Many Pathways in Laboratory Evolution Can Lead to Improved Enzymes: How to Escape from Local Minima

ChemBioChem

Volumn 13, Issue 7, 2012, Pages 1060-1066

  Gumulya, Yosephine ^a   Sanchis, Joaquin ^a   Reetz, Manfred T ^a,b  

^a MAX PLANCK INSTITUT FÜR KOHLENFORSCHUNG   (Germany)

^b PHILIPPS UNIVERSITY MARBURG   (Germany)

Author keywords

Directed evolution; Enantioselectivity; Enzyme catalysis; Fitness landscapes; Iterative saturation mutagenesis

Indexed keywords

ENZYME; EPOXIDE; EPOXIDE HYDROLASE;

ARTICLE; ASPERGILLUS NIGER; CATALYST; CHIRALITY; CODON; DNA TEMPLATE; ENZYME MECHANISM; HYDROLYSIS; MOLECULAR EVOLUTION; MUTAGENESIS; MUTANT; NONHUMAN; ORGANIC CHEMISTRY; PRIORITY JOURNAL; PROTEIN ENGINEERING; STEREOCHEMISTRY; THERMAL ANALYSIS;

AMINO ACID SEQUENCE; DIRECTED MOLECULAR EVOLUTION; ENZYMES; GENE LIBRARY; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS; MUTATION; PROTEIN ENGINEERING; STEREOISOMERISM;

ASPERGILLUS NIGER;

EID: 84860234014     PISSN: 14394227     EISSN: 14397633     Source Type: Journal    
DOI: 10.1002/cbic.201100784     Document Type: Article

References (71)

1. T. W. Johannes, H. Zhao, Curr. Opin. Microbiol. 2006, 9, 261-267;
2. Protein Engineering Handbook, Vols. 1-2 (Eds.: S. Lutz, U. T. Bornscheuer), Wiley-VCH, Weinheim, 2009;
3. N. J. Turner, Nat. Chem. Biol. 2009, 5, 567-573;
4. C. Jäckel, P. Kast, D. Hilvert, Annu. Rev. Biophys. 2008, 37, 153-173;
5. S. Bershtein, D. S. Tawfik, Curr. Opin. Chem. Biol. 2008, 12, 151-158;
6. P. A. Romero, F. H. Arnold, Nat. Rev. Mol. Cell Biol. 2009, 10, 866-876;
7. M. T. Reetz in Asymmetric Organic Synthesis with Enzymes (Eds.: V. Gotor, I. Alfonso, E. García-Urdiales), Wiley-VCH, Weinheim, 2008, pp. 21-63;
8. L. G. Otten, F. Hollmann, I. W. C. E. Arends, Trends Biotechnol. 2010, 28, 46-54;
9. A. V. Shivange, J. Marienhagen, H. Mundhada, A. Schenk, U. Schwaneberg, Curr. Opin. Chem. Biol. 2009, 13, 19-25;
10. A. S. Bommarius, J. K. Blum, M. J. Abrahamson, Curr. Opin. Chem. Biol. 2011, 15, 194-200.
11. Reviews covering protein engineering of thermostability:
12. T. Oshima, Curr. Opin. Struct. Biol. 1994, 4, 623-628;
13. C. Ó'Fágáin, Enzyme Microb. Technol. 2003, 33, 137-149;
14. V. G. H. Eijsink, S. Gåseidnes, T. V. Borchert, B. van den Burg, Biomol. Eng. 2005, 22, 21-30;
15. A. S. Bommarius, J. M. Broering, Biocatal. Biotransform. 2005, 23, 125-139;
16. N. Amin, A. D. Liu, S. Ramer, W. Aehle, D. Meijer, M. Metin, S. Wong, P. Gualfetti, V. Schellenberger, Protein Eng. Des. Sel. 2004, 17, 787-793;
17. P. L. Wintrode, F. H. Arnold, Adv. Protein Chem. 2001, 55, 161-225.
18. M. T. Reetz, Angew. Chem. 2011, 123, 144-182; Angew. Chem. Int. Ed. 2011, 50, 138-174.
19. K. Faber, Biotransformations in Organic Chemistry, 5th ed., Springer, Berlin, 2004;
20. Enzyme Catalysis in Organic Synthesis: A Comprehensive Handbook, Vols. I-III (Eds.: K. Drauz, H. Waldmann), 2nd ed., Wiley-VCH, Weinheim, 2002;
21. Industrial Biotransformations (Eds.: A. Liese, K. Seelbach, C. Wandrey), 2nd ed., Wiley-VCH, Weinheim, 2006;
22. J. Tao, G.-Q. Lin, A. Liese, Biocatalysis for the Pharmaceutical Industry, Wiley-VCH, Weinheim, 2009;
23. V. Gotor, I. Alfonso, E. García-Urdiales, Asymmetric Organic Synthesis with Enzymes, Wiley-VCH Weinheim, 2008.
24. S. Lutz, W. M. Patrick, Curr. Opin. Biotechnol. 2004, 15, 291-297.
25. M. R. Parikh, I. Matsumura, J. Mol. Biol. 2005, 352, 621-628.
26. R. J. Kazlauskas, U. T. Bornscheuer, Nat. Chem. Biol. 2009, 5, 526-5297.
27. R. J. Fox, G. W. Huisman, Trends Biotechnol. 2008, 26, 132-138.
28. M. T. Reetz, L.-W. Wang, M. Bocola, Angew. Chem. 2006, 118, 1258-1263, Erratum 2556; Angew. Chem. Int. Ed. 2006, 45, 1236-1241, Erratum 2494.
29. M. T. Reetz, J. D. Carballeira, Nat. Protoc. 2007, 2, 891-903.
30. M. T. Reetz, M. Bocola, J. D. Carballeira, D. Zha, A. Vogel, Angew. Chem. 2005, 117, 4264-4268; Angew. Chem. Int. Ed. 2005, 44, 4192-4196.
31. J. Zou, B. M. Hallberg, T. Bergfors, F. Oesch, M. Arand, S. L. Mowbray, T. A. Jones, Structure 2000, 8, 111-122.
32. M. T. Reetz, D. Kahakeaw, R. Lohmer, ChemBioChem 2008, 9, 1797-1804;
33. M. T. Reetz, D. Kahakeaw, J. Sanchis, Mol. BioSyst. 2009, 5, 115-122.
34. M. T. Reetz, M. Bocola, L.-W. Wang, J. Sanchis, A. Cronin, M. Arand, J. Zou, A. Archelas, A.-L. Bottalla, A. Naworyta, S. L. Mowbray, J. Am. Chem. Soc. 2009, 131, 7334-7343.
35. K. Engström, J. Nyhlén, A. G. Sandström, J.-E. Bäckvall, J. Am. Chem. Soc. 2010, 132, 7038-7042.
36. K. Okrasa, C. Levy, M. Wilding, M. Goodall, N. Baudendistel, B. Hauer, D. Leys, J. Micklefield, Angew. Chem. 2009, 121, 7827-7830; Angew. Chem. Int. Ed. 2009, 48, 7691-7694.
37. R. Hawwa, S. D. Larsen, K. Ratia, A. D. Mesecar, J. Mol. Biol. 2009, 393, 36-57.
38. L. Liang, J. Zhang, Z. Lin, Microb. Cell Fact. 2007, 6, 36.
39. M. R. M. De Groeve, M. De Baere, L. Hoflack, T. Desmet, E. J. Vandamme, W. Soetaert, Protein Eng. Des. Sel. 2009, 22, 393-399.
40. M.-W. Bhuiya, C.-J. Liu, J. Biol. Chem. 2010, 285, 277-285.
41. R. M. Kelly, H. Leemhuis, L. Dijkhuizen, Biochemistry 2007, 46, 11216-11222.
42. M. Ivancic, G. Valinger, K. Gruber, H. Schwab, J. Biotechnol. 2007, 129, 109-122.
43. D. F. Visser, F. Hennessy, J. Rashamuse, B. Pletschke, D. Brady, J. Mol. Catal. B 2011, 68, 279-285.
44. D. J. Bougioukou, S. Kille, A. Taglieber, M. T. Reetz, Adv. Synth. Catal. 2009, 351, 3287-3305.
45. M. T. Reetz, S. Prasad, J. D. Carballeira, Y. Gumulya, M. Bocola, J. Am. Chem. Soc. 2010, 132, 9144-9152.
46. H. Zheng, M. T. Reetz, J. Am. Chem. Soc. 2010, 132, 15744-15751.
47. S. Prasad, M. Bocola, M. T. Reetz, ChemPhysChem 2011, 12, 1550-1557.
48. Y. Miyauchi, R. Kourist, D. Uemura, K. Miyamoto, Chem. Commun. 2011, 47, 7503-7505;
49. M. A. Norrgård, B. Mannervik, J. Mol. Biol. 2011, 412, 111-120.
50. M. T. Reetz, J. Sanchis, ChemBioChem 2008, 9, 2260-2267.
51. M. T. Reetz, S. Wilensek, D. Zha, K.-E. Jaeger, Angew. Chem. 2001, 113, 3701-3703; Angew. Chem. Int. Ed. 2001, 40, 3589-3591.
52. M. T. Reetz, M. Puls, J. D. Carballeira, A. Vogel, K.-E. Jaeger, T. Eggert, W. Thiel, M. Bocola, N. Otte, ChemBioChem 2007, 8, 106-112.
53. S. Park, K. L. Morley, G. P. Horsman, M. Holmquist, K. Hult, R. J. Kazlauskas, Chem. Biol. 2005, 12, 45-54.
54. M. T. Reetz, S. Wu, Chem. Commun. 2008, 5499-5501;
55. A. G. Sandström, Y. Wikmark, K. Engstöm, J. Nyhlén, J.-E. Bäckvall, Proc. Natl. Acad. Sci. USA 2012, 109, 78-83.
56. K. U. Walter, K. Vamvaca, D. Hilvert, J. Biol. Chem. 2005, 280, 37742-37746.
57. Y. Gumulya, M. T. Reetz, ChemBioChem 2011, 12, 2502-2510;
58. for a probabilistic look at saturation mutagenesis, see: Y. Nov, Appl. Environ. Microbiol. 2012, 78, 258-262.
59. S. G. Peisajovich, D. S. Tawfik, Nat. Methods 2007, 4, 991-994.
60. M. A. DePristo, HFSP J. 2007, 1, 94-98.
61. M. Eigen, J. McCaskill, P. Schuster, J. Phys. Chem. 1988, 92, 6881-6891.
62. L. O. Emrén, S. Kurtovic, A. Runarsdottir, A.-K. Larsson, B. Mannervik, Proc. Natl. Acad. Sci. USA 2006, 103, 10866-10870;
63. S. Kurtovic, B. Mannervik, Biochemistry 2009, 48, 9330-9339.
64. R. E. Lenski, C. Ofria, R. T. Pennock, C. Adami, Nature 2003, 423, 139-144.
65. M. T. Reetz, H. Höbenreich, P. Soni, L. Fernández, Chem. Commun. 2008, 5502-5504;
66. Y. L. Boersma, M. J. Dröge, A. M. van der Sloot, T. Pijning, R. H. Cool, B. W. Dijkstra, W. J. Quax, ChemBioChem 2008, 9, 1110-1115.
67. D. M. Weinreich, N. F. Delaney, M. A. DePristo, D. L. Hartl, Science 2006, 312, 111-114;
68. F. J. Poelwijk, D. J. Kiviet, D. M. Weinreich, S. J. Tans, Nature 2007, 445, 383-386.
69. W. P. C. Stemmer, Nature 1994, 370, 389-391.
70. A. I. Khan, D. M. Dinh, D. Schneider, R. E. Lenski, T. F. Cooper, Science 2011, 332, 1193-1196.
71. M. L. M. Salverda, E. Dellus, F. A. Gorter, A. J. M. Debets, J. van der Oost, R. F. Hoekstra, D. S. Tawfik, J. A. G. M. de Visser, PLoS Genet. 2011, 7, e1001321.