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Volumn 44, Issue 9, 2016, Pages 4266-4277

DNA motifs determining the accuracy of repeat duplication during CRISPR adaptation in Haloarcula hispanica

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ADAPTIVE IMMUNITY; AMINO ACID SUBSTITUTION; ARTICLE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; COMPLEX FORMATION; CONTROLLED STUDY; DNA INTEGRATION; DNA SEQUENCE; DNA TRANSPOSITION; EVOLUTIONARY ADAPTATION; GENE DUPLICATION; GENETIC MANIPULATION; HALOARCULA HISPANICA; NONHUMAN; PERIODICITY; PRIORITY JOURNAL; ARCHAEAL GENE; DNA REPLICATION; GENETICS; HALOARCULA; NUCLEOTIDE MOTIF; NUCLEOTIDE SEQUENCE;

EID: 84971201881     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw260     Document Type: Article
Times cited : (39)

References (43)
  • 2
    • 84954214717 scopus 로고    scopus 로고
    • Biology and applications of CRISPR systems: Harnessing nature's toolbox for genome engineering
    • Wright, A.V., Nũ nez, J.K., Doudna, J.A. (2016) Biology and applications of CRISPR systems: harnessing nature's toolbox for genome engineering. Cell, 164, 29-44.
    • (2016) Cell , vol.164 , pp. 29-44
    • Wright, A.V.1    Nuñez, J.K.2    Doudna, J.A.3
  • 5
    • 57849137502 scopus 로고    scopus 로고
    • CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA
    • Marraffini, L.A., Sontheimer, E.J. (2008) CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science, 322, 1843-1845.
    • (2008) Science , vol.322 , pp. 1843-1845
    • Marraffini, L.A.1    Sontheimer, E.J.2
  • 6
    • 84857097177 scopus 로고    scopus 로고
    • RNA-guided genetic silencing systems in bacteria and archaea
    • Wiedenheft, B., Sternberg, S.H., Doudna, J.A. (2012) RNA-guided genetic silencing systems in bacteria and archaea. Nature, 482, 331-338.
    • (2012) Nature , vol.482 , pp. 331-338
    • Wiedenheft, B.1    Sternberg, S.H.2    Doudna, J.A.3
  • 7
    • 84899134190 scopus 로고    scopus 로고
    • CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity
    • Barrangou, R., Marraffini, L.A. (2014) CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Mol. Cell., 54, 234-244.
    • (2014) Mol. Cell. , vol.54 , pp. 234-244
    • Barrangou, R.1    Marraffini, L.A.2
  • 9
    • 39149142575 scopus 로고    scopus 로고
    • CRISPR-A widespread system that provides acquired resistance against phages in bacteria and archaea
    • 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.
    • (2008) Nat. Rev. Microbiol. , vol.6 , pp. 181-186
    • Sorek, R.1    Kunin, V.2    Hugenholtz, P.3
  • 10
    • 23844505202 scopus 로고    scopus 로고
    • Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin
    • Bolotin, A., Ouinquis, B., Sorokin, A., Ehrlich, S.D. (2005) Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology, 151, 2551-2561.
    • (2005) Microbiology , vol.151 , pp. 2551-2561
    • Bolotin, A.1    Ouinquis, B.2    Sorokin, A.3    Ehrlich, S.D.4
  • 11
    • 16444385662 scopus 로고    scopus 로고
    • Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements
    • Mojica, F.J.M., D?ez-Villase ñor, C., Garć?a-Mart?nez, J., Soria, E. (2005) Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol., 60, 174-182.
    • (2005) J. Mol. Evol. , vol.60 , pp. 174-182
    • Mojica, F.J.M.1    Déz-Villaseñor, C.2    Garcá-Martńez, J.3    Soria, E.4
  • 12
    • 15844390228 scopus 로고    scopus 로고
    • CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, provide additional tools for evolutionary studies
    • Pourcel, C., Salvignol, G., Vergnaud, G. (2005) CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, provide additional tools for evolutionary studies. Microbiology, 151, 653-663.
    • (2005) Microbiology , vol.151 , pp. 653-663
    • Pourcel, C.1    Salvignol, G.2    Vergnaud, G.3
  • 13
    • 34248400310 scopus 로고    scopus 로고
    • A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes
    • Haft, D.H., Selengut, J., Mongodin, E.F., Nelson, K.E. (2005) A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput. Biol., 1, 474-483.
    • (2005) PLoS Comput. Biol. , vol.1 , pp. 474-483
    • Haft, D.H.1    Selengut, J.2    Mongodin, E.F.3    Nelson, K.E.4
  • 14
    • 0036267740 scopus 로고    scopus 로고
    • Identification of genes that are associated with DNA repeats in prokaryotes
    • Jansen, R., van Embden, J.D.A., Gaastra, W., Schouls, L.M. (2002) Identification of genes that are associated with DNA repeats in prokaryotes. Mol. Microbiol., 43, 1565-1575.
    • (2002) Mol. Microbiol. , vol.43 , pp. 1565-1575
    • Jansen, R.1    Van Embden, J.D.A.2    Gaastra, W.3    Schouls, L.M.4
  • 15
    • 77956498326 scopus 로고    scopus 로고
    • Sequence-and structure-specific RNA processing by a CRISPR endonuclease
    • Haurwitz, R.E., Jinek, M., Wiedenheft, B., Zhou, K.H., Doudna, J.A. (2010) Sequence-and structure-specific RNA processing by a CRISPR endonuclease. Science, 329, 1355-1358.
    • (2010) Science , vol.329 , pp. 1355-1358
    • Haurwitz, R.E.1    Jinek, M.2    Wiedenheft, B.3    Zhou, K.H.4    Doudna, J.A.5
  • 16
    • 84873528026 scopus 로고    scopus 로고
    • Characterization of CRISPR RNA biogenesis and Cas6 cleavage-mediated inhibition of a provirus in the haloarchaeon Haloferax mediterranei
    • Li, M., Liu, H.L., Han, J., Liu, J.F., Wang, R., Zhao, D.H., Zhou, J., Xiang, H. (2013) Characterization of CRISPR RNA biogenesis and Cas6 cleavage-mediated inhibition of a provirus in the haloarchaeon Haloferax mediterranei. J. Bacteriol., 195, 867-875.
    • (2013) J. Bacteriol. , vol.195 , pp. 867-875
    • Li, M.1    Liu, H.L.2    Han, J.3    Liu, J.F.4    Wang, R.5    Zhao, D.H.6    Zhou, J.7    Xiang, H.8
  • 20
    • 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. (2012) Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res., 40, 5569-5576.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 5569-5576
    • Yosef, I.1    Goren, M.G.2    Qimron, U.3
  • 21
    • 84870718176 scopus 로고    scopus 로고
    • Memory of viral infections by CRISPR-Cas adaptive immune systems: Acquisition of new information
    • Fineran, P.C., Charpentier, E. (2012) Memory of viral infections by CRISPR-Cas adaptive immune systems: acquisition of new information. Virology, 434, 202-209.
    • (2012) Virology , vol.434 , pp. 202-209
    • Fineran, P.C.1    Charpentier, E.2
  • 22
    • 84860433123 scopus 로고    scopus 로고
    • CRISPR interference directs strand specific spacer acquisition
    • Swarts, D.C., Mosterd, C., van Passel, M.W.J., Brouns, S.J.J. (2012) CRISPR interference directs strand specific spacer acquisition. PLoS One, 7, e35888.
    • (2012) PLoS One , vol.7 , pp. e35888
    • Swarts, D.C.1    Mosterd, C.2    Van Passel, M.W.J.3    Brouns, S.J.J.4
  • 23
    • 84864864464 scopus 로고    scopus 로고
    • Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system
    • Datsenko, K.A., Pougach, K., Tikhonov, A., Wanner, B.L., Severinov, K., Semenova, E. (2012) Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nat. Commun., 3, 945.
    • (2012) Nat. Commun. , vol.3 , pp. 945
    • Datsenko, K.A.1    Pougach, K.2    Tikhonov, A.3    Wanner, B.L.4    Severinov, K.5    Semenova, E.6
  • 24
    • 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.H., Xiang, H. (2014) Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process. Nucleic Acids Res., 42, 2483-2492.
    • (2014) Nucleic Acids Res. , vol.42 , pp. 2483-2492
    • Li, M.1    Wang, R.2    Zhao, D.H.3    Xiang, H.4
  • 27
    • 64049118040 scopus 로고    scopus 로고
    • Short motif sequences determine the targets of the prokaryotic CRISPR defence system
    • Mojica, F.J.M., D?ez-Villase ñor, C., Garć?a-Mart?nez, J., Almendros, C. (2009) Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology, 155, 733-740.
    • (2009) Microbiology , vol.155 , pp. 733-740
    • Mojica, F.J.M.1    Déz-Villaseñor, C.2    Garcá-Martńez, J.3    Almendros, C.4
  • 28
    • 84879026965 scopus 로고    scopus 로고
    • Protospacer recognition motifs: Mixed identities and functional diversity
    • Shah, S.A., Erdmann, S., Mojica, F.J.M., Garrett, R.A. (2013) Protospacer recognition motifs: mixed identities and functional diversity. RNA Biol., 10, 891-899.
    • (2013) RNA Biol. , vol.10 , pp. 891-899
    • Shah, S.A.1    Erdmann, S.2    Mojica, F.J.M.3    Garrett, R.A.4
  • 29
    • 84884687531 scopus 로고    scopus 로고
    • Type I-E CRISPR-Cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition
    • Westra, E.R., Semenova, E., Datsenko, K.A., Jackson, R.N., Wiedenheft, B., Severinov, K., Brouns, S.J.J. (2013) Type I-E CRISPR-Cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition. PLoS Genet., 9, e1003742.
    • (2013) PLoS Genet. , vol.9 , pp. e1003742
    • Westra, E.R.1    Semenova, E.2    Datsenko, K.A.3    Jackson, R.N.4    Wiedenheft, B.5    Severinov, K.6    Brouns, S.J.J.7
  • 30
    • 84879032247 scopus 로고    scopus 로고
    • CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli
    • D?ez-Villase ñor, C., Guzmán, N.M., Almendros, C., Garć?a-Mart?nez, J., Mojica, F.J.M. (2013) CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli. RNA Biol., 10, 792-802.
    • (2013) RNA Biol. , vol.10 , pp. 792-802
    • Dez-Villaseñor, C.1
  • 32
    • 84903175627 scopus 로고    scopus 로고
    • Haloarcula hispanica CRISPR authenticates PAM of a target sequence to prime discriminative adaptation
    • Li, M., Wang, R., Xiang, H. (2014) Haloarcula hispanica CRISPR authenticates PAM of a target sequence to prime discriminative adaptation. Nucleic Acids Res., 42, 7226-7235.
    • (2014) Nucleic Acids Res. , vol.42 , pp. 7226-7235
    • Li, M.1    Wang, R.2    Xiang, H.3
  • 33
    • 84904019733 scopus 로고    scopus 로고
    • Detection and characterization of spacer integration intermediates in type I-E CRISPR-Cas system
    • Arslan, Z., Hermanns, V., Wurm, R., Wagner, R., Pul, Ü. (2014) Detection and characterization of spacer integration intermediates in type I-E CRISPR-Cas system. Nucleic Acids Res., 42, 7884-7893.
    • (2014) Nucleic Acids Res. , vol.42 , pp. 7884-7893
    • Arslan, Z.1    Hermanns, V.2    Wurm, R.3    Wagner, R.4    Pul, Ü.5
  • 34
    • 84924664059 scopus 로고    scopus 로고
    • Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity
    • Nũ nez, J.K., Lee, A.S.Y., Engelman, A., Doudna, J.A. (2015) Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity. Nature, 519, 193-198.
    • (2015) Nature , vol.519 , pp. 193-198
    • Nuñez, J.K.1
  • 35
    • 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. (2015) Intrinsic sequence specificity of the Cas1 integrase directs new spacer acquisition. eLife, 4, e08716.
    • (2015) ELife , vol.4 , pp. e08716
    • Rollie, C.1    Schneider, S.2    Brinkmann, A.S.3    Bolt, E.L.4    White, M.F.5
  • 36
    • 84922978235 scopus 로고    scopus 로고
    • Sequences spanning the leader-repeat junction mediate CRISPR adaptation to phage in Streptococcus thermophilus
    • Wei, Y.Z., Chesne, M.T., Terns, R.M., Terns, M.P. (2015) Sequences spanning the leader-repeat junction mediate CRISPR adaptation to phage in Streptococcus thermophilus. Nucleic Acids Res., 43, 1749-1758.
    • (2015) Nucleic Acids Res. , vol.43 , pp. 1749-1758
    • Wei, Y.Z.1    Chesne, M.T.2    Terns, R.M.3    Terns, M.P.4
  • 37
    • 79959374305 scopus 로고    scopus 로고
    • Development of pyrF-based gene knockout systems for genome-wide manipulation of the archaea Haloferax mediterranei and Haloarcula hispanica
    • Liu, H.L., Han, J., Liu, X.Q., Zhou, J., Xiang, H. (2011) Development of pyrF-based gene knockout systems for genome-wide manipulation of the archaea Haloferax mediterranei and Haloarcula hispanica. J. Genet. Genomics, 38, 261-269.
    • (2011) J. Genet. Genomics , vol.38 , pp. 261-269
    • Liu, H.L.1    Han, J.2    Liu, X.Q.3    Zhou, J.4    Xiang, H.5
  • 38
    • 84917734270 scopus 로고    scopus 로고
    • A novel DNA-binding protein, PhaR, plays a central role in the regulation of polyhydroxyalkanoate accumulation and granule formation in the haloarchaeon Haloferax mediterranei
    • Cai, S., Cai, L., Zhao, D., Liu, G., Han, J., Zhou, J., Xiang, H. (2015) A novel DNA-binding protein, PhaR, plays a central role in the regulation of polyhydroxyalkanoate accumulation and granule formation in the haloarchaeon Haloferax mediterranei. Appl. Environ. Microbiol., 81, 373-385.
    • (2015) Appl. Environ. Microbiol. , vol.81 , pp. 373-385
    • Cai, S.1    Cai, L.2    Zhao, D.3    Liu, G.4    Han, J.5    Zhou, J.6    Xiang, H.7
  • 39
    • 84866313681 scopus 로고    scopus 로고
    • Experimental definition of a clustered regularly interspaced short palindromic duplicon in Escherichia coli
    • Goren, M.G., Yosef, I., Auster, O., Qimron, U. (2012) Experimental definition of a clustered regularly interspaced short palindromic duplicon in Escherichia coli. J. Mol. Biol., 423, 14-16.
    • (2012) J. Mol. Biol. , vol.423 , pp. 14-16
    • Goren, M.G.1    Yosef, I.2    Auster, O.3    Qimron, U.4
  • 40
    • 77958451348 scopus 로고    scopus 로고
    • Phantom, a new subclass of mutator DNA transposons found in insect viruses and widely distributed in animals
    • Marquez, C.P., Pritham, E.J. (2010) Phantom, a new subclass of mutator DNA transposons found in insect viruses and widely distributed in animals. Genetics, 185, 1507-1582.
    • (2010) Genetics , vol.185 , pp. 1507-1582
    • Marquez, C.P.1    Pritham, E.J.2
  • 41
    • 34447644810 scopus 로고    scopus 로고
    • CRISPR recognition tool (CRT): A tool for automatic detection of clustered regularly interspaced palindromic repeats
    • Bland, C., Ramsey, T.L., Sabree, F., Lowe, M., Brown, K., Kyrpides, N.C., Hugenholtz, P. (2007) CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics, 8, 209.
    • (2007) BMC Bioinformatics , vol.8 , pp. 209
    • Bland, C.1    Ramsey, T.L.2    Sabree, F.3    Lowe, M.4    Brown, K.5    Kyrpides, N.C.6    Hugenholtz, P.7
  • 42
    • 84961336907 scopus 로고    scopus 로고
    • The casposon-encoded Cas1 protein from Aciduliprofundum boonei is a DNA integrase that generates target site duplications
    • Hickman, A.B., Dyda, F. (2015) The casposon-encoded Cas1 protein from Aciduliprofundum boonei is a DNA integrase that generates target site duplications. Nucleic Acids Res., 43, 10576-10587.
    • (2015) Nucleic Acids Res. , vol.43 , pp. 10576-10587
    • Hickman, A.B.1    Dyda, F.2
  • 43
    • 35748974534 scopus 로고    scopus 로고
    • Evolutionary conservation of sequence and secondary structures in CRISPR repeats
    • Kunin, V., Sorek, R., Hugenholtz, P. (2007) Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol., 8, R61.
    • (2007) Genome Biol. , vol.8 , pp. R61
    • Kunin, V.1    Sorek, R.2    Hugenholtz, P.3


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