Cited by 161RNA and protein synthesis mechanismsRNA modifications and cancerDNA and Nucleic Acid Chemistry

The DOI matches its Crossref record; 136 of the 136 references it cites were found in a registry or an index.

Metabolite Recognition Principles and Molecular Mechanisms Underlying Riboswitch Function

Open access

Serganov, Alexander, Patel, Dinshaw J.·2012·Annual Review of Biophysics

DOI 10.1146/annurev-biophys-101211-113224PMC PMC4696762

Open this paper in CoChat — free account

Abstract

Riboswitches are mRNA elements capable of modulating gene expression in response to specific binding by cellular metabolites. Riboswitches exert their function through the interplay of alternative ligand-free and ligand-bound conformations of the metabolite-sensing domain, which in turn modulate the formation of adjacent gene expression controlling elements. X-ray crystallography and NMR spectroscopy have determined three-dimensional structures of virtually all the major riboswitch classes in the ligand-bound state and, for several riboswitches, in the ligand-free state. The resulting spatial topologies have demonstrated the wide diversity of riboswitch folds and revealed structural principles for specific recognition by cognate metabolites. The available three-dimensional information, supplemented by structure-guided biophysical and biochemical experimentation, has led to an improved understanding of how riboswitches fold, what RNA conformations are required for ligand recognition, and how ligand binding can be transduced into gene expression modulation. These studies have greatly facilitated the dissection of molecular mechanisms underlying riboswitch action and should in turn guide the anticipated development of tools for manipulating gene regulatory circuits.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1146/annurev-biophys-101211-113224

Cites

136 of 136 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

The role of dynamic conformational ensembles in biomolecular recognition
Boehr, D. D., Nussinov, R., & Wright, P. E. (2009) · Nature Chemical Biology · doi:10.1038/nchembio.232 · Cited by 2,008
Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression
Winkler, W. C., Nahvi, A., & Breaker, R. R. (2002) · Nature · doi:10.1038/nature01145 · Cited by 1,267
Control of gene expression by a natural metabolite-responsive ribozyme
Winkler, W. C., Nahvi, A., Roth, A., Collins, J. A., & Breaker, R. R. (2004) · Nature · doi:10.1038/nature02362 · Cited by 976
Genetic Control by a Metabolite Binding mRNA
Nahvi, A., Sudarsan, N., Ebert, M. S., Zou, X., Brown, K. L., & Breaker, R. R. (2002) · Chemistry & Biology · doi:10.1016/s1074-5521(02)00224-7 · Cited by 820
RNA Structure Analysis at Single Nucleotide Resolution by Selective 2‘-Hydroxyl Acylation and Primer Extension (SHAPE)
Merino, E. J., Wilkinson, K. A., Coughlan, J. L., & Weeks, K. M. (2005) · Journal of the American Chemical Society · doi:10.1021/ja043822v · Cited by 791
REGULATION OF BACTERIAL GENE EXPRESSION BY RIBOSWITCHES
Winkler, W. C., & Breaker, R. R. (2005) · Annual Review of Microbiology · doi:10.1146/annurev.micro.59.030804.121336 · Cited by 740
The kink‐turn: a new RNA secondary structure motif
Klein, D. J., Schmeing, T. M., Moore, P. B., & Steitz, T. A. (2001) · The EMBO Journal · doi:10.1093/emboj/20.15.4214 · Cited by 740
Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria
Mandal, M., Boese, B. J., Barrick, J. E., Winkler, W. C., & Breaker, R. R. (2003) · Cell · doi:10.1016/s0092-8674(03)00391-x · Cited by 737
Riboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP
Sudarsan, N., Lee, E. R., Zasha Weinberg, A., Moy, R. H., Kim, J. N., Link, K. H., & Breaker, R. R. (2008) · Science · doi:10.1126/science.1159519 · Cited by 720
An mRNA structure that controls gene expression by binding FMN
Winkler, W. C., Cohen‐Chalamish, S., & Breaker, R. R. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.212628899 · Cited by 698
Sensing Small Molecules by Nascent RNA
Mironov, A. S., Gusarov, I., Rafikov, R., Errais, L. L., Shatalin, K. Y., Kreneva, R. A., Perumov, D. A., & Nudler, E. (2002) · Cell · doi:10.1016/s0092-8674(02)01134-0 · Cited by 682
RNA tertiary interactions in the large ribosomal subunit: The A-minor motif
Nissen, P., Ippolito, J. A., Ban, N., Moore, P. B., & Steitz, T. A. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.081082398 · Cited by 659
The riboswitch control of bacterial metabolism
Nudler, E. (2003) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2003.11.004 · Cited by 574
Structural Basis for Discriminative Regulation of Gene Expression by Adenine- and Guanine-Sensing mRNAs
Serganov, A., Yuan, Y.-R., Pikovskaya, O., Polonskaia, A., Malinina, L. V., Phan, A. T., Höbartner, C., Micura, R., Breaker, R. R., & Patel, D. J. (2004) · Chemistry & Biology · doi:10.1016/j.chembiol.2004.11.018 · Cited by 561
Self-citation
The Structural and Functional Diversity of Metabolite-Binding Riboswitches
Roth, A., & Breaker, R. R. (2009) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.78.070507.135656 · Cited by 557
A Glycine-Dependent Riboswitch That Uses Cooperative Binding to Control Gene Expression
Mandal, M., Lee, M. N., Barrick, J. E., Weinberg, Z., Emilsson, G. M., Ruzzo, W. L., & Breaker, R. R. (2004) · Science · doi:10.1126/science.1100829 · Cited by 554
Relationship between internucleotide linkage geometry and the stability of RNA
Soukup, G. A., & Breaker, R. R. (1999) · RNA · doi:10.1017/s1355838299990891 · Cited by 549
Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine
Batey, R., Gilbert, S. D., & Montange, R. K. (2004) · Nature · doi:10.1038/nature03037 · Cited by 517
Adenine riboswitches and gene activation by disruption of a transcription terminator
Mandal, M., & Breaker, R. R. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb710 · Cited by 514
The Speed of RNA Transcription and Metabolite Binding Kinetics Operate an FMN Riboswitch
Wickiser, J. K., Winkler, W. C., Breaker, R. R., & Crothers, D. M. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.02.032 · Cited by 483
An mRNA structure that controls gene expression by binding S-adenosylmethionine
Winkler, W. C., Nahvi, A., Sudarsan, N., Barrick, J. E., & Breaker, R. R. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb967 · Cited by 463
Ribozymes, riboswitches and beyond: regulation of gene expression without proteins
Serganov, A., & Patel, D. J. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2172 · Cited by 448
Self-citation
Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch
Serganov, A., Polonskaia, A., Phan, A. T., Breaker, R. R., & Patel, D. J. (2006) · Nature · doi:10.1038/nature04740 · Cited by 443
Self-citation
Widespread genetic switches and toxicity resistance proteins for fluoride
Baker, J. L., Sudarsan, N., Weinberg, Z., Roth, A., Stockbridge, R. B., & Breaker, R. R. (2012) · Science · doi:10.1126/science.1215063 · Cited by 438
Metabolite-binding RNA domains are present in the genes of eukaryotes
Sudarsan, N., Barrick, J. E., & Breaker, R. R. (2003) · RNA · doi:10.1261/rna.5090103 · Cited by 422
Structure of the S-adenosylmethionine riboswitch regulatory mRNA element
Montange, R. K., & Batey, R. (2006) · Nature · doi:10.1038/nature04819 · Cited by 405
Metals, Motifs, and Recognition in the Crystal Structure of a 5S rRNA Domain
Correll, C. C., Freeborn, B., Moore, P. B., & Steitz, T. A. (1997) · Cell · doi:10.1016/s0092-8674(00)80457-2 · Cited by 393
Direct Observation of Hierarchical Folding in Single Riboswitch Aptamers
Greenleaf, W. J., Frieda, K. L., Foster, D. A. N., Woodside, M. T., & Block, S. M. (2008) · Science · doi:10.1126/science.1151298 · Cited by 387
Structure and Mechanism of a Metal-Sensing Regulatory RNA
Dann, C. E., Wakeman, C. A., Sieling, C. L., Baker, S. C., Irnov, I., & Winkler, W. C. (2007) · Cell · doi:10.1016/j.cell.2007.06.051 · Cited by 386
Riboswitches: Emerging Themes in RNA Structure and Function
Montange, R. K., & Batey, R. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.032807.130000 · Cited by 386
Structural Basis of glmS Ribozyme Activation by Glucosamine-6-Phosphate
Klein, D. J., & Ferré-D’Amaré, A. R. (2006) · Science · doi:10.1126/science.1129666 · Cited by 381
A trans-Acting Riboswitch Controls Expression of the Virulence Regulator PrfA in Listeria monocytogenes
Loh, E., Dussurget, O., Gripenland, J., Vaitkevicius, K., Tiensuu, T., Mandin, P., Repoila, F., Buchrieser, C., Cossart, P., & Johansson, J. (2009) · Cell · doi:10.1016/j.cell.2009.08.046 · Cited by 379
An mRNA structure in bacteria that controls gene expression by binding lysinePreprint
Sudarsan, N., Wickiser, J. K., Nakamura, S., Ebert, M. S., & Breaker, R. R. (2003) · Genes & Development · doi:10.1101/gad.1140003 · Cited by 357
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes
Weinberg, Z., Wang, J. X., Bogue, J., Yang, J., Corbino, K., Moy, R. H., & Breaker, R. R. (2010) · Genome Biology · doi:10.1186/gb-2010-11-3-r31 · Cited by 354
Structure of the Eukaryotic Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand
Thore, S., Leibundgut, M., & Ban, N. (2006) · Science · doi:10.1126/science.1128451 · Cited by 352
An Allosteric Self-Splicing Ribozyme Triggered by a Bacterial Second Messenger
Lee, E. R., Baker, J. L., Zasha Weinberg, A., Sudarsan, N., & Breaker, R. R. (2010) · Science · doi:10.1126/science.1190713 · Cited by 348
Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes
Nahvi, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh167 · Cited by 327
An RNA Sensor for Intracellular Mg2+
Cromie, M. J., Shi, Y., Latifi, T. N., & Groisman, E. A. (2006) · Cell · doi:10.1016/j.cell.2006.01.043 · Cited by 325
RNA dynamics: it is about time
Al‐Hashimi, H. M., & Walter, N. G. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.04.004 · Cited by 323
Structural basis of ligand binding by a c-di-GMP riboswitch
Smith, K. D., Lipchock, S. V., Ames, T. D., Wang, J., Breaker, R. R., & Strobel, S. A. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1702 · Cited by 291
Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch
Serganov, A., Huang, L., & Patel, D. J. (2009) · Nature · doi:10.1038/nature07642 · Cited by 290
Self-citation
Folding of the Adenine Riboswitch
Lemay, J., Penedo, J. C., Tremblay, R., Lilley, D. M. J., & Lafontaine, D. A. (2006) · Chemistry & Biology · doi:10.1016/j.chembiol.2006.06.010 · Cited by 280
The Kinetics of Ligand Binding by an Adenine-Sensing Riboswitch
Wickiser, J. K., Cheah, M. T., Breaker, R. R., & Crothers, D. M. (2005) · Biochemistry · doi:10.1021/bi051008u · Cited by 276
tRNA as a positive regulator of transcription antitermination in B. subtilis
Grundy, F. J., & Henkin, T. M. (1993) · Cell · doi:10.1016/0092-8674(93)80049-k · Cited by 273
Thermodynamic and Kinetic Characterization of Ligand Binding to the Purine Riboswitch Aptamer Domain
Gilbert, S. D., Stoddard, C. D., Wise, S. J., & Batey, R. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.04.003 · Cited by 267
Structural Investigation of the GlmS Ribozyme Bound to Its Catalytic Cofactor
Cochrane, J. C., Lipchock, S. V., & Strobel, S. A. (2006) · Chemistry & Biology · doi:10.1016/j.chembiol.2006.12.005 · Cited by 267
Tandem Riboswitch Architectures Exhibit Complex Gene Control Functions
Sudarsan, N., Hammond, M. C., Block, K. F., Welz, R., Barrick, J. E., Roth, A., & Breaker, R. R. (2006) · Science · doi:10.1126/science.1130716 · Cited by 264
Structure of the SAM-II riboswitch bound to S-adenosylmethionine
Gilbert, S. D., Rambo, R. P., Tyne, D. V., & Batey, R. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1371 · Cited by 255
Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive RNA-Small Molecule Recognition
Edwards, T. E., & Ferré-D’Amaré, A. R. (2006) · Structure · doi:10.1016/j.str.2006.07.008 · Cited by 252
Structural insights into amino acid binding and gene control by a lysine riboswitch
Serganov, A., Huang, L., & Patel, D. J. (2008) · Nature · doi:10.1038/nature07326 · Cited by 251
Self-citation
The riboswitch-mediated control of sulfur metabolism in bacteria
Epshtein, V., Mironov, A. S., & Nudler, E. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0531307100 · Cited by 250
Mechanism of mRNA destabilization by the glmS ribozymePreprint
Collins, J. A., Irnov, I., Baker, S. C., & Winkler, W. C. (2007) · Genes & Development · doi:10.1101/gad.1605307 · Cited by 247
Transcription termination control of the S box system: Direct measurement of S -adenosylmethionine by the leader RNA
McDaniel, B. A., Grundy, F. J., Artsimovitch, I., & Henkin, T. M. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0630422100 · Cited by 246
A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain
Roth, A., Winkler, W. C., Regulski, E. E., Lee, B. W. K., Lim, J., Jona, I., Barrick, J. E., Ritwik, A., Kim, J. N., Welz, R., et al. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1224 · Cited by 245
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., Puskarz, I., Mandal, M., Rudnick, N. D., & Breaker, R. R. (2005) · Genome biology · doi:10.1186/gb-2005-6-8-r70 · Cited by 241
The SMK box is a new SAM-binding RNA for translational regulation of SAM synthetase
Fuchs, R. T., Grundy, F. J., & Henkin, T. M. (2006) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1059 · Cited by 204
Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch
Kulshina, N., Baird, N., & Ferré-D’Amaré, A. R. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1701 · Cited by 197
Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain
Stoddard, C. D., Montange, R. K., Hennelly, S. P., Rambo, R. P., Sanbonmatsu, K. Y., & Batey, R. (2010) · Structure · doi:10.1016/j.str.2010.04.006 · Cited by 194
Crystal Structure of the Lysine Riboswitch Regulatory mRNA Element
Garst, A. D., Heroux, A., Rambo, R. P., & Batey, R. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.c800120200 · Cited by 189
The L box regulon: Lysine sensing by leader RNAs of bacterial lysine biosynthesis genes
Grundy, F. J., Lehman, S. C., & Henkin, T. M. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2133705100 · Cited by 186
Novel Riboswitch Ligand Analogs as Selective Inhibitors of Guanine-Related Metabolic Pathways
Mulhbacher, J., Brouillette, É., Allard, M., Fortier, L., Malouin, F., & Lafontaine, D. A. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1000865 · Cited by 184
The Dynamic Nature of RNA as Key to Understanding Riboswitch Mechanisms
Haller, A., Soulière, M. F., & Micura, R. (2011) · Accounts of Chemical Research · doi:10.1021/ar200035g · Cited by 184
Comparative Study between Transcriptionally- and Translationally-Acting Adenine Riboswitches Reveals Key Differences in Riboswitch Regulatory Mechanisms
Lemay, J., Desnoyers, G., Blouin, S., Heppell, B., Bastet, L., St-Pierre, P., Massé, É., & Lafontaine, D. A. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001278 · Cited by 181
Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?
Rodionov, D. A., Vitreschak, A. G., Mironov, A. A., & Gelfand, M. S. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg900 · Cited by 178
Ligand‐Induced Folding of the Adenosine Deaminase A‐Riboswitch and Implications on Riboswitch Translational Control
Rieder, R., Lang, K., Graber, D., & Micura, R. (2007) · ChemBioChem · doi:10.1002/cbic.200700057 · Cited by 177
Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase
Klein, D. J., Edwards, T. E., & Ferré-D’Amaré, A. R. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1563 · Cited by 175
Crystal structures of the SAM-III/SMK riboswitch reveal the SAM-dependent translation inhibition mechanism
Lu, C., Smith, A. M., Fuchs, R. T., Ding, F., Rajashankar, K. R., Henkin, T. M., & Ke, A. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1494 · Cited by 174
Reengineering orthogonally selective riboswitches
Dixon, N., Duncan, J. N., Geerlings, T. H., Dunstan, M. S., McCarthy, J. E. G., Leys, D., & Micklefield, J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0911209107 · Cited by 173
Conformational capture of the SAM-II riboswitch
Haller, A., Rieder, U., Aigner, M., Blanchard, S. C., & Micura, R. (2011) · Nature Chemical Biology · doi:10.1038/nchembio.562 · Cited by 166
A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism
Regulski, E. E., Moy, R. H., Zasha Weinberg, A., Barrick, J. E., Yao, Z., Ruzzo, W. L., & Breaker, R. R. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06208.x · Cited by 162
Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach
Lang, K., Rieder, R., & Micura, R. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm580 · Cited by 154
Structural Insights into Ligand Recognition by a Sensing Domain of the Cooperative Glycine Riboswitch
Huang, L., Serganov, A., & Patel, D. J. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.11.026 · Cited by 152
Self-citation
An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs
Noeske, J., Richter, C. P., Grundl, M. A., Nasiri, H. R., Schwalbe, H., & Wöhnert, J. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0406347102 · Cited by 147
Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch
Noeske, J., Buck, J., Fürtig, B., Nasiri, H. R., Schwalbe, H., & Wöhnert, J. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl1094 · Cited by 147
Ribozymes and Riboswitches: Modulation of RNA Function by Small Molecules
Zhang, J., Lau, M. W. L., & Ferré-D’Amaré, A. R. (2010) · Biochemistry · doi:10.1021/bi1012645 · Cited by 146
Structural Insights into Riboswitch Control of the Biosynthesis of Queuosine, a Modified Nucleotide Found in the Anticodon of tRNA
Kang, M., Peterson, R. D., & Feigon, J. F. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.02.019 · Cited by 146
Ligand Requirements for glmS Ribozyme Self-Cleavage
McCarthy, T. J., Plog, M. A., Floy, S. A., Jansen, J. A., Strauss-Soukup, J. K., & Soukup, G. A. (2005) · Chemistry & Biology · doi:10.1016/j.chembiol.2005.09.006 · Cited by 146
Riboswitches: small-molecule recognition by gene regulatory RNAs
Edwards, T. E., Klein, D. J., & Ferré-D’Amaré, A. R. (2007) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2007.05.004 · Cited by 144
Guanine riboswitch variants from Mesoplasma florum selectively recognize 2′-deoxyguanosine
Kim, J. N., Roth, A., & Breaker, R. R. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0705884104 · Cited by 141
Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution
Buck, J., Fürtig, B., Noeske, J., Wöhnert, J., & Schwalbe, H. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0703182104 · Cited by 138
Comparison of a PreQ1 Riboswitch Aptamer in Metabolite-bound and Free States with Implications for Gene Regulation
Jenkins, J. L., Krucinska, J., McCarty, R. M., Bandarian, V., & Wedekind, J. E. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.230375 · Cited by 137
The Structure of a Tetrahydrofolate-Sensing Riboswitch Reveals Two Ligand Binding Sites in a Single Aptamer
Trausch, J. J., Ceres, P., Reyes, F. E., & Batey, R. (2011) · Structure · doi:10.1016/j.str.2011.06.019 · Cited by 134
Design and Antimicrobial Action of Purine Analogues That Bind Guanine Riboswitches
Kim, J. N., Blount, K., Puskarz, I., Lim, J., Link, K. H., & Breaker, R. R. (2009) · ACS Chemical Biology · doi:10.1021/cb900146k · Cited by 126
Single-molecule force spectroscopy of the add adenine riboswitch relates folding to regulatory mechanism
Neupane, K., Yu, H., Foster, D. A. N., Wang, F., & Woodside, M. T. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr305 · Cited by 123
Structural Transitions and Thermodynamics of a Glycine-Dependent Riboswitch from Vibrio cholerae
Lipfert, J., Das, R., Chu, V. B., Kudaravalli, M., Boyd, N., Herschlag, D., & Doniach, S. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.10.022 · Cited by 117
Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria
Meyer, M. M., Roth, A., Chervin, S. M., Garcia, G. A., & Breaker, R. R. (2008) · RNA · doi:10.1261/rna.937308 · Cited by 117
Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection
Vicens, Q., Mondragón, E., & Batey, R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr565 · Cited by 116
Structural basis of differential ligand recognition by two classes of bis-(3′-5′)-cyclic dimeric guanosine monophosphate-binding riboswitches
Smith, K. D., Shanahan, C. A., Moore, E. L., Simon, A. C., & Strobel, S. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1018857108 · Cited by 115
A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria
Poiata, E., Meyer, M. M., Ames, T. D., & Breaker, R. R. (2009) · RNA · doi:10.1261/rna.1824209 · Cited by 113
Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteineThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Systems and Chemical Biology, and has undergone the Journal's usual peer review process.
Wang, J. X., & Breaker, R. R. (2008) · Biochemistry and Cell Biology · doi:10.1139/o08-008 · Cited by 113
A Bacterial mRNA Leader that Employs Different Mechanisms to Sense Disparate Intracellular Signals
Park, S.-Y., Cromie, M. J., Lee, E., & Groisman, E. A. (2010) · Cell · doi:10.1016/j.cell.2010.07.046 · Cited by 113
Novel Ligands for a Purine Riboswitch Discovered by RNA-Ligand Docking
Daldrop, P., Reyes, F. E., Robinson, D. A., Hammond, C. M., Lilley, D. M. J., Batey, R., & Brenk, R. (2011) · Chemistry & Biology · doi:10.1016/j.chembiol.2010.12.020 · Cited by 111
The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches
Zasha Weinberg, A., Regulski, E. E., Hammond, M. C., Barrick, J. E., Yao, Z., Ruzzo, W. L., & Breaker, R. R. (2008) · RNA · doi:10.1261/rna.988608 · Cited by 111
Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions
Roth, A., Nahvi, A., Lee, M. N., Jona, I., & Breaker, R. R. (2006) · RNA · doi:10.1261/rna.2266506 · Cited by 110
Molecular insights into the ligand-controlled organization of the SAM-I riboswitch
Heppell, B., Blouin, S., Dussault, A.-M., Mulhbacher, J., Ennifar, E., Penedo, J. C., & Lafontaine, D. A. (2011) · Nature Chemical Biology · doi:10.1038/nchembio.563 · Cited by 110
Real-time multidimensional NMR follows RNA folding with second resolution
Lee, M., Gal, M., Frydman, L., & Varani, G. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1001195107 · Cited by 105
Structural Basis of Cooperative Ligand Binding by the Glycine Riboswitch
Butler, E. B., Xiong, Y., Wang, J., & Strobel, S. A. (2011) · Chemistry & Biology · doi:10.1016/j.chembiol.2011.01.013 · Cited by 104
A Eubacterial Riboswitch Class That Senses the Coenzyme Tetrahydrofolate
Ames, T. D., Rodionov, D. A., Weinberg, Z., & Breaker, R. R. (2010) · Chemistry & Biology · doi:10.1016/j.chembiol.2010.05.020 · Cited by 104
Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis
Baird, N., & Ferré-D’Amaré, A. R. (2010) · RNA · doi:10.1261/rna.1852310 · Cited by 104
Folding of a transcriptionally acting PreQ 1 riboswitch
Rieder, U., Kreutz, C., & Micura, R. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914925107 · Cited by 103
Ligand-dependent folding of the three-way junction in the purine riboswitch
Stoddard, C. D., Gilbert, S. D., & Batey, R. (2008) · RNA · doi:10.1261/rna.736908 · Cited by 103
Bacterial aptamers that selectively bind glutamine
Ames, T. D., & Breaker, R. R. (2011) · RNA Biology · doi:10.4161/rna.8.1.13864 · Cited by 101
Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch
Thore, S., Frick, C., & Ban, N. (2008) · Journal of the American Chemical Society · doi:10.1021/ja801708e · Cited by 101
The Structural Basis for Recognition of the PreQ0 Metabolite by an Unusually Small Riboswitch Aptamer Domain
Spitale, R. C., Torelli, A. T., Krucinska, J., Bandarian, V., & Wedekind, J. E. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.c900024200 · Cited by 100
Riboswitch-mediated control of gene expression in eukaryotes
Wachter, A. (2010) · RNA Biology · doi:10.4161/rna.7.1.10489 · Cited by 100
Evidence for Preorganization of the glmS Ribozyme Ligand Binding Pocket
Hampel, K. J., & Tinsley, M. M. (2006) · Biochemistry · doi:10.1021/bi060337z · Cited by 95
Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined–induced fit mechanism
Ottink, O. M., Rampersad, S. M., Tessari, M., Zaman, G. J. R., Heus, H. A., & Wijmenga, S. S. (2007) · RNA · doi:10.1261/rna.635307 · Cited by 90
The UA_handle: a versatile submotif in stable RNA architectures†
Jaeger, L., Verzemnieks, E., & Geary, C. W. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn911 · Cited by 87
The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo
Watson, P. Y., & Fedor, M. J. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1989 · Cited by 86
Structural principles of nucleoside selectivity in a 2′-deoxyguanosine riboswitch
Pikovskaya, O., Polonskaia, A., Patel, D. J., & Serganov, A. (2011) · Nature Chemical Biology · doi:10.1038/nchembio.631 · Cited by 83
Self-citation
On the occurrence of the T-loop RNA folding motif in large RNA molecules
Krasilnikov, A. S., & Mondragón, A. (2003) · RNA · doi:10.1261/rna.2202703 · Cited by 81
Structural basis for recognition ofS-adenosylhomocysteine by riboswitches
Edwards, A. L., Reyes, F. E., Heroux, A., & Batey, R. (2010) · RNA · doi:10.1261/rna.2341610 · Cited by 81
Requirement of Helix P2.2 and Nucleotide G1 for Positioning the Cleavage Site and Cofactor of the glmS Ribozyme
Klein, D. J., Wilkinson, S. R., Been, M. D., & Ferré-D’Amaré, A. R. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.07.062 · Cited by 78
Chemical basis of glycine riboswitch cooperativity
Kwon, M., & Strobel, S. A. (2007) · RNA · doi:10.1261/rna.771608 · Cited by 75
Core requirements of the adenine riboswitch aptamer for ligand binding
Lemay, J., & Lafontaine, D. A. (2007) · RNA · doi:10.1261/rna.142007 · Cited by 74
Ligand recognition determinants of guanine riboswitches
Mulhbacher, J., & Lafontaine, D. A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm572 · Cited by 73
Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs
Nagaswamy, U., & Fox, G. E. (2002) · RNA · doi:10.1017/s135583820202006x · Cited by 72
A Structural Basis for the Recognition of 2′-Deoxyguanosine by the Purine Riboswitch
Edwards, A. L., & Batey, R. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.10.074 · Cited by 70
Differential Analogue Binding by Two Classes of c-di-GMP Riboswitches
Shanahan, C. A., Gaffney, B. L., Jones, R. A., & Strobel, S. A. (2011) · Journal of the American Chemical Society · doi:10.1021/ja204650q · Cited by 67
The Ligand-Free State of the TPP Riboswitch: A Partially Folded RNA Structure
Ali, M., Lipfert, J., Seifert, S., Herschlag, D., & Doniach, S. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.11.030 · Cited by 66
Regulation of magnesium homeostasis in Salmonella: Mg2+ targets the mgtA transcript for degradation by RNase E
Spinelli, S. V., Pontel, L. B., Véscovi, E. G., & Soncini, F. C. (2008) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2008.01065.x · Cited by 65
Trans-acting glmS catalytic riboswitch: Locked and loaded
Tinsley, R. A., Furchak, J. R. W., & Walter, N. G. (2007) · RNA · doi:10.1261/rna.341807 · Cited by 64
Multivector Fluorescence Analysis of the xpt Guanine Riboswitch Aptamer Domain and the Conformational Role of Guanine
Brenner, M. D., Scanlan, M. S., Nahas, M. K., Ha, T., & Silverman, S. K. (2010) · Biochemistry · doi:10.1021/bi9019912 · Cited by 62
Switching the light on plant riboswitches
Bocobza, S. E., & Aharoni, A. (2008) · Trends in Plant Science · doi:10.1016/j.tplants.2008.07.004 · Cited by 60
Characteristics of Ligand Recognition by a glmS Self‐Cleaving Ribozyme
Lim, J., Grove, B. C., Roth, A., & Breaker, R. R. (2006) · Angewandte Chemie International Edition · doi:10.1002/anie.200602534 · Cited by 57
Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch
Huang, L., Ishibe-Murakami, S., Patel, D. J., & Serganov, A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1111701108 · Cited by 54
Self-citation
Tuning Riboswitch Regulation through Conformational Selection
Wilson, R. C., Smith, A. M., Fuchs, R. T., Kleckner, I. R., Henkin, T. M., & Foster, M. P. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.10.056 · Cited by 51
A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm
Huang, W., Kim, J., Jha, S., & Aboul‐ela, F. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp664 · Cited by 50
Riboswitch structure: an internal residue mimicking the purine ligand
Delfosse, V., Bouchard, P., Bonneau, É., Dagenais, P., Lemay, J., Lafontaine, D. A., & Legault, P. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1080 · Cited by 50
Insights into Metalloregulation by M-box Riboswitch RNAs via Structural Analysis of Manganese-Bound Complexes
Ramesh, A., Wakeman, C. A., & Winkler, W. C. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.01.049 · Cited by 49
glmS Riboswitch Binding to the Glucosamine-6-phosphate α-Anomer Shifts the pKa toward Neutrality
Davis, J., Dunican, B. F., & Strobel, S. A. (2011) · Biochemistry · doi:10.1021/bi200471c · Cited by 41
Mg2+ facilitates leader peptide translation to induce riboswitch‐mediated transcription termination
Zhao, G., Kong, W., Weatherspoon‐Griffin, N., Clark‐Curtiss, J. E., & Shi, Y. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.66 · Cited by 33
Multiple Metal-Binding Cores Are Required for Metalloregulation by M-box Riboswitch RNAs
Wakeman, C. A., Ramesh, A., & Winkler, W. C. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.07.033 · Cited by 32
Heterogeneity and Dynamics of the Ligand Recognition Mode in Purine-Sensing Riboswitches
Jain, N., Zhao, L., Liu, J. D., & Xia, T. (2010) · Biochemistry · doi:10.1021/bi1000036 · Cited by 23
Constitutive Regulatory Activity of an Evolutionarily Excluded Riboswitch Variant
Tremblay, R., Lemay, J., Blouin, S., Mulhbacher, J., Bonneau, É., Legault, P., Dupont, P., Penedo, J. C., & Lafontaine, D. A. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.229047 · Cited by 22
Analysis of Metal Ion Dependence in glmS Ribozyme Self‐Cleavage and Coenzyme Binding
Klawuhn, K., Jansen, J. A., Souchek, J. J., Soukup, G. A., & Strauss-Soukup, J. K. (2010) · ChemBioChem · doi:10.1002/cbic.201000544 · Cited by 22

Sorted by citations

A triple helix stabilizes the 3′ ends of long noncoding RNAs that lack poly(A) tailsPreprint
Wilusz, J. E., JnBaptiste, C. K., Lu, L. Y., Kuhn, C., Joshua‐Tor, L., & Sharp, P. A. (2012) · Genes & Development · doi:10.1101/gad.204438.112 · Cited by 487
Riboswitch diversity and distribution
McCown, P. J., Corbino, K. A., Stav, S., Sherlock, M. E., & Breaker, R. R. (2017) · RNA · doi:10.1261/rna.061234.117 · Cited by 479
Regulation of Bacterial Virulence by Csr (Rsm) Systems
Vakulskas, C. A., Potts, A. H., Babitzke, P., Ahmer, B. M. M., & Romeo, T. (2015) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00052-14 · Cited by 333
Automated physics-based design of synthetic riboswitches from diverse RNA aptamers
Borujeni, A. E., Mishler, D. M., Wang, J., Huso, W. D., & Salis, H. M. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1289 · Cited by 265
Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes
Micura, R., & Höbartner, C. (2020) · Chemical Society Reviews · doi:10.1039/d0cs00617c · Cited by 265

See all 161

Authors: Serganov, A., & Patel, D. J.
Affiliations: New York University (US)
Memorial Sloan Kettering Cancer Center (US)
ORCID: Serganov, Alexander
Patel, Dinshaw J.
Venue: Annual Review of Biophysics
Publisher: Annual Reviews
Published: 2012-06-09
Volume: 41
Issue: 1
Pages: 343-370
ISSN: 1936-122X (ISSN-L)
1936-1238
DOI: 10.1146/annurev-biophys-101211-113224
PMC: PMC4696762
OpenAlex: W2129215648
Cited by: 160
References: 136
Citations by year: 2026: 4 · 2025: 6 · 2024: 8 · 2023: 8 · 2022: 10 · 2021: 6 · 2020: 13 · 2019: 12 · 2018: 9 · 2017: 10 · 2016: 13 · 2015: 24 · 2014: 27 · 2013: 9 · 2012: 1
FWCI: 1.78
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Annual Review of Biophysics (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Funders: National Cancer Institute (P30CA008748)
National Institute of General Medical Sciences (P41GM066354, GM 66354, R01GM034504)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
Keywords: riboswitches, ligand binding, RNA conformational change, gene expression regulation, RNA folding, ligand-free state, ligand-bound state, riboswitch structure, RNA-ligand interactions, gene regulatory circuits
MeSH terms: Bacteria, Ligands, Nucleic Acid Conformation, RNA, Messenger, Gene Expression Regulation, Bacterial, Crystallography, X-Ray, Riboswitch

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Metabolite Recognition Principles and Molecular Mechanisms Underlying Riboswitch Function

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks