Novel method for genomic promoter shuffling by using recyclable cassettes

Applied and Environmental Microbiology

Volumn 79, Issue 22, 2013, Pages 7042-7047

  Tian, Xuelei ^a   Xu, Xin ^a,b   Xiao, Wei ^a,b  

^a CAPITAL NORMAL UNIVERSITY   (China)

^b UNIVERSITY OF SASKATCHEWAN   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

GENETIC ELEMENTS; HOMOLOGOUS RECOMBINATION; MARKER GENES; NOVEL CONCEPT; PROOF OF PRINCIPLES; SACCHAROMYCES CEREVISIAE GENOME; SELECTABLE MARKER GENES; TANDEM REPEATS;

YEAST;

GENES;

BIOENGINEERING; CHROMOSOME; GENETIC ANALYSIS; GENETIC MARKER; GENOME; GENOMICS; HOMOLOGY; INTEGRATED APPROACH; RECOMBINATION; YEAST;

FUNGAL DNA;

ARTICLE; DNA SEQUENCE; FLUORESCENCE MICROSCOPY; FUNGAL GENE; GENE EXPRESSION REGULATION; GENE LOCUS; GENETIC ENGINEERING; GENETIC MARKER; GENETIC RECOMBINATION; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; PLASMID; PROMOTER REGION; REPORTER GENE; SACCHAROMYCES CEREVISIAE;

DNA, FUNGAL; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; GENES, REPORTER; GENETIC ENGINEERING; GENETIC LOCI; GENETIC MARKERS; MICROSCOPY, FLUORESCENCE; PLASMIDS; PROMOTER REGIONS, GENETIC; RECOMBINATION, GENETIC; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, DNA;

EID: 84886667629     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02159-13     Document Type: Article

References (35)

1. Orr-Weaver TL, Szostak JW. 1983. Yeast recombination: the association between double-strand gap repair and crossing-over. Proc. Natl. Acad. Sci. U. S. A. 80:4417-4421.
2. Orr-Weaver TL, Szostak JW, Rothstein RJ. 1981. Yeast transformation: a model system for the study of recombination. Proc. Natl. Acad. Sci. U. S. A. 78:6354-6358.
3. Szostak JW, Orr-Weaver TL, Rothstein RJ, Stahl FW. 1983. The doublestrand- break repair model for recombination. Cell 33:25-35.
4. Knop M, Siegers K, Pereira G, Zachariae W, Winsor B, Nasmyth K, Schiebel E. 1999. Epitope tagging of yeast genes using a PCR-based strategy: more tags and improved practical routines. Yeast 15:963-972.
5. Orr-Weaver TL, Szostak JW, Rothstein RJ. 1983. Genetic applications of yeast transformation with linear and gapped plasmids. Methods Enzymol. 101:228-245.
6. Rothstein RJ. 1983. One-step gene disruption in yeast. Methods Enzymol. 101:202-211.
7. Scherer S, Davis RW. 1979. Replacement of chromosome segments with altered DNA sequences constructed in vitro. Proc. Natl. Acad. Sci. U. S. A. 76:4951-4955.
8. Brachmann CB, Davies A, Cost GJ, Caputo E, Li J, Hieter P, Boeke JD. 1998. Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14:115-132.
9. Christianson TW, Sikorski RS, Dante M, Shero JH, Hieter P. 1992. Multifunctional yeast high-copy-number shuttle vectors. Gene 110:119- 122.
10. Fang F, Salmon K, Shen MW, Aeling KA, Ito E, Irwin B, Tran UP, Hatfield GW, Da Silva NA, Sandmeyer S. 2011. A vector set for systematic metabolic engineering in Saccharomyces cerevisiae. Yeast 28:123-136.
11. Gueldener U, Heinisch J, Koehler GJ, Voss D, Hegemann JH. 2002. A second set of loxP marker cassettes for Cre-mediated multiple gene knockouts in budding yeast. Nucleic Acids Res. 30:e23. doi:10.1093/nar/30.6.e23.
12. Da Silva NA, Srikrishnan S. 2012. Introduction and expression of genes for metabolic engineering applications in Saccharomyces cerevisiae. FEMS Yeast Res. 12:197-214.
13. Alani E, Cao L, Kleckner N. 1987. A method for gene disruption that allows repeated use of URA3 selection in the construction of multiply disrupted yeast strains. Genetics 116:541-545.
14. Boeke JD, LaCroute F, Fink GR. 1984. A positive selection for mutants lacking orotidine-5'-phosphate decarboxylase activity in yeast: 5-fluoroorotic acid resistance. Mol. Gen. Genet. 197:345-346.
15. Guldener U, Heck S, Fielder T, Beinhauer J, Hegemann JH. 1996. A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res. 24:2519-2524.
16. Voth WP, Richards JD, Shaw JM, Stillman DJ. 2001. Yeast vectors for integration at the HO locus. Nucleic Acids Res. 29:E59. doi:10.1093/nar/29.12.e59.
17. Deng C, Xiong X, Krutchinsky AN. 2009. Unifying fluorescence microscopy and mass spectrometry for studying protein complexes in cells. Mol. Cell. Proteomics 8:1413-1423.
18. Hanna M, Xiao W. 2006. Isolation of nucleic acids. Methods Mol. Biol. 313:15-20.
19. Fu Y, Xiao W. 2006. Identification and characterization of CRT10 as a novel regulator of Saccharomyces cerevisiae ribonucleotide reductase genes. Nucleic Acids Res. 34:1876-1883.
20. Fu Y, Zhu Y, Zhang K, Yeung M, Durocher D, Xiao W. 2008. Rad6- Rad18 mediates a eukaryotic SOS response by ubiquitinating the 9-1-1 checkpoint clamp. Cell 133:601-611.
21. Ogden JE, Stanway C, Kim S, Mellor J, Kingsman AJ, Kingsman SM. 1986. Efficient expression of the Saccharomyces cerevisiae PGK gene depends on an upstream activation sequence but does not require TATA sequences. Mol. Cell. Biol. 6:4335-4343.
22. Partow S, Siewers V, Bjorn S, Nielsen J, Maury J. 2010. Characterization of different promoters for designing a new expression vector in Saccharomyces cerevisiae. Yeast 27:955-964.
23. Gerami-Nejad M, Hausauer D, McClellan M, Berman J, Gale C. 2004. Cassettes for the PCR-mediated construction of regulatable alleles in Candida albicans. Yeast 21:429-436.
24. Johnston M, Flick JS, Pexton T. 1994. Multiple mechanisms provide rapid and stringent glucose repression of GAL gene expression in Saccharomyces cerevisiae. Mol. Cell. Biol. 14:3834-3841.
25. Yocum RR, Hanley S, West R, Jr, Ptashne M. 1984. Use of lacZ fusions to delimit regulatory elements of the inducible divergent GAL1-GAL10 promoter in Saccharomyces cerevisiae. Mol. Cell. Biol. 4:1985-1998.
26. Gari E, Piedrafita L, Aldea M, Herrero E. 1997. A set of vectors with a tetracycline-regulatable promoter system for modulated gene expression in Saccharomyces cerevisiae. Yeast 13:837-848.
27. Gossen M, Bujard H. 1992. Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proc. Natl. Acad. Sci. U. S. A. 89:5547-5551.
28. Mnaimneh S, Davierwala AP, Haynes J, Moffat J, Peng WT, Zhang W, Yang X, Pootoolal J, Chua G, Lopez A, Trochesset M, Morse D, Krogan NJ, Hiley SL, Li Z, Morris Q, Grigull J, Mitsakakis N, Roberts CJ, Greenblatt JF, Boone C, Kaiser CA, Andrews BJ, Hughes TR. 2004. Exploration of essential gene functions via titratable promoter alleles. Cell 118:31-44.
29. Erdeniz N, Mortensen UH, Rothstein R. 1997. Cloning-free PCR-based allele replacement methods. Genome Res. 7:1174-1183.
30. Manivasakam P, Weber SC, McElver J, Schiestl RH. 1995. Microhomology mediated PCR targeting in Saccharomyces cerevisiae. Nucleic Acids Res. 23:2799-2800.
31. Oldenburg KR, Vo KT, Michaelis S, Paddon C. 1997. Recombinationmediated PCR-directed plasmid construction in vivo in yeast. Nucleic Acids Res. 25:451-452.
32. Adams BG. 1972. Induction of galactokinase in Saccharomyces cerevisiae: kinetics of induction and glucose effects. J. Bacteriol. 111:308-315.
33. Choi PJ, Cai L, Frieda K, Xie XS. 2008. A stochastic single-molecule event triggers phenotype switching of a bacterial cell. Science 322:442-446.
34. Lenfant F, Mann RK, Thomsen B, Ling X, Grunstein M. 1996. All four core histone N-termini contain sequences required for the repression of basal transcription in yeast. EMBO J. 15:3974-3985.
35. Mann RK, Grunstein M. 1992. Histone H3 N-terminal mutations allow hyperactivation of the yeast GAL1 gene in vivo. EMBO J. 11:3297-3306.