Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems

Cell

Volumn 163, Issue 4, 2015, Pages 840-853

  Wang, Jiuyu ^a,b   Li, Jiazhi ^a,b,c   Zhao, Hongtu ^a,b,c   Sheng, Gang ^a,b   Wang, Min ^a,b,c   Yin, Maolu ^a,b,c   Wang, Yanli ^a,b  

^a Key Laboratory of RNA Biology   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN; DNA; TYROSINE; CAS2 PROTEIN, E COLI; CRISPR ASSOCIATED PROTEIN; DEOXYRIBONUCLEASE; ENDONUCLEASE; ESCHERICHIA COLI PROTEIN; YGBT PROTEIN, E COLI;

ARTICLE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CRISPR CAS SYSTEM; CRYSTAL STRUCTURE; DNA BINDING; DNA FLANKING REGION; DNA SEQUENCE; ENZYME ACTIVE SITE; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; STRUCTURE ANALYSIS; AMINO ACID SEQUENCE; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; ESCHERICHIA COLI; GENETICS; IMMUNOLOGY; METABOLISM; MOLECULAR GENETICS; SEQUENCE ALIGNMENT; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; CRISPR-ASSOCIATED PROTEINS; CRISPR-CAS SYSTEMS; CRYSTALLOGRAPHY, X-RAY; ENDODEOXYRIBONUCLEASES; ENDONUCLEASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT;

EID: 84946130269     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2015.10.008     Document Type: Article

References (35)

1. C. Anders, O. Niewoehner, A. Duerst, and M. Jinek Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease Nature 513 2014 569 573
2. Z. Arslan, V. Hermanns, R. Wurm, R. Wagner, and Ü. Pul Detection and characterization of spacer integration intermediates in type I-E CRISPR-Cas system Nucleic Acids Res. 42 2014 7884 7893
3. M. Babu, N. Beloglazova, R. Flick, C. Graham, T. Skarina, B. Nocek, A. Gagarinova, O. Pogoutse, G. Brown, A. Binkowski, and et al. A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair Mol. Microbiol. 79 2011 484 502
4. R. Barrangou, and L.A. Marraffini CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity Mol. Cell 54 2014 234 244
5. R. Barrangou, C. Fremaux, H. Deveau, M. Richards, P. Boyaval, S. Moineau, D.A. Romero, and P. Horvath CRISPR provides acquired resistance against viruses in prokaryotes Science 315 2007 1709 1712
6. N. Beloglazova, G. Brown, M.D. Zimmerman, M. Proudfoot, K.S. Makarova, M. Kudritska, S. Kochinyan, S. Wang, M. Chruszcz, W. Minor, and et al. A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats J. Biol. Chem. 283 2008 20361 20371
7. S.J. Brouns, M.M. Jore, M. Lundgren, E.R. Westra, R.J. Slijkhuis, A.P. Snijders, M.J. Dickman, K.S. Makarova, E.V. Koonin, and J. van der Oost Small CRISPR RNAs guide antiviral defense in prokaryotes Science 321 2008 960 964
8. K.A. Datsenko, K. Pougach, A. Tikhonov, B.L. Wanner, K. Severinov, and E. Semenova Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system Nat. Commun. 3 2012 945
9. H. Deveau, R. Barrangou, J.E. Garneau, J. Labonté, C. Fremaux, P. Boyaval, D.A. Romero, P. Horvath, and S. Moineau Phage response to CRISPR-encoded resistance in Streptococcus thermophilus J. Bacteriol. 190 2008 1390 1400
10. C. Díez-Villaseñor, N.M. Guzmán, C. Almendros, J. García-Martínez, and F.J. Mojica CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli RNA Biol. 10 2013 792 802
11. P.C. Fineran, and E. Charpentier Memory of viral infections by CRISPR-Cas adaptive immune systems: acquisition of new information Virology 434 2012 202 209
12. J.E. Garneau, M.E. Dupuis, M. Villion, D.A. Romero, R. Barrangou, P. Boyaval, C. Fremaux, P. Horvath, A.H. Magadán, and S. Moineau The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA Nature 468 2010 67 71
13. M.G. Goren, I. Yosef, O. Auster, and U. Qimron Experimental definition of a clustered regularly interspaced short palindromic duplicon in Escherichia coli J. Mol. Biol. 423 2012 14 16
14. F.F. Gunderson, C.A. Mallama, S.G. Fairbairn, and N.P. Cianciotto Nuclease activity of Legionella pneumophila Cas2 promotes intracellular infection of amoebal host cells Infect. Immun. 83 2015 1008 1018
15. C.R. Hale, P. Zhao, S. Olson, M.O. Duff, B.R. Graveley, L. Wells, R.M. Terns, and M.P. Terns RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex Cell 139 2009 945 956
16. R. Heler, P. Samai, J.W. Modell, C. Weiner, G.W. Goldberg, D. Bikard, and L.A. Marraffini Cas9 specifies functional viral targets during CRISPR-Cas adaptation Nature 519 2015 199 202
17. P. Horvath, D.A. Romero, A.C. Coûté-Monvoisin, M. Richards, H. Deveau, S. Moineau, P. Boyaval, C. Fremaux, and R. Barrangou Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus J. Bacteriol. 190 2008 1401 1412
18. D. Ka, D. Kim, G. Baek, and E. Bae Structural and functional characterization of Streptococcus pyogenes Cas2 protein under different pH conditions Biochem. Biophys. Res. Commun. 451 2014 152 157
19. T.Y. Kim, M. Shin, L. Huynh Thi Yen, and J.S. Kim Crystal structure of Cas1 from Archaeoglobus fulgidus and characterization of its nucleolytic activity Biochem. Biophys. Res. Commun. 441 2013 720 725
20. A. Levy, M.G. Goren, I. Yosef, O. Auster, M. Manor, G. Amitai, R. Edgar, U. Qimron, and R. Sorek CRISPR adaptation biases explain preference for acquisition of foreign DNA Nature 520 2015 505 510
21. K.S. Makarova, D.H. Haft, R. Barrangou, S.J. Brouns, E. Charpentier, P. Horvath, S. Moineau, F.J. Mojica, Y.I. Wolf, A.F. Yakunin, and et al. Evolution and classification of the CRISPR-Cas systems Nat. Rev. Microbiol. 9 2011 467 477
22. L.A. Marraffini, and E.J. Sontheimer CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA Science 322 2008 1843 1845
23. F.J. Mojica, C. Díez-Villaseñor, J. García-Martínez, and C. Almendros Short motif sequences determine the targets of the prokaryotic CRISPR defence system Microbiology 155 2009 733 740
24. K.H. Nam, F. Ding, C. Haitjema, Q. Huang, M.P. DeLisa, and A. Ke Double-stranded endonuclease activity in Bacillus halodurans clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas2 protein J. Biol. Chem. 287 2012 35943 35952
25. J.K. Nuñez, P.J. Kranzusch, J. Noeske, A.V. Wright, C.W. Davies, and J.A. Doudna Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity Nat. Struct. Mol. Biol. 21 2014 528 534
26. J.K. Nuñez, A.S. Lee, A. Engelman, and J.A. Doudna Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity Nature 519 2015 193 198
27. D. Paez-Espino, W. Morovic, C.L. Sun, B.C. Thomas, K. Ueda, B. Stahl, R. Barrangou, and J.F. Banfield Strong bias in the bacterial CRISPR elements that confer immunity to phage Nat. Commun. 4 2013 1430
28. K. Pougach, E. Semenova, E. Bogdanova, K.A. Datsenko, M. Djordjevic, B.L. Wanner, and K. Severinov Transcription, processing and function of CRISPR cassettes in Escherichia coli Mol. Microbiol. 77 2010 1367 1379
29. C. Rollie, S. Schneider, A.S. Brinkmann, E.L. Bolt, and M.F. White Intrinsic sequence specificity of the Cas1 integrase directs new spacer acquisition eLife 4 2015 e08716
30. P. Samai, P. Smith, and S. Shuman Structure of a CRISPR-associated protein Cas2 from Desulfovibrio vulgaris Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66 2010 1552 1556
31. D.C. Swarts, C. Mosterd, M.W. van Passel, and S.J. Brouns CRISPR interference directs strand specific spacer acquisition PLoS ONE 7 2012 e35888
32. J. van der Oost, E.R. Westra, R.N. Jackson, and B. Wiedenheft Unravelling the structural and mechanistic basis of CRISPR-Cas systems Nat. Rev. Microbiol. 12 2014 479 492
33. B. Wiedenheft, K. Zhou, M. Jinek, S.M. Coyle, W. Ma, and J.A. Doudna Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense Structure 17 2009 904 912
34. I. Yosef, M.G. Goren, and U. Qimron Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli Nucleic Acids Res. 40 2012 5569 5576
35. I. Yosef, D. Shitrit, M.G. Goren, D. Burstein, T. Pupko, and U. Qimron DNA motifs determining the efficiency of adaptation into the Escherichia coli CRISPR array Proc. Natl. Acad. Sci. USA 110 2013 14396 14401