A two-step integration method for seamless gene deletion in baker's yeast

Analytical Biochemistry

Volumn 439, Issue 1, 2013, Pages 30-36

  Dong, Jian ^a   Wang, Guanglu ^a   Zhang, Cuiying ^a   Tan, Haigang ^a   Sun, Xi ^a   Wu, Mingyue ^a   Xiao, Dongguang ^a  

^a TIANJIN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

Baker's yeast; Freezing tolerance; Fusion PCR; Gene deletion; Integration

Indexed keywords

DNA; DNA SEQUENCES; FREEZING; GENES; GENETIC ENGINEERING; INTEGRATION; YEAST;

BAKER'S YEAST; FREEZING TOLERANCE; GENE DELETION; INTEGRATION METHOD; SELECTION MARKER; SEQUENCE ANALYSIS; UPSTREAM SEQUENCE; WILD-TYPE STRAIN;

POLYMERASE CHAIN REACTION;

DNA; PLASMID VECTOR; TREHALOSE;

ARTICLE; DNA FLANKING REGION; DNA SEQUENCE; FREEZING; FREEZING TOLERANCE; FUNGAL GENE; GENE DELETION; GENE DISRUPTION; GENE LOCUS; GENETIC ENGINEERING; GENETIC RECOMBINATION; HOMOLOGOUS RECOMBINATION; NONHUMAN; NTH1 GENE; PLASMID; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; TANDEM REPEAT; YEAST CELL;

BASE SEQUENCE; FREEZING; GENE DELETION; GENETIC TECHNIQUES; INDUSTRY; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TREHALOSE;

EID: 84884916322     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2013.04.005     Document Type: Article

References (39)

1. E.A. Winzeler, D.D. Shoemaker, A. Astromoff, H. Liang, K. Anderson, B. Andre, R. Bangham, R. Benito, J.D. Boeke, H. Bussey, et al., Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis, Science 285 (1999) 901-906. (Pubitemid 29381993)
2. A. Baudin, O. Ozier-Kalogeropoulos, A. Denouel, F. Lacroute, C. Cullin, A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae, Nucleic Acids Res. 21 (1993) 3329-3330. (Pubitemid 23230516)
3. M.C. Lorenz, R.S. Muir, E. Lim, J. McElver, S.C. Weber, J. Heitman, Gene disruption with PCR products in Saccharomyces cerevisiae, Gene 158 (1995) 113-117.
4. A. Wach, A. Brachat, R. Pohlmann, P. Philippsen, New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae, Yeast 10 (1994) 1793-1808.
5. E. Alani, L. Cao, N. Kleckner, A method for gene disruption that allows repeated use of URA3 selection in the construction of multiply disrupted yeast strains, Genetics 116 (1987) 541-545.
6. R. Akada, I. Hirosawa, M. Kawahata, H. Hoshida, Y. Nishizawa, Sets of integrating plasmids and gene disruption cassettes containing improved counter-selection markers designed for repeated use in budding yeast, Yeast 19 (2002) 393-402. (Pubitemid 34284882)
7. U. Guldener, S. Heck, T. Fielder, J. Beinhauer, J.H. Hegemann, A new efficient gene disruption cassette for repeated use in budding yeast, Nucleic Acids Res. 24 (1996) 2519-2524. (Pubitemid 26237149)
8. J. Roca, M.R. Gartenberg, Y. Oshima, J.C. Wang, A hit-And-run system for targeted genetic manipulations in yeast, Nucleic Acids Res. 20 (1992) 4671-4672.
9. B. Sauer, Recycling selectable markers in yeast, Biotechniques 16 (1994) 1086-1088. (Pubitemid 24184634)
10. T. Iwaki, K. Takegawa, A set of loxP marker cassettes for Cre-mediated multiple gene disruption in Schizosaccharomyces pombe, Biosci. Biotechnol. Biochem. 68 (2004) 545-550. (Pubitemid 39251490)
11. F. Storici, M. Coglievina, C.V. Bruschi, A 2-micron DNA-based marker recycling system for multiple gene disruption in the yeast Saccharomyces cerevisiae, Yeast 15 (1999) 271-283. (Pubitemid 29132370)
12. J.H. Hegemann, S.B. Heick, Delete and repeat: A comprehensive toolkit for sequential gene knockout in the budding yeast Saccharomyces cerevisiae, Methods Mol. Biol. 765 (2011) 189-206.
13. F. Fang, K. Salmon, M.W. Shen, K.A. Aeling, E. Ito, B. Irwin, U.P. Tran, G.W. Hatfield, N.A. Da Silva, S. Sandmeyer, A vector set for systematic metabolic engineering in Saccharomyces cerevisiae, Yeast 28 (2011) 123-136.
14. R.D. Patel, J.K. Lodge, L.G. Baker, Going green in Cryptococcus neoformans: the recycling of a selectable drug marker, Fungal Genet. Biol. 47 (2010) 191-198.
15. F. Estruch, J.A. Prieto, Construction of a Trp commercial baker's yeast strain by using food-safe-grade dominant drug resistance cassettes, FEMS Yeast Res. 4 (2003) 329-338. (Pubitemid 37494732)
16. R. Akada, T. Kitagawa, S. Kaneko, D. Toyonaga, S. Ito, Y. Kakihara, H. Hoshida, S. Morimura, A. Kondo, K. Kida, PCR-mediated seamless gene deletion and marker recycling in Saccharomyces cerevisiae, Yeast 23 (2006) 399-405.
17. J.D. Boeke, F. LaCroute, G.R. Fink, A positive selection for mutants lacking orotidine-50-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance, Mol. Gen. Genet. 197 (1984) 345-346.
18. P. Klaassen, Y.J. Blankwater, L.P. van Marrewijk, K.A. Osinga, R. Baankreis, Effects of the NTH1 gene disruption in baker's yeast, Folia Microbiol. 39 (1994) 524-526.
19. E. Garre, E. Matallana, The three trehalases Nth1p, Nth2p, and Ath1p participate in the mobilization of intracellular trehalose required for recovery from saline stress in Saccharomyces cerevisiae, Microbiology 155 (2009) 3092-3099.
20. Y. Sasano, Y. Haitani, K. Hashida, I. Ohtsu, J. Shima, H. Takagi, Simultaneous accumulation of proline and trehalose in industrial baker's yeast enhances fermentation ability in frozen dough, J. Biosci. Bioeng. 113 (2012) 592-595.
21. R.D. Gietz, A. Sugino, New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites, Gene 74 (1988) 527-534. (Pubitemid 19060666)
22. X. Sun, C.Y. Zhang, J. Dong, M.Y. Wu, Y. Zhang, D.G. Xiao, Enhanced leavening properties of baker's yeast overexpressing MAL62 with deletion of MIG1 in lean dough, J. Ind. Microbiol. Biotechnol. 39 (2012) 1533-1539.
23. R.D. Gietz, R.H. Schiestl, A.R. Willems, R.A. Woods, Studies on the transformation of intact yeast cells by the LiAc/SS-DNA/PEG procedure, Yeast 11 (1995) 355-360.
24. R. Akada, T. Murakane, Y. Nishizawa, DNA extraction method for screening yeast clones by PCR, Biotechniques 28 (2000) 668-674. (Pubitemid 30198602)
25. J.G. Lewis, R.P. Learmonth, K. Watson, Role of growth phase and ethanol in freeze-Thaw stress resistance of Saccharomyces cerevisiae, Appl. Environ. Microbiol. 59 (1993) 1065-1071. (Pubitemid 23096644)
26. J. Shima, A. Hino, C. Yamada-Iyo, Y. Suzuki, R. Nakajima, H. Watanabe, K. Mori, H. Takano, Stress tolerance in doughs of Saccharomyces cerevisiae trehalase mutants derived from commercial baker's yeast, Appl. Environ. Microbiol. 65 (1999) 2841-2846. (Pubitemid 29315550)
27. R. Akada, K. Matsuo, K. Aritomi, Y. Nishizawa, Construction of recombinant sake yeast containing a dominant FAS2 mutation without extraneous sequences by a two-step gene replacement protocol, J. Biosci. Bioeng. 87 (1999) 43-48. (Pubitemid 29162229)
28. C. Jacq, J. Alt-Morbe, B. Andre, W. Arnold, A. Bahr, J.P. Ballesta, M. Bargues, L. Baron, A. Becker, N. Biteau, et al., The nucleotide sequence of Saccharomyces cerevisiae chromosome IV, Nature 387 (1997) 75-78. (Pubitemid 27334669)
29. R. Walgate, Genetic manipulation: Britain may exempt ''self-cloning'', Nature 277 (1979) 589.
30. M. Walker, A. Vystavelova, S. Pedler, J. Eglinton, V. Jiranek, PCR-based gene disruption and recombinatory marker excision to produce modified industrial Saccharomyces cerevisiae without added sequences, J. Microbiol. Methods 63 (2005) 193-204. (Pubitemid 41443328)
31. F. Storici, L.K. Lewis, M.A. Resnick, In vivo site-directed mutagenesis using oligonucleotides, Nat. Biotechnol. 19 (2001) 773-776. (Pubitemid 32729542)
32. J.F. Davidson, R.H. Schiestl, Mis-Targeting of multiple gene disruption constructs containing hisG, Curr. Genet. 38 (2000) 188-190.
33. B.L. Schneider, B. Steiner, W. Seufert, A.B. Futcher, PMPY-ZAP: a reusable polymerase chain reaction-directed gene disruption cassette for Saccharomyces cerevisiae, Yeast 12 (1996) 129-134. (Pubitemid 26058232)
34. D. Delneri, G.C. Tomlin, J.L. Wixon, A. Hutter, M. Sefton, E.J. Louis, S.G. Oliver, Exploring redundancy in the yeast genome: an improved strategy for use of the Cre-loxP system, Gene 252 (2000) 127-135. (Pubitemid 30618819)
35. S. Dequin, The potential of genetic engineering for improving brewing, winemaking, and baking yeasts, Appl. Microbiol. Biotechnol. 56 (2001) 577-588. (Pubitemid 32831582)
36. W.A. Fonzi, M.Y. Irwin, Isogenic strain construction and gene mapping in Candida albicans, Genetics 134 (1993) 717-728. (Pubitemid 23193572)
37. S. Hashimoto, M. Ogura, K. Aritomi, H. Hoshida, Y. Nishizawa, R. Akada, Isolation of auxotrophic mutants of diploid industrial yeast strains after UV mutagenesis, Appl. Environ. Microbiol. 71 (2005) 312-319. (Pubitemid 40116283)
38. B. Regenberg, J. Hansen, GAP1, a novel selection and counter-selection marker for multiple gene disruptions in Saccharomyces cerevisiae, Yeast 16 (2000) 1111-1119.
39. I. Hirosawa, K. Aritomi, H. Hoshida, S. Kashiwagi, Y. Nishizawa, R. Akada, Construction of a self-cloning sake yeast that overexpresses alcohol acetyltransferase gene by a two-step gene replacement protocol, Appl. Microbiol. Biotechnol. 65 (2004) 68-73. (Pubitemid 39044313)