메뉴 건너뛰기




Volumn 108, Issue 30, 2011, Pages 12473-12478

Quantifying the sequence-function relation in gene silencing by bacterial small RNAs

Author keywords

Gene regulation; Noncoding RNA; Posttranscriptional control; Quantitative biology; RNA interaction

Indexed keywords

BACTERIAL RNA; CHAPERONE; COMPLEMENTARY RNA; MESSENGER RNA; RNA; SMALL RNA; SMALL RNA HFQ; SMALL RNA RYHB; UNCLASSIFIED DRUG;

EID: 79961098409     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1100432108     Document Type: Article
Times cited : (42)

References (50)
  • 1
    • 4344682527 scopus 로고    scopus 로고
    • The small RNA regulators of Escherichia coli: Roles and mechanisms
    • Gottesman S (2004) The small RNA regulators of Escherichia coli: Roles and mechanisms. Annu Rev Microbiol 58:303-328.
    • (2004) Annu Rev Microbiol , vol.58 , pp. 303-328
    • Gottesman, S.1
  • 2
    • 54149095553 scopus 로고    scopus 로고
    • Biological principles of microRNA-mediated regulation: Shared themes amid diversity
    • Flynt AS, Lai EC (2008) Biological principles of microRNA-mediated regulation: shared themes amid diversity. Nat Rev Genet 9:831-842.
    • (2008) Nat Rev Genet , vol.9 , pp. 831-842
    • Flynt, A.S.1    Lai, E.C.2
  • 3
    • 60149089144 scopus 로고    scopus 로고
    • Regulatory RNAs in bacteria
    • Waters LS, Storz G (2009) Regulatory RNAs in bacteria. Cell 136:615-628.
    • (2009) Cell , vol.136 , pp. 615-628
    • Waters, L.S.1    Storz, G.2
  • 4
    • 0031459386 scopus 로고    scopus 로고
    • A small, stable RNA induced by oxidative stress: Role as a pleiotropic regulator and antimutator
    • DOI 10.1016/S0092-8674(00)80312-8
    • Altuvia S, Weinstein-Fischer D, Zhang A, Postow L, Storz G (1997) A small, stable RNA induced by oxidative stress: Role as a pleiotropic regulator and antimutator. Cell 90:43-53. (Pubitemid 28009417)
    • (1997) Cell , vol.90 , Issue.1 , pp. 43-53
    • Altuvia, S.1    Weinstein-Fischer, D.2    Zhang, A.3    Postow, L.4    Storz, G.5
  • 7
    • 0036645490 scopus 로고    scopus 로고
    • Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon
    • DOI 10.1101/gad.231702
    • Møller T, Franch T, Udesen C, Gerdes K, Valentin-Hansen P (2002) Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon. Genes Dev 16:1696-1706. (Pubitemid 34743329)
    • (2002) Genes and Development , vol.16 , Issue.13 , pp. 1696-1706
    • Moller, T.1    Franch, T.2    Udesen, C.3    Gerdes, K.4    Valentin-Hansen, P.5
  • 8
    • 8544271637 scopus 로고    scopus 로고
    • Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system
    • DOI 10.1111/j.1365-2958.2004.04348.x
    • Vanderpool CK, Gottesman S (2004) Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system. Mol Microbiol 54:1076-1089. (Pubitemid 39491039)
    • (2004) Molecular Microbiology , vol.54 , Issue.4 , pp. 1076-1089
    • Vanderpool, C.K.1    Gottesman, S.2
  • 9
    • 3142564584 scopus 로고    scopus 로고
    • The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae
    • DOI 10.1016/j.cell.2004.06.009, PII S0092867404005732
    • Lenz DH, et al. (2004) The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell 118:69-82. (Pubitemid 38902815)
    • (2004) Cell , vol.118 , Issue.1 , pp. 69-82
    • Lenz, D.H.1    Mok, K.C.2    Lilley, B.N.3    Kulkarni, R.V.4    Wingreen, N.S.5    Bassler, B.L.6
  • 10
    • 4944236203 scopus 로고    scopus 로고
    • MicC, a second small-RNA regulator of omp protein expression in Escherichia coli
    • DOI 10.1128/JB.186.20.6689-6697.2004
    • Chen S, Zhang A, Blyn LB, Storz G (2004) MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli. J Bacteriol 186:6689-6697. (Pubitemid 39332105)
    • (2004) Journal of Bacteriology , vol.186 , Issue.20 , pp. 6689-6697
    • Chen, S.1    Zhang, A.2    Blyn, L.B.3    Storz, G.4
  • 12
    • 33751202938 scopus 로고    scopus 로고
    • Small non-coding RNAs and the bacterial outer membrane
    • DOI 10.1016/j.mib.2006.10.006, PII S1369527406001585, Growth and Development
    • Vogel J, Papenfort K (2006) Small non-coding RNAs and the bacterial outer membrane. Curr Opin Microbiol 9:605-611. (Pubitemid 44791989)
    • (2006) Current Opinion in Microbiology , vol.9 , Issue.6 , pp. 605-611
    • Vogel, J.1    Papenfort, K.2
  • 13
    • 33746553370 scopus 로고    scopus 로고
    • Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq
    • DOI 10.1111/j.1365-2958.2006.05288.x
    • Kawamoto H, Koide Y, Morita T, Aiba H (2006) Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq. Mol Microbiol 61:1013-1022. (Pubitemid 44134177)
    • (2006) Molecular Microbiology , vol.61 , Issue.4 , pp. 1013-1022
    • Kawamoto, H.1    Koide, Y.2    Morita, T.3    Aiba, H.4
  • 14
    • 34247148876 scopus 로고    scopus 로고
    • RNA antitoxins
    • DOI 10.1016/j.mib.2007.03.003, PII S1369527407000203, Cell Regulation (RNA Special Issue)
    • Gerdes K, Wagner EG (2007) RNA antitoxins. Curr Opin Microbiol 10:117-124. (Pubitemid 46590043)
    • (2007) Current Opinion in Microbiology , vol.10 , Issue.2 , pp. 117-124
    • Gerdes, K.1    Wagner, E.G.H.2
  • 15
    • 70350176597 scopus 로고    scopus 로고
    • Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA
    • Papenfort K, et al. (2009) Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA. Mol Microbiol 74:139-158.
    • (2009) Mol Microbiol , vol.74 , pp. 139-158
    • Papenfort, K.1
  • 16
    • 34548668642 scopus 로고    scopus 로고
    • Quantitative characteristics of gene regulation by small RNA
    • Levine E, Zhang Z, Kuhlman T, Hwa T (2007) Quantitative characteristics of gene regulation by small RNA. PLoS Biol 5:e229.
    • (2007) PLoS Biol , vol.5
    • Levine, E.1    Zhang, Z.2    Kuhlman, T.3    Hwa, T.4
  • 17
    • 34748871477 scopus 로고    scopus 로고
    • Regulation of gene expression by small non-coding RNAs: A quantitative view
    • Shimoni Y, et al. (2007) Regulation of gene expression by small non-coding RNAs: A quantitative view. Mol Syst Biol 3:138.
    • (2007) Mol Syst Biol , vol.3 , pp. 138
    • Shimoni, Y.1
  • 18
    • 56949096652 scopus 로고    scopus 로고
    • Small RNAs establish gene expression thresholds
    • Levine E, Hwa T (2008) Small RNAs establish gene expression thresholds. Curr Opin Microbiol 11:574-579.
    • (2008) Curr Opin Microbiol , vol.11 , pp. 574-579
    • Levine, E.1    Hwa, T.2
  • 19
    • 54049118804 scopus 로고    scopus 로고
    • A quantitative comparison of sRNA-based and protein-based gene regulation
    • Mehta P, Goyal S, Wingreen NS (2008) A quantitative comparison of sRNA-based and protein-based gene regulation. Mol Syst Biol 4:221.
    • (2008) Mol Syst Biol , vol.4 , pp. 221
    • Mehta, P.1    Goyal, S.2    Wingreen, N.S.3
  • 20
    • 67649784872 scopus 로고    scopus 로고
    • Dynamic features of gene expression control by small regulatory RNAs
    • Mitarai N, et al. (2009) Dynamic features of gene expression control by small regulatory RNAs. Proc Natl Acad Sci USA 106:10655-10659.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 10655-10659
    • Mitarai, N.1
  • 21
    • 0023894726 scopus 로고
    • Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites
    • Berg OG, von Hippel PH (1988) Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites. J Mol Biol 200:709-723.
    • (1988) J Mol Biol , vol.200 , pp. 709-723
    • Berg, O.G.1    Von Hippel, P.H.2
  • 22
    • 0022884567 scopus 로고
    • Base substitution mutants of the lac operator: In vivo and in vitro affinities for lac repressor
    • DOI 10.1016/0378-1119(86)90317-3
    • Betz JL, Sasmor HM, Buck F, Insley MY, Caruthers MH (1986) Base substitution mutants of the lac operator: In vivo and in vitro affinities for lac repressor. Gene 50:123-132. (Pubitemid 17041744)
    • (1986) Gene , vol.50 , Issue.1-3 , pp. 123-132
    • Betz, J.L.1    Sasmor, H.M.2    Buck, F.3
  • 24
    • 0037126028 scopus 로고    scopus 로고
    • Physical constraints and functional characteristics of transcription factor-DNA interaction
    • Gerland U, Moroz JD, Hwa T (2002) Physical constraints and functional characteristics of transcription factor-DNA interaction. Proc Natl Acad Sci USA 99:12015-12020.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 12015-12020
    • Gerland, U.1    Moroz, J.D.2    Hwa, T.3
  • 26
    • 77958493458 scopus 로고    scopus 로고
    • Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes
    • Sahota G, Stormo GD (2010) Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes. Bioinformatics 26:2672-2677.
    • (2010) Bioinformatics , vol.26 , pp. 2672-2677
    • Sahota, G.1    Stormo, G.D.2
  • 27
    • 0036787402 scopus 로고    scopus 로고
    • On the selection and evolution of regulatory DNA motifs
    • Gerland U, Hwa T (2002) On the selection and evolution of regulatory DNA motifs. J Mol Evol 55:386-400.
    • (2002) J Mol Ev , vol.55 , pp. 386-400
    • Gerland, U.1    Hwa, T.2
  • 29
    • 34247158257 scopus 로고    scopus 로고
    • Mechanism of RNA silencing by Hfq-binding small RNAs
    • Aiba H (2007) Mechanism of RNA silencing by Hfq-binding small RNAs. Curr Opin Microbiol 10:134-139.
    • (2007) Curr Opin Microbiol , vol.10 , pp. 134-139
    • Aiba, H.1
  • 30
    • 0036163624 scopus 로고    scopus 로고
    • The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs
    • DOI 10.1016/S1097-2765(01)00437-3
    • Zhang A, Wassarman KM, Ortega J, Steven AC, Storz G (2002) The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Mol Cell 9:11-22. (Pubitemid 34127767)
    • (2002) Molecular Cell , vol.9 , Issue.1 , pp. 11-22
    • Zhang, A.1    Wassarman, K.M.2    Ortega, J.3    Steven, A.C.4    Storz, G.5
  • 31
    • 0035104707 scopus 로고    scopus 로고
    • Hfq is necessary for regulation by the untranslated RNA DsrA
    • DOI 10.1128/JB.183.6.1997-2005.2001
    • Sledjeski DD, Whitman C, Zhang A (2001) Hfq is necessary for regulation by the untranslated RNA DsrA. J Bacteriol 183:1997-2005. (Pubitemid 32225995)
    • (2001) Journal of Bacteriology , vol.183 , Issue.6 , pp. 1997-2005
    • Sledjeski, D.D.1    Whitman, C.2    Zhang, A.3
  • 32
    • 0141860088 scopus 로고    scopus 로고
    • Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli
    • DOI 10.1101/gad.1127103
    • Massé E, Escorcia FE, Gottesman S (2003) Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes Dev 17:2374-2383. (Pubitemid 37214786)
    • (2003) Genes and Development , vol.17 , Issue.19 , pp. 2374-2383
    • Masse, E.1    Escorcia, F.E.2    Gottesman, S.3
  • 33
    • 50849105413 scopus 로고    scopus 로고
    • Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq
    • Sittka A, et al. (2008) Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet 4:e1000163.
    • (2008) PLoS Genet , vol.4
    • Sittka, A.1
  • 34
    • 0142240435 scopus 로고    scopus 로고
    • Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs
    • DOI 10.1261/rna.5850703
    • Moll I, Afonyushkin T, Vytvytska O, Kaberdin VR, Bläsi U (2003) Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs. RNA 9:1308-1314. (Pubitemid 37310861)
    • (2003) RNA , vol.9 , Issue.11 , pp. 1308-1314
    • Moll, I.1    Afonyushkin, T.2    Vytvytska, O.3    Kaberdin, V.R.4    Blasi, U.5
  • 35
    • 1542320707 scopus 로고    scopus 로고
    • Hfq, a new chaperoning role: Binding to messenger RNA determines access for small RNA regulator
    • DOI 10.1038/sj.emboj.7600058
    • Geissmann TA, Touati D (2004) Hfq, a new chaperoning role: Binding to messenger RNA determines access for small RNA regulator. EMBO J 23:396-405. (Pubitemid 38294504)
    • (2004) EMBO Journal , vol.23 , Issue.2 , pp. 396-405
    • Geissmann, T.A.1    Touati, D.2
  • 36
    • 50649097486 scopus 로고    scopus 로고
    • The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA
    • Soper TJ, Woodson SA (2008) The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA. RNA 14:1907-1917.
    • (2008) RNA , vol.14 , pp. 1907-1917
    • Soper, T.J.1    Woodson, S.A.2
  • 37
    • 57149111586 scopus 로고    scopus 로고
    • Small RNA binding to 5′ mRNA coding region inhibits translational initiation
    • Bouvier M, Sharma CM, Mika F, Nierhaus KH, Vogel J (2008) Small RNA binding to 5′ mRNA coding region inhibits translational initiation. Mol Cell 32:827-837.
    • (2008) Mol Cell , vol.32 , pp. 827-837
    • Bouvier, M.1    Sharma, C.M.2    Mika, F.3    Nierhaus, K.H.4    Vogel, J.5
  • 38
    • 68249156618 scopus 로고    scopus 로고
    • Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation
    • Pfeiffer V, Papenfort K, Lucchini S, Hinton JC, Vogel J (2009) Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat Struct Mol Biol 16:840-846.
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 840-846
    • Pfeiffer, V.1    Papenfort, K.2    Lucchini, S.3    Hinton, J.C.4    Vogel, J.5
  • 39
    • 77951519861 scopus 로고    scopus 로고
    • A minimal base-pairing region of a bacterial small RNA SgrS required for translational repression of ptsG mRNA
    • Maki K, Morita T, Otaka H, Aiba H (2010) A minimal base-pairing region of a bacterial small RNA SgrS required for translational repression of ptsG mRNA. Mol Microbiol 76:782-792.
    • (2010) Mol Microbiol , vol.76 , pp. 782-792
    • Maki, K.1    Morita, T.2    Otaka, H.3    Aiba, H.4
  • 40
    • 34247109118 scopus 로고    scopus 로고
    • Hfq structure, function and ligand binding
    • DOI 10.1016/j.mib.2007.03.015, PII S1369527407000331, Cell Regulation (RNA Special Issue)
    • Brennan RG, Link TM (2007) Hfq structure, function and ligand binding. Curr Opin Microbiol 10:125-133. (Pubitemid 46590055)
    • (2007) Current Opinion in Microbiology , vol.10 , Issue.2 , pp. 125-133
    • Brennan, R.G.1    Link, T.M.2
  • 41
    • 26444505976 scopus 로고    scopus 로고
    • Effect of RyhB small RNA on global iron use in Escherichia coli
    • DOI 10.1128/JB.187.20.6962-6971.2005
    • Massé E, Vanderpool CK, Gottesman S (2005) Effect of RyhB small RNA on global iron use in Escherichia coli. J Bacteriol 187:6962-6971. (Pubitemid 41428872)
    • (2005) Journal of Bacteriology , vol.187 , Issue.20 , pp. 6962-6971
    • Masse, E.1    Vanderpool, C.K.2    Gottesman, S.3
  • 42
    • 85011941303 scopus 로고    scopus 로고
    • Computational prediction of sRNAs and their targets in bacteria
    • Backofen R, Hess WR (2010) Computational prediction of sRNAs and their targets in bacteria. RNA Biol 7:33-42.
    • (2010) RNA Biol , vol.7 , pp. 33-42
    • Backofen, R.1    Hess, W.R.2
  • 43
    • 34548679810 scopus 로고    scopus 로고
    • Computational approaches for the discovery of bacterial small RNAs
    • DOI 10.1016/j.ymeth.2007.04.001, PII S1046202307000837
    • Kulkarni RV, Kulkarni PR (2007) Computational approaches for the discovery of bacterial small RNAs. Methods 43:131-139. (Pubitemid 47419356)
    • (2007) Methods , vol.43 , Issue.2 , pp. 131-139
    • Kulkarni, R.V.1    Kulkarni, P.R.2
  • 44
    • 77951204983 scopus 로고    scopus 로고
    • Prediction of small non-coding RNA in bacterial genomes using support vector machines
    • Chang TH, et al. (2010) Prediction of small non-coding RNA in bacterial genomes using support vector machines. Expert Syst Appl 37:5549-5557.
    • (2010) Expert Syst Appl , vol.37 , pp. 5549-5557
    • Chang, T.H.1
  • 45
    • 0032729689 scopus 로고    scopus 로고
    • Predicting oligonucleotide affinity to nucleic acid targets
    • DOI 10.1017/S1355838299991148
    • Mathews DH, Burkard ME, Freier SM, Wyatt JR, Turner DH (1999) Predicting oligonucleotide affinity to nucleic acid targets. RNA 5:1458-1469. (Pubitemid 29530490)
    • (1999) RNA , vol.5 , Issue.11 , pp. 1458-1469
    • Mathews, D.H.1    Burkard, M.E.2    Freier, S.M.3    Wyatt, J.R.4    Turner, D.H.5
  • 46
    • 0033527352 scopus 로고    scopus 로고
    • Prediction of antisense oligonucleotide binding affinity to a structured RNA target
    • DOI 10.1002/(SICI)1097-0290(19991005)65:1<1::AID-BIT1>3.0.CO;2-F
    • Walton SP, Stephanopoulos GN, Yarmush ML, Roth CM (1999) Prediction of antisense oligonucleotide binding affinity to a structured RNA target. Biotechnol Bioeng 65:1-9. (Pubitemid 29406765)
    • (1999) Biotechnology and Bioengineering , vol.65 , Issue.1 , pp. 1-9
    • Walton, S.P.1    Stephanopoulos, G.N.2    Yarmush, M.L.3    Roth, C.M.4
  • 47
    • 0036217930 scopus 로고    scopus 로고
    • Thermodynamic and kinetic characterization of antisense oligodeoxynucleotide binding to a structured mRNA
    • Walton SP, Stephanopoulos GN, Yarmush ML, Roth CM (2002) Thermodynamic and kinetic characterization of antisense oligodeoxynucleotide binding to a structured mRNA. Biophys J 82:366-377. (Pubitemid 34289809)
    • (2002) Biophysical Journal , vol.82 , Issue.1 , pp. 366-377
    • Patrick, W.S.1    Stephanopoulos, G.N.2    Yarmush, M.L.3    Roth, C.M.4
  • 48
    • 46349106221 scopus 로고    scopus 로고
    • Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design
    • DOI 10.1093/nar/gkn266
    • Lu ZJ, Mathews DH (2008) Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design. Nucleic Acids Res 36:3738-3745. (Pubitemid 351917535)
    • (2008) Nucleic Acids Research , vol.36 , Issue.11 , pp. 3738-3745
    • Lu, Z.J.1    Mathews, D.H.2
  • 49
    • 51649090185 scopus 로고    scopus 로고
    • A new Vibrio cholerae sRNA modulates colonization and affects release of outer membrane vesicles
    • Song T, et al. (2008) A new Vibrio cholerae sRNA modulates colonization and affects release of outer membrane vesicles. Mol Microbiol 70:100-111.
    • (2008) Mol Microbiol , vol.70 , pp. 100-111
    • Song, T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.