Constructing and analyzing the fitness landscape of an experimental evolutionary process

ChemBioChem

Volumn 9, Issue 14, 2008, Pages 2260-2267

  Reetz, Manfred T ^a   Sanchis, Joaquin ^a  

^a MAX PLANCK INSTITUT FÜR KOHLENFORSCHUNG   (Germany)

Author keywords

Directed evolution; Enantioselectivity; Evolutionary pathways; Fitness landscape; Saturation mutagenesis

Indexed keywords

ARTICLE; BACTERIAL GENETICS; CONTROLLED STUDY; DIRECTED MOLECULAR EVOLUTION; ENANTIOSELECTIVITY; GENE MUTATION; GENETIC EPISTASIS; MUTANT; NONHUMAN; PRIORITY JOURNAL; SITE DIRECTED MUTAGENESIS; WILD TYPE;

CATALYTIC DOMAIN; DIRECTED MOLECULAR EVOLUTION; EPISTASIS, GENETIC; MUTAGENESIS; MUTATION; THERMODYNAMICS;

EID: 54349117265     PISSN: 14394227     EISSN: 14397633     Source Type: Journal    
DOI: 10.1002/cbic.200800371     Document Type: Article

References (57)

1. Reviews of directed evolution: a) K. M. Arndt,K. M. Müller, Methods in Molecular Biology, Vol. 352: Protein Engineering Protocols, Humana, Totowa, 2007;
2. b) F. H. Arnold,G. Georgiou, Screening and Selection Methods, Vol. 230: Directed Enzyme Evolution, Humana, Totowa, 2003;
3. c) N. J. Turner, Trends Biotechnol. 2003, 21, 474-478;
4. d) S. V. Taylor, P. Kast, D. Hilvert, Angew. Chem. 2001, 113, 3408-3436; Angew. Chem. Int. Ed. 2001, 40, 3310-3335;
5. e) S. Brakmann, A. Schwienhorst, Evolutionary Methods in Biotechnology: Clever Tricks for Directed Evolution, Wiley -VCH, Weinheim, 2004;
6. f) E. G. Hibbert, F. Baganz, H. C. Hailes,J. M. Ward, G. J. Lye, J. M. Woodley, P. A. Dalby, Biomol. Eng. 2005, 22, 11-19
7. g) S. B. Rubin-Pitel,H. Zhao, Comb. Chem. High Throughput Screening 2006, 9, 247-257;
8. h) J. Kaur, R. Sharma, Crit. Rev. Biotechnol. 2006, 26, 165-199;
9. i) S. Bershtein,D. S. Tawfik, Curr. Opin. Chem. Biol. 2008, 12, 151-158;
10. j) M. T. Reetz, Proc. Natl. Acad. Sci. USA 2004, 101, 5716-5722;
11. k) M. T. Reetz in Advances in Catalysis, Vol. 49 (Eds.: B. C. Gates,H. Knözinger), Elsevier, San Diego, 2006, pp. 1-69;
12. l) M. T. Reetz in Asymmetric Organic Synthesis with Enzymes (Eds.: V. Gotor, I. Alfonso, E. García-Urdiales), Wiley-VCH, Weinheim, 2008, pp. 21-63.
13. a) D. W. Leung,E. Chen, D. V. Goeddel, Technique (Philadelphia) 1989, 1, 11-15;
14. b) R. C. Cadwell,G. F. Joyce, PCR Methods Appl. 1992, 2, 28-33.
15. a) H. H. Hogrefe, J. Cline, G. L. Youngblood, R. M. Allen, BioTechniques 2002, 33, 1158-1165;
16. b) C. N. Dominy, D. W. Andrews in Methods Molecular Biology, Vol. 235: E. coli Plasmid Vectors: Methods and Applications (Eds.: N. Casali, A. Preston), Humana, Totowa, 2003, pp. 209-223;
17. c) R. Georgescu, G. Bandara, L. Sun in Directed Evolution Library Creation (Eds.: F. H. Arnold,G. Georgiou) Humana, Totowa, 2003, pp. 75-84;
18. d) R. D. Kirsch, E. Joly, Nucleic Acids Res. 1998, 26, 1848-1850.
19. a) W. P. C. Stemmer, Nature 1994, 370, 389-391;
20. b) K. A. Powell, S. W. Ramer, S. B. del Cardayré, W. P. C. Stemmer, M. B. Tobin, P. F. Longchamp, G. W. Huisman, Angew. Chem. 2001, 113, 4068-40 80; Angew. Chem. Int. Ed. 2001, 40, 3948-3959.
21. a) S. Lutz, W.M. Patrick, Curr. Opin. Biotechnol. 2004, 15, 291-297
22. b) R. J. Fox, G. W. Huisman, Trends Biotechnol. 2008, 26, 132-13 8;
23. c) A. Herman, D. S. Tawfik, Protein Eng. Des. Sel. 2007, 20, 219-226
24. d) J. D. Bloom, M. M. Meyer, P. Meinhold, C. R. Otey, D. MacMillan, F. H. Arnold, Curr. Opin. Struct. Biol. 2005, 15, 447-452.
25. 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.
26. M. T. Reetz, L.-W. Wang, M. Bocola, Angew. Chem. 2006, 118, 1258-1263; Angew. Chem. Int. Ed. 2006, 45, 1236-1241.
27. a) M. T. Reetz, J. D. Carballeira, A. Vogel, Angew. Chem. 2006, 118, 7909-7915; Angew. Chem. Int Ed. 2006, 45, 7745-7751;
28. b) M. T. Reetz, J. D. Carballeira, Not Protoc. 2007, 2, 891-903.
29. [6-8,15a] a) M.S. Warren, S. J. Benkovic, Protein Eng. 1997, 10, 63-68
30. b) Y. Koga, K. Kato, H. Nakano, T. Yamane, J. Mol. Biol. 2003, 331, 585-592
31. c) G. P. Horsman, A. M. F. Liu, E. Henke, U. T. Bornscheuer, R. J. Kazlauskas, Chem. Eur. J. 2003, 9, 1933-1939
32. d) C. Nowlan, Y. Li, J. C. Hermann, T. Evans, J. Carpenter, E. Ghanem, B. K. Shoichet, F. M. Raushel, J. Am. Chem. Soc. 2006, 128, 15892-15902
33. e) K. Miyazaki, F. H. Arnold, J. Mol. Evol. 1999, 49, 716-720
34. L. Rui, L. Cao, W. Chen, K. F. Reardon, T. K. Wood, J. Biol. Chem. 2004, 279, 46810-46817
35. g) S. Bartsch, R. Kourist, U. Bornscheuer, Angew. Chem. 2008, 120, 1531-1534; Angew. Chem. Int. Ed. 2008, 47, 1508-1511
36. h) L. Liang, J. Zhang, Z. Lin, Microb. Cell Fact. 2007, 6, 36
37. i) E. M. Gabor, D. B. Janssen, Protein Eng. Des. Sel. 2004, 17, 571-579
38. j) A. Juillerat, T. Gronerneyer, A. Keppler, S. Gendreizig, H. Pick, H. Vogel, K. Johnsson, Chem. Biol. 2003, 10, 313-317
39. k) N. U. Nair, H. Zhao, ChemBioChem 2008, 9, 1213-1215.
40. M. T Reetz, J. D. Carballeira, J. J.-P. Peyralans, H. Höbenreich, A. Maichele, A. Vogel, Chem. Eur. J. 2006, 12, 6031-6038.
41. Y. Zou, B. M. Hallberg, T. Bergfors, F. Oesch, M. Arand, S. L. Mowbray, T. A. Jones, Structure 2000, 8, 111-122.
42. M. T. Reetz, C. Torre, A. Eipper, R. Lohmer, M. Hermes, B. Brunner, A. Maichele, M. Bocola, M. Arand, A. Cronin, Y. Genzel, A. Archelas, R. Furstoss, Org. Lett. 2004, 6, 177-180.
43. a) D. M. Weinreich, N. F. Delaney, M. A. DePristo, D. L. Hard, Science 2006, 312, 111-114;
44. b) F. J. Poelwijk, D. J. Kiviet, D. M. Weinreich, S. J. Tans, Nature 2007, 445, 383-386.
45. a) D. C. Carter, G. Winter, A. J. Wilkinson, A. R. Fersht, Cell 1984, 38, 835-840;
46. b) J. A. Wells, Biochemistry 1990, 29, 8509-8517;
47. c) A. Horovitz, Curr. Biol. 1996, 6, 11121-11126.
48. a) M. T. Reetz, S. Wilensek, D. Zha, K.-E. Jaeger, Angew. Chem. 2001, 113, 3701-3703; Angew. Chem. Int. Ed. 2001, 40, 3589-3591;
49. b) M. Bocola, N. Otte, K.-E. Jaeger, M. J. Reetz, W. Thiel, ChemBioChem 2004, 5, 214-223;
50. c) 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.
51. A. S. Mildvan, Biochemistry 2004, 43, 14517-14520.
52. Examples of remote effects regarding enantioselectivity/substrate acceptance: a) C.-C. Hsu, Z. Hong, M. Wada, D. Franke, C.-H. Wong, Proc. Natl. Acad. Sci. USA 2005, 102, 9122-9126;
53. b) I. Lavandera, S. Fernández, J. Magdalena, M. Ferrero, H. Grewal, C. K Savile, R. J. Kazlauskas, V. Gotor, ChemBioChem 2006, 7, 693-698;
54. c) S. Oue, A. Okamoto, T. Yano, H. Kagamiyama, J. Biol. Chem. 1999, 274, 2344-2349;
55. d) S. Park, K. L. Morley, G. P. Horsman, M. Holmquist, K. Hult, R. J. Kazlauskas, Chem. Biol. 2005, 12, 45-54.
56. F. Cedrone, S. Niel, S. Roca, T. Bhatnagar, N. Ait-Abdelkader, C. Torre, H. Krumm, A. Maichele, M. T Reetz, J. C. Baratti, Biocatal. Biotransform. 2003, 21, 357-364.
57. K. Faber, Biotransformations in Organic Chemistry, 5th ed., Springer, Berlin, 2004.