Multiplex engineering of industrial yeast genomes using CRISPRm

Methods in Enzymology

Volumn 546, Issue C, 2014, Pages 473-489

  Ryan, Owen W ^a   Cate, Jamie H D ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

Cas9 Multiplex genome editing; Chromosomal integration; CRISPRm; Directed evolution; DNA libraries; Homology directed repair; Industrial yeast; Saccharomyces cerevisiae; Synthetic biology

Indexed keywords

CASPASE 9; DOUBLE STRANDED DNA; FUNGAL DNA; FUNGAL ENZYME; FUNGAL RNA; GUIDE RNA; CRISPR ASSOCIATED PROTEIN; ENDONUCLEASE;

ARTICLE; CHROMOSOME; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; DNA REPAIR; DNA TEMPLATE; ENZYME ENGINEERING; FUNGAL GENOME; GENE EXPRESSION; GENE SEQUENCE; GENE TARGETING; GENETIC SCREENING; GENETIC TRANSFORMATION; INDUSTRIAL YEAST; MOLECULAR CLONING; NONHUMAN; PLASMID; PRIORITY JOURNAL; PROTEIN EXPRESSION; YEAST; YEAST CHROMOSOME; CRISPR CAS SYSTEM; DIRECTED MOLECULAR EVOLUTION; GENE LIBRARY; GENETIC ENGINEERING; GENETICS; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE;

BASE SEQUENCE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CRISPR-ASSOCIATED PROTEINS; CRISPR-CAS SYSTEMS; DIRECTED MOLECULAR EVOLUTION; ENDONUCLEASES; GENE LIBRARY; GENETIC ENGINEERING; GENOME, FUNGAL; INDUSTRIAL MICROBIOLOGY; MOLECULAR SEQUENCE DATA; PLASMIDS; RNA, GUIDE; SACCHAROMYCES CEREVISIAE;

EID: 84925451973     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-801185-0.00023-4     Document Type: Chapter

References (28)

1. J.D. Boeke, F. LaCroute, and G.R. Fink A positive selection for mutants lacking orotidine-5′-phosphate decarboxylase activity in yeast: 5-Fluoro-orotic acid resistance Molecular & General Genetics 197 2 1984 345 346
2. L. Cong, F.A. Ran, D. Cox, S. Lin, R. Barretto, and N. Habib Multiplex genome engineering using CRISPR/Cas systems Science 339 6121 2013 819 823
3. K.A. Curran, A.S. Karim, A. Gupta, and H.S. Alper Use of expression-enhancing terminators in Saccharomyces cerevisiae to increase mRNA half-life and improve gene expression control for metabolic engineering applications Metabolic Engineering 19 2013 88 97
4. 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 Research 41 7 2013 4336 4343
5. R.D. Dowell, O. Ryan, A. Jansen, D. Cheung, S. Agarwala, and T. Danford Genotype to phenotype: A complex problem Science 328 5977 2010 469
6. A.E. Farrell, R.J. Plevin, B.T. Turner, A.D. Jones, M. O'Hare, and D.M. Kammen Ethanol can contribute to energy and environmental goals Science 311 5760 2006 506 508
7. J.M. Galazka, C. Tian, W.T. Beeson, B. Martinez, N.L. Glass, and J.H.D. Cate Cellodextrin transport in yeast for improved biofuel production Science 330 6000 2010 84 86
8. G. Giaever, and A.M. Chu Functional profiling of the Saccharomyces cerevisiae genome Nature 418 6896 2002 387 391
9. J. Houseley, and D. Tollervey The many pathways of RNA degradation Cell 136 4 2009 763 776
10. P.D. Hsu, D.A. Scott, J.A. Weinstein, F.A. Ran, S. Konermann, and V. Agarwala DNA targeting specificity of RNA-guided Cas9 nucleases Nature Biotechnology 31 9 2013 827 832
11. 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 6096 2012 816 821
12. M. Jinek, A. East, A. Cheng, S. Lin, E. Ma, and J.A. Doudna RNA-programmed genome editing in human cells Elife 2 2013 e00471
13. M. Jinek, F. Jiang, D.W. Taylor, S.H. Sternberg, E. Kaya, and E. Ma Structures of Cas9 endonucleases reveal RNA-mediated conformational activation Science 343 6176 2014 1247997
14. A. Ke, F. Ding, J.D. Batchelor, and J.A. Doudna Structural roles of monovalent cations in the HDV ribozyme Structure 15 3 2007 281 287
15. A. Kohler, and E. Hurt Exporting RNA from the nucleus to the cytoplasm Nature Reviews. Molecular Cell Biology 8 10 2007 761 773
16. H. Krugel, G. Fiedler, I. Haut, E. Sarfert, and H. Simon Analysis of the nourseothricin-resistance gene (nat) of Streptomyces noursei Gene 62 2 1988 209 217
17. P. Mali, K.M. Esvelt, and G.M. Church Cas9 as a versatile tool for engineering biology Nature Methods 10 10 2013 957 963
18. P. Mali, L. Yang, K.M. Esvelt, J. Aach, M. Guell, and J.E. DiCarlo RNA-guided human genome engineering via Cas9 Science 339 6121 2013 823 826
19. C. Marck, R. Kachouri-Lafond, I. Lafontaine, E. Westhof, B. Dujon, and H. Grosjean The RNA polymerase III-dependent family of genes in hemiascomycetes: Comparative RNomics, decoding strategies, transcription and evolutionary implications Nucleic Acids Research 34 6 2006 1816 1835
20. S.A. Parent, C.M. Fenimore, and K.A. Bostian Vector systems for the expression, analysis and cloning of DNA sequences in S. cerevisiae Yeast 1 2 1985 83 138
21. E.M. Rubin Genomics of cellulosic biofuels Nature 454 7206 2008 841 845
22. O.W. Ryan, J.M. Skerker, M.J. Maurer, X. Li, J.C. Tsai, and S. Poddar Selection of chromosomal DNA libraries using a multiplex CRISPR system Elife 2014 e03703 10.7554/eLife.03703 [Epub ahead of print]
23. D. Solis-Escalante, N.G. Kuijpers, F.H. van der Linden, J.T. Pronk, and P. Daran-Lapujade Efficient simultaneous excision of multiple selectable marker cassettes using I-SceI-induced double-strand DNA breaks in Saccharomyces cerevisiae FEMS Yeast Research 14 5 2014 741 754
24. R. Sopko, D. Huang, N. Preston, G. Chua, B. Papp, and K. Kafadar Mapping pathways and phenotypes by systematic gene overexpression Molecular Cell 21 3 2006 319 330
25. S.H. Sternberg, S. Redding, M. Jinek, E.C. Greene, and J.A. Doudna DNA interrogation by the CRISPR RNA-guided endonuclease Cas9 Nature 507 7490 2014 62 67
26. F. van den Ent, and J. Lowe RF cloning: A restriction-free method for inserting target genes into plasmids Journal of Biochemical and Biophysical Methods 67 1 2006 67 74
27. C.H. Webb, N.J. Riccitelli, D.J. Ruminski, and A. Luptak Widespread occurrence of self-cleaving ribozymes Science 326 5955 2009 953
28. L.M. Wingler, and V.W. Cornish Reiterative recombination for the in vivo assembly of libraries of multigene pathways Proceedings of the National Academy of Sciences of the United States of America 108 37 2011 15135 15140