Efficient Multiplexed Integration of Synergistic Alleles and Metabolic Pathways in Yeasts via CRISPR-Cas

Cell Systems

Volumn 1, Issue 1, 2015, Pages 88-96

  Horwitz, Andrew A ^a   Walter, Jessica M ^a   Schubert, Max G ^a   Kung, Stephanie H ^a   Hawkins, Kristy ^a   Platt, Darren M ^a   Hernday, Aaron D ^a   Mahatdejkul Meadows, Tina ^a   Szeto, Wayne ^a   Chandran, Sunil S ^a   Newman, Jack D ^a  

^a Amyris Inc ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; MUCONIC ACID;

ALLELE; AMINO ACID SUBSTITUTION; ARTICLE; CONTROLLED STUDY; CRISPR CAS SYSTEM; DNA MODIFICATION; FERMENTATION; FUNGAL GENOME; FUNGAL METABOLISM; GENE LOCUS; GENETIC ENGINEERING; KLUYVEROMYCES LACTIS; NONHUMAN; PHENOTYPE; POINT MUTATION; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE;

KLUYVEROMYCES LACTIS; SACCHAROMYCES CEREVISIAE;

EID: 84935513637     PISSN: 24054712     EISSN: 24054720     Source Type: Journal    
DOI: 10.1016/j.cels.2015.02.001     Document Type: Article

References (39)

1. H. Alper, J. Moxley, E. Nevoigt, G.R. Fink, and G. Stephanopoulos Engineering yeast transcription machinery for improved ethanol tolerance and production Science 314 2006 1565 1568
2. Z. Bao, H. Xiao, J. Liang, L. Zhang, X. Xiong, N. Sun, T. Si, and H. Zhao Homology-integrated CRISPR-Cas (HI-CRISPR) system for one-step multigene disruption in Saccharomyces cerevisiae ACS Synth Biol 2014 10.1021/sb500255k
3. X.J. Chen, M. Wésolowski-Louvel, C. Tanguy-Rougeau, M.M. Bianchi, L. Fabiani, M. Saliola, C. Falcone, L. Frontali, and H. Fukuhara A gene-cloning system for Kluyveromyces lactis and isolation of a chromosomal gene required for killer toxin production J. Basic Microbiol. 28 1988 211 220
4. S.W. Cho, S. Kim, J.M. Kim, and J.S. Kim Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease Nat. Biotechnol. 31 2013 230 232
5. L. Cong, F.A. Ran, D. Cox, S. Lin, R. Barretto, N. Habib, P.D. Hsu, X. Wu, W. Jiang, L.A. Marraffini, and F. Zhang Multiplex genome engineering using CRISPR/Cas systems Science 339 2013 819 823
6. K.A. Curran, J.M. Leavitt, A.S. Karim, and H.S. Alper Metabolic engineering of muconic acid production in Saccharomyces cerevisiae Metab. Eng. 15 2013 55 66
7. J.E. DiCarlo, J.E. Norville, P. Mali, X. Rios, J. Aach, and G.M. Church Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems Nucleic Acids Res. 41 2013 4336 4343
8. J.E. DiCarlo, A.J. Conley, M. Penttilä, J. Jäntti, H.H. Wang, and G.M. Church Yeast oligo-mediated genome engineering (YOGE) ACS Synth Biol 2 2013 741 749
9. Y. Fu, J.A. Foden, C. Khayter, M.L. Maeder, D. Reyon, J.K. Joung, and J.D. Sander High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells Nat. Biotechnol. 31 2013 822 826
10. R.D. Gietz, and R.A. Woods Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method Methods Enzymol. 350 2002 87 96
11. D.W. Griggs, and M. Johnston Regulated expression of the GAL4 activator gene in yeast provides a sensitive genetic switch for glucose repression Proc. Natl. Acad. Sci. USA 88 1991 8597 8601
12. P.D. Hsu, D.A. Scott, J.A. Weinstein, F.A. Ran, S. Konermann, V. Agarwala, Y. Li, E.J. Fine, X. Wu, O. Shalem, and et al. DNA targeting specificity of RNA-guided Cas9 nucleases Nat. Biotechnol. 31 2013 827 832
13. J.Z. Jacobs, K.M. Ciccaglione, V. Tournier, and M. Zaratiegui Implementation of the CRISPR-Cas9 system in fission yeast Nat. Commun. 5 2014 5344
14. L.E. Jao, S.R. Wente, and W. Chen Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system Proc. Natl. Acad. Sci. USA 110 2013 13904 13909
15. M. Jinek, K. Chylinski, I. Fonfara, M. Hauer, J.A. Doudna, and E. Charpentier A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity Science 337 2012 816 821
16. R. Kooistra, P.J. Hooykaas, and H.Y. Steensma Efficient gene targeting in Kluyveromyces lactis Yeast 21 2004 781 792
17. S. Lin, B.T. Staahl, R.K. Alla, and J.A. Doudna Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery Elife 3 2014 e04766 10.7554/eLife.04766
18. A.T. Lörincz, and S.I. Reed Sequence analysis of temperature-sensitive mutations in the Saccharomyces cerevisiae gene CDC28 Mol. Cell. Biol. 6 1986 4099 4103
19. W. Mandecki Oligonucleotide-directed double-strand break repair in plasmids of Escherichia coli: a method for site-specific mutagenesis Proc. Natl. Acad. Sci. USA 83 1986 7177 7181
20. Z. Moqtaderi, and J.V. Geisberg Construction of mutant alleles in Saccharomyces cerevisiae without cloning: overview and the delitto perfetto method Curr. Protoc. Mol. Biol. 104 2013 10C
21. W. Niu, K.M. Draths, and J.W. Frost Benzene-free synthesis of adipic acid Biotechnol. Prog. 18 2002 201 211
22. T.L. Orr-Weaver, J.W. Szostak, and R.J. Rothstein Genetic applications of yeast transformation with linear and gapped plasmids Methods Enzymol. 101 1983 228 245
23. B. Oud, V. Guadalupe-Medina, J.F. Nijkamp, D. de Ridder, J.T. Pronk, A.J. van Maris, and J.M. Daran Genome duplication and mutations in ACE2 cause multicellular, fast-sedimenting phenotypes in evolved Saccharomyces cerevisiae Proc. Natl. Acad. Sci. USA 110 2013 E4223 E4231
24. F.A. Ran, P.D. Hsu, J. Wright, V. Agarwala, D.A. Scott, and F. Zhang Genome engineering using the CRISPR-Cas9 system Nat. Protoc. 8 2013 2281 2308
25. O. Roumanie, H. Wu, J.N. Molk, G. Rossi, K. Bloom, and P. Brennwald Rho GTPase regulation of exocytosis in yeast is independent of GTP hydrolysis and polarization of the exocyst complex J. Cell Biol. 170 2005 583 594
26. O.W. Ryan, J.M. Skerker, M.J. Maurer, X. Li, J.C. Tsai, S. Poddar, M.E. Lee, W. DeLoache, J.E. Dueber, A.P. Arkin, and J.H. Cate Selection of chromosomal DNA libraries using a multiplex CRISPR system Elife 3 2014 10.7554/eLife.03703
27. N. Saleh-Gohari, and T. Helleday Conservative homologous recombination preferentially repairs DNA double-strand breaks in the S phase of the cell cycle in human cells Nucleic Acids Res. 32 2004 3683 3688
28. R.S. Sikorski, and P. Hieter A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae Genetics 122 1989 19 27
29. H. Sinha, L. David, R.C. Pascon, S. Clauder-Münster, S. Krishnakumar, M. Nguyen, G. Shi, J. Dean, R.W. Davis, P.J. Oefner, and et al. Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeast Genetics 180 2008 1661 1670
30. L.S. Symington, and J. Gautier Double-strand break end resection and repair pathway choice Annu. Rev. Genet. 45 2011 247 271
31. H. Takagi, M. Takaoka, A. Kawaguchi, and Y. Kubo Effect of L-proline on sake brewing and ethanol stress in Saccharomyces cerevisiae Appl. Environ. Microbiol. 71 2005 8656 8662
32. M.H. Thiemens, and W.C. Trogler Nylon production: an unknown source of atmospheric nitrous oxide Science 251 1991 932 934
33. A. Toulmay, and R. Schneiter A two-step method for the introduction of single or multiple defined point mutations into the genome of Saccharomyces cerevisiae Yeast 23 2006 825 831
34. J.P. van Dijken, J. Bauer, L. Brambilla, P. Duboc, J.M. Francois, C. Gancedo, M.L. Giuseppin, J.J. Heijnen, M. Hoare, H.C. Lange, and et al. An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains Enzyme Microb. Technol. 26 2000 706 714
35. H. Wang, H. Yang, C.S. Shivalila, M.M. Dawlaty, A.W. Cheng, F. Zhang, and R. Jaenisch One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering Cell 153 2013 910 918
36. H.H. Wang, F.J. Isaacs, P.A. Carr, Z.Z. Sun, G. Xu, C.R. Forest, and G.M. Church Programming cells by multiplex genome engineering and accelerated evolution Nature 460 2009 894 898
37. C. Weber, C. Brückner, S. Weinreb, C. Lehr, C. Essl, and E. Boles Biosynthesis of cis,cis-muconic acid and its aromatic precursors, catechol and protocatechuic acid, from renewable feedstocks by Saccharomyces cerevisiae Appl. Environ. Microbiol. 78 2012 8421 8430
38. M. Wésolowski-Louvel An efficient method to optimize Kluyveromyces lactis gene targeting FEMS Yeast Res. 11 2011 509 513
39. Y. Yang, M.R. Foulquié-Moreno, L. Clement, E. Erdei, A. Tanghe, K. Schaerlaekens, F. Dumortier, and J.M. Thevelein QTL analysis of high thermotolerance with superior and downgraded parental yeast strains reveals new minor QTLs and converges on novel causative alleles involved in RNA processing PLoS Genet. 9 2013 e1003693