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Volumn 110, Issue 37, 2013, Pages

Comparative genomics boosts target prediction for bacterial small RNAs

Author keywords

E. coli; Regulatory RNA; RNA RNA interaction

Indexed keywords

AMINO ACID; BACTERIAL RNA; IRON BINDING PROTEIN; MESSENGER RNA; SUCCINATE DEHYDROGENASE; TRANSCRIPTION FACTOR; TRANSCRIPTOME; TRANSFER RNA;

EID: 84883772639     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1303248110     Document Type: Article
Times cited : (183)

References (52)
  • 1
    • 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(6):880-891.
    • (2011) Mol Cell , vol.43 , Issue.6 , pp. 880-891
    • Storz, G.1    Vogel, J.2    Wassarman, K.M.3
  • 2
    • 84863924309 scopus 로고    scopus 로고
    • Bacterial small RNA regulators: Versatile roles and rapidly evolving variations
    • Gottesman S, Storz G (2011) Bacterial small RNA regulators: Versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 3(12):a003798.
    • (2011) Cold Spring Harb Perspect Biol , vol.3 , Issue.12
    • Gottesman, S.1    Storz, G.2
  • 3
    • 77958028354 scopus 로고    scopus 로고
    • Regulatory RNA in bacterial pathogens
    • Papenfort K, Vogel J (2010) Regulatory RNA in bacterial pathogens. Cell Host Microbe 8(1):116-127.
    • (2010) Cell Host Microbe , vol.8 , Issue.1 , pp. 116-127
    • Papenfort, K.1    Vogel, J.2
  • 4
    • 80051929071 scopus 로고    scopus 로고
    • Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA
    • Sharma CM, et al. (2011) Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA. Mol Microbiol 81(5):1144-1165.
    • (2011) Mol Microbiol , vol.81 , Issue.5 , pp. 1144-1165
    • Sharma, C.M.1
  • 5
    • 79961239912 scopus 로고    scopus 로고
    • Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon
    • Gogol EB, Rhodius VA, Papenfort K, Vogel J, Gross CA (2011) Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon. Proc Natl Acad Sci USA 108(31):12875-12880.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.31 , pp. 12875-12880
    • Gogol, E.B.1    Rhodius, V.A.2    Papenfort, K.3    Vogel, J.4    Gross, C.A.5
  • 6
    • 79251559383 scopus 로고    scopus 로고
    • The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli
    • Beisel CL, Storz G (2011) The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli. Mol Cell 41(3):286-297.
    • (2011) Mol Cell , vol.41 , Issue.3 , pp. 286-297
    • Beisel, C.L.1    Storz, G.2
  • 7
    • 77949425194 scopus 로고    scopus 로고
    • The primary transcriptome of the major human pathogen Helicobacter pylori
    • Sharma CM, et al. (2010) The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464(7286):250-255.
    • (2010) Nature , vol.464 , Issue.7286 , pp. 250-255
    • Sharma, C.M.1
  • 8
    • 79952174199 scopus 로고    scopus 로고
    • An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803
    • Mitschke J, et al. (2011) An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proc Natl Acad Sci USA 108(5):2124-2129.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.5 , pp. 2124-2129
    • Mitschke, J.1
  • 9
    • 78650532236 scopus 로고    scopus 로고
    • Evidence for an autonomous 5′ target recognition domain in an Hfq-associated small RNA
    • Papenfort K, Bouvier M, Mika F, Sharma CM, Vogel J (2010) Evidence for an autonomous 5′ target recognition domain in an Hfq-associated small RNA. Proc Natl Acad Sci USA 107(47):20435-20440.
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.47 , pp. 20435-20440
    • Papenfort, K.1    Bouvier, M.2    Mika, F.3    Sharma, C.M.4    Vogel, J.5
  • 11
    • 79959937873 scopus 로고    scopus 로고
    • RNApredator: Fast accessibility-based prediction of sRNA targets
    • Eggenhofer F, Tafer H, Stadler PF, Hofacker IL (2011) RNApredator: Fast accessibility-based prediction of sRNA targets. Nucleic Acids Res 39(Web Server issue):W149-W154.
    • (2011) Nucleic Acids Res , vol.39 , Issue.WEB SERVER ISSUE
    • Eggenhofer, F.1    Tafer, H.2    Stadler, P.F.3    Hofacker, I.L.4
  • 12
    • 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(24):2849-2856.
    • (2008) Bioinformatics , vol.24 , Issue.24 , pp. 2849-2856
    • Busch, A.1    Richter, A.S.2    Backofen, R.3
  • 13
    • 4644237189 scopus 로고    scopus 로고
    • Fast and effective prediction of microRNA/target duplexes
    • DOI 10.1261/rna.5248604
    • Rehmsmeier M, Steffen P, Höchsmann M, Giegerich R (2004) Fast and effective prediction of microRNA/target duplexes. RNA 10(10):1507-1517. (Pubitemid 39288185)
    • (2004) RNA , vol.10 , Issue.10 , pp. 1507-1517
    • Rehmsmeier, M.1    Steffen, P.2    Hochsmann, M.3    Giegerich, R.4
  • 14
    • 79961098409 scopus 로고    scopus 로고
    • Quantifying the sequence-function relation in gene silencing by bacterial small RNAs
    • Hao Y, et al. (2011) Quantifying the sequence-function relation in gene silencing by bacterial small RNAs. Proc Natl Acad Sci USA 108(30):12473-12478.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.30 , pp. 12473-12478
    • Hao, Y.1
  • 15
    • 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(1):33-42.
    • (2010) RNA Biol , vol.7 , Issue.1 , pp. 33-42
    • Backofen, R.1    Hess, W.R.2
  • 16
    • 84865302975 scopus 로고    scopus 로고
    • Accessibility and conservation: General features of bacterial small RNA-mRNA interactions?
    • Richter AS, Backofen R (2012) Accessibility and conservation: General features of bacterial small RNA-mRNA interactions? RNA Biol 9(7):954-965.
    • (2012) RNA Biol , vol.9 , Issue.7 , pp. 954-965
    • Richter, A.S.1    Backofen, R.2
  • 17
    • 84859915108 scopus 로고    scopus 로고
    • Multiple factors dictate target selection by Hfq-binding small RNAs
    • Beisel CL, Updegrove TB, Janson BJ, Storz G (2012) Multiple factors dictate target selection by Hfq-binding small RNAs. EMBO J 31(8):1961-1974.
    • (2012) EMBO J , vol.31 , Issue.8 , pp. 1961-1974
    • Beisel, C.L.1    Updegrove, T.B.2    Janson, B.J.3    Storz, G.4
  • 18
    • 58649085492 scopus 로고    scopus 로고
    • The Crp-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior
    • De Lay N, Gottesman S (2009) The Crp-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior. J Bacteriol 191(2):461-476.
    • (2009) J Bacteriol , vol.191 , Issue.2 , pp. 461-476
    • De Lay, N.1    Gottesman, S.2
  • 19
    • 42549165769 scopus 로고    scopus 로고
    • Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP-dependent riboregulator of OmpX synthesis
    • DOI 10.1111/j.1365-2958.2008.06189.x
    • Papenfort K, et al. (2008) Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP-dependent riboregulator of OmpX synthesis. Mol Microbiol 68(4):890-906. (Pubitemid 351581055)
    • (2008) Molecular Microbiology , vol.68 , Issue.4 , pp. 890-906
    • Papenfort, K.1    Pfeiffer, V.2    Lucchini, S.3    Sonawane, A.4    Hinton, J.C.D.5    Vogel, J.6
  • 20
    • 77349101808 scopus 로고    scopus 로고
    • Translational regulation of gene expression by an anaerobically induced small non-coding RNA in Escherichia coli
    • Boysen A, Møller-Jensen J, Kallipolitis B, Valentin-Hansen P, Overgaard M (2010) Translational regulation of gene expression by an anaerobically induced small non-coding RNA in Escherichia coli. J Biol Chem 285(14):10690-10702.
    • (2010) J Biol Chem , vol.285 , Issue.14 , pp. 10690-10702
    • Boysen, A.1    Møller-Jensen, J.2    Kallipolitis, B.3    Valentin-Hansen, P.4    Overgaard, M.5
  • 21
    • 77349104885 scopus 로고    scopus 로고
    • Reprogramming of anaerobic metabolism by the FnrS small RNA
    • Durand S, Storz G (2010) Reprogramming of anaerobic metabolism by the FnrS small RNA. Mol Microbiol 75(5):1215-1231.
    • (2010) Mol Microbiol , vol.75 , Issue.5 , pp. 1215-1231
    • Durand, S.1    Storz, G.2
  • 22
    • 84859988230 scopus 로고    scopus 로고
    • Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA
    • Corcoran CP, et al. (2012) Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA. Mol Microbiol 84(3):428-445.
    • (2012) Mol Microbiol , vol.84 , Issue.3 , pp. 428-445
    • Corcoran, C.P.1
  • 23
    • 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(20):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
  • 24
    • 84859451156 scopus 로고    scopus 로고
    • The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair
    • Papenfort K, Podkaminski D, Hinton JCD, Vogel J (2012) The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair. Proc Natl Acad Sci USA 109(13):E757-E764.
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.13
    • Papenfort, K.1    Podkaminski, D.2    Hinton, J.C.D.3    Vogel, J.4
  • 25
    • 33846034308 scopus 로고    scopus 로고
    • MBGD: A platform for microbial comparative genomics based on the automated construction of orthologous groups
    • Uchiyama I (2007) MBGD: A platform for microbial comparative genomics based on the automated construction of orthologous groups. Nucleic Acids Res 35(Database issue):D343-D346.
    • (2007) Nucleic Acids Res , vol.35 , Issue.DATABASE ISSUE
    • Uchiyama, I.1
  • 26
    • 0033448847 scopus 로고    scopus 로고
    • A note on combining dependent tests of signi fi cance
    • Hartung J (1999) A note on combining dependent tests of signi fi cance. Biom J 41:849-855.
    • (1999) Biom J , vol.41 , pp. 849-855
    • Hartung, J.1
  • 28
    • 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(6):827-837.
    • (2008) Mol Cell , vol.32 , Issue.6 , pp. 827-837
    • Bouvier, M.1    Sharma, C.M.2    Mika, F.3    Nierhaus, K.H.4    Vogel, J.5
  • 30
    • 84861442326 scopus 로고    scopus 로고
    • Regulating iron storage and metabolism with RNA: An overview of posttranscriptional controls of intracellular iron homeostasis
    • Salvail H, Massé E (2012) Regulating iron storage and metabolism with RNA: An overview of posttranscriptional controls of intracellular iron homeostasis. Wiley Interdiscip Rev RNA 3(1):26-36.
    • (2012) Wiley Interdiscip Rev RNA , vol.3 , Issue.1 , pp. 26-36
    • Salvail, H.1    Massé, E.2
  • 31
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4(1):44-57.
    • (2009) Nat Protoc , vol.4 , Issue.1 , pp. 44-57
    • Huang, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 32
    • 84858862917 scopus 로고    scopus 로고
    • Small regulatory RNAs control the multi-cellular adhesive lifestyle of Escherichia coli
    • Jørgensen MG, et al. (2012) Small regulatory RNAs control the multi-cellular adhesive lifestyle of Escherichia coli. Mol Microbiol 84(1):36-50.
    • (2012) Mol Microbiol , vol.84 , Issue.1 , pp. 36-50
    • Jørgensen, M.G.1
  • 33
    • 84858866772 scopus 로고    scopus 로고
    • A small RNA that regulates motility and biofilm formation in response to changes in nutrient availability in Escherichia coli
    • Thomason MK, Fontaine F, De Lay N, Storz G (2012) A small RNA that regulates motility and biofilm formation in response to changes in nutrient availability in Escherichia coli. Mol Microbiol 84(1):17-35.
    • (2012) Mol Microbiol , vol.84 , Issue.1 , pp. 17-35
    • Thomason, M.K.1    Fontaine, F.2    De Lay, N.3    Storz, G.4
  • 34
    • 77953120292 scopus 로고    scopus 로고
    • Two antisense RNAs target the transcriptional regulator CsgD to inhibit curli synthesis
    • Holmqvist E, et al. (2010) Two antisense RNAs target the transcriptional regulator CsgD to inhibit curli synthesis. EMBO J 29(11):1840-1850.
    • (2010) EMBO J , vol.29 , Issue.11 , pp. 1840-1850
    • Holmqvist, E.1
  • 35
    • 84858863122 scopus 로고    scopus 로고
    • Targeting of csgD by the small regulatory RNA RprA links stationary phase, biofilm formation and cell envelope stress in Escherichia coli
    • Mika F, et al. (2012) Targeting of csgD by the small regulatory RNA RprA links stationary phase, biofilm formation and cell envelope stress in Escherichia coli. Mol Microbiol 84(1):51-65.
    • (2012) Mol Microbiol , vol.84 , Issue.1 , pp. 51-65
    • Mika, F.1
  • 36
    • 84859996025 scopus 로고    scopus 로고
    • A mixed double negative feedback loop between the sRNA MicF and the global regulator Lrp
    • Holmqvist E, Unoson C, Reimegård J, Wagner EGH (2012) A mixed double negative feedback loop between the sRNA MicF and the global regulator Lrp. Mol Microbiol 84(3):414-427.
    • (2012) Mol Microbiol , vol.84 , Issue.3 , pp. 414-427
    • Holmqvist, E.1    Unoson, C.2    Reimegård, J.3    Wagner, E.G.H.4
  • 37
    • 84859365433 scopus 로고    scopus 로고
    • Noncanonical repression of translation initiation through small RNA recruitment of the RNA chaperone Hfq
    • Desnoyers G, Massé E (2012) Noncanonical repression of translation initiation through small RNA recruitment of the RNA chaperone Hfq. Genes Dev 26(7):726-739.
    • (2012) Genes Dev , vol.26 , Issue.7 , pp. 726-739
    • Desnoyers, G.1    Massé, E.2
  • 38
    • 67349095027 scopus 로고    scopus 로고
    • Small RNA-induced differential degradation of the polycistronic mRNA iscRSUA
    • Desnoyers G, Morissette A, Prévost K, Massé E (2009) Small RNA-induced differential degradation of the polycistronic mRNA iscRSUA. EMBO J 28(11):1551-1561.
    • (2009) EMBO J , vol.28 , Issue.11 , pp. 1551-1561
    • Desnoyers, G.1    Morissette, A.2    Prévost, K.3    Massé, E.4
  • 39
    • 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 JCD, Vogel J (2009) Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat Struct Mol Biol 16(8):840-846.
    • (2009) Nat Struct Mol Biol , vol.16 , Issue.8 , pp. 840-846
    • Pfeiffer, V.1    Papenfort, K.2    Lucchini, S.3    Hinton, J.C.D.4    Vogel, J.5
  • 40
    • 84866788439 scopus 로고    scopus 로고
    • The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E
    • Bandyra KJ, et al. (2012) The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E. Mol Cell 47(6):943-953.
    • (2012) Mol Cell , vol.47 , Issue.6 , pp. 943-953
    • Bandyra, K.J.1
  • 41
    • 84883147219 scopus 로고    scopus 로고
    • Iron deprivation in Synechocystis: Inference of pathways, non-coding RNAs, and regulatory elements from comprehensive expression profiling
    • Hernández-Prieto MA, et al. (2012) Iron deprivation in Synechocystis: Inference of pathways, non-coding RNAs, and regulatory elements from comprehensive expression profiling. G3 (Bethesda) 2(12):1475-1495.
    • (2012) G3 (Bethesda) , vol.2 , Issue.12 , pp. 1475-1495
    • Hernández-Prieto, M.A.1
  • 43
    • 77956879952 scopus 로고    scopus 로고
    • Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA
    • Mandin P, Gottesman S (2010) Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA. EMBO J 29(18):3094-3107.
    • (2010) EMBO J , vol.29 , Issue.18 , pp. 3094-3107
    • Mandin, P.1    Gottesman, S.2
  • 44
    • 77957252762 scopus 로고    scopus 로고
    • CspC regulates rpoS transcript levels and complements hfq deletions
    • Cohen-Or I, Shenhar Y, Biran D, Ron EZ (2010) CspC regulates rpoS transcript levels and complements hfq deletions. Res Microbiol 161(8):694-700.
    • (2010) Res Microbiol , vol.161 , Issue.8 , pp. 694-700
    • Cohen-Or, I.1    Shenhar, Y.2    Biran, D.3    Ron, E.Z.4
  • 45
    • 78651299341 scopus 로고    scopus 로고
    • RegulonDB version 7.0: Transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)
    • Gama-Castro S, et al. (2011) RegulonDB version 7.0: Transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic Acids Res 39(Database issue):D98-D105.
    • (2011) Nucleic Acids Res , vol.39 , Issue.DATABASE ISSUE
    • Gama-Castro, S.1
  • 46
    • 78650887552 scopus 로고    scopus 로고
    • Promoter discrimination at class I MarA regulon promoters mediated by glutamic acid 89 of the MarA transcriptional activator of Escherichia coli
    • Martin RG, Rosner JL (2011) Promoter discrimination at class I MarA regulon promoters mediated by glutamic acid 89 of the MarA transcriptional activator of Escherichia coli. J Bacteriol 193(2):506-515.
    • (2011) J Bacteriol , vol.193 , Issue.2 , pp. 506-515
    • Martin, R.G.1    Rosner, J.L.2
  • 48
    • 77956128431 scopus 로고    scopus 로고
    • NagZ inactivation prevents and reverts β-lactam resistance, driven by AmpD and PBP 4 mutations, in Pseudomonas aeruginosa
    • Zamorano L, et al. (2010) NagZ inactivation prevents and reverts β-lactam resistance, driven by AmpD and PBP 4 mutations, in Pseudomonas aeruginosa. Antimicrob Agents Chemother 54(9):3557-3563.
    • (2010) Antimicrob Agents Chemother , vol.54 , Issue.9 , pp. 3557-3563
    • Zamorano, L.1
  • 49
    • 84855895055 scopus 로고    scopus 로고
    • A-type carrier protein ErpA is essential for formation of an active formate-nitrate respiratory pathway in Escherichia coli K-12
    • Pinske C, Sawers RG (2012) A-type carrier protein ErpA is essential for formation of an active formate-nitrate respiratory pathway in Escherichia coli K-12. J Bacteriol 194(2):346-353.
    • (2012) J Bacteriol , vol.194 , Issue.2 , pp. 346-353
    • Pinske, C.1    Sawers, R.G.2
  • 50
    • 84876234571 scopus 로고    scopus 로고
    • Small RNA-mediated activation of sugar phosphatase mRNA regulates glucose homeostasis
    • Papenfort K, Sun Y, Miyakoshi M, Vanderpool CK, Vogel J (2013) Small RNA-mediated activation of sugar phosphatase mRNA regulates glucose homeostasis. Cell 153(2):426-437.
    • (2013) Cell , vol.153 , Issue.2 , pp. 426-437
    • Papenfort, K.1    Sun, Y.2    Miyakoshi, M.3    Vanderpool, C.K.4    Vogel, J.5
  • 51
    • 38449101120 scopus 로고    scopus 로고
    • Integration of biological networks and gene expression data using Cytoscape
    • Cline MS, et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2(10):2366-2382.
    • (2007) Nat Protoc , vol.2 , Issue.10 , pp. 2366-2382
    • Cline, M.S.1
  • 52
    • 84876556918 scopus 로고    scopus 로고
    • EcoCyc: Fusing model organism databases with systems biology
    • Keseler IM, et al. (2013) EcoCyc: Fusing model organism databases with systems biology. Nucleic Acids Res 41(Database issue):D605-D612.
    • (2013) Nucleic Acids Res , vol.41 , Issue.DATABASE ISSUE
    • Keseler, I.M.1


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