Optimization of ordered plasmid assembly by gap repair in Saccharomyces cerevisiae

Yeast

Volumn 29, Issue 8, 2012, Pages 323-334

  Eckert Boulet, Nadine ^a   Pedersen, Mette Louise ^a,b   Krogh, Berit Olsen ^b   Lisby, Michael ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b NOVO NORDISK A S   (Denmark)

Author keywords

Combinatorial libraries; Gap repair; Homologous recombination; Saccharomyces cerevisiae

Indexed keywords

DNA FRAGMENT; HELICASE; LITHIUM ACETATE; PLASMID VECTOR;

ARTICLE; COMBINATORIAL LIBRARY; CONTROLLED STUDY; DNA LIBRARY; GENE DELETION; GENETIC TRANSFORMATION; HOMOLOGOUS RECOMBINATION; IN VIVO STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; REACTION OPTIMIZATION; RECOMBINATION REPAIR; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY;

DNA, FUNGAL; GENETIC VECTORS; GENETICS, MICROBIAL; MOLECULAR BIOLOGY; MUTATION; PLASMIDS; RECOMBINATION, GENETIC; SACCHAROMYCES CEREVISIAE; SEQUENCE DELETION;

SACCHAROMYCES CEREVISIAE;

EID: 84865067659     PISSN: 0749503X     EISSN: 10970061     Source Type: Journal    
DOI: 10.1002/yea.2912     Document Type: Article

References (53)

1. Altmannova V, Eckert-Boulet N, Arneric M, et al. 2010. Rad52 SUMOylation affects the efficiency of the DNA repair. Nucleic Acids Res 38: 4708-4721.
2. An Y, Wu W, Lv A. 2010. A convenient and robust method for construction of combinatorial and random mutant libraries. Biochimie 92: 1081-1084.
3. Aylon Y, Kupiec M. 2004. DSB repair: the yeast paradigm. DNA Repair (Amst) 3: 797-815.
4. Bachrati CZ, Hickson ID. 2003. RecQ helicases: suppressors of tumorigenesis and premature aging. Biochem J 374: 577-606.
5. Boder ET, Wittrup KD. 1997. Yeast surface display for screening combinatorial polypeptide libraries. Nat Biotechnol 15: 553-557.
6. Clausing E, Mayer A, Chanarat S, et al. 2010. The transcription elongation factor Bur1-Bur2 interacts with replication protein A and maintains genome stability during replication stress. J Biol Chem 285: 41665-41674.
7. Davis AP, Symington LS. 2001. The yeast recombinational repair protein Rad59 interacts with Rad52 and stimulates single-strand annealing. Genetics 159: 515-525.
8. De Antoni A, Gallwitz D. 2000. A novel multi-purpose cassette for repeated integrative epitope tagging of genes in Saccharomyces cerevisiae. Gene 246: 179-185.
9. Dong Z, Fasullo M. 2003. Multiple recombination pathways for sister chromatid exchange in Saccharomyces cerevisiae: role of RAD1 and the RAD52 epistasis group genes. Nucleic Acids Res 31: 2576-2585.
10. Dudasova Z, Dudas A, Chovanec M. 2004. Non-homologous end-joining factors of Saccharomyces cerevisiae. FEMS Microbiol Rev 28: 581-601.
11. Dufner P, Jermutus L, Minter RR. 2006. Harnessing phage and ribosome display for antibody optimisation. Trends Biotechnol 24: 523-529.
12. Erdeniz N, Mortensen UH, Rothstein R. 1997. Cloning-free PCR-based allele replacement methods. Genome Res 7: 1174-1183.
13. Falco SC, Rose M, Rothstein R. 1983. Homologous recombination between episomal plasmids and chromosomes in yeast. Genetics 105: 843-856.
14. Game JC, Birrell GW, Brown JA, et al. 2003. Use of a genome-wide approach to identify new genes that control resistance of Saccharomyces cerevisiae to ionizing radiation. Radiat Res 160: 14-24.
15. Game JC, Mortimer RK. 1974. A genetic study of X-ray sensitive mutants in yeast. Mutat Res 24: 281-292.
16. Garufi G, Minenkova O, Lo Passo C, et al. 2005. Display libraries on bacteriophage-λ capsid. Biotechnol Annu Rev 11: 153-190.
17. Glaser VM, Glasunov AV, Tevzadze GG, et al. 1990. Genetic control of plasmid DNA double-strand gap repair in yeast, Saccharomyces cerevisiae. Curr Genet 18: 1-5.
18. Gravel S, Chapman JR, Magill C, Jackson SP. 2008. DNA helicases Sgs1 and BLM promote DNA double-strand break resection. Genes Dev 22: 2767-2772.
19. Guldener U, Heck S, Fielder T, et al. 1996. A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res 24: 2519-2524.
20. Hackel BJ, Kapila A, Wittrup KD. 2008. Picomolar affinity fibronectin domains engineered utilizing loop length diversity, recursive mutagenesis, and loop shuffling. J Mol Biol 381: 1238-1252.
21. Hanes J, Jermutus L, Pluckthun A. 2000. Selecting and evolving functional proteins in vitro by ribosome display. Methods Enzymol 328: 404-430.
22. Ho M, Nagata S, Pastan I. 2006. Isolation of anti-CD22 Fv with high affinity by Fv display on human cells. Proc Natl Acad Sci USA 103: 9637-9642.
23. Hurt JA, Thibodeau SA, Hirsh AS, et al. 2003. Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection. Proc Natl Acad Sci USA 100: 12271-12276.
24. Jose J. 2006. Autodisplay: efficient bacterial surface display of recombinant proteins. Appl Microbiol Biotechnol 69: 607-614.
25. Kim J, Schumann W. 2009. Display of proteins on Bacillus subtilis endospores. Cell Mol Life Sci 66: 3127-3136.
26. Krejci L, Van Komen S, Li Y, et al. 2003. DNA helicase Srs2 disrupts the Rad51 presynaptic filament. Nature 423: 305-309.
27. Krogh BO, Llorente B, Lam A, Symington LS. 2005. Mutations in Mre11 phosphoesterase motif I that impair Saccharomyces cerevisiae Mre11-Rad50-Xrs2 complex stability in addition to nuclease activity. Genetics 171: 1561-1570.
28. Kuepper MB, Huhn M, Spiegel H, et al. 2005. Generation of human antibody fragments against Streptococcus mutans using a phage display chain shuffling approach. BMC Biotechnol 5: 4.
29. Lawrence CW, Christensen RB. 1976. Metabolic suppressors of trimethoprim and ultraviolet light sensitivities of Saccharomyces cerevisiae rad6 mutants. J Bacteriol 139: 866-876.
30. 2/M arrest after DNA damage. Cell 94: 399-409.
31. Lisby M, Barlow JH, Burgess RC, Rothstein R. 2004. Choreography of the DNA damage response; spatiotemporal relationships among checkpoint and repair proteins. Cell 118: 699-713.
32. Lisby M, Mortensen UH, Rothstein R. 2003. Colocalization of multiple DNA double-strand breaks at a single Rad52 repair centre. Nat Cell Biol 5: 572-577.
33. Ma H, Kunes S, Schatz PJ, Bothstein D. 1987. Plasmid construction by homologous recombination in yeast. Gene 58: 201-216
34. Mimitou EP, Symington LS. 2009a. DNA end resection: many nucleases make light work. DNA Repair (Amst) 8: 983-995.
35. Mimitou EP, Symington LS. 2009b. Nucleases and helicases take center stage in homologous recombination. Trends Biochem Sci 34: 264-272.
36. Muhlrad D, Hunter R, Parker R. 1992. A rapid method for localized mutagenesis of yeast genes. Yeast 8: 79-82.
37. Nour-Eldin HH, Geu-Flores F, Halkier BA. 2010. USER cloning and USER fusion: the ideal cloning techniques for small and big laboratories. Methods Mol Biol 643: 185-200.
38. Orr-Weaver TL, Szostak JW, Rothstein RJ. 1983. Genetic applications of yeast transformation with linear and gapped plasmids. Methods Enzymol 101: 228-245.
39. Pande J, Szewczyk MM, Grover AK. 2010. Phage display: concept, innovations, applications and future. Biotechnol Adv 28: 849-858.
40. Schiestl RH, Gietz RD. 1989. High efficiency transformation of intact yeast cells using single stranded nucleic acids as a carrier. Curr Genet 16: 339-346.
41. Sherman F, Fink GR, Hicks JB. 1986. Methods in Yeast Genetics. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY.
42. Shibasaki S, Maeda H, Ueda M. 2009. Molecular display technology using yeast-arming technology. Anal Sci 25: 41-49.
43. Solinger JA, Heyer WD. 2001. Rad54 protein stimulates the postsynaptic phase of Rad51 protein-mediated DNA strand exchange. Proc Natl Acad Sci USA 98: 8447-8453.
44. Sugawara N, Haber JE. 1992. Characterization of double-strand break-induced recombination: homology requirements and single-stranded DNA formation. Mol Cell Biol 12: 563-575.
45. Sugawara N, Ira G, Haber JE. 2000. DNA length dependence of the single-strand annealing pathway and the role of Saccharomyces cerevisiae RAD59 in double-strand break repair. Mol Cell Biol 20: 5300-5309.
46. Sung P. 1994. Catalysis of ATP-dependent homologous DNA pairing and strand exchange by yeast RAD51 protein. Science 265: 1241-1243.
47. Swers JS, Kellogg BA, Wittrup KD. 2004. Shuffled antibody libraries created by in vivo homologous recombination and yeast surface display. Nucleic Acids Res 32: e36.
48. Thomas BJ, Rothstein R. 1989. Elevated recombination rates in transcriptionally active DNA. Cell 56: 619-630.
49. Torres-Rosell J, Sunjevaric I, De Piccoli G, et al. 2007. The Smc5-Smc6 complex and SUMO modification of Rad52 regulates recombinational repair at the ribosomal gene locus. Nat Cell Biol 9: 923-931.
50. van der Veen BA, Potocki-Veronese G, Albenne C, et al. 2004. Combinatorial engineering to enhance amylosucrase performance: construction, selection, and screening of variant libraries for increased activity. FEBS Lett 560: 91-97.
51. Veaute X, Jeusset J, Soustelle C, et al. 2003. The Srs2 helicase prevents recombination by disrupting Rad51 nucleoprotein filaments. Nature 423: 309-312.
52. Villiers BR, Stein V, Hollfelder F. 2010. USER friendly DNA recombination (USERec): a simple and flexible near homology-independent method for gene library construction. Protein Eng Des Sel 23: 1-8.
53. Zhu Z, Chung WH, Shim EY, et al. 2008. Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double-strand break ends. Cell 134: 981-994.