메뉴 건너뛰기




Volumn 17, Issue 1, 2016, Pages

Comparative genomic analysis identifies structural features of CRISPR-Cas systems in Riemerella anatipestifer

Author keywords

cas gene; CRISPR Cas system; Phylogenetic analysis; Repeat sequence; Riemerella anatipestifer; Spacer sequence

Indexed keywords

ADAPTIVE IMMUNITY; AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENETICS; BACTERIOPHAGE; CAS1 GENE; CAS2 GENE; CAS9 GENE; COMPARATIVE STUDY; CRISPR CAS SYSTEM; DNA FLANKING REGION; GENE; GENE LOCATION; GENE LOCUS; GENE STRUCTURE; GENETIC ANALYSIS; HIGH THROUGHPUT SEQUENCING; NONHUMAN; OPERON; PHYLOGENY; PROKARYOTE; RIEMERELLA ANATIPESTIFER; SEQUENCE ALIGNMENT; COMPARATIVE GENOMIC HYBRIDIZATION; GENETIC VARIATION; GENETICS; GENOMICS; PATHOGENICITY; PLASMID; RIEMERELLA;

EID: 84984639985     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-016-3040-4     Document Type: Article
Times cited : (17)

References (57)
  • 1
    • 84919424243 scopus 로고    scopus 로고
    • Riemerella anatipestifer Infection. In: Swayne DE, Glisson JR, McDougald LR, Nolan LK, Suarez DL, Nair VL, editors
    • Diseases of poultry. 13th ed. Hoboken: John Wiley & Sons, Inc
    • Ruiz JA, Sandhu TS. Riemerella anatipestifer Infection. In: Swayne DE, Glisson JR, McDougald LR, Nolan LK, Suarez DL, Nair VL, editors. Diseases of poultry. 13th ed. Hoboken: John Wiley & Sons, Inc; 2013. p. 823-8.
    • (2013) , pp. 823-828
    • Ruiz, J.A.1    Sandhu, T.S.2
  • 2
    • 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(3):181-90.
    • (2010) Nat Rev Genet , vol.11 , Issue.3 , pp. 181-190
    • Marraffini, L.A.1    Sontheimer, E.J.2
  • 3
    • 84899134190 scopus 로고    scopus 로고
    • CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity
    • Barrangou R, Marraffini LA. CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity. Mol Cell. 2014;54(2):234-44.
    • (2014) Mol Cell , vol.54 , Issue.2 , pp. 234-244
    • Barrangou, R.1    Marraffini, L.A.2
  • 4
    • 84920871112 scopus 로고    scopus 로고
    • The roles of CRISPR-Cas systems in adaptive immunity and beyond
    • Barrangou R. The roles of CRISPR-Cas systems in adaptive immunity and beyond. Curr Opin Immunol. 2015;32:36-41.
    • (2015) Curr Opin Immunol , vol.32 , pp. 36-41
    • Barrangou, R.1
  • 6
    • 84877304698 scopus 로고    scopus 로고
    • Comparative genomics of defense systems in archaea and bacteria
    • Makarova KS, Wolf YI, Koonin EV. Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Res. 2013;41(8):4360-77.
    • (2013) Nucleic Acids Res , vol.41 , Issue.8 , pp. 4360-4377
    • Makarova, K.S.1    Wolf, Y.I.2    Koonin, E.V.3
  • 8
    • 84922978235 scopus 로고    scopus 로고
    • Sequences spanning the leader-repeat junction mediate CRISPR adaptation to phage in Streptococcus thermophilus
    • Wei Y, Chesne MT, Terns RM, Terns MP. Sequences spanning the leader-repeat junction mediate CRISPR adaptation to phage in Streptococcus thermophilus. Nucleic Acids Res. 2015;43(3):1749-58.
    • (2015) Nucleic Acids Res , vol.43 , Issue.3 , pp. 1749-1758
    • Wei, Y.1    Chesne, M.T.2    Terns, R.M.3    Terns, M.P.4
  • 9
    • 84861014892 scopus 로고    scopus 로고
    • Comparative genomic structures of Mycobacterium CRISPR-Cas
    • He L, Fan X, Xie J. Comparative genomic structures of Mycobacterium CRISPR-Cas. J Cell Biochem. 2012;113(7):2464-73.
    • (2012) J Cell Biochem , vol.113 , Issue.7 , pp. 2464-2473
    • He, L.1    Fan, X.2    Xie, J.3
  • 10
    • 84910022269 scopus 로고    scopus 로고
    • Whole genome sequencing reveals a novel CRISPR system in industrial Clostridium acetobutylicum
    • Peng L, Pei J, Hao P, Yuan G, Lin L, Huang R. Whole genome sequencing reveals a novel CRISPR system in industrial Clostridium acetobutylicum. J Ind Microbiol Biotechnol. 2014;41(11):1677-85.
    • (2014) J Ind Microbiol Biotechnol , vol.41 , Issue.11 , pp. 1677-1685
    • Peng, L.1    Pei, J.2    Hao, P.3    Yuan, G.4    Lin, L.5    Huang, R.6
  • 11
    • 77949398275 scopus 로고    scopus 로고
    • Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS
    • Pul U, Wurm RZ, Geissen R, Hofmann N, Wagner R. Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS. Mol Microbiol. 2010;75(6):1495-512.
    • (2010) Mol Microbiol , vol.75 , Issue.6 , pp. 1495-1512
    • Pul, U.1    Wurm, R.Z.2    Geissen, R.3    Hofmann, N.4    Wagner, R.5
  • 12
    • 23844505202 scopus 로고    scopus 로고
    • Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin
    • Bolotin A, Quinquis B, Sorokin A, Ehrlich SD. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology. 2005;151(Pt 8):2551-61.
    • (2005) Microbiology , vol.151 , pp. 2551-2561
    • Bolotin, A.1    Quinquis, B.2    Sorokin, A.3    Ehrlich, S.D.4
  • 13
    • 16444385662 scopus 로고    scopus 로고
    • Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements
    • Mojica FJM, Díez-Villaseñor C, García-Martínez J, Soria E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol. 2005;60(2):174-82.
    • (2005) J Mol Evol , vol.60 , Issue.2 , pp. 174-182
    • Mojica, F.J.M.1    Díez-Villaseñor, C.2    García-Martínez, J.3    Soria, E.4
  • 14
    • 84964370937 scopus 로고    scopus 로고
    • The bacteriophage carrier state of campylobacter jejuni features changes in host Non-coding RNAs and the acquisition of New host-derived CRISPR spacer sequences
    • Hooton SP, Brathwaite KJ, Connerton IF. The bacteriophage carrier state of campylobacter jejuni features changes in host Non-coding RNAs and the acquisition of New host-derived CRISPR spacer sequences. Front Microbiol. 2016;7:355.
    • (2016) Front Microbiol , vol.7 , pp. 355
    • Hooton, S.P.1    Brathwaite, K.J.2    Connerton, I.F.3
  • 15
    • 84942279889 scopus 로고    scopus 로고
    • Regulation of the Type I-F CRISPR-Cas system by CRP-cAMP and GalM controls spacer acquisition and interference
    • Patterson AG, Chang JT, Taylor C, Fineran PC. Regulation of the Type I-F CRISPR-Cas system by CRP-cAMP and GalM controls spacer acquisition and interference. Nucleic Acids Res. 2015;43(12):6038-48.
    • (2015) Nucleic Acids Res , vol.43 , Issue.12 , pp. 6038-6048
    • Patterson, A.G.1    Chang, J.T.2    Taylor, C.3    Fineran, P.C.4
  • 16
    • 84945533699 scopus 로고    scopus 로고
    • Campylobacter jejuni acquire new host-derived CRISPR spacers when in association with bacteriophages harboring a CRISPR-like Cas4 protein
    • Hooton SP, Connerton IF. Campylobacter jejuni acquire new host-derived CRISPR spacers when in association with bacteriophages harboring a CRISPR-like Cas4 protein. Front Microbiol. 2014;5:744.
    • (2014) Front Microbiol , vol.5 , pp. 744
    • Hooton, S.P.1    Connerton, I.F.2
  • 17
    • 84861639567 scopus 로고    scopus 로고
    • Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli
    • Yosef I, Goren MG, Qimron U. Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res. 2012;40(12):5569-76.
    • (2012) Nucleic Acids Res , vol.40 , Issue.12 , pp. 5569-5576
    • Yosef, I.1    Goren, M.G.2    Qimron, U.3
  • 19
    • 79551694059 scopus 로고    scopus 로고
    • Interaction of the Cas6 riboendonuclease with CRISPR RNAs: recognition and cleavage
    • Wang R, Preamplume G, Terns MP, Terns RM, Li H. Interaction of the Cas6 riboendonuclease with CRISPR RNAs: recognition and cleavage. Structure. 2011;19(2):257-64.
    • (2011) Structure , vol.19 , Issue.2 , pp. 257-264
    • Wang, R.1    Preamplume, G.2    Terns, M.P.3    Terns, R.M.4    Li, H.5
  • 22
    • 84864085433 scopus 로고    scopus 로고
    • Cleavage of Phage DNA by the Streptococcus thermophilus CRISPR3-Cas System
    • Magadán AH, Dupuis M, Villion M, Moineau S. Cleavage of Phage DNA by the Streptococcus thermophilus CRISPR3-Cas System. PLoS One. 2012;7(7), e40913.
    • (2012) PLoS One , vol.7 , Issue.7
    • Magadán, A.H.1    Dupuis, M.2    Villion, M.3    Moineau, S.4
  • 23
    • 84865070369 scopus 로고    scopus 로고
    • A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity
    • Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337(6096):816-21.
    • (2012) Science , vol.337 , Issue.6096 , pp. 816-821
    • Jinek, M.1    Chylinski, K.2    Fonfara, I.3    Hauer, M.4    Doudna, J.A.5    Charpentier, E.6
  • 24
  • 25
    • 84878211288 scopus 로고    scopus 로고
    • The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems
    • Chylinski K, Le Rhun A, Charpentier E. The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems. RNA Biol. 2013;10(5):726-37.
    • (2013) RNA Biol , vol.10 , Issue.5 , pp. 726-737
    • Chylinski, K.1    Rhun, A.2    Charpentier, E.3
  • 27
    • 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(Pt 3):733-40.
    • (2009) Microbiology , vol.155 , pp. 733-740
    • Mojica, F.J.1    Diez-Villasenor, C.2    Garcia-Martinez, J.3    Almendros, C.4
  • 28
    • 84879026965 scopus 로고    scopus 로고
    • Protospacer recognition motifs: mixed identities and functional diversity
    • Shah SA, Erdmann S, Mojica FJ, Garrett RA. Protospacer recognition motifs: mixed identities and functional diversity. RNA Biol. 2013;10(10):891-9.
    • (2013) RNA Biol , vol.10 , Issue.10 , pp. 891-899
    • Shah, S.A.1    Erdmann, S.2    Mojica, F.J.3    Garrett, R.A.4
  • 29
    • 75749118174 scopus 로고    scopus 로고
    • Self versus non-self discrimination during CRISPR RNA-directed immunity
    • Marraffini LA, Sontheimer EJ. Self versus non-self discrimination during CRISPR RNA-directed immunity. Nature. 2010;463(7280):568-71.
    • (2010) Nature , vol.463 , Issue.7280 , pp. 568-571
    • Marraffini, L.A.1    Sontheimer, E.J.2
  • 32
    • 84887971081 scopus 로고    scopus 로고
    • The basic building blocks and evolution of CRISPR-CAS systems
    • Makarova KS, Wolf YI, Koonin EV. The basic building blocks and evolution of CRISPR-CAS systems. Biochem Soc Trans. 2013;41(6):1392-400.
    • (2013) Biochem Soc Trans , vol.41 , Issue.6 , pp. 1392-1400
    • Makarova, K.S.1    Wolf, Y.I.2    Koonin, E.V.3
  • 33
    • 0025323593 scopus 로고
    • The National Center for Biotechnology Information
    • Benson D, Boguski M, Lipman D, Ostell J. The National Center for Biotechnology Information. Genomics. 1990;6(2):389-91.
    • (1990) Genomics , vol.6 , Issue.2 , pp. 389-391
    • Benson, D.1    Boguski, M.2    Lipman, D.3    Ostell, J.4
  • 34
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18(5):821-9.
    • (2008) Genome Res , vol.18 , Issue.5 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 35
    • 84969673075 scopus 로고    scopus 로고
    • BPGA- an ultra-fast pan-genome analysis pipeline
    • Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep. 2016;6.
    • Sci Rep , vol.2016 , pp. 6
    • Chaudhari, N.M.1    Gupta, V.K.2    Dutta, C.3
  • 36
    • 34250662138 scopus 로고    scopus 로고
    • The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
    • Grissa I, Vergnaud G, Pourcel C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics. 2007;8:172.
    • (2007) BMC Bioinformatics , vol.8 , pp. 172
    • Grissa, I.1    Vergnaud, G.2    Pourcel, C.3
  • 39
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31(13):3406-15.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3406-3415
    • Zuker, M.1
  • 40
    • 84879014174 scopus 로고    scopus 로고
    • CRISPRTarget: bioinformatic prediction and analysis of crRNA targets
    • Biswas A, Gagnon JN, Brouns SJ, Fineran PC, Brown CM. CRISPRTarget: bioinformatic prediction and analysis of crRNA targets. RNA Biol. 2013;10(5):817-27.
    • (2013) RNA Biol , vol.10 , Issue.5 , pp. 817-827
    • Biswas, A.1    Gagnon, J.N.2    Brouns, S.J.3    Fineran, P.C.4    Brown, C.M.5
  • 41
    • 54049108449 scopus 로고    scopus 로고
    • Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics 2002, Chapter 2:Unit
    • Thompson JD, Gibson TJ, Higgins DG: Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics 2002, Chapter 2:Unit 2.3.
    • Thompson, J.D.1    Gibson, T.J.2    Higgins, D.G.3
  • 42
    • 0034740227 scopus 로고    scopus 로고
    • Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome
    • Reese MG. Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput Chem. 2001;26(1):51-6.
    • (2001) Comput Chem , vol.26 , Issue.1 , pp. 51-56
    • Reese, M.G.1
  • 44
    • 45949109669 scopus 로고    scopus 로고
    • MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences
    • Kumar S, Nei M, Dudley J, Tamura K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform. 2008;9(4):299-306.
    • (2008) Brief Bioinform , vol.9 , Issue.4 , pp. 299-306
    • Kumar, S.1    Nei, M.2    Dudley, J.3    Tamura, K.4
  • 45
    • 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(4):R61.
    • (2007) Genome Biol , vol.8 , Issue.4 , pp. R61
    • Kunin, V.1    Sorek, R.2    Hugenholtz, P.3
  • 46
    • 33744941078 scopus 로고    scopus 로고
    • The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes
    • Godde JS, Bickerton A. The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes. J Mol Evol. 2006;62(6):718-29.
    • (2006) J Mol Evol , vol.62 , Issue.6 , pp. 718-729
    • Godde, J.S.1    Bickerton, A.2
  • 48
  • 49
    • 84879032247 scopus 로고    scopus 로고
    • CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli
    • Diez-Villasenor C, Guzman NM, Almendros C, Garcia-Martinez J, Mojica FJ. CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli. RNA Biol. 2013;10(5):792-802.
    • (2013) RNA Biol , vol.10 , Issue.5 , pp. 792-802
    • Diez-Villasenor, C.1    Guzman, N.M.2    Almendros, C.3    Garcia-Martinez, J.4    Mojica, F.J.5
  • 54
    • 84879016248 scopus 로고    scopus 로고
    • crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus
    • Karvelis T, Gasiunas G, Miksys A, Barrangou R, Horvath P, Siksnys V. crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus. RNA Biol. 2013;10(5):841-51.
    • (2013) RNA Biol , vol.10 , Issue.5 , pp. 841-851
    • Karvelis, T.1    Gasiunas, G.2    Miksys, A.3    Barrangou, R.4    Horvath, P.5    Siksnys, V.6
  • 56
    • 84863662334 scopus 로고    scopus 로고
    • Complete genomic sequence of the virulent bacteriophage RAP44 of Riemerella anatipestifer
    • Cheng LF, Chen HM, Zheng T, Fu GH, Shi SH, Wan CH, Huang Y. Complete genomic sequence of the virulent bacteriophage RAP44 of Riemerella anatipestifer. Avian Dis. 2012;56(2):321-7.
    • (2012) Avian Dis , vol.56 , Issue.2 , pp. 321-327
    • Cheng, L.F.1    Chen, H.M.2    Zheng, T.3    Fu, G.H.4    Shi, S.H.5    Wan, C.H.6    Huang, Y.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.