Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae

Metabolic Engineering - Tập 28 - Trang 213-222 - 2015
Tadas Jakočiūnas1, Ida Bonde1, Markus Herrgård1, Scott J. Harrison1, Mette Kristensen1, Lasse E. Pedersen1, Michael K. Jensen1, Jay D. Keasling1,2,3,4
1The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
2Joint BioEnergy Institute, Emeryville, CA, USA
3Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
4Department of Chemical and Biomolecular Engineering & Department of Bioengineering University of California, Berkeley, CA, USA

Tài liệu tham khảo

Alani, 1987, A method for gene disruption that allows repeated use of URA3 selection in the construction of multiply disrupted yeast strains, Genetics, 116, 541, 10.1093/genetics/116.4.541 Asadollahi, 2010, Enhancement of farnesyl diphosphate pool as direct precursor of sesquiterpenes through metabolic engineering of the mevalonate pathway in Saccharomyces cerevisiae, Biotechnol. Bioeng., 106, 86 Bao, 2014, A Homology Integrated CRISPR–Cas (HI-CRISPR) system for one-step multi-gene disruptions in Saccharomyces cerevisiae, ACS Synth. Biol. Bitinaite, 2007, USER friendly DNA engineering and cloning method by uracil excision, Nucleic Acids Res., 35, 1992, 10.1093/nar/gkm041 Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170 Bonde, 2014, Direct mutagenesis of thousands of genomic targets using microarray-derived oligonucleotides, ACS Synth. Biol, 4, 17, 10.1021/sb5001565 Brenneman, 1996, Stimulation of intrachromosomal homologous recombination in human cells by electroporation with site-specific endonucleases, Proc. Natl. Acad. Sci. USA, 93, 3608, 10.1073/pnas.93.8.3608 Cong, 2013, Multiplex genome engineering using CRISPR/Cas systems, Science, 339, 819, 10.1126/science.1231143 Da Silva, 2012, Introduction and expression of genes for metabolic engineering applications in Saccharomyces cerevisiae, FEMS Yeast Res., 12, 197, 10.1111/j.1567-1364.2011.00769.x Deatherage, 2014, Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq, Methods Mol. Biol., 1151, 165, 10.1007/978-1-4939-0554-6_12 Delneri, 2000, Exploring redundancy in the yeast genome: an improved strategy for use of the cre-loxP system, Gene, 252, 127, 10.1016/S0378-1119(00)00217-1 Dicarlo, 2013, Yeast oligo-mediated genome engineering (YOGE), ACS Synth. Biol., 2, 741, 10.1021/sb400117c DiCarlo, 2013, Genome engineering in Saccharomyces cerevisiae using CRISPR–Cas systems, Nucleic Acids Res., 41, 4336, 10.1093/nar/gkt135 Engels, 2008, Metabolic engineering of taxadiene biosynthesis in yeast as a first step towards Taxol (Paclitaxel) production, Metab. Eng., 10, 201, 10.1016/j.ymben.2008.03.001 Fang, 2011, A vector set for systematic metabolic engineering in Saccharomyces cerevisiae, Yeast, 28, 123, 10.1002/yea.1824 Fu, 2013, High-frequency off-target mutagenesis induced by CRISPR–Cas nucleases in human cells, Nat. Biotechnol., 31, 822, 10.1038/nbt.2623 Gao, 2014, Self-processing of ribozyme-flanked RNAs into guide RNAs in vitro and in vivo for CRISPR-mediated genome editing, J. Integr. Plant Biol., 56, 343, 10.1111/jipb.12152 Gietz, 2007, Large-scale high-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method, Nat. Protoc., 2, 38, 10.1038/nprot.2007.15 Gueldener, 2002, A second set of loxP marker cassettes for Cre-mediated multiple gene knockouts in budding yeast, Nucleic Acids Res., 30, e23, 10.1093/nar/30.6.e23 Henry, 2002, ROX1 and ERG regulation in Saccharomyces cerevisiae: implications for antifungal susceptibility, Eukaryot. Cell, 1, 1041, 10.1128/EC.1.6.1041-1044.2002 Hsu, 2013, DNA targeting specificity of RNA-guided Cas9 nucleases, Nat. Biotechnol., 31, 827, 10.1038/nbt.2647 Iida, 2004, Noncompetitive counteractions of DNA polymerase epsilon and ISW2/yCHRAC for epigenetic inheritance of telomere position effect in Saccharomyces cerevisiae, Mol. Cell. Biol., 24, 217, 10.1128/MCB.24.1.217-227.2004 Jacobs, 2014, Implementation of the CRISPR–Cas9 system in fission yeast, Nat. Commun., 5, 5344, 10.1038/ncomms6344 Jennings, 1991, Molecular cloning and characterization of the yeast gene for squalene synthetase, Proc. Natl. Acad. Sci. USA, 88, 6038, 10.1073/pnas.88.14.6038 Jensen, 2014, EasyClone: method for iterative chromosomal integration of multiple genes in Saccharomyces cerevisiae, FEMS Yeast Res., 14, 238, 10.1111/1567-1364.12118 Jiang, 2013, RNA-guided editing of bacterial genomes using CRISPR–Cas systems, Nat. Biotechnol., 31, 233, 10.1038/nbt.2508 Jiang, 1995, BTS1 encodes a geranylgeranyl diphosphate synthase in Saccharomyces cerevisiae, J. Biol. Chem., 270, 21793, 10.1074/jbc.270.37.21793 Jinek, 2012, A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Science, 337, 816, 10.1126/science.1225829 Kennedy, 2001, Positive and negative regulation of squalene synthase (ERG9), an ergosterol biosynthetic gene, in Saccharomyces cerevisiae, Biochim. Biophys. Acta – Gene Struct. Expr., 1517, 177, 10.1016/S0167-4781(00)00246-3 Li, 2013, Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9, Nat. Biotechnol., 31, 688, 10.1038/nbt.2654 Liang, 1998, Homology-directed repair is a major double-strand break repair pathway in mammalian cells, Proc. Natl. Acad. Sci. USA, 95, 5172, 10.1073/pnas.95.9.5172 Lin, 2014, CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences, Nucleic Acids Res., 10.1093/nar/gku402 Liu, 2014, Highly efficient multiplex targeted mutagenesis and genomic structure variation in Bombyx mori cells using CRISPR/Cas9, Insect Biochem. Mol. Biol., 49, 35, 10.1016/j.ibmb.2014.03.010 Mali, 2013, RNA-guided human genome engineering via Cas9, Science, 339, 823, 10.1126/science.1232033 Matsubara, 2014, Transcription activator-like effector nuclease-mediated transduction of exogenous gene into IL2RG locus, Sci. Rep., 4, 5043, 10.1038/srep05043 Montañés, 2011, Repression of ergosterol biosynthesis is essential for stress resistance and is mediated by the Hog1 MAP kinase and the Mot3 and Rox1 transcription factors, Mol. Microbiol., 79, 1008, 10.1111/j.1365-2958.2010.07502.x Moore, 1996, Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae, Mol. Cell. Biol., 16, 2164, 10.1128/MCB.16.5.2164 Nijkamp, 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, 10.1186/1475-2859-11-36 Özaydın, 2013, Carotenoid-based phenotypic screen of the yeast deletion collection reveals new genes with roles in isoprenoid production, Metab. Eng., 15, 174, 10.1016/j.ymben.2012.07.010 Pâques, 1999, Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae, Microbiol. Mol. Biol. Rev., 63, 349, 10.1128/MMBR.63.2.349-404.1999 Paradise, 2008, Redirection of flux through the FPP branch-point in Saccharomyces cerevisiae by down-regulating squalene synthase, Biotechnol. Bioeng., 100, 371, 10.1002/bit.21766 Pattanayak, 2013, High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity, Nat. Biotechnol., 31, 839, 10.1038/nbt.2673 Peralta-Yahya, 2011, Identification and microbial production of a terpene-based advanced biofuel, Nat. Commun., 2, 483, 10.1038/ncomms1494 Ro, 2006, Production of the antimalarial drug precursor artemisinic acid in engineered yeast, Nature, 440, 940, 10.1038/nature04640 Rodriguez, 2014, Production and quantification of sesquiterpenes in Saccharomyces cerevisiae, including extraction, detection and quantification of terpene products and key related metabolites, Nat. Protoc., 9, 1980, 10.1038/nprot.2014.132 Ronda, 2014, Accelerating genome editing in CHO cells using CRISPR Cas9 and CRISPy, a web-based target finding tool, Biotechnol. Bioeng., 111, 1604, 10.1002/bit.25233 Rouet, 1994, Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease, Mol. Cell. Biol., 14, 8096 Ryan, 2014, Selection of chromosomal DNA libraries using a multiplex CRISPR system, Elife, e03703, 10.7554/eLife.03703 Sakuma, 2014, Multiplex genome engineering in human cells using all-in-one CRISPR/Cas9 vector system, Sci. Rep., 4, 5400, 10.1038/srep05400 Sander, 2014, CRISPR–Cas systems for editing, regulating and targeting genomes, Nat. Biotechnol., 32, 347, 10.1038/nbt.2842 Scalcinati, 2012, Dynamic control of gene expression in Saccharomyces cerevisiae engineered for the production of plant sesquitepene α-santalene in a fed-batch mode, Metab. Eng., 14, 91, 10.1016/j.ymben.2012.01.007 Schiestl, 1993, Transformation of Saccharomyces cerevisiae with nonhomologous DNA: illegitimate integration of transforming DNA into yeast chromosomes and in vivo ligation of transforming DNA to mitochondrial DNA sequences, Mol. Cell. Biol., 13, 2697 Solis-Escalante, 2014, Efficient simultaneous excision of multiple selectable marker cassettes using I-SceI-induced double-strand breaks in Saccharomyces cerevisiae, FEMS Yeast Res., 14, 741, 10.1111/1567-1364.12162 Storici, 2003, Chromosomal site-specific double-strand breaks are efficiently targeted for repair by oligonucleotides in yeast, Proc. Natl. Acad. Sci. USA, 100, 14994, 10.1073/pnas.2036296100 Storici, 2006, The delitto perfetto approach to in vivo site-directed mutagenesis and chromosome rearrangements with synthetic oligonucleotides in yeast, Methods Enzymol., 409, 329, 10.1016/S0076-6879(05)09019-1 Tian, 2013, Novel method for genomic promoter shuffling by using recyclable cassettes, Appl. Environ. Microbiol., 79, 7042, 10.1128/AEM.02159-13 Van Dien, 2013, From the first drop to the first truckload: commercialization of microbial processes for renewable chemicals, Curr. Opin. Biotechnol., 24, 1061, 10.1016/j.copbio.2013.03.002 Verwaal, 2007, High-level production of beta-carotene in Saccharomyces cerevisiae by successive transformation with carotenogenic genes from Xanthophyllomyces dendrorhous, Appl. Environ. Microbiol., 73, 4342, 10.1128/AEM.02759-06 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 Wilson, 2002, Systematic identification of the genes affecting glycogen storage in the yeast Saccharomyces cerevisiae: implication of the vacuole as a determinant of glycogen level, Mol. Cell. Proteomics, 1, 232, 10.1074/mcp.M100024-MCP200 Wu, 2004, High efficiency transformation by electroporation of Pichia pastoris pretreated with lithium acetate and dithiothreitol, Biotechniques, 36, 152, 10.2144/04361DD02 Wu, 2014, TALE nickase mediates high efficient targeted transgene integration at the human multi-copy ribosomal DNA locus, Biochem. Biophys. Res. Commun., 446, 261, 10.1016/j.bbrc.2014.02.099 Xu, 2014, Efficient genome engineering in eukaryotes using Cas9 from Streptococcus thermophilus, Cell. Mol. Life Sci., 72, 383, 10.1007/s00018-014-1679-z Yang, 2014, CRISPR–Cas-mediated targeted genome editing in human cells, Methods Mol. Biol., 1114, 245, 10.1007/978-1-62703-761-7_16 Yu, 2013, Highly efficient genome modifications mediated by CRISPR/Cas9 in Drosophila, Genetics, 195, 289, 10.1534/genetics.113.153825