Amino acid recognition and gene regulation by riboswitches
Open accessAbstract
Riboswitches specifically control expression of genes predominantly involved in biosynthesis, catabolism and transport of various cellular metabolites in organisms from all three kingdoms of life. Among many classes of identified riboswitches, two riboswitches respond to amino acids lysine and glycine to date. Though these riboswitches recognize small compounds, they both belong to the largest riboswitches and have unique structural and functional characteristics. In this review, we attempt to characterize molecular recognition principles employed by amino acid-responsive riboswitches to selectively bind their cognate ligands and to effectively perform a gene regulation function. We summarize up-to-date biochemical and genetic data available for the lysine and glycine riboswitches and correlate these results with recent high-resolution structural information obtained for the lysine riboswitch. We also discuss the contribution of lysine riboswitches to antibiotic resistance and outline potential applications of riboswitches in biotechnology and medicine.
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
Cites
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?
Direct recognition of amino acids by RNA molecules survives in other functional spheres of modern cells, in particular, as amino acid-binding riboswitches.
“It seems interesting to note that, although direct recognition of amino acids by RNA molecules seems to be banished from the modern translation system, it survives in other functional spheres of modern cells, in particular, as amino acid-binding riboswitches [96,97].”
From Frozen Accident Pushing 50: Stereochemistry, Expansion, and Chance in the Evolution of the Genetic Code (2017) · cites this paper as [96]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Environmental genome shotgun sequencing of the sargasso sea
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376 · see citing works
Gilbert, W. (1986) · Nature · Cited by 1,941 · see citing works
Rfam: annotating non-coding RNAs in complete genomes
Griffiths‐Jones, S. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki081 · Cited by 1,701 · see citing works
Comparative Metagenomics of Microbial Communities
Tringe, S. G., von Mering, C., Kobayashi, A., Salamov, A. A., Chen, K., Chang, H. W., Podar, M., Short, J. M., Mathur, E. J., Detter, J. C., et al. (2005) · Science · doi:10.1126/science.1107851 · Cited by 1,694 · see citing works
Femtomolar Sensitivity of Metalloregulatory Proteins Controlling Zinc Homeostasis
Outten, C. E., & O'Halloran, A. T. V. (2001) · Science · doi:10.1126/science.1060331 · Cited by 1,489 · see citing works
Essential Bacillus subtilis genes
Kobayashi, K., Ehrlich, S. D., Albertini, A., Amati, G., Andersen, K. K., Arnaud, M., Asai, K., Ashikaga, S., Aymerich, S., Bessières, P., et al. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0730515100 · Cited by 1,331 · see citing works
Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing
Cate, J. H. D., Gooding, A. R., Podell, E. R., Zhou, K., Golden, B. L., Kundrot, C. E., Cech, T. R., & Doudna, J. A. (1996) · Science · doi:10.1126/science.273.5282.1678 · Cited by 1,249 · see citing works
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 1,241 · see citing works
SAR11 clade dominates ocean surface bacterioplankton communities
Morris, R. M., Rappé, M. S., Connon, S. A., Vergin, K. L., Siebold, W. A., Carlson, C. A., & Giovannoni, S. J. (2002) · Nature · doi:10.1038/nature01240 · Cited by 1,129 · see citing works
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 953 · see citing works
Rfam: updates to the RNA families database
Gardner, P. P., Daub, J., Tate, J. G., Nawrocki, E. P., Kolbe, D. L., Lindgreen, S., Wilkinson, A. C., Finn, R. D., Griffiths‐Jones, S., Eddy, S. R., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn766 · Cited by 923 · see citing works
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 802 · see citing works
Wilkinson, K. A., Merino, E. J., & Weeks, K. M. (2006) · Nature Protocols · doi:10.1038/nprot.2006.249 · Cited by 775 · see citing works
Attenuation in the control of expression of bacterial operons
Yanofsky, C. (1981) · Nature · doi:10.1038/289751a0 · Cited by 759 · see citing works
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 · see citing works
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 729 · see citing works
Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655
Gerdes, S., Scholle, M. D., Campbell, J. W., Balázsi, G., Ravasz, E., Daugherty, M. D., Somera, A. L., Kyrpides, N. C., Anderson, I., Gelfand, M. S., et al. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.19.5673-5684.2003 · Cited by 726 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
Riboswitches and the RNA WorldPreprint
Breaker, R. R. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a003566 · Cited by 679 · see citing works
Bacillus Subtilis and Its Closest Relatives: From Genes to Cells
Sonenshein, A. L., Hoch, J. A., & Losick, R. M. (2001) · Cited by 674 · see citing works
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 · see citing works
Histone lysine demethylases: emerging roles in development, physiology and disease
Shi, Y. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2218 · Cited by 603 · see citing works
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 560 · see citing works
Self-citationThe 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 555 · see citing works
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 · see citing works
A Glycine-Dependent Riboswitch That Uses Cooperative Binding to Control Gene Expression
Mandal, M., Lee, M. N., Barrick, J. E., Zasha Weinberg, A., Emilsson, G. M., Ruzzo, W. L., & Breaker, R. R. (2004) · Science · doi:10.1126/science.1100829 · Cited by 545 · see citing works
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 · see citing works
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 509 · see citing works
New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control
Barrick, J. E., Corbino, K. A., Winkler, W. C., Nahvi, A., Mandal, M., Collins, J. A., Lee, M. N., Roth, A., Sudarsan, N., Jona, I., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0308014101 · Cited by 498 · see citing works
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 · see citing works
The distributions, mechanisms, and structures of metabolite-binding riboswitches
Barrick, J. E., & Breaker, R. R. (2007) · Genome biology · doi:10.1186/gb-2007-8-11-r239 · Cited by 482 · see citing works
Riboswitches as antibacterial drug targets
Blount, K., & Breaker, R. R. (2006) · Nature Biotechnology · doi:10.1038/nbt1268 · Cited by 470 · see citing works
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 458 · see citing works
Crystal structure of a self-splicing group I intron with both exons
Adams, P. L., Stahley, M. R., Kosek, A. B., Wang, J., & Strobel, S. A. (2004) · Nature · doi:10.1038/nature02642 · Cited by 458 · see citing works
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 · see citing works
Self-citationRibozymes, riboswitches and beyond: regulation of gene expression without proteins
Serganov, A., & Patel, D. J. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2172 · Cited by 438 · see citing works
Self-citationMetabolite-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 418 · see citing works
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 · see citing works
Dinnbier, U., Limpinsel, E., Schmid, R., & Bakker, E. P. (1988) · Archives of Microbiology · doi:10.1007/bf00408306 · Cited by 392 · see citing works
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 · see citing works
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 · see citing works
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 385 · see citing works
Glycine cleavage system: reaction mechanism, physiological significance, and hyperglycinemia
Kikuchi, G., Motokawa, Y., Yoshida, T., & Hiraga, K. (2008) · Proceedings of the Japan Academy Series B · doi:10.2183/pjab.84.246 · Cited by 381 · see citing works
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 377 · see citing works
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 · see citing works
Metal ions and RNA folding: a highly charged topic with a dynamic future
Woodson, S. A. (2005) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2005.02.004 · Cited by 355 · see citing works
Comparative Genomics of Thiamin Biosynthesis in Procaryotes
Rodionov, D. A., Vitreschak, A. G., Mironov, A. A., & Gelfand, M. S. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m208965200 · Cited by 354 · see citing works
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 345 · see citing works
CRC handbook of food additives
Furia, T. E. (1968) · CRC Press eBooks · Cited by 342 · see citing works
Robust Salmonella metabolism limits possibilities for new antimicrobials
Becker, D., Selbach, M., Rollenhagen, C., Ballmaier, M., Meyer, T. F., Mann, M., & Bumann, D. (2006) · Nature · doi:10.1038/nature04616 · Cited by 335 · see citing works
Vitreschak, A. G. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf433 · Cited by 327 · see citing works
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 · see citing works
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 · see citing works
Self-citationFolding 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 282 · see citing works
Narberhaus, F., Waldminghaus, T., & Chowdhury, S. (2005) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2005.004.x · Cited by 282 · see citing works
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 280 · see citing works
Riboswitch RNAs: using RNA to sense cellular metabolismPreprint
Henkin, T. M. (2008) · Genes & Development · doi:10.1101/gad.1747308 · Cited by 277 · see citing works
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 · see citing works
Thiamine Pyrophosphate Riboswitches Are Targets for the Antimicrobial Compound Pyrithiamine
Sudarsan, N., Cohen‐Chalamish, S., Nakamura, S., Emilsson, G. M., & Breaker, R. R. (2005) · Chemistry & Biology · doi:10.1016/j.chembiol.2005.10.007 · Cited by 268 · see citing works
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 · see citing works
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 · see citing works
Edwards, T. E., & Ferré-D’Amaré, A. R. (2006) · Structure · doi:10.1016/j.str.2006.07.008 · Cited by 252 · see citing works
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 · see citing works
Self-citationThe 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 · see citing works
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 · see citing works
Henkin, T. M., & Yanofsky, C. (2002) · BioEssays · doi:10.1002/bies.10125 · Cited by 244 · see citing works
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 242 · see citing works
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 236 · see citing works
Determination of turgor pressure in Bacillus subtilis: a possible role for K+ in turgor regulation
Whatmore, A. M., & Reed, R. H. (1990) · Journal of General Microbiology · doi:10.1099/00221287-136-12-2521 · Cited by 236 · see citing works
Lee, E. R., Blount, K., & Breaker, R. R. (2009) · RNA Biology · doi:10.4161/rna.6.2.7727 · Cited by 235 · see citing works
ANTIBIOTICS TARGETING RIBOSOMES: Resistance, Selectivity, Synergism, and Cellular Regulation
Yonath, A. (2005) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.74.082803.133130 · Cited by 231 · see citing works
Antibacterial lysine analogs that target lysine riboswitches
Blount, K., Wang, J. X., Lim, J., Sudarsan, N., & Breaker, R. R. (2006) · Nature Chemical Biology · doi:10.1038/nchembio842 · Cited by 231 · see citing works
A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor
Basu, S., Rambo, R. P., Strauss-Soukup, J. K., Cate, J. H. D., Ferré-D’Amaré, A. R., Strobel, S. A., & Doudna, J. A. (1998) · Nature Structural Biology · doi:10.1038/2960 · Cited by 211 · see citing works
Vitreschak, A. G., Rodionov, D. A., Mironov, A. A., & Gelfand, M. S. (2003) · RNA · doi:10.1261/rna.5710303 · Cited by 207 · see citing works
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 · see citing works
Ennifar, E., Walter, P., Ehresmann, B., Ehresmann, C., & Dumas, P. (2001) · Nature Structural Biology · doi:10.1038/nsb727 · Cited by 199 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
Mapping nucleic acid structure by hydroxyl radical cleavage
Tullius, T. D., & Greenbaum, J. (2005) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2005.02.009 · Cited by 178 · see citing works
Rieder, R., Lang, K., Graber, D., & Micura, R. (2007) · ChemBioChem · doi:10.1002/cbic.200700057 · Cited by 175 · see citing works
Klein, D. J., Edwards, T. E., & Ferré-D’Amaré, A. R. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1563 · Cited by 175 · see citing works
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 171 · see citing works
Structures of RNA Switches: Insight into Molecular Recognition and Tertiary Structure
Schwalbe, H., Buck, J., Fürtig, B., Noeske, J., & Wöhnert, J. (2007) · Angewandte Chemie International Edition · doi:10.1002/anie.200604163 · Cited by 167 · see citing works
Inhibition of lysine biosynthesis: an evolving antibiotic strategy
Hutton, C. A., Perugini, M. A., & Gerrard, J. A. (2007) · Molecular BioSystems · doi:10.1039/b705624a · Cited by 164 · see citing works
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 · see citing works
Cooperative Interactions of Hemoglobin
Edelstein, S. J. (1975) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.44.070175.001233 · Cited by 160 · see citing works
Riboswitches that Sense S-adenosylhomocysteine and Activate Genes Involved in Coenzyme Recycling
Wang, J. X., Lee, E. R., Morales, D. R., Lim, J., & Breaker, R. R. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.01.012 · Cited by 155 · see citing works
Lang, K., Rieder, R., & Micura, R. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm580 · Cited by 154 · see citing works
Biochemical Features and Functional Implications of the RNA-Based T-Box Regulatory Mechanism
Gutiérrez‐Preciado, A., Henkin, T. M., Grundy, F. J., Yanofsky, C., & Merino, E. (2009) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00026-08 · Cited by 149 · see citing works
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 · see citing works
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 · see citing works
Kang, M., Peterson, R. D., & Feigon, J. F. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.02.019 · Cited by 142 · see citing works
The intricate world of riboswitches
Coppins, R. L., Hall, K. B., & Groisman, E. A. (2007) · Current Opinion in Microbiology · doi:10.1016/j.mib.2007.03.006 · Cited by 139 · see citing works
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 138 · see citing works
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 135 · see citing works
Metal-ion binding and metal-ion induced folding of the adenine-sensing riboswitch aptamer domain
Noeske, J., Schwalbe, H., & Wöhnert, J. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm565 · Cited by 135 · see citing works
Comparative genomic analysis of T-box regulatory systems in bacteria
Vitreschak, A. G., Mironov, A. A., Lyubetsky, V., & Gelfand, M. S. (2008) · RNA · doi:10.1261/rna.819308 · Cited by 134 · see citing works
Artificial Ribozyme Switches Containing Natural Riboswitch Aptamer Domains
Wieland, M., Benz, A., Klauser, B., & Hartig, J. S. (2009) · Angewandte Chemie International Edition · doi:10.1002/anie.200805311 · Cited by 126 · see citing works
Xiao, H., Edwards, T. E., & Ferré-D’Amaré, A. R. (2008) · Chemistry & Biology · doi:10.1016/j.chembiol.2008.09.004 · Cited by 124 · see citing works
Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis
Welz, R., & Breaker, R. R. (2007) · RNA · doi:10.1261/rna.407707 · Cited by 124 · see citing works
The 5S rRNA loop E: Chemical probing and phylogenetic data versus crystal structure
Leontis, N. B., & Westhof, É. (1998) · RNA · doi:10.1017/s1355838298980566 · Cited by 121 · see citing works
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 · see citing works
Unique glycine‐activated riboswitch linked to glycine–serine auxotrophy in SAR11
Tripp, H. J., Schwalbach, M. S., Meyer, M. M., Kitner, J. B., Breaker, R. R., & Giovannoni, S. J. (2008) · Environmental Microbiology · doi:10.1111/j.1462-2920.2008.01758.x · Cited by 113 · see citing works
Wang, J. X., & Breaker, R. R. (2008) · Biochemistry and Cell Biology · doi:10.1139/o08-008 · Cited by 112 · see citing works
The Na+-dependence of alkaliphily in Bacillus
KRULWICH, T. A., Ito, M., & Guffanti, A. A. (2001) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/s0005-2728(00)00285-1 · Cited by 111 · see citing works
The long and the short of riboswitches
Serganov, A. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2009.02.002 · Cited by 111 · see citing works
Self-citationCooperative hemoglobins: conserved fold, diverse quaternary assemblies and allosteric mechanisms
Royer, W. E., Knapp, J. E., Strand, K., & Soutter, H. H. (2001) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(01)01811-4 · Cited by 110 · see citing works
Artificial Ribozyme Switches Containing Natural Riboswitch Aptamer Domains
Wieland, M., Benz, A., Klauser, B., & Hartig, J. S. (2009) · Angewandte Chemie · doi:10.1002/ange.200805311 · Cited by 110 · see citing works
Purine sensing by riboswitches
Kim, J. N., & Breaker, R. R. (2007) · Biology of the Cell · doi:10.1042/bc20070088 · Cited by 107 · see citing works
Ott, E., Stolz, J., & Mack, M. (2009) · RNA Biology · doi:10.4161/rna.6.3.8342 · Cited by 104 · see citing works
Role of the nhaC-encoded Na+/H+ antiporter of alkaliphilic Bacillus firmus OF4
Ito, M., Guffanti, A. A., Zemsky, J., Ivey, D. M., & KRULWICH, T. A. (1997) · Journal of Bacteriology · doi:10.1128/jb.179.12.3851-3857.1997 · Cited by 104 · see citing works
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 · see citing works
Inhibitors of Lysine Biosynthesis as Antibacterial Agents
Hutton, C. A., Southwood, T. J., & Turner, J. (2003) · Mini-Reviews in Medicinal Chemistry · doi:10.2174/1389557033405359 · Cited by 99 · see citing works
Expanding roles for metabolite-sensing regulatory RNAs
Dambach, M., & Winkler, W. C. (2009) · Current Opinion in Microbiology · doi:10.1016/j.mib.2009.01.012 · Cited by 95 · see citing works
Breaker, R. R. (2008) · Science · doi:10.1126/science.1152621 · Cited by 92 · see citing works
Regulation of diaminopimelate decarboxylase synthesis in Escherichia coli
Stragier, P., Richaud, F., Borne, F., & Patte, J.-C. (1983) · Journal of Molecular Biology · doi:10.1016/s0022-2836(83)80020-5 · Cited by 89 · see citing works
Anastassiadis, S. (2007) · Recent Patents on Biotechnology · doi:10.2174/187220807779813947 · Cited by 88 · see citing works
Blouin, S., & Lafontaine, D. A. (2007) · RNA · doi:10.1261/rna.560307 · Cited by 83 · see citing works
Riboswitches: Ancient and Promising Genetic Regulators
Blouin, S., Mulhbacher, J., Penedo, J. C., & Lafontaine, D. A. (2008) · ChemBioChem · doi:10.1002/cbic.200800593 · Cited by 82 · see citing works
Babitzke, P., & Gollnick, P. D. (2001) · Journal of Bacteriology · doi:10.1128/jb.183.20.5795-5802.2001 · Cited by 82 · see citing works
Structure-based drug design meets the ribosome
Franceschi, F. J., & Duffy, E. M. (2006) · Biochemical Pharmacology · doi:10.1016/j.bcp.2005.12.026 · Cited by 80 · see citing works
Roles of Mg2+ in TPP‐dependent riboswitch
Yamauchi, T., Miyoshi, D., Kubodera, T., Nishimura, A., Nakai, S., & Sugimoto, N. (2005) · FEBS Letters · doi:10.1016/j.febslet.2005.03.074 · Cited by 79 · see citing works
High magnesium content ofEscherichia coli B
Moncany, M. L. J., & Kellenberger, E. (1981) · Cellular and Molecular Life Sciences · doi:10.1007/bf01985672 · Cited by 76 · see citing works
Chemical basis of glycine riboswitch cooperativity
Kwon, M., & Strobel, S. A. (2007) · RNA · doi:10.1261/rna.771608 · Cited by 75 · see citing works
Nucleotide Analog Interference Mapping
Ryder, S. P., & Strobel, S. A. (1999) · Methods · doi:10.1006/meth.1999.0755 · Cited by 75 · see citing works
Chang, C. H., & Frey, P. A. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.1.106 · Cited by 74 · see citing works
12 The Role of Metal Ions in RNA Biochemistry
Feig, A. L., & Uhlenbeck, O. C. (1999) · doi:10.1101/087969589.37.287 · Cited by 74 · see citing works
Towards the discovery of drug-like RNA ligands?
Foloppe, N., Matassova, N., & Aboul‐ela, F. (2006) · Drug Discovery Today · doi:10.1016/j.drudis.2006.09.001 · Cited by 73 · see citing works
Mäder, U., Homuth, G., Scharf, C., Büttner, K., Bode, R., & Hecker, M. (2002) · Journal of Bacteriology · doi:10.1128/jb.184.15.4288-4295.2002 · Cited by 72 · see citing works
Structural features of metabolite-sensing riboswitches
Wakeman, C. A., Winkler, W. C., & Dann, C. E. (2007) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2007.08.005 · Cited by 70 · see citing works
Kalinowski, J., Bachmann, B., Thierbach, G., & Pühler, A. (1990) · Molecular and General Genetics MGG · doi:10.1007/bf00262424 · Cited by 67 · see citing works
Structures of regulatory elements in mRNAs
Batey, R. (2006) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2006.05.001 · Cited by 64 · see citing works
Serganov, A., Polonskaia, A., Ehresmann, B., Ehresmann, C., & Patel, D. J. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg170 · Cited by 64 · see citing works
Self-citationAbundance and functional diversity of riboswitches in microbial communities
Kazanov, M. D., Vitreschak, A. G., & Gelfand, M. S. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-347 · Cited by 62 · see citing works
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 59 · see citing works
Chen, H., Wu, S., Lin, Y.-L., Chen, C., & Tsay, S. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m108365200 · Cited by 57 · see citing works
Regulation of diaminopimelate decarboxylase synthesis in Escherichia coli
Stragier, P., Danos, O., & Patte, J.-C. (1983) · Journal of Molecular Biology · doi:10.1016/s0022-2836(83)80021-7 · Cited by 55 · see citing works
Chen, N. Y., Hu, F. M., & Paulus, H. (1987) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)47484-4 · Cited by 54 · see citing works
RNA as a target for small-molecule therapeutics
Hermann, T. M., & Tor, Y. (2005) · Expert Opinion on Therapeutic Patents · doi:10.1517/13543776.15.1.49 · Cited by 49 · see citing works
Mechanisms of Resistance to an Amino Acid Antibiotic That Targets Translation
Ataide, S. F., Wilson, S. N., Dang, S., Rogers, T. E., Roy, B., Banerjee, R., Henkin, T. M., & Ibba, M. (2007) · ACS Chemical Biology · doi:10.1021/cb7002253 · Cited by 49 · see citing works
Host–microbe interactions: bacteria
Kenny, B., & Valdivia, R. H. (2009) · Current Opinion in Microbiology · doi:10.1016/j.mib.2009.01.002 · Cited by 46 · see citing works
Evidence for Pseudoknot Formation of Class I preQ1 Riboswitch Aptamers
Rieder, U., Lang, K., Kreutz, C., Polacek, N., & Micura, R. (2009) · ChemBioChem · doi:10.1002/cbic.200900155 · Cited by 43 · see citing works
Hirshfield, I. N., & Zamecnik, P. C. (1972) · Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis · doi:10.1016/0005-2787(72)90308-5 · Cited by 41 · see citing works
Structural and Energetic Analysis of Metal Ions Essential to SRP Signal Recognition Domain Assembly
Batey, R., & Doudna, J. A. (2002) · Biochemistry · doi:10.1021/bi026163c · Cited by 40 · see citing works
Development of a glycine-inducible expression system for Bacillus subtilis
Phan, T. T. P., & Schumann, W. (2006) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2006.12.007 · Cited by 40 · see citing works
Regulation of dihydrodipicolinate synthase and aspartate kinase in Bacillus subtilis
Vold, B. S., Szulmajster, J., & Carbone, A. (1975) · Journal of Bacteriology · doi:10.1128/jb.121.3.970-974.1975 · Cited by 37 · see citing works
Lysine-induced premature transcription termination in the lysC operon of Bacillus subtilis
Kochhar, S., & Paulus, H. (1996) · Microbiology · doi:10.1099/13500872-142-7-1635 · Cited by 37 · see citing works
Wang, W., Guffanti, A. A., Wei, Y., Ito, M., & KRULWICH, T. A. (2000) · Journal of Bacteriology · doi:10.1128/jb.182.8.2088-2095.2000 · Cited by 36 · see citing works
The leader sequence of theEscherichia coli lysCgene is involved in the regulation of LysC synthesis
Patte, J.-C., Akrim, M., & Méjean, V. (1998) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1998.tb13313.x · Cited by 33 · see citing works
Rosner, A. (1975) · Journal of Bacteriology · doi:10.1128/jb.121.1.20-28.1975 · Cited by 31 · see citing works
The cad locus of Enterobacteriaceae: More than just lysine decarboxylation
Torres, A. G. (2008) · Anaerobe · doi:10.1016/j.anaerobe.2008.05.002 · Cited by 31 · see citing works
Lu, Y., Chen, N.-Y., & Paulus, H. (1991) · Journal of General Microbiology · doi:10.1099/00221287-137-5-1135 · Cited by 31 · see citing works
Transcriptional regulation of the methionine and cysteine transport and metabolism in streptococci
Kovaleva, G. Y., & Gelfand, M. S. (2007) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2007.00934.x · Cited by 29 · see citing works
l-Arginine influences the structure and function of arginase mRNA in Aspergillus nidulans
Borsuk, P., Przykorska, A., Błachnio, K., Koper, M., Pawlowicz, J. M., Pękala, M., & Węgleński, P. (2007) · Biological Chemistry · doi:10.1515/bc.2007.015 · Cited by 27 · see citing works
Forman, M., & Aronson, A. I. (1972) · Biochemical Journal · doi:10.1042/bj1260503 · Cited by 26 · see citing works
Fine-structure mapping ofcis-acting control sites in thelysCoperon ofBacillus subtilis
Lu, Y., Shevtchenko, T. N., & Paulus, H. (1992) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1992.tb05230.x · Cited by 26 · see citing works
Probing mRNA Structure and sRNA–mRNA Interactions in Bacteria Using Enzymes and Lead(II)
Chevalier, C., Geissmann, T., Helfer, A., & Romby, P. (2009) · Methods in molecular biology · doi:10.1007/978-1-59745-558-9_16 · Cited by 26 · see citing works
Riboswitch Conformations Revealed by Small-Angle X-Ray Scattering
Lipfert, J., Herschlag, D., & Doniach, S. (2009) · Methods in molecular biology · doi:10.1007/978-1-59745-558-9_11 · Cited by 25 · see citing works
Hirshfield, I. N., Tomford, J. W., & Zamecnik, P. C. (1972) · Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis · doi:10.1016/0005-2787(72)90309-7 · Cited by 24 · see citing works
Towards deciphering the principles underlying an mRNA recognition code
Serganov, A., & Patel, D. J. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2007.12.006 · Cited by 24 · see citing works
Self-citationSchendel, F. J., & Flickinger, M. C. (1992) · Applied and Environmental Microbiology · doi:10.1128/aem.58.9.2806-2814.1992 · Cited by 22 · see citing works
Boy, E., Borne, F., & Patte, J.-C. (1980) · Biochimie · doi:10.1016/s0300-9084(80)80228-8 · Cited by 22 · see citing works
Genetic and Biochemical Properties of Thialysine-resistant Mutants of Saccharomyces cerevisiae
Zwolshen, J. H., & Bhattacharjee, J. K. (1981) · Microbiology · doi:10.1099/00221287-122-2-281 · Cited by 18 · see citing works
4 Riboswitches and the RNA WorldPreprint
Breaker, R. R. (2006) · Cold Spring Harbor Monograph Archive · doi:10.1101/087969739.43.89 · Cited by 18 · see citing works
Wakeman, C. A., & Winkler, W. C. (2009) · Methods in molecular biology · doi:10.1007/978-1-59745-558-9_13 · Cited by 18 · see citing works
Bacterial cis-regulatory RNA structures
Gelfand, M. S. (2006) · Molecular Biology · doi:10.1134/s0026893306040066 · Cited by 9 · see citing works
Aspartokinase III repression and lysine analogs utilization for protein synthesis.
Girolamo, M. D., Busiello, V., Coccia, R., & Foppoli, C. (1990) · PubMed · Cited by 9 · see citing works
Analysis of the regulatory region of thelysCgene ofEscherichia coli
Liao, H.-H., & Hseu, T. (1998) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1998.tb13251.x · Cited by 7 · see citing works
Degradation of thialysine- or selenalysine-containing abnormal proteins in CHO cells.
Girolamo, M. D., Busiello, V., Girolamo, A. D., Marco, C. D., & Cini, C. (1987) · PubMed · Cited by 4 · see citing works
Strauss-Soukup, J. K., & Soukup, G. A. (2009) · Methods in molecular biology · doi:10.1007/978-1-59745-558-9_14 · Cited by 3 · see citing works
Aspartokinase III repression in a thialysine-resistant mutant of E. coli.
Girolamo, M. D., Busiello, V., Girolamo, A. D., Foppoli, C., & Marco, C. D. (1988) · PubMed · Cited by 3 · see citing works
Structural Probing of RNA Thermosensors
Chiaruttini, C., Allem, F., & Springer, M. (2009) · Methods in molecular biology · doi:10.1007/978-1-59745-558-9_17 · Cited by 2 · see citing works
Flagged first, then by citations
1 of the 176 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
The mononuclear molybdenum enzymes
Hille, R., Hall, J., & Basu, P. (2014) · Chemical Reviews · doi:10.1021/cr400443z · Cited by 1,738 · see citing works
Huang, L., Serganov, A., & Patel, D. J. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.11.026 · Cited by 147 · see citing works
Self-citationGenome-wide detection of novel regulatory RNAs in E. coliPreprint
Raghavan, R., Groisman, E. A., & Ochman, H. (2011) · Genome Research · doi:10.1101/gr.119370.110 · Cited by 146 · see citing works
Molybdenum enzymes in bacteria and their maturation
Magalon, A., Fedor, J. G., Walburger, A., & Weiner, J. H. (2011) · Coordination Chemistry Reviews · doi:10.1016/j.ccr.2010.12.031 · Cited by 114 · see citing works
Zhou, L., & Zeng, A. (2015) · ACS Synthetic Biology · doi:10.1021/acssynbio.5b00075 · Cited by 112 · see citing works
Lu, C., Ding, F., Chowdhury, A., Pradhan, V., Tomšič, J., Holmes, W. M., Henkin, T. M., & Ke, A. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.09.059 · Cited by 99 · see citing works
Riboflavin as a promising antimicrobial agent? A multi-perspective review
Farah, N., Chin, V. K., Chong, P. P., Lim, W. F., Lim, J. C. W., Basir, R., Chang, S. K., & Lee, T. Y. (2022) · Current Research in Microbial Sciences · doi:10.1016/j.crmicr.2022.100111 · Cited by 94 · see citing works
Koonin, E. (2017) · Life · doi:10.3390/life7020022 · Cited by 85 · see citing works
“It seems interesting to note that, although direct recognition of amino acids by RNA molecules seems to be banished from the modern translation system, it survives in other functional spheres of modern cells, in particular, as amino acid-binding riboswitches [96,97].”
BackgroundLong-Range Interactions in Riboswitch Control of Gene Expression
Jones, C. P., & Ferré-D’Amaré, A. R. (2017) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-070816-034042 · Cited by 77 · see citing works
Emerging applications of riboswitches – from antibacterial targets to molecular tools
Machtel, P., Bąkowska‐Żywicka, K., & Żywicki, M. (2016) · Journal of Applied Genetics · doi:10.1007/s13353-016-0341-x · Cited by 77 · see citing works
Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions
Li, S., Su, Z., Lehmann, J., Stamatopoulou, V., Γιαρίμογλου, Ν., Henderson, F. E., Fan, L., Pintilie, G. D., Zhang, K., Chen, M., et al. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0326-7 · Cited by 76 · see citing works
Characterization and application of a DNA aptamer binding to l-tryptophan
Yang, X., Bing, T., Mei, H., Fang, C., Cao, Z. C., & Shangguan, D. (2010) · The Analyst · doi:10.1039/c0an00550a · Cited by 70 · see citing works
Riboswitch structure in the ligand‐free state
Liberman, J. A., & Wedekind, J. E. (2011) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.114 · Cited by 67 · see citing works
Zhang, J., & Ferré-D’Amaré, A. R. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.05.017 · Cited by 57 · see citing works
Li, S., Su, Z., Zhang, J., & Chiu, W. (2019) · Worldwide Protein Data Bank · doi:10.2210/pdb6pom/pdb · Cited by 52 · see citing works
Zhang, Q., Kang, M., Peterson, R. D., & Feigon, J. F. (2011) · Journal of the American Chemical Society · doi:10.1021/ja111769g · Cited by 50 · see citing works
Structure and mechanism of the T‐box riboswitches
Zhang, J., & Ferré-D’Amaré, A. R. (2015) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1285 · Cited by 46 · see citing works
Probing Translation with Small-Molecule Inhibitors
Blanchard, S. C., Cooperman, B. S., & Wilson, D. N. (2010) · Chemistry & Biology · doi:10.1016/j.chembiol.2010.06.003 · Cited by 44 · see citing works
RNA-mediated regulation in bacteria: from natural to artificial systems
Lioliou, E. E., Romilly, C., Romby, P., & Fechter, P. (2010) · New Biotechnology · doi:10.1016/j.nbt.2010.03.002 · Cited by 43 · see citing works
Biosynthesis and Insertion of the Molybdenum Cofactor
Magalon, A., & Mendel, R. R. (2015) · EcoSal Plus · doi:10.1128/ecosalplus.esp-0006-2013 · Cited by 38 · see citing works
Erion, T., & Strobel, S. A. (2010) · RNA · doi:10.1261/rna.2271511 · Cited by 36 · see citing works
Schroeder, G. M., Dutta, D., Cavender, C. E., Jenkins, J. L., Pritchett, E. M., Baker, C. D., Ashton, J. M., Mathews, D. H., & Wedekind, J. E. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa546 · Cited by 35 · see citing works
Mechanism and Distribution of glmS Ribozymes
McCown, P. J., Winkler, W. C., & Breaker, R. R. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-545-9_8 · Cited by 32 · see citing works
Sung, H.-L., & Nesbitt, D. J. (2019) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.8b11841 · Cited by 31 · see citing works
Cooperativity, allostery and synergism in ligand binding to riboswitches
Peselis, A., Gao, A., & Serganov, A. (2015) · Biochimie · doi:10.1016/j.biochi.2015.06.028 · Cited by 31 · see citing works
Self-citationTwo-codon T-box riboswitch binding two tRNAs
Saad, N. Y., Stamatopoulou, V., Brayé, M., Drainas, D., Stathopoulos, C., & Becker, H. D. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1304307110 · Cited by 29 · see citing works
McCluskey, K., Boudreault, J., St-Pierre, P., Pérez‐González, C., Chauvier, A., Rizzi, A., Beauregard, P. B., Lafontaine, D. A., & Penedo, J. C. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz316 · Cited by 28 · see citing works
Engineering and characterization of fluorogenic glycine riboswitches
Ketterer, S., Gladis, L., Kozica, A., & Meier, M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw465 · Cited by 27 · see citing works
Small molecule signaling, regulation, and potential applications in cellular therapeutics
McNerney, M. P., & Styczynski, M. P. (2017) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1405 · Cited by 24 · see citing works
Khani, A., Popp, N., Kreikemeyer, B., & Patenge, N. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00200 · Cited by 23 · see citing works
A riboswitch gives rise to multi-generational phenotypic heterogeneity in an auxotrophic bacterium
Hernandez‐Valdes, J. A., van Gestel, J., & Kuipers, O. P. (2020) · Nature Communications · doi:10.1038/s41467-020-15017-1 · Cited by 22 · see citing works
Schamber, T., Binas, O., Schlundt, A., Wacker, A., & Schwalbe, H. (2021) · ChemBioChem · doi:10.1002/cbic.202100564 · Cited by 20 · see citing works
Liberman, J. A., & Wedekind, J. E. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.03.016 · Cited by 20 · see citing works
Brautaset, T., & Ellingsen, T. E. (2011) · Elsevier eBooks · doi:10.1016/b978-0-08-088504-9.00220-8 · Cited by 18 · see citing works
Riboswitch-mediated regulation of riboflavin biosynthesis genes in prokaryotes
Vikram, V., Mishra, V., Rana, A., & Ahire, J. J. (2022) · 3 Biotech · doi:10.1007/s13205-022-03348-3 · Cited by 16 · see citing works
Pavlova, N., Traykovska, M., & Prof. Robert Penchovsky, D. R. N. (2023) · Antibiotics · doi:10.3390/antibiotics12111607 · Cited by 17 · see citing works
Molina-Quintero, L. R., Elío, P. L., & Sánchez-Amat, A. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.00690-10 · Cited by 16 · see citing works
Comparative genomics and phylogenomic analyses of lysine riboswitch distributions in bacteria
Mukherjee, S., Barash, D., & Sengupta, S. (2017) · PLoS ONE · doi:10.1371/journal.pone.0184314 · Cited by 16 · see citing works
Jiang, Q., Geng, F., Shen, J., Ping, Z., Lu, Z., Zhou, L., & Lü, F. (2024) · Microorganisms · doi:10.3390/microorganisms12030606 · Cited by 15 · see citing works
Analysis of lysine recognition and specificity of the Bacillus subtilis L box riboswitch
Wilson-Mitchell, S. N., Grundy, F. J., & Henkin, T. M. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks212 · Cited by 15 · see citing works
Multidimensional Applications and Challenges of Riboswitches in Biosensing and Biotherapy
Wu, Y., Zhu, L., Zhang, Y., & Xu, W. (2023) · Small · doi:10.1002/smll.202304852 · Cited by 11 · see citing works
Abavisani, M., Sajjadi, S. M., Ebadpour, N., Kesharwani, P., Karav, S., & Sahebkar, A. (2025) · Chemical Engineering Journal · doi:10.1016/j.cej.2025.165777 · Cited by 10 · see citing works
Direct structural analysis of modified RNA by fluorescent in-line probing
Strauss, B., Nierth, A., Singer, M., & Jäschke, A. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr733 · Cited by 10 · see citing works
An integrated perspective on RNA aptamer ligand-recognition models: clearing muddy waters
McCluskey, K., & Penedo, J. C. (2017) · Physical Chemistry Chemical Physics · doi:10.1039/c6cp08798a · Cited by 9 · see citing works
Ligation of RNA Oligomers by the Schistosoma mansoni Hammerhead Ribozyme in Frozen Solution
Lie, L., Biliya, S., Vannberg, F. O., & Wartell, R. M. (2016) · Journal of Molecular Evolution · doi:10.1007/s00239-016-9729-9 · Cited by 9 · see citing works
Lysine Industrial Uses and Production
Brautaset, T., Ellingsen, T. E., & Eggeling, L. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.09172-x · Cited by 9 · see citing works
Evolution of the RNA world: From signals to codes
Spirov, A. V. (2023) · Biosystems · doi:10.1016/j.biosystems.2023.105043 · Cited by 7 · see citing works
Regulatory Components for Bacterial Cell-Free Systems Engineering
Lee, P., & Maerkl, S. J. (2024) · ACS Synthetic Biology · doi:10.1021/acssynbio.4c00574 · Cited by 8 · see citing works
Dahedl, E. K., Hancock, T. L., Kratz, M. A., & Urakawa, H. (2024) · Journal of Environmental Management · doi:10.1016/j.jenvman.2024.123503 · Cited by 7 · see citing works
Munyati-Othman, N., Appasamy, S. D., Damiri, N., Emrizal, R., Alipiah, N. M., Ramlan, E. I., & Firdaus‐Raih, M. (2021) · Current Microbiology · doi:10.1007/s00284-021-02550-5 · Cited by 7 · see citing works
Droste, J., Rückert, C., Kalinowski, J., Hamed, M. B., Anné, J., Simoens, K., Bernaerts, K., Economou, A., & Busche, T. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.604034 · Cited by 7 · see citing works
From the RNA world to the RNA/protein world: Contribution of some riboswitch-binding species?
da Silva, J. A. L. (2015) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2014.12.013 · Cited by 7 · see citing works
Zhang, J., Wang, D., Liang, Y., Zhong, W.-Y., Ming, Z., Tang, D., & Tang, J. (2018) · Microbiology · doi:10.1099/mic.0.000690 · Cited by 6 · see citing works
Aghdam, E. M., Barzegar, A., & Hejazi, M. S. (2014) · Europe PMC (PubMed Central) · doi:10.5681/apb.2014.033 · Cited by 6 · see citing works
Dahedl, E. K., Hancock, T. L., & Urakawa, H. (2025) · Harmful Algae · doi:10.1016/j.hal.2025.102992 · Cited by 5 · see citing works
Sung, H.-L., & Nesbitt, D. J. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c06579 · Cited by 4 · see citing works
The current riboswitch landscape in Clostridioides difficile
Badilla-Lobo, A., Soutourina, O. A., & Johann, P. (2024) · Microbiology · doi:10.1099/mic.0.001508 · Cited by 3 · see citing works
Kenesheva, S. T., Turganbay, S., Jumagaziyeva, A. B., Askhatkyzy, G., Askarova, D. A., Azembayev, A., Ilin, A. I., Reva, O. N., & Karpenyuk, T. A. (2025) · Biomedicines · doi:10.3390/biomedicines13081790 · Cited by 2 · see citing works
Recent Advances, Challenges, and Opportunities in Riboswitches
Ramakrishnan, C., Kesharwani, M., & Velmurugan, D. (2020) · Springer eBooks · doi:10.1007/978-981-15-0081-7_11 · Cited by 2 · see citing works
Origin of ribonucleotide recognition motifs through ligand mimicry at early earth
Mozumdar, D., & Roy, R. N. (2024) · RNA Biology · doi:10.1080/15476286.2024.2423149 · Cited by 1 · see citing works
Deciphering the metabolic details of L-lysine toxicity in cyanobacteria
Enkerlin, A. M., Hoffmann, U. A., Rapp, J., Miao, R., Postma, J., Feldbrügge, M., Link, H., Hudson, E. P., & Selim, K. A. (2026) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiag106 · Cited by 1 · see citing works
Riboswitches as Molecular Tools for Microbial Bioprospecting
Gupta, J., & Peerzada, T. (2018) · Springer eBooks · doi:10.1007/978-981-13-0053-0_17 · Cited by 1 · see citing works
Alam, K. M., Yan, Y., Lin, M., Islam, M. A., Gaber, A., & Hossain, A. (2022) · Archives of Microbiology · doi:10.1007/s00203-022-03064-9 · Cited by 1 · see citing works
Bio-engineering of antibiotic enduracidin biosynthetic pathways and PreQ1 riboswitch
Wu, M. (2011) · Research Explorer (The University of Manchester)
Structural Insights into Ligand Recognition by a Sensing Domain of the Cooperative
Huang, L., Serganov, A., & Patel, D. J. (2010)
Self-citationStudying Parasite Gene Function and Interaction Through Ribozymes and Riboswitches Design Mechanism
Shukla, H., & Tripathi, T. (2018) · Springer eBooks · doi:10.1007/978-981-10-8693-9_4
Structure and function of non-coding regulatory RNA domains
Smith, N. L. (2012) · doi:10.54014/gcn7-s2yt
- Authors
- Serganov, A., & Patel, D. J.
- Affiliations
- Memorial Sloan Kettering Cancer Center (US)
- Corresponding author
- Serganov, Alexander
- Venue
- Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
- Publisher
- Elsevier BV
- Published
- 2009-09
- Volume
- 1789
- Issue
- 9-10
- Pages
- 592-611
- ISSN
- 1874-9399 (ISSN-L)
- PMC
- PMC3744886
- OpenAlex
- W1969810565
- Cited by
- 69
- References
- 176
- Citations by year
- 2026: 1 · 2025: 3 · 2024: 6 · 2023: 3 · 2022: 4 · 2021: 3 · 2020: 3 · 2019: 3 · 2018: 4 · 2017: 7 · 2016: 3 · 2015: 5 · 2014: 3 · 2013: 1 · 2012: 3
- FWCI
- 0.51
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of General Medical Sciences (GM073618, R01GM073618, 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 › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- riboswitches, amino acid recognition, glycine riboswitch, ligand binding, gene expression regulation, riboswitch structure, antibiotic resistance
- MeSH terms
- Amino Acids, Bacillus subtilis, Base Sequence, Binding Sites, Biochemistry, Glycine, Hydrogen Bonding, Ligands, Lysine, Molecular Sequence Data, Nucleic Acid Conformation, Phylogeny, Ribosomes, RNA, RNA, Bacterial, Gene Expression Regulation, Bacterial, Crystallography, X-Ray, 5' Untranslated Regions
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