Recognition and cleavage of a nonstructured CRISPR RNA by its processing endoribonuclease Cas6

Structure

Volumn 21, Issue 3, 2013, Pages 385-393

  Shao, Yaming ^a   Li, Hong ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBONUCLEASE; RIBONUCLEASE CAS6; RNA; UNCLASSIFIED DRUG;

ARTICLE; CLUSTERED REGULARLY INTERSPACED PALINDROMIC REPEAT; CRYSTAL STRUCTURE; ENZYME STABILITY; MOLECULAR MECHANICS; PRIORITY JOURNAL; PROTEIN PROCESSING; RNA BINDING; RNA CLEAVAGE; RNA PROCESSING; RNA STRUCTURE;

ARCHAEAL PROTEINS; BASE SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; ENDORIBONUCLEASES; ESCHERICHIA COLI; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN STRUCTURE, SECONDARY; PROTEIN SUBUNITS; RECOMBINANT PROTEINS; RNA CLEAVAGE; RNA STABILITY; RNA, ARCHAEAL; SULFOLOBUS SOLFATARICUS;

PROKARYOTA;

EID: 84874930818     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2013.01.010     Document Type: Article

References (42)

1. P.D. Adams, P.V. Afonine, G. Bunkóczi, V.B. Chen, N. Echols, J.J. Headd, L.W. Hung, S. Jain, G.J. Kapral, and R.W. Grosse Kunstleve The Phenix software for automated determination of macromolecular structures Methods 55 2011 94 106
2. R. Barrangou, and P. Horvath CRISPR: new horizons in phage resistance and strain identification Annu Rev Food Sci Technol 3 2012 143 162
3. 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
4. D. Bhaya, M. Davison, and R. Barrangou CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation Annu. Rev. Genet. 45 2011 273 297
5. 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
6. J. Carte, R. Wang, H. Li, R.M. Terns, and M.P. Terns Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes Genes Dev. 22 2008 3489 3496
7. J. Carte, N.T. Pfister, M.M. Compton, R.M. Terns, and M.P. Terns Binding and cleavage of CRISPR RNA by Cas6 RNA 16 2010 2181 2188
8. J.C. Cochrane, and S.A. Strobel Catalytic strategies of self-cleaving ribozymes Acc. Chem. Res. 41 2008 1027 1035
9. H. Deveau, J.E. Garneau, and S. Moineau CRISPR/Cas system and its role in phage-bacteria interactions Annu. Rev. Microbiol. 64 2010 475 493
10. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr. D Biol. Crystallogr. 60 2004 2126 2132
11. E.M. Gesner, M.J. Schellenberg, E.L. Garside, M.M. George, and A.M. Macmillan Recognition and maturation of effector RNAs in a CRISPR interference pathway Nat. Struct. Mol. Biol. 18 2011 688 692
12. D.H. Haft, J. Selengut, E.F. Mongodin, and K.E. Nelson A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes PLoS Comput. Biol. 1 2005 e60
13. C. Hale, K. Kleppe, R.M. Terns, and M.P. Terns Prokaryotic silencing (psi)RNAs in Pyrococcus furiosus RNA 14 2008 2572 2579
14. 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
15. R.E. Haurwitz, M. Jinek, B. Wiedenheft, K. Zhou, and J.A. Doudna Sequence- and structure-specific RNA processing by a CRISPR endonuclease Science 329 2010 1355 1358
16. R.E. Haurwitz, S.H. Sternberg, and J.A. Doudna Csy4 relies on an unusual catalytic dyad to position and cleave CRISPR RNA EMBO J. 31 2012 2824 2832
17. P. Horvath, and R. Barrangou CRISPR/Cas, the immune system of bacteria and archaea Science 327 2010 167 170
18. F.V. Karginov, and G.J. Hannon The CRISPR system: small RNA-guided defense in bacteria and archaea Mol. Cell 37 2010 7 19
19. V. Kunin, R. Sorek, and P. Hugenholtz Evolutionary conservation of sequence and secondary structures in CRISPR repeats Genome Biol. 8 2007 R61
20. R.K. Lillestøl, S.A. Shah, K. Brügger, P. Redder, H. Phan, J. Christiansen, and R.A. Garrett CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties Mol. Microbiol. 72 2009 259 272
21. N.G. Lintner, M. Kerou, S.K. Brumfield, S. Graham, H. Liu, J.H. Naismith, M. Sdano, N. Peng, Q. She, and V. Copié Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE) J. Biol. Chem. 286 2011 21643 21656
22. K.S. Makarova, N.V. Grishin, S.A. Shabalina, Y.I. Wolf, and E.V. Koonin 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 2006 7
23. K.S. Makarova, L. Aravind, Y.I. Wolf, and E.V. Koonin Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems Biol. Direct 6 2011 38
24. L.A. Marraffini, and E.J. Sontheimer CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea Nat. Rev. Genet. 11 2010 181 190
25. D. Min, S. Xue, H. Li, and W. Yang 'In-line attack' conformational effect plays a modest role in an enzyme-catalyzed RNA cleavage: a free energy simulation study Nucleic Acids Res. 35 2007 4001 4006
26. F.J. Mojica, C. Díez-Villaseñor, J. García- Martínez, and E. Soria Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements J. Mol. Evol. 60 2005 174 182
27. Z. Otwinowski, and W. Minor Processing of x-ray diffraction data collected in the oscillation mode Methods Enzymol. 276 1997 307 326
28. C. Pourcel, G. Salvignol, and G. Vergnaud CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies Microbiology 151 2005 653 663
29. R.T. Raines Ribonuclease A Chem. Rev. 98 1998 1045 1066
30. H. Richter, J. Zoephel, J. Schermuly, D. Maticzka, R. Backofen, and L. Randau Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis Nucleic Acids Res. 40 2012 9887 9896
31. D.G. Sashital, M. Jinek, and J.A. Doudna An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3 Nat. Struct. Mol. Biol. 18 2011 680 687
32. R. Sorek, V. Kunin, and P. Hugenholtz CRISPR - a widespread system that provides acquired resistance against phages in bacteria and archaea Nat. Rev. Microbiol. 6 2008 181 186
33. M.P. Terns, and R.M. Terns CRISPR-based adaptive immune systems Curr. Opin. Microbiol. 14 2011 321 327
34. J. van der Oost, M.M. Jore, E.R. Westra, M. Lundgren, and S.J. Brouns CRISPR-based adaptive and heritable immunity in prokaryotes Trends Biochem. Sci. 34 2009 401 407
35. R. Wang, G. Preamplume, M.P. Terns, R.M. Terns, and H. Li Interaction of the Cas6 riboendonuclease with CRISPR RNAs: recognition and cleavage Structure 19 2011 257 264
36. R. Wang, H. Zheng, G. Preamplume, Y. Shao, and H. Li The impact of CRISPR repeat sequence on structures of a Cas6 protein-RNA complex Protein Sci. 21 2012 405 422
37. B. Wiedenheft, G.C. Lander, K. Zhou, M.M. Jore, S.J. Brouns, J. van der Oost, J.A. Doudna, and E. Nogales Structures of the RNA-guided surveillance complex from a bacterial immune system Nature 477 2011 486 489
38. B. Wiedenheft, E. van Duijn, J.B. Bultema, S.P. Waghmare, K. Zhou, A. Barendregt, W. Westphal, A.J. Heck, E.J. Boekema, M.J. Dickman, and J.A. Doudna RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions Proc. Natl. Acad. Sci. USA 108 2011 10092 10097
39. B. Wiedenheft, S.H. Sternberg, and J.A. Doudna RNA-guided genetic silencing systems in bacteria and archaea Nature 482 2012 331 338
40. S. Xue, K. Calvin, and H. Li RNA recognition and cleavage by a splicing endonuclease Science 312 2006 906 910
41. J. Zhang, C. Rouillon, M. Kerou, J. Reeks, K. Brugger, S. Graham, J. Reimann, G. Cannone, H. Liu, and S.-V. Albers Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity Mol. Cell 45 2012 303 313
42. M. Zuker Mfold web server for nucleic acid folding and hybridization prediction Nucleic Acids Res. 31 2003 3406 3415