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Volumn 55, Issue 1, 2014, Pages 148-155

Direct evaluation of tRNA aminoacylation status by the T-Box riboswitch using tRNA-mRNA stacking and steric readout

Author keywords

[No Author keywords available]

Indexed keywords

AMINOACYL TRANSFER RNA; MESSENGER RNA; RNA BINDING PROTEIN; T BOX TRANSCRIPTION FACTOR;

EID: 84903768300     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2014.05.017     Document Type: Article
Times cited : (47)

References (46)
  • 1
    • 0037133662 scopus 로고    scopus 로고
    • The tRNA specificity of Thermus thermophilus EF-Tu
    • Asahara H., Uhlenbeck O.C. The tRNA specificity of Thermus thermophilus EF-Tu. Proc. Natl. Acad. Sci. USA 2002, 99:3499-3504.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 3499-3504
    • Asahara, H.1    Uhlenbeck, O.C.2
  • 2
    • 84857431262 scopus 로고    scopus 로고
    • Folding of the hammerhead ribozyme: pyrrolo-cytosine fluorescence separates core folding from global folding and reveals a pH-dependent conformational change
    • Buskiewicz I.A., Burke J.M. Folding of the hammerhead ribozyme: pyrrolo-cytosine fluorescence separates core folding from global folding and reveals a pH-dependent conformational change. RNA 2012, 18:434-448.
    • (2012) RNA , vol.18 , pp. 434-448
    • Buskiewicz, I.A.1    Burke, J.M.2
  • 4
    • 0033635215 scopus 로고    scopus 로고
    • Uncharged tRNA activates GCN2 by displacing the protein kinase moiety from a bipartite tRNA-binding domain
    • Dong J., Qiu H., Garcia-Barrio M., Anderson J., Hinnebusch A.G. Uncharged tRNA activates GCN2 by displacing the protein kinase moiety from a bipartite tRNA-binding domain. Mol. Cell 2000, 6:269-279.
    • (2000) Mol. Cell , vol.6 , pp. 269-279
    • Dong, J.1    Qiu, H.2    Garcia-Barrio, M.3    Anderson, J.4    Hinnebusch, A.G.5
  • 5
    • 0038476616 scopus 로고    scopus 로고
    • The riboswitch-mediated control of sulfur metabolism in bacteria
    • Epshtein V., Mironov A.S., Nudler E. The riboswitch-mediated control of sulfur metabolism in bacteria. Proc. Natl. Acad. Sci. USA 2003, 100:5052-5056.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 5052-5056
    • Epshtein, V.1    Mironov, A.S.2    Nudler, E.3
  • 6
    • 61449157240 scopus 로고    scopus 로고
    • T box transcription antitermination riboswitch: influence of nucleotide sequence and orientation on tRNA binding by the antiterminator element
    • Fauzi H., Agyeman A., Hines J.V. T box transcription antitermination riboswitch: influence of nucleotide sequence and orientation on tRNA binding by the antiterminator element. Biochim. Biophys. Acta 2009, 1789:185-191.
    • (2009) Biochim. Biophys. Acta , vol.1789 , pp. 185-191
    • Fauzi, H.1    Agyeman, A.2    Hines, J.V.3
  • 7
    • 0037423679 scopus 로고    scopus 로고
    • Solution structure of the Bacillus subtilis T-box antiterminator RNA: seven nucleotide bulge characterized by stacking and flexibility
    • Gerdeman M.S., Henkin T.M., Hines J.V. Solution structure of the Bacillus subtilis T-box antiterminator RNA: seven nucleotide bulge characterized by stacking and flexibility. J.Mol. Biol. 2003, 326:189-201.
    • (2003) J.Mol. Biol. , vol.326 , pp. 189-201
    • Gerdeman, M.S.1    Henkin, T.M.2    Hines, J.V.3
  • 8
    • 80053649204 scopus 로고    scopus 로고
    • TRNA: Vast reservoir of RNA molecules with unexpected regulatory function
    • Geslain R., Pan T. tRNA: Vast reservoir of RNA molecules with unexpected regulatory function. Proc. Natl. Acad. Sci. USA 2011, 108:16489-16490.
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 16489-16490
    • Geslain, R.1    Pan, T.2
  • 9
    • 79958158209 scopus 로고    scopus 로고
    • Flexizymes for genetic code reprogramming
    • Goto Y., Katoh T., Suga H. Flexizymes for genetic code reprogramming. Nat. Protoc. 2011, 6:779-790.
    • (2011) Nat. Protoc. , vol.6 , pp. 779-790
    • Goto, Y.1    Katoh, T.2    Suga, H.3
  • 10
    • 71549138669 scopus 로고    scopus 로고
    • The T box mechanism: tRNA as a regulatory molecule
    • Green N.J., Grundy F.J., Henkin T.M. The T box mechanism: tRNA as a regulatory molecule. FEBS Lett. 2010, 584:318-324.
    • (2010) FEBS Lett. , vol.584 , pp. 318-324
    • Green, N.J.1    Grundy, F.J.2    Henkin, T.M.3
  • 11
    • 84887407372 scopus 로고    scopus 로고
    • Structural determinants for geometry and information decoding of tRNA by T box leader RNA
    • Grigg J.C., Ke A. Structural determinants for geometry and information decoding of tRNA by T box leader RNA. Structure 2013, 21:2025-2032.
    • (2013) Structure , vol.21 , pp. 2025-2032
    • Grigg, J.C.1    Ke, A.2
  • 12
    • 0027234192 scopus 로고
    • TRNA as a positive regulator of transcription antitermination in B. subtilis
    • Grundy F.J., Henkin T.M. tRNA as a positive regulator of transcription antitermination in B. subtilis. Cell 1993, 74:475-482.
    • (1993) Cell , vol.74 , pp. 475-482
    • Grundy, F.J.1    Henkin, T.M.2
  • 13
    • 0036529579 scopus 로고    scopus 로고
    • Sequence requirements for terminators and antiterminators in the T box transcription antitermination system: disparity between conservation and functional requirements
    • Grundy F.J., Moir T.R., Haldeman M.T., Henkin T.M. Sequence requirements for terminators and antiterminators in the T box transcription antitermination system: disparity between conservation and functional requirements. Nucleic Acids Res. 2002, 30:1646-1655.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 1646-1655
    • Grundy, F.J.1    Moir, T.R.2    Haldeman, M.T.3    Henkin, T.M.4
  • 14
    • 0037143628 scopus 로고    scopus 로고
    • TRNA-mediated transcription antitermination invitro: codon-anticodon pairing independent of the ribosome
    • Grundy F.J., Winkler W.C., Henkin T.M. tRNA-mediated transcription antitermination invitro: codon-anticodon pairing independent of the ribosome. Proc. Natl. Acad. Sci. USA 2002, 99:11121-11126.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 11121-11126
    • Grundy, F.J.1    Winkler, W.C.2    Henkin, T.M.3
  • 15
    • 12344255940 scopus 로고    scopus 로고
    • Monitoring uncharged tRNA during transcription of the Bacillus subtilis glyQS gene
    • Grundy F.J., Yousef M.R., Henkin T.M. Monitoring uncharged tRNA during transcription of the Bacillus subtilis glyQS gene. J.Mol. Biol. 2005, 346:73-81.
    • (2005) J.Mol. Biol. , vol.346 , pp. 73-81
    • Grundy, F.J.1    Yousef, M.R.2    Henkin, T.M.3
  • 17
    • 33746601044 scopus 로고    scopus 로고
    • Influence of base stacking and hydrogen bonding on the fluorescence of 2-aminopurine and pyrrolocytosine in nucleic acids
    • Hardman S.J., Thompson K.C. Influence of base stacking and hydrogen bonding on the fluorescence of 2-aminopurine and pyrrolocytosine in nucleic acids. Biochemistry 2006, 45:9145-9155.
    • (2006) Biochemistry , vol.45 , pp. 9145-9155
    • Hardman, S.J.1    Thompson, K.C.2
  • 18
    • 55649100267 scopus 로고    scopus 로고
    • Evidence for anonbase stacking effect for the environment-sensitive fluorescent base pyrrolocytosine-comparison with 2-aminopurine
    • Hardman S.J., Botchway S.W., Thompson K.C. Evidence for anonbase stacking effect for the environment-sensitive fluorescent base pyrrolocytosine-comparison with 2-aminopurine. Photochem. Photobiol. 2008, 84:1473-1479.
    • (2008) Photochem. Photobiol. , vol.84 , pp. 1473-1479
    • Hardman, S.J.1    Botchway, S.W.2    Thompson, K.C.3
  • 19
    • 0033544719 scopus 로고    scopus 로고
    • Stitching together RNA tertiary architectures
    • Hermann T., Patel D.J. Stitching together RNA tertiary architectures. J.Mol. Biol. 1999, 294:829-849.
    • (1999) J.Mol. Biol. , vol.294 , pp. 829-849
    • Hermann, T.1    Patel, D.J.2
  • 20
    • 27144510561 scopus 로고    scopus 로고
    • Translational regulation of GCN4 and the general amino acid control of yeast
    • Hinnebusch A.G. Translational regulation of GCN4 and the general amino acid control of yeast. Annu. Rev. Microbiol. 2005, 59:407-450.
    • (2005) Annu. Rev. Microbiol. , vol.59 , pp. 407-450
    • Hinnebusch, A.G.1
  • 22
    • 0025280236 scopus 로고
    • Fluorescence characterization of the interaction of various transfer RNA species with elongation factor Tu.GTP: evidence for anew functional role for elongation factor Tu in protein biosynthesis
    • Janiak F., Dell V.A., Abrahamson J.K., Watson B.S., Miller D.L., Johnson A.E. Fluorescence characterization of the interaction of various transfer RNA species with elongation factor Tu.GTP: evidence for anew functional role for elongation factor Tu in protein biosynthesis. Biochemistry 1990, 29:4268-4277.
    • (1990) Biochemistry , vol.29 , pp. 4268-4277
    • Janiak, F.1    Dell, V.A.2    Abrahamson, J.K.3    Watson, B.S.4    Miller, D.L.5    Johnson, A.E.6
  • 23
    • 0035793105 scopus 로고    scopus 로고
    • 2-Aminopurine fluorescence quenching and lifetimes: role of base stacking
    • Jean J.M., Hall K.B. 2-Aminopurine fluorescence quenching and lifetimes: role of base stacking. Proc. Natl. Acad. Sci. USA 2001, 98:37-41.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 37-41
    • Jean, J.M.1    Hall, K.B.2
  • 24
    • 0035912786 scopus 로고    scopus 로고
    • RNA-catalyzed amino acid activation
    • Kumar R.K., Yarus M. RNA-catalyzed amino acid activation. Biochemistry 2001, 40:6998-7004.
    • (2001) Biochemistry , vol.40 , pp. 6998-7004
    • Kumar, R.K.1    Yarus, M.2
  • 25
    • 0035812828 scopus 로고    scopus 로고
    • Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation
    • LaRiviere F.J., Wolfson A.D., Uhlenbeck O.C. Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation. Science 2001, 294:165-168.
    • (2001) Science , vol.294 , pp. 165-168
    • LaRiviere, F.J.1    Wolfson, A.D.2    Uhlenbeck, O.C.3
  • 27
    • 23044446600 scopus 로고    scopus 로고
    • The N-pentenoyl protecting group for aminoacyl-tRNAs
    • Lodder M., Wang B., Hecht S.M. The N-pentenoyl protecting group for aminoacyl-tRNAs. Methods 2005, 36:245-251.
    • (2005) Methods , vol.36 , pp. 245-251
    • Lodder, M.1    Wang, B.2    Hecht, S.M.3
  • 29
    • 0021344828 scopus 로고
    • Relative affinities ofall Escherichia coli aminoacyl-tRNAs for elongation factor Tu-GTP
    • Louie A., Ribeiro N.S., Reid B.R., Jurnak F. Relative affinities ofall Escherichia coli aminoacyl-tRNAs for elongation factor Tu-GTP. J.Biol. Chem. 1984, 259:5010-5016.
    • (1984) J.Biol. Chem. , vol.259 , pp. 5010-5016
    • Louie, A.1    Ribeiro, N.S.2    Reid, B.R.3    Jurnak, F.4
  • 30
    • 78650649651 scopus 로고    scopus 로고
    • Proofreading in translation: dynamics of the double-sieve model
    • Moras D. Proofreading in translation: dynamics of the double-sieve model. Proc. Natl. Acad. Sci. USA 2010, 107:21949-21950.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 21949-21950
    • Moras, D.1
  • 31
    • 0026639881 scopus 로고
    • Unusual resistance of peptidyl transferase to protein extraction procedures
    • Noller H.F., Hoffarth V., Zimniak L. Unusual resistance of peptidyl transferase to protein extraction procedures. Science 1992, 256:1416-1419.
    • (1992) Science , vol.256 , pp. 1416-1419
    • Noller, H.F.1    Hoffarth, V.2    Zimniak, L.3
  • 32
    • 77955225547 scopus 로고    scopus 로고
    • Use of EF-Tu mutants for determining and improving aminoacylation efficiency and for purifying aminoacyl tRNAs with non-natural amino acids
    • Ohtsuki T., Yamamoto H., Doi Y., Sisido M. Use of EF-Tu mutants for determining and improving aminoacylation efficiency and for purifying aminoacyl tRNAs with non-natural amino acids. J.Biochem. 2010, 148:239-246.
    • (2010) J.Biochem. , vol.148 , pp. 239-246
    • Ohtsuki, T.1    Yamamoto, H.2    Doi, Y.3    Sisido, M.4
  • 33
    • 79960395328 scopus 로고    scopus 로고
    • Bacterial transcription terminators: the RNA 3'-end chronicles
    • Peters J.M., Vangeloff A.D., Landick R. Bacterial transcription terminators: the RNA 3'-end chronicles. J.Mol. Biol. 2011, 412:793-813.
    • (2011) J.Mol. Biol. , vol.412 , pp. 793-813
    • Peters, J.M.1    Vangeloff, A.D.2    Landick, R.3
  • 35
    • 42449118064 scopus 로고    scopus 로고
    • RNA-dependent lipid remodeling by bacterial multiple peptide resistance factors
    • Roy H., Ibba M. RNA-dependent lipid remodeling by bacterial multiple peptide resistance factors. Proc. Natl. Acad. Sci. USA 2008, 105:4667-4672.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 4667-4672
    • Roy, H.1    Ibba, M.2
  • 36
    • 71849091911 scopus 로고    scopus 로고
    • Amino acid recognition and gene regulation by riboswitches
    • Serganov A., Patel D.J. Amino acid recognition and gene regulation by riboswitches. Biochim. Biophys. Acta 2009, 1789:592-611.
    • (2009) Biochim. Biophys. Acta , vol.1789 , pp. 592-611
    • Serganov, A.1    Patel, D.J.2
  • 37
    • 0023653195 scopus 로고
    • Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid
    • Sugimoto N., Kierzek R., Turner D.H. Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid. Biochemistry 1987, 26:4554-4558.
    • (1987) Biochemistry , vol.26 , pp. 4554-4558
    • Sugimoto, N.1    Kierzek, R.2    Turner, D.H.3
  • 38
    • 33344477201 scopus 로고    scopus 로고
    • Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation
    • Tinsley R.A., Walter N.G. Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation. RNA 2006, 12:522-529.
    • (2006) RNA , vol.12 , pp. 522-529
    • Tinsley, R.A.1    Walter, N.G.2
  • 39
    • 0019844454 scopus 로고
    • Probing the principles of amino acid selection using the alanyl-tRNA synthetase from Escherichia coli
    • Tsui W.C., Fersht A.R. Probing the principles of amino acid selection using the alanyl-tRNA synthetase from Escherichia coli. Nucleic Acids Res. 1981, 9:4627-4637.
    • (1981) Nucleic Acids Res. , vol.9 , pp. 4627-4637
    • Tsui, W.C.1    Fersht, A.R.2
  • 40
    • 41649115061 scopus 로고    scopus 로고
    • Comparative genomic analysis of T-box regulatory systems in bacteria
    • Vitreschak A.G., Mironov A.A., Lyubetsky V.A., Gelfand M.S. Comparative genomic analysis of T-box regulatory systems in bacteria. RNA 2008, 14:717-735.
    • (2008) RNA , vol.14 , pp. 717-735
    • Vitreschak, A.G.1    Mironov, A.A.2    Lyubetsky, V.A.3    Gelfand, M.S.4
  • 41
    • 47549110353 scopus 로고    scopus 로고
    • Structural basis of specific tRNA aminoacylation by a small invitro selected ribozyme
    • Xiao H., Murakami H., Suga H., Ferré-D'Amaré A.R. Structural basis of specific tRNA aminoacylation by a small invitro selected ribozyme. Nature 2008, 454:358-361.
    • (2008) Nature , vol.454 , pp. 358-361
    • Xiao, H.1    Murakami, H.2    Suga, H.3    Ferré-D'Amaré, A.R.4
  • 43
    • 65549106053 scopus 로고    scopus 로고
    • DNA hairpins containing the cytidine analog pyrrolo-dC: structural, thermodynamic, and spectroscopic studies
    • Zhang X., Wadkins R.M. DNA hairpins containing the cytidine analog pyrrolo-dC: structural, thermodynamic, and spectroscopic studies. Biophys. J. 2009, 96:1884-1891.
    • (2009) Biophys. J. , vol.96 , pp. 1884-1891
    • Zhang, X.1    Wadkins, R.M.2
  • 44
    • 84881665997 scopus 로고    scopus 로고
    • Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA
    • Zhang J., Ferré-D'Amaré A.R. Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA. Nature 2013, 500:363-366.
    • (2013) Nature , vol.500 , pp. 363-366
    • Zhang, J.1    Ferré-D'Amaré, A.R.2
  • 46
    • 78049276834 scopus 로고    scopus 로고
    • Ribozymes and riboswitches: modulation of RNA function by small molecules
    • Zhang J., Lau M.W., Ferré-D'Amaré A.R. Ribozymes and riboswitches: modulation of RNA function by small molecules. Biochemistry 2010, 49:9123-9131.
    • (2010) Biochemistry , vol.49 , pp. 9123-9131
    • Zhang, J.1    Lau, M.W.2    Ferré-D'Amaré, A.R.3


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