The impact of CRISPR repeat sequence on structures of a Cas6 protein-RNA complex

Protein Science

Volumn 21, Issue 3, 2012, Pages 405-417

  Wang, Ruiying ^a   Zheng, Han ^a   Preamplume, Gan ^a   Shao, Yaming ^a   Li, Hong ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

Author keywords

CRISPR Cas; Protein RNA interactions; RAMP proteins; RNA mediated prokaryotic immunity; RRM fold

Indexed keywords

CAS6 PROTEIN; DIMER; SHORT HAIRPIN RNA; SINGLE STRANDED RNA; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL ANALYSIS; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; COMPLEX FORMATION; OLIGOMERIZATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN RNA BINDING; PROTEIN STRUCTURE; PYROCOCCUS HORIKOSHII; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ANALYSIS;

ARCHAEAL PROTEINS; BASE SEQUENCE; INVERTED REPEAT SEQUENCES; MODELS, MOLECULAR; PYROCOCCUS FURIOSUS; PYROCOCCUS HORIKOSHII; RNA;

EID: 84863116866     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.2028     Document Type: Article

References (28)

1. Bolotin A, Quinquis B, Sorokin A, Ehrlich SD (2005) Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151:2551-2561. (Pubitemid 41149778)
2. Mojica FJ, Diez-Villasenor C, Garcia-Martinez J, Soria E (2005) Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 60:174-182. (Pubitemid 40568857)
3. Sorek R, Kunin V, Hugenholtz P (2008) CRISPR - a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol 6:181-186. (Pubitemid 351256313)
4. van der Oost J, Jore MM, Westra ER, Lundgren M, Brouns SJ (2009) CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem Sci 34: 401-407.
5. Marraffini LA, Sontheimer EJ (2010) CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet 11:181-190.
6. Karginov FV, Hannon GJ (2010) The CRISPR system: small RNA-guided defense in bacteria and archaea. Mol Cell 37:7-19.
7. Horvath P, Barrangou R (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327: 167-170.
8. Waters LS, Storz G (2009) Regulatory RNAs in bacteria. Cell 136:615-628.
9. Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV (2006) 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.
10. Haft DH, Selengut J, Mongodin EF, Nelson KE (2005) A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol 1:e60.
11. Pourcel C, Salvignol G, Vergnaud G (2005) 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. (Pubitemid 40425001)
12. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709-1712. (Pubitemid 46515624)
13. Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, Dickman MJ, Makarova KS, Koonin EV, van der Oost J (2008) Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321: 960-964.
14. Marraffini LA, Sontheimer EJ (2008) CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322:1843-1845.
15. Hale CR, Zhao P, Olson S, Duff MO, Graveley BR, Wells L, Terns RM, Terns MP (2009) RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139:945-956.
16. Carte J, Wang R, Li H, Terns RM, Terns MP (2008) Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev 22:3489-3496.
17. Makarova KS, Aravind L, Grishin NV, Rogozin IB, Koonin EV (2002) A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res 30:482-496. (Pubitemid 34679610)
18. Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA (2010) Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 329:1355-1358.
19. Ebihara A, Yao M, Masui R, Tanaka I, Yokoyama S, Kuramitsu S (2006) 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. (Pubitemid 43800020)
20. Kunin V, Sorek R, Hugenholtz P (2007) Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol 8:R61.
21. Wang R, Preamplume G, Terns MP, Terns RM, Li H (2011) Interaction of the Cas6 Riboendonuclease with CRISPR RNAs: Recognition and Cleavage. Structure 19:257-264.
22. Gesner EM, Schellenberg MJ, Garside EL, George MM, Macmillan AM (2011) Recognition and maturation of effector RNAs in a CRISPR interference pathway. Nat Struct Mol Biol 18:688-692.
23. Sashital DG, Jinek M, Doudna JA (2011) An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3. Nat Struct Mol Biol 18:680-687.
24. Maris C, Dominguez C, Allain FH (2005) The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. FEBS J 272: 2118-2131. (Pubitemid 40655326)
25. Otwinowski Z, Minor W. 1997. Processing of X-ray diffraction data collected in oscillation mode, San Diego: Academic Press.
26. Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC (2002) PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr 58: 1948-1954. (Pubitemid 35337293)
27. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126-2132. (Pubitemid 41742764)
28. Jones TA, Zou JY, Cowan SW, Kjeldgaard M (1991) Improved methods for binding protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 47:110-119.