General method for sequence-independent site-directed chimeragenesis

Journal of Molecular Biology

Volumn 330, Issue 2, 2003, Pages 287-296

  Hiraga, Kaori ^a   Arnold, Frances H ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Directed evolution; DNA shuffling; Non homologous recombination; SCHEMA

Indexed keywords

BETA LACTAMASE; CHIMERIC PROTEIN; RECOMBINANT ENZYME;

ALGORITHM; ARTICLE; CALCULATION; CHIMERA; CLONE; CONTROLLED STUDY; ENZYME ACTIVITY; GENE DISRUPTION; GENE LIBRARY; GENE PROBE; GENE SEQUENCE; GENE TARGETING; GENETIC CODE; GENETIC PROCEDURES; GENETIC RECOMBINATION; HYBRIDIZATION; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROCESSING; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SEQUENCE INDEPENDENT SITE DIRECTED CHIMERAGENESIS;

EID: 0038799745     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00590-4     Document Type: Article

References (30)

1. Minshull J., Stemmer W.P.C. Protein evolution by molecular breeding. Curr. Opin. Chem. Biol. 3:1999;284-290.
2. Stevenson J.D., Benkovic S.J. Combinatorial approaches to engineering hybrid enzymes. J. Chem. Soc. 2:2002;1483-1493.
3. Coco W.M., Levinson W.E., Crist M.J., Hektor H.J., Darzins A., Pienkos P.T., et al. DNA shuffling method for generating highly recombined genes and evolved enzymes. Nature Biotechnol. 19:2001;354-359.
4. Crameri A., Raillard S.A., Bermudez E., Stemmer W.P.C. DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature. 391:1998;288-291.
5. Moore J.C., Jin H.M., Kuchner O., Arnold F.H. Strategies for the in vitro evolution of protein function: enzyme evolution by random recombination of improved sequences. J. Mol. Biol. 272:1997;336-347.
6. Shao Z., Zhao H., Giver L., Arnold F.H. Random-priming in vitro recombination: an effective tool for directed evolution. Nucl. Acids Res. 26:1998;681-683.
7. Stemmer W.P.C. Rapid evolution of a protein in vitro by DNA shuffling. Nature. 370:1994;389-391.
8. Zhao H., Giver L., Shao Z., Affholter J.A., Arnold F.H. Molecular evolution by staggered extension process (StEP) in vitro recombination. Nature Biotechnol. 16:1998;258-261.
9. Joern J.M., Meinhold P., Arnold F.H. Analysis of shuffled gene libraries. J. Mol. Biol. 316:2002;643-656.
10. Ostermeier M., Shim J.H., Benkovic S.J. A combinatorial approach to hybrid enzymes independent of DNA homology. Nature Biotechnol. 17:1999;1205-1209.
11. Lutz S., Ostermeier M., Moore G.L., Maranas C.D., Benkovic S.J. Creating multiple-crossover DNA libraries independent of sequence identity. Proc. Natl Acad. Sci. USA. 98:2001;11248-11253.
12. Sieber V., Martinez C.A., Arnold F.H. Libraries of hybrid proteins from distantly related sequences. Nature Biotechnol. 19:2001;456-460.
13. Apic G., Gough J., Teichmann S.A. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J. Mol. Biol. 310:2001;311-325.
14. de Souza S.J., Long M., Gilbert W. Introns and gene evolution. Genes Cells. 1:1996;493-505.
15. Doolittle R.F. The multiplicity of domains in proteins. Annu. Rev. Biochem. 64:1995;287-314.
16. Gilbert W. Why genes in pieces? Nature. 271:1978;501.
17. Thornton J.M., Orengo C.A., Todd A.E., Pearl F.M.G. Protein folds, functions and evolution. J. Mol. Biol. 293:1999;333-342.
18. O'Maille P.E., Bakhtina M., Tsai M.D. Structure-based combinatorial protein engineering (SCOPE). J. Mol. Biol. 321:2002;677-691.
19. Tsuji T., Onimaru M., Yanagawa H. Random multi-recombinant PCR for the construction of combinatorial protein libraries. Nucl. Acids Res. 29:2001;E97.
20. Voigt C.A., Martinez C., Wang Z.G., Mayo S.L., Arnold F.H. Protein building blocks preserved by recombination. Nature Struct. Biol. 9:2002;553-558.
21. Kolkman J.A., Stemmer W.P.C. Directed evolution of proteins by exon shuffling. Nature Biotechnol. 19:2001;423-428.
22. Tsuji T., Yoshida K., Satoh A., Kohno T., Kobayashi K., Yanagawa H. Foldability of barnase mutants obtained by permutation of modules or secondary structure units. J. Mol. Biol. 286:1999;1581-1596.
23. Horton R.M., Hunt H.D., Ho S.N., Pullen J.K., Pease L.R. Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene. 77:1989;61-68.
24. Cho G., Keefe A.D., Liu R., Wilson D.S., Szostak J.W. Constructing high complexity synthetic libraries of long ORFs using in vitro selection. J. Mol. Biol. 297:2000;309-319.
25. Riechmann L., Winter G. Novel folded protein domains generated by combinatorial shuffling of polypeptide segments. Proc. Natl Acad. Sci. USA. 97:2000;10068-10073.
26. Jelsch C., Mourey L., Masson J.M., Samama J.P. Crystal structure of Escherichia coli TEM1 β-lactamase at 1.8 Å resolution. Proteins: Struct. Funct. Genet. 16:1993;364-383.
27. Lim D., Sanschagrin F., Passmore L., De Castro L., Levesque R.C., Strynadka N.C.J. Insights into the molecular basis for the carbenicillinase activity of PSE-4 β-lactamase from crystallographic and kinetic studies. Biochemistry. 40:2001;395-402.
28. Sears L.E., Zhou B., Aliotta J.M., Morgan R.D., Kong H. BaeI, another unusual BcgI-like restriction endonuclease. Nucl. Acids Res. 24:1996;3590-3592.
29. In the press Meyer M.M., Silberg J.J., Voigt C.A., Endelman J.B., Mayo S.L., Wang Z.-G., Arnold F.H. Library analysis of SCHEMA-guided protein recombination. Protein Sci. 2003.
30. Sabbagh Y., Theriault E., Sanschagrin F., Voyer N., Palzkill T., Levesque R.C. Characterization of a PSE-4 mutant with different properties in relation to penicillanic acid sulfones: importance of residues 216-218 in class A β-lactamases. Antimicrob. Agents Chemother. 42:1998;2319-2325.