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Volumn 22, Issue 11, 2016, Pages 1728-1738

Singlet glycine riboswitches bind ligand as well as tandem riboswitches

Author keywords

Aptamer; Gene control; Glycine; Metabolite; Riboswitch

Indexed keywords

APTAMER; GLYCINE; LIGAND; RIBOSWITCH;

EID: 84992663900     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.057935.116     Document Type: Article
Times cited : (17)

References (38)
  • 1
    • 85011940614 scopus 로고    scopus 로고
    • Bacterial aptamers that selectively bind glutamine
    • Ames TD, Breaker RR. 2011. Bacterial aptamers that selectively bind glutamine. RNA Biol 8: 82-89.
    • (2011) RNA Biol , vol.8 , pp. 82-89
    • Ames, T.D.1    Breaker, R.R.2
  • 2
    • 84872517135 scopus 로고    scopus 로고
    • Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches
    • Baird NJ, Ferré-D'Amaré AR. 2013. Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches. RNA 19: 167-176.
    • (2013) RNA , vol.19 , pp. 167-176
    • Baird, N.J.1    Ferré-D'Amaré, A.R.2
  • 3
    • 46349083026 scopus 로고    scopus 로고
    • The distributions, mechanisms, and structures of metabolite-binding riboswitches
    • Barrick JE, Breaker RR. 2007. The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol 8: R239.
    • (2007) Genome Biol , vol.8 , pp. R239
    • Barrick, J.E.1    Breaker, R.R.2
  • 5
    • 80052973462 scopus 로고    scopus 로고
    • Prospects for riboswitch discovery and analysis
    • Breaker RR. 2011. Prospects for riboswitch discovery and analysis. Mol Cell 43: 867-879.
    • (2011) Mol Cell , vol.43 , pp. 867-879
    • Breaker, R.R.1
  • 7
    • 79953052076 scopus 로고    scopus 로고
    • Structural basis of cooperative ligand binding by the glycine riboswitch
    • Butler EB, Xiong Y, Wang J, Strobel SA. 2011. Structural basis of cooperative ligand binding by the glycine riboswitch. Chem Biol 18: 293-298.
    • (2011) Chem Biol , vol.18 , pp. 293-298
    • Butler, E.B.1    Xiong, Y.2    Wang, J.3    Strobel, S.A.4
  • 8
    • 17444453249 scopus 로고    scopus 로고
    • Revised UV extinction coefficients for nucleoside-5′-monophosphates and unpaired DNA and RNA
    • Cavaluzzi MJ, Borer PN. 2004. Revised UV extinction coefficients for nucleoside-5′-monophosphates and unpaired DNA and RNA. Nucleic Acids Res 32: e13-e13.
    • (2004) Nucleic Acids Res , vol.32 , pp. e13
    • Cavaluzzi, M.J.1    Borer, P.N.2
  • 9
    • 84937061323 scopus 로고    scopus 로고
    • Consistent global structures of complex RNA states through multidimensional chemical mapping
    • Cheng CY, Chou F-C, Kladwang W, Tian S, Cordero P, Das R. 2015. Consistent global structures of complex RNA states through multidimensional chemical mapping. Elife 4: e07600.
    • (2015) Elife , vol.4
    • Cheng, C.Y.1    Chou, F.-C.2    Kladwang, W.3    Tian, S.4    Cordero, P.5    Das, R.6
  • 11
    • 78650424317 scopus 로고    scopus 로고
    • Identification of a tertiary interaction important for cooperative ligand binding by the glycine riboswitch
    • Erion TV, Strobel SA. 2011. Identification of a tertiary interaction important for cooperative ligand binding by the glycine riboswitch. RNA 17: 74-84.
    • (2011) RNA , vol.17 , pp. 74-84
    • Erion, T.V.1    Strobel, S.A.2
  • 12
    • 84902197971 scopus 로고    scopus 로고
    • Characterizing the dynamics of the leader-linker interaction in the glycine riboswitch with site-directed spin labeling
    • Esquiaqui JM, Sherman EM, Ionescu SA, Ye J-D, Fanucci GE. 2014. Characterizing the dynamics of the leader-linker interaction in the glycine riboswitch with site-directed spin labeling. Biochemistry 53: 3526-3528.
    • (2014) Biochemistry , vol.53 , pp. 3526-3528
    • Esquiaqui, J.M.1    Sherman, E.M.2    Ionescu, S.A.3    Ye, J.-D.4    Fanucci, G.E.5
  • 13
    • 84906311591 scopus 로고    scopus 로고
    • Structural insights into recognition of c-di-AMP by the ydaO riboswitch
    • Gao A, Serganov A. 2014. Structural insights into recognition of c-di-AMP by the ydaO riboswitch. Nat Chem Biol 10: 787-792.
    • (2014) Nat Chem Biol , vol.10 , pp. 787-792
    • Gao, A.1    Serganov, A.2
  • 15
    • 78649970557 scopus 로고    scopus 로고
    • Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch
    • Huang L, Serganov A, Patel DJ. 2010. Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch. Mol Cell 40: 774-786.
    • (2010) Mol Cell , vol.40 , pp. 774-786
    • Huang, L.1    Serganov, A.2    Patel, D.J.3
  • 16
    • 38549119502 scopus 로고    scopus 로고
    • Abundance and functional diversity of riboswitches in microbial communities
    • Kazanov MD, Vitreschak AG, Gelfand MS. 2007. Abundance and functional diversity of riboswitches in microbial communities. BMC Genomics 8: 347.
    • (2007) BMC Genomics , vol.8 , pp. 347
    • Kazanov, M.D.1    Vitreschak, A.G.2    Gelfand, M.S.3
  • 17
    • 84856246110 scopus 로고    scopus 로고
    • Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches
    • Kladwang W, Chou F-C, Das R. 2012. Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches. J Am Chem Soc 134: 1404-1407.
    • (2012) J Am Chem Soc , vol.134 , pp. 1404-1407
    • Kladwang, W.1    Chou, F.-C.2    Das, R.3
  • 18
    • 38049025288 scopus 로고    scopus 로고
    • Chemical basis of glycine riboswitch cooperativity
    • Kwon M, Strobel SA. 2008. Chemical basis of glycine riboswitch cooperativity. RNA 14: 25-34.
    • (2008) RNA , vol.14 , pp. 25-34
    • Kwon, M.1    Strobel, S.A.2
  • 19
    • 33845971464 scopus 로고    scopus 로고
    • Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae
    • Lipfert J, Das R, Chu VB, Kudaravalli M, Boyd N, Herschlag D, Doniach S. 2007. Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. J Mol Biol 365: 1393-1406.
    • (2007) J Mol Biol , vol.365 , pp. 1393-1406
    • Lipfert, J.1    Das, R.2    Chu, V.B.3    Kudaravalli, M.4    Boyd, N.5    Herschlag, D.6    Doniach, S.7
  • 21
    • 79952996320 scopus 로고    scopus 로고
    • An expanded collection and refined consensus model of glmS ribozymes
    • McCown PJ, Roth A, Breaker RR. 2011. An expanded collection and refined consensus model of glmS ribozymes. RNA 17: 728-736.
    • (2011) RNA , vol.17 , pp. 728-736
    • McCown, P.J.1    Roth, A.2    Breaker, R.R.3
  • 22
    • 84904555761 scopus 로고    scopus 로고
    • Structural, functional, and taxonomic diversity of three preQ1 riboswitch classes
    • McCown PJ, Liang JJ, Weinberg Z, Breaker RR. 2014. Structural, functional, and taxonomic diversity of three preQ1 riboswitch classes. Chem Biol 21: 880-889.
    • (2014) Chem Biol , vol.21 , pp. 880-889
    • McCown, P.J.1    Liang, J.J.2    Weinberg, Z.3    Breaker, R.R.4
  • 23
    • 84958767485 scopus 로고    scopus 로고
    • Nuclease-resistant c-di-AMP derivatives that differentially recognize RNA and protein receptors
    • Meehan RE, Torgerson CD, Gaffney BL, Jones RA, Strobel SA. 2016. Nuclease-resistant c-di-AMP derivatives that differentially recognize RNA and protein receptors. Biochemistry 55: 837-849.
    • (2016) Biochemistry , vol.55 , pp. 837-849
    • Meehan, R.E.1    Torgerson, C.D.2    Gaffney, B.L.3    Jones, R.A.4    Strobel, S.A.5
  • 24
    • 84941598803 scopus 로고    scopus 로고
    • Cooperativity, allostery and synergism in ligand binding to riboswitches
    • Peselis A, Gao A, Serganov A. 2015. Cooperativity, allostery and synergism in ligand binding to riboswitches. Biochimie 117: 100-109.
    • (2015) Biochimie , vol.117 , pp. 100-109
    • Peselis, A.1    Gao, A.2    Serganov, A.3
  • 25
    • 70350111141 scopus 로고    scopus 로고
    • A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria
    • Poiata E, Meyer MM, Ames TD, Breaker RR. 2009. A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria. RNA 15: 2046-2056.
    • (2009) RNA , vol.15 , pp. 2046-2056
    • Poiata, E.1    Meyer, M.M.2    Ames, T.D.3    Breaker, R.R.4
  • 26
    • 84906313473 scopus 로고    scopus 로고
    • c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets
    • Ren A, Patel DJ. 2014. c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets. Nat Chem Biol 10: 780-786.
    • (2014) Nat Chem Biol , vol.10 , pp. 780-786
    • Ren, A.1    Patel, D.J.2
  • 27
    • 84908133094 scopus 로고    scopus 로고
    • Ligand binding by the tandem glycine riboswitch depends on aptamer dimerization but not double ligand occupancy
    • Ruff KM, Strobel SA. 2014. Ligand binding by the tandem glycine riboswitch depends on aptamer dimerization but not double ligand occupancy. RNA 20: 1775-1788.
    • (2014) RNA , vol.20 , pp. 1775-1788
    • Ruff, K.M.1    Strobel, S.A.2
  • 28
    • 84857438025 scopus 로고    scopus 로고
    • An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches
    • Sherman EM, Esquiaqui J, Elsayed G, Ye J-D. 2012. An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches. RNA 18: 496-507.
    • (2012) RNA , vol.18 , pp. 496-507
    • Sherman, E.M.1    Esquiaqui, J.2    Elsayed, G.3    Ye, J.-D.4
  • 30
    • 84895737813 scopus 로고    scopus 로고
    • Two glycine riboswitches activate the glycine cleavage system essential for glycine detoxification in Streptomyces griseus
    • Tezuka T, Ohnishi Y. 2014. Two glycine riboswitches activate the glycine cleavage system essential for glycine detoxification in Streptomyces griseus. J Bacteriol 196: 1369-1376.
    • (2014) J Bacteriol , vol.196 , pp. 1369-1376
    • Tezuka, T.1    Ohnishi, Y.2
  • 31
    • 84894462887 scopus 로고    scopus 로고
    • A disconnect between high-affinity binding and efficient regulation by antifolates and purines in the tetrahydrofolate riboswitch
    • Trausch JJ, Batey RT. 2014. A disconnect between high-affinity binding and efficient regulation by antifolates and purines in the tetrahydrofolate riboswitch. Chem Biol 21: 205-216.
    • (2014) Chem Biol , vol.21 , pp. 205-216
    • Trausch, J.J.1    Batey, R.T.2
  • 32
    • 80054074740 scopus 로고    scopus 로고
    • The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer
    • Trausch JJ, Ceres P, Reyes FE, Batey RT. 2011. The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer. Structure 19: 1413-1423.
    • (2011) Structure , vol.19 , pp. 1413-1423
    • Trausch, J.J.1    Ceres, P.2    Reyes, F.E.3    Batey, R.T.4
  • 33
    • 0037100667 scopus 로고    scopus 로고
    • Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation
    • Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS. 2002. Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. Nucleic Acids Res 30: 3141-3151.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3141-3151
    • Vitreschak, A.G.1    Rodionov, D.A.2    Mironov, A.A.3    Gelfand, M.S.4
  • 34
    • 78650791283 scopus 로고    scopus 로고
    • R2R - Software to speed the depiction of aesthetic consensus RNA secondary structures
    • Weinberg Z, Breaker RR. 2011. R2R - software to speed the depiction of aesthetic consensus RNA secondary structures. BMC Bioinformatics 12: 3.
    • (2011) BMC Bioinformatics , vol.12 , pp. 3
    • Weinberg, Z.1    Breaker, R.R.2
  • 35
    • 33947714417 scopus 로고    scopus 로고
    • Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis
    • Welz R, Breaker RR. 2007. Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis. RNA 13: 573-582.
    • (2007) RNA , vol.13 , pp. 573-582
    • Welz, R.1    Breaker, R.R.2
  • 36
    • 84902688021 scopus 로고    scopus 로고
    • A neutral pH thermal hydrolysis method for quantification of structured RNAs
    • Wilson SC, Cohen DT, Wang XC, Hammond MC. 2014. A neutral pH thermal hydrolysis method for quantification of structured RNAs. RNA 20: 1153-1160.
    • (2014) RNA , vol.20 , pp. 1153-1160
    • Wilson, S.C.1    Cohen, D.T.2    Wang, X.C.3    Hammond, M.C.4
  • 37
    • 32544452741 scopus 로고    scopus 로고
    • CMfinder - A covariance model based RNA motif finding algorithm
    • Yao Z, Weinberg Z, Ruzzo WL. 2006. CMfinder - a covariance model based RNA motif finding algorithm. Bioinformatics 22: 445-452.
    • (2006) Bioinformatics , vol.22 , pp. 445-452
    • Yao, Z.1    Weinberg, Z.2    Ruzzo, W.L.3
  • 38
    • 84908321643 scopus 로고    scopus 로고
    • Global analysis of riboswitches by small-angle X-ray scattering and calorimetry
    • Zhang J, Jones CP, Ferré-D'Amaré AR. 2014. Global analysis of riboswitches by small-angle X-ray scattering and calorimetry. Biochim Biophys Acta 1839: 1020-1029.
    • (2014) Biochim Biophys Acta , vol.1839 , pp. 1020-1029
    • Zhang, J.1    Jones, C.P.2    Ferré-D'Amaré, A.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.