Unravelling the structural and mechanistic basis of CRISPR-Cas systems

Nature Reviews Microbiology

Volumn 12, Issue 7, 2014, Pages 479-492

  Van Der Oost, John ^a   Westra, Edze R ^a,b   Jackson, Ryan N ^c   Wiedenheft, Blake ^c  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b UNIVERSITY OF EXETER   (United Kingdom)

^c MONTANA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAS1 PROTEIN; CAS2 PROTEIN; CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN; HETERODUPLEX; RIBONUCLEOPROTEIN; RNA; UNCLASSIFIED DRUG; CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN 1; CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN 2; CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN 3; CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN 5; CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN 6; CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN 7; CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN 9; NUCLEIC ACID; RIBONUCLEASE; RIBONUCLEASE III; RNA PRECURSOR;

ADAPTIVE IMMUNITY; ARCHAEON; BACTERIAL IMMUNITY; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CONFORMATIONAL TRANSITION; CRISPR CAS SYSTEM; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; REVIEW; RNA INTERFERENCE; RNA PROCESSING; BACTERIUM; BIOGENESIS; GENE EXPRESSION; GENE LOCUS; RNA TRANSCRIPTION; TYPE I SECRETION SYSTEM; TYPE II SECRETION SYSTEM; TYPE III SECRETION SYSTEM; VIRUS;

ARCHAEA; BACTERIA; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CRISPR-CAS SYSTEMS; MODELS, MOLECULAR; PLASMIDS; RIBONUCLEOPROTEINS; RNA, BACTERIAL; VIRUSES;

EID: 84902533278     PISSN: 17401526     EISSN: 17401534     Source Type: Journal    
DOI: 10.1038/nrmicro3279     Document Type: Review

References (128)

1. Suttle, C. A. Marine viruses -major players in the global ecosystem. Nature Rev. Microbiol. 5, 801-812 (2007).
2. Samson, J. E., Magadan, A. H., Sabri, M. &Moineau, S. Revenge of the phages: defeating bacterial defences. Nature Rev. Microbiol. 11, 675-687 (2013).
3. Makarova, K. S., Wolf, Y. I. &Koonin, E. V. Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Res. 41, 4360-4377 (2013).
4. Mojica, F. J., Diez-Villasenor, C., Garcia-Martinez, J. &Soria, E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 60, 174-182 (2005).
5. Bolotin, A., Quinquis, B., Sorokin, A. &Ehrlich, S. D. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151, 2551-2561 (2005).
6. Pourcel, C., Salvignol, G. &Vergnaud, G. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology 151, 653-663 (2005).
7. Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709-1712 (2007).
8. Kunin, V., Sorek, R. &Hugenholtz, P. Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol. 8, R61 (2007).
9. Jansen, R., Embden, J. D., Gaastra, W. &Schouls, L. M. Identification of genes that are associated with DNA repeats in prokaryotes. Mol. Microbiol. 43, 1565-1575 (2002).
10. Haft, D. H., Selengut, J., Mongodin, E. F. &Nelson, K. E. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput. Biol. 1, e60 (2005).
11. Makarova, K. S., Grishin, N. V., Shabalina, S. A., Wolf, Y. I. &Koonin, E. V. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol. Direct 1, 7 (2006).
12. Makarova, K. S. et al. Evolution and classification of the CRISPR-Cas systems. Nature Rev. Microbiol. 9, 467-477 (2011).
13. Heidrich, N. &Vogel, J. Same same but different: new structural insight into CRISPR-Cas complexes. Mol. Cell 52, 4-7 (2013).
14. Fonfara, I. et al. Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic Acids Res. 42, 2577-2590 (2013).
15. Godde, J. S. &Bickerton, A. The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes. J. Mol. Evol. 62, 718-729 (2006).
16. Lillestol, R. K. et al. CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties. Mol. Microbiol. 72, 259-272 (2009).
17. Seed, K. D., Lazinski, D. W., Calderwood, S. B. &Camilli, A. A bacteriophage encodes its own CRISPR-Cas adaptive response to evade host innate immunity. Nature 494, 489-491 (2013).
18. Minot, S. et al. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res. 21, 1616-1625 (2011).
19. Minot, S. et al. Rapid evolution of the human gut virome. Proc. Natl Acad. Sci. USA 110, 12450-12455 (2013).
20. Tyson, G. W. &Banfield, J. F. Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ. Microbiol. 10, 200-207 (2008).
21. Dupuis, M. E., Villion, M., Magadan, A. H. &Moineau, S. CRISPR-Cas and restriction-modification systems are compatible and increase phage resistance. Nature Commun. 4, 2087 (2013).
22. Deveau, H. et al. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J. Bacteriol. 190, 1390-1400 (2008).
23. Mojica, F. J., Diez-Villasenor, C., Garcia-Martinez, J. &Almendros, C. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155, 733-740 (2009).
24. Shah, S. A., Erdmann, S., Mojica, F. J. &Garrett, R. A. Protospacer recognition motifs: mixed identities and functional diversity. RNA Biol. 10, 891-899 (2013).
25. Swarts, D. C., Mosterd, C., van Passel, M. W. &Brouns, S. J. CRISPR interference directs strand specific spacer acquisition. PLoS ONE 7, e35888 (2012).
26. Diez-Villasenor, C., Guzman, N. M., Almendros, C., Garcia-Martinez, J. &Mojica, F. J. CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli. RNA Biol. 10, 792-802 (2013).
27. Erdmann, S. &Garrett, R. A. Selective and hyperactive uptake of foreign DNA by adaptive immune systems of an archaeon via two distinct mechanisms. Mol. Microbiol. 85, 1044-1056 (2012).
28. Yosef, I., Goren, M. G. &Qimron, U. Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res. 40, 5569-5576 (2012).
29. Vercoe, R. B. et al. Cytotoxic chromosomal targeting by CRISPR/Cas systems can reshape bacterial genomes and expel or remodel pathogenicity islands. PLoS Genet. 9, e1003454 (2013).
30. Stern, A., Keren, L., Wurtzel, O., Amitai, G. &Sorek, R. Self-targeting by CRISPR: gene regulation or autoimmunity? Trends Genet. 26, 335-340 (2010).
31. Wiedenheft, B. et al. Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure 17, 904-912 (2009).
32. Babu, M. et al. A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol. Microbiol. 79, 484-502 (2011).
33. Wiedenheft, B., Sternberg, S. H. &Doudna, J. A. RNA-guided genetic silencing systems in bacteria and archaea. Nature 482, 331-338 (2012).
34. Reeks, J., Naismith, J. H. &White, M. F. CRISPR interference: a structural perspective. Biochem. J. 453, 155-166 (2013).
35. Beloglazova, N. et al. A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats. J. Biol. Chem. 283, 20361-20371 (2008).
36. Samai, P., Smith, P. &Shuman, S. Structure of a CRISPR-associated protein Cas2 from Desulfovibrio vulgaris. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66, 1552-1556 (2010).
37. Nam, K. H. et al. Double-stranded endonuclease activity in Bacillus halodurans clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas2 protein. J. Biol. Chem. 287, 35943-35952 (2012).
38. van der Oost, J., Jore, M. M., Westra, E. R., Lundgren, M. &Brouns, S. J. CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem. Sci. 34, 401-407 (2009).
39. Arslan, Z. et al. Double-strand DNA end-binding and sliding of the toroidal CRISPR-associated protein Csn2. Nucleic Acids Res. 41, 6347-6359 (2013).
40. Nam, K. H., Kurinov, I. &Ke, A. Crystal structure of clustered regularly interspaced short palindromic repeats (CRISPR)-associated Csn2 protein revealed Ca2+-dependent double-stranded DNA binding activity. J. Biol. Chem. 286, 30759-30768 (2011).
41. Ellinger, P. et al. The crystal structure of the CRISPR-associated protein Csn2 from Streptococcus agalactiae. J. Struct. Biol. 178, 350-362 (2012).
42. Koo, Y., Jung, D. K. &Bae, E. Crystal structure of Streptococcus pyogenes Csn2 reveals calcium-dependent conformational changes in its tertiary and quaternary structure. PLoS ONE 7, e33401 (2012).
43. Lee, K. H. et al. Identification, structural, and biochemical characterization of a group of large Csn2 proteins involved in CRISPR-mediated bacterial immunity. Proteins 80, 2573-2582 (2012).
44. Zhang, J., Kasciukovic, T. &White, M. F. The CRISPR associated protein Cas4 is a 5? to 3? DNA exonuclease with an iron-sulfur cluster. PLoS ONE 7, e47232 (2012).
45. Lemak, S. et al. Toroidal structure and DNA cleavage by the CRISPR-associated [4Fe-4S] cluster containing Cas4 nuclease SSO0001 from Sulfolobus solfataricus. J. Am. Chem. Soc. 135, 17476-17487 (2013).
46. Plagens, A., Tjaden, B., Hagemann, A., Randau, L. &Hensel, R. Characterization of the CRISPR/Cas subtype I-A system of the hyperthermophilic crenarchaeon Thermoproteus tenax. J. Bacteriol. 194, 2491-2500 (2012).
47. Jackson, R. N., Lavin, M., Carter, J. &Wiedenheft, B. Fitting CRISPR-associated Cas3 into the helicase family tree. Curr. Opin. Struct. Biol. 24C, 106-114 (2014).
48. Richter, C., Gristwood, T., Clulow, J. S. &Fineran, P. C. In vivo protein interactions and complex formation in the Pectobacterium atrosepticum subtype I-F CRISPR/Cas System. PLoS ONE 7, e49549 (2012).
49. Datsenko, K. A. et al. Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nature Commun. 3, 945 (2012).
50. Fineran, P. C. et al. Degenerate target sites mediate rapid primed CRISPR adaptation. Proc. Natl Acad. Sci. USA 111, E1629-E1638 (2014).
51. Niewoehner, O., Jinek, M. &Doudna, J. A. Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases. Nucleic Acids Res. 42, 1341-1353 (2014).
52. Jore, M. M. et al. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nature Struct. Mol. Biol. 18, 529-536 (2011).
53. Wiedenheft, B. et al. RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions. Proc. Natl Acad. Sci. USA 108, 10092-10097 (2011).
54. Sinkunas, T. et al. In vitro reconstitution of Cascade-mediated CRISPR immunity in Streptococcus thermophilus. EMBO J. 32, 385-394 (2013).
55. Carte, J., Wang, R., Li, H., Terns, R. M. &Terns, M. P. Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev. 22, 3489-3496 (2008).
56. Sashital, D. G., Jinek, M. &Doudna, J. A. An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3. Nature Struct. Mol. Biol. 18, 680-687 (2011).
57. Reeks, J. et al. Structure of a dimeric crenarchaeal Cas6 enzyme with an atypical active site for CRISPR RNA processing. Biochem. J. 452, 223-230 (2013).
58. Ebihara, A. et al. Crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 reveals a new protein family with an RNA recognition motif-like domain. Protein Sci. 15, 1494-1499 (2006).
59. Gesner, E. M., Schellenberg, M. J., Garside, E. L., George, M. M. &Macmillan, A. M. Recognition and maturation of effector RNAs in a CRISPR interference pathway. Nature Struct. Mol. Biol. 18, 688-692 (2011).
60. Haurwitz, R. E., Jinek, M., Wiedenheft, B., Zhou, K. &Doudna, J. A. Sequence-and structure-specific RNA processing by a CRISPR endonuclease. Science 329, 1355-1358 (2010).
61. Przybilski, R. et al. Csy4 is responsible for CRISPR RNA processing in Pectobacterium atrosepticum. RNA Biol. 8, 517-528 (2011).
62. Haurwitz, R. E., Sternberg, S. H. &Doudna, J. A. Csy4 relies on an unusual catalytic dyad to position and cleave CRISPR RNA. EMBO J. 31, 2824-2832 (2012).
63. Sternberg, S. H., Haurwitz, R. E. &Doudna, J. A. Mechanism of substrate selection by a highly specific CRISPR endoribonuclease. RNA 18, 661-672 (2012).
64. Carte, J., Pfister, N. T., Compton, M. M., Terns, R. M. &Terns, M. P. Binding and cleavage of CRISPR RNA by Cas6. RNA 16, 2181-2188 (2010).
65. Wang, R., Preamplume, G., Terns, M. P., Terns, R. M. &Li, H. Interaction of the Cas6 riboendonuclease with CRISPR RNAs: recognition and cleavage. Structure 19, 257-264 (2011).
66. Hatoum-Aslan, A., Maniv, I. &Marraffini, L. A. Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site. Proc. Natl Acad. Sci. USA 108, 21218-21222 (2011).
67. Hatoum-Aslan, A., Samai, P., Maniv, I., Jiang, W. &Marraffini, L. A. A ruler protein in a complex for antiviral defense determines the length of small interfering CRISPR RNAs. J. Biol. Chem. 288, 27888-27897 (2013).
68. Zhang, J. et al. Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity. Mol. Cell 45, 303-313 (2012).
69. Staals, R. H. et al. Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus. Mol. Cell 52, 135-145 (2013).
70. Hale, C. R. et al. Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs. Mol. Cell 45, 292-302 (2012).
71. Garside, E. L. et al. Cas5d processes pre-crRNA and is a member of a larger family of CRISPR RNA endonucleases. RNA 18, 2020-2028 (2012).
72. Nam, K. H. et al. Cas5d protein processes pre-crRNA and assembles into a cascade-like interference complex in subtype I-C/Dvulg CRISPR-Cas system. Structure 20, 1574-1584 (2012).
73. Koo, Y., Ka, D., Kim, E. J., Suh, N. &Bae, E. Conservation and variability in the structure and function of the Cas5d endoribonuclease in the CRISPR-mediated microbial immune system. J. Mol. Biol. 425, 3799-3810 (2013).
74. Wiedenheft, B. et al. Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature 477, 486-489 (2011).
75. Deltcheva, E. et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471, 602-607 (2011).
76. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821 (2012).
77. Gasiunas, G., Barrangou, R., Horvath, P. &Siksnys, V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc. Natl Acad. Sci. USA 109, E2579-E2586 (2012).
78. Rouillon, C. et al. Structure of the CRISPR interference complex CSM reveals key similarities with Cascade. Mol. Cell 52, 124-134 (2013).
79. Spilman, M. et al. Structure of an RNA silencing complex of the CRISPR-Cas immune system. Mol. Cell 52, 146-152 (2013).
80. Jinek, M. et al. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343, 1247997 (2014).
81. Nishimasu, H. et al. Crystal structure of cas9 in complex with guide RNA and target DNA. Cell 156, 935-949 (2014).
82. Westra, E. R. et al. The CRISPRs, they are a-changin': how prokaryotes generate adaptive immunity. Annu. Rev. Genet. 46, 311-339 (2012).
83. Brouns, S. J. et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321, 960-964 (2008).
84. Sashital, D. G., Wiedenheft, B. &Doudna, J. A. Mechanism of foreign DNA selection in a bacterial adaptive immune system. Mol. Cell 46, 606-615 (2012).
85. van Duijn, E. et al. Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced shot-palindromic-repeats (CRISPR)-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa. Mol. Cell Proteom. 11, 1430-1441 (2012).
86. Quax, T. E. et al. Differential translation tunes uneven production of operon-encoded proteins. Cell Rep. 4, 938-944 (2013).
87. Lintner, N. G. et al. Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE). J. Biol. Chem. 286, 21643-21656 (2011).
88. Maris, C., Dominguez, C. &Allain, F. H. The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. FEBS J. 272, 2118-2131 (2005).
89. Hochstrasser, M. L. et al. CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference. Proc. Natl Acad. Sci. USA 111, 6618-6623 (2014).
90. Hrle, A. et al. Structure and RNA-binding properties of the Type III-A CRISPR-associated protein Csm3. RNA Biol. 10, 1670-1678 (2013).
91. Makarova, K. S., Aravind, L., Wolf, Y. I. &Koonin, E. V. Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol. Direct 6, 38 (2011).
92. Osawa, T., Inanaga, H. &Numata, T. Crystal structure of the Cmr2-Cmr3 subcomplex in the CRISPR-Cas RNA silencing effector complex. J. Mol. Biol. 425, 3811-3823 (2013).
93. Shao, Y. et al. Structure of the Cmr2-Cmr3 subcomplex of the Cmr RNA silencing complex. Structure 21, 376-384 (2013).
94. Mulepati, S., Orr, A. &Bailey, S. Crystal structure of the largest subunit of a bacterial RNA-guided immune complex and its role in DNA target binding. J. Biol. Chem. 287, 22445-22449 (2012).
95. Zhu, X. &Ye, K. Crystal structure of Cmr2 suggests a nucleotide cyclase-related enzyme in type III CRISPR-Cas systems. FEBS Lett. 586, 939-945 (2012).
96. Cocozaki, A. I. et al. Structure of the Cmr2 subunit of the CRISPR-Cas RNA silencing complex. Structure 20, 545-553 (2012).
97. Makarova, K. S., Wolf, Y. I. &Koonin, E. V. The basic building blocks and evolution of CRISPR-Cas systems. Biochem. Soc. Trans. 41, 1392-1400 (2013).
98. Westra, E. R. et al. Cascade-mediated binding and bending of negatively supercoiled DNA. RNA Biol. 9, 1134-1138 (2012).
99. Semenova, E. et al. Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence. Proc. Natl Acad. Sci. USA 108, 10098-10103 (2011).
100. Sorek, R., Lawrence, C. M. &Wiedenheft, B. CRISPR-mediated adaptive immune systems in bacteria and archaea. Annu. Rev. Biochem. 82, 237-266 (2013).
101. Westra, E. R. et al. Type I-E CRISPR-Cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition. PLoS Genet. 9, e1003742 (2013).
102. Kunne, T., Swarts, D. C. &Brouns, S. J. Planting the seed: target recognition of short guide RNAs. Trends Microbiol. 22, 74-83 (2014).
103. Westra, E. R. et al. CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3. Mol. Cell 46, 595-605 (2012).
104. Beloglazova, N. et al. Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference. EMBO J. 30, 4616-4627 (2011).
105. Mulepati, S. &Bailey, S. Structural and biochemical analysis of nuclease domain of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 3 (Cas3). J. Biol. Chem. 286, 31896-31903 (2011).
106. Sinkunas, T. et al. Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system. EMBO J. 30, 1335-1342 (2011).
107. Garneau, J. E. et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 67-71 (2010).
108. Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C. &Doudna, J. A. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507, 62-67 (2014).
109. Jiang, W., Bikard, D., Cox, D., Zhang, F. &Marraffini, L. A. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nature Biotech. 31, 233-239 (2013).
110. Magadan, A. H., Dupuis, M. E., Villion, M. &Moineau, S. Cleavage of phage DNA by the Streptococcus thermophilus CRISPR3-Cas system. PLoS ONE 7, e40913 (2012).
111. Marraffini, L. A. &Sontheimer, E. J. Self versus non-self discrimination during CRISPR RNA-directed immunity. Nature 463, 568-571 (2010).
112. Hatoum-Aslan, A., Maniv, I., Samai, P. &Marraffini, L. A. Genetic characterization of antiplasmid immunity through a type III-A CRISPR-Cas system. J. Bacteriol. 196, 310-317 (2014).
113. Marraffini, L. A. &Sontheimer, E. J. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322, 1843-1845 (2008).
114. Deng, L., Garrett, R. A., Shah, S. A., Peng, X. &She, Q. A novel interference mechanism by a type IIIB CRISPR-Cmr module in Sulfolobus. Mol. Microbiol. 87, 1088-1099 (2013).
115. Hale, C. R. et al. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139, 945-956 (2009).
116. Stoll, B. et al. Requirements for a successful defence reaction by the CRISPR-Cas subtype I-B system. Biochem. Soc. Trans. 41, 1444-1448 (2013).
117. Story, R. M., Weber, I. T. &Steitz, T. A. The structure of the E. coli recA protein monomer and polymer. Nature 355, 318-325 (1992).
118. Sheng, G. et al. Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proc. Natl Acad. Sci. USA 111, 652-657 (2014).
119. Pennisi, E. The CRISPR craze. Science 341, 833-836 (2013).
120. Wilkinson, R. &Wiedenheft, B. A. CRISPR method for genome engineering. F1000Prime Rep. 6, 3 (2014).
121. Gomaa, A. A. et al. Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems. mBio 5, e00928-13 (2014).
122. Bikard, D. et al. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res. 41, 7429-7437 (2013).
123. Qi, L. S. et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173-1183 (2013).
124. Sampson, T. R. &Weiss, D. S. Exploiting CRISPR/Cas systems for biotechnology. Bioessays 36, 34-38 (2014).
125. Almendros, C., Guzman, N. M., Diez-Villasenor, C., Garcia-Martinez, J. &Mojica, F. J. Target motifs affecting natural immunity by a constitutive CRISPR-Cas system in Escherichia coli. PLoS ONE 7, e50797 (2012).
126. Horvath, P. et al. Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J. Bacteriol. 190, 1401-1412 (2008).
127. Plagens, A. et al. In vitro assembly and activity of an archaeal CRISPR-Cas type I-A Cascade interference complex. Nucleic Acids Res. 42, 5125-5138 (2014).
128. Nuñez J. K. et al. Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity. Nature Struct. Mol. Biol. http://dx.doi.org/10.1038/nsmb.2820 (2014)