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Volumn 44, Issue 40, 2005, Pages 13404-13414

The kinetics of ligand binding by an adenine-sensing riboswitch

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; CONCENTRATION (PROCESS); PROTEINS; RNA; THERMODYNAMICS;

EID: 26444620938     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi051008u     Document Type: Article
Times cited : (240)

References (37)
  • 1
    • 0142075327 scopus 로고    scopus 로고
    • Genetic control by metabolite-binding riboswitches
    • Winkler, W. C., and Breaker, R. R. (2003) Genetic control by metabolite-binding riboswitches, ChemBioChem 4, 1024-1032.
    • (2003) ChemBioChem , vol.4 , pp. 1024-1032
    • Winkler, W.C.1    Breaker, R.R.2
  • 3
    • 5044234799 scopus 로고    scopus 로고
    • A glycine-dependent riboswitch that uses cooperative binding to control gene expression
    • Mandal, M., Lee, M., Barrick, J. E., Weinberg, Z., Emilsson, G. M., Ruzzo, W. L., and Breaker, R. R. (2004) A glycine-dependent riboswitch that uses cooperative binding to control gene expression, Science 306, 275-279.
    • (2004) Science , vol.306 , pp. 275-279
    • Mandal, M.1    Lee, M.2    Barrick, J.E.3    Weinberg, Z.4    Emilsson, G.M.5    Ruzzo, W.L.6    Breaker, R.R.7
  • 4
    • 0346687595 scopus 로고    scopus 로고
    • The riboswitch control of bacterial metabolism
    • Nudler, E., and Mironov, A. S. (2004) The riboswitch control of bacterial metabolism, Trends Biochem. Sci. 29, 11-17.
    • (2004) Trends Biochem. Sci. , vol.29 , pp. 11-17
    • Nudler, E.1    Mironov, A.S.2
  • 5
    • 0347418195 scopus 로고    scopus 로고
    • Riboswitches: The oldest mechanism for the regulation of gene expression?
    • Vitreschak, A. G., Rodionov, D. A., Mironov, A. A., and Gelfand, M. S. (2004) Riboswitches: the oldest mechanism for the regulation of gene expression?, Trends Genet. 20, 44-50.
    • (2004) Trends Genet. , vol.20 , pp. 44-50
    • Vitreschak, A.G.1    Rodionov, D.A.2    Mironov, A.A.3    Gelfand, M.S.4
  • 6
    • 1642586299 scopus 로고    scopus 로고
    • Control of gene expression by a natural metabolite-responsive ribozyme
    • Winkler, W. C., Nahvi, A., Roth, A., Collins, J. A., and Breaker, R. R. (2004) Control of gene expression by a natural metabolite-responsive ribozyme, Nature 428, 281-286.
    • (2004) Nature , vol.428 , pp. 281-286
    • Winkler, W.C.1    Nahvi, A.2    Roth, A.3    Collins, J.A.4    Breaker, R.R.5
  • 7
    • 0037206833 scopus 로고    scopus 로고
    • Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression
    • Winkler, W. C., Nahvi, A., and Breaker, R. R. (2002) Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression, Nature 419, 952-956.
    • (2002) Nature , vol.419 , pp. 952-956
    • Winkler, W.C.1    Nahvi, A.2    Breaker, R.R.3
  • 9
    • 0346366823 scopus 로고    scopus 로고
    • Thiamine-regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5′-UTR
    • Kubodera, T., Watanabe, M., Yoshiuchi, K., Yamashita, N., Nishimura, A., Nakai, S., Gomi, K., and Hanamoto, H. (2003) Thiamine-regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5′-UTR, FEBS Lett. 555, 516-520.
    • (2003) FEBS Lett. , vol.555 , pp. 516-520
    • Kubodera, T.1    Watanabe, M.2    Yoshiuchi, K.3    Yamashita, N.4    Nishimura, A.5    Nakai, S.6    Gomi, K.7    Hanamoto, H.8
  • 10
    • 0038136962 scopus 로고    scopus 로고
    • Metabolite-binding RNA domains are present in the genes of eukaryotes
    • Sudarsan, N., Barrick, J. E., and Breaker, R. R. (2003) Metabolite-binding RNA domains are present in the genes of eukaryotes, RNA 9, 644-647.
    • (2003) RNA , vol.9 , pp. 644-647
    • Sudarsan, N.1    Barrick, J.E.2    Breaker, R.R.3
  • 11
    • 15944382675 scopus 로고    scopus 로고
    • The speed of RNA transcription and ligand binding kinetics operate an FMN binding riboswitch
    • Wickiser, J. K., Winkler, W. C., Breaker, R. R., and Crothers, D. M. (2005) The speed of RNA transcription and ligand binding kinetics operate an FMN binding riboswitch, Mol. Cell 18, 49-60.
    • (2005) Mol. Cell , vol.18 , pp. 49-60
    • Wickiser, J.K.1    Winkler, W.C.2    Breaker, R.R.3    Crothers, D.M.4
  • 12
    • 0242298623 scopus 로고    scopus 로고
    • An mRNA structure in bacteria that controls gene expression by binding lysine
    • Sudarsan, N., Wickiser, J. K., Nakamura, S., Ebert, M. S., and Breaker, R. R. (2003) An mRNA structure in bacteria that controls gene expression by binding lysine, Genes Dev. 17, 2688-2697.
    • (2003) Genes Dev. , vol.17 , pp. 2688-2697
    • Sudarsan, N.1    Wickiser, J.K.2    Nakamura, S.3    Ebert, M.S.4    Breaker, R.R.5
  • 13
    • 0042890402 scopus 로고    scopus 로고
    • Definition of a second Bacillus subtilis pur regulon comprising the pur and xpt-pbuX operons plus pbuG, nupG (yxjA), and pbuE (ydhL)
    • Johansen, L. E., Nygaard, P., Lassen, C., Agerso, Y., and Saxild, H. H. (2003) Definition of a second Bacillus subtilis pur regulon comprising the pur and xpt-pbuX operons plus pbuG, nupG (yxjA), and pbuE (ydhL), J. Bacteriol. 185, 5200-5209.
    • (2003) J. Bacteriol. , vol.185 , pp. 5200-5209
    • Johansen, L.E.1    Nygaard, P.2    Lassen, C.3    Agerso, Y.4    Saxild, H.H.5
  • 14
    • 11844290117 scopus 로고    scopus 로고
    • The purine efflux pump PbuE in Bacillus subtilis modulates expression of the PurR and G-Box (XptR) regulons by adjusting the purine base pool size
    • Nygaard, P., and Saxild, H. H. (2005) The purine efflux pump PbuE in Bacillus subtilis modulates expression of the PurR and G-Box (XptR) regulons by adjusting the purine base pool size, J. Bacteriol. 187, 791-794.
    • (2005) J. Bacteriol. , vol.187 , pp. 791-794
    • Nygaard, P.1    Saxild, H.H.2
  • 15
    • 0038210214 scopus 로고    scopus 로고
    • Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria
    • Mandal, M., Boese, B., Barrick, J. E., Winkler, W. C., and Breaker, R. R. (2003) Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria, Cell 113, 577-586.
    • (2003) Cell , vol.113 , pp. 577-586
    • Mandal, M.1    Boese, B.2    Barrick, J.E.3    Winkler, W.C.4    Breaker, R.R.5
  • 17
    • 9244225713 scopus 로고    scopus 로고
    • Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine
    • Batey, R. T., Gilbert, S. D., and Montange, R. K. (2004) Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine, Nature 432, 411-415.
    • (2004) Nature , vol.432 , pp. 411-415
    • Batey, R.T.1    Gilbert, S.D.2    Montange, R.K.3
  • 18
    • 12344273534 scopus 로고    scopus 로고
    • Riboswitch structures: Purine ligands replace tertiary contacts
    • Lescoute, A., and Westhof, E. (2005) Riboswitch structures: purine ligands replace tertiary contacts, Chem. Biol. 12, 10-13.
    • (2005) Chem. Biol. , vol.12 , pp. 10-13
    • Lescoute, A.1    Westhof, E.2
  • 19
    • 13444271576 scopus 로고    scopus 로고
    • An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs
    • Noeske, J., Richter, C., Grundl, M. A., Nasiri, H. R., Schwalbe, H., and Wohnert, J. (2005) An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs, Proc. Natl. Acad. Sci. U.S.A. 102, 1372-1377.
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 1372-1377
    • Noeske, J.1    Richter, C.2    Grundl, M.A.3    Nasiri, H.R.4    Schwalbe, H.5    Wohnert, J.6
  • 20
    • 0842334528 scopus 로고    scopus 로고
    • Adenine riboswitches and gene activation by disruption of a transcription terminator
    • Mandal, M., and Breaker, R. R. (2004) Adenine riboswitches and gene activation by disruption of a transcription terminator, Nat. Struct. Mol. Biol. 11, 29-35.
    • (2004) Nat. Struct. Mol. Biol. , vol.11 , pp. 29-35
    • Mandal, M.1    Breaker, R.R.2
  • 22
    • 2442626706 scopus 로고    scopus 로고
    • Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
    • Mathews, D. H., Disney, M. D., Childs, J. L., Schroeder, S. J., Zuker, M., and Turner, D. H. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure, Proc. Natl. Acad. Sci. U.S.A. 101, 7287-7292.
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 7287-7292
    • Mathews, D.H.1    Disney, M.D.2    Childs, J.L.3    Schroeder, S.J.4    Zuker, M.5    Turner, D.H.6
  • 23
    • 0032831634 scopus 로고    scopus 로고
    • Relationship between internucleotide linkage geometry and the stability of RNA
    • Soukup, G. A., and Breaker, R. R. (1999) Relationship between internucleotide linkage geometry and the stability of RNA, RNA 5, 1308-1325.
    • (1999) RNA , vol.5 , pp. 1308-1325
    • Soukup, G.A.1    Breaker, R.R.2
  • 24
    • 0014669561 scopus 로고
    • Fluorescence studies of nucleotides and polynucleotides. I. Formycin 2-aminopurine riboside 2,6-diaminopurine riboside and their derivatives
    • Ward, D. C., Reich, E., and Stryer, L. (1969) Fluorescence studies of nucleotides and polynucleotides. I. Formycin 2-aminopurine riboside 2,6-diaminopurine riboside and their derivatives, J. Biol. Chem. 244, 1228-1237.
    • (1969) J. Biol. Chem. , vol.244 , pp. 1228-1237
    • Ward, D.C.1    Reich, E.2    Stryer, L.3
  • 25
  • 26
    • 0014674138 scopus 로고
    • Relaxation studies of the proflavine-DNA complex: The kinetics of an intercalation reaction
    • Li, H. J., and Crothers, D. M. (1969) Relaxation studies of the proflavine-DNA complex: the kinetics of an intercalation reaction, J. Mol. Biol. 39, 461-477.
    • (1969) J. Mol. Biol. , vol.39 , pp. 461-477
    • Li, H.J.1    Crothers, D.M.2
  • 27
    • 0032516019 scopus 로고    scopus 로고
    • Simultaneous determination of helical unwinding angles and intrinsic association constants in ligand-DNA complexes: The interaction between DNA and calichearubicin B
    • Zeman, S. M., Depew, K. M., Danishefsky, S. J., and Crothers, D. M. (1998) Simultaneous determination of helical unwinding angles and intrinsic association constants in ligand-DNA complexes: The interaction between DNA and calichearubicin B, Proc. Natl. Acad. Sci. U.S.A. 95, 4327-4332.
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.95 , pp. 4327-4332
    • Zeman, S.M.1    Depew, K.M.2    Danishefsky, S.J.3    Crothers, D.M.4
  • 28
    • 0019886894 scopus 로고
    • Pausing of RNA polymerase during in vitro transcription of the tryptophan operon leader region
    • Winkler, M. E., and Yanofsky, C. (1981) Pausing of RNA polymerase during in vitro transcription of the tryptophan operon leader region, Biochemistry 20, 3738-3744.
    • (1981) Biochemistry , vol.20 , pp. 3738-3744
    • Winkler, M.E.1    Yanofsky, C.2
  • 29
    • 10044287423 scopus 로고    scopus 로고
    • Single molecule studies of sequence-dependent transcription pausing
    • Shundrovsky, A., Santangelo, T. J., Roberts, J. W., and Wang, M. D. (2004) Single molecule studies of sequence-dependent transcription pausing, Biophys. J. 87, 3945-3953.
    • (2004) Biophys. J. , vol.87 , pp. 3945-3953
    • Shundrovsky, A.1    Santangelo, T.J.2    Roberts, J.W.3    Wang, M.D.4
  • 30
    • 0033578330 scopus 로고    scopus 로고
    • Folding of a large ribozyme during transcription and the effect of the elongation factor NusA
    • Pan, T., Artsimovitch, I., Fang, X. W., Landick, R., and Sosnick, T. R. (1999) Folding of a large ribozyme during transcription and the effect of the elongation factor NusA, Proc. Natl. Acad. Sci. U.S.A. 96, 9545-9550.
    • (1999) Proc. Natl. Acad. Sci. U.S.A. , vol.96 , pp. 9545-9550
    • Pan, T.1    Artsimovitch, I.2    Fang, X.W.3    Landick, R.4    Sosnick, T.R.5
  • 31
    • 0025082365 scopus 로고
    • RNA folding during transcription by Escherichia coli RNA polymerase analyzed by RNA self-cleavage
    • Monforte, J. A., Kahn, J. D., and Hearst, J. E. (1990) RNA folding during transcription by Escherichia coli RNA polymerase analyzed by RNA self-cleavage, Biochemistry 29, 7882-7890.
    • (1990) Biochemistry , vol.29 , pp. 7882-7890
    • Monforte, J.A.1    Kahn, J.D.2    Hearst, J.E.3
  • 32
    • 0032438195 scopus 로고    scopus 로고
    • Functional topography of nascent RNA in elongation intermediates of RNA polymerase
    • Komissarova, N., and Kashlev, M. (1998) Functional topography of nascent RNA in elongation intermediates of RNA polymerase, Proc. Natl. Acad. Sci. U.S.A. 95, 14699-14704.
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.95 , pp. 14699-14704
    • Komissarova, N.1    Kashlev, M.2
  • 34
    • 19244382579 scopus 로고    scopus 로고
    • Diversity in the rates of transcript elongation by single RNA polymerase molecules
    • Tolic-Norrelykke, S. F., Engh, A. M., Landick, R., and Gelles, J. (2004) Diversity in the rates of transcript elongation by single RNA polymerase molecules, J. Biol. Chem. 279, 3292-3299.
    • (2004) J. Biol. Chem. , vol.279 , pp. 3292-3299
    • Tolic-Norrelykke, S.F.1    Engh, A.M.2    Landick, R.3    Gelles, J.4
  • 35
    • 0027173194 scopus 로고
    • The Leptomonas collosoma spliced leader RNA can switch between 2 alternate structural forms
    • Lecuyer, K. A., and Crothers, D. M. (1993) The Leptomonas collosoma spliced leader RNA can switch between 2 alternate structural forms, Biochemistry 32, 5301-5311.
    • (1993) Biochemistry , vol.32 , pp. 5301-5311
    • Lecuyer, K.A.1    Crothers, D.M.2
  • 37
    • 0037143667 scopus 로고    scopus 로고
    • NusA-stimulated RNA polymerase pausing and termination participates in the Bacillus subtilis trp operon attenuation mechanism in vitro
    • Yakhnin, A. V., and Babitzke, P. (2002) NusA-stimulated RNA polymerase pausing and termination participates in the Bacillus subtilis trp operon attenuation mechanism in vitro, Proc. Natl. Acad. Sci. U.S.A. 99, 11067-72.
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 11067-11072
    • Yakhnin, A.V.1    Babitzke, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.