메뉴 건너뛰기




Volumn 52, Issue 48, 2013, Pages 8777-8785

The cellular environment stabilizes adenine riboswitch RNA structure

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR ENVIRONMENT; ESCHERICHIA COLI CELLS; IN-VITRO ANALYSIS; LIGAND BINDING; PRIMER EXTENSION; RIBOSWITCHES; RNA STRUCTURES; TIME-SCALES;

EID: 84889243990     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi401207q     Document Type: Article
Times cited : (92)

References (55)
  • 1
    • 0026344818 scopus 로고
    • Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli
    • Zimmerman, S. B. and Trach, S. O. (1991) Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli J. Mol. Biol. 222, 599-620
    • (1991) J. Mol. Biol. , vol.222 , pp. 599-620
    • Zimmerman, S.B.1    Trach, S.O.2
  • 2
    • 0022001625 scopus 로고
    • Polyamines in microorganisms
    • Tabor, C. W. and Tabor, H. (1985) Polyamines in microorganisms Microbiol. Rev. 49, 81-99 (Pubitemid 15134122)
    • (1985) Microbiological Reviews , vol.49 , Issue.1 , pp. 81-99
    • Tabor, C.W.1    Tabor, H.2
  • 3
    • 0027265852 scopus 로고
    • Estimation of polyamine distribution and polyamine stimulation of protein synthesis in Escherichia coli
    • DOI 10.1006/abbi.1993.1009
    • Miyamoto, S., Kashiwagi, K., Ito, K., Watanabe, S., and Igarashi, K. (1993) Estimation of polyamine distribution and polyamine stimulation of protein synthesis in Escherichia coli Arch. Biochem. Biophys. 300, 63-68 (Pubitemid 23225718)
    • (1993) Archives of Biochemistry and Biophysics , vol.300 , Issue.1 , pp. 63-68
    • Miyamoto, S.1    Kashiwagi, K.2    Ito, K.3    Watanabe, S.4    Igarashi, K.5
  • 4
    • 68049100110 scopus 로고    scopus 로고
    • Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
    • Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., and Rabinowitz, J. D. (2009) Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli Nat. Chem. Biol. 5, 593-599
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 593-599
    • Bennett, B.D.1    Kimball, E.H.2    Gao, M.3    Osterhout, R.4    Van Dien, S.J.5    Rabinowitz, J.D.6
  • 6
    • 84985735713 scopus 로고
    • Excluded volume as a determinant of macromolecular structure and reactivity
    • Minton, A. P. (1981) Excluded volume as a determinant of macromolecular structure and reactivity Biopolymers 20, 2093-2120
    • (1981) Biopolymers , vol.20 , pp. 2093-2120
    • Minton, A.P.1
  • 7
    • 41049090929 scopus 로고    scopus 로고
    • Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences
    • Zhou, H. X., Rivas, G., and Minton, A. P. (2008) Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences Annu. Rev. Biophys. 37, 375-397
    • (2008) Annu. Rev. Biophys. , vol.37 , pp. 375-397
    • Zhou, H.X.1    Rivas, G.2    Minton, A.P.3
  • 9
    • 84877014249 scopus 로고    scopus 로고
    • Soft interactions and crowding
    • Sarkar, M., Li, C., and Pielak, G. J. (2013) Soft interactions and crowding Biophys. Rev. 5, 187-194
    • (2013) Biophys. Rev. , vol.5 , pp. 187-194
    • Sarkar, M.1    Li, C.2    Pielak, G.J.3
  • 10
    • 70450159038 scopus 로고    scopus 로고
    • Facilitation of RNA enzyme activity in the molecular crowding media of cosolutes
    • Nakano, S., Karimata, H. T., Kitagawa, Y., and Sugimoto, N. (2009) Facilitation of RNA enzyme activity in the molecular crowding media of cosolutes J. Am. Chem. Soc. 131, 16881-16888
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 16881-16888
    • Nakano, S.1    Karimata, H.T.2    Kitagawa, Y.3    Sugimoto, N.4
  • 11
    • 79961136147 scopus 로고    scopus 로고
    • Crowding promotes the switch from hairpin to pseudoknot conformation in human telomerase RNA
    • Denesyuk, N. A. and Thirumalai, D. (2011) Crowding promotes the switch from hairpin to pseudoknot conformation in human telomerase RNA J. Am. Chem. Soc. 133, 11858-11861
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 11858-11861
    • Denesyuk, N.A.1    Thirumalai, D.2
  • 12
    • 77953900637 scopus 로고    scopus 로고
    • Molecular crowding stabilizes folded RNA structure by the excluded volume effect
    • Kilburn, D., Roh, J. H., Guo, L., Briber, R. M., and Woodson, S. A. (2011) Molecular crowding stabilizes folded RNA structure by the excluded volume effect J. Am. Chem. Soc. 132, 8690-8696
    • (2011) J. Am. Chem. Soc. , vol.132 , pp. 8690-8696
    • Kilburn, D.1    Roh, J.H.2    Guo, L.3    Briber, R.M.4    Woodson, S.A.5
  • 13
    • 1242274330 scopus 로고    scopus 로고
    • A guide to ions and RNA structure
    • DOI 10.1261/rna.5205404
    • Draper, D. E. (2004) A guide to ions and RNA structure RNA 10, 335-343 (Pubitemid 38240993)
    • (2004) RNA , vol.10 , Issue.3 , pp. 335-343
    • Draper, D.E.1
  • 14
    • 84883214087 scopus 로고    scopus 로고
    • 2+ with RNA rertiary structures: Similar versus differential effects on the stabilities of diverse RNA folds
    • 2+ with RNA rertiary structures: Similar versus differential effects on the stabilities of diverse RNA folds Biochemistry 52, 5911-5919
    • (2013) Biochemistry , vol.52 , pp. 5911-5919
    • Trachman III, R.J.1    Draper, D.E.2
  • 15
  • 16
    • 78049279838 scopus 로고    scopus 로고
    • Probing RNA structure within living cells
    • Liebeg, A. and Waldsich, C. (2009) Probing RNA structure within living cells Methods Enzymol. 468, 219-238
    • (2009) Methods Enzymol. , vol.468 , pp. 219-238
    • Liebeg, A.1    Waldsich, C.2
  • 17
    • 67649371451 scopus 로고    scopus 로고
    • Influence of nucleotide identity on ribose 2′-hydroxyl reactivity in RNA
    • Wilkinson, K. A., Vasa, S. M., Deigan, K. E., Mortimer, S. A., Giddings, M. C., and Weeks, K. M. (2009) Influence of nucleotide identity on ribose 2′-hydroxyl reactivity in RNA RNA 15, 1314-1321
    • (2009) RNA , vol.15 , pp. 1314-1321
    • Wilkinson, K.A.1    Vasa, S.M.2    Deigan, K.E.3    Mortimer, S.A.4    Giddings, M.C.5    Weeks, K.M.6
  • 18
    • 16244412610 scopus 로고    scopus 로고
    • RNA structure analysis at single nucleotide resolution by Selective 2′-Hydroxyl Acylation and Primer Extension (SHAPE)
    • DOI 10.1021/ja043822v
    • Merino, E. J., Wilkinson, K. A., Coughlan, J. L., and Weeks, K. M. (2005) RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE) J. Am. Chem. Soc. 127, 4223-4231 (Pubitemid 40463047)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.12 , pp. 4223-4231
    • Merino, E.J.1    Wilkinson, K.A.2    Coughlan, J.L.3    Weeks, K.M.4
  • 19
    • 40849118189 scopus 로고    scopus 로고
    • Asp revealed by single-nucleotide resolution SHAPE chemistry
    • DOI 10.1021/bi702372x
    • Wang, B., Wilkinson, K. A., and Weeks, K. M. (2008) Complex ligand-induced conformational changes in tRNA(Asp) revealed by single-nucleotide resolution SHAPE chemistry Biochemistry 47, 3454-3461 (Pubitemid 351399234)
    • (2008) Biochemistry , vol.47 , Issue.11 , pp. 3454-3461
    • Wang, B.1    Wilkinson, K.A.2    Weeks, K.M.3
  • 20
    • 79960611669 scopus 로고    scopus 로고
    • Exploring RNA structural codes with SHAPE chemistry
    • Weeks, K. M. and Mauger, D. M. (2011) Exploring RNA structural codes with SHAPE chemistry Acc. Chem. Res. 44, 1280-1291
    • (2011) Acc. Chem. Res. , vol.44 , pp. 1280-1291
    • Weeks, K.M.1    Mauger, D.M.2
  • 23
    • 40849123031 scopus 로고    scopus 로고
    • High-Throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states
    • Wilkinson, K. A., Gorelick, R. J., Vasa, S. M., Guex, N., Rein, A., Mathews, D. H., Giddings, M. C., and Weeks, K. M. (2008) High-Throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states PLoS Biol. 6, e96
    • (2008) PLoS Biol. , vol.6 , pp. 96
    • Wilkinson, K.A.1    Gorelick, R.J.2    Vasa, S.M.3    Guex, N.4    Rein, A.5    Mathews, D.H.6    Giddings, M.C.7    Weeks, K.M.8
  • 28
    • 34447548824 scopus 로고    scopus 로고
    • Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control
    • DOI 10.1002/cbic.200700057
    • Rieder, R., Lang, K., Graber, D., and Micura, R. (2007) Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control ChemBioChem 8, 896-902 (Pubitemid 47194838)
    • (2007) ChemBioChem , vol.8 , Issue.8 , pp. 896-902
    • Rieder, R.1    Lang, K.2    Graber, D.3    Micura, R.4
  • 29
    • 54849437727 scopus 로고    scopus 로고
    • Relative stability of helices determines the folding landscape of adenine riboswitch aptamers
    • Lin, J. C. and Thirumalai, D. (2008) Relative stability of helices determines the folding landscape of adenine riboswitch aptamers J. Am. Chem. Soc. 130, 14080-14081
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 14080-14081
    • Lin, J.C.1    Thirumalai, D.2
  • 30
    • 77952700860 scopus 로고    scopus 로고
    • Real-time multidimensional NMR follows RNA folding with second resolution
    • Lee, M. K., Gal, M., Frydman, L., and Varani, G. (2010) Real-time multidimensional NMR follows RNA folding with second resolution Proc. Natl. Acad. Sci. U.S.A. 107, 9192-9197
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 9192-9197
    • Lee, M.K.1    Gal, M.2    Frydman, L.3    Varani, G.4
  • 31
    • 79953682254 scopus 로고    scopus 로고
    • 2+ on the free energy landscape for folding a purine riboswitch RNA
    • 2+ on the free energy landscape for folding a purine riboswitch RNA Biochemistry 50, 2790-2799
    • (2011) Biochemistry , vol.50 , pp. 2790-2799
    • Leipply, D.1    Draper, D.E.2
  • 35
    • 34547659860 scopus 로고    scopus 로고
    • Recombinant RNA technology: The tRNA scaffold
    • DOI 10.1038/nmeth1058, PII NMETH1058
    • Ponchon, L. and Dardel, F. (2007) Recombinant RNA technology: The tRNA scaffold Nat. Methods 4, 571-576 (Pubitemid 47214776)
    • (2007) Nature Methods , vol.4 , Issue.7 , pp. 571-576
    • Ponchon, L.1    Dardel, F.2
  • 36
    • 66749152587 scopus 로고    scopus 로고
    • A generic protocol for the expression and purification of recombinant RNA in Escherichia coli using a tRNA scaffold
    • Ponchon, L., Beauvais, G., Nonin-Lecomte, S., and Dardel, F. (2009) A generic protocol for the expression and purification of recombinant RNA in Escherichia coli using a tRNA scaffold Nat. Protoc. 4, 947-959
    • (2009) Nat. Protoc. , vol.4 , pp. 947-959
    • Ponchon, L.1    Beauvais, G.2    Nonin-Lecomte, S.3    Dardel, F.4
  • 38
    • 0026409841 scopus 로고
    • Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity: Implications for protein-DNA interactions in vivo
    • Cayley, S., Lewis, B. A., Guttman, H. J., and Record, M. T., Jr. (1991) Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity. Implications for protein-DNA interactions in vivo J. Mol. Biol. 222, 281-300 (Pubitemid 121004007)
    • (1991) Journal of Molecular Biology , vol.222 , Issue.2 , pp. 281-300
    • Cayley, S.1    Lewis, B.A.2    Guttman, H.J.3    Record Jr., M.T.4
  • 39
    • 84871411741 scopus 로고    scopus 로고
    • QuShape: Rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis
    • Karabiber, F., McGinnis, J. L., Favorov, O. V., and Weeks, K. M. (2013) QuShape: Rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis RNA 19, 63-73
    • (2013) RNA , vol.19 , pp. 63-73
    • Karabiber, F.1    McGinnis, J.L.2    Favorov, O.V.3    Weeks, K.M.4
  • 40
    • 0012444011 scopus 로고
    • Insights into the cell envelope of Paracoccus denitrificans, a member of the α-subdivision of purple bacteria, through studies of its lysozyme susceptibility
    • Wee, S. and Wilkinson, B. J. (1988) Insights into the cell envelope of Paracoccus denitrificans, a member of the α-subdivision of purple bacteria, through studies of its lysozyme susceptibility Can. J. Microbiol. 34, 952-959
    • (1988) Can. J. Microbiol. , vol.34 , pp. 952-959
    • Wee, S.1    Wilkinson, B.J.2
  • 41
    • 0026036451 scopus 로고
    • Methods for measurement of intracellular magnesium: NMR and fluorescence
    • London, R. E. (1991) Methods for measurement of intracellular magnesium: NMR and fluorescence Annu. Rev. Physiol. 53, 241-258
    • (1991) Annu. Rev. Physiol. , vol.53 , pp. 241-258
    • London, R.E.1
  • 43
    • 0030783372 scopus 로고    scopus 로고
    • 2+ concentration in smooth muscle cells of guinea pig tenia cecum: Intracellular calibration of the fluorescent indicator furaptra
    • 2+ concentration in smooth muscle cells of guinea pig tenia cecum: Intracellular calibration of the fluorescent indicator furaptra Biophys. J. 73, 3358-3370 (Pubitemid 27525798)
    • (1997) Biophysical Journal , vol.73 , Issue.6 , pp. 3358-3370
    • Tashiro, M.1    Konishi, M.2
  • 44
    • 34247162792 scopus 로고    scopus 로고
    • A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry
    • DOI 10.1021/ja0704028
    • Mortimer, S. A. and Weeks, K. M. (2007) A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry J. Am. Chem. Soc. 129, 4144-4145 (Pubitemid 46595421)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.14 , pp. 4144-4145
    • Mortimer, S.A.1    Weeks, K.M.2
  • 46
    • 0021920739 scopus 로고
    • Rates of diffusion of fluorescent molecules via cell-to-cell membrane channels in a developing tissue
    • DOI 10.1083/jcb.100.3.736
    • Safranyos, R. G. and Caveney, S. (1985) Rates of diffusion of fluorescent molecules via cell-to-cell membrane channels in a developing tissue J. Cell Biol. 100, 736-747 (Pubitemid 15135333)
    • (1985) Journal of Cell Biology , vol.100 , Issue.3 , pp. 736-747
    • Safranyos, R.G.A.1    Caveney, S.2
  • 47
    • 44649148267 scopus 로고    scopus 로고
    • Down to atomic-scale intracellular water dynamics
    • DOI 10.1038/embor.2008.50, PII EMBOR200850
    • Jasnin, M., Moulin, M., Haertlein, M., Zaccai, G., and Tehei, M. (2008) Down to atomic-scale intracellular water dynamics EMBO Rep. 9, 543-547 (Pubitemid 351772917)
    • (2008) EMBO Reports , vol.9 , Issue.6 , pp. 543-547
    • Jasnin, M.1    Moulin, M.2    Haertlein, M.3    Zaccai, G.4    Tehei, M.5
  • 48
    • 77954011992 scopus 로고    scopus 로고
    • Molecular sieving properties of the cytoplasm of Escherichia coli and consequences of osmotic stress
    • Mika, J. T., Van Den Bogaart, G., Veenhoff, L., Krasnikov, V., and Poolman, B. (2010) Molecular sieving properties of the cytoplasm of Escherichia coli and consequences of osmotic stress Mol. Microbiol. 77, 200-207
    • (2010) Mol. Microbiol. , vol.77 , pp. 200-207
    • Mika, J.T.1    Van Den Bogaart, G.2    Veenhoff, L.3    Krasnikov, V.4    Poolman, B.5
  • 49
    • 79551523648 scopus 로고    scopus 로고
    • Macromolecule diffusion and confinement in prokaryotic cells
    • Mika, J. T. and Poolman, B. (2011) Macromolecule diffusion and confinement in prokaryotic cells Curr. Opin. Biotechnol. 22, 117-126
    • (2011) Curr. Opin. Biotechnol. , vol.22 , pp. 117-126
    • Mika, J.T.1    Poolman, B.2
  • 51
    • 70349459246 scopus 로고    scopus 로고
    • C2′-endo nucleotides as molecular timers suggested by the folding of an RNA domain
    • Mortimer, S. A. and Weeks, K. M. (2009) C2′-endo nucleotides as molecular timers suggested by the folding of an RNA domain Proc. Natl. Acad. Sci. U.S.A. 106, 15622-15627
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 15622-15627
    • Mortimer, S.A.1    Weeks, K.M.2
  • 52
    • 84865133584 scopus 로고    scopus 로고
    • Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity
    • Steen, K. A., Rice, G. M., and Weeks, K. M. (2012) Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity J. Am. Chem. Soc. 134, 13160-13163
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 13160-13163
    • Steen, K.A.1    Rice, G.M.2    Weeks, K.M.3
  • 54
    • 33847308180 scopus 로고    scopus 로고
    • Core requirements of the adenine riboswitch aptamer for ligand binding
    • Lemay, J. F. and Lafontaine, D. A. (2007) Core requirements of the adenine riboswitch aptamer for ligand binding RNA 13, 339-350
    • (2007) RNA , vol.13 , pp. 339-350
    • Lemay, J.F.1    Lafontaine, D.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.