Interaction of the Cas6 riboendonuclease with CRISPR RNAs: Recognition and cleavage

Structure

Volumn 19, Issue 2, 2011, Pages 257-264

  Wang, Ruiying ^a   Preamplume, Gan ^a   Terns, Michael P ^b   Terns, Rebecca M ^b   Li, Hong ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN; CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN 6; ENDONUCLEASE; FERREDOXIN; NUCLEOTIDE; UNCLASSIFIED DRUG;

ARTICLE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; MUTAGENESIS; NONHUMAN; NUCLEOTIDE REPEAT; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN RNA BINDING; PYROCOCCUS FURIOSUS; RNA BINDING; RNA CLEAVAGE; RNA PROCESSING; RNA STRUCTURE;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE SEQUENCE; ENDONUCLEASES; INVERTED REPEAT SEQUENCES; MICROBIAL INTERACTIONS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR SEQUENCE DATA; NUCLEOTIDES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PYROCOCCUS FURIOSUS; RNA, BACTERIAL;

PROKARYOTA; PYROCOCCUS FURIOSUS;

EID: 79551694059     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2010.11.014     Document Type: Article

References (38)

1. P.D. Adams, R.W. Grosse-Kunstleve, L.W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.J. Read, J.C. Sacchettini, N.K. Sauter, and T.C. Terwilliger PHENIX: building new software for automated crystallographic structure determination Acta Crystallogr. D Biol. Crystallogr. 58 2002 1948 1954 (Pubitemid 35337293)
2. A.F. Andersson, and J.F. Banfield Virus population dynamics and acquired virus resistance in natural microbial communities Science 320 2008 1047 1050 (Pubitemid 351929541)
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 (Pubitemid 46515624)
4. A. Bolotin, B. Quinquis, A. Sorokin, and S.D. Ehrlich Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin Microbiology 151 2005 2551 2561 (Pubitemid 41149778)
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, 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
7. 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
8. J.R. Driscoll Spoligotyping for molecular epidemiology of the Mycobacterium tuberculosis complex Methods Mol. Biol. 551 2009 117 128
9. A. Ebihara, M. Yao, R. Masui, I. Tanaka, S. Yokoyama, and S. Kuramitsu 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 2006 1494 1499 (Pubitemid 43800020)
10. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr. D Biol. Crystallogr. 60 2004 2126 2132 (Pubitemid 41742764)
11. I. Grissa, G. Vergnaud, and C. Pourcel The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats BMC Bioinformatics 8 2007 172
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.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
14. 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
15. J.F. Heidelberg, W.C. Nelson, T. Schoenfeld, and D. Bhaya Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes PLoS ONE 4 2009 e4169
16. P. Horvath, and R. Barrangou CRISPR/Cas, the immune system of bacteria and archaea Science 327 2010 167 170
17. J. Janin, S. Miller, and C. Chothia Surface, subunit interfaces and interior of oligomeric proteins J. Mol. Biol. 204 1988 155 164 (Pubitemid 19011740)
18. R. Jansen, J.D. Embden, W. Gaastra, and L.M. Schouls Identification of genes that are associated with DNA repeats in prokaryotes Mol. Microbiol. 43 2002 1565 1575 (Pubitemid 34595547)
19. T.A. Jones, J.Y. Zou, S.W. Cowan, and M. Kjeldgaard Improved methods for binding protein models in electron density maps and the location of errors in these models Acta Crystallogr. A 47 1991 110 119
20. F.V. Karginov, and G.J. Hannon The CRISPR system: small RNA-guided defense in bacteria and archaea Mol. Cell 37 2010 7 19
21. V. Kunin, R. Sorek, and P. Hugenholtz Evolutionary conservation of sequence and secondary structures in CRISPR repeats Genome Biol. 8 2007 R61
22. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26 1993 283 291
23. 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
24. C. Maris, C. Dominguez, and F.H. Allain The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression FEBS J. 272 2005 2118 2131 (Pubitemid 40655326)
25. L.A. Marraffini, and E.J. Sontheimer CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA Science 322 2008 1843 1845
26. L.A. Marraffini, and E.J. Sontheimer CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea Nat. Rev. Genet. 11 2010 181 190
27. L.A. Marraffini, and E.J. Sontheimer Self versus non-self discrimination during CRISPR RNA-directed immunity Nature 463 2010 568 571
28. S. Mills, C. Griffin, A. Coffey, W.C. Meijer, B. Hafkamp, and R.P. Ross CRISPR analysis of bacteriophage-insensitive mutants (BIMs) of industrial Streptococcus thermophilus- implications for starter design J. Appl. Microbiol. 2009
29. F.J. Mojica, C. Diez-Villasenor, J. Garcia-Martinez, and E. Soria Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements J. Mol. Evol. 60 2005 174 182 (Pubitemid 40568857)
30. I. Mokrousov, E. Limeschenko, A. Vyazovaya, and O. Narvskaya Corynebacterium diphtheriae spoligotyping based on combined use of two CRISPR loci Biotechnol. J. 2 2007 901 906 (Pubitemid 47161995)
31. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326 (Pubitemid 27085611)
32. 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 (Pubitemid 40425001)
33. V. Ramakrishnan, and V. Biou Treatment of multiwavelength anomalous diffraction data as a special case of multiple isomorphous replacement Methods Enzymol. 276 1997 538 557 (Pubitemid 27085622)
34. J.C. Snyder, M.M. Bateson, M. Lavin, and M.J. Young Use of cellular CRISPR (clusters of regularly interspaced short palindromic repeats) spacer-based microarrays for detection of viruses in environmental samples Appl. Environ. Microbiol. 76 2010 7251 7258
35. 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 (Pubitemid 351256313)
36. G.W. Tyson, and J.F. Banfield Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses Environ. Microbiol. 10 2008 200 207
37. 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
38. L.S. Waters, and G. Storz Regulatory RNAs in bacteria Cell 136 2009 615 628