activity and selectivity in organic media by imprinting with nucleophilic substrates. J. Am. Chem. Soc. 119, 3245–3252 (1997).

    CAS  Google Scholar 

  61. Slade C.J. & Vulfson, E.N. Induction of catalytic activity in proteins by lyophilization in the presence of a transition state analogue. Biotechnol. Bioeng. 57, 211–215 (1998).

    CAS  PubMed  Google Scholar 

  62. Reetz, M.T., Zonta, A., Schimossek, K., Liebeton, K. & Jaeger, K.-E. Creation of enantioselective biocatalysts for organic chemistry by in vitro evolution. Angew. Chem., Int. Edn. Engl. 36, 2830–2833 (1997).

    CAS  Google Scholar 

  63. Bornscheuer, U.T, Altenbuchner, J. & Meyer, H.H. Directed evolution of an esterase for the stereoselective resolution of a key intermediate in synthesis of epithilones. Biotechnol. Bioeng. 58, 554–559 (1998).

    CAS  PubMed  Google Scholar 

  64. Sutherland, J.D. Evolutionary optimization of enzymes. Curr. Opin. Chem. Biol. 4, 263–269 (2000).

    CAS  PubMed  Google Scholar 

  65. Broun, P., Shanklin, J., Whittle, E. & Somerville, C. Catalytic plasticity of fatty acid modification enzymes underlying chemical diversity of plant lipids. Science 282, 1315–1317 (1998).

    CAS  PubMed  Google Scholar 

  66. Zhang, J.H., Dawes, G., & Stemmer, W.P. Directed evolution of a fucosidase from a galactosidase by DNS shuffling and screening. Proc. Natl. Acad. Sci. USA 94, 4504–4509 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  67. Zhao, H. & Arnold, F. Directed evolution converts subtilisin E into a functional equivalent of thermitase. Protein Eng. 12, 47–52 (1999).

    CAS  PubMed  Google Scholar 

  68. Fernandez-Lafuente, R., Cowan, D.A. & Wood, A.N.P. Hyperstabilisation of a thermophilic esterase by multipoint covalent attachment. Enz. Microb. Technol. 17, 366–372 (1995).

    Google Scholar 

  69. Kazan, D., Ertan, H. & Eraslan, A. Stabilisation of Escherichia coli penicillin G acylase against thermal inactivation by cross-linking with dextran dialdehyde polymers. Appl. Microbiol. Biotechnol. 48, 191–197 (1997).

    CAS  PubMed  Google Scholar 

  70. Häring, D. & Schreier, P. Novel biocatalysts by chemical modification of known enzymes: cross-linked microcrystals of the semi-synthetic peroxidase seleno-subtilisin. Agnew. Chem. Int. Edn. Engl. 37, 2471–2473 (1998).

    Google Scholar 

  71. Mori, T. & Okahata, Y. A variety of lipid-coated glycoside hydrolases as effective glycosyl transfer catalysts in homogenous organic solvents. Tetrahedron Lett. 38, 1971–1974 (1997).

    CAS  Google Scholar 

  72. Jene, O., Pearson, J.C. & Lowe, C.R. Surfactant modified enzymes: solubility and activity of surfactant-modified catalase in organic solvents. Enz. Microb. Technol. 20, 69–74 (2000).

    Google Scholar 

  73. Moore, J.C. & Arnold, F.H. Directed evolution of a para-nitrobenzyl esterase for aqueous–organic solvents. Nat. Biotechnol. 14, 458–462 (1996).

    CAS  PubMed  Google Scholar 

  74. Bull, A.T., Goodfellow, M. & Slater, J.H. Biodiversity as a source of innovation in biotechnology. Ann. Rev. Microbiol. 46, 219–252 (1992)

    CAS  Google Scholar 

  75. Margesin, R. & Schinner, F. Characterization of a metalloprotease from psychrophilic Xanthomonas maltophilia. FEMS Microbiol. Lett. 79, 257–261 (1991).

    CAS  Google Scholar 

  76. Giménez, M.I., Studdert, C.A., Sánchez, J.J. & De Castro, R.E. Extracellular protease of Natrialba magadii: purification and biochemical characterisation. Extremophiles 4, 181–188 (2000).

    PubMed  Google Scholar 

  77. Cowan, D.A. & Daniel, R.M. Purification and some properties of an extracellular protease (Caldolysin) from an extreme thermophile. Biochim. Biophys. Acta. 705, 293–305 (1982).

    CAS  PubMed  Google Scholar 

  78. Cowan, D.A., Smolenski, K.A., Daniel, R.M. & Morgan, H.W. An extremely thermostable extracellular protease from a strain of the archaebacterium Desulfurococcus growing at 88°C. Biochem. J. 247, 121–133 (1987).

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The authors gratefully acknowledge the financial support for their research from the UK Biotechnology and Biological Sciences Research Council and the South African National Research Foundation.

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Burton, S., Cowan, D. & Woodley, J. The search for the ideal biocatalyst. Nat Biotechnol 20, 37–45 (2002). https://doi.org/10.1038/nbt0102-37

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