메뉴 건너뛰기




Volumn 21, Issue 5, 2015, Pages 1005-1017

SRD: A Staphylococcus regulatory RNA database

Author keywords

Bacteria; Database; RNA seq; Small regulatory RNAs; sRNA identification; sRNA targets; Staphylococcus aureus

Indexed keywords

TRANSFER RNA; BACTERIAL RNA; SMALL UNTRANSLATED RNA;

EID: 84928029323     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.049346.114     Document Type: Article
Times cited : (52)

References (60)
  • 3
    • 84928987900 scopus 로고    scopus 로고
    • HTSeq - A Python framework to work with high-throughput sequencing data
    • Anders S, Pyl PT, Huber W. 2014. HTSeq - a Python framework to work with high-throughput sequencing data. Bioinformatics 31: 166-169.
    • (2014) Bioinformatics , vol.31 , pp. 166-169
    • Anders, S.1    Pyl, P.T.2    Huber, W.3
  • 4
    • 33749316678 scopus 로고    scopus 로고
    • Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover
    • Anderson KL, Roberts C, Disz T, Vonstein V, Hwang K, Overbeek R, Olson PD, Projan SJ, Dunman PM. 2006. Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover. J Bacteriol 188: 6739-6756.
    • (2006) J Bacteriol , vol.188 , pp. 6739-6756
    • Anderson, K.L.1    Roberts, C.2    Disz, T.3    Vonstein, V.4    Hwang, K.5    Overbeek, R.6    Olson, P.D.7    Projan, S.J.8    Dunman, P.M.9
  • 5
    • 37549035397 scopus 로고    scopus 로고
    • Genome sequence of Staphylococcus aureus strain Newman and comparative analysis of staphylococcal genomes: Polymorphism and evolution of two major pathogenicity islands
    • Baba T, Bae T, Schneewind O, Takeuchi F, Hiramatsu K. 2008. Genome sequence of Staphylococcus aureus strain Newman and comparative analysis of staphylococcal genomes: polymorphism and evolution of two major pathogenicity islands. J Bacteriol 190: 300-310.
    • (2008) J Bacteriol , vol.190 , pp. 300-310
    • Baba, T.1    Bae, T.2    Schneewind, O.3    Takeuchi, F.4    Hiramatsu, K.5
  • 6
    • 77956278172 scopus 로고    scopus 로고
    • Cartography of methicillin-resistant S. aureus transcripts: Detection, orientation and temporal expression during growth phase and stress conditions
    • Beaume M, Hernandez D, Farinelli L, Deluen C, Linder P, Gaspin C, Romby P, Schrenzel J, Francois P. 2010. Cartography of methicillin-resistant S. aureus transcripts: detection, orientation and temporal expression during growth phase and stress conditions. PLoS One 5: e10725.
    • (2010) PLoS One , vol.5 , pp. e10725
    • Beaume, M.1    Hernandez, D.2    Farinelli, L.3    Deluen, C.4    Linder, P.5    Gaspin, C.6    Romby, P.7    Schrenzel, J.8    Francois, P.9
  • 8
    • 84906355091 scopus 로고    scopus 로고
    • Small regulatory RNAs from low-GC Grampositive bacteria
    • Brantl S, Brückner R. 2014. Small regulatory RNAs from low-GC Grampositive bacteria. RNA Biol 11: 443-456.
    • (2014) RNA Biol , vol.11 , pp. 443-456
    • Brantl, S.1    Brückner, R.2
  • 10
    • 57249083988 scopus 로고    scopus 로고
    • IntaRNA: Efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
    • Busch A, Richter AS, Backofen R. 2008. IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics 24: 2849-2856.
    • (2008) Bioinformatics , vol.24 , pp. 2849-2856
    • Busch, A.1    Richter, A.S.2    Backofen, R.3
  • 12
    • 78149343511 scopus 로고    scopus 로고
    • sRNATarBase: A comprehensive database of bacterial sRNA targets verified by experiments
    • Cao Y, Wu J, Liu Q, Zhao Y, Ying X, Cha L, Wang L, Li W. 2010. sRNATarBase: a comprehensive database of bacterial sRNA targets verified by experiments. RNA 16: 2051-2057.
    • (2010) RNA , vol.16 , pp. 2051-2057
    • Cao, Y.1    Wu, J.2    Liu, Q.3    Zhao, Y.4    Ying, X.5    Cha, L.6    Wang, L.7    Li, W.8
  • 13
    • 84857188863 scopus 로고    scopus 로고
    • Artemis: An integrated platform for visualization and analysis of high-throughput sequence-based experimental data
    • Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA. 2012. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 28: 464-469.
    • (2012) Bioinformatics , vol.28 , pp. 464-469
    • Carver, T.1    Harris, S.R.2    Berriman, M.3    Parkhill, J.4    McQuillan, J.A.5
  • 14
    • 77954665866 scopus 로고    scopus 로고
    • A Staphylococcus aureus small RNA is required for bacterial virulence and regulates the expression of an immune-evasion molecule
    • Chabelskaya S, Gaillot O, Felden B. 2010. A Staphylococcus aureus small RNA is required for bacterial virulence and regulates the expression of an immune-evasion molecule. PLoS Pathog 6: e1000927.
    • (2010) PLoS Pathog , vol.6 , pp. e1000927
    • Chabelskaya, S.1    Gaillot, O.2    Felden, B.3
  • 16
    • 77956193448 scopus 로고    scopus 로고
    • ProgressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement
    • Darling AE, Mau B, Perna NT. 2010. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5: e11147.
    • (2010) PLoS One , vol.5 , pp. e11147
    • Darling, A.E.1    Mau, B.2    Perna, N.T.3
  • 17
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • Edgar R, Domrachev M, Lash AE. 2002. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210.
    • (2002) Nucleic Acids Res , vol.30 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 19
    • 84904253051 scopus 로고    scopus 로고
    • Novel aspects of RNA regulation in Staphylococcus aureus
    • Fechter P, Caldelari I, Lioliou E, Romby P. 2014. Novel aspects of RNA regulation in Staphylococcus aureus. FEBS Lett 588: 2523-2529.
    • (2014) FEBS Lett , vol.588 , pp. 2523-2529
    • Fechter, P.1    Caldelari, I.2    Lioliou, E.3    Romby, P.4
  • 20
    • 79953268826 scopus 로고    scopus 로고
    • The Staphylococcus aureus RNome and its commitment to virulence
    • Felden B, Vandenesch F, Bouloc P, Romby P. 2011. The Staphylococcus aureus RNome and its commitment to virulence. PLoS Pathog 7: e1002006.
    • (2011) PLoS Pathog , vol.7 , pp. e1002006
    • Felden, B.1    Vandenesch, F.2    Bouloc, P.3    Romby, P.4
  • 23
    • 84892854028 scopus 로고    scopus 로고
    • Emerging functions for the Staphylococcus aureus RNome
    • Guillet J, Hallier M, Felden B. 2013. Emerging functions for the Staphylococcus aureus RNome. PLoS Pathog 9: e1003767.
    • (2013) PLoS Pathog , vol.9 , pp. e1003767
    • Guillet, J.1    Hallier, M.2    Felden, B.3
  • 26
    • 30744470609 scopus 로고    scopus 로고
    • Application of phylogenetic networks in evolutionary studies
    • Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23: 254-267.
    • (2006) Mol Biol Evol , vol.23 , pp. 254-267
    • Huson, D.H.1    Bryant, D.2
  • 27
    • 84904813263 scopus 로고    scopus 로고
    • Target RNA2: Identifying targets of small regulatory RNAs in bacteria
    • Kery MB, Feldman M, Livny J, Tjaden B. 2014. TargetRNA2: identifying targets of small regulatory RNAs in bacteria. Nucleic Acids Res 42: W124-W129.
    • (2014) Nucleic Acids Res , vol.42 , pp. W124-W129
    • Kery, M.B.1    Feldman, M.2    Livny, J.3    Tjaden, B.4
  • 28
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14: R36.
    • (2013) Genome Biol , vol.14 , pp. R36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6
  • 30
    • 35748954014 scopus 로고    scopus 로고
    • Prokaryotic taxonomy and phylogeny in the genomic era: Advancements and challenges ahead
    • Konstantinidis KT, Tiedje JM. 2007. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 10: 504-509.
    • (2007) Curr Opin Microbiol , vol.10 , pp. 504-509
    • Konstantinidis, K.T.1    Tiedje, J.M.2
  • 34
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589-595.
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 38
    • 64549149245 scopus 로고    scopus 로고
    • Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing
    • Liu JM, Livny J, Lawrence MS, Kimball MD, Waldor MK, Camilli A. 2009. Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing. Nucleic Acids Res 37: e46.
    • (2009) Nucleic Acids Res , vol.37 , pp. e46
    • Liu, J.M.1    Livny, J.2    Lawrence, M.S.3    Kimball, M.D.4    Waldor, M.K.5    Camilli, A.6
  • 39
    • 66449091512 scopus 로고    scopus 로고
    • Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles
    • Marchais A, Naville M, Bohn C, Bouloc P, Gautheret D. 2009. Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles. Genome Res 19: 1084-1092.
    • (2009) Genome Res , vol.19 , pp. 1084-1092
    • Marchais, A.1    Naville, M.2    Bohn, C.3    Bouloc, P.4    Gautheret, D.5
  • 40
    • 0344363037 scopus 로고
    • A unique mechanism regulating gene expression: Translational inhibition by a complementary RNA transcript (micRNA)
    • Mizuno T, Chou MY, Inouye M. 1984. A unique mechanism regulating gene expression: translational inhibition by a complementary RNA transcript (micRNA). Proc Natl Acad Sci 81: 1966-1970.
    • (1984) Proc Natl Acad Sci , vol.81 , pp. 1966-1970
    • Mizuno, T.1    Chou, M.Y.2    Inouye, M.3
  • 41
    • 84864015491 scopus 로고    scopus 로고
    • Characterization of SSR42, a novel virulence factor regulatory RNA that contributes to the pathogenesis of a Staphylococcus aureus USA300 representative
    • Morrison JM, Miller EW, Benson MA, Alonzo F III, Yoong P, Torres VJ, Hinrichs SH, Dunman PM. 2012. Characterization of SSR42, a novel virulence factor regulatory RNA that contributes to the pathogenesis of a Staphylococcus aureus USA300 representative. J Bacteriol 194: 2924-2938.
    • (2012) J Bacteriol , vol.194 , pp. 2924-2938
    • Morrison, J.M.1    Miller, E.W.2    Benson, M.A.3    Alonzo, F.4    Yoong, P.5    Torres, V.J.6    Hinrichs, S.H.7    Dunman, P.M.8
  • 43
    • 0024473736 scopus 로고
    • pT181 plasmid replication is regulated by a countertranscript-driven transcriptional attenuator
    • Novick RP, Iordanescu S, Projan SJ, Kornblum J, Edelman I. 1989. pT181 plasmid replication is regulated by a countertranscript-driven transcriptional attenuator. Cell 59: 395-404.
    • (1989) Cell , vol.59 , pp. 395-404
    • Novick, R.P.1    Iordanescu, S.2    Projan, S.J.3    Kornblum, J.4    Edelman, I.5
  • 44
    • 0027180031 scopus 로고
    • Synthesis of staphylococcal virulence factors is controlled by a regulatory RNA molecule
    • Novick RP, Ross HF, Projan SJ, Kornblum J, Kreiswirth B, Moghazeh S. 1993. Synthesis of staphylococcal virulence factors is controlled by a regulatory RNA molecule. EMBO J 12: 3967-3975.
    • (1993) EMBO J , vol.12 , pp. 3967-3975
    • Novick, R.P.1    Ross, H.F.2    Projan, S.J.3    Kornblum, J.4    Kreiswirth, B.5    Moghazeh, S.6
  • 46
    • 26444600764 scopus 로고    scopus 로고
    • Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains
    • Pichon C, Felden B. 2005. Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains. Proc Natl Acad Sci 102: 14249-14254.
    • (2005) Proc Natl Acad Sci , vol.102 , pp. 14249-14254
    • Pichon, C.1    Felden, B.2
  • 47
    • 84899628221 scopus 로고    scopus 로고
    • Dual toxic peptide-coding Staphylococcus aureus RNA under antisense regulation targets host cells and bacterial rivals unequally
    • Pinel-Marie ML, Brielle R, Felden B. 2014. Dual toxic peptide-coding Staphylococcus aureus RNA under antisense regulation targets host cells and bacterial rivals unequally. Cell Rep 7: 424-435.
    • (2014) Cell Rep , vol.7 , pp. 424-435
    • Pinel-Marie, M.L.1    Brielle, R.2    Felden, B.3
  • 50
    • 84860769484 scopus 로고    scopus 로고
    • Current knowledge on regulatory RNAs and their machineries in Staphylococcus aureus
    • Romilly C, Caldelari I, Parmentier D, Lioliou E, Romby P, Fechter P. 2012. Current knowledge on regulatory RNAs and their machineries in Staphylococcus aureus. RNA Biol 9: 402-413.
    • (2012) RNA Biol , vol.9 , pp. 402-413
    • Romilly, C.1    Caldelari, I.2    Parmentier, D.3    Lioliou, E.4    Romby, P.5    Fechter, P.6
  • 51
    • 84855464046 scopus 로고    scopus 로고
    • A cis-antisense RNA acts in trans in Staphylococcus aureus to control translation of a human cytolytic peptide
    • Sayed N, Jousselin A, Felden B. 2012. A cis-antisense RNA acts in trans in Staphylococcus aureus to control translation of a human cytolytic peptide. Nat Struct Mol Biol 19: 105-112.
    • (2012) Nat Struct Mol Biol , vol.19 , pp. 105-112
    • Sayed, N.1    Jousselin, A.2    Felden, B.3
  • 52
    • 84882623924 scopus 로고    scopus 로고
    • Advantages and limitations of genomics in prokaryotic taxonomy
    • Sentausa E, Fournier PE. 2013. Advantages and limitations of genomics in prokaryotic taxonomy. Clin Microbiol Infect 19: 790-795.
    • (2013) Clin Microbiol Infect , vol.19 , pp. 790-795
    • Sentausa, E.1    Fournier, P.E.2
  • 53
    • 0032900532 scopus 로고    scopus 로고
    • Genome phylogeny based on gene content
    • Snel B, Bork P, Huynen MA. 1999. Genome phylogeny based on gene content. Nat Genet 21: 108-110.
    • (1999) Nat Genet , vol.21 , pp. 108-110
    • Snel, B.1    Bork, P.2    Huynen, M.A.3
  • 54
    • 27144493223 scopus 로고    scopus 로고
    • Genome trees and the nature of genome evolution
    • Snel B, Huynen MA, Dutilh BE. 2005. Genome trees and the nature of genome evolution. Annu Rev Microbiol 59: 191-209.
    • (2005) Annu Rev Microbiol , vol.59 , pp. 191-209
    • Snel, B.1    Huynen, M.A.2    Dutilh, B.E.3
  • 55
    • 80053019485 scopus 로고    scopus 로고
    • Regulation by small RNAs in bacteria: Expanding frontiers
    • Storz G, Vogel J, Wassarman KM. 2011. Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 43: 880-891.
    • (2011) Mol Cell , vol.43 , pp. 880-891
    • Storz, G.1    Vogel, J.2    Wassarman, K.M.3
  • 58
    • 84894252717 scopus 로고    scopus 로고
    • ArtR, a novel sRNA of Staphylococcus aureus, regulates α-toxin expression by targeting the 5′ UTR of sarT mRNA
    • Xue T, Zhang X, Sun H, Sun B. 2014. ArtR, a novel sRNA of Staphylococcus aureus, regulates α-toxin expression by targeting the 5′ UTR of sarT mRNA. Med Microbiol Immunol 203: 1-12.
    • (2014) Med Microbiol Immunol , vol.203 , pp. 1-12
    • Xue, T.1    Zhang, X.2    Sun, H.3    Sun, B.4
  • 60
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3406-3415
    • Zuker, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.