메뉴 건너뛰기




Volumn 14, Issue 4, 2013, Pages

CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes

Author keywords

CRISPR Cas system; Human microbiome; Mobile genetic element (MGE)

Indexed keywords

BACTERIOPHAGE; CRISPR CAS SYSTEM; FECES; HUMAN; JOINT; METAGENOMICS; MICROBIOME; PLASMID; BACTERIA; GENETICS; INTERSPERSED REPEAT; MICROBIAL GENE; MICROFLORA; PROPHAGE;

EID: 84876800205     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2013-14-4-r40     Document Type: Article
Times cited : (48)

References (76)
  • 1
    • 31344459549 scopus 로고    scopus 로고
    • Antimicrobial-resistant bacteria in the community setting
    • Furuya EY, Lowy FD: Antimicrobial-resistant bacteria in the community setting. Nat Rev Microbiol 2006, 4:36-45.
    • (2006) Nat Rev Microbiol , vol.4 , pp. 36-45
    • Furuya, E.Y.1    Lowy, F.D.2
  • 2
    • 57849137502 scopus 로고    scopus 로고
    • CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA
    • Marraffini LA, Sontheimer EJ: CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 2008, 322:1843-1845.
    • (2008) Science , vol.322 , pp. 1843-1845
    • Marraffini, L.A.1    Sontheimer, E.J.2
  • 4
    • 79952168979 scopus 로고    scopus 로고
    • Multidrug-resistant enterococci lack CRISPR-cas
    • Palmer KL, Gilmore MS: Multidrug-resistant enterococci lack CRISPR-cas. MBio 2010, 1(pii):e00227-10.
    • (2010) MBio , vol.1
    • Palmer, K.L.1    Gilmore, M.S.2
  • 5
    • 77954761569 scopus 로고    scopus 로고
    • Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow
    • Wozniak RA, Waldor MK: Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat Rev Microbiol 2010, 8:552-563.
    • (2010) Nat Rev Microbiol , vol.8 , pp. 552-563
    • Wozniak, R.A.1    Waldor, M.K.2
  • 8
    • 74249095519 scopus 로고    scopus 로고
    • CRISPR/Cas, the immune system of bacteria and archaea
    • Horvath P, Barrangou R: CRISPR/Cas, the immune system of bacteria and archaea. Science 2010, 327:167-170.
    • (2010) Science , vol.327 , pp. 167-170
    • Horvath, P.1    Barrangou, R.2
  • 11
    • 77249170201 scopus 로고    scopus 로고
    • CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea
    • Marraffini LA, Sontheimer EJ: CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet 2010, 11:181-190.
    • (2010) Nat Rev Genet , vol.11 , pp. 181-190
    • Marraffini, L.A.1    Sontheimer, E.J.2
  • 13
    • 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: CRISPR-a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol 2008, 6:181-186.
    • (2008) Nat Rev Microbiol , vol.6 , pp. 181-186
    • Sorek, R.1    Kunin, V.2    Hugenholtz, P.3
  • 15
    • 0036267740 scopus 로고    scopus 로고
    • Identification of genes that are associated with DNA repeats in prokaryotes
    • Jansen R, Embden JD, Gaastra W, Schouls LM: Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 2002, 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
  • 16
    • 84969323736 scopus 로고    scopus 로고
    • CRISPRs web server. [http://crispr.u-psud.fr/crispr/].
  • 21
    • 84874687019 scopus 로고    scopus 로고
    • Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression
    • Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA: Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 2013, 152:1173-1183.
    • (2013) Cell , vol.152 , pp. 1173-1183
    • Qi, L.S.1    Larson, M.H.2    Gilbert, L.A.3    Doudna, J.A.4    Weissman, J.S.5    Arkin, A.P.6    Lim, W.A.7
  • 24
    • 78651482834 scopus 로고    scopus 로고
    • Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time
    • Pride DT, Sun CL, Salzman J, Rao N, Loomer P, Armitage GC, Banfield JF, Relman DA: Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time. Genome Res 2011, 21:126-136.
    • (2011) Genome Res , vol.21 , pp. 126-136
    • Pride, D.T.1    Sun, C.L.2    Salzman, J.3    Rao, N.4    Loomer, P.5    Armitage, G.C.6    Banfield, J.F.7    Relman, D.A.8
  • 25
    • 84861539064 scopus 로고    scopus 로고
    • Bacterial 'immunity' against bacteriophages
    • Abedon ST: Bacterial 'immunity' against bacteriophages. Bacteriophage 2012, 2:50-54.
    • (2012) Bacteriophage , vol.2 , pp. 50-54
    • Abedon, S.T.1
  • 27
    • 0026903941 scopus 로고
    • Different bacteriophage resistance mechanisms in Streptococcus salivarius subsp. thermophilus
    • Larbi D, Decaris B, Simonet JM: Different bacteriophage resistance mechanisms in Streptococcus salivarius subsp. thermophilus. J Dairy Res 1992, 59:349-357.
    • (1992) J Dairy Res , vol.59 , pp. 349-357
    • Larbi, D.1    Decaris, B.2    Simonet, J.M.3
  • 28
    • 0034198173 scopus 로고    scopus 로고
    • Protection against bacteriophage contamination in industrial fermentation processes-investigation and applications of phage resistance mechanisms in bacteria
    • Ogata S, Eguchi T, Doi K: Protection against bacteriophage contamination in industrial fermentation processes-investigation and applications of phage resistance mechanisms in bacteria. Uirusu 2000, 50:17-26.
    • (2000) Uirusu , vol.50 , pp. 17-26
    • Ogata, S.1    Eguchi, T.2    Doi, K.3
  • 29
    • 44449133775 scopus 로고    scopus 로고
    • Virus population dynamics and acquired virus resistance in natural microbial communities
    • Andersson AF, Banfield JF: Virus population dynamics and acquired virus resistance in natural microbial communities. Science 2008, 320:1047-1050.
    • (2008) Science , vol.320 , pp. 1047-1050
    • Andersson, A.F.1    Banfield, J.F.2
  • 33
    • 84865795822 scopus 로고    scopus 로고
    • Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses
    • Pride DT, Salzman J, Relman DA: Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses. Environ Microbiol 2012, 14:2564-2576.
    • (2012) Environ Microbiol , vol.14 , pp. 2564-2576
    • Pride, D.T.1    Salzman, J.2    Relman, D.A.3
  • 34
    • 84865169354 scopus 로고    scopus 로고
    • CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome
    • Stern A, Mick E, Tirosh I, Sagy O, Sorek R: CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome. Genome Res 2012, 22:1985-1994.
    • (2012) Genome Res , vol.22 , pp. 1985-1994
    • Stern, A.1    Mick, E.2    Tirosh, I.3    Sagy, O.4    Sorek, R.5
  • 35
    • 84862276328 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • Human Microbiome Project Consortium: Structure, function and diversity of the healthy human microbiome. Nature 2012, 486:207-214.
    • (2012) Nature , vol.486 , pp. 207-214
  • 36
    • 84862286169 scopus 로고    scopus 로고
    • A framework for human microbiome research
    • Human Microbiome Project Consortium: A framework for human microbiome research. Nature 2012, 486:215-221.
    • (2012) Nature , vol.486 , pp. 215-221
  • 38
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li W, Godzik A: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 39
    • 77955085897 scopus 로고    scopus 로고
    • Self-targeting by CRISPR: gene regulation or autoimmunity?
    • Stern A, Keren L, Wurtzel O, Amitai G, Sorek R: Self-targeting by CRISPR: gene regulation or autoimmunity?. Trends Genet 2010, 26:335-340.
    • (2010) Trends Genet , vol.26 , pp. 335-340
    • Stern, A.1    Keren, L.2    Wurtzel, O.3    Amitai, G.4    Sorek, R.5
  • 40
    • 84969317703 scopus 로고    scopus 로고
    • ICTV website. [http://www.ictvdb.org].
  • 41
    • 75549086985 scopus 로고    scopus 로고
    • ACLAME: a CLAssification of Mobile genetic Elements, update 2010
    • Leplae R, Lima-Mendez G, Toussaint A: ACLAME: a CLAssification of Mobile genetic Elements, update 2010. Nucleic Acids Res 2010, 38:D57-61.
    • (2010) Nucleic Acids Res , vol.38 , pp. D57-D61
    • Leplae, R.1    Lima-Mendez, G.2    Toussaint, A.3
  • 42
    • 84969321715 scopus 로고    scopus 로고
    • DACC website. [http://www.hmpdacc.org/].
  • 43
    • 78651326786 scopus 로고    scopus 로고
    • FragGeneScan: predicting genes in short and errorprone reads
    • Rho M, Tang H, Ye Y: FragGeneScan: predicting genes in short and errorprone reads. Nucleic Acids Res 2010, 38:e191.
    • (2010) Nucleic Acids Res , vol.38
    • Rho, M.1    Tang, H.2    Ye, Y.3
  • 44
    • 61449201423 scopus 로고    scopus 로고
    • IslandViewer: an integrated interface for computational identification and visualization of genomic islands
    • Langille MG, Brinkman FS: IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 2009, 25:664-665.
    • (2009) Bioinformatics , vol.25 , pp. 664-665
    • Langille, M.G.1    Brinkman, F.S.2
  • 45
    • 50149094265 scopus 로고    scopus 로고
    • Evaluation of genomic island predictors using a comparative genomics approach
    • Langille MG, Hsiao WW, Brinkman FS: Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinformatics 2008, 9:329.
    • (2008) BMC Bioinformatics , vol.9 , pp. 329
    • Langille, M.G.1    Hsiao, W.W.2    Brinkman, F.S.3
  • 47
    • 0345237922 scopus 로고    scopus 로고
    • IslandPath: aiding detection of genomic islands in prokaryotes
    • Hsiao W, Wan I, Jones SJ, Brinkman FS: IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics 2003, 19:418-420.
    • (2003) Bioinformatics , vol.19 , pp. 418-420
    • Hsiao, W.1    Wan, I.2    Jones, S.J.3    Brinkman, F.S.4
  • 48
    • 84969326100 scopus 로고    scopus 로고
    • IslandViewer server. [http://www.pathogenomics.sfu.ca/islandviewer/genome_submit.php].
  • 49
    • 60349094186 scopus 로고    scopus 로고
    • Atypical association of DDE transposition with conjugation specifies a new family of mobile elements
    • Brochet M, Da Cunha V, Couve E, Rusniok C, Trieu-Cuot P, Glaser P: Atypical association of DDE transposition with conjugation specifies a new family of mobile elements. Mol Microbiol 2009, 71:948-959.
    • (2009) Mol Microbiol , vol.71 , pp. 948-959
    • Brochet, M.1    Da Cunha, V.2    Couve, E.3    Rusniok, C.4    Trieu-Cuot, P.5    Glaser, P.6
  • 51
    • 64049118040 scopus 로고    scopus 로고
    • Short motif sequences determine the targets of the prokaryotic CRISPR defence system
    • Mojica FJ, Diez-Villasenor C, Garcia-Martinez J, Almendros C: Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 2009, 155:733-740.
    • (2009) Microbiology , vol.155 , pp. 733-740
    • Mojica, F.J.1    Diez-Villasenor, C.2    Garcia-Martinez, J.3    Almendros, C.4
  • 52
    • 84857097177 scopus 로고    scopus 로고
    • RNA-guided genetic silencing systems in bacteria and archaea
    • Wiedenheft B, Sternberg SH, Doudna JA: RNA-guided genetic silencing systems in bacteria and archaea. Nature 2012, 482:331-338.
    • (2012) Nature , vol.482 , pp. 331-338
    • Wiedenheft, B.1    Sternberg, S.H.2    Doudna, J.A.3
  • 53
    • 34248400310 scopus 로고    scopus 로고
    • A guild of 45 CRISPRassociated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes
    • Haft DH, Selengut J, Mongodin EF, Nelson KE: A guild of 45 CRISPRassociated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol 2005, 1:e60.
    • (2005) PLoS Comput Biol , vol.1
    • Haft, D.H.1    Selengut, J.2    Mongodin, E.F.3    Nelson, K.E.4
  • 54
    • 35748974534 scopus 로고    scopus 로고
    • Evolutionary conservation of sequence and secondary structures in CRISPR repeats
    • Kunin V, Sorek R, Hugenholtz P: Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol 2007, 8:R61.
    • (2007) Genome Biol , vol.8 , pp. R61
    • Kunin, V.1    Sorek, R.2    Hugenholtz, P.3
  • 55
    • 35748931450 scopus 로고    scopus 로고
    • Identification of compositionally distinct regions in genomes using the centroid method
    • Rajan I, Aravamuthan S, Mande SS: Identification of compositionally distinct regions in genomes using the centroid method. Bioinformatics 2007, 23:2672-2677.
    • (2007) Bioinformatics , vol.23 , pp. 2672-2677
    • Rajan, I.1    Aravamuthan, S.2    Mande, S.S.3
  • 57
    • 84872607723 scopus 로고    scopus 로고
    • Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system
    • Bondy-Denomy J, Pawluk A, Maxwell KL, Davidson AR: Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature 2013, 493:429-432.
    • (2013) Nature , vol.493 , pp. 429-432
    • Bondy-Denomy, J.1    Pawluk, A.2    Maxwell, K.L.3    Davidson, A.R.4
  • 59
    • 84969313349 scopus 로고    scopus 로고
    • NCBI ftp site. [http://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?taxid=10239].
  • 62
    • 84969325481 scopus 로고    scopus 로고
    • ICEberg server. [http://http:db-mml.sjtu.edu.cn/ICEberg/].
  • 63
    • 0030854739 scopus 로고    scopus 로고
    • tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    • Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25:955-964.
    • (1997) Nucleic Acids Res , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 64
    • 84969322213 scopus 로고    scopus 로고
    • ACLAME database. [http://aclame.ulb.ac.be/].
  • 65
    • 84969313347 scopus 로고    scopus 로고
    • PFAM ftp site. [ftp://ftp.sanger.ac.uk/pub/databases/Pfam/].
  • 68
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: a multiple sequence alignment method with reduced time and space complexity
    • Edgar RC: MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004, 5:113.
    • (2004) BMC Bioinformatics , vol.5 , pp. 113
    • Edgar, R.C.1
  • 69
    • 77952988108 scopus 로고    scopus 로고
    • A new generation of homology search tools based on probabilistic inference
    • Eddy SR: A new generation of homology search tools based on probabilistic inference. Genome Inform 2009, 23:205-211.
    • (2009) Genome Inform , vol.23 , pp. 205-211
    • Eddy, S.R.1
  • 70
    • 84855167751 scopus 로고    scopus 로고
    • RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data
    • Zhao Y, Tang H, Ye Y: RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics 2012, 28:125-126.
    • (2012) Bioinformatics , vol.28 , pp. 125-126
    • Zhao, Y.1    Tang, H.2    Ye, Y.3
  • 72
    • 84969321700 scopus 로고    scopus 로고
    • Weblogo server. [http://weblogo.berkeley.edu/].
  • 74
    • 33749431828 scopus 로고    scopus 로고
    • Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences
    • Bose M, Barber RD: Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences. In Silico Biol 2006, 6:223-227.
    • (2006) In Silico Biol , vol.6 , pp. 223-227
    • Bose, M.1    Barber, R.D.2
  • 75
    • 84969317699 scopus 로고    scopus 로고
    • Prophage Finder server. [http://bioinformatics.uwp.edu/~phage/help.htm].
  • 76
    • 84969323747 scopus 로고    scopus 로고
    • PHAST server. [http://phast.wishartlab.com/].


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.