Random mutagenesis methods for in vitro directed enzyme evolution

Current Protein and Peptide Science

Volumn 11, Issue 1, 2010, Pages 91-100

  Labrou, Nikolaos E ^a  

^a AGRICULTURAL UNIVERSITY OF ATHENS   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL MUTAGEN; DNA; ENZYME;

ANALYTICAL ERROR; CHEMICAL MUTAGENESIS; COMBINATORIAL LIBRARY; DIRECTED MOLECULAR EVOLUTION; DNA REPLICATION; DNA SEQUENCE; ENZYME ACTIVITY; ENZYME STRUCTURE; ESCHERICHIA COLI; GENE AMPLIFICATION; GENETIC STRAIN; GENETIC VARIABILITY; IN VITRO STUDY; MOLECULAR CLONING; MUTAGENESIS; MUTATOR GENE; NONHUMAN; POLYMERASE CHAIN REACTION; REVIEW; ROLLING CIRCLE AMPLIFICATION; SATURATION MUTAGENESIS; SITE DIRECTED MUTAGENESIS; SITE SATURATIONN MUTAGENESIS;

DIRECTED MOLECULAR EVOLUTION; ENZYMES; GENE LIBRARY; HUMANS; MUTAGENESIS;

EID: 77950164392     PISSN: 13892037     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920310790274617     Document Type: Review

References (84)

1. Sen, S.; Venkata Dasu, V.; Mandal, B. Developments in directed evolution for improving enzyme functions. Appl. Biochem. Biotechnol., 2007, 143, 212-223
2. Haseltine, E.L.; Arnold, F.H. Synthetic gene circuits: design with directed evolution. Annu. Rev. Biophys. Biomol. Struct., 2007, 36, 1-19
3. Hida, K.; Hanes, J.; Ostermeier, M. Directed evolution for drug and nucleic acid delivery. Adv. Drug Deliv. Rev., 2007, 59, 1562-1578.
4. Bershtein, S.; Tawfik, D.S. Advances in laboratory evolution of enzymes. Curr. Opin. Chem. Biol. 2008, 12,151-158.
5. Zhao, H.; Giver, L.; Shao, Z. Affholter, J.A., Arnold, F.H. Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat. Biotechnol., 1998, 16, 258-261.
6. Rubin-Pitel, S.B.; Cho, C.M-H.; Chen, W.; Zhao, H. In Bioprocessing for value-added products from renewable resources. Shang-Tian Yang, Ed., New Technologies and Applications, Elsevier B.V., USA, 2007, pp. 49-72.
7. Hibbert, E.G.; Baganz, F.; Hailes, H.C.; Ward, J.M.; Lye, G.J; Woodley, J.M.; Dalby, P.A. Directed evolution of biocatalytic processes. Biomol. Eng., 2005, 22, 11-19.
8. Jäckel, C.; Kast, P.; Hilvert, D. Protein design by directed evolution. Annu. Rev. Biophys., 2008, 37, 153-173.
9. Kaur, J.; Sharma, R. Directed evolution: an approach to engineer enzymes. Crit. Rev. Biotechnol., 2006, 26,165-99.
10. Stemmer, W.P. Rapid evolution of a protein in vitro by DNA shuffling. Nature, 1994, 370, 389-391.
11. Arnold, F.H. Combinatorial and computational challenges for biocatalyst design. Nature, 2001, 409, 253-257.
12. Plückthun, A.; Schaffitzel, C.; Hanes, J.; Jermutus, L. In vitro selection and evolution of proteins. Adv. Protein Chem., 2001, 55, 367-403.
13. Kotzia, G.A.; Labrou, N.E. Engineering thermal stability of L-asparaginase by in vitro directed evolution. FEBS J., 2009, 276, 1750-1761.
14. Fox, R.J.; Huisman, G.W. Enzyme optimization: moving from blind evolution to statistical exploration of sequence-function space. Trends Biotechnol., 2008, 26, 132-138.
15. Gillam, E.M. Engineering cytochrome P450 enzymes. Chem. Res. Toxicol., 2008, 21, 220-31.
16. Chaput, J.C.; Woodbury, N.W.; Stearns, L.A. Williams BA. Creating protein biocatalysts as tools for future industrial applications. Expert Opin. Biol. Ther., 2008, 8, 1087-1098.
17. Bershtein, S.; Tawfik, D.S. Advances in laboratory evolution of enzymes. Curr. Opin. Chem. Biol., 2008, 12, 151-158.
18. Jin, Z.H.; Xu, B.; Lin, S.Z.; Jin, Q.C.; Cen, P.L. Enhanced Production of Spinosad in Saccharopolyspora spinosa by Genome Shuffling. Appl. Biochem. Biotechnol., 2009 (in press).
19. Johannes, T.W.; Zhao, H. Directed evolution of enzymes and biosynthetic pathways. Curr. Opin. Microbiol., 2006, 9, 261-267.
20. Hou, L. Novel methods of genome shuffling in Saccharomyces cerevisiae. Biotechnol. Lett., 2009, 31, 671-7.
21. Xu, B.; Jin, Z.; Wang, H.; Jin, Q.; Jin, X.; Cen, P. Evolution of Streptomyces pristinaespiralis for resistance and production of pristinamycin by genome shuffling. Appl. Microbiol. Biotechnol., 2008, 80, 261-267.
22. Yu, L.; Pei, X.; Lei, T.; Wang, Y.; Feng, Y. Genome shuffling enhanced L-lactic acid production by improving glucose tolerance of Lactobacillus rhamnosus. J Biotechnol., 2008, 134, 154-159.
23. Deshler, J.O. A simple method for randomly mutating cloned DNA fragments by using chemical mutagens and the polymerase chain reaction. Genet. Anal. Tech. Appl., 1992, 9, 103-106.
24. Ryu, D.D.Y.; Nam, D.-H. Recent progress in biomolecular engineering. Biotechnol. Prog., 2000, 16, 2-16.
25. Salazar, O.; Sun, L. In: directed enzyme evolution: screening and selection methods. methods in molecular biology, Arnold, F.H. Georgiou, G. Eds; Evaluating a Screen and Analysis of Mutant Libraries. Humana Press, Totowa, NJ, 2003. Vol. 230, pp. 85-97.
26. Cirino, P.; Mayer, K.; Umeno, D. In: Directed Evolution Library Creation: Methods and Protocols. Methods in Molecular Biology, Arnold, F.H.; Georgiou, G.; Eds. Generating Mutants Libraries Using Error-Prone PCR. Humana Press, Totowa, NJ. 2003, Vol. 231, pp. 3-9.
27. Schuster. P. In Directed Molecular Evolution of Proteins: or How to Improve Enzymes for Biocatalysis, Brackmann, S.; Johnsson, K.; Eds; Evolutionary Biotechnology - From Ideas and Concepts to Experiments and Computer Simulations. Wiley-VCH, Weinheim, Germany. 2002, pp. 5-28.
28. Brakmann, S.; Lindemann, B.F. In: Evolutionary Methods in Biotechnology, Brakmann, S.; Schwienhorst, A.; Eds., Generation of Mutant Libraries Using Random Mutagenesis. Wiley-VCH Verlag GmbH & Co. KGaA, 2004, pp. 5-11.
29. Shortle, D.; Nathans, D. Local mutagenesis: a method for generating viral mutants with base substitutions in preselected regions of the viral genome. Proc. Natl. Acad. Sci. USA, 1978, 75, 2170-2174.
30. Kadonaga, J.T., Knowles, J.R. A simple and efficient method for chemical mutagenesis of DNA. Nucleic Acids Res., 1985, 13, 1733-1745.
31. Cox, E.C. Bacterial mutator genes and the control of spontaneous mutation. Annu. Rev. Genet., 1976, 10, 135-156.
32. Greener, A.; Callahan, M.; Jerpseth B. An efficient random mutagenesis technique using an E. coli mutator strain. Methods Mol. Biol., 1996, 57, 375-385.
33. Leung, D.W.; Chen, E.; Goeddel, D.V. A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction. Technique, 1989, 1, 11-15.
34. Cadwell, R.C.; Joyce, G.F. Randomization of genes by PCR mutagenesis. PCR Methods Appl., 1992, 2, 28-33.
35. Vartanian, J.P.; Henry, M.; Wain-Hobson. S. Hypermutagenic PCR involving all four transitions and a sizeable proportion of transversions. Nucleic Acids Res., 1996, 24, 2627-2631.
36. Patrick, W.M.; Firth, A.E. Strategies and computational tools for improving randomized protein libraries. Biomol. Eng., 2005, 22, 105-12.
37. Fujii, R., Kitaoka, M., Hayashi, K. One-step random mutagenesis by error-prone rolling circle amplification. Nucleic Acids Res., 2004, 32, e145.
38. Selifonova, O.; Valle, F.; Schellenberger, V. Rapid evolution of novel traits in microorganisms. Appl. Environ. Microbiol., 2001, 67, 3645-3652.
39. Kadonaga, J.T.; Knowles, J.R. A simple and efficient method for chemical mutagenesis of DNA. Nucleic Acids Res., 1985, 13, 1733-1742.
40. Ermakova-Gerdes, S.; Shestakov, S.; Vermaas, W. Random chemical mutagenesis of a specific psbDI region coding for a lumenal loop of the D2 protein of photosystem II in Synechocystis sp. PCC. Plant Mol. Biol., 1996, 30, 6803.
41. Mohan, U.; Banerjee, U.C. Molecular evolution of a defined DNA sequence with accumulation of mutations in a single round by a dual approach to random chemical mutagenesis (DuARCheM). Chembiochem., 2008, 9, 2238-2243.
42. Bornscheuer, U.T.; Altenbuchner, J.; Meyer, H.H. Directed evolution of an esterase for the stereoselective resolution of a key intermediate in the synthesis of epothilones. Biotechnol. Bioeng., 1998, 58, 554-559.
43. Henke, E.; Bornscheuer, U.T. Directed evolution of an esterase from Pseudomonas fluorescens. Random mutagenesis by errorprone PCR or a mutator strain and identification of mutants showing enhanced enantioselectivity by a resorufin-based fluorescence assay. Biol. Chem., 1999, 380, 1029-1033.
44. Callanan, M.J.; Russell, W.M.; Klaenhammer, T.R. Modification of Lactobacillus beta-glucuronidase activity by random mutagenesis. Gene, 2007, 389, 122-127.
45. Tindall, K.R.; Kunkel, T.A. Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase. Biochemistry. 1988, 27, 6008-6013.
46. Cline, J.; Braman, J.C.; Hogrefe, H.H. PCR fidelity of Pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Res., 1996, 24, 3546-3551.
47. Beckman, R.A.; Mildvan, A.S.; Loeb, L.A. On the fidelity of DNA replication: manganese mutagenesis in vitro. Biochemistry, 1985, 24, 5810-5817.
48. Eckert, K.A.; Kunkel, T.A. DNA polymerase fidelity and the polymerase chain reaction. PCR Methods Appl., 1991, 1, 17-24.
49. Vanhercke, T.; Ampe, C.; Tirry, L.; Denolf P. Reducing mutational bias in random protein libraries. Anal. Biochem., 2005, 339, 9-14.
50. Biles, B.D.; Connolly, B.A. Low-fidelity Pyrococcus furiosus DNA polymerase mutants useful in error-prone PCR. Nucleic Acids Res., 2004, 32, e176 1-7.
51. Axarli, I.; Prigipaki, A.; Labrou, N.E. Engineering the substrate specificity of cytochrome P450 CYP102A2 by directed evolution: production of an efficient enzyme for bioconversion of fine chemicals. Biomol. Eng., 2005, 22, 81-88.
52. Kim, M.S.; Lei, X.G. Enhancing thermostability of Escherichia coli phytase AppA2 by error-prone PCR. Appl. Microbiol. Biotechnol., 2008, 79, 69-75.
53. Maeda, T.; Sanchez-Torres, V.; Wood, T.K. Protein engineering of hydrogenase 3 to enhance hydrogen production. Appl. Microbiol. Biotechnol., 2008, 79, 77-86.
54. Emond, S.; Mondon, P.; Pizzut-Serin, S.; Douchy, L.; Crozet, F.; Bouayadi, K.; Kharrat, H.; Potocki-Véronèse, G.; Monsan, P.; Remaud-Simeon, M. A novel random mutagenesis approach using human mutagenic DNA polymerases to generate enzyme variant libraries. Protein Eng. Des. Sel., 2008, 21, 267-74.
55. Asano, Y.; Kira, I.; Yokozeki, K. Alteration of substrate specificity of aspartase by directed evolution. Biomol. Eng., 2005, 22, 95-101.
56. Kashiwagi, K.; Isogai, Y.; Nishiguchi, K.-I.; Shiba, K. Frame shuffling: a novel method for in vitro protein evolution. Protein Eng. Des. Sel., 2006, 19, 135-140.
57. Fire, A.; Xu, S.Q. Rolling replication of short DNA cir-cles. Proc. Natl. Acad. Sci. USA, 1995, 92, 4641-4645.
58. +. FEBS J., 2008, 275, 3859-3869.
59. Reetz, M.T.; Wu, S. Greatly reduced amino acid alphabets in directed evolution: making the right choice for saturation mutagenesis at homologous enzyme positions. Chem. Commun. (Camb)., 2008, 43, 5499-501.
60. Matsumura, I.; Rowe, L.A. Whole plasmid mutagenic PCR for directed protein evolution. Biomol. Eng., 2005, 22, 73-9.
61. Gratz, A.; Jose, J. Protein domain library generation by overlap extension (PDLGO): a tool for enzyme engineering. Anal. Biochem., 2008, 378, 171-176.
62. Alcalde, M.; Zumárraga, M.; Polaina, J.; Ballesteros, A.; Plou, F.J. Combinatorial saturation mutagenesis by in vivo overlap extension for the engineering of fungal laccases. Comb. Chem. High Throughput Screen., 2006, 9, 719-27.
63. Reidhaar-Olson, J.F.; Sauer, R.T. Combinatorial cassette mutagenesis as a probe of the informational content of protein sequences, Science, 1988, 241, 53-58.
64. Arkin, A.P.; Youvan, D.C. A combinatorial optimization procedure for protein engineering: simulation of recursive ensemble mutagenesis. Proc. Natl. Acad. Sci. USA, 1992, 89, 7811-7815.
65. Maynard, J.A.; Chen, G.; Georgiou, G.; Iverson, B.L. In vitro scanning -saturation mutagenesis. Methods Mol. Biol., 2002, 182, 149-163.
66. Kegler-Ebo, D.M.; Docktor, C.M.; DiMaio, D. Codon cassette mutagenesis: a general method to insert or replace individual codons by using universal mutagenic cassettes. Nucleic Acids Res., 1994, 22, 1593-1599.
67. Reetz, M.T.; Kahakeaw, D.; Sanchis, J. Shedding light on the efficacy of laboratory evolution based on iterative saturation mutagenesis. Mol. Biosyst., 2009, 5, 115-22.
68. Reetz, M.T.; Carballeira, J.D. Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat. Protoc., 2007, 2, 891-903.
69. Wong, T.S.; Tee, K.L.; Hauer, B.; Schwaneberg, U. Sequence saturation mutagenesis (SeSaM): a novel method for directed evolution. Nucleic Acids Res., 2004, 32, e26.
70. Ang, E.L.; Obbard, J.P.; Zhao, H.. Directed evolution of aniline dioxygenase for enhanced bioremediation of aromatic amines. Appl. Microbiol. Biotechnol., 2009, 81, 1063-1070.
71. Li, H.M.; Mei, L.H.; Urlacher, V.B.; Schmid, R.D. Cytochrome P450 BM-3 evolved by random and saturation mutagenesis as an effective indole-hydroxylating catalyst. Appl. Biochem. Biotechnol., 2008, 144, 27-36.
72. Voigt, C.A.; Kauffman, S.; Wang, Z.G. Rational evolutionary design: the theory of in vitro protein evolution. Adv. Protein Chem., 2000, 55, 79-160.
73. Holm, L.; Sander, C. Protein folds and families: sequence and structure alignments. Nucleic Acids Res., 1999, 27, 244-7.
74. Meyer, M.M.; Hochrein, L.; Arnold, F.H. Structure-guided SCHEMA recombination of distantly related beta-lactamases. Protein Eng. Des. Sel., 2006, 19, 563-570.
75. Glaser, F.; Pupko, T.; Paz, I.; Bell, R.E.; Bechor-Shental, D.; Martz, E.; Ben-Tal, N. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics, 2003, 19, 163-164.
76. Patrick, W.M.; Firth, A.E.; Blackburn, J.M. User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries. Protein Eng., 2003, 16, 451-457.
77. Firth, A.E.; Patrick, W.M. Statistics of protein library construction. Bioinformatics, 2005, 21, 3314-3315.
78. Firth, A.E.; Patrick, W.M. GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries. Nucleic Acids Res., 2008, 36(Web Server issue), 281-285.
79. Reetz, M.T.; Jaeger, K.E. Enantioselective enzymes for organic synthesis created by directed evolution. Chemistry, 2000, 6, 407-412.
80. Zhao, H.; Zha, W. In: Evolutionary Methods for Protein Engineering, Svendsen, A.; Ed.; Marcel Dekker, Inc: New York, 2004, pp. 353-365.
81. Callanan, M.J.; Russell, W.M.; Klaenhammer, T.R. Modification of Lactobacillus beta-glucuronidase activity by random mutagenesis. Gene, 2007, 389, 122-127.
82. Altreuter, D.H.; Clark, D.S. Combinatorial biocatalysis: taking the lead from nature. Curr. Opin. Biotechnol., 1999, 10, 130-136.
83. Liang, S.M.; Lee, N.; Zoon, K.C.; Manischewitz, J.F.; Chollet, A.; Liang, C.M.; Quinnan, G.V. Biological characterization of human interleukin-2 mutant proteins: structure-activity relationship studies. J. Biol. Chem., 1988, 263, 4768-4772.
84. +-specific formate dehydrogenases. Biotechnol. Bioeng., 1999, 64, 187-193.