메뉴 건너뛰기




Volumn 25, Issue 2, 2019, Pages 250-260.e4

Imprecise Spacer Acquisition Generates CRISPR-Cas Immune Diversity through Primed Adaptation

Author keywords

adaptation; coevolution; CRISPR Cas; diversity; phage; primed; priming; slipping; spacer acquisition

Indexed keywords

ARTICLE; BACTERIOPHAGE; COEVOLUTION; CRISPR CAS SYSTEM; IMMUNE SYSTEM; MEMORY; NONHUMAN; GENETIC VARIATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; MOLECULAR EVOLUTION; PECTOBACTERIUM; SERRATIA; VIROLOGY;

EID: 85060878990     PISSN: 19313128     EISSN: 19346069     Source Type: Journal    
DOI: 10.1016/j.chom.2018.12.014     Document Type: Article
Times cited : (49)

References (56)
  • 1
    • 84954537942 scopus 로고    scopus 로고
    • CRISPR-Cas adaptation: insights into the mechanism of action
    • Amitai, G., Sorek, R., CRISPR-Cas adaptation: insights into the mechanism of action. Nat. Rev. Microbiol. 14 (2016), 67–76.
    • (2016) Nat. Rev. Microbiol. , vol.14 , pp. 67-76
    • Amitai, G.1    Sorek, R.2
  • 2
    • 44449133775 scopus 로고    scopus 로고
    • Virus population dynamics and acquired virus resistance in natural microbial communities
    • Andersson, A.F., Banfield, J.F., Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320 (2008), 1047–1050.
    • (2008) Science , vol.320 , pp. 1047-1050
    • Andersson, A.F.1    Banfield, J.F.2
  • 5
    • 84868143545 scopus 로고    scopus 로고
    • The CRISPR/Cas adaptive immune system of Pseudomonas aeruginosa mediates resistance to naturally occurring and engineered phages
    • Cady, K.C., Bondy-Denomy, J., Heussler, G.E., Davidson, A.R., O'Toole, G.A., The CRISPR/Cas adaptive immune system of Pseudomonas aeruginosa mediates resistance to naturally occurring and engineered phages. J. Bacteriol. 194 (2012), 5728–5738.
    • (2012) J. Bacteriol. , vol.194 , pp. 5728-5738
    • Cady, K.C.1    Bondy-Denomy, J.2    Heussler, G.E.3    Davidson, A.R.4    O'Toole, G.A.5
  • 8
    • 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., Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nat. Commun., 3, 2012, 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
  • 12
  • 13
    • 84865798438 scopus 로고    scopus 로고
    • Spatial structure and Lamarckian adaptation explain extreme genetic diversity at CRISPR locus
    • e00126–12
    • Haerter, J.O., Sneppen, K., Spatial structure and Lamarckian adaptation explain extreme genetic diversity at CRISPR locus. MBio, 3, 2012 e00126–12.
    • (2012) MBio , vol.3
    • Haerter, J.O.1    Sneppen, K.2
  • 14
    • 80054971915 scopus 로고    scopus 로고
    • Targeted bacterial immunity buffers phage diversity
    • Haerter, J.O., Trusina, A., Sneppen, K., Targeted bacterial immunity buffers phage diversity. J. Virol. 85 (2011), 10554–10560.
    • (2011) J. Virol. , vol.85 , pp. 10554-10560
    • Haerter, J.O.1    Trusina, A.2    Sneppen, K.3
  • 15
    • 77649097737 scopus 로고    scopus 로고
    • Sustainability of virulence in a phage-bacterial ecosystem
    • Heilmann, S., Sneppen, K., Krishna, S., Sustainability of virulence in a phage-bacterial ecosystem. J. Virol. 84 (2010), 3016–3022.
    • (2010) J. Virol. , vol.84 , pp. 3016-3022
    • Heilmann, S.1    Sneppen, K.2    Krishna, S.3
  • 16
    • 77958590947 scopus 로고    scopus 로고
    • CRISPR associated diversity within a population of Sulfolobus islandicus
    • Held, N.L., Herrera, A., Cadillo-Quiroz, H., Whitaker, R.J., CRISPR associated diversity within a population of Sulfolobus islandicus. PLoS One, 5, 2010, e12988.
    • (2010) PLoS One , vol.5 , pp. e12988
    • Held, N.L.1    Herrera, A.2    Cadillo-Quiroz, H.3    Whitaker, R.J.4
  • 17
    • 84994662819 scopus 로고    scopus 로고
    • Requirements for Pseudomonas aeruginosa type I-F CRISPR-cas adaptation determined using a biofilm enrichment assay
    • Heussler, G.E., Miller, J.L., Price, C.E., Collins, A.J., O'Toole, G.A., Requirements for Pseudomonas aeruginosa type I-F CRISPR-cas adaptation determined using a biofilm enrichment assay. J. Bacteriol. 198 (2016), 3080–3090.
    • (2016) J. Bacteriol. , vol.198 , pp. 3080-3090
    • Heussler, G.E.1    Miller, J.L.2    Price, C.E.3    Collins, A.J.4    O'Toole, G.A.5
  • 19
    • 84883510431 scopus 로고    scopus 로고
    • Evolutionary dynamics of the prokaryotic adaptive immunity system CRISPR-Cas in an explicit ecological context
    • Iranzo, J., Lobkovsky, A.E., Wolf, Y.I., Koonin, E.V., Evolutionary dynamics of the prokaryotic adaptive immunity system CRISPR-Cas in an explicit ecological context. J. Bacteriol. 195 (2013), 3834–3844.
    • (2013) J. Bacteriol. , vol.195 , pp. 3834-3844
    • Iranzo, J.1    Lobkovsky, A.E.2    Wolf, Y.I.3    Koonin, E.V.4
  • 21
    • 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
  • 22
    • 85052592154 scopus 로고    scopus 로고
    • Primed CRISPR adaptation in Escherichia coli cells does not depend on conformational changes in the Cascade effector complex detected in vitro
    • Krivoy, A., Rutkauskas, M., Kuznedelov, K., Musharova, O., Rouillon, C., Severinov, K., Seidel, R., Primed CRISPR adaptation in Escherichia coli cells does not depend on conformational changes in the Cascade effector complex detected in vitro. Nucleic Acids Res. 46 (2018), 4087–4098.
    • (2018) Nucleic Acids Res. , vol.46 , pp. 4087-4098
    • Krivoy, A.1    Rutkauskas, M.2    Kuznedelov, K.3    Musharova, O.4    Rouillon, C.5    Severinov, K.6    Seidel, R.7
  • 24
    • 84876001507 scopus 로고    scopus 로고
    • The population and evolutionary dynamics of phage and bacteria with CRISPR-mediated immunity
    • Levin, B.R., Moineau, S., Bushman, M., Barrangou, R., The population and evolutionary dynamics of phage and bacteria with CRISPR-mediated immunity. PLoS Genet., 9, 2013, e1003312.
    • (2013) PLoS Genet. , vol.9 , pp. e1003312
    • Levin, B.R.1    Moineau, S.2    Bushman, M.3    Barrangou, R.4
  • 25
    • 85020266476 scopus 로고    scopus 로고
    • The spacer size of I-B CRISPR is modulated by the terminal sequence of the protospacer
    • Li, M., Gong, L., Zhao, D., Zhou, J., Xiang, H., The spacer size of I-B CRISPR is modulated by the terminal sequence of the protospacer. Nucleic Acids Res. 45 (2017), 4642–4654.
    • (2017) Nucleic Acids Res. , vol.45 , pp. 4642-4654
    • Li, M.1    Gong, L.2    Zhao, D.3    Zhou, J.4    Xiang, H.5
  • 27
    • 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
  • 34
    • 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), 525–1538.
    • (2017) RNA , vol.23 , pp. 525-1538
    • Rao, C.1    Chin, D.2    Ensminger, A.W.3
  • 35
    • 84905594146 scopus 로고    scopus 로고
    • Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer
    • Richter, C., Dy, R.L., McKenzie, R.E., Watson, B.N., Taylor, C., Chang, J.T., McNeil, M.B., Staals, R.H., Fineran, P.C., Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer. Nucleic Acids Res. 42 (2014), 8516–8526.
    • (2014) Nucleic Acids Res. , vol.42 , pp. 8516-8526
    • Richter, C.1    Dy, R.L.2    McKenzie, R.E.3    Watson, B.N.4    Taylor, C.5    Chang, J.T.6    McNeil, M.B.7    Staals, R.H.8    Fineran, P.C.9
  • 36
    • 84879021475 scopus 로고    scopus 로고
    • High-throughput analysis of type I-E CRISPR/Cas spacer acquisition in E. coli
    • Savitskaya, E., Semenova, E., Dedkov, V., Metlitskaya, A., Severinov, K., High-throughput analysis of type I-E CRISPR/Cas spacer acquisition in E. coli. RNA Biol. 10 (2013), 716–725.
    • (2013) RNA Biol. , vol.10 , pp. 716-725
    • Savitskaya, E.1    Semenova, E.2    Dedkov, V.3    Metlitskaya, A.4    Severinov, K.5
  • 39
    • 85016138679 scopus 로고    scopus 로고
    • The influence of copy-number of targeted extrachromosomal genetic elements on the outcome of CRISPR-cas defense
    • Severinov, K., Ispolatov, I., Semenova, E., The influence of copy-number of targeted extrachromosomal genetic elements on the outcome of CRISPR-cas defense. Front. Mol. Biosci., 3, 2016, 45.
    • (2016) Front. Mol. Biosci. , vol.3 , pp. 45
    • Severinov, K.1    Ispolatov, I.2    Semenova, E.3
  • 42
    • 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., 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.1    Jackson, S.A.2    Biswas, A.3    Brouns, S.J.4    Brown, C.M.5    Fineran, P.C.6
  • 44
    • 84860433123 scopus 로고    scopus 로고
    • CRISPR interference directs strand specific spacer acquisition
    • Swarts, D.C., Mosterd, C., van Passel, M.W., Brouns, S.J., CRISPR interference directs strand specific spacer acquisition. PLoS One, 7, 2012, e35888.
    • (2012) PLoS One , vol.7 , pp. e35888
    • Swarts, D.C.1    Mosterd, C.2    van Passel, M.W.3    Brouns, S.J.4
  • 45
    • 64549143788 scopus 로고    scopus 로고
    • An improved Escherichia coli donor strain for diparental mating
    • Thoma, S., Schobert, M., An improved Escherichia coli donor strain for diparental mating. FEMS Microbiol. Lett. 294 (2009), 127–132.
    • (2009) FEMS Microbiol. Lett. , vol.294 , pp. 127-132
    • Thoma, S.1    Schobert, M.2
  • 46
    • 0034016854 scopus 로고    scopus 로고
    • Biosynthesis of carbapenem antibiotic and prodigiosin pigment in Serratia is under quorum sensing control
    • Thomson, N.R., Crow, M.A., McGowan, S.J., Cox, A., Salmond, G.P., Biosynthesis of carbapenem antibiotic and prodigiosin pigment in Serratia is under quorum sensing control. Mol. Microbiol. 36 (2000), 539–556.
    • (2000) Mol. Microbiol. , vol.36 , pp. 539-556
    • Thomson, N.R.1    Crow, M.A.2    McGowan, S.J.3    Cox, A.4    Salmond, G.P.5
  • 48
    • 84922998282 scopus 로고    scopus 로고
    • Cas9 function and host genome sampling in Type II-A CRISPR-Cas adaptation
    • Wei, Y., Terns, R.M., Terns, M.P., Cas9 function and host genome sampling in Type II-A CRISPR-Cas adaptation. Genes Dev. 29 (2015), 356–361.
    • (2015) Genes Dev. , vol.29 , pp. 356-361
    • Wei, Y.1    Terns, R.M.2    Terns, M.P.3
  • 53
    • 0141877349 scopus 로고    scopus 로고
    • NetLogo
    • Center for Connected Learning and Computer-Based Modeling, Northwestern University
    • Wilensky, U., NetLogo. 1999, Center for Connected Learning and Computer-Based Modeling, Northwestern University http://ccl.northwestern.edu/netlogo/.
    • (1999)
    • Wilensky, U.1
  • 55
    • 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
  • 56
    • 84897676120 scopus 로고    scopus 로고
    • PEAR: a fast and accurate Illumina Paired-End reAd mergeR
    • Zhang, J., Kobert, K., Flouri, T., Stamatakis, A., PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30 (2014), 614–620.
    • (2014) Bioinformatics , vol.30 , pp. 614-620
    • Zhang, J.1    Kobert, K.2    Flouri, T.3    Stamatakis, A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.