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Volumn 5, Issue 1, 2014, Pages

CRISPR-cas functional module exchange in Escherichia coli

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; CAS E GENE; CAS F GENE; CRISPR GENE; ESCHERICHIA COLI; GENE INSERTION SEQUENCE; GENE LOCUS; GENETIC VARIABILITY; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

EID: 84903363942     PISSN: 21612129     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.00767-13     Document Type: Article
Times cited : (31)

References (56)
  • 1
    • 0034034401 scopus 로고    scopus 로고
    • Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria
    • Mojica FJ, Díez-Villaseñor C, Soria E, Juez G. 2000. Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol. Microbiol. 36:244-246.
    • (2000) Mol. Microbiol. , vol.36 , pp. 244-246
    • Mojica, F.J.1    Díez-Villaseñor, C.2    Soria, E.3    Juez, G.4
  • 2
    • 0036267740 scopus 로고    scopus 로고
    • Identification of genes that are associated with DNA repeats in prokaryotes
    • Jansen R, Embden JD, Gaastra W, Schouls LM. 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    Embden, J.D.2    Gaastra, W.3    Schouls, L.M.4
  • 4
    • 79960393323 scopus 로고    scopus 로고
    • Non-identity-mediated CRISPRbacteriophage interaction mediated via the Csy and Cas3 proteins
    • Cady KC, O'Toole GA. 2011. Non-identity-mediated CRISPRbacteriophage interaction mediated via the Csy and Cas3 proteins. J. Bacteriol. 193:3433-3445.
    • (2011) J. Bacteriol. , vol.193 , pp. 3433-3445
    • Cady, K.C.1    O'Toole, G.A.2
  • 5
    • 0029166294 scopus 로고
    • Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning
    • Mojica FJ, Ferrer C, Juez G, Rodríguez-Valera F. 1995. Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning. Mol. Microbiol. 17:85-93.
    • (1995) Mol. Microbiol. , vol.17 , pp. 85-93
    • Mojica, F.J.1    Ferrer, C.2    Juez, G.3    Rodríguez-Valera, F.4
  • 6
    • 34248331654 scopus 로고    scopus 로고
    • Regulation of dev, an operon that includes genes essential for Myxococcus xanthus development and CRISPR-associated genes and repeats
    • Viswanathan P, Murphy K, Julien B, Garza AG, Kroos L. 2007. Regulation of dev, an operon that includes genes essential for Myxococcus xanthus development and CRISPR-associated genes and repeats. J. Bacteriol. 189:3738-3750.
    • (2007) J. Bacteriol. , vol.189 , pp. 3738-3750
    • Viswanathan, P.1    Murphy, K.2    Julien, B.3    Garza, A.G.4    Kroos, L.5
  • 8
    • 77249170201 scopus 로고    scopus 로고
    • CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea
    • Marraffini LA, Sontheimer EJ. 2010. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat. Rev. Genet. 11:181-190.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 181-190
    • Marraffini, L.A.1    Sontheimer, E.J.2
  • 10
    • 84857097177 scopus 로고    scopus 로고
    • RNA-guided genetic silencing systems in bacteria and archaea
    • Wiedenheft B, Sternberg SH, Doudna JA. 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
  • 12
    • 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 RM, Terns MP. 2008. Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev. 22:3489-3496.
    • (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
  • 14
    • 84860433123 scopus 로고    scopus 로고
    • CRISPR interference directs strand specific spacer acquisition
    • Swarts DC, Mosterd C, van Passel MW, Brouns SJ. 2012. CRISPR interference directs strand specific spacer acquisition. PLoS One 7:e35888. http://dx.doi.org/10.1371/journal.pone.0035888.
    • (2012) PLoS One , vol.7
    • Swarts, D.C.1    Mosterd, C.2    van Passel, M.W.3    Brouns, S.J.4
  • 15
    • 84861639567 scopus 로고    scopus 로고
    • Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli
    • Yosef I, Goren MG, 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
  • 17
    • 84864425353 scopus 로고    scopus 로고
    • Erwinia amylovora CRISPR elements provide new tools for evaluating strain diversity and for microbial source tracking
    • McGhee GC, Sundin GW. 2012. Erwinia amylovora CRISPR elements provide new tools for evaluating strain diversity and for microbial source tracking. PLoS One 7:e41706. http://dx.doi.org/10.1371/ journal.pone.0041706.
    • (2012) PLoS One , vol.7
    • McGhee, G.C.1    Sundin, G.W.2
  • 18
    • 79958285933 scopus 로고    scopus 로고
    • Diversity, evolution, and functionality of clustered regularly interspaced short palindromic repeat (CRISPR) regions in the fire blight pathogen Erwinia amylovora
    • Rezzonico F, Smits TH, Duffy B. 2011. Diversity, evolution, and functionality of clustered regularly interspaced short palindromic repeat (CRISPR) regions in the fire blight pathogen Erwinia amylovora. Appl. Environ. Microbiol. 77:3819-3829.
    • (2011) Appl. Environ. Microbiol. , vol.77 , pp. 3819-3829
    • Rezzonico, F.1    Smits, T.H.2    Duffy, B.3
  • 20
    • 79956154321 scopus 로고    scopus 로고
    • CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection
    • Touchon M, Charpentier S, Clermont O, Rocha EP, Denamur E, Branger C. 2011. CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection. J. Bacteriol. 193:2460-2467.
    • (2011) J. Bacteriol. , vol.193 , pp. 2460-2467
    • Touchon, M.1    Charpentier, S.2    Clermont, O.3    Rocha, E.P.4    Denamur, E.5    Branger, C.6
  • 22
    • 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. http://dx.doi.org/10.1186/gb-2007-8-4-r61.
    • (2007) Genome Biol. , vol.8
    • Kunin, V.1    Sorek, R.2    Hugenholtz, P.3
  • 23
  • 25
    • 77949398275 scopus 로고    scopus 로고
    • Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS
    • Pul U, Wurm R, Arslan Z, Geissen R, Hofmann N, Wagner R. 2010. Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS. Mol. Microbiol. 75:1495-1512.
    • (2010) Mol. Microbiol. , vol.75 , pp. 1495-1512
    • Pul, U.1    Wurm, R.2    Arslan, Z.3    Geissen, R.4    Hofmann, N.5    Wagner, R.6
  • 28
    • 84869997748 scopus 로고    scopus 로고
    • Target motifs affecting natural immunity by a constitutive CRISPR-Cas system in Escherichia coli
    • Almendros C, Guzmán NM, Díez-Villaseñor C, García-Martínez J, Mojica FJ. 2012. Target motifs affecting natural immunity by a constitutive CRISPR-Cas system in Escherichia coli. PLoS One 7:e50797. http:// dx.doi.org/10.1371/journal.pone.0050797.
    • (2012) PLoS One , vol.7
    • Almendros, C.1    Guzmán, N.M.2    Díez-Villaseñor, C.3    García-Martínez, J.4    Mojica, F.J.5
  • 29
    • 77956624244 scopus 로고    scopus 로고
    • The on-off switch of CRISPR immunity against phages in Escherichia coli
    • Mojica FJ, Díez-Villaseñor C. 2010. The on-off switch of CRISPR immunity against phages in Escherichia coli. Mol. Microbiol. 77:1341-1345.
    • (2010) Mol. Microbiol. , vol.77 , pp. 1341-1345
    • Mojica, F.J.1    Díez-Villaseñor, C.2
  • 30
    • 0021367325 scopus 로고
    • Standard reference strains of Escherichia coli from natural populations
    • Ochman H, Selander RK. 1984. Standard reference strains of Escherichia coli from natural populations. J. Bacteriol. 157:690-693.
    • (1984) J. Bacteriol. , vol.157 , pp. 690-693
    • Ochman, H.1    Selander, R.K.2
  • 32
    • 53849112279 scopus 로고    scopus 로고
    • Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5
    • Fricke WF, Wright MS, Lindell AH, Harkins DM, Baker-Austin C, Ravel J, Stepanauskas R. 2008. Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5. J. Bacteriol. 190:6779-6794.
    • (2008) J. Bacteriol. , vol.190 , pp. 6779-6794
    • Fricke, W.F.1    Wright, M.S.2    Lindell, A.H.3    Harkins, D.M.4    Baker-Austin, C.5    Ravel, J.6    Stepanauskas, R.7
  • 35
    • 74249095519 scopus 로고    scopus 로고
    • CRISPR/Cas, the immune system of Bacteria and Archaea
    • Horvath P, Barrangou R. 2010. CRISPR/Cas, the immune system of Bacteria and Archaea. Science 327:167-170.
    • (2010) Science , vol.327 , pp. 167-170
    • Horvath, P.1    Barrangou, R.2
  • 39
    • 11944272751 scopus 로고
    • Statistical significance of the matrix correlation coefficient for comparing independent phylogenetic trees
    • Lapointe FJ, Legendre P. 1992. Statistical significance of the matrix correlation coefficient for comparing independent phylogenetic trees. Syst. Biol. 41:378-384.
    • (1992) Syst. Biol. , vol.41 , pp. 378-384
    • Lapointe, F.J.1    Legendre, P.2
  • 40
    • 78650254130 scopus 로고    scopus 로고
    • CRISPR/Cas and Cmr modules, mobility and evolution of adaptive immune systems
    • Shah SA, Garrett RA. 2011. CRISPR/Cas and Cmr modules, mobility and evolution of adaptive immune systems. Res. Microbiol. 162:27-38.
    • (2011) Res. Microbiol. , vol.162 , pp. 27-38
    • Shah, S.A.1    Garrett, R.A.2
  • 42
    • 0023650543 scopus 로고
    • The codon adaptation index--a measure of directional synonymous codon usage bias, and its potential applications
    • Sharp PM, Li WH. 1987. The codon adaptation index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15:1281-1295.
    • (1987) Nucleic Acids Res. , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 43
    • 33845874641 scopus 로고    scopus 로고
    • Predicting gene expression level from codon usage bias
    • Henry I, Sharp PM. 2007. Predicting gene expression level from codon usage bias. Mol. Biol. Evol. 24:10-12.
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 10-12
    • Henry, I.1    Sharp, P.M.2
  • 44
    • 0030994798 scopus 로고    scopus 로고
    • Amelioration of bacterial genomes: Rates of change and exchange
    • Lawrence JG, Ochman H. 1997. Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol. 44:383-397.
    • (1997) J. Mol. Evol. , vol.44 , pp. 383-397
    • Lawrence, J.G.1    Ochman, H.2
  • 45
    • 40749101805 scopus 로고    scopus 로고
    • Gene amelioration demonstrated: The journey of nascent genes in bacteria
    • Marri PR, Golding GB. 2008. Gene amelioration demonstrated: the journey of nascent genes in bacteria. Genome 51:164-168.
    • (2008) Genome , vol.51 , pp. 164-168
    • Marri, P.R.1    Golding, G.B.2
  • 46
    • 0021992145 scopus 로고
    • Stable inheritance of plasmid R1 requires two different loci
    • Gerdes K, Larsen JE, Molin S. 1985. Stable inheritance of plasmid R1 requires two different loci. J. Bacteriol. 161:292-298.
    • (1985) J. Bacteriol. , vol.161 , pp. 292-298
    • Gerdes, K.1    Larsen, J.E.2    Molin, S.3
  • 48
    • 84870521184 scopus 로고    scopus 로고
    • Genomics of Escherichia and Shigella
    • In Wiedmann M, Zhang W (ed), Springer Science & Business Media, New York, NY
    • Perna NT. 2011. Genomics of Escherichia and Shigella, p 119-139. In Wiedmann M, Zhang W (ed), Genomics of foodborne bacterial pathogens. Food microbiology and food safety. Springer Science & Business Media, New York, NY. http://dx.doi.org/10.1007/978-1-4419-7686-4_5.
    • (2011) Genomics of foodborne bacterial pathogens. Food microbiology and food safety. , pp. 119-139
    • Perna, N.T.1
  • 49
    • 53149111160 scopus 로고    scopus 로고
    • CAIcal: A combined set of tools to assess codon usage adaptation
    • Puigbò P, Bravo IG, Garcia-Vallve S. 2008. CAIcal: a combined set of tools to assess codon usage adaptation. Biol. Direct 3:38. http://dx.doi.org/ 10.1186/1745-6150-3-38.
    • (2008) Biol. Direct , vol.3 , pp. 38
    • Puigbò, P.1    Bravo, I.G.2    Garcia-Vallve, S.3
  • 50
    • 77956213914 scopus 로고    scopus 로고
    • The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella
    • Touchon M, Rocha EP. 2010. The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella. PLoS One 5:e11126. http://dx.doi.org/10.1371/journal.pone.0011126.
    • (2010) PLoS One , vol.5
    • Touchon, M.1    Rocha, E.P.2
  • 51
    • 84879032247 scopus 로고    scopus 로고
    • CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli
    • Díez-Villaseñor C, Guzmán NM, Almendros C, García-Martínez J, Mojica FJ. 2013. CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli. RNA Biol. 10:57-67.
    • (2013) RNA Biol. , vol.10 , pp. 57-67
    • Díez-Villaseñor, C.1    Guzmán, N.M.2    Almendros, C.3    García-Martínez, J.4    Mojica, F.J.5
  • 52
    • 34447546660 scopus 로고    scopus 로고
    • The distribution of fitness effects of new mutations
    • Eyre-Walker A, Keightley PD. 2007. The distribution of fitness effects of new mutations. Nat. Rev. Genet. 8:610-618.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 610-618
    • Eyre-Walker, A.1    Keightley, P.D.2
  • 53
    • 0022367323 scopus 로고
    • Structural analysis of a new GC-specific insertion element IS186
    • Chong P, Hui I, Loo T, Gillam S. 1985. Structural analysis of a new GC-specific insertion element IS186. FEBS Lett. 192:47-52.
    • (1985) FEBS Lett. , vol.192 , pp. 47-52
    • Chong, P.1    Hui, I.2    Loo, T.3    Gillam, S.4
  • 54
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0
    • Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 55
    • 0025886466 scopus 로고
    • A constant rate of spontaneous mutation in DNA-based microbes
    • Drake JW. 1991. A constant rate of spontaneous mutation in DNA-based microbes. Proc. Natl. Acad. Sci. U. S. A. 88:7160-7164.
    • (1991) Proc. Natl. Acad. Sci. U. S. A. , vol.88 , pp. 7160-7164
    • Drake, J.W.1
  • 56
    • 31144444027 scopus 로고    scopus 로고
    • Genomic divergence of Escherichia coli strains: Evidence for horizontal transfer and variation in mutation rates
    • Elena SF, Whittam TS, Winkworth CL, Riley MA, Lenski RE. 2005. Genomic divergence of Escherichia coli strains: evidence for horizontal transfer and variation in mutation rates. Int. Microbiol. 8:271-278.
    • (2005) Int. Microbiol. , vol.8 , pp. 271-278
    • Elena, S.F.1    Whittam, T.S.2    Winkworth, C.L.3    Riley, M.A.4    Lenski, R.E.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.