Mutant library construction in directed molecular evolution

详细信息    查看全文

• 作者：Tian-Wen Wang (1)
  Hu Zhu (1)
  Xing-Yuan Ma (1)
  Ting Zhang (1)
  Yu-Shu Ma (1)
  Dong-Zhi Wei (1)
  
• 关键词：Directed molecular evolution ; error ; prone PCR ; oligonucleotide ; based mutagenesis ; DNA shuffling ; mutator strain ; somatic hypermutation
• 刊名：Molecular Biotechnology
• 出版年：2006
• 出版时间：September 2006
• 年：2006
• 卷：34
• 期：1
• 页码：55-68
• 全文大小：293KB
• 参考文献：1. Chen K. Q. and Arnold, F. H. (1993) Tuning the activity of an enzyme for unusual environments鈥攕equential random mutagenesis of subtilisin, E for catalysis in dimethylformamide. / Proc. Natl. Acad. Sci. USA 90, 5618鈥?622. CrossRef
  2. Reetz, M. T., Zonta, A., Schimossek, K., Liebeton, K., and Jaeger, K. E. (1997) Creation of enantioselective biocatalysts for organic chemistry by in vitro evolution. / Angew. Chem. Int. Ed. Engl. 36, 2830鈥?832. CrossRef
  3. Stemmer, W. P. C. (1994) Rapid evolution of a protein in vitro by DNA shuffling. / Nature 370, 389鈥?91. CrossRef
  4. Zhao, H., Giyer, L., Affholter, J. A. and Arnold, F. H. (1998). Molecular evolution by staggered extension process (StEP) in vitro recombination. / Nat. Biotechniol. 16, 258鈥?61. CrossRef
  5. Crameri, A., Raillard, S. A., Bermudez, E., and Stemmer, W. P. C. (1998). DNA shuffling of a family of genes from diverse species accelerates directed evolution. / Nature 391, 288鈥?91. CrossRef
  6. Williams, G. J., Nelson, A. S., and Berry, A. (2004) Directed evolution of enzymes for biocatalysis and the life sciences. / Cell Mol. Life Sci. 61, 3034鈥?046. CrossRef
  7. Dahiyat, B. I. and Mayo, S. L. (1997) / De novo protein design: fully automated sequence selection. / Science 278, 82鈥?7. CrossRef
  8. Root, M. J., Kay, M. S., and Kim, P. S. (2001). Protein design of an HIV-1 entry inhibitor. / Science 291, 884鈥?88. CrossRef
  9. Arnold, F. H. (2001) Combinatorial and computational challenges for biocatalyst design. / Nature 409, 253鈥?57. CrossRef
  10. Wahler, D. and Reymond, J. L. (2001) High-throughput screening for biocatalysts. / Curr. Opin. Biotechnol. 12, 535鈥?44. CrossRef
  11. Wahler, D. and Reymond, J. L. (2001) Novel methods for biocatalyst screening. / Curr. Opin. Chem. Biol. 5, 152鈥?58. CrossRef
  12. Olsen, M., Iverson, B., and Georgiou, G. (2000) High-throughput screening of enzyme libraries. / Curr. Opin. Biotechnol. 11, 331鈥?37. CrossRef
  13. Becker, S., Schmoldt, H. U., Adams, T. M., Wilhelm, S., and Kolmar, H. (2004) Ultra-high-throughput screening based on cell-surface display and fluorescence-activated cell sorting for the identification of novel biocatalysts. / Curr. Opin. Biotechnol. 15, 323鈥?29. CrossRef
  14. Cohen, N., Abramov, S., Dror, Y., and Freeman, A. (2001). / In vitro enzyme evolution: the screening challenge of isolating the one in a million. / Trends Biotechnol. 19, 507鈥?10. CrossRef
  15. Schmidt, M. and Bornscheuer, U. T. (2005). High-throughput assays for lipases and esterases. / Biomol. Eng. 22, 51鈥?6. CrossRef
  16. Aharoni, A., Griffiths, A. D., and Tawfik, D. S. (2005). High-throughput screens and selections of enzyme-encoding genes. / Curr. Opin. Chem. Biol. 9, 210鈥?16. CrossRef
  17. Mullis, K. B. and Faloona, F. A. (1987). Specific synthesis of DNA / in vitro via a polymerase catalyzed chain reaction. / Methods Enzymol. 155, 335鈥?51. CrossRef
  18. Sun, F. (1995) The polymerase chain reaction and branching processes. / J. Comput. Biol. 2, 63鈥?6. CrossRef
  19. Echert, K. A., and Kunkel, T. A. (1991). DNA polymerase fidelity and the polymerase chain reaction. / PCR Methods Appl. 1, 17鈥?4.
  20. Brakmann, S. (2001). Discovery of superior enzymes by directed molecular evolution. / Chem. Biochem. 2, 865鈥?71.
  21. Cadwell, C. and Joyce, G. F. (1992) Randomization of genes by PCR mutagenesis. / PCR Methods Appl. 2, 28鈥?3.
  22. Cadwell, R. C. and Joyce, G. F. (1995) Mutagenic PCR. / PCR Methods Appl. 3, 136鈥?40.
  23. Vartanian, J. P., Henry, M., and Wain-Hobson, S. (1996). Hypermutagenic PCR involving all four transitions and a sizeable proportion of transversions. / Nucleic Acids Res. 24, 2627鈥?631. CrossRef
  24. Shafikhani, S., Siegel, R. A., Ferrari, E., and Schellenberger, V. (1997). Generation of large libraries of random mutants in / Bacillus subtilis by PCR-based plasmid multimerization. / Bio Techniques 23, 304鈥?10.
  25. Lin-Goerke, J. L. Robbins, D. J., and Burczak, J. D. (1997) PCR-based random mutagenesis using manganese and reduced dNTP concentration. / BioTechniques 23, 409鈥?12.
  26. McCarthy, J. K., Uzelac, A., Davis, D. F., and Eveleigh, D. E. (2004) Improved catalytic efficiency and active site modification of 1,4-beta-D-glucan glucohydrolase A from / Thermotoga neapolitana by directed evolution. / J. Biol. Chem. 279, 11495鈥?1502. CrossRef
  27. Ling, L. L., Keohavong, P., Dias, C., and Thilly, W. G. (1991). Optimization of the polymerase chain reaction with regard to fidelity: modified T7, Taq, and vent DNA polymerases. / PCR Methods Appl. 1, 63鈥?9.
  28. Beckman, R. A., Mildvan, A. S., and Loeb, L. A. (1985) On the fidelity of DNA replication: manganese mutagenesis in vitro. / Biochemistry 24, 5810鈥?817. CrossRef
  29. Leung D. W., Chen, E., and Goeddel, D. V. (1989) A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction. / Techniques 1, 11鈥?5.
  30. Zaccolo, M., Williams, D. M., Brown, D. M., and Gherardi, E. (1996). An approach to random mutagenesis of DNA using mixtures of triphosphate derivatives of nucleoside analogues. / J. Mol. Biol. 255, 589鈥?03. CrossRef
  31. Xu, H., Petersen, E. I., Petersen, S. B. and el-Gewely, M. R. (1999) Random mutagenesis libraries: optimization and simplification by PCR. / Bio Techniques 27, 1102鈥?104, 1106, 1108.
  32. Neylon, C. (2004) Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: library construction methods for directed evolution. / Nucleic Acids Res. 32, 1448鈥?459. CrossRef
  33. Gelfand, D. H. and White, T. J. (1990) A guide to methods and applications. In / PCR Protocols (Innis, M. A., ed). Academic Press Inc., California, pp. 129鈥?41.
  34. Biles, B. D. and Connolly, B. A. (2004) Low-fidelity / Pyrococcus furiosus DNA polymerase mutants useful in error-prone PCR. / Nucleic Acids Res. 32, e176. CrossRef
  35. Ghadessy, F. J., Ramsay, N., Boudsocq, E., et al. (2004) Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution. / Nat. Biotechnol. 22, 755鈥?59. CrossRef
  36. Wong, T. S., Tee, K. L., Hauer, B., and Schwaneberg, U. (2004) Sequence saturation mutagenesis (SeSaM): a novel method for directed evolution. / Nucleic Acids Res. 32, e26. CrossRef
  37. Wong, T. S., Tee, K. L., Hauer, B., and Schwaneberg, U. (2005) Sequence saturation mutagenesis with tunable mutation frequencies. / Anal Biochem. 341, 187鈥?89. CrossRef
  38. Spee, J. H., de Vos, W. M., and Kuipers, O. P. (1993). Efficient random mutagenesis method with adjustable mutation frequency by use of PCR and dITP / Nucleic Acids Res. 21, 777鈥?78. CrossRef
  39. Ward, B. and Juehne, T. (1998) Combinatorial library diversity: probability assessment of library populations. / Nucleic Acids Res. 26, 879鈥?86. CrossRef
  40. Palfrey, D., Picardo, M., and Hine, A. V. (2000) A new randomization assay reveals unexpected elements of sequence bias in model 鈥榬andomized鈥?gene libraries: implications for biopanning. / Gene 251, 91鈥?9. CrossRef
  41. Miyazaki, K. and Takenouchi, M. (2002) Creating random mutagenesis libraries using megaprimer PCR of whole plasmid. / Bio Techniques 33, 1033鈥?034, 1036鈥?038.
  42. Angelaccio, S. and Bonaccorsi di Patti, M. C. (2002) Site-directed mutagenesis by the megaprimer PCR method: variations on a theme for simultaneous introduction of multiple mutations. / Anal. Biochem. 306, 346鈥?49. CrossRef
  43. Choi, K. H. and Schweizer, H. P. (2005) An improved method for rapid generation of unmarked / Pseudomonas aeruginosa deletion mutants. / BMC Microbiol. 5, 30. CrossRef
  44. Hogrefe, H. H., Cline, J., Youngblood, G. L., and Allen, R. M. (2002) Creating randomized amino acid libraries with the QuickChange Multi Site-Directed Mutagenesis Kit. / Bio Techniques 33, 1158鈥?160, 1162, 1164鈥?165.
  45. Zha, D., Eipper, A., and Reetz, M. T. (2003). Assembly of designed oligonucleotides as an efficient method for gene recombination: a new tool in directed evolution. / ChemBioChem., 4, 34鈥?9. CrossRef
  46. Boder, E. T., Midelfort, K. S., and Witrup, K. D. (2000) Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity. / Proc Natl. Acad. Sci. USA 97, 10701鈥?0705. CrossRef
  47. Cho, C. M., Mulchandani, A., and Chen, W. (2004) Altering the substrate specificity of organophosphorus hydrolase for enhanced hydrolysis of chlorpyrifos. / Appl. Environ. Microbiol. 70, 4681鈥?685. CrossRef
  48. Castle, L. A., Siehl, D. L., Gorton, R., et al. (2004) Discovery and directed evolution of a glyphosate tolerance gene. / Science, 304, 1151鈥?154. CrossRef
  49. Reetz, M. T. (2004) Controlling the enantioselectivity of enzymes by directed evolution: practical and theoretical ramifications. / Proc. Natl. Acad. Sci. USA 101, 5716鈥?722. CrossRef
  50. Bessler, C., Schmitt, J., Maurer, K. H., and Schmid, R. D. (2003) Directed evolution of a bacterial alpha-amylase: toward enhanced pH-performance and higher specific activity. / Protein Sci. 12, 2141鈥?149. CrossRef
  51. Hatanaka, T. (2005) Identification of a key amino acid residue of / Streotomyces phospholipase D for thermostability by / in vivo DNA shuffling. / Biochim. Biophys. Acta. 1722, 331鈥?42.
  52. Moore, G. L., Maranas, C. D., Lutz, S., and Benkovic, S. J. (2001) Predicting crossover generation in DNA shuffling. / Proc. Natl. Acad. Sci. USA 98, 3226鈥?231. CrossRef
  53. Sieber, V., Martinez, C. A., and Arnold, F. H. (2001). Libraries of hybrid proteins from distantly related sequences. / Nat. Biotechnol. 19, 456鈥?60. CrossRef
  54. Ostermeier, M., Nixon, A. E., and Benkovic, S. J. (1999) Incremental truncation as a strategy in the engineering of novel biocatalysts. / Bioorg. Med. Chem. 7, 2139鈥?144. CrossRef
  55. Ostermeier, M., Nixon, A. E., Shim, J. H., and Benkovic, S. J. (1999) Combinatorial protein engineering by incremental truncation. / Proc. Natl. Acad. Sci. USA 96, 3562鈥?567. CrossRef
  56. Ostermeier, M., Shim, J. H., and Benkovic, S. J. (1999) A combinatorial approach to hybrid enzymes independent of DNA homology. / Nat. Biotechnol. 17, 1205鈥?209. CrossRef
  57. Lutz, S., Ostermeier, M., Moore, G. L., Maranas, C. D., and Benkovic, S. J. (2001) Creating multiple-cross-over DNA libraries independent of sequence identity. / Proc. Natl. Acad. Sci. USA 98, 11248鈥?1253. CrossRef
  58. Walton, C. R., Booth, K., and Stockley, P. G. (1991) in / Directed mutagenesis: a practical approach (McPherson, M. J., ed), IRL Press, Oxford, pp. 135鈥?62.
  59. Lai, Y. P., Huang, J., Wang, L. F., Li, J., and Wu, Z. R. (2004) A new approach to random mutagenesis / in vitro. / Biotechnol. Bioeng. 86, 622鈥?27. CrossRef
  60. Coia, G, Ayres, A., Lilley, G. G., Hudson, P. J., and Irving, R. A. (1997). Use of mutator cells as a means for increasing production levels of a recombinant anti-body directed against Hepatitis B. / Gene 201, 203鈥?09. CrossRef
  61. Sleator, R. D., Gahan, C. G., and Hill, C. (2001) Mutations in the listerial proB gene leading to proline overproduction: effects on salt tolerance and murine infection. / Appl. Environ. Microbiol. 67, 4560鈥?565. CrossRef
  62. Farrow, K. A., Lyras, D., Polekhina, G., Koutsis, K., Parker, M. W., and Rood, J. I. (2002) Identification of essential residues in the Erm(B) rRNA methyltransferase of / Clostridium perfringens. / Antimicrob. Agents Chemother. 46, 1253鈥?261. CrossRef
  63. Chusacultanachai, S. and Yuthavong, Y. (2004) Random mutagenesis strategies for construction of large and diverse clone libraries of mutated DNA fragments. / Methods Mol. Biol. 270, 319鈥?34.
  64. Belanger, F., Theberge-Julien, G., Cunningham, P. R., and Brakier-Gingras, L. (2005) A functional relationship between helix 1 and the 900 tetraloop of 16S ribosomal RNA within the bacterial ribosome. / RNA 11, 906鈥?13. CrossRef
  65. Bornscheuer, U. T., Altenbuchner, J., and Meyer, H. H. (1999) Directed evolution of an esterase: screening of enzyme libraries based on pH-indicators and a growth assay. / Bioorg. Med. Chem. 7, 2169鈥?173. CrossRef
  66. Amara, A. A., Steinbuchel, A., and Rehm, B. H. (2002) / In vivo evolution of the / Aeromonas punctata polyhydroxyalkanote (PHA) synthase: isolation and characterization of modified PHA synthases with enhanced activity. / Appl. Microbiol. Biotechnol. 59, 477鈥?82. CrossRef
  67. Lu, X., Hirata, H., Yamaji, Y., Ugaki, M., and Namba, S. (2001) Random mutagenesis in a plant viral genome using a DNA repair-deficient mutator / Escherichia coli strain. / J. Virol. Methods 94, 37鈥?3. CrossRef
  68. Bachl, J., Carlson, C., Gray-Schopfer, V., Dessing, M., and Olsson, C. (2001) Increased transcription levels induce higher mutation rates in a hypermutating cell line. / J. Immunol. 166, 5051鈥?057.
  69. Papavasiliou, F. N., and Schatz, D. G. (2002) Somatic hypermutation of immunoglobulin genes merging mechanisms for genetic diversity. / Cell 109, S35-S44. CrossRef
  70. Martin, A., and Scharff, M. D. (2002) AID and mismatch repair in antibody diversification. / Nat. Rev. Immunol. 2, 605鈥?14. CrossRef
  71. Neuberger, M. S., Harris, R. S., Di Noia, J., and Petersen-Mahrst S. K. (2003) Immunity through DNA deamination. / Trends Biochem. Sci. 28, 305鈥?12. CrossRef
  72. Wang, C. L., Harper, R. A., and Wabl, M. (2004) Genome-wide somatic hypermutation. / Proc. Natl. Acad. Sci. USA 101, 7352鈥?356. CrossRef
  73. Wang, C. L., Yang, D. C., and Wabl, M. (2004) Directed molecular evolution by somatic hypermutation. / Protein. Eng. Des. Set. 17, 659鈥?64. CrossRef
  74. Wang, L., Jackson, W. C., Steinbach, P. A., and Tsien, R. Y. (2004) Evolution of new nonantibody proteins via iterative somatic hypermutation. / Proc. Natl. Acad. Sci. USA 101, 16745鈥?6749. CrossRef
  
• 作者单位：Tian-Wen Wang (1)
  Hu Zhu (1)
  Xing-Yuan Ma (1)
  Ting Zhang (1)
  Yu-Shu Ma (1)
  Dong-Zhi Wei (1)
  
  1. State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 200237, Shanghai, P. R. China
  

文摘

Directed molecular evolution imitates the natural selection process in the laboratory to find mutant proteins with improved properties in the expected aspects by exploring the encoding sequence space. The success of directed molecular evolution experiment depends on the quality of artificially prepared mutant libraries and the availability of convenient high-throughput screening methods. Well-prepared libraries promise the possibility of obtaining desired mutants by screening a library containing a relatively small number of mutants. This article summarizes and reviews the currently available methodologies widely used in directed evolution practices in the hope of providing a general reference for library construction. These methods include error-prone polymerase chain reaction (epPCR), oligonucleotide-based mutagenesis, and genetic recombination exemplified by DNA shuffling and its derivatives. Another designed method is also discussed, in which B-lymphocytes are fooled to mutate nonantibody foreign proteins through somatic hypermutation (SHM).