DC-Analyzer-facilitated combinatorial strategy for rapid directed evolution of functional enzymes with multiple mutagenesis sites

Journal of Biotechnology

Volumn 192, Issue Part A, 2014, Pages 102-107

  Wang, Xiong ^a   Zheng, Kai ^a   Zheng, Huayu ^a   Nie, Hongli ^a   Yang, Zujun ^a   Tang, Lixia ^a  

^a UNIVERSITY OF ELECTRONIC SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

Combinatorial library; DC Analyzer; Directed evolution; Iterative saturation mutagenesis

Indexed keywords

CLONING; ENZYMES; ITERATIVE METHODS; RANDOM PROCESSES;

1 ,3-DICHLORO-2-PROPANOL; AGROBACTERIUM RADIOBACTER AD1; COMBINATORIAL LIBRARY; COMBINATORIAL STRATEGIES; DC-ANALYZER; DIRECTED EVOLUTION; HALOHYDRIN DEHALOGENASE; SATURATION MUTAGENESIS;

MUTAGENESIS;

1,3 DICHLORO 2 PROPANOL; HALOHYDRIN DEHALOGENASE; LYASE; PROPANOL; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; HYDROLASE;

AGROBACTERIUM TUMEFACIENS; ANALYZER; ARTICLE; BIOCATALYST; COMPUTER PROGRAM; DC ANALYZER; ITERATIVE SATURATION MUTAGENESIS; MODIFIED ITERATIVE SATURATION MUTAGENESIS; MUTAGENESIS; RANDOMIZATION; DIRECTED MOLECULAR EVOLUTION; ENZYMOLOGY; ESCHERICHIA COLI; GENETICS;

AGROBACTERIUM TUMEFACIENS; BACTERIAL PROTEINS; DIRECTED MOLECULAR EVOLUTION; ESCHERICHIA COLI; HYDROLASES; MUTAGENESIS;

EID: 84909640175     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2014.10.023     Document Type: Article

References (34)

1. Andrews F.H., McLeish M.J. Using site-saturation mutagenesis to explore mechanism and substrate specificity in thiamin diphosphate-dependent enzymes. FEBS J. 2013, 280:6395-6411.
2. Ba L., Li P., Zhang H., Duan Y., Lin Z. Semi-rational engineering of cytochrome P450sca-2 in a hybrid system for enhanced catalytic activity: insights into the important role of electron transfer. Biotechnol. Bioeng. 2013, 110:2815-2825.
3. Bergmann J., Sanik J. Determination of trace amounts of chlorine in naphtha. Anal. Chem. 1957, 29:241-243.
4. Bhuiya M.W., Liu C.J. Engineering monolignol 4-O-methyltransferases to modulate lignin biosynthesis. J. Biol. Chem. 2010, 285:277-285.
5. Brustad E.M., Arnold F.H. Optimizing non-natural protein function with directed evolution. Curr. Opin. Chem. Biol. 2011, 15:201-210.
6. Dalby P.A. Strategy and success for the directed evolution of enzymes. Curr. Opin. Struct. Biol. 2011, 21:473-480.
7. de Jong R.M., Tiesinga J.J., Villa A., Tang L., Janssen D.B., Dijkstra B.W. Structural basis for the enantioselectivity of an epoxide ring opening reaction catalyzed by halo alcohol dehalogenase HheC. J. Am. Chem. Soc. 2005, 127:13338-13343.
8. Fox R.J., Davis S.C., Mundorff E.C., Newman L.M., Gavrilovic V., Ma S.K., Chung L.M., Ching C., Tam S., Muley S., Grate J., Gruber J., Whitman J.C., Sheldon R.A., Huisman G.W. Improving catalytic function by ProSAR-driven enzyme evolution. Nat. Biotechnol. 2007, 25:338-344.
9. Gumulya Y., Reetz M.T. Enhancing the thermal robustness of an enzyme by directed evolution: least favorable starting points and inferior mutants can map superior evolutionary pathways. Chembiochem 2011, 12:2502-2510.
10. Gumulya Y., Sanchis J., Reetz M.T. Many pathways in laboratory evolution can lead to improved enzymes: how to escape from local minima. Chembiochem 2012, 13:1060-1066.
11. Han R., Liu L., Shin H.D., Chen R.R., Li J., Du G., Chen J. Iterative saturation mutagenesis of -6 subsite residues in cyclodextrin glycosyltransferase from Paenibacillus macerans to improve maltodextrin specificity for 2-O-d-glucopyranosyl-l-ascorbic acid synthesis. Appl. Environ. Microbiol. 2013, 79:7562-7568.
12. Hasnaoui-Dijoux G., Majeric Elenkov M., Lutje Spelberg J.H., Hauer B., Janssen D.B. Catalytic promiscuity of halohydrin dehalogenase and its application in enantioselective epoxide ring opening. Chembiochem 2008, 9:1048-1051.
13. Janssen D.B., Majeric-Elenkov M., Hasnaoui G., Hauer B., Lutje Spelberg J.H. Enantioselective formation and ring-opening of epoxides catalysed by halohydrin dehalogenases. Biochem. Soc. Trans. 2006, 34:291-295.
14. Kille S., Acevedo-Rocha C.G., Parra L.P., Zhang Z.G., Opperman D.J., Reetz M.T., Acevedo J.P. Reducing codon redundancy and screening effort of combinatorial protein libraries created by saturation mutagenesis. ACS Synth. Biol. 2013, 2:83-92.
15. Majeric Elenkov M., Primozic I., Hrenar T., Smolko A., Dokli I., Salopek-Sondi B., Tang L. Catalytic activity of halohydrin dehalogenases towards spiroepoxides. Org. Biomol. Chem. 2012, 10:5063-5072.
16. Majeric Elenkov M., Tang L., Meetsma A., Hauer B., Janssen D.B. Formation of enantiopure 5-substituted oxazolidinones through enzyme-catalysed kinetic resolution of epoxides. Org. Lett. 2008, 10:2417-2420.
17. Martinez R., Schwaneberg U. A roadmap to directed enzyme evolution and screening systems for biotechnological applications. Biol. Res. 2013, 46:395-405.
18. Parra L.P., Agudo R., Reetz M.T. Directed evolution by using iterative saturation mutagenesis based on multiresidue sites. Chembiochem 2013, 14:2301-2309.
19. Reetz M.T., Carballeira J.D. Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat. Protoc. 2007, 2:891-903.
20. 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.
21. Reetz M.T., Kahakeaw D., Lohmer R. Addressing the numbers problem in directed evolution. Chembiochem 2008, 9:1797-1804.
22. Reetz M.T., Kahakeaw D., Sanchis J. Shedding light on the efficacy of laboratory evolution based on iterative saturation mutagenesis. Mol. Biosyst. 2009, 5:115-122.
23. Reetz M.T., Zheng H. Manipulating the expression rate and enantioselectivity of an epoxide hydrolase by using directed evolution. Chembiochem 2011, 12:1529-1535.
24. Shivange A.V., Marienhagen J., Mundhada H., Schenk A., Schwaneberg U. Advances in generating functional diversity for directed protein evolution. Curr. Opin. Chem. Biol. 2009, 13:19-25.
25. Siloto R.M., Weselake R.J. Site saturation mutagenesis: methods and applications in protein engineering. Biocatal. Agric. Biotechnol. 2012, 1:181-189.
26. Tang L., Gao H., Zhu X., Wang X., Zhou M., Jiang R. Construction of "small-intelligent" focused mutagenesis libraries using well-designed combinatorial degenerate primers. Biotechniques 2012, 52:149-158.
27. Tang L., Li Y., Wang X. A high-throughput colorimetric assay for screening halohydrin dehalogenase saturation mutagenesis libraries. J. Biotechnol. 2010, 147:164-168.
28. Tang L., Lutje Spelberg J.H., Fraaije M.W., Janssen D.B. Kinetic mechanism and enantioselectivity of halohydrin dehalogenase from Agrobacterium radiobacter. Biochemistry 2003, 42:5378-5386.
29. Turner N.J. Directed evolution drives the next generation of biocatalysts. Nat. Chem. Biol. 2009, 5:567-573.
30. van Hylckama Vlieg J.E., Tang L., Lutje Spelberg J.H., Smilda T., Poelarends G.J., Bosma T., van Merode A.E., Fraaije M.W., Janssen D.B. Halohydrin dehalogenases are structurally and mechanistically related to short-chain dehydrogenases/reductases. J. Bacteriol. 2001, 183:5058-5066.
31. Wong T.S., Roccatano D., Schwaneberg U. Steering directed protein evolution: strategies to manage combinatorial complexity of mutant libraries. Environ. Microbiol. 2007, 9:2645-2659.
32. Wu Q., Soni P., Reetz M.T. Laboratory evolution of enantiocomplementary Candida antarctica lipase B mutants with broad substrate scope. J. Am. Chem. Soc. 2013, 135:1872-1881.
33. Xie Y., An J., Yang G., Wu G., Zhang Y., Cui L., Feng Y. Enhanced enzyme kinetic stability by increasing rigidity within the active site. J. Biol. Chem. 2014, 289:7994-8006.
34. Zheng H., Reetz M.T. Manipulating the stereoselectivity of limonene epoxide hydrolase by directed evolution based on iterative saturation mutagenesis. J. Am. Chem. Soc. 2010, 132:15744-15751.