One-step assembly and targeted integration of multigene constructs assisted by the I-SceI meganuclease in Saccharomyces cerevisiae

FEMS Yeast Research

Volumn 13, Issue 8, 2013, Pages 769-781

  Kuijpers, Niels G A ^a,b   Chroumpi, Soultana ^a,b   Vos, Tim ^a,b   Solis Escalante, Daniel ^a,b   Bosman, Lizanne ^a,b   Pronk, Jack T ^a,b,c   Daran, Jean Marc ^a,b,c   Daran Lapujade, Pascale ^a,b  

^a DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

^b KLUYVER CENTRE FOR GENOMICS OF INDUSTRIAL FERMENTATION   (Netherlands)

^c Platform Green Synthetic Biology   (Netherlands)

Author keywords

Homologous recombination; in vivo assembly; Pathway engineering; Synthetic biology

Indexed keywords

CANAVANINE; DNA FRAGMENT; FUNGAL DNA; GENOMIC DNA; I SCEI PROTEIN; NITROGEN; NUCLEASE; UNCLASSIFIED DRUG;

ARTICLE; DNA INTEGRATION; DNA STRAND BREAKAGE; DOUBLE STRANDED DNA BREAK; FUNGAL GENE; GENE CASSETTE; GENE CONSTRUCT; GENE EXPRESSION; GENE LOCUS; HOMOLOGOUS RECOMBINATION; MITOCHONDRIAL GENE; MULTIGENE FAMILY; MULTIPLEX POLYMERASE CHAIN REACTION; NONHUMAN; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE;

HOMOLOGOUS RECOMBINATION; IN VIVO ASSEMBLY; PATHWAY ENGINEERING; SYNTHETIC BIOLOGY;

AMINO ACID TRANSPORT SYSTEMS, BASIC; CELL CYCLE PROTEINS; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA BREAKS, DOUBLE-STRANDED; GENE ORDER; GENE TARGETING; GLYCOLYSIS; GTP PHOSPHOHYDROLASES; HOMOLOGOUS RECOMBINATION; MUTAGENESIS, INSERTIONAL; QUANTITATIVE TRAIT LOCI; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84887606266     PISSN: 15671356     EISSN: 15671364     Source Type: Journal    
DOI: 10.1111/1567-1364.12087     Document Type: Article

References (41)

1. Alberti S, Gitler AD & Lindquist S (2007) A suite of Gateway cloning vectors for high-throughput genetic analysis in Saccharomyces cerevisiae. Yeast 24: 913-919.
2. Benoit RM, Wilhelm RN, Scherer-Becker D & Ostermeier C (2006) An improved method for fast, robust, and seamless integration of DNA fragments into multiple plasmids. Protein Expr Purif 45: 66-71.
3. Choulika A, Perrin A, Dujon B & Nicolas JF (1995) Induction of homologous recombination in mammalian chromosomes by using the I-SceI system of Saccharomyces cerevisiae. Mol Cell Biol 15: 1968-1973.
4. Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Bogdanove AJ & Voytas DF (2010) Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186: 757-761.
5. Cong L, Ran FA, Cox D et al. (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339: 819-823.
6. Ellis T, Adie T & Baldwin GS (2011) DNA assembly for synthetic biology: from parts to pathways and beyond. Integr Biol (Camb) 3: 109-118.
7. Entian KD & Kotter P (2007) Yeast genetic strain and plasmid collections. Method Microbiol, Vol. 36 (Stansfield I & Stark MJR, eds), pp. 629-666. Academic Press, Amsterdam, The Netherlands.
8. Gibson DG, Benders G, Axelrod KC, Zaveri J, Algire M, Moodie M, Montague MG, Venter JC, Smith HO & Hutchison C (2008) One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. P Natl Acad Sci USA 105: 20404-20409.
9. Gibson DG, Young L, Chuang RY, Venter JC, Iii CAH, Smith HO & America N (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6: 12-16.
10. Gietz RD & Woods R (2002) Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol 350: 87-96.
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.
12. Kandavelou K, Mani M, Durai S & Chandrasegaran S (2005) "Magic" scissors for genome surgery. Nat Biotechnol 23: 686-687.
13. Khmelinskii A, Meurer M, Duishoev N, Delhomme N & Knop M (2011) Seamless gene tagging by endonuclease-driven homologous recombination. PLoS ONE 6: e23794.
14. Kooistra R, Hooykaas PJ & Steensma HY (2004) Efficient gene targeting in Kluyveromyces lactis. Yeast 21: 781-792.
15. Koopman F, Beekwilder J, Crimi B, van Houwelingen A, Hall RD, Bosch D, van Maris AJ, Pronk JT & Daran JM (2012) De novo production of the flavonoid naringenin in engineered Saccharomyces cerevisiae. Microb Cell Fact 11: 155.
16. Krappmann S, Sasse C & Braus GH (2006) Gene targeting in Aspergillus fumigatus by homologous recombination is facilitated in a nonhomologous end-joining-deficient genetic background. Eukaryot Cell 5: 212-215.
17. Kuijpers NGA, Solis-Escalante D, Bosman L, van den Broek M, Pronk JT, Daran JM & Daran-Lapujade P (2013) A versatile, efficient strategy for assembly of multi-fragment expression vectors in Saccharomyces cerevisiae using 60 bp synthetic recombination sequences. Microb Cell Fact 12: 47.
18. Leem SH, Noskov VN, Park JE, Kim SI, Larionov V & Kouprina N (2003) Optimum conditions for selective isolation of genes from complex genomes by transformation-associated recombination cloning. Nucleic Acids Res 31: e29.
19. Li MZ & Elledge SJ (2007) Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat Methods 4: 251-256.
20. Monteilhet C, Perrin A, Thierry A, Colleaux L & Dujon B (1990) Purification and characterization of the in vitro activity of I-Sce I, a novel and highly specific endonuclease encoded by a group I intron. Nucleic Acids Res 18: 1407-1413.
21. Nijkamp JF, van den Broek M, Datema E et al. (2012) De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology. Microb Cell Fact 11: 36.
22. Ninomiya Y, Suzuki K, Ishii C & Inoue H (2004) Highly efficient gene replacements in Neurospora strains deficient for nonhomologous end-joining. P Natl Acad Sci USA 101: 12248-12253.
23. Noskov VN, Segall-Shapiro TH & Chuang RY (2010) Tandem repeat coupled with endonuclease cleavage (TREC): a seamless modification tool for genome engineering in yeast. Nucleic Acids Res 38: 2570-2576.
24. Orr-Weaver TL, Szostak JW & Rothstein RJ (1981) Yeast transformation: a model system for the study of recombination. P Natl Acad Sci USA 78: 6354-6358.
25. Plessis A, Perrin A, Haber JE & Dujon B (1992) Site-specific recombination determined by I-SceI, a mitochondrial group I intron-encoded endonuclease expressed in the yeast nucleus. Genetics 130: 451-460.
26. Pronk JT (2002) Auxotrophic yeast strains in fundamental and applied research. Appl Environ Microbiol 68: 2095-2100.
27. Ro DK, Paradise EM, Ouellet M et al. (2006) Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440: 940-943.
28. Rouet P, Smih F & Jasin M (1994) Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. Mol Cell Biol 14: 8096-8106.
29. Schiestl RH & Petes TD (1991) Integration of DNA fragments by illegitimate recombination in Saccharomyces cerevisiae. P Natl Acad Sci USA 88: 7585-7589.
30. Shao Z, Zhao H & Zhao H (2009) DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Res 37: e16.
31. Shevchuk NA, Bryksin AV, Nusinovich YA, Cabello FC, Sutherland M & Ladisch S (2004) Construction of long DNA molecules using long PCR-based fusion of several fragments simultaneously. Nucleic Acids Res 32: e19.
32. Shibata T, Watabe H, Kaneko T, Iino T & Ando T (1984) On the nucleotide sequence recognized by a eukaryotic site-specific endonuclease, Endo.SceI from yeast. J Biol Chem 259: 10499-10506.
33. Snoek IS, van der Krogt ZA, Touw H, Kerkman R, Pronk JT, Bovenberg RA, van den Berg MA & Daran JM (2009) Construction of an hdfA Penicillium chrysogenum strain impaired in non-homologous end-joining and analysis of its potential for functional analysis studies. Fungal Genet Biol 46: 418-426.
34. Solis-Escalante D, Kuijpers NGA, Bongaerts N, Bolat I, Bosman L, Pronk JT, Daran JM & Daran-Lapujade P (2013) amdSYM, a new dominant recyclable marker cassette for Saccharomyces cerevisiae. FEMS Yeast Res 13: 126-139.
35. Storici F, Durham CL, Gordenin DA & Resnick MA (2003) Chromosomal site-specific double-strand breaks are efficiently targeted for repair by oligonucleotides in yeast. P Natl Acad Sci USA 100: 14994-14999.
36. van Dijken JP, Bauer J, Brambilla L et al. (2000) An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme Microb Technol 26: 706-714.
37. Verduyn C, Postma E, Scheffers W & van Dijken JP (1992) Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8: 501-517.
38. Watabe H, Iino T, Kaneko T, Shibata T & Ando T (1983) A new class of site-specific endodeoxyribonucleases. Endo. Sce I isolated from a eukaryote, Saccharomyces cerevisiae. J Biol Chem 258: 4663-4665.
39. Whelan WL, Gocke E & Manney TR (1979) The CAN1 Locus of Saccharomyces cerevisiae: fine-structure analysis and forward mutation rates. Genetics 91: 35-51.
40. Wingler LM & Cornish VW (2011) Reiterative recombination for the in vivo assembly of libraries of multigene pathways. P Natl Acad Sci USA 108: 15135-15140.
41. Zhang Z, Moo-Young M & Chisti Y (1996) Plasmid stability in recombinant Saccharomyces cerevisiae. Biotechnol Adv 14: 401-435.