메뉴 건너뛰기




Volumn 113, Issue 26, 2016, Pages 7237-7242

Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis

Author keywords

Rna structure; Rna thermometer; Temperature; Translational control; Virulence

Indexed keywords

EXODEOXYRIBONUCLEASE VIII; NUCLEASE S1; RNA; BACTERIAL RNA; BETA GALACTOSIDASE; TRANSCRIPTOME;

EID: 84976576475     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1523004113     Document Type: Article
Times cited : (72)

References (49)
  • 1
    • 84872543206 scopus 로고    scopus 로고
    • A decade of riboswitches
    • Serganov A, Nudler E (2013) A decade of riboswitches. Cell 152(1-2):17-24.
    • (2013) Cell , vol.152 , Issue.1-2 , pp. 17-24
    • Serganov, A.1    Nudler, E.2
  • 2
    • 84858436083 scopus 로고    scopus 로고
    • Bacterial RNA thermometers: Molecular zippers and switches
    • Kortmann J, Narberhaus F (2012) Bacterial RNA thermometers: Molecular zippers and switches. Nat Rev Microbiol 10(4):255-265.
    • (2012) Nat Rev Microbiol , vol.10 , Issue.4 , pp. 255-265
    • Kortmann, J.1    Narberhaus, F.2
  • 3
    • 84908067413 scopus 로고    scopus 로고
    • Temperature-driven differential gene expression by RNA thermosensors
    • Krajewski SS, Narberhaus F (2014) Temperature-driven differential gene expression by RNA thermosensors. Biochim Biophys Acta 1839(10):978-988.
    • (2014) Biochim Biophys Acta , vol.1839 , Issue.10 , pp. 978-988
    • Krajewski, S.S.1    Narberhaus, F.2
  • 4
    • 0037031594 scopus 로고    scopus 로고
    • An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes
    • Johansson J, et al. (2002) An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes. Cell 110(5):551-561.
    • (2002) Cell , vol.110 , Issue.5 , pp. 551-561
    • Johansson, J.1
  • 5
    • 0027141070 scopus 로고
    • Temperature sensing in Yersinia pestis: Translation of the LcrF activator protein is thermally regulated
    • Hoe NP, Goguen JD (1993) Temperature sensing in Yersinia pestis: Translation of the LcrF activator protein is thermally regulated. J Bacteriol 175(24):7901-7909.
    • (1993) J Bacteriol , vol.175 , Issue.24 , pp. 7901-7909
    • Hoe, N.P.1    Goguen, J.D.2
  • 6
    • 84871714811 scopus 로고    scopus 로고
    • Concerted actions of a thermo-labile regulator and a unique intergenic RNA thermosensor control Yersinia virulence
    • Böhme K, et al. (2012) Concerted actions of a thermo-labile regulator and a unique intergenic RNA thermosensor control Yersinia virulence. PLoS Pathog 8(2):e1002518.
    • (2012) PLoS Pathog , vol.8 , Issue.2 , pp. e1002518
    • Böhme, K.1
  • 7
    • 84887247958 scopus 로고    scopus 로고
    • Role for cis-acting RNA sequences in the temperature-dependent expression of the multiadhesive lig proteins in Leptospira interrogans
    • Matsunaga J, Schlax PJ, Haake DA (2013) Role for cis-acting RNA sequences in the temperature-dependent expression of the multiadhesive lig proteins in Leptospira interrogans. J Bacteriol 195(22):5092-5101.
    • (2013) J Bacteriol , vol.195 , Issue.22 , pp. 5092-5101
    • Matsunaga, J.1    Schlax, P.J.2    Haake, D.A.3
  • 8
    • 84877989981 scopus 로고    scopus 로고
    • RNA-mediated thermoregulation of iron-acquisition genes in Shigella dysenteriae and pathogenic Escherichia coli
    • Kouse AB, Righetti F, Kortmann J, Narberhaus F, Murphy ER (2013) RNA-mediated thermoregulation of iron-acquisition genes in Shigella dysenteriae and pathogenic Escherichia coli. PLoS One 8(5):e63781.
    • (2013) PLoS One , vol.8 , Issue.5 , pp. e63781
    • Kouse, A.B.1    Righetti, F.2    Kortmann, J.3    Narberhaus, F.4    Murphy, E.R.5
  • 9
    • 84885611420 scopus 로고    scopus 로고
    • Temperature triggers immune evasion by Neisseria meningitidis
    • Loh E, et al. (2013) Temperature triggers immune evasion by Neisseria meningitidis. Nature 502(7470):237-240.
    • (2013) Nature , vol.502 , Issue.7470 , pp. 237-240
    • Loh, E.1
  • 10
    • 84908434445 scopus 로고    scopus 로고
    • Regulation of Pseudomonas aeruginosa virulence factors by two novel RNA thermometers
    • Grosso-Becerra MV, et al. (2014) Regulation of Pseudomonas aeruginosa virulence factors by two novel RNA thermometers. Proc Natl Acad Sci USA 111(43):15562-15567.
    • (2014) Proc Natl Acad Sci USA , vol.111 , Issue.43 , pp. 15562-15567
    • Grosso-Becerra, M.V.1
  • 11
    • 84907584473 scopus 로고    scopus 로고
    • RNA thermometer controls temperature-dependent virulence factor expression in Vibrio cholerae
    • Weber GG, Kortmann J, Narberhaus F, Klose KE (2014) RNA thermometer controls temperature-dependent virulence factor expression in Vibrio cholerae. Proc Natl Acad Sci USA 111(39):14241-14246.
    • (2014) Proc Natl Acad Sci USA , vol.111 , Issue.39 , pp. 14241-14246
    • Weber, G.G.1    Kortmann, J.2    Narberhaus, F.3    Klose, K.E.4
  • 13
    • 77956306662 scopus 로고    scopus 로고
    • Genome-wide measurement of RNA secondary structure in yeast
    • Kertesz M, et al. (2010) Genome-wide measurement of RNA secondary structure in yeast. Nature 467(7311):103-107.
    • (2010) Nature , vol.467 , Issue.7311 , pp. 103-107
    • Kertesz, M.1
  • 14
    • 84868009378 scopus 로고    scopus 로고
    • Genome-wide measurement of RNA folding energies
    • Wan Y, et al. (2012) Genome-wide measurement of RNA folding energies. Mol Cell 48(2):169-181.
    • (2012) Mol Cell , vol.48 , Issue.2 , pp. 169-181
    • Wan, Y.1
  • 15
    • 84898949357 scopus 로고    scopus 로고
    • Mod-seq: Highthroughput sequencing for chemical probing of RNA structure
    • Talkish J, May G, Lin Y, Woolford JL, Jr, McManus CJ (2014) Mod-seq: Highthroughput sequencing for chemical probing of RNA structure. RNA 20(5):713-720.
    • (2014) RNA , vol.20 , Issue.5 , pp. 713-720
    • Talkish, J.1    May, G.2    Lin, Y.3    Woolford, J.L.4    McManus, C.J.5
  • 16
    • 84861121932 scopus 로고    scopus 로고
    • Global analysis of RNA secondary structure in two metazoans
    • Li F, et al. (2012) Global analysis of RNA secondary structure in two metazoans. Cell Reports 1(1):69-82.
    • (2012) Cell Reports , vol.1 , Issue.1 , pp. 69-82
    • Li, F.1
  • 17
    • 78049445573 scopus 로고    scopus 로고
    • Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis
    • Zheng Q, et al. (2010) Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. PLoS Genet 6(9):e1001141.
    • (2010) PLoS Genet , vol.6 , Issue.9 , pp. e1001141
    • Zheng, Q.1
  • 18
    • 84871887837 scopus 로고    scopus 로고
    • Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome
    • Li F, et al. (2012) Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome. Plant Cell 24(11):4346-4359.
    • (2012) Plant Cell , vol.24 , Issue.11 , pp. 4346-4359
    • Li, F.1
  • 19
    • 84893427735 scopus 로고    scopus 로고
    • In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features
    • Ding Y, et al. (2014) In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature 505(7485):696-700.
    • (2014) Nature , vol.505 , Issue.7485 , pp. 696-700
    • Ding, Y.1
  • 20
    • 78649690492 scopus 로고    scopus 로고
    • FragSeq: Transcriptome-wide RNA structure probing using high-throughput sequencing
    • Underwood JG, et al. (2010) FragSeq: Transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods 7(12):995-1001.
    • (2010) Nat Methods , vol.7 , Issue.12 , pp. 995-1001
    • Underwood, J.G.1
  • 21
    • 84924584607 scopus 로고    scopus 로고
    • Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome
    • Incarnato D, Neri F, Anselmi F, Oliviero S (2014) Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome. Genome Biol 15(10):491.
    • (2014) Genome Biol , vol.15 , Issue.10 , pp. 491
    • Incarnato, D.1    Neri, F.2    Anselmi, F.3    Oliviero, S.4
  • 22
    • 84925777836 scopus 로고    scopus 로고
    • Structural imprints in vivo decode RNA regulatory mechanisms
    • Spitale RC, et al. (2015) Structural imprints in vivo decode RNA regulatory mechanisms. Nature 519(7544):486-490.
    • (2015) Nature , vol.519 , Issue.7544 , pp. 486-490
    • Spitale, R.C.1
  • 23
    • 84893351549 scopus 로고    scopus 로고
    • Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo
    • Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman JS (2014) Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature 505(7485): 701-705.
    • (2014) Nature , vol.505 , Issue.7485 , pp. 701-705
    • Rouskin, S.1    Zubradt, M.2    Washietl, S.3    Kellis, M.4    Weissman, J.S.5
  • 24
    • 84893358533 scopus 로고    scopus 로고
    • Landscape and variation of RNA secondary structure across the human transcriptome
    • Wan Y, et al. (2014) Landscape and variation of RNA secondary structure across the human transcriptome. Nature 505(7485):706-709.
    • (2014) Nature , vol.505 , Issue.7485 , pp. 706-709
    • Wan, Y.1
  • 25
    • 84946606812 scopus 로고    scopus 로고
    • Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function
    • Del Campo C, Bartholomäus A, Fedyunin I, Ignatova Z (2015) Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function. PLoS Genet 11(10):e1005613.
    • (2015) PLoS Genet , vol.11 , Issue.10 , pp. e1005613
    • Del Campo, C.1    Bartholomäus, A.2    Fedyunin, I.3    Ignatova, Z.4
  • 26
    • 67249097456 scopus 로고    scopus 로고
    • Intrinsic thermal sensing controls proteolysis of Yersinia virulence regulator RovA
    • Herbst K, et al. (2009) Intrinsic thermal sensing controls proteolysis of Yersinia virulence regulator RovA. PLoS Pathog 5(5):e1000435.
    • (2009) PLoS Pathog , vol.5 , Issue.5 , pp. e1000435
    • Herbst, K.1
  • 27
    • 84987949523 scopus 로고    scopus 로고
    • Coregulation of host-adapted metabolism and virulence by pathogenic yersiniae
    • Heroven AK, Dersch P (2014) Coregulation of host-adapted metabolism and virulence by pathogenic yersiniae. Front Cell Infect Microbiol 4:146.
    • (2014) Front Cell Infect Microbiol , vol.4 , pp. 146
    • Heroven, A.K.1    Dersch, P.2
  • 28
    • 84926333299 scopus 로고    scopus 로고
    • Transcriptomic profiling of Yersinia pseudotuberculosis reveals reprogramming of the Crp regulon by temperature and uncovers Crp as a master regulator of small RNAs
    • Nuss AM, et al. (2015) Transcriptomic profiling of Yersinia pseudotuberculosis reveals reprogramming of the Crp regulon by temperature and uncovers Crp as a master regulator of small RNAs. PLoS Genet 11(3):e1005087.
    • (2015) PLoS Genet , vol.11 , Issue.3 , pp. e1005087
    • Nuss, A.M.1
  • 29
    • 13944268797 scopus 로고    scopus 로고
    • A novel method for accurate operon predictions in all sequenced prokaryotes
    • Price MN, Huang KH, Alm EJ, Arkin AP (2005) A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res 33(3):880-892.
    • (2005) Nucleic Acids Res , vol.33 , Issue.3 , pp. 880-892
    • Price, M.N.1    Huang, K.H.2    Alm, E.J.3    Arkin, A.P.4
  • 30
    • 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
  • 31
    • 84906346426 scopus 로고    scopus 로고
    • A direct link between the global regulator PhoP and the Csr regulon in Y. Pseudotuberculosis through the small regulatory RNA CsrC
    • Nuss AM, et al. (2014) A direct link between the global regulator PhoP and the Csr regulon in Y. pseudotuberculosis through the small regulatory RNA CsrC. RNA Biol 11(5):580-593.
    • (2014) RNA Biol , vol.11 , Issue.5 , pp. 580-593
    • Nuss, A.M.1
  • 33
    • 84862156384 scopus 로고    scopus 로고
    • Thermogenetic tools to monitor temperature-dependent gene expression in bacteria
    • Klinkert B, et al. (2012) Thermogenetic tools to monitor temperature-dependent gene expression in bacteria. J Biotechnol 160(1-2):55-63.
    • (2012) J Biotechnol , vol.160 , Issue.1-2 , pp. 55-63
    • Klinkert, B.1
  • 34
    • 0025166089 scopus 로고
    • Secondary structure of the ribosome binding site determines translational efficiency: A quantitative analysis
    • de Smit MH, van Duin J (1990) Secondary structure of the ribosome binding site determines translational efficiency: A quantitative analysis. Proc Natl Acad Sci USA 87(19):7668-7672.
    • (1990) Proc Natl Acad Sci USA , vol.87 , Issue.19 , pp. 7668-7672
    • De Smit, M.H.1    Van Duin, J.2
  • 35
    • 84909993101 scopus 로고    scopus 로고
    • The PqsR and RhlR transcriptional regulators determine the level of Pseudomonas quinolone signal synthesis in Pseudomonas aeruginosa by producing two different pqsABCDE mRNA isoforms
    • Brouwer S, et al. (2014) The PqsR and RhlR transcriptional regulators determine the level of Pseudomonas quinolone signal synthesis in Pseudomonas aeruginosa by producing two different pqsABCDE mRNA isoforms. J Bacteriol 196(23):4163-4171.
    • (2014) J Bacteriol , vol.196 , Issue.23 , pp. 4163-4171
    • Brouwer, S.1
  • 36
    • 84888227426 scopus 로고    scopus 로고
    • The cytotoxic necrotizing factor of Yersinia pseudotuberculosis (CNFY) enhances inflammation and Yop delivery during infection by activation of Rho GTPases
    • Schweer J, et al. (2013) The cytotoxic necrotizing factor of Yersinia pseudotuberculosis (CNFY) enhances inflammation and Yop delivery during infection by activation of Rho GTPases. PLoS Pathog 9(11):e1003746.
    • (2013) PLoS Pathog , vol.9 , Issue.11 , pp. e1003746
    • Schweer, J.1
  • 37
    • 84881469450 scopus 로고    scopus 로고
    • Cytotoxic necrotizing factor-Y boosts Yersinia effector translocation by activating Rac protein
    • Wolters M, et al. (2013) Cytotoxic necrotizing factor-Y boosts Yersinia effector translocation by activating Rac protein. J Biol Chem 288(32):23543-23553.
    • (2013) J Biol Chem , vol.288 , Issue.32 , pp. 23543-23553
    • Wolters, M.1
  • 38
    • 60549117099 scopus 로고    scopus 로고
    • The Yersinia pestis Ail protein mediates binding and Yop delivery to host cells required for plague virulence
    • Felek S, Krukonis ES (2009) The Yersinia pestis Ail protein mediates binding and Yop delivery to host cells required for plague virulence. Infect Immun 77(2):825-836.
    • (2009) Infect Immun , vol.77 , Issue.2 , pp. 825-836
    • Felek, S.1    Krukonis, E.S.2
  • 39
    • 77955292889 scopus 로고    scopus 로고
    • Ail binding to fibronectin facilitates Yersinia pestis binding to host cells and Yop delivery
    • Tsang TM, Felek S, Krukonis ES (2010) Ail binding to fibronectin facilitates Yersinia pestis binding to host cells and Yop delivery. Infect Immun 78(8):3358-3368.
    • (2010) Infect Immun , vol.78 , Issue.8 , pp. 3358-3368
    • Tsang, T.M.1    Felek, S.2    Krukonis, E.S.3
  • 41
    • 84892475803 scopus 로고    scopus 로고
    • Yersinia pseudotuberculosis uses Ail and YadA to circumvent neutrophils by directing Yop translocation during lung infection
    • Paczosa MK, Fisher ML, Maldonado-Arocho FJ, Mecsas J (2014) Yersinia pseudotuberculosis uses Ail and YadA to circumvent neutrophils by directing Yop translocation during lung infection. Cell Microbiol 16(2):247-268.
    • (2014) Cell Microbiol , vol.16 , Issue.2 , pp. 247-268
    • Paczosa, M.K.1    Fisher, M.L.2    Maldonado-Arocho, F.J.3    Mecsas, J.4
  • 42
    • 79960571755 scopus 로고    scopus 로고
    • Multiplexed RNA structure characterization with selective 2?-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)
    • Lucks JB, et al. (2011) Multiplexed RNA structure characterization with selective 2?-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc Natl Acad Sci USA 108(27):11063-11068.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.27 , pp. 11063-11068
    • Lucks, J.B.1
  • 43
    • 84928259454 scopus 로고    scopus 로고
    • Constitutive production of c-di-GMP is associated with mutations in a variant of Pseudomonas aeruginosa with altered membrane composition
    • Blanka A, et al. (2015) Constitutive production of c-di-GMP is associated with mutations in a variant of Pseudomonas aeruginosa with altered membrane composition. Sci Signal 8(372):ra36.
    • (2015) Sci Signal , vol.8 , Issue.372 , pp. ra36
    • Blanka, A.1
  • 44
    • 84877063192 scopus 로고    scopus 로고
    • Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing
    • Wan Y, Qu K, Ouyang Z, Chang HY (2013) Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing. Nat Protoc 8(5):849-869.
    • (2013) Nat Protoc , vol.8 , Issue.5 , pp. 849-869
    • Wan, Y.1    Qu, K.2    Ouyang, Z.3    Chang, H.Y.4
  • 45
    • 70349667200 scopus 로고    scopus 로고
    • Fast mapping of short sequences with mismatches, insertions and deletions using index structures
    • Hoffmann S, et al. (2009) Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLOS Comput Biol 5(9):e1000502.
    • (2009) PLOS Comput Biol , vol.5 , Issue.9 , pp. e1000502
    • Hoffmann, S.1
  • 46
    • 82055164092 scopus 로고    scopus 로고
    • ViennaRNA Package 2.0
    • Lorenz R, et al. (2011) ViennaRNA Package 2.0. Algorithms Mol Biol 6:26.
    • (2011) Algorithms Mol Biol , vol.6 , pp. 26
    • Lorenz, R.1
  • 47
    • 67650727366 scopus 로고    scopus 로고
    • VARNA: Interactive drawing and editing of the RNA secondary structure
    • Darty K, Denise A, Ponty Y (2009) VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 25(15):1974-1975.
    • (2009) Bioinformatics , vol.25 , Issue.15 , pp. 1974-1975
    • Darty, K.1    Denise, A.2    Ponty, Y.3
  • 48
    • 78650749888 scopus 로고    scopus 로고
    • Multiple layers of control govern expression of the Escherichia coli ibpAB heat-shock operon
    • Gaubig LC, Waldminghaus T, Narberhaus F (2011) Multiple layers of control govern expression of the Escherichia coli ibpAB heat-shock operon. Microbiology 157(Pt 1):66-76.
    • (2011) Microbiology , vol.157 , pp. 66-76
    • Gaubig, L.C.1    Waldminghaus, T.2    Narberhaus, F.3
  • 49
    • 0024252185 scopus 로고
    • Extension inhibition analysis of translation initiation complexes
    • Hartz D, McPheeters DS, Traut R, Gold L (1988) Extension inhibition analysis of translation initiation complexes. Methods Enzymol 164:419-425.
    • (1988) Methods Enzymol , vol.164 , pp. 419-425
    • Hartz, D.1    McPheeters, D.S.2    Traut, R.3    Gold, L.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.