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Volumn 23, Issue 1, 2015, Pages 13-20

Structural principles of CRISPR RNA processing

Author keywords

[No Author keywords available]

Indexed keywords

CAS5D PROTEIN; CAS6 PROTEIN; CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN; CRISPR ASSOCIATED PROTEIN; DNA; DOUBLE STRANDED RNA; FERREDOXIN; RIBONUCLEASE A; RIBONUCLEASE III; RNA; UNCLASSIFIED DRUG; HEMOCYANIN;

EID: 84920939515     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2014.10.006     Document Type: Review
Times cited : (35)

References (55)
  • 1
    • 84899134190 scopus 로고    scopus 로고
    • CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity
    • R. Barrangou, and L.A. Marraffini CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity Mol. Cell 54 2014 234 244
    • (2014) Mol. Cell , vol.54 , pp. 234-244
    • Barrangou, R.1    Marraffini, L.A.2
  • 3
    • 58049191229 scopus 로고    scopus 로고
    • Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes
    • 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
    • (2008) Genes Dev. , vol.22 , pp. 3489-3496
    • Carte, J.1    Wang, R.2    Li, H.3    Terns, R.M.4    Terns, M.P.5
  • 5
    • 80052710778 scopus 로고    scopus 로고
    • Bovine pancreatic ribonuclease: Fifty years of the first enzymatic reaction mechanism
    • C.M. Cuchillo, M.V. Nogués, and R.T. Raines Bovine pancreatic ribonuclease: fifty years of the first enzymatic reaction mechanism Biochemistry 50 2011 7835 7841
    • (2011) Biochemistry , vol.50 , pp. 7835-7841
    • Cuchillo, C.M.1    Nogués, M.V.2    Raines, R.T.3
  • 7
    • 33744503676 scopus 로고    scopus 로고
    • Crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 reveals a new protein family with an RNA recognition motif-like domain
    • 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
    • (2006) Protein Sci. , vol.15 , pp. 1494-1499
    • Ebihara, A.1    Yao, M.2    Masui, R.3    Tanaka, I.4    Yokoyama, S.5    Kuramitsu, S.6
  • 9
    • 84892804564 scopus 로고    scopus 로고
    • Molecular mechanisms of CRISPR-mediated microbial immunity
    • G. Gasiunas, T. Sinkunas, and V. Siksnys Molecular mechanisms of CRISPR-mediated microbial immunity Cell. Mol. Life Sci. 71 2014 449 465
    • (2014) Cell. Mol. Life Sci. , vol.71 , pp. 449-465
    • Gasiunas, G.1    Sinkunas, T.2    Siksnys, V.3
  • 11
    • 34248400310 scopus 로고    scopus 로고
    • A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes
    • 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
    • (2005) PLoS Comput. Biol. , vol.1 , pp. e60
    • Haft, D.H.1    Selengut, J.2    Mongodin, E.F.3    Nelson, K.E.4
  • 12
    • 77956498326 scopus 로고    scopus 로고
    • Sequence- and structure-specific RNA processing by a CRISPR endonuclease
    • 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
    • (2010) Science , vol.329 , pp. 1355-1358
    • Haurwitz, R.E.1    Jinek, M.2    Wiedenheft, B.3    Zhou, K.4    Doudna, J.A.5
  • 13
    • 84862190458 scopus 로고    scopus 로고
    • Csy4 relies on an unusual catalytic dyad to position and cleave CRISPR RNA
    • 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
    • (2012) EMBO J. , vol.31 , pp. 2824-2832
    • Haurwitz, R.E.1    Sternberg, S.H.2    Doudna, J.A.3
  • 14
    • 0036568328 scopus 로고    scopus 로고
    • Structural genomics analysis: Characteristics of atypical, common, and horizontally transferred folds
    • H. Hegyi, J. Lin, D. Greenbaum, and M. Gerstein Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds Proteins 47 2002 126 141
    • (2002) Proteins , vol.47 , pp. 126-141
    • Hegyi, H.1    Lin, J.2    Greenbaum, D.3    Gerstein, M.4
  • 17
    • 0036267740 scopus 로고    scopus 로고
    • Identification of genes that are associated with DNA repeats in prokaryotes
    • 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
    • (2002) Mol. Microbiol. , vol.43 , pp. 1565-1575
    • Jansen, R.1    Embden, J.D.2    Gaastra, W.3    Schouls, L.M.4
  • 18
    • 84885180803 scopus 로고    scopus 로고
    • Conservation and variability in the structure and function of the Cas5d endoribonuclease in the CRISPR-mediated microbial immune system
    • Y. Koo, D. Ka, E.J. Kim, N. Suh, and E. Bae Conservation and variability in the structure and function of the Cas5d endoribonuclease in the CRISPR-mediated microbial immune system J. Mol. Biol. 425 2013 3799 3810
    • (2013) J. Mol. Biol. , vol.425 , pp. 3799-3810
    • Koo, Y.1    Ka, D.2    Kim, E.J.3    Suh, N.4    Bae, E.5
  • 19
    • 84878168552 scopus 로고    scopus 로고
    • CRISPR-Cas: Evolution of an RNA-based adaptive immunity system in prokaryotes
    • E.V. Koonin, and K.S. Makarova CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes RNA Biol. 10 2013 679 686
    • (2013) RNA Biol. , vol.10 , pp. 679-686
    • Koonin, E.V.1    Makarova, K.S.2
  • 20
    • 35748974534 scopus 로고    scopus 로고
    • Evolutionary conservation of sequence and secondary structures in CRISPR repeats
    • V. Kunin, R. Sorek, and P. Hugenholtz Evolutionary conservation of sequence and secondary structures in CRISPR repeats Genome Biol. 8 2007 R61
    • (2007) Genome Biol. , vol.8 , pp. R61
    • Kunin, V.1    Sorek, R.2    Hugenholtz, P.3
  • 21
    • 79551716585 scopus 로고    scopus 로고
    • Recognition of archaeal CRISPR RNA: No P in the alindromic repeat?
    • C.M. Lawrence, and M.F. White Recognition of archaeal CRISPR RNA: No P in the alindromic repeat? Structure 19 2011 142 144
    • (2011) Structure , vol.19 , pp. 142-144
    • Lawrence, C.M.1    White, M.F.2
  • 23
    • 34248374277 scopus 로고    scopus 로고
    • 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
    • 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
    • (2006) Biol. Direct , vol.1 , pp. 7
    • Makarova, K.S.1    Grishin, N.V.2    Shabalina, S.A.3    Wolf, Y.I.4    Koonin, E.V.5
  • 25
    • 84887971081 scopus 로고    scopus 로고
    • The basic building blocks and evolution of CRISPR-CAS systems
    • K.S. Makarova, Y.I. Wolf, and E.V. Koonin The basic building blocks and evolution of CRISPR-CAS systems Biochem. Soc. Trans. 41 2013 1392 1400
    • (2013) Biochem. Soc. Trans. , vol.41 , pp. 1392-1400
    • Makarova, K.S.1    Wolf, Y.I.2    Koonin, E.V.3
  • 26
    • 18544377013 scopus 로고    scopus 로고
    • The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression
    • 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
    • (2005) FEBS J. , vol.272 , pp. 2118-2131
    • Maris, C.1    Dominguez, C.2    Allain, F.H.3
  • 27
    • 34547622435 scopus 로고    scopus 로고
    • 'In-line attack' conformational effect plays a modest role in an enzyme-catalyzed RNA cleavage: A free energy simulation study
    • 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
    • (2007) Nucleic Acids Res. , vol.35 , pp. 4001-4006
    • Min, D.1    Xue, S.2    Li, H.3    Yang, W.4
  • 28
    • 84907204893 scopus 로고    scopus 로고
    • Structural biology. Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target
    • S. Mulepati, A. Héroux, and S. Bailey Structural biology. Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target Science 345 2014 1479 1484
    • (2014) Science , vol.345 , pp. 1479-1484
    • Mulepati, S.1    Héroux, A.2    Bailey, S.3
  • 29
    • 84865704094 scopus 로고    scopus 로고
    • Cas5d protein processes pre-crRNA and assembles into a cascade-like interference complex in subtype I-C/Dvulg CRISPR-Cas system
    • K.H. Nam, C. Haitjema, X. Liu, F. Ding, H. Wang, M.P. DeLisa, and A. Ke Cas5d protein processes pre-crRNA and assembles into a cascade-like interference complex in subtype I-C/Dvulg CRISPR-Cas system Structure 20 2012 1574 1584
    • (2012) Structure , vol.20 , pp. 1574-1584
    • Nam, K.H.1    Haitjema, C.2    Liu, X.3    Ding, F.4    Wang, H.5    Delisa, M.P.6    Ke, A.7
  • 30
    • 84890287379 scopus 로고    scopus 로고
    • Ribonuclease III mechanisms of double-stranded RNA cleavage
    • A.W. Nicholson Ribonuclease III mechanisms of double-stranded RNA cleavage Wiley Interdiscip. Rev. RNA 5 2014 31 48
    • (2014) Wiley Interdiscip. Rev. RNA , vol.5 , pp. 31-48
    • Nicholson, A.W.1
  • 31
    • 84893230222 scopus 로고    scopus 로고
    • Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases
    • O. Niewoehner, M. Jinek, and J.A. Doudna Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases Nucleic Acids Res. 42 2014 1341 1353
    • (2014) Nucleic Acids Res. , vol.42 , pp. 1341-1353
    • Niewoehner, O.1    Jinek, M.2    Doudna, J.A.3
  • 32
    • 84901195977 scopus 로고    scopus 로고
    • Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells
    • L. Nissim, S.D. Perli, A. Fridkin, P. Perez-Pinera, and T.K. Lu Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells Mol. Cell 54 2014 698 710
    • (2014) Mol. Cell , vol.54 , pp. 698-710
    • Nissim, L.1    Perli, S.D.2    Fridkin, A.3    Perez-Pinera, P.4    Lu, T.K.5
  • 34
    • 84879584456 scopus 로고    scopus 로고
    • CRISPR interference: A structural perspective
    • J. Reeks, J.H. Naismith, and M.F. White CRISPR interference: a structural perspective Biochem. J. 453 2013 155 166
    • (2013) Biochem. J. , vol.453 , pp. 155-166
    • Reeks, J.1    Naismith, J.H.2    White, M.F.3
  • 35
    • 84877757610 scopus 로고    scopus 로고
    • Structure of a dimeric crenarchaeal Cas6 enzyme with an atypical active site for CRISPR RNA processing
    • J. Reeks, R.D. Sokolowski, S. Graham, H. Liu, J.H. Naismith, and M.F. White Structure of a dimeric crenarchaeal Cas6 enzyme with an atypical active site for CRISPR RNA processing Biochem. J. 452 2013 223 230
    • (2013) Biochem. J. , vol.452 , pp. 223-230
    • Reeks, J.1    Sokolowski, R.D.2    Graham, S.3    Liu, H.4    Naismith, J.H.5    White, M.F.6
  • 36
    • 84868111481 scopus 로고    scopus 로고
    • Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis
    • 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
    • (2012) Nucleic Acids Res. , vol.40 , pp. 9887-9896
    • Richter, H.1    Zoephel, J.2    Schermuly, J.3    Maticzka, D.4    Backofen, R.5    Randau, L.6
  • 37
    • 79958825675 scopus 로고    scopus 로고
    • An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3
    • 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
    • (2011) Nat. Struct. Mol. Biol. , vol.18 , pp. 680-687
    • Sashital, D.G.1    Jinek, M.2    Doudna, J.A.3
  • 38
    • 84874930818 scopus 로고    scopus 로고
    • Recognition and cleavage of a nonstructured CRISPR RNA by its processing endoribonuclease Cas6
    • Y. Shao, and H. Li Recognition and cleavage of a nonstructured CRISPR RNA by its processing endoribonuclease Cas6 Structure 21 2013 385 393
    • (2013) Structure , vol.21 , pp. 385-393
    • Shao, Y.1    Li, H.2
  • 39
    • 84903202938 scopus 로고    scopus 로고
    • Cas6 specificity and CRISPR RNA loading in a complex CRISPR-Cas system
    • R.D. Sokolowski, S. Graham, and M.F. White Cas6 specificity and CRISPR RNA loading in a complex CRISPR-Cas system Nucleic Acids Res. 42 2014 6532 6541
    • (2014) Nucleic Acids Res. , vol.42 , pp. 6532-6541
    • Sokolowski, R.D.1    Graham, S.2    White, M.F.3
  • 40
    • 84878936806 scopus 로고    scopus 로고
    • CRISPR-mediated adaptive immune systems in bacteria and archaea
    • R. Sorek, C.M. Lawrence, and B. Wiedenheft CRISPR-mediated adaptive immune systems in bacteria and archaea Annu. Rev. Biochem. 82 2013 237 266
    • (2013) Annu. Rev. Biochem. , vol.82 , pp. 237-266
    • Sorek, R.1    Lawrence, C.M.2    Wiedenheft, B.3
  • 41
    • 0032831634 scopus 로고    scopus 로고
    • Relationship between internucleotide linkage geometry and the stability of RNA
    • G.A. Soukup, and R.R. Breaker Relationship between internucleotide linkage geometry and the stability of RNA RNA 5 1999 1308 1325
    • (1999) RNA , vol.5 , pp. 1308-1325
    • Soukup, G.A.1    Breaker, R.R.2
  • 44
    • 84858659496 scopus 로고    scopus 로고
    • Mechanism of substrate selection by a highly specific CRISPR endoribonuclease
    • S.H. Sternberg, R.E. Haurwitz, and J.A. Doudna Mechanism of substrate selection by a highly specific CRISPR endoribonuclease RNA 18 2012 661 672
    • (2012) RNA , vol.18 , pp. 661-672
    • Sternberg, S.H.1    Haurwitz, R.E.2    Doudna, J.A.3
  • 45
    • 79959319829 scopus 로고    scopus 로고
    • CRISPR-based adaptive immune systems
    • M.P. Terns, and R.M. Terns CRISPR-based adaptive immune systems Curr. Opin. Microbiol. 14 2011 321 327
    • (2011) Curr. Opin. Microbiol. , vol.14 , pp. 321-327
    • Terns, M.P.1    Terns, R.M.2
  • 47
    • 84863371175 scopus 로고    scopus 로고
    • The mysterious RAMP proteins and their roles in small RNA-based immunity
    • R. Wang, and H. Li The mysterious RAMP proteins and their roles in small RNA-based immunity Protein Sci. 21 2012 463 470
    • (2012) Protein Sci. , vol.21 , pp. 463-470
    • Wang, R.1    Li, H.2
  • 48
    • 79551694059 scopus 로고    scopus 로고
    • Interaction of the Cas6 riboendonuclease with CRISPR RNAs: Recognition and cleavage
    • 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
    • (2011) Structure , vol.19 , pp. 257-264
    • Wang, R.1    Preamplume, G.2    Terns, M.P.3    Terns, R.M.4    Li, H.5
  • 49
    • 84863116866 scopus 로고    scopus 로고
    • The impact of CRISPR repeat sequence on structures of a Cas6 protein-RNA complex
    • 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 405 417
    • (2012) Protein Sci. , vol.21 , pp. 405-417
    • Wang, R.1    Zheng, H.2    Preamplume, G.3    Shao, Y.4    Li, H.5
  • 52
    • 84857097177 scopus 로고    scopus 로고
    • RNA-guided genetic silencing systems in bacteria and archaea
    • B. Wiedenheft, S.H. Sternberg, and J.A. Doudna RNA-guided genetic silencing systems in bacteria and archaea Nature 482 2012 331 338
    • (2012) Nature , vol.482 , pp. 331-338
    • Wiedenheft, B.1    Sternberg, S.H.2    Doudna, J.A.3
  • 53
    • 0035128549 scopus 로고    scopus 로고
    • Protein folds: Molecular systematics in three dimensions
    • C. Zhang, and C. DeLisi Protein folds: molecular systematics in three dimensions Cell. Mol. Life Sci. 58 2001 72 79
    • (2001) Cell. Mol. Life Sci. , vol.58 , pp. 72-79
    • Zhang, C.1    Delisi, C.2
  • 55
    • 84908445494 scopus 로고    scopus 로고
    • Crystal structure of the RNA-guided immune surveillance Cascade complex in Escherichia coli
    • Published online August 12, 2014
    • H. Zhao, G. Sheng, J. Wang, M. Wang, G. Bunkoczi, W. Gong, Z. Wei, and Y. Wang Crystal structure of the RNA-guided immune surveillance Cascade complex in Escherichia coli Nature 2014 10.1038/nature13733 Published online August 12, 2014
    • (2014) Nature
    • Zhao, H.1    Sheng, G.2    Wang, J.3    Wang, M.4    Bunkoczi, G.5    Gong, W.6    Wei, Z.7    Wang, Y.8


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