Directed protein evolution

Molecular Biomethods Handbook: Second Edition

Volumn , Issue , 2008, Pages 631-656

  Stebel, Sabine C ^a   Gaida, Annette ^a   Arndt, Katja M ^a   Müller, Kristian M ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79959442578     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-60327-375-6_36     Document Type: Chapter

References (48)

1. Seyffert W, Ed. (1998) Lehrbuch der Genetik. Gustav Fischer Verlag, Stuttgart, Jena, Lübeck, Ulm
2. Cadwell RC, Joyce GF (1992) Randomization of genes by PCR mutagenesis PCR. Methods Appl 2:28-33
3. Wong TS, Tee KL, Hauer B, Schwaneberg U (2004) Sequence saturation mutagenesis (SeSaM): A novel method for directed evolution. Nucleic Acids Res 32:e26
4. Hayes F, Hallet B (2000) Pentapeptide scanning mutagenesis: encouraging old proteins to execute unusual tricks. Trends Microbiol 8:571-577
5. Fujii R, Kitaoka M, Hayashi K (2006) RAISE: A simple and novel method of generating random insertion and deletion mutations. Nucleic Acids Res 34:e30
6. Murakami H, Hohsaka T, Sisido M (2002) Random insertion and deletion of arbitrary number of bases for codon-based random mutation of DNAs. Nat Biotechnol 20:76-81
7. Stemmer WP (1994) DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc Natl Acad Sci USA 91:10,747-10,751
8. Stebel SC, Arndt KM, Müller KM (2006) Versatile DNA fragmentation and directed evolution with nucleotide exchange and excision technology. Methods Mol Biol 352:167-190
9. Müller KM, Stebel SC, Knall S, Zipf G, Bernauer HS, Arndt KM (2005) Nucleotide exchange and excision technology (NExT) DNA shuffling: A robust method for DNA fragmentation and directed evolution. Nucleic Acids Res 33:e117
10. Zhao H, Giver L, Shao Z, Affholter JA, Arnold FH (1998) Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat Biotechnol 16:258-261
11. Ikeuchi A, Kawarasaki Y, Shinbata T, Yamane T (2003) Chimeric gene library construction by a simple and highly versatile method using recombination dependent exponential amplification. Biotechnol Prog 19:1460-1467
12. Coco WM, Levinson WE, Crist MJ, Hektor HJ, Darzins A, Pienkos PT, Squires CH, Monticello DJ (2001) DNA shuffling method for generating highly recombined genes and evolved enzymes. Nat Biotechnol 19:354-359
13. Lee SH, Ryu EJ, Kang MJ, Wang ES, Piao Z, Choi YJ, Jung KH, Jeon JYJ, Shin YC (2003) A new approach to directed gene evolution by recombined extension on truncated templates (RETT). J Mol Catalysis B-Enzymatic 26:119-129
14. Song JK, Chung B, Oh YH, Rhee JS (2002) Construction of DNA-shuffled and incrementally truncated libraries by a mutagenic and unidirectional reassembly method: changing from a substrate specificity of phospholipase to that of lipase. Appl Environ Microbiol 68:6146-6151
15. Eggert T, Funke SA, Rao NM, Acharya P, Krumm H, Reetz MT, Jaeger KE (2005) Multiplex-PCR-based recombination as a novel high-fidelity method for directed evolution. Chembiochem 6:1062-1067
16. Chamberlain JS, Gibbs RA, Ranier JE, Nguyen PN, Caskey CT (1988) Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification. Nucleic Acids Res 16:11,141-11,156
17. Shao Z, Zhao H, Giver L, Arnold FH (1998) Random-priming in vitro recombination: An effective tool for directed evolution. Nucleic Acids Res 26: 681-683
18. Volkov AA, Shao Z, Arnold FH (1999) Recombination and chimeragenesis by in vitro heteroduplex formation and in vivo repair. Nucleic Acids Res 27:e18
19. Voigt CA, Martinez C, Wang ZG, Mayo SL, Arnold FH (2002) Protein building blocks preserved by recombination. Nat Struct Biol 9:553-558
20. Ostermeier M, Shim JH, Benkovic SJ (1999) A combinatorial approach to hybrid enzymes independent of DNA homology. Nat Biotechnol 17:1205-1209
21. Ostermeier M, Nixon AE, Shim JH, Benkovic SJ (1999) Combinatorial protein engineering by incremental truncation. Proc Natl Acad Sci USA 96:3562-3567
22. Lutz S, Ostermeier M (2003) Preparation of SCRATCHY hybrid protein libraries: size-and in-frame selection of nucleic acid sequences. Methods Mol Biol 231:143-151
23. Sieber V, Martinez CA, Arnold FH (2001) Libraries of hybrid proteins from distantly related sequences. Nat Biotechnol 19:456-460
24. Ness JE, Kim S, Gottman A, Pak R, Krebber A, Borchert TV, Govindarajan S, Mundorff EC, Minshull J (2002) Synthetic shuffling expands functional protein diversity by allowing amino acids to recombine independently. Nat Biotechnol 20:1251-1255
25. Zha D, Eipper A, Reetz MT (2003) Assembly of designed oligonucleotides as an efficient method for gene recombination: A new tool in directed evolution. Chembiochem 4:34-39
26. Gibbs MD, Nevalainen KM, Bergquist PL (2001) Degenerate oligonucleotide gene shuffling (DOGS): A method for enhancing the frequency of recombination with family shuffling. Gene 271:13-20
27. OMaille PE, Bakhtina M, Tsai MD (2002) Structure-based combinatorial protein engineering (SCOPE). J Mol Biol 321:677-691
28. Hiraga K, Arnold FH (2003) General method for sequence-independent sitedirected chimeragenesis. J Mol Biol 330:287-296
29. Kolkman JA, Stemmer WP (2001) Directed evolution of proteins by exon shuffling. Nat Biotechnol 19:423-428
30. Liao H, McKenzie T, Hageman R (1986) Isolation of a thermostable enzyme variant by cloning and selection in a thermophile. Proc Natl Acad Sci USA 83:576-580
31. Bornscheuer UT, Altenbuchner J, Meyer HH (1998) Directed evolution of an esterase for the stereoselective resolution of a key intermediate in the synthesis of epothilones. Biotechnol Bioeng 58:554-559
32. Taguchi S, Ozaki A, Momose H (1998) Engineering of a cold-Adapted protease by sequential random mutagenesis and a screening system. Appl Environ Microbiol 64:492-495
33. Kano H, Taguchi S, Momose H (1997) Cold adaptation of a mesophilic serine protease, subtilisin, by in vitro random mutagenesis. Appl Microbiol Biotechnol 47:46-51
34. Chen K, Arnold FH (1993) Tuning the activity of an enzyme for unusual environments: sequential random mutagenesis of subtilisin E for catalysis in dimethylformamide. Proc Natl Acad Sci USA 90:5618-5622
35. You L, Arnold FH (1996) Directed evolution of subtilisin E in Bacillus subtilis to enhance total activity in aqueous dimethylformamide. Protein Eng 9:77-83
36. Ness JE, Welch M, Giver L, Bueno M, Cherry JR, Borchert TV, Stemmer WP, Minshull J (1999) DNA shuffling of subgenomic sequences of subtilisin. Nat Biotechnol 17:893-896
37. Zhang JH, Dawes G, Stemmer WP (1997) Directed evolution of a fucosidase from a galactosidase by DNA shuffling and screening. Proc Natl Acad Sci USA 94:4504-4509
38. Carter P, Presta L, Gorman CM, Ridgway JB, Henner D, Wong WL, Rowland AM, Kotts C, Carver ME, Shepard HM (1992) Humanization of an anti-p185HER2 antibody for human cancer therapy. Proc Natl Acad Sci USA 89:4285-4289
39. Locher CP, Heinrichs V, Apt D, Whalen RG (2004) Overcoming antigenic diversity and improving vaccines using DNA shuffling and screening technologies. Expert Opin Biol Ther 4:589-597
40. Apt D, Raviprakash K, Brinkman A, Semyonov A, Yang S, Skinner C, Diehl L, Lyons R, Porter K, Punnonen J (2006) Tetravalent neutralizing antibody response against four dengue serotypes by a single chimeric dengue envelope antigen. Vaccine 24:335-344
41. Raviprakash K, Apt D, Brinkman A, Skinner C, Yang S, Dawes G, Ewing D, Wu SJ, Bass S, Punnonen J, Porter K (2006) A chimeric tetravalent dengue DNA vaccine elicits neutralizing antibody to all four virus serotypes in rhesus macaques. Virology 353:166-173
42. Dua M, Singh A, Sethunathan N, Johri AK (2002) Biotechnology and bioremediation: successes and limitations. Appl Microbiol Biotechnol 59:143-152
43. Dai M, Copley SD (2004) Genome shuffling improves degradation of the anthropogenic pesticide pentachlorophenol by Sphingobium chlorophenolicum ATCC 39723. Appl Environ Microbiol 70:2391-2397
44. Cho CM, Mulchandani A, Chen W (2002) Bacterial cell surface display of organophosphorus hydrolase for selective screening of improved hydrolysis of organophosphate nerve agents. Appl Environ Microbiol 68:2026-2030
45. Chang CC, Chen TT, Cox BW, Dawes GN, Stemmer WP, Punnonen J, Patten PA (1999) Evolution of a cytokine using DNA family shuffling. Nat Biotechnol 17:793-797
46. Griswold KE, Kawarasaki Y, Ghoneim N, Benkovic SJ, Iverson BL, Georgiou G (2005) Evolution of highly active enzymes by homology-independent recombination. Proc Natl Acad Sci USA 102:10,082-10,087
47. Hecky J, Mason JM, Arndt KM, Müller KM (2007) A general method of terminal truncation, evolution, and re-elongation to generate enzymes of enhanced stability. Methods Mol Biol 352:275-304
48. Hecky J, Müller KM (2005) Structural perturbation and compensation by directed evolution at physiological temperature leads to thermostabilization of beta-lactamase. Biochemistry 44:12,640-12,654