CRISPR-Cas-Assisted Multiplexing (CAM): Simple Same-Day Multi-Locus Engineering in Yeast

Journal of Cellular Physiology

Volumn 231, Issue 12, 2016, Pages 2563-2569

  Walter, Jessica M ^a   Chandran, Sunil S ^a   Horwitz, Andrew A ^a  

^a Amyris Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL RNA; GUIDE RNA;

ALLELE; ARTICLE; CRISPR CAS ASSISTED MULTIPLEXING; CRISPR CAS SYSTEM; FUNGAL GENE; FUNGAL STRAIN; GENE CASSETTE; GENE LOCUS; GENETIC ENGINEERING; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE;

EID: 84983246741     PISSN: 00219541     EISSN: 10974652     Source Type: Journal    
DOI: 10.1002/jcp.25375     Document Type: Article

References (32)

1. Bao Z, Xiao H, Liang J, Zhang L, Xiong X, Sun N, Si T, Zhao H. 2014. Homology-integrated CRISPR-Cas (HI-CRISPR) system for one-step multigene disruption in Saccharomyces cerevisiae. ACS Synth Biol 4: 585–594.
2. Botstein D, Fink GR. 2011. Yeast: An experimental organism for 21st century biology. Genetics 189:695–704.
3. Chen XJ, Wésolowski-Louvel M, Tanguy-Rougeau C, Bianchi MM, Fabiani L, Saliola M, Falcone C, Frontali L, Fukuhara H. 1988. A gene-cloning system for Kluyveromyces lactis and isolation of a chromosomal gene required for killer toxin production. J Basic Microbiol 28:211–220.
4. Chu VT, Weber T, Wefers B, Wurst W, Sander S, Rajewsky K, Kühn R. 2015. Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat Biotechnol 33:543–548.
5. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–823.
6. Curran KA, Leavitt JM, Karim AS, Alper HS. 2013. Metabolic engineering of muconic acid production in Saccharomyces cerevisiae. Metab Eng 15:55–66.
7. de Kok S, Yilmaz D, Suir E, Pronk JT, Daran J-M, van Maris AJA. 2011. Increasing free-energy (ATP) conservation in maltose-grown Saccharomyces cerevisiae by expression of a heterologous maltose phosphorylase. Metab Eng 13:518–526.
8. DiCarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM. 2013. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res 41:4336–4343.
9. Fuller KK, Chen S, Loros JJ, Dunlap JC. 2015. Development of the CRISPR/Cas9 system for targeted gene disruption in Aspergillus fumigatus. Eukaryot Cell 14:1073–1080.
10. Horwitz AA, Walter JM, Schubert MG, Kung SH, Hawkins K, Platt DM, Hernday AD, Mahatdejkul-Meadows T, Szeto W, Chandran SS, Newman JD. 2015. Efficient multiplexed integration of synergistic alleles and metabolic pathways in yeasts via CRISPR-Cas. Cell Syst 1:88–96.
11. Hsu PD, Lander ES, Zhang F. 2014. Development and applications of CRISPR-Cas9 for genome engineering. Cell 157:1262–1278.
12. Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh J-RJ, Joung JK. 2013. Efficient in vivo genome editing using RNA-guided nucleases. Nat Biotechnol 31:227–229.
13. Jacobs JZ, Ciccaglione KM, Tournier V, Zaratiegui M. 2014. Implementation of the CRISPR-Cas9 system in fission yeast. Nat Commun 5:5344.
14. Jakočiu̅nas T, Rajkumar AS, Zhang J, Arsovska D, Rodriguez A, Jendresen CB, Skjødt ML, Nielsen AT, Borodina I, Jensen MK, Keasling JD. 2015. CasEMBLR: Cas9-facilitated multiloci genomic integration of in vivo assembled DNA parts in Saccharomyces cerevisiae. ACS Synth Biol 4:1226–1234.
15. Jao L-E, Wente SR, Chen W. 2013. Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc Natl Acad Sci USA 110:13904–13909.
16. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. 2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821.
17. Keasling JD. 2010. Manufacturing molecules through metabolic engineering. Science 330:1355–1358.
18. Kim H, Kim J-S. 2014. A guide to genome engineering with programmable nucleases. Nat Rev Genet 15:321–334.
19. Lin S, Staahl BT, Alla RK, Doudna JA. 2014. Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. eLife 3:e04766.
20. Mager WH, Winderickx J. 2005. Yeast as a model for medical and medicinal research. Trends Pharmacol Sci 26:265–273.
21. Maruyama T, Dougan SK, Truttmann MC, Bilate AM, Ingram JR, Ploegh HL. 2015. Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat Biotechnol 33:538–542.
22. Orr-Weaver TL, Szostak JW, Rothstein RJ. 1983. [14] Genetic applications of yeast transformation with linear and gapped plasmids. In: Wu R, Grossman L, Moldave K, editors. Methods in Enzymology. New York: Academic Press. pp 228–245.
23. Ryan OW, Skerker JM, Maurer MJ, Li X, Tsai JC, Poddar S, Lee ME, Loache De, DeLoache W, Dueber JE, Arkin, AP, Cate JHD. 2014. Selection of chromosomal DNA libraries using a multiplex CRISPR system. eLife 3:e03703.
24. Saleh-Gohari N, Helleday T. 2004. Conservative homologous recombination preferentially repairs DNA double-strand breaks in the S phase of the cell cycle in human cells. Nucleic Acids Res 32:3683–3688.
25. Schwartz CM, Hussain MS, Blenner M, Wheeldon I. 2015. Synthetic RNA polymerase III promoters facilitate high-efficiency CRISPR–Cas9-mediated genome editing in Yarrowia lipolytica. ACS Synth Biol. [Epub ahead of print].
26. Shapland EB, Holmes V, Reeves CD, Sorokin E, Durot M, Platt D, Allen C, Dean J, Serber Z, Newman J, Chandran SS. 2015. Low-cost, high-throughput sequencing of dna assemblies using a highly multiplexed nextera process. ACS Synth Biol 4:860–866.
27. Storici F, Resnick MA. 2006. The delitto perfetto approach to in vivo site-directed mutagenesis and chromosome rearrangements with synthetic oligonucleotides in yeast. Methods Enzymol 409:329–345.
28. Symington LS, Gautier J. 2011. Double-strand break end resection and repair pathway choice. Annu Rev Genet 45:247–271.
29. Vyas VK, Barrasa MI, Fink GR. 2015. A Candida albicans CRISPR system permits genetic engineering of essential genes and gene families. Sci Adv 1:e1500248.
30. Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R. 2013. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153:910–918.
31. Weber C, Bruckner C, Weinreb S, Lehr C, Essl C, Boles E. 2012. Biosynthesis of cis, cis-Muconic acid and its aromatic precursors, catechol and protocatechuic acid, from renewable feedstocks by saccharomyces cerevisiae. Appl Environ Microbiol 78:8421–8430.
32. Wilson EH, Sagawa S, Weis JW, Schubert MG, Bissell M, Hawthorne B, Reeves CD, Dean J, Platt D. 2016. Genotype specification language. ACS Synth Biol. [Epub ahead of print].