메뉴 건너뛰기




Volumn 70, Issue 1, 2018, Pages 48-59.e5

Cas4-Dependent Prespacer Processing Ensures High-Fidelity Programming of CRISPR Arrays

Author keywords

Cas1 Cas2; Cas4; CRISPR Cas; DNA cleavage; DNA integration; negative stain EM

Indexed keywords

CAS1 INTEGRASE; CAS2 PROTEIN; CAS4 PROTEIN; CRISPR ASSOCIATED PROTEIN; DIMER; INTEGRASE; UNCLASSIFIED DRUG; BACTERIAL DNA; DEOXYRIBONUCLEASE; ESCHERICHIA COLI PROTEIN; MULTIENZYME COMPLEX; YGBT PROTEIN, E COLI;

EID: 85044055719     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2018.03.003     Document Type: Article
Times cited : (81)

References (64)
  • 2
    • 23844505202 scopus 로고    scopus 로고
    • Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin
    • Bolotin, A., Quinquis, B., Sorokin, A., Ehrlich, S.D., Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151 (2005), 2551–2561.
    • (2005) Microbiology , vol.151 , pp. 2551-2561
    • Bolotin, A.1    Quinquis, B.2    Sorokin, A.3    Ehrlich, S.D.4
  • 4
    • 58049191229 scopus 로고    scopus 로고
    • Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes
    • Carte, J., Wang, R., Li, H., Terns, R.M., Terns, M.P., 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
  • 6
    • 85023759619 scopus 로고    scopus 로고
    • Functional characterization of hormone sensitive-like lipase from Bacillus halodurans : synthesis and recovery of pNP-laurate with high yields
    • Dua, A., Gupta, R., Functional characterization of hormone sensitive-like lipase from Bacillus halodurans : synthesis and recovery of pNP-laurate with high yields. Extremophiles 21 (2017), 871–889.
    • (2017) Extremophiles , vol.21 , pp. 871-889
    • Dua, A.1    Gupta, R.2
  • 10
    • 84991299011 scopus 로고    scopus 로고
    • Repeat size determination by two molecular rulers in the type I-E CRISPR array
    • Goren, M.G., Doron, S., Globus, R., Amitai, G., Sorek, R., Qimron, U., Repeat size determination by two molecular rulers in the type I-E CRISPR array. Cell Rep. 16 (2016), 2811–2818.
    • (2016) Cell Rep. , vol.16 , pp. 2811-2818
    • Goren, M.G.1    Doron, S.2    Globus, R.3    Amitai, G.4    Sorek, R.5    Qimron, U.6
  • 11
    • 84884765703 scopus 로고    scopus 로고
    • A ruler protein in a complex for antiviral defense determines the length of small interfering CRISPR RNAs
    • Hatoum-Aslan, A., Samai, P., Maniv, I., Jiang, W., Marraffini, L.A., A ruler protein in a complex for antiviral defense determines the length of small interfering CRISPR RNAs. J. Biol. Chem. 288 (2013), 27888–27897.
    • (2013) J. Biol. Chem. , vol.288 , pp. 27888-27897
    • Hatoum-Aslan, A.1    Samai, P.2    Maniv, I.3    Jiang, W.4    Marraffini, L.A.5
  • 12
    • 77956498326 scopus 로고    scopus 로고
    • Sequence- and structure-specific RNA processing by a CRISPR endonuclease
    • Haurwitz, R.E., Jinek, M., Wiedenheft, B., Zhou, K., Doudna, J.A., 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
    • 84924740446 scopus 로고    scopus 로고
    • Cutting it close: CRISPR-associated endoribonuclease structure and function
    • Hochstrasser, M.L., Doudna, J.A., Cutting it close: CRISPR-associated endoribonuclease structure and function. Trends Biochem. Sci. 40 (2015), 58–66.
    • (2015) Trends Biochem. Sci. , vol.40 , pp. 58-66
    • Hochstrasser, M.L.1    Doudna, J.A.2
  • 15
    • 84946498330 scopus 로고    scopus 로고
    • A Conserved Structural Chassis for Mounting Versatile CRISPR RNA-Guided Immune Responses
    • Jackson, R.N., Wiedenheft, B., A Conserved Structural Chassis for Mounting Versatile CRISPR RNA-Guided Immune Responses. Mol. Cell 58 (2015), 722–728.
    • (2015) Mol. Cell , vol.58 , pp. 722-728
    • Jackson, R.N.1    Wiedenheft, B.2
  • 18
    • 84888838217 scopus 로고    scopus 로고
    • Crystal structure of Cas1 from Archaeoglobus fulgidus and characterization of its nucleolytic activity
    • Kim, T.Y., Shin, M., Huynh Thi Yen, L., Kim, J.S., Crystal structure of Cas1 from Archaeoglobus fulgidus and characterization of its nucleolytic activity. Biochem. Biophys. Res. Commun. 441 (2013), 720–725.
    • (2013) Biochem. Biophys. Res. Commun. , vol.441 , pp. 720-725
    • Kim, T.Y.1    Shin, M.2    Huynh Thi Yen, L.3    Kim, J.S.4
  • 19
    • 85020445396 scopus 로고    scopus 로고
    • Diversity, classification and evolution of CRISPR-Cas systems
    • Koonin, E.V., Makarova, K.S., Zhang, F., Diversity, classification and evolution of CRISPR-Cas systems. Curr. Opin. Microbiol. 37 (2017), 67–78.
    • (2017) Curr. Opin. Microbiol. , vol.37 , pp. 67-78
    • Koonin, E.V.1    Makarova, K.S.2    Zhang, F.3
  • 24
    • 84945540442 scopus 로고    scopus 로고
    • The CRISPR-associated Cas4 protein Pcal 0546 from Pyrobaculum calidifontis contains a [2Fe-2S] cluster: crystal structure and nuclease activity
    • Lemak, S., Nocek, B., Beloglazova, N., Skarina, T., Flick, R., Brown, G., Joachimiak, A., Savchenko, A., Yakunin, A.F., The CRISPR-associated Cas4 protein Pcal 0546 from Pyrobaculum calidifontis contains a [2Fe-2S] cluster: crystal structure and nuclease activity. Nucleic Acids Res. 42 (2014), 11144–11155.
    • (2014) Nucleic Acids Res. , vol.42 , pp. 11144-11155
    • Lemak, S.1    Nocek, B.2    Beloglazova, N.3    Skarina, T.4    Flick, R.5    Brown, G.6    Joachimiak, A.7    Savchenko, A.8    Yakunin, A.F.9
  • 26
    • 84895823059 scopus 로고    scopus 로고
    • Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process
    • Li, M., Wang, R., Zhao, D., Xiang, H., Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process. Nucleic Acids Res. 42 (2014), 2483–2492.
    • (2014) Nucleic Acids Res. , vol.42 , pp. 2483-2492
    • Li, M.1    Wang, R.2    Zhao, D.3    Xiang, H.4
  • 27
    • 84943160849 scopus 로고    scopus 로고
    • CRISPR-Cas immunity in prokaryotes
    • Marraffini, L.A., CRISPR-Cas immunity in prokaryotes. Nature 526 (2015), 55–61.
    • (2015) Nature , vol.526 , pp. 55-61
    • Marraffini, L.A.1
  • 28
    • 57849137502 scopus 로고    scopus 로고
    • CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA
    • Marraffini, L.A., Sontheimer, E.J., CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322 (2008), 1843–1845.
    • (2008) Science , vol.322 , pp. 1843-1845
    • Marraffini, L.A.1    Sontheimer, E.J.2
  • 29
    • 84994798354 scopus 로고    scopus 로고
    • CRISPR-Cas systems optimize their immune response by specifying the site of spacer integration
    • McGinn, J., Marraffini, L.A., CRISPR-Cas systems optimize their immune response by specifying the site of spacer integration. Mol. Cell 64 (2016), 616–623.
    • (2016) Mol. Cell , vol.64 , pp. 616-623
    • McGinn, J.1    Marraffini, L.A.2
  • 30
  • 31
    • 16444385662 scopus 로고    scopus 로고
    • Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements
    • Mojica, F.J.M., Díez-Villaseñor, C., García-Martínez, J., Soria, E., Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 60 (2005), 174–182.
    • (2005) J. Mol. Evol. , vol.60 , pp. 174-182
    • Mojica, F.J.M.1    Díez-Villaseñor, C.2    García-Martínez, J.3    Soria, E.4
  • 32
    • 64049118040 scopus 로고    scopus 로고
    • Short motif sequences determine the targets of the prokaryotic CRISPR defence system
    • Mojica, F.J.M., Díez-Villaseñor, C., García-Martínez, J., Almendros, C., Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155 (2009), 733–740.
    • (2009) Microbiology , vol.155 , pp. 733-740
    • Mojica, F.J.M.1    Díez-Villaseñor, C.2    García-Martínez, J.3    Almendros, C.4
  • 33
    • 84867818484 scopus 로고    scopus 로고
    • Double-stranded endonuclease activity in Bacillus halodurans clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas2 protein
    • Nam, K.H., Ding, F., Haitjema, C., Huang, Q., DeLisa, M.P., Ke, A., Double-stranded endonuclease activity in Bacillus halodurans clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas2 protein. J. Biol. Chem. 287 (2012), 35943–35952.
    • (2012) J. Biol. Chem. , vol.287 , pp. 35943-35952
    • Nam, K.H.1    Ding, F.2    Haitjema, C.3    Huang, Q.4    DeLisa, M.P.5    Ke, A.6
  • 36
    • 84924664059 scopus 로고    scopus 로고
    • Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity
    • Nuñez, J.K., Lee, A.S., Engelman, A., Doudna, J.A., Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity. Nature 519 (2015), 193–198.
    • (2015) Nature , vol.519 , pp. 193-198
    • Nuñez, J.K.1    Lee, A.S.2    Engelman, A.3    Doudna, J.A.4
  • 37
    • 84974693401 scopus 로고    scopus 로고
    • CRISPR immunological memory requires a host factor for specificity
    • Nuñez, J.K., Bai, L., Harrington, L.B., Hinder, T.L., Doudna, J.A., CRISPR immunological memory requires a host factor for specificity. Mol. Cell 62 (2016), 824–833.
    • (2016) Mol. Cell , vol.62 , pp. 824-833
    • Nuñez, J.K.1    Bai, L.2    Harrington, L.B.3    Hinder, T.L.4    Doudna, J.A.5
  • 39
    • 77952581453 scopus 로고    scopus 로고
    • Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions
    • Pintilie, G.D., Zhang, J., Goddard, T.D., Chiu, W., Gossard, D.C., Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. J. Struct. Biol. 170 (2010), 427–438.
    • (2010) J. Struct. Biol. , vol.170 , pp. 427-438
    • Pintilie, G.D.1    Zhang, J.2    Goddard, T.D.3    Chiu, W.4    Gossard, D.C.5
  • 40
    • 84861357119 scopus 로고    scopus 로고
    • Characterization of the CRISPR/Cas subtype I-A system of the hyperthermophilic crenarchaeon Thermoproteus tenax
    • Plagens, A., Tjaden, B., Hagemann, A., Randau, L., Hensel, R., Characterization of the CRISPR/Cas subtype I-A system of the hyperthermophilic crenarchaeon Thermoproteus tenax. J. Bacteriol. 194 (2012), 2491–2500.
    • (2012) J. Bacteriol. , vol.194 , pp. 2491-2500
    • Plagens, A.1    Tjaden, B.2    Hagemann, A.3    Randau, L.4    Hensel, R.5
  • 41
    • 15844390228 scopus 로고    scopus 로고
    • CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies
    • Pourcel, C., Salvignol, G., Vergnaud, G., 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.
    • (2005) Microbiology , vol.151 , pp. 653-663
    • Pourcel, C.1    Salvignol, G.2    Vergnaud, G.3
  • 42
    • 85011645437 scopus 로고    scopus 로고
    • cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
    • Punjani, A., Rubinstein, J.L., Fleet, D.J., Brubaker, M.A., cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14 (2017), 290–296.
    • (2017) Nat. Methods , vol.14 , pp. 290-296
    • Punjani, A.1    Rubinstein, J.L.2    Fleet, D.J.3    Brubaker, M.A.4
  • 43
    • 85029643760 scopus 로고    scopus 로고
    • Priming in a permissive type I-C CRISPR-Cas system reveals distinct dynamics of spacer acquisition and loss
    • Rao, C., Chin, D., Ensminger, A.W., Priming in a permissive type I-C CRISPR-Cas system reveals distinct dynamics of spacer acquisition and loss. RNA 23 (2017), 1525–1538.
    • (2017) RNA , vol.23 , pp. 1525-1538
    • Rao, C.1    Chin, D.2    Ensminger, A.W.3
  • 45
    • 84941907747 scopus 로고    scopus 로고
    • Intrinsic sequence specificity of the Cas1 integrase directs new spacer acquisition
    • Rollie, C., Schneider, S., Brinkmann, A.S., Bolt, E.L., White, M.F., Intrinsic sequence specificity of the Cas1 integrase directs new spacer acquisition. eLife, 4, 2015, 10.7554/eLife.08716.
    • (2015) eLife , vol.4
    • Rollie, C.1    Schneider, S.2    Brinkmann, A.S.3    Bolt, E.L.4    White, M.F.5
  • 46
    • 85044551490 scopus 로고    scopus 로고
    • Prespacer processing and specific integration in a Type I-A CRISPR system
    • Rollie, C., Graham, S., Rouillon, C., White, M.F., Prespacer processing and specific integration in a Type I-A CRISPR system. Nucleic Acids Res. 46 (2017), 1007–1020.
    • (2017) Nucleic Acids Res. , vol.46 , pp. 1007-1020
    • Rollie, C.1    Graham, S.2    Rouillon, C.3    White, M.F.4
  • 48
    • 79958825675 scopus 로고    scopus 로고
    • An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3
    • Sashital, D.G., Jinek, M., Doudna, J.A., 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
  • 49
    • 84868444740 scopus 로고    scopus 로고
    • RELION: implementation of a Bayesian approach to cryo-EM structure determination
    • Scheres, S.H.W., RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180 (2012), 519–530.
    • (2012) J. Struct. Biol. , vol.180 , pp. 519-530
    • Scheres, S.H.W.1
  • 51
    • 33947654156 scopus 로고    scopus 로고
    • Expression in Escherichia coli and characterization of beta-xylosidases GH39 and GH-43 from Bacillus halodurans C-125
    • Smaali, I., Rémond, C., O'Donohue, M.J., Expression in Escherichia coli and characterization of beta-xylosidases GH39 and GH-43 from Bacillus halodurans C-125. Appl. Microbiol. Biotechnol. 73 (2006), 582–590.
    • (2006) Appl. Microbiol. Biotechnol. , vol.73 , pp. 582-590
    • Smaali, I.1    Rémond, C.2    O'Donohue, M.J.3
  • 52
    • 84990860399 scopus 로고    scopus 로고
    • Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR-Cas system
    • Staals, R.H.J., Jackson, S.A., Biswas, A., Brouns, S.J., Brown, C.M., Fineran, P.C., Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR-Cas system. Nat. Commun., 7, 2016, 12853.
    • (2016) Nat. Commun. , vol.7 , pp. 12853
    • Staals, R.H.J.1    Jackson, S.A.2    Biswas, A.3    Brouns, S.J.4    Brown, C.M.5    Fineran, P.C.6
  • 53
    • 84895871173 scopus 로고    scopus 로고
    • DNA interrogation by the CRISPR RNA-guided endonuclease Cas9
    • Sternberg, S.H., Redding, S., Jinek, M., Greene, E.C., Doudna, J.A., DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507 (2014), 62–67.
    • (2014) Nature , vol.507 , pp. 62-67
    • Sternberg, S.H.1    Redding, S.2    Jinek, M.3    Greene, E.C.4    Doudna, J.A.5
  • 54
    • 0037047411 scopus 로고    scopus 로고
    • A third bacterial system for the assembly of iron-sulfur clusters with homologs in archaea and plastids
    • Takahashi, Y., Tokumoto, U., A third bacterial system for the assembly of iron-sulfur clusters with homologs in archaea and plastids. J. Biol. Chem. 277 (2002), 28380–28383.
    • (2002) J. Biol. Chem. , vol.277 , pp. 28380-28383
    • Takahashi, Y.1    Tokumoto, U.2
  • 55
    • 84946130269 scopus 로고    scopus 로고
    • Structural and mechanistic basis of PAM-dependent spacer acquisition in CRISPR-Cas systems
    • Wang, J., Li, J., Zhao, H., Sheng, G., Wang, M., Yin, M., Wang, Y., Structural and mechanistic basis of PAM-dependent spacer acquisition in CRISPR-Cas systems. Cell 163 (2015), 840–853.
    • (2015) Cell , vol.163 , pp. 840-853
    • Wang, J.1    Li, J.2    Zhao, H.3    Sheng, G.4    Wang, M.5    Yin, M.6    Wang, Y.7
  • 56
    • 84971201881 scopus 로고    scopus 로고
    • DNA motifs determining the accuracy of repeat duplication during CRISPR adaptation in Haloarcula hispanica
    • Wang, R., Li, M., Gong, L., Hu, S., Xiang, H., DNA motifs determining the accuracy of repeat duplication during CRISPR adaptation in Haloarcula hispanica. Nucleic Acids Res. 44 (2016), 4266–4277.
    • (2016) Nucleic Acids Res. , vol.44 , pp. 4266-4277
    • Wang, R.1    Li, M.2    Gong, L.3    Hu, S.4    Xiang, H.5
  • 58
    • 84990233575 scopus 로고    scopus 로고
    • Protecting genome integrity during CRISPR immune adaptation
    • Wright, A.V., Doudna, J.A., Protecting genome integrity during CRISPR immune adaptation. Nat. Struct. Mol. Biol. 23 (2016), 876–883.
    • (2016) Nat. Struct. Mol. Biol. , vol.23 , pp. 876-883
    • Wright, A.V.1    Doudna, J.A.2
  • 60
    • 18744383071 scopus 로고    scopus 로고
    • GMAP: a genomic mapping and alignment program for mRNA and EST sequences
    • Wu, T.D., Watanabe, C.K., GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21 (2005), 1859–1875.
    • (2005) Bioinformatics , vol.21 , pp. 1859-1875
    • Wu, T.D.1    Watanabe, C.K.2
  • 61
    • 85030696100 scopus 로고    scopus 로고
    • How type II CRISPR-Cas establish immunity through Cas1-Cas2-mediated spacer integration
    • Xiao, Y., Ng, S., Nam, K.H., Ke, A., How type II CRISPR-Cas establish immunity through Cas1-Cas2-mediated spacer integration. Nature 550 (2017), 137–141.
    • (2017) Nature , vol.550 , pp. 137-141
    • Xiao, Y.1    Ng, S.2    Nam, K.H.3    Ke, A.4
  • 62
    • 85039973114 scopus 로고    scopus 로고
    • Real-time observation of target search by the CRISPR Surveillance Complex Cascade
    • Xue, C., Zhu, Y., Zhang, X., Shin, Y.K., Sashital, D.G., Real-time observation of target search by the CRISPR Surveillance Complex Cascade. Cell Rep. 21 (2017), 3717–3727.
    • (2017) Cell Rep. , vol.21 , pp. 3717-3727
    • Xue, C.1    Zhu, Y.2    Zhang, X.3    Shin, Y.K.4    Sashital, D.G.5
  • 63
    • 84861639567 scopus 로고    scopus 로고
    • Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli
    • Yosef, I., Goren, M.G., Qimron, U., Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res. 40 (2012), 5569–5576.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 5569-5576
    • Yosef, I.1    Goren, M.G.2    Qimron, U.3
  • 64
    • 84867325709 scopus 로고    scopus 로고
    • The CRISPR associated protein Cas4 Is a 5′ to 3′ DNA exonuclease with an iron-sulfur cluster
    • Zhang, J., Kasciukovic, T., White, M.F., The CRISPR associated protein Cas4 Is a 5′ to 3′ DNA exonuclease with an iron-sulfur cluster. PLoS ONE, 7, 2012, e47232.
    • (2012) PLoS ONE , vol.7 , pp. e47232
    • Zhang, J.1    Kasciukovic, T.2    White, M.F.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.