Bacterial CRISPR: Accomplishments and prospects

Current Opinion in Microbiology

Volumn 27, Issue , 2015, Pages 121-126

  Peters, Jason M ^a   Silvis, Melanie R ^a,b   Zhao, Dehua ^c,d   Hawkins, John S ^a,b   Gross, Carol A ^a   Qi, Lei S ^c,d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c Stanford University   (United States)

^d STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; SINGLE GUIDE RNA; UNCLASSIFIED DRUG;

ACTINOMYCETALES; BACILLUS SUBTILIS; BACTERIOIDES THETAIOTAOMICRON; BACTERIUM; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; GENE ACTIVATION; GENE FUNCTION; GENOME; MYCOBACTERIUM SMEGMATIS; NONHUMAN; REVIEW; SITE DIRECTED MUTAGENESIS; BACTERIAL GENOME; CRISPR CAS SYSTEM; GENETIC ENGINEERING; GENETICS; PROCEDURES;

BACTERIA; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CRISPR-CAS SYSTEMS; GENETIC ENGINEERING; GENOME, BACTERIAL;

EID: 84941285455     PISSN: 13695274     EISSN: 18790364     Source Type: Journal    
DOI: 10.1016/j.mib.2015.08.007     Document Type: Review

References (53)

1. Bhaya D., Davison M., Barrangou R. CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu Rev Genet 2011, 45:273-297.
2. Brouns S.J.J., Jore M.M., Lundgren M., Westra E.R., Slijkhuis R.J.H., Snijders A.P.L., Dickman M.J., Makarova K.S., Koonin E.V., van der Oost J. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 2008, 321:960-964.
3. Wiedenheft B., Sternberg S.H., Doudna J.A. RNA-guided genetic silencing systems in bacteria and archaea. Nature 2012, 482:331-338.
4. Chylinski K., Makarova K.S., Charpentier E., Koonin E.V. Classification and evolution of type II CRISPR-Cas systems. Nucleic Acids Res 2014, 42:6091-6105.
5. Westra E.R., Buckling A., Fineran P.C. CRISPR-Cas systems: beyond adaptive immunity. Nat Rev Microbiol 2014, 12:317-326.
6. Barrangou R. The roles of CRISPR-Cas systems in adaptive immunity and beyond. Curr Opin Immunol 2015, 32:36-41.
7. Bondy-Denomy J., Davidson A.R. To acquire or resist: the complex biological effects of CRISPR-Cas systems. Trends Microbiol 2014, 22:218-225.
8. Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J.A., Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012, 337:816-821.
9. Jinek M., Jiang F., Taylor D.W., Sternberg S.H., Kaya E., Ma E., Anders C., Hauer M., Zhou K., Lin S., et al. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 2014, 343:1247997.
10. Nishimasu H., Ran F.A., Hsu P.D., Konermann S., Shehata S.I., Dohmae N., Ishitani R., Zhang F., Nureki O. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 2014, 156:935-949.
11. Jiang F., Doudna J.A. The structural biology of CRISPR-Cas systems. Curr Opin Struct Biol 2015, 30:100-111.
12. Sternberg S.H., Redding S., Jinek M., Greene E.C., Doudna J.A. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 2014, 507:62-67.
13. Qi L.S., Larson M.H., Gilbert L.A., Doudna J.A., Weissman J.S., Arkin A.P., Lim W.A. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 2013, 152:1173-1183.
14. Bikard D., Jiang W., Samai P., Hochschild A., Zhang F., Marraffini L.A. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res 2013, 41:7429-7437.
15. Sternberg S.H., Doudna J.A. Expanding the Biologist's Toolkit with CRISPR-Cas9. Mol Cell 2015, 58:568-574.
16. Shalem O., Sanjana N.E., Zhang F. High-throughput functional genomics using CRISPR-Cas9. Nat Rev Genet 2015, 16:299-311.
17. Doudna J.A., Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 2014, 346:1258096.
18. Harrison M.M., Jenkins B.V., O'Connor-Giles K.M., Wildonger J. A CRISPR view of development. Genes Dev 2014, 28:1859-1872.
19. Hsu P.D., Lander E.S., Zhang F. Development and applications of CRISPR-Cas9 for genome engineering. Cell 2014, 157:1262-1278.
20. Selle K., Barrangou R. Harnessing CRISPR-Cas systems for bacterial genome editing. Trends Microbiol 2015, 23:225-232.
21. Jiang W., Bikard D., Cox D., Zhang F., Marraffini L.A. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 2013, 31:233-239.
22. Vercoe R.B., Chang J.T., Dy R.L., Taylor C., Gristwood T., Clulow J.S., Richter C., Przybilski R., Pitman A.R., Fineran P.C. Cytotoxic chromosomal targeting by CRISPR/Cas systems can reshape bacterial genomes and expel or remodel pathogenicity islands. PLoS Genet 2013, 9:e1003454.
23. Jiang Y., Chen B., Duan C., Sun B., Yang J., Yang S. Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system. Appl Environ Microbiol 2015, 81:2506-2514.
24. Oh J.-H., van Pijkeren J.-P. CRISPR-Cas9-assisted recombineering in Lactobacillus reuteri. Nucleic Acids Res 2014, 42:e131.
25. Wang Y., Zhang Z-T., Seo S-O., Choi K., Lu T., Jin Y-S., Blaschek H.P. Markerless chromosomal gene deletion in Clostridium beijerinckii using CRISPR/Cas9 system. J Biotechnol 2015, 200:1-5.
26. Cobb R.E., Wang Y., Zhao H. High-efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system. ACS Synth Biol 2015, 4:723-728.
27. Huang H., Zheng G., Jiang W., Hu H., Lu Y. One-step high-efficiency CRISPR/Cas9-mediated genome editing in Streptomyces. Acta Biochim Biophys Sin 2015, 47:231-243.
28. Yu D., Ellis H.M., Lee E.C., Jenkins N.A., Copeland N.G., Court D.L. An efficient recombination system for chromosome engineering in Escherichia coli. Proc Natl Acad Sci U S A 2000, 97:5978-5983.
29. Bikard D., Euler C.W., Jiang W., Nussenzweig P.M., Goldberg G.W., Duportet X., Fischetti V.A., Marraffini L.A. Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials. Nat Biotechnol 2014, 32:1146-1150.
30. Cho S.W., Lee J., Carroll D., Kim J-S., Lee J. Heritable gene knockout in Caenorhabditis elegans by direct injection of Cas9-sgRNA ribonucleoproteins. Genetics 2013, 195:1177-1180.
31. Sung Y.H., Kim J.M., Kim H-T., Lee J., Jeon J., Jin Y., Choi J-H., Ban Y.H., Ha S-J., Kim C-H., et al. Highly efficient gene knockout in mice and zebrafish with RNA-guided endonucleases. Genome Res 2014, 24:125-131.
32. Lv L., Ren Y-L., Chen J-C., Wu Q., Chen G-Q. Application of CRISPRi for prokaryotic metabolic engineering involving multiple genes, a case study: controllable P(3HB-co-4HB) biosynthesis. Metab Eng 2015, 29:160-168.
33. Qi L.S., Arkin A.P. A versatile framework for microbial engineering using synthetic non-coding RNAs. Nat Rev Microbiol 2014, 12:341-354.
34. Choudhary E., Thakur P., Pareek M., Agarwal N. Gene silencing by CRISPR interference in mycobacteria. Nat Commun 2015, 6:6267.
35. Larson M.H., Gilbert L.A., Wang X., Lim W.A., Weissman J.S., Qi L.S. CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nat Protoc 2013, 8:2180-2196.
36. Hawkins J.S., Wong S., Peters J.M., Almeida R., Qi L.S. Targeted transcriptional repression in bacteria using CRISPR interference (CRISPRi). Methods Mol Biol 2015, 1311:349-362.
37. Cleary M.A., Kilian K., Wang Y., Bradshaw J., Cavet G., Ge W., Kulkarni A., Paddison P.J., Chang K., Sheth N., et al. Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis. Nat Methods 2004, 1:241-248.
38. LeProust E.M., Peck B.J., Spirin K., McCuen H.B., Moore B., Namsaraev E., Caruthers M.H. Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process. Nucleic Acids Res 2010, 38:2522-2540.
39. Gilbert L.A., Horlbeck M.A., Adamson B., Villalta J.E., Chen Y., Whitehead E.H., Guimaraes C., Panning B., Ploegh H.L., Bassik M.C., et al. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 2014, 159:647-661.
40. Konermann S., Brigham M.D., Trevino A.E., Joung J., Abudayyeh O.O., Barcena C., Hsu P.D., Habib N., Gootenberg J.S., Nishimasu H., et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 2015, 517:583-588.
41. Tanenbaum M.E., Gilbert L.A., Qi L.S., Weissman J.S., Vale R.D. A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 2014, 159:635-646.
42. Vrentas C.E., Gaal T., Ross W., Ebright R.H., Gourse R.L. Response of RNA polymerase to ppGpp: requirement for the omega subunit and relief of this requirement by DksA. Genes Dev 2005, 19:2378-2387.
43. Langmead B., Trapnell C., Pop M., Salzberg S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25.
44. Kuscu C., Arslan S., Singh R., Thorpe J., Adli M. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat Biotechnol 2014, 32:677-683.
45. Singh R., Kuscu C., Quinlan A., Qi Y., Adli M. Cas9-chromatin binding information enables more accurate CRISPR off-target prediction. Nucleic Acids Res 2015, 10.1093/nar/gkv575.
46. Aravind L., Koonin E.V. Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system. Genome Res 2001, 11:1365-1374.
47. Wang S.T., Setlow B., Conlon E.M., Lyon J.L., Imamura D., Sato T., Setlow P., Losick R., Eichenberger P. The forespore line of gene expression in Bacillus subtilis. J Mol Biol 2006, 358:16-37.
48. Shuman S., Glickman M.S. Bacterial DNA repair by non-homologous end joining. Nat Rev Microbiol 2007, 5:852-861.
49. Stephanou N.C., Gao F., Bongiorno P., Ehrt S., Schnappinger D., Shuman S., Glickman M.S. Mycobacterial nonhomologous end joining mediates mutagenic repair of chromosomal double-strand DNA breaks. J Bacteriol 2007, 189:5237-5246.
50. Gilbert L.A., Larson M.H., Morsut L., Liu Z., Brar G.A., Torres S.E., Stern-Ginossar N., Brandman O., Whitehead E.H., Doudna J.A., et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 2013, 154:442-451.
51. Ji W., Lee D., Wong E., Dadlani P., Dinh D., Huang V., Kearns K., Teng S., Chen S., Haliburton J., et al. Specific gene repression by CRISPRi system transferred through bacterial conjugation. ACS Synth Biol 2014, 3:929-931.
52. Mimee M., Tucker A.C., Voigt C.A., Lu T.K. Programming a human commensal bacterium, Bacteroides thetaiotaomicron, to sense and respond to stimuli in the murine gut microbiota. Cell Sys 2015, 1-11. 10.1016/j.cels.2015.06.001.
53. Tong Y., Charusanti P., Zhang L., Weber T., Lee S.Y. CRISPR-Cas9 based engineering of Actinomycetal genomes. ACS Synth Biol 2015, 10.1021/acssynbio.5b00038.