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Volumn 409, Issue 5, 2011, Pages 786-799

Variable sequences outside the sam-binding core critically influence the conformational dynamics of the SAM-III/SMK box riboswitch

Author keywords

induced fit; riboswitch; SAM III; SHAPE; SMK

Indexed keywords

RNA; S ADENOSYLMETHIONINE;

EID: 79958031831     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.04.039     Document Type: Article
Times cited : (34)

References (46)
  • 1
    • 20444478991 scopus 로고    scopus 로고
    • Riboswitches as versatile gene control elements
    • DOI 10.1016/j.sbi.2005.05.003, PII S0959440X05000874
    • Tucker B.J., and Breaker R.R. Riboswitches as versatile gene control elements Curr. Opin. Struct. Biol. 15 2005 342 348 (Pubitemid 40826454)
    • (2005) Current Opinion in Structural Biology , vol.15 , Issue.3 SPEC. ISS. , pp. 342-348
    • Tucker, B.J.1    Breaker, R.R.2
  • 2
    • 33750874085 scopus 로고    scopus 로고
    • From ribosome to riboswitch: Control of gene expression in bacteria by RNA structural rearrangements
    • DOI 10.1080/10409230600914294, PII N30R7131220Q9161
    • Grundy F.J., and Henkin T.M. From ribosome to riboswitch: control of gene expression in bacteria by RNA structural rearrangements Crit. Rev. Biochem. Mol. Biol. 41 2006 329 338 (Pubitemid 44722139)
    • (2006) Critical Reviews in Biochemistry and Molecular Biology , vol.41 , Issue.6 , pp. 329-338
    • Grundy, F.J.1    Henkin, T.M.2
  • 3
    • 0347418195 scopus 로고    scopus 로고
    • Riboswitches: The oldest mechanism for the regulation of gene expression?
    • DOI 10.1016/j.tig.2003.11.008
    • Vitreschak A.G., Rodionov D.A., Mironov A.A., and Gelfand M.S. Riboswitches: the oldest mechanism for the regulation of gene expression? Trends Genet. 20 2004 44 50 (Pubitemid 38032819)
    • (2004) Trends in Genetics , vol.20 , Issue.1 , pp. 44-50
    • Vitreschak, A.G.1    Rodionov, D.A.2    Mironov, A.A.3    Gelfand, M.S.4
  • 4
    • 17444403921 scopus 로고    scopus 로고
    • Metabolic monitoring by bacterial mRNAs
    • DOI 10.1007/s00203-005-0758-9
    • Winkler W.C. Metabolic monitoring by bacterial mRNAs Arch. Microbiol. 183 2005 151 159 (Pubitemid 40543777)
    • (2005) Archives of Microbiology , vol.183 , Issue.3 , pp. 151-159
    • Winkler, W.C.1
  • 5
    • 27144527479 scopus 로고    scopus 로고
    • Regulation of bacterial gene expression by riboswitches
    • DOI 10.1146/annurev.micro.59.030804.121336
    • Winkler W.C., and Breaker R.R. Regulation of bacterial gene expression by riboswitches Annu. Rev. Microbiol. 59 2005 487 517 (Pubitemid 41507440)
    • (2005) Annual Review of Microbiology , vol.59 , pp. 487-517
    • Winkler, W.C.1    Breaker, R.R.2
  • 6
    • 0031735563 scopus 로고    scopus 로고
    • The S box regulon: A new global transcription termination control system for methionine and cysteine biosynthesis genes in Gram-positive bacteria
    • DOI 10.1046/j.1365-2958.1998.01105.x
    • Grundy F.J., and Henkin T.M. The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in Gram-positive bacteria Mol. Microbiol. 30 1998 737 749 (Pubitemid 28528593)
    • (1998) Molecular Microbiology , vol.30 , Issue.4 , pp. 737-749
    • Grundy, F.J.1    Henkin, T.M.2
  • 7
    • 0042320361 scopus 로고    scopus 로고
    • An mRNA structure that controls gene expression by binding S-adenosylmethionine
    • DOI 10.1038/nsb967
    • Winkler W.C., Nahvi A., Sudarsan N., Barrick J.E., and Breaker R.R. An mRNA structure that controls gene expression by binding S-adenosylmethionine Nat. Struct. Biol. 10 2003 701 707 (Pubitemid 37052407)
    • (2003) Nature Structural Biology , vol.10 , Issue.9 , pp. 701-707
    • Winkler, W.C.1    Nahvi, A.2    Sudarsan, N.3    Barrick, J.E.4    Breaker, R.R.5
  • 11
    • 40849104495 scopus 로고    scopus 로고
    • The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches
    • DOI 10.1261/rna.988608
    • Weinberg Z., Regulski E.E., Hammond M.C., Barrick J.E., Yao Z., Ruzzo W.L., and Breaker R.R. The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches RNA 14 2008 822 828 (Pubitemid 351574903)
    • (2008) RNA , vol.14 , Issue.5 , pp. 822-828
    • Weinberg, Z.1    Regulski, E.E.2    Hammond, M.C.3    Barrick, J.E.4    Yao, Z.5    Ruzzo, W.L.6    Breaker, R.R.7
  • 12
    • 33644792751 scopus 로고    scopus 로고
    • MK box is a new SAM-binding RNA for translational regulation of SAM synthetase
    • DOI 10.1038/nsmb1059, PII N1059
    • Fuchs R.T., Grundy F.J., and Henkin T.M. The SMK box is a new SAM-binding RNA for translational regulation of SAM synthetase Nat. Struct. Mol. Biol. 13 2006 226 233 (Pubitemid 43348508)
    • (2006) Nature Structural and Molecular Biology , vol.13 , Issue.3 , pp. 226-233
    • Fuchs, R.T.1    Grundy, F.J.2    Henkin, T.M.3
  • 13
    • 41649108068 scopus 로고    scopus 로고
    • 1 aptamer class in Streptococcaceae bacteria
    • DOI 10.1261/rna.937308
    • Meyer M.M., Roth A., Chervin S.M., Garcia G.A., and Breaker R.R. Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria RNA 14 2008 685 695 (Pubitemid 351480881)
    • (2008) RNA , vol.14 , Issue.4 , pp. 685-695
    • Meyer, M.M.1    Roth, A.2    Chervin, S.M.3    Garcia, G.A.4    Breaker, R.R.5
  • 14
    • 32044442926 scopus 로고    scopus 로고
    • Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria
    • Corbino K.A., Barrick J.E., Lim J., Welz R., Tucker B.J., and Puskarz I. Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria Genome Biol. 6 2005 R70
    • (2005) Genome Biol. , vol.6 , pp. 70
    • Corbino, K.A.1    Barrick, J.E.2    Lim, J.3    Welz, R.4    Tucker, B.J.5    Puskarz, I.6
  • 15
    • 70350111141 scopus 로고    scopus 로고
    • A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria
    • Poiata E., Meyer M.M., Ames T.D., and Breaker R.R. A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria RNA 15 2009 2046 2056
    • (2009) RNA , vol.15 , pp. 2046-2056
    • Poiata, E.1    Meyer, M.M.2    Ames, T.D.3    Breaker, R.R.4
  • 17
    • 33745628336 scopus 로고    scopus 로고
    • Structure of the S-adenosylmethionine riboswitch regulatory mRNA element
    • DOI 10.1038/nature04819, PII N04819
    • Montange R.K., and Batey R.T. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element Nature 441 2006 1172 1175 (Pubitemid 43990740)
    • (2006) Nature , vol.441 , Issue.7097 , pp. 1172-1175
    • Montange, R.K.1    Batey, R.T.2
  • 18
    • 48249104039 scopus 로고    scopus 로고
    • Riboswitches: Emerging themes in RNA structure and function
    • Montange R.K., and Batey R.T. Riboswitches: emerging themes in RNA structure and function Annu. Rev. Biophys. 37 2008 117 133
    • (2008) Annu. Rev. Biophys. , vol.37 , pp. 117-133
    • Montange, R.K.1    Batey, R.T.2
  • 20
    • 53549089576 scopus 로고    scopus 로고
    • Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism
    • Lu C., Smith A.M., Fuchs R.T., Ding F., Rajashankar K., Henkin T.M., and Ke A. Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism Nat. Struct. Mol. Biol. 15 2008 1076 1083
    • (2008) Nat. Struct. Mol. Biol. , vol.15 , pp. 1076-1083
    • Lu, C.1    Smith, A.M.2    Fuchs, R.T.3    Ding, F.4    Rajashankar, K.5    Henkin, T.M.6    Ke, A.7
  • 24
    • 70349145411 scopus 로고    scopus 로고
    • Time-resolved RNA SHAPE chemistry: Quantitative RNA structure analysis in one-second snapshots and at single-nucleotide resolution
    • Mortimer S.A., and Weeks K.M. Time-resolved RNA SHAPE chemistry: quantitative RNA structure analysis in one-second snapshots and at single-nucleotide resolution Nat. Protoc. 4 2009 1413 1421
    • (2009) Nat. Protoc. , vol.4 , pp. 1413-1421
    • Mortimer, S.A.1    Weeks, K.M.2
  • 26
    • 0025264854 scopus 로고
    • The equilibrium partition function and base pair binding probabilities for RNA secondary structure
    • McCaskill J.S. The equilibrium partition function and base pair binding probabilities for RNA secondary structure Biopolymers 29 1990 1105 1119 (Pubitemid 20145703)
    • (1990) Biopolymers , vol.29 , Issue.6-7 , pp. 1105-1119
    • McCaskill, J.S.1
  • 29
    • 23144463133 scopus 로고    scopus 로고
    • Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots
    • Xayaphoummine A., Bucher T., and Isambert H. Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots Nucleic Acids Res. 33 2005 W605 W610
    • (2005) Nucleic Acids Res. , vol.33
    • Xayaphoummine, A.1    Bucher, T.2    Isambert, H.3
  • 31
    • 38649086717 scopus 로고    scopus 로고
    • Natural variability in S-adenosylmethionine (SAM)-dependent riboswitches: S-box elements in Bacillus subtilis exhibit differential sensitivity to SAM in vivo and in vitro
    • DOI 10.1128/JB.01034-07
    • Tomsic J., McDaniel B.A., Grundy F.J., and Henkin T.M. Natural variability in S-adenosylmethionine (SAM)-dependent riboswitches: S-box elements in Bacillus subtilis exhibit differential sensitivity to SAM in vivo and in vitro J. Bacteriol. 190 2008 823 833 (Pubitemid 351170925)
    • (2008) Journal of Bacteriology , vol.190 , Issue.3 , pp. 823-833
    • Tomsic, J.1    McDaniel, B.A.2    Grundy, F.J.3    Henkin, T.M.4
  • 32
    • 0024024568 scopus 로고
    • Genetic mapping and physiological consequences of metE mutations of Bacillus subtilis
    • Wabiko H., Ochi K., Nguyen D.M., Allen E.R., and Freese E. Genetic mapping and physiological consequences of metE mutations of Bacillus subtilis J. Bacteriol. 170 1988 2705 2710
    • (1988) J. Bacteriol. , vol.170 , pp. 2705-2710
    • Wabiko, H.1    Ochi, K.2    Nguyen, D.M.3    Allen, E.R.4    Freese, E.5
  • 33
    • 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. RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE) J. Am. Chem. Soc. 127 2005 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
  • 34
    • 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. A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry J. Am. Chem. Soc. 129 2007 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
  • 35
    • 78650007560 scopus 로고    scopus 로고
    • The SAM-responsive S(MK) box is a reversible riboswitch
    • Smith A.M., Fuchs R.T., Grundy F.J., and Henkin T.M. The SAM-responsive S(MK) box is a reversible riboswitch Mol. Microbiol. 78 2010 1393 1402
    • (2010) Mol. Microbiol. , vol.78 , pp. 1393-1402
    • Smith, A.M.1    Fuchs, R.T.2    Grundy, F.J.3    Henkin, T.M.4
  • 36
    • 78649529299 scopus 로고    scopus 로고
    • SAM recognition and conformational switching mechanism in the Bacillus subtilis yitJ S box/SAM-I riboswitch
    • Lu C., Ding F., Chowdhury A., Pradhan V., Tomsic J., and Holmes W.M. SAM recognition and conformational switching mechanism in the Bacillus subtilis yitJ S box/SAM-I riboswitch J. Mol. Biol. 404 2010 803 818
    • (2010) J. Mol. Biol. , vol.404 , pp. 803-818
    • Lu, C.1    Ding, F.2    Chowdhury, A.3    Pradhan, V.4    Tomsic, J.5    Holmes, W.M.6
  • 38
    • 78650007560 scopus 로고    scopus 로고
    • The SAM-responsive S(MK) box is a reversible riboswitch
    • Smith A.M., Fuchs R.T., Grundy F.J., and Henkin T.M. The SAM-responsive S(MK) box is a reversible riboswitch Mol. Microbiol. 78 2010 1393 1402
    • (2010) Mol. Microbiol. , vol.78 , pp. 1393-1402
    • Smith, A.M.1    Fuchs, R.T.2    Grundy, F.J.3    Henkin, T.M.4
  • 39
    • 4344596976 scopus 로고    scopus 로고
    • Crystallization of RNA and RNA-protein complexes
    • DOI 10.1016/j.ymeth.2004.03.027, PII S1046202304001215
    • Ke A., and Doudna J.A. Crystallization of RNA and RNA-protein complexes Methods (San Diego) 34 2004 408 414 (Pubitemid 39119821)
    • (2004) Methods , vol.34 , Issue.3 , pp. 408-414
    • Ke, A.1    Doudna, J.A.2
  • 40
    • 33947720028 scopus 로고    scopus 로고
    • Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): Quantitative RNA structure analysis at single nucleotide resolution
    • Wilkinson K.A., Merino E.J., and Weeks K.M. Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution Nat Protoc 1 2006 1610 1616
    • (2006) Nat Protoc , vol.1 , pp. 1610-1616
    • Wilkinson, K.A.1    Merino, E.J.2    Weeks, K.M.3
  • 41
    • 16344370497 scopus 로고    scopus 로고
    • Asp transcripts
    • DOI 10.1021/ja0436749
    • Wilkinson K.A., Merino E.J., and Weeks K.M. RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts J. Am. Chem. Soc. 127 2005 4659 4667 (Pubitemid 40489622)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.13 , pp. 4659-4667
    • Wilkinson, K.A.1    Merino, E.J.2    Weeks, K.M.3
  • 42
    • 13944278373 scopus 로고    scopus 로고
    • SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments
    • DOI 10.1261/rna.7214405
    • Das R., Laederach A., Pearlman S.M., Herschlag D., and Altman R.B. SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments RNA 11 2005 344 354 (Pubitemid 40270826)
    • (2005) RNA , vol.11 , Issue.3 , pp. 344-354
    • Das, R.1    Laederach, A.2    Pearlman, S.M.3    Herschlag, D.4    Altman, R.B.5
  • 43
    • 0003785155 scopus 로고
    • Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY
    • Miller J. Experiments in Molecular Genetics 1972 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY
    • (1972) Experiments in Molecular Genetics
    • Miller, J.1
  • 44
    • 0027234192 scopus 로고
    • tRNA as a positive regulator of transcription antitermination in B. subtilis
    • Grundy F.J., and Henkin T.M. tRNA as a positive regulator of transcription antitermination in B. subtilis Cell 74 1993 475 482 (Pubitemid 23244613)
    • (1993) Cell , vol.74 , Issue.3 , pp. 475-482
    • Grundy, F.J.1    Henkin, T.M.2
  • 45
    • 0021331731 scopus 로고
    • Genetic mapping of a mutation causing an alteration in Bacillus subtilis ribosomal protein S4
    • DOI 10.1007/BF00330694
    • Henkin T.M., and Chambliss G.H. Genetic mapping of a mutation causing an alteration in Bacillus subtilis ribosomal protein S4 Mol. Gen. Genet. 193 1984 364 369 (Pubitemid 14153316)
    • (1984) Molecular and General Genetics , vol.193 , Issue.2 , pp. 364-369
    • Henkin, T.M.1    Chambliss, G.H.2
  • 46
    • 0001134202 scopus 로고
    • Requirements for transformation in Bacillus subtilis
    • Anagnostopoulos C., and Spizizen J. Requirements for transformation in Bacillus subtilis J. Bacteriol. 81 1961 741 746
    • (1961) J. Bacteriol. , vol.81 , pp. 741-746
    • Anagnostopoulos, C.1    Spizizen, J.2


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