Site saturation mutagenesis: Methods and applications in protein engineering

Biocatalysis and Agricultural Biotechnology

Volumn 1, Issue 3, 2012, Pages 181-189

  Siloto, Rodrigo M P ^a   Weselake, Randall J ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Biocatalysis; Codon degeneracy; Directed evolution; Mutagenesis; Protein engineering; Structure function

Indexed keywords

EID: 84861228538     PISSN: 18788181     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bcab.2012.03.010     Document Type: Review

References (66)

1. An Y., Ji J., Wu W., Lv A., Huang R., Wei Y. A rapid and efficient method for multiple-site mutagenesis with a modified overlap extension PCR. Appl. Microbiol. Biotechnol. 2005, 68:774-778.
2. +. FEBS J. 2008, 275:3859-3869.
3. Arendt C.S., Ri K., Yates P.A., Ullman B. Genetic selection for a highly functional cysteine-less membrane protein using site saturation mutagenesis. Anal. Biochem. 2007, 365:185-193.
4. Blanusa M., Schenk A., Sadeghi H., Marienhagen J., Schwaneberg U. Phosphorothioate-based ligase-independent gene cloning (PLICing): an enzyme-free and sequence-independent cloning method. Anal. Biochem. 2010, 406:141-146.
5. Burley S.K., Bonanno J.B. Structuring the universe of proteins. Annu. Rev. Genomics Hum. Genet. 2002, 3:243-262.
6. Byrappa S., Gavin D.K., Gupta K.C. A highly efficient procedure for site-specific mutagenesis of full-length plasmids using Vent DNA polymerase. Genome Res. 1995, 5:404-407.
7. Caglio R., Valetti F., Caposio P., Gribaudo G., Pessione E., Giunta C. Fine-tuning of catalytic properties of catechol 1,2-dioxygenase by active site tailoring. Chembiochem. 2009, 10:1015-1024.
8. Chen R. Enzyme engineering: rational redesign versus directed evolution. Trends Biotechnol. 2001, 19:13-14.
9. Chiang L.W., Kovari I., Howe M.M. Mutagenic oligonucleotide-directed PCR amplification (Mod-PCR): an efficient method for generating random base substitution mutations in a DNA sequence element. PCR Methods Appl. 1993, 2:210-217.
10. Dalby P.A. Strategy and success for the directed evolution of enzymes. Curr. Opin. Struct. Biol. 2011, 21:473-480.
11. De Groeve M.R.M., De Baere M., Hoflack L., Desmet T., Vandamme E.J., Soetaert W. Creating lactose phosphorylase enzymes by directed evolution of cellobiose phosphorylase. Protein Eng. Des. Sel. 2009, 22:393-399.
12. De Groeve M.R.M., Remmery L., Van Hoorebeke A., Stout J., Desmet T., Savvides S.N., Soetaert W. Construction of cellobiose phosphorylase variants with broadened acceptor specificity towards anomerically substituted glucosides. Biotechnol. Bioeng. 2010, 107:413-420.
13. Delagrave S., Youvan D.C. Searching sequence space to engineer proteins: exponential ensemble mutagenesis. Biotechnology (N. Y) 1993, 11:1548-1552.
14. Dennig A., Shivange A.V., Marienhagen J., Schwaneberg U. OmniChange: the sequence independent method for simultaneous site-saturation of five codons. PLoS One 2011, 6:e26222.
15. Farinas E.T., Bulter T., Arnold F.H. Directed enzyme evolution. Curr. Opin. Biotechnol. 2001, 12:545-551.
16. Guo Z.Y., Lin S., Heinen J.A., Chang C.C., Chang T.Y. The active site His-460 of human acyl-coenzyme A:cholesterol acyltransferase 1 resides in a hitherto undisclosed transmembrane domain. J. Biol. Chem. 2005, 280:37814-37826.
17. von Heijne G. Membrane proteins: from bench to bits. Biochem. Soc. Trans. 2011, 39:747-750.
18. Herman A., Tawfik D.S. Incorporating synthetic oligonucleotides via gene reassembly (ISOR): a versatile tool for generating targeted libraries. Protein Eng. Des. Sel. 2007, 20:219-226.
19. Higuchi R., Krummel B., Saiki R.K. A general method of in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions. Nucleic Acids Res. 1988, 16:7351-7367.
20. Ho S.N., Hunt H.D., Horton R.M., Pullen J.K., Pease L.R. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 1989, 77:51-59.
21. Huang W., Petrosino J., Hirsch M., Shenkin P.S., Palzkill T. Amino acid sequence determinants of beta-lactamase structure and activity. J. Mol. Biol. 1996, 258:688-703.
22. Jochens H., Bornscheuer U.T. Natural diversity to guide focused directed evolution. Chembiochem. 2010, 11:1861-1866.
23. Kazlauskas R.J., Bornscheuer U.T. Finding better protein engineering strategies. Nat. Chem. Biol. 2009, 5:526-529.
24. 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.
25. Kim H.J., Kang S.Y., Park J.J., Kim P. Novel activity of UDP-galactose-4-epimerase for free monosaccharide and activity improvement by active site-saturation mutagenesis. Appl. Biochem. Biotechnol. 2011, 163:444-451.
26. Koga Y., Kato K., Nakano H., Yamane T. Inverting enantioselectivity of Burkholderia cepacia KWI-56 lipase by combinatorial mutation and high-throughput screening using single-molecule PCR and in vitro expression. J. Mol. Biol. 2003, 331:585-592.
27. Kotzia G.A., Labrou N.E. Engineering thermal stability of l-asparaginase by in vitro directed evolution. FEBS J. 2009, 276:1750-1761.
28. Li H., Yang Y., Zhu D., Hua L., Kantardjieff K. Highly enantioselective mutant carbonyl reductases created via structure-based site-saturation mutagenesis. J. Org. Chem. 2010, 75:7559-7564.
29. Lin M.G., Chen B.E., Liang W.C., Chou W.M., Chen J.H., Kuo L.Y., Lin L.L. Site-saturation mutagenesis of leucine 134 of Bacillus licheniformis nucleotide exchange factor GrpE reveals the importance of this residue to the co-chaperone activity. Protein J. 2010, 29:365-372.
30. Liu D., Trodler P., Eiben S., Koschorreck K., Muller M., Pleiss J., Maurer S.C., Branneby C., Schmid R.D., Hauer B. Rational design of Pseudozyma antarctica lipase B yielding a general esterification catalyst. Chembiochem 2010, 11:789-795.
31. Liu Q., Siloto R.M., Snyder C.L., Weselake R.J. Functional and topological analysis of yeast acyl-CoA: diacylglycerol acyltransferase 2, an endoplasmic reticulum enzyme essential for triacylglycerol biosynthesis. J. Biol. Chem. 2011, 286:13115-13126.
32. Malhotra K.T., Nicholas R.A. Substitution of lysine 213 with arginine in penicillin-binding protein 5 of Escherichia coli abolishes d-alanine carboxypeptidase activity without affecting penicillin binding. J. Biol. Chem. 1992, 267:11386-11391.
33. Matsumura I., Rowe L.A. Whole plasmid mutagenic PCR for directed protein evolution. Biomol. Eng. 2005, 22:73-79.
34. Moreira I.S., Fernandes P.A., Ramos M.J. Computational alanine scanning mutagenesis-an improved methodological approach. J. Comput. Chem. 2007, 28:644-654.
35. Morley K.L., Kazlauskas R.J. Improving enzyme properties: when are closer mutations better?. Trends Biotechnol. 2005, 23:231-237.
36. Paes G., Tran V., Takahashi M., Boukari I., O'Donohue M.J. New insights into the role of the thumb-like loop in GH-11 xylanases. Protein Eng. Des. Sel. 2007, 20:15-23.
37. Parikh M.R., Matsumura I. Site-saturation mutagenesis is more efficient than DNA shuffling for the directed evolution of beta-fucosidase from beta-galactosidase. J. Mol. Biol. 2005, 352:621-628.
38. Pei X.Q., Yi Z.L., Tang C.G., Wu Z.L. Three amino acid changes contribute markedly to the thermostability of beta-glucosidase BglC from Thermobifida fusca. Bioresour. Technol. 2011, 102:3337-3342.
39. Peng R.H., Xiong A.S., Yao Q.H. A direct and efficient PAGE-mediated overlap extension PCR method for gene multiple-site mutagenesis. Appl. Microbiol. Biotechnol. 2006, 73:234-240.
40. Reetz M.T. Laboratory evolution of stereoselective enzymes: a prolific source of catalysts for asymmetric reactions. Angew. Chem. Int. Ed. Engl. 2011, 50:138-174.
41. Reetz M.T., Carballeira J.D. Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat. Protoc. 2007, 2:891-903.
42. 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, 43:5499-5501.
43. Reetz M.T., Wu S. Laboratory evolution of robust and enantioselective Baeyer-Villiger monooxygenases for asymmetric catalysis. J. Am. Chem. Soc. 2009, 131:15424-15432.
44. Reetz M.T., Torre C., Eipper A., Lohmer R., Hermes M., Brunner B., Maichele A., Bocola M., Arand M., Cronin A., Genzel Y., Archelas A., Furstoss R. Enhancing the enantioselectivity of an epoxide hydrolase by directed evolution. Org. Lett. 2004, 6:177-180.
45. Reetz M.T., Bocola M., Carballeira J.D., Zha D., Vogel A. Expanding the range of substrate acceptance of enzymes: combinatorial active-site saturation test. Angew. Chem. Int. Ed. Engl. 2005, 44:4192-4196.
46. Reetz M.T., Wang L.W., Bocola M. Directed evolution of enantioselective enzymes: iterative cycles of CASTing for probing protein-sequence space. Angew. Chem. Int. Ed. Engl. 2006, 45:1236-1241.
47. Reetz M.T., Carballeira J.D., Vogel A. Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability. Angew. Chem. Int. Ed. Engl. 2006, 45:7745-7751.
48. Reetz M.T., Kahakeaw D., Lohmer R. Addressing the numbers problem in directed evolution. Chembiochem. 2008, 9:1797-1804.
49. Reetz M.T., Soni P., Fernandez L. Knowledge-guided laboratory evolution of protein thermolability. Biotechnol. Bioeng. 2009, 102:1712-1717.
50. Reetz M.T., Prasad S., Carballeira J.D., Gumulya Y., Bocola M. Iterative saturation mutagenesis accelerates laboratory evolution of enzyme stereoselectivity: rigorous comparison with traditional methods. J. Am. Chem. Soc. 2010, 132:9144-9152.
51. Sarkar G., Sommer S.S. The "megaprimer" method of site-directed mutagenesis. BioTechniques 1990, 8:404-407.
52. Seyfang A., Jin J.H. Multiple site-directed mutagenesis of more than 10 sites simultaneously and in a single round. Anal. Biochem. 2004, 324:285-291.
53. Steffens D.L., Williams J.G. Efficient site-directed saturation mutagenesis using degenerate oligonucleotides. J. Biomol. Tech. 2007, 18:147-149.
54. Stemmer W.P. Rapid evolution of a protein in vitro by DNA shuffling. Nature 1994, 370:389-391.
55. Svendsen A. Enzyme Functionality: Design, Engineering, and Screening 2004, Marcel Dekker, New York.
56. Tao S., Chen X., Liu J., Ming M., Chong N., Chen D. Characterization of Ser73 in Arabidopsis thaliana Glutathione S-transferase zeta class. J. Genet. Genom. 2008, 35:507-512.
57. Tseng W.C., Lin J.W., Wei T.Y., Fang T.Y. A novel megaprimed and ligase-free, PCR-based, site-directed mutagenesis method. Anal. Biochem. 2008, 375:376-378.
58. Turner N.J. Directed evolution drives the next generation of biocatalysts. Nat. Chem. Biol. 2009, 5:567-573.
59. 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.
60. Walsh C. Enabling the chemistry of life. Nature 2001, 409:226-231.
61. Wang Y., Toei M., Forgac M. Analysis of the membrane topology of transmembrane segments in the C-terminal hydrophobic domain of the yeast vacuolar ATPase subunit a (Vph1p) by chemical modification. J. Biol. Chem. 2008, 283:20696-20702.
62. Warren M.S., Benkovic S.J. Combinatorial manipulation of three key active site residues in glycinamide ribonucleotide transformylase. Protein Eng. 1997, 10:63-68.
63. Wu S., Acevedo J.P., Reetz M.T. Induced allostery in the directed evolution of an enantioselective Baeyer-Villiger monooxygenase. Proc. Natl. Acad. Sci. USA 2010, 107:2775-2780.
64. Yep A., McLeish M.J. Engineering the substrate binding site of benzoylformate decarboxylase. Biochemistry 2009, 48:8387-8395.
65. Zhang J.H., Dawes G., Stemmer W.P. Directed evolution of a fucosidase from a galactosidase by DNA shuffling and screening. Proc. Natl. Acad. Sci. USA 1997, 94:4504-4509.
66. Zheng L., Baumann U., Reymond J.L. An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic Acids Res. 2004, 32:e115.