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

Cell Systems - Tập 1 - Trang 88-96 - 2015
Andrew A. Horwitz1, Jessica M. Walter1, Max G. Schubert1, Stephanie H. Kung1, Kristy Hawkins1, Darren M. Platt1, Aaron D. Hernday1, Tina Mahatdejkul-Meadows1, Wayne Szeto1, Sunil S. Chandran1, Jack D. Newman1
1Amyris, Inc., Emeryville, CA 94608, USA

Tài liệu tham khảo

Alper, 2006, Engineering yeast transcription machinery for improved ethanol tolerance and production, Science, 314, 1565, 10.1126/science.1131969 Bao, 2014, Homology-integrated CRISPR-Cas (HI-CRISPR) system for one-step multigene disruption in Saccharomyces cerevisiae, ACS Synth Biol Chen, 1988, A gene-cloning system for Kluyveromyces lactis and isolation of a chromosomal gene required for killer toxin production, J. Basic Microbiol., 28, 211, 10.1002/jobm.3620280402 Cho, 2013, Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease, Nat. Biotechnol., 31, 230, 10.1038/nbt.2507 Cong, 2013, Multiplex genome engineering using CRISPR/Cas systems, Science, 339, 819, 10.1126/science.1231143 Curran, 2013, Metabolic engineering of muconic acid production in Saccharomyces cerevisiae, Metab. Eng., 15, 55, 10.1016/j.ymben.2012.10.003 DiCarlo, 2013, Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems, Nucleic Acids Res., 41, 4336, 10.1093/nar/gkt135 DiCarlo, 2013, Yeast oligo-mediated genome engineering (YOGE), ACS Synth Biol, 2, 741, 10.1021/sb400117c Fu, 2013, High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells, Nat. Biotechnol., 31, 822, 10.1038/nbt.2623 Gietz, 2002, Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method, Methods Enzymol., 350, 87, 10.1016/S0076-6879(02)50957-5 Griggs, 1991, Regulated expression of the GAL4 activator gene in yeast provides a sensitive genetic switch for glucose repression, Proc. Natl. Acad. Sci. USA, 88, 8597, 10.1073/pnas.88.19.8597 Hsu, 2013, DNA targeting specificity of RNA-guided Cas9 nucleases, Nat. Biotechnol., 31, 827, 10.1038/nbt.2647 Jacobs, 2014, Implementation of the CRISPR-Cas9 system in fission yeast, Nat. Commun., 5, 5344, 10.1038/ncomms6344 Jao, 2013, Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system, Proc. Natl. Acad. Sci. USA, 110, 13904, 10.1073/pnas.1308335110 Jinek, 2012, A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Science, 337, 816, 10.1126/science.1225829 Kooistra, 2004, Efficient gene targeting in Kluyveromyces lactis, Yeast, 21, 781, 10.1002/yea.1131 Lin, 2014, Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery, Elife, 3, e04766, 10.7554/eLife.04766 Lörincz, 1986, Sequence analysis of temperature-sensitive mutations in the Saccharomyces cerevisiae gene CDC28, Mol. Cell. Biol., 6, 4099, 10.1128/MCB.6.11.4099 Mandecki, 1986, Oligonucleotide-directed double-strand break repair in plasmids of Escherichia coli: a method for site-specific mutagenesis, Proc. Natl. Acad. Sci. USA, 83, 7177, 10.1073/pnas.83.19.7177 Moqtaderi, 2013, Construction of mutant alleles in Saccharomyces cerevisiae without cloning: overview and the delitto perfetto method, Curr. Protoc. Mol. Biol., 104, 10C, 10.1002/0471142727.mb1310cs104 Niu, 2002, Benzene-free synthesis of adipic acid, Biotechnol. Prog., 18, 201, 10.1021/bp010179x Orr-Weaver, 1983, Genetic applications of yeast transformation with linear and gapped plasmids, Methods Enzymol., 101, 228, 10.1016/0076-6879(83)01017-4 Oud, 2013, Genome duplication and mutations in ACE2 cause multicellular, fast-sedimenting phenotypes in evolved Saccharomyces cerevisiae, Proc. Natl. Acad. Sci. USA, 110, E4223, 10.1073/pnas.1305949110 Ran, 2013, Genome engineering using the CRISPR-Cas9 system, Nat. Protoc., 8, 2281, 10.1038/nprot.2013.143 Roumanie, 2005, Rho GTPase regulation of exocytosis in yeast is independent of GTP hydrolysis and polarization of the exocyst complex, J. Cell Biol., 170, 583, 10.1083/jcb.200504108 Ryan, 2014, Selection of chromosomal DNA libraries using a multiplex CRISPR system, Elife, 3, 10.7554/eLife.03703 Saleh-Gohari, 2004, Conservative homologous recombination preferentially repairs DNA double-strand breaks in the S phase of the cell cycle in human cells, Nucleic Acids Res., 32, 3683, 10.1093/nar/gkh703 Sikorski, 1989, A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae, Genetics, 122, 19, 10.1093/genetics/122.1.19 Sinha, 2008, Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeast, Genetics, 180, 1661, 10.1534/genetics.108.092932 Symington, 2011, Double-strand break end resection and repair pathway choice, Annu. Rev. Genet., 45, 247, 10.1146/annurev-genet-110410-132435 Takagi, 2005, Effect of L-proline on sake brewing and ethanol stress in Saccharomyces cerevisiae, Appl. Environ. Microbiol., 71, 8656, 10.1128/AEM.71.12.8656-8662.2005 Thiemens, 1991, Nylon production: an unknown source of atmospheric nitrous oxide, Science, 251, 932, 10.1126/science.251.4996.932 Toulmay, 2006, A two-step method for the introduction of single or multiple defined point mutations into the genome of Saccharomyces cerevisiae, Yeast, 23, 825, 10.1002/yea.1397 van Dijken, 2000, An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains, Enzyme Microb. Technol., 26, 706, 10.1016/S0141-0229(00)00162-9 Wang, 2013, One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering, Cell, 153, 910, 10.1016/j.cell.2013.04.025 Wang, 2009, Programming cells by multiplex genome engineering and accelerated evolution, Nature, 460, 894, 10.1038/nature08187 Weber, 2012, Biosynthesis of cis,cis-muconic acid and its aromatic precursors, catechol and protocatechuic acid, from renewable feedstocks by Saccharomyces cerevisiae, Appl. Environ. Microbiol., 78, 8421, 10.1128/AEM.01983-12 Wésolowski-Louvel, 2011, An efficient method to optimize Kluyveromyces lactis gene targeting, FEMS Yeast Res., 11, 509, 10.1111/j.1567-1364.2011.00741.x Yang, 2013, 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, e1003693, 10.1371/journal.pgen.1003693