메뉴 건너뛰기




Volumn 326, Issue 1, 2003, Pages 189-201

Solution structure of the Bacillus subtilis T-box antiterminator RNA: Seven nucleotide bulge characterized by stacking and flexibility

Author keywords

Antitermination; NMR; RNA binding; RNA bulge; Structure

Indexed keywords

NUCLEOTIDE; RNA; T BOX TRANSCRIPTION FACTOR; TRANSFER RNA;

EID: 0037423679     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)01339-6     Document Type: Article
Times cited : (53)

References (59)
  • 1
    • 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. 74:1993;475-482.
    • (1993) Cell , vol.74 , pp. 475-482
    • Grundy, F.J.1    Henkin, T.M.2
  • 2
    • 0033867256 scopus 로고    scopus 로고
    • TRNA determinants for transcription antitermination of the Bacillus subtilis tyrS gene
    • Grundy F.J., Collins J.A., Rollins S.M., Henkin T.M. tRNA determinants for transcription antitermination of the Bacillus subtilis tyrS gene. RNA. 6:2000;1131-1141.
    • (2000) RNA , vol.6 , pp. 1131-1141
    • Grundy, F.J.1    Collins, J.A.2    Rollins, S.M.3    Henkin, T.M.4
  • 3
    • 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. Nucl. Acids Res. 30:2002;1646-1655.
    • (2002) Nucl. Acids Res. , vol.30 , pp. 1646-1655
    • Grundy, F.J.1    Moir, T.R.2    Haldeman, M.T.3    Henkin, T.M.4
  • 4
    • 0028025386 scopus 로고
    • Interaction between the acceptor end of tRNA and the T-box stimulates antitermination in the Bacillus subtilis tyrS gene: A new role for the discriminator base
    • Grundy F.J., Rollins S.M., Henkin T.M. Interaction between the acceptor end of tRNA and the T-box stimulates antitermination in the Bacillus subtilis tyrS gene: a new role for the discriminator base. J. Bacteriol. 176:1994;4518-4526.
    • (1994) J. Bacteriol. , vol.176 , pp. 4518-4526
    • Grundy, F.J.1    Rollins, S.M.2    Henkin, T.M.3
  • 5
    • 0037082440 scopus 로고    scopus 로고
    • In vitro structure-function studies of the Bacillus subtilis tyrS mRNA antiterminator: Evidence for factor independent tRNA acceptor stem binding specificity
    • Gerdeman M.S., Henkin T.M., Hines J.V. In vitro structure-function studies of the Bacillus subtilis tyrS mRNA antiterminator: evidence for factor independent tRNA acceptor stem binding specificity. Nucl. Acids Res. 30:2002;1065-1072.
    • (2002) Nucl. Acids Res. , vol.30 , pp. 1065-1072
    • Gerdeman, M.S.1    Henkin, T.M.2    Hines, J.V.3
  • 6
    • 0037143628 scopus 로고    scopus 로고
    • TRNA-mediated transcription antitermination in vitro: Codon-anticodon pairing independent of the ribosome
    • Grundy F.J., Winkler W.C., Henkin T.M. tRNA-mediated transcription antitermination in vitro: codon-anticodon pairing independent of the ribosome. Proc. Natl Acad. Sci. USA. 99:2002;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
  • 7
    • 0034653899 scopus 로고    scopus 로고
    • RNA bulges as architectural and recognition motifs
    • Hermann T., Patel D.J. RNA bulges as architectural and recognition motifs. Structure. 8:2000;R47-R54.
    • (2000) Structure , vol.8
    • Hermann, T.1    Patel, D.J.2
  • 8
    • 0029024877 scopus 로고
    • Proton NMR and structural features of a 24-nucleotide RNA hairpin
    • Borer P.N., Pelcer I. Proton NMR and structural features of a 24-nucleotide RNA hairpin. Biochemistry. 34:1995;6488-6503.
    • (1995) Biochemistry , vol.34 , pp. 6488-6503
    • Borer, P.N.1    Pelcer, I.2
  • 9
    • 0029111762 scopus 로고
    • Kinking of DNA and RNA by base bulges
    • Lilley D.M.J. Kinking of DNA and RNA by base bulges. Proc. Natl Acad. Sci. USA. 92:1995;7140-7142.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 7140-7142
    • Lilley, D.M.J.1
  • 10
    • 0030874397 scopus 로고    scopus 로고
    • Solution conformation of a five-nucleotide RNA bulge loop from a group I intron
    • Luebke K.J., Landry S.M., Tinoco I. Jr. Solution conformation of a five-nucleotide RNA bulge loop from a group I intron. Biochemistry. 36:1997;10246-10255.
    • (1997) Biochemistry , vol.36 , pp. 10246-10255
    • Luebke, K.J.1    Landry, S.M.2    Tinoco I., Jr.3
  • 11
    • 0033529304 scopus 로고    scopus 로고
    • Structure of tau exon 10 spilcing regulatory element RNA and destabilization by mutations of frontotemperal dementia and Parkinsonism linked to chromosome 17
    • Varani L., Varani G. Structure of tau exon 10 spilcing regulatory element RNA and destabilization by mutations of frontotemperal dementia and Parkinsonism linked to chromosome 17. Proc. Natl Acad. Sci. USA. 96:1999;8229-8234.
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 8229-8234
    • Varani, L.1    Varani, G.2
  • 12
    • 0030090986 scopus 로고    scopus 로고
    • Crystal structure of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage
    • Portman S., Grimm S., Workman C., Usman N., Egli M. Crystal structure of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage. Chem. Biol. 3:1996;173-184.
    • (1996) Chem. Biol. , vol.3 , pp. 173-184
    • Portman, S.1    Grimm, S.2    Workman, C.3    Usman, N.4    Egli, M.5
  • 13
    • 0030585428 scopus 로고    scopus 로고
    • Solution structure of the donor site of a trans-splicing RNA
    • Greenbaum N.L., Radhakrishnan I., Patel D.J., Hirsh D. Solution structure of the donor site of a trans-splicing RNA. Structure. 4:1996;725-733.
    • (1996) Structure , vol.4 , pp. 725-733
    • Greenbaum, N.L.1    Radhakrishnan, I.2    Patel, D.J.3    Hirsh, D.4
  • 14
    • 0024426629 scopus 로고
    • The contrasting structures of mismatched DNA sequences containing looped-out bases (bulges) and multiple mismatches (bubbles)
    • Bhattacharyya A., Lilley D.M.J. The contrasting structures of mismatched DNA sequences containing looped-out bases (bulges) and multiple mismatches (bubbles). Nucl. Acids Res. 17:1989;6821-6840.
    • (1989) Nucl. Acids Res. , vol.17 , pp. 6821-6840
    • Bhattacharyya, A.1    Lilley, D.M.J.2
  • 15
    • 0022470564 scopus 로고
    • Interconversion of active and inactive 30 S ribosomal subunits is accompanied by a conformational change in decoding region of 16 S RNA
    • Moazed D., Stern S., Noller H.F. Interconversion of active and inactive 30 S ribosomal subunits is accompanied by a conformational change in decoding region of 16 S RNA. J. Mol. Biol. 187:1986;399-416.
    • (1986) J. Mol. Biol. , vol.187 , pp. 399-416
    • Moazed, D.1    Stern, S.2    Noller, H.F.3
  • 16
    • 0029820625 scopus 로고    scopus 로고
    • Crystal structure of a group I ribozyme domain: Principles of RNA packing
    • Cate J.H., Gooding A.R., Podel E., Zhou K., Golden B.L., Kundrot C.E., et al. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 273:1996;1678-1685.
    • (1996) Science , vol.273 , pp. 1678-1685
    • Cate, J.H.1    Gooding, A.R.2    Podel, E.3    Zhou, K.4    Golden, B.L.5    Kundrot, C.E.6
  • 20
    • 0029082529 scopus 로고
    • Structure of the P1 Helix from Group 1 self-splicing introns
    • Allain F.H.-T., Varani G. Structure of the P1 Helix from Group 1 self-splicing introns. J. Mol. Biol. 250:1995;333-353.
    • (1995) J. Mol. Biol. , vol.250 , pp. 333-353
    • Allain, F.H.-T.1    Varani, G.2
  • 21
    • 0025811124 scopus 로고
    • Structure of an unusually stable RNA hairpin
    • Varani G., Cheong C., Tinoco I. Jr. Structure of an unusually stable RNA hairpin. Biochemistry. 30:1991;3280-3289.
    • (1991) Biochemistry , vol.30 , pp. 3280-3289
    • Varani, G.1    Cheong, C.2    Tinoco I., Jr.3
  • 24
    • 0026676167 scopus 로고
    • Sampling and efficiency of metric matrix distance geometry: A novel partial meterization algorithm
    • Kuszewski J., Nilges M., Brunger A.T. Sampling and efficiency of metric matrix distance geometry: a novel partial meterization algorithm. J. Biomol. NMR. 2:1992;33-56.
    • (1992) J. Biomol. NMR , vol.2 , pp. 33-56
    • Kuszewski, J.1    Nilges, M.2    Brunger, A.T.3
  • 25
    • 0031569392 scopus 로고    scopus 로고
    • New applications of simulated annealing in X-ray crystallography and solution NMR
    • Brunger A.T., Adams P.D., Rice L.M. New applications of simulated annealing in X-ray crystallography and solution NMR. Structure. 5:1997;325-336.
    • (1997) Structure , vol.5 , pp. 325-336
    • Brunger, A.T.1    Adams, P.D.2    Rice, L.M.3
  • 26
    • 0024285896 scopus 로고
    • Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations
    • Nilges M., Clore G.M., Gronenborn A.M. Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Letters. 229:1988;317-324.
    • (1988) FEBS Letters , vol.229 , pp. 317-324
    • Nilges, M.1    Clore, G.M.2    Gronenborn, A.M.3
  • 28
    • 0031037836 scopus 로고    scopus 로고
    • Solution Structure of an Intramolecular DNA Triplex Containing an N7-Glycosylated Guanine which Mimics a Protonated Cytosine
    • Koshlap K.M., Schultze P., Brunar H., Dervan P.B., Feigon J. Solution Structure of an Intramolecular DNA Triplex Containing an N7-Glycosylated Guanine which Mimics a Protonated Cytosine. Biochemistry. 36:1997;2659-2668.
    • (1997) Biochemistry , vol.36 , pp. 2659-2668
    • Koshlap, K.M.1    Schultze, P.2    Brunar, H.3    Dervan, P.B.4    Feigon, J.5
  • 29
    • 0035965142 scopus 로고    scopus 로고
    • The structure of helix III in Xenopus oocyte 5 S rRNA: An RNA stem containing a two-nucleotide bulge
    • Huber P.W., Rife J.P., Moore P.B. The structure of helix III in Xenopus oocyte 5 S rRNA: an RNA stem containing a two-nucleotide bulge. J. Mol. Biol. 312:2001;823-832.
    • (2001) J. Mol. Biol. , vol.312 , pp. 823-832
    • Huber, P.W.1    Rife, J.P.2    Moore, P.B.3
  • 30
    • 0034975454 scopus 로고    scopus 로고
    • A conserved pseudouridine modification in eukaryotic U2 snRNA induces a change in branch-site architecture
    • Newby M.I., Greenbaum N.L. A conserved pseudouridine modification in eukaryotic U2 snRNA induces a change in branch-site architecture. RNA. 7:2001;833-845.
    • (2001) RNA , vol.7 , pp. 833-845
    • Newby, M.I.1    Greenbaum, N.L.2
  • 31
    • 0030069826 scopus 로고    scopus 로고
    • Structure of the polyadenylation regulatory element of the human U1A pre-mRNA 3′ untranslated region and interaction with the U1A protein
    • Gubser C.C., Varani G. Structure of the polyadenylation regulatory element of the human U1A pre-mRNA 3′ untranslated region and interaction with the U1A protein. Biochemistry. 35:1996;2253-2267.
    • (1996) Biochemistry , vol.35 , pp. 2253-2267
    • Gubser, C.C.1    Varani, G.2
  • 32
    • 0024058085 scopus 로고
    • The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
    • Lavery R., Sklenar H. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. Biol. Struct. Dynam. 6:1988;63-91.
    • (1988) Biol. Struct. Dynam. , vol.6 , pp. 63-91
    • Lavery, R.1    Sklenar, H.2
  • 33
    • 0032999204 scopus 로고    scopus 로고
    • Refinement of the structure of protein-RNA complexes by residual dipolar coupling analysis
    • Bayer P., Varani L., Varani G. Refinement of the structure of protein-RNA complexes by residual dipolar coupling analysis. J. Biomol. NMR. 14:1999;149-155.
    • (1999) J. Biomol. NMR , vol.14 , pp. 149-155
    • Bayer, P.1    Varani, L.2    Varani, G.3
  • 34
    • 0034130999 scopus 로고    scopus 로고
    • Filamentous bacteriophage for aligning RNA, DNA, and proteins for measurement of nuclear magnetic resonance dipolar coupling interactions
    • Hansen M., Hansen P., Pardi A. Filamentous bacteriophage for aligning RNA, DNA, and proteins for measurement of nuclear magnetic resonance dipolar coupling interactions. Methods Enzymol. 317:2000;220-240.
    • (2000) Methods Enzymol. , vol.317 , pp. 220-240
    • Hansen, M.1    Hansen, P.2    Pardi, A.3
  • 35
    • 0034638401 scopus 로고    scopus 로고
    • Determining DNA global structure and DNA bending by application of NMR residual dipolar couplings
    • Vermeulen A., Zhou H., Pardi A. Determining DNA global structure and DNA bending by application of NMR residual dipolar couplings. J. Am. Chem. Soc. 122:2000;9638-9647.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 9638-9647
    • Vermeulen, A.1    Zhou, H.2    Pardi, A.3
  • 36
    • 0032580790 scopus 로고    scopus 로고
    • 13C relaxation and dynamics of the purine bases in the iron responsive element RNA hairpin
    • Hall K.B., Tang C. 13C relaxation and dynamics of the purine bases in the iron responsive element RNA hairpin. Biochemistry. 37:1998;9323-9332.
    • (1998) Biochemistry , vol.37 , pp. 9323-9332
    • Hall, K.B.1    Tang, C.2
  • 38
    • 0028268016 scopus 로고
    • Binding of an HIV-Rev peptide to Rev response element RNA induces formation of purine-purine base pairs
    • Battiste J.L., Rao N.S., Frankel A.D., Williamson J.R. Binding of an HIV-Rev peptide to Rev response element RNA induces formation of purine-purine base pairs. Biochemistry. 33:1994;2741-2747.
    • (1994) Biochemistry , vol.33 , pp. 2741-2747
    • Battiste, J.L.1    Rao, N.S.2    Frankel, A.D.3    Williamson, J.R.4
  • 40
    • 0027960331 scopus 로고
    • Crystal structure of an RNA bacteriophage coat protein-operator complex
    • Valegard K., Murray J.B., Stockely P.G., Stonehouse J., Liljas L. Crystal structure of an RNA bacteriophage coat protein-operator complex. Nature. 371:1994;623-626.
    • (1994) Nature , vol.371 , pp. 623-626
    • Valegard, K.1    Murray, J.B.2    Stockely, P.G.3    Stonehouse, J.4    Liljas, L.5
  • 41
    • 0030795362 scopus 로고    scopus 로고
    • Analysis of cis-acting sequence and structural elements required for antitermination of the Bacillus subtilis tyrS gene
    • Rollins S.M., Grundy F.J., Henkin T.M. Analysis of cis-acting sequence and structural elements required for antitermination of the Bacillus subtilis tyrS gene. Mol. Microbiol. 25:1997;411-421.
    • (1997) Mol. Microbiol. , vol.25 , pp. 411-421
    • Rollins, S.M.1    Grundy, F.J.2    Henkin, T.M.3
  • 42
    • 0032533772 scopus 로고    scopus 로고
    • RNA bulge entropies in the unbound state correlate with peptide binding strengths for HIV-1 and BIV TAR RNA because of improved conformational access
    • Lustig B., Bahar I., Jernigan R. RNA bulge entropies in the unbound state correlate with peptide binding strengths for HIV-1 and BIV TAR RNA because of improved conformational access. Nucl. Acids Res. 26:1998;5212-5217.
    • (1998) Nucl. Acids Res. , vol.26 , pp. 5212-5217
    • Lustig, B.1    Bahar, I.2    Jernigan, R.3
  • 43
    • 0036290269 scopus 로고    scopus 로고
    • Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings
    • Al-Hashimi H.M., Gosser Y., Gorin A., Hu W., Majumdar A., Patel D.J. Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings. J. Mol. Biol. 315:2002;95-102.
    • (2002) J. Mol. Biol. , vol.315 , pp. 95-102
    • Al-Hashimi, H.M.1    Gosser, Y.2    Gorin, A.3    Hu, W.4    Majumdar, A.5    Patel, D.J.6
  • 44
    • 0035838382 scopus 로고    scopus 로고
    • Current topics in RNA-protein recognition: Control of specificity and biological function through induced fit and conformational capture
    • Leulliot N., Varani G. Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture. Biochemistry. 40:2001;7947-7956.
    • (2001) Biochemistry , vol.40 , pp. 7947-7956
    • Leulliot, N.1    Varani, G.2
  • 47
    • 0024819449 scopus 로고
    • Synthesis of small RNAs using T7 RNA polymerase
    • Milligan J.F., Uhlenbeck O.C. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol. 180:1989;51-62.
    • (1989) Methods Enzymol. , vol.180 , pp. 51-62
    • Milligan, J.F.1    Uhlenbeck, O.C.2
  • 48
    • 0028803380 scopus 로고
    • Preparation of isotopically enriched RNAs for heteronuclear NMR
    • Batey R.T., Battiste J.L., Williamson J.R. Preparation of isotopically enriched RNAs for heteronuclear NMR. Methods Enzymol. 261:1995;300.
    • (1995) Methods Enzymol. , vol.261 , pp. 300
    • Batey, R.T.1    Battiste, J.L.2    Williamson, J.R.3
  • 49
    • 0001591905 scopus 로고
    • Separation and suppression of coherent transfer effects in two-dimenstional NOE and chemical exchange spectroscopy
    • Macura S., Wüthrich K., Ernst R.R. Separation and suppression of coherent transfer effects in two-dimenstional NOE and chemical exchange spectroscopy. J. Magn. Reson. 46:1982;269-282.
    • (1982) J. Magn. Reson. , vol.46 , pp. 269-282
    • Macura, S.1    Wüthrich, K.2    Ernst, R.R.3
  • 51
    • 0021114895 scopus 로고
    • Application of phase-sensitive two-dimensional correlated spectroscopy COSY for measurements of proton-proton spin-spin couplings in proteins
    • Marion D., Wüthrich K. Application of phase-sensitive two-dimensional correlated spectroscopy COSY for measurements of proton-proton spin-spin couplings in proteins. Biochem. Biophys. Res. Commun. 113:1983;967-974.
    • (1983) Biochem. Biophys. Res. Commun. , vol.113 , pp. 967-974
    • Marion, D.1    Wüthrich, K.2
  • 52
    • 48749147783 scopus 로고
    • An improved sequence for broadband decoupling: WALTZ16
    • Shaka A.J., Keeler J., Frenkeil T., Freeman R. An improved sequence for broadband decoupling: WALTZ16. J. Magn. Res. 52:1983;335-338.
    • (1983) J. Magn. Res. , vol.52 , pp. 335-338
    • Shaka, A.J.1    Keeler, J.2    Frenkeil, T.3    Freeman, R.4
  • 53
    • 0006925492 scopus 로고
    • Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity
    • Kay L.E., Keifer P., Saarinen T. Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity. J. Am. Chem. Soc. 114:1992;10663-10665.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 10663-10665
    • Kay, L.E.1    Keifer, P.2    Saarinen, T.3
  • 54
    • 44949276869 scopus 로고
    • Sensitivity improvement inproon detected two dimensional heteronuclear NMR spectroscopy
    • Palmer A.G. III, Cavanagh J., Wright P.E., Rance M. Sensitivity improvement inproon detected two dimensional heteronuclear NMR spectroscopy. J. Magn. Reson. 93:1991;151-170.
    • (1991) J. Magn. Reson. , vol.93 , pp. 151-170
    • Palmer A.G. III1    Cavanagh, J.2    Wright, P.E.3    Rance, M.4
  • 56
    • 45249127991 scopus 로고
    • Rapid recording of 2D NMR spectra without phase cycling; Application to the study of hydrogen exchange in proteins
    • Marion D., Ikura M., Tschudin R., Bax A. Rapid recording of 2D NMR spectra without phase cycling; application to the study of hydrogen exchange in proteins. J. Magn. Reson. 85:1989;393-399.
    • (1989) J. Magn. Reson. , vol.85 , pp. 393-399
    • Marion, D.1    Ikura, M.2    Tschudin, R.3    Bax, A.4
  • 57
    • 0000492963 scopus 로고
    • Broadband homonuclear cross polarization in 2D NMR using DIPSI-2
    • Rucker S.P., Shaka A.J. Broadband homonuclear cross polarization in 2D NMR using DIPSI-2. Mol. Phys. 68:1989;509-517.
    • (1989) Mol. Phys. , vol.68 , pp. 509-517
    • Rucker, S.P.1    Shaka, A.J.2
  • 58
    • 0030918784 scopus 로고    scopus 로고
    • Chirality errors in nucleic acid structures
    • Schultze P., Feigon J. Chirality errors in nucleic acid structures. Nature. 387:1997;668.
    • (1997) Nature , vol.387 , pp. 668
    • Schultze, P.1    Feigon, J.2
  • 59
    • 0024556774 scopus 로고
    • Conformational and helicoidal analysis of 30 ps of molecular dynamics on the d(CGCGAATTCGCG) double helix: "Curves", dials and windows
    • Ravishankar G., Swaminathan S., Beveridge D.L., Lavery R., Sklenar H. Conformational and helicoidal analysis of 30 ps of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows. J. Biomol. Struct. Dynam. 6:1989;669-699.
    • (1989) J. Biomol. Struct. Dynam. , vol.6 , pp. 669-699
    • Ravishankar, G.1    Swaminathan, S.2    Beveridge, D.L.3    Lavery, R.4    Sklenar, H.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.