Protein engineering of Cas9 for enhanced function

Methods in Enzymology

Volumn 546, Issue C, 2014, Pages 491-511

  Oakes, Benjamin L ^a   Nadler, Dana C ^a   Savage, David F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Cas9; CRISPR; Gene activation repression; Genome editing; Nuclease; PDZ; Protein engineering; Synthetic biology

Indexed keywords

CRISPR ASSOCIATED PROTEIN; CRISPR ASSOCIATED PROTEIN 9; MUTANT PROTEIN; UNCLASSIFIED DRUG; DEOXYRIBONUCLEASE I;

ARTICLE; CONTROLLED STUDY; CRISPR CAS SYSTEM; DIRECTED MOLECULAR EVOLUTION; ENZYME ACTIVE SITE; GENE INSERTION; GENETIC ENGINEERING; GENOME ANALYSIS; HETEROLOGOUS EXPRESSION; MOLECULAR CLONING; NEXT GENERATION SEQUENCING; NONHUMAN; PDZ DOMAIN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ENGINEERING; PROTEIN FUNCTION; PROTEIN ISOLATION; PROTEIN STRUCTURE; AMINO ACID SEQUENCE; BACTERIUM; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; GENETICS; METABOLISM; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; PROCEDURES; PROTEIN CONFORMATION; STREPTOCOCCUS PYOGENES;

BACTERIA (MICROORGANISMS);

AMINO ACID SEQUENCE; BACTERIA; BASE SEQUENCE; CRISPR-ASSOCIATED PROTEINS; CRISPR-CAS SYSTEMS; DEOXYRIBONUCLEASE I; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; PDZ DOMAINS; PROTEIN CONFORMATION; PROTEIN ENGINEERING; STREPTOCOCCUS PYOGENES;

EID: 84925437370     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-801185-0.00024-6     Document Type: Chapter

References (47)

1. R. Barrangou, C. Fremaux, H. Deveau, M. Richards, P. Boyaval, and S. Moineau CRISPR provides acquired resistance against viruses in prokaryotes Science (New York) 315 5819 2007 1709 1712 10.1126/science.1138140
2. D. Bikard, W. Jiang, P. Samai, A. Hochschild, F. Zhang, and L.A. Marraffini Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system Nucleic Acids Research 41 15 2013 7429 7437 10.1093/nar/gkt520
3. 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 and General Genetics 197 2 1984 345 346
4. J.D. Boeke, J. Trueheart, G. Natsoulis, and G.R. Fink 5-fluoroorotic acid as a selective agent in yeast molecular genetics Methods in Enzymology 154 1987 164 175
5. D. Carroll Genome engineering with targetable nucleases Annual Review of Biochemistry 83 1 2014 409 439 10.1146/annurev-biochem-060713-035418
6. K. Chylinski, A. Le Rhun, and E. Charpentier The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems RNA Biology 10 2013 726 737
7. K. Chylinski, K.S. Makarova, E. Charpentier, and E.V. Koonin Classification and evolution of type II CRISPR-Cas systems Nucleic Acids Research 42 2014 6091 6105
8. L. Cong, F.A. Ran, D. Cox, S. Lin, R. Barretto, and N. Habib Multiplex genome engineering using CRISPR/Cas systems Science (New York) 339 6121 2013 819 823 10.1126/science.1231143
9. E. Deltcheva, K. Chylinski, C.M. Sharma, K. Gonzales, Y. Chao, and Z.A. Pirzada CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III Nature 471 7340 2011 602 607 10.1038/nature09886
10. J.E. Dueber, E.A. Mirsky, and W.A. Lim Engineering synthetic signaling proteins with ultrasensitive input/output control Nature Biotechnology 25 6 2007 660 662 10.1038/nbt1308
11. J.E. Dueber, B.J. Yeh, K. Chak, and W.A. Lim Reprogramming control of an allosteric signaling switch through modular recombination Science (New York) 301 5641 2003 1904 1908 10.1126/science.1085945
12. W.R. Edwards, K. Busse, R.K. Allemann, and D.D. Jones Linking the functions of unrelated proteins using a novel directed evolution domain insertion method Nucleic Acids Research 36 13 2008 e78 10.1093/nar/gkn363
13. M.B. Elowitz, A.J. Levine, E.D. Siggia, and P.S. Swain Stochastic gene expression in a single cell Science (New York) 297 5584 2002 1183 1186 10.1126/science.1070919
14. K.M. Esvelt, P. Mali, J.L. Braff, M. Moosburner, S.J. Yaung, and G.M. Church Orthogonal Cas9 proteins for RNA-guided gene regulation and editing Nature Methods 10 11 2013 1116 1121 10.1038/nmeth.2681
15. A.E. Friedland, Y.B. Tzur, K.M. Esvelt, M.P. Colaiácovo, G.M. Church, and J.A. Calarco Heritable genome editing in C. elegans via a CRISPR-Cas9 system Nature Methods 10 8 2013 741 743 10.1038/nmeth.2532
16. Y. Fu, J.D. Sander, D. Reyon, V.M. Cascio, and J.K. Joung Improving CRISPR-Cas nuclease specificity using truncated guide RNAs Nat Biotechnology 32 2014 279 284
17. T.C. Galvao, and V. de Lorenzo Adaptation of the yeast URA3 selection system to Gram-negative bacteria and generation of a betCDE Pseudomonas putida strain Applied and Environmental Microbiology 71 2 2005 883 892 10.1128/AEM.71.2.883-892.2005
18. L.A. Gilbert, M.H. Larson, L. Morsut, Z. Liu, G.A. Brar, and S.E. Torres CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes Cell 154 2 2013 442 451 10.1016/j.cell.2013.06.044
19. S.J. Gratz, A.M. Cummings, J.N. Nguyen, D.C. Hamm, L.K. Donohue, and M.M. Harrison Genome engineering of drosophila with the CRISPR RNA-guided Cas9 nuclease Genetics 194 4 2013 1029 1035 10.1534/genetics.113.152710
20. J.P. Guilinger, D.B. Thompson, and D.R. Liu Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification Nature Biotechnology 32 6 2014 577 582 10.1038/nbt.2909
21. Z. Hou, Y. Zhang, N.E. Propson, S.E. Howden, L.-F. Chu, and E.J. Sontheimer Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis Proceedings of the National Academy of Sciences of the United States of America 110 39 2013 15644 15649 10.1073/pnas.1313587110
22. 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 10.1038/nbt.2647
23. W.Y. Hwang, Y. Fu, D. Reyon, M.L. Maeder, S.Q. Tsai, and J.D. Sander Efficient genome editing in zebrafish using a CRISPR-Cas system Nature Biotechnology 31 3 2013 227 229 10.1038/nbt.2501
24. 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 (New York) 337 6096 2012 816 821 10.1126/science.1225829
25. 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 (New York) 343 6176 2014 1247997 10.1126/science.1247997
26. E.S. Lander, L.M. Linton, B. Birren, C. Nusbaum, M.C. Zody, and J. Baldwin Initial sequencing and analysis of the human genome Nature 409 6822 2001 860 921 10.1038/35057062
27. P. Mali, J. Aach, P.B. Stranges, K.M. Esvelt, M. Moosburner, and S. Kosuri CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering Nature Biotechnology 31 9 2013 833 838 10.1038/nbt.2675
28. P. Mali, K.M. Esvelt, and G.M. Church Cas9 as a versatile tool for engineering biology Nature Methods 10 10 2013 957 963 10.1038/nmeth.2649
29. P. Mali, L. Yang, K.M. Esvelt, J. Aach, M. Guell, and J.E. DiCarlo RNA-guided human genome engineering via Cas9 Science (New York) 339 6121 2013 823 826 10.1126/science.1232033
30. H. Nishimasu, F.A. Ran, P.D. Hsu, S. Konermann, S.I. Shehata, and N. Dohmae Crystal structure of Cas9 in complex with guide RNA and target DNA Cell 156 5 2014 935 949 10.1016/j.cell.2014.02.001
31. Y. Niu, Bin Shen, Y. Cui, Y. Chen, J. Wang, and L. Wang Generation of gene-modified cynomolgus monkey via Cas9/RNA-mediated gene targeting in one-cell embryos Cell 156 4 2014 836 843 10.1016/j.cell.2014.01.027
32. C. Nourry, S.G.N. Grant, and J.-P. Borg PDZ domain proteins: Plug and play! Science's STKE 2003 179 2003 RE7 10.1126/stke.2003.179.re7
33. M.R. O'Connell, B.L. Oakes, S.H. Sternberg, A. East-Seletsky, M. Kaplan, and J.A. Doudna Programmable RNA recognition and cleavage by CRISPR/Cas9 Nature 2014 10.1038/nature13769
34. E.J. Olson, and J.J. Tabor Post-translational tools expand the scope of synthetic biology Current Opinion in Chemical Biology 16 3-4 2012 300 306 10.1016/j.cbpa.2012.06.003
35. V. Pattanayak, S. Lin, J.P. Guilinger, E. Ma, J.A. Doudna, and D.R. Liu High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity Nat Biotechnology 31 2013 839 843
36. A.V. Persikov, E.F. Rowland, B.L. Oakes, M. Singh, and M.B. Noyes Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets Nucleic Acids Research 42 3 2014 1497 1508 10.1093/nar/gkt1034
37. L.S. Qi, M.H. Larson, L.A. Gilbert, J.A. Doudna, J.S. Weissman, and A.P. Arkin Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression Cell 152 5 2013 1173 1183 10.1016/j.cell.2013.02.022
38. F.A. Ran, P.D. Hsu, C.-Y. Lin, J.S. Gootenberg, S. Konermann, and A.E. Trevino Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity Cell 154 2013 1380 1389
39. C. Schmidt-Dannert, and F.H. Arnold Directed evolution of industrial enzymes Trends in Biotechnology 17 4 1999 135 136
40. O. Shalem, N.E. Sanjana, E. Hartenian, X. Shi, D.A. Scott, and T.S. Mikkelsen Genome-scale CRISPR-Cas9 knockout screening in human cells Science (New York) 343 6166 2014 84 87 10.1126/science.1247005
41. Q. Shan, Y. Wang, J. Li, Y. Zhang, K. Chen, and Z. Liang Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9 Nature Biotechnology 31 8 2013 688 691 10.1038/nbt.2654
42. 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 10.1038/nature13011
43. S.Q. Tsai, N. Wyvekens, C. Khayter, J.A. Foden, V. Thapar, and D. Reyon Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing Nature Biotechnology 32 6 2014 569 576 10.1038/nbt.2908
44. H. Wang, H. Yang, C.S. Shivalila, M.M. Dawlaty, A.W. Cheng, and F. Zhang One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering Cell 153 4 2013 910 918 10.1016/j.cell.2013.04.025
45. B. Wiedenheft, S.H. Sternberg, and J.A. Doudna RNA-guided genetic silencing systems in bacteria and archaea Nature 482 7385 2012 331 338 10.1038/nature10886
46. T. Yano, C. Sanders, J. Catalano, and F. Daldal SacB-5-fluoroorotic acid-pyrE-based bidirectional selection for integration of unmarked alleles into the chromosome of Rhodobacter capsulatus Applied and Environmental Microbiology 71 6 2005 3014 3024 10.1128/AEM.71.6.3014-3024.2005
47. Y. Zhou, S. Zhu, C. Cai, P. Yuan, C. Li, and Y. Huang High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells Nature 509 7501 2014 487 491 10.1038/nature13166