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Research Paper

Structure and RNA-binding properties of the Type III-A CRISPR-associated protein Csm3

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Pages 1670-1678 | Received 15 Aug 2013, Accepted 16 Sep 2013, Published online: 30 Sep 2013

References

  • Labrie SJ, Samson JE, Moineau S. Bacteriophage resistance mechanisms. Nat Rev Microbiol 2010; 8:317 - 27; http://dx.doi.org/10.1038/nrmicro2315; PMID: 20348932
  • Makarova KS, Wolf YI, Koonin EV. Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Res 2013; 41:4360 - 77; http://dx.doi.org/10.1093/nar/gkt157; PMID: 23470997
  • Mojica FJ, Díez-Villaseñor C, García-Martínez J, Soria E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 2005; 60:174 - 82; http://dx.doi.org/10.1007/s00239-004-0046-3; PMID: 15791728
  • Mojica FJ, Díez-Villaseñor C, Soria E, Juez G. Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol Microbiol 2000; 36:244 - 6; http://dx.doi.org/10.1046/j.1365-2958.2000.01838.x; PMID: 10760181
  • Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P. CRISPR provides acquired resistance against viruses in prokaryotes. Science 2007; 315:1709 - 12; http://dx.doi.org/10.1126/science.1138140; PMID: 17379808
  • Marraffini LA, Sontheimer EJ. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet 2010; 11:181 - 90; http://dx.doi.org/10.1038/nrg2749; PMID: 20125085
  • Wiedenheft B, Sternberg SH, Doudna JA. RNA-guided genetic silencing systems in bacteria and archaea. Nature 2012; 482:331 - 8; http://dx.doi.org/10.1038/nature10886; PMID: 22337052
  • Carte J, Wang R, Li H, Terns RM, Terns MP. Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev 2008; 22:3489 - 96; http://dx.doi.org/10.1101/gad.1742908; PMID: 19141480
  • Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 2010; 329:1355 - 8; http://dx.doi.org/10.1126/science.1192272; PMID: 20829488
  • Richter H, Zoephel J, Schermuly J, Maticzka D, Backofen R, Randau L. Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis. Nucleic Acids Res 2012; 40:9887 - 96; http://dx.doi.org/10.1093/nar/gks737; PMID: 22879377
  • Marraffini LA, Sontheimer EJ. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 2008; 322:1843 - 5; http://dx.doi.org/10.1126/science.1165771; PMID: 19095942
  • Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 2007; 35:Web Server issue W52-7; http://dx.doi.org/10.1093/nar/gkm360; PMID: 17537822
  • Jansen R, Embden JD, Gaastra W, Schouls LM. Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 2002; 43:1565 - 75; http://dx.doi.org/10.1046/j.1365-2958.2002.02839.x; PMID: 11952905
  • Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV. 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 2006; 1:7; http://dx.doi.org/10.1186/1745-6150-1-7; PMID: 16545108
  • Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, et al. Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 2011; 9:467 - 77; http://dx.doi.org/10.1038/nrmicro2577; PMID: 21552286
  • Bhaya D, Davison M, Barrangou R. CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu Rev Genet 2011; 45:273 - 97; http://dx.doi.org/10.1146/annurev-genet-110410-132430; PMID: 22060043
  • Hale CR, Zhao P, Olson S, Duff MO, Graveley BR, Wells L, Terns RM, Terns MP. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 2009; 139:945 - 56; http://dx.doi.org/10.1016/j.cell.2009.07.040; PMID: 19945378
  • Garside EL, Schellenberg MJ, Gesner EM, Bonanno JB, Sauder JM, Burley SK, Almo SC, Mehta G, MacMillan AM. Cas5d processes pre-crRNA and is a member of a larger family of CRISPR RNA endonucleases. RNA 2012; 18:2020 - 8; http://dx.doi.org/10.1261/rna.033100.112; PMID: 23006625
  • Nam KH, Haitjema C, Liu X, Ding F, Wang H, DeLisa MP, Ke A. Cas5d protein processes pre-crRNA and assembles into a cascade-like interference complex in subtype I-C/Dvulg CRISPR-Cas system. Structure 2012; 20:1574 - 84; http://dx.doi.org/10.1016/j.str.2012.06.016; PMID: 22841292
  • 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 2011; 286:31896 - 903; http://dx.doi.org/10.1074/jbc.M111.270017; PMID: 21775431
  • Wang R, Preamplume G, Terns MP, Terns RM, Li H. Interaction of the Cas6 riboendonuclease with CRISPR RNAs: recognition and cleavage. Structure 2011; 19:257 - 64; http://dx.doi.org/10.1016/j.str.2010.11.014; PMID: 21300293
  • Reeks J, Naismith JH, White MF. CRISPR interference: a structural perspective. Biochem J 2013; 453:155 - 66; http://dx.doi.org/10.1042/BJ20130316; PMID: 23805973
  • Wiedenheft B, Lander GC, Zhou K, Jore MM, Brouns SJ, van der Oost J, Doudna JA, Nogales E. Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature 2011; 477:486 - 9; http://dx.doi.org/10.1038/nature10402; PMID: 21938068
  • Wiedenheft B, Zhou K, Jinek M, Coyle SM, Ma W, Doudna JA. Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure 2009; 17:904 - 12; http://dx.doi.org/10.1016/j.str.2009.03.019; PMID: 19523907
  • Zhu X, Ye K. Crystal structure of Cmr2 suggests a nucleotide cyclase-related enzyme in type III CRISPR-Cas systems. FEBS Lett 2012; 586:939 - 45; http://dx.doi.org/10.1016/j.febslet.2012.02.036; PMID: 22449983
  • Osawa T, Inanaga H, Numata T. Crystal Structure of the Cmr2-Cmr3 Subcomplex in the CRISPR-Cas RNA Silencing Effector Complex. J Mol Biol 2013; Forthcoming http://dx.doi.org/10.1016/j.jmb.2013.03.042; PMID: 23583914
  • Cocozaki AI, Ramia NF, Shao Y, Hale CR, Terns RM, Terns MP, Li H. Structure of the Cmr2 subunit of the CRISPR-Cas RNA silencing complex. Structure 2012; 20:545 - 53; http://dx.doi.org/10.1016/j.str.2012.01.018; PMID: 22405013
  • Zhang J, Rouillon C, Kerou M, Reeks J, Brugger K, Graham S, Reimann J, Cannone G, Liu H, Albers SV, et al. Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity. Mol Cell 2012; 45:303 - 13; http://dx.doi.org/10.1016/j.molcel.2011.12.013; PMID: 22227115
  • Lintner NG, Kerou M, Brumfield SK, Graham S, Liu H, Naismith JH, Sdano M, Peng N, She Q, Copié V, 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 2011; 286:21643 - 56; http://dx.doi.org/10.1074/jbc.M111.238485; PMID: 21507944
  • van Duijn E, Barbu IM, Barendregt A, Jore MM, Wiedenheft B, Lundgren M, Westra ER, Brouns SJ, Doudna JA, van der Oost J, 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 Proteomics 2012; 11:1430 - 41; http://dx.doi.org/10.1074/mcp.M112.020263; PMID: 22918228
  • Nam KH, Haitjema C, Liu X, Ding F, Wang H, DeLisa MP, Ke A. Cas5d protein processes pre-crRNA and assembles into a cascade-like interference complex in subtype I-C/Dvulg CRISPR-Cas system. Structure 2012; 20:1574 - 84; http://dx.doi.org/10.1016/j.str.2012.06.016; PMID: 22841292
  • Wiedenheft B, van Duijn E, Bultema JB, Waghmare SP, Zhou K, Barendregt A, Westphal W, Heck AJ, Boekema EJ, Dickman MJ, et al. RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions. Proc Natl Acad Sci U S A 2011; 108:10092 - 7; http://dx.doi.org/10.1073/pnas.1102716108; PMID: 21536913
  • Koonin EV, Makarova KS. CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes. RNA Biol 2013; 10:679 - 86; http://dx.doi.org/10.4161/rna.24022; PMID: 23439366
  • Hatoum-Aslan A, Samai P, Maniv I, Jiang W, Marraffini LA. A ruler protein in a complex for antiviral defense determines the length of small interfering CRISPR RNAs. J Biol Chem 2013; (Forthcoming)
  • Maris C, Dominguez C, Allain FH. The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. FEBS J 2005; 272:2118 - 31; http://dx.doi.org/10.1111/j.1742-4658.2005.04653.x; PMID: 15853797
  • Fribourg S, Gatfield D, Izaurralde E, Conti E. A novel mode of RBD-protein recognition in the Y14-Mago complex. Nat Struct Biol 2003; 10:433 - 9; http://dx.doi.org/10.1038/nsb926; PMID: 12730685
  • Kadlec J, Izaurralde E, Cusack S. The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3. Nat Struct Mol Biol 2004; 11:330 - 7; http://dx.doi.org/10.1038/nsmb741; PMID: 15004547
  • Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 2004; 60:2126 - 32; http://dx.doi.org/10.1107/S0907444904019158; PMID: 15572765
  • Makarova KS, Aravind L, Wolf YI, Koonin EV. Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct 2011; 6:38; http://dx.doi.org/10.1186/1745-6150-6-38; PMID: 21756346
  • Su AA, Tripp V, Randau L. RNA-Seq analyses reveal the order of tRNA processing events and the maturation of C/D box and CRISPR RNAs in the hyperthermophile Methanopyrus kandleri. Nucleic Acids Res 2013; 41:6250 - 8; http://dx.doi.org/10.1093/nar/gkt317; PMID: 23620296
  • Hatoum-Aslan A, Maniv I, Marraffini LA. 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 U S A 2011; 108:21218 - 22; http://dx.doi.org/10.1073/pnas.1112832108; PMID: 22160698
  • Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul U, Wurm R, Wagner R, et al. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol 2011; 18:529 - 36; http://dx.doi.org/10.1038/nsmb.2019; PMID: 21460843
  • Kabsch W. XDS. Acta Crystallogr D Biol Crystallogr 2010; 66:125 - 32; http://dx.doi.org/10.1107/S0907444909047337; PMID: 20124692
  • McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ. Phaser crystallographic software. J Appl Crystallogr 2007; 40:658 - 74; http://dx.doi.org/10.1107/S0021889807021206; PMID: 19461840
  • Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 2010; 66:213 - 21; http://dx.doi.org/10.1107/S0907444909052925; PMID: 20124702