A Decade of Riboswitches

Baker, 2012, Widespread genetic switches and toxicity resistance proteins for fluoride, Science, 335, 233, 10.1126/science.1215063

Batey, 2004, Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine, Nature, 432, 411, 10.1038/nature03037

Bocobza, 2007, Riboswitch-dependent gene regulation and its evolution in the plant kingdom, Genes Dev., 21, 2874, 10.1101/gad.443907

Breaker, 2006, Riboswitches and the RNA world, 89

Breaker, 2011, Prospects for riboswitch discovery and analysis, Mol. Cell, 43, 867, 10.1016/j.molcel.2011.08.024

Butler, 2011, Structural basis of cooperative ligand binding by the glycine riboswitch, Chem. Biol., 18, 293, 10.1016/j.chembiol.2011.01.013

Cheah, 2007, Control of alternative RNA splicing and gene expression by eukaryotic riboswitches, Nature, 447, 497, 10.1038/nature05769

Chen, 2011, Mechanism for gene control by a natural allosteric group I ribozyme, RNA, 17, 1967, 10.1261/rna.2757311

Cochrane, 2007, Structural investigation of the GlmS ribozyme bound to its catalytic cofactor, Chem. Biol., 14, 97, 10.1016/j.chembiol.2006.12.005

Collins, 2007, Mechanism of mRNA destabilization by the glmS ribozyme, Genes Dev., 21, 3356, 10.1101/gad.1605307

Corbino, 2005, Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria, Genome Biol., 6, R70, 10.1186/gb-2005-6-8-r70

Croft, 2007, Thiamine biosynthesis in algae is regulated by riboswitches, Proc. Natl. Acad. Sci. USA, 104, 20770, 10.1073/pnas.0705786105

Cromie, 2006, An RNA sensor for intracellular Mg(2+), Cell, 125, 71, 10.1016/j.cell.2006.01.043

Dann, 2007, Structure and mechanism of a metal-sensing regulatory RNA, Cell, 130, 878, 10.1016/j.cell.2007.06.051

Dixon, 2010, Reengineering orthogonally selective riboswitches, Proc. Natl. Acad. Sci. USA, 107, 2830, 10.1073/pnas.0911209107

Dixon, 2012, Orthogonal riboswitches for tuneable coexpression in bacteria, Angew. Chem. Int. Ed. Engl., 51, 3620, 10.1002/anie.201109106

Edwards, 2006, Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition, Structure, 14, 1459, 10.1016/j.str.2006.07.008

Ellington, 1990, In vitro selection of RNA molecules that bind specific ligands, Nature, 346, 818, 10.1038/346818a0

Epshtein, 2003, The riboswitch-mediated control of sulfur metabolism in bacteria, Proc. Natl. Acad. Sci. USA, 100, 5052, 10.1073/pnas.0531307100

Fox, 2009, Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in Enterococcus faecalis, Proc. Natl. Acad. Sci. USA, 106, 4435, 10.1073/pnas.0812194106

Fuchs, 2006, The S(MK) box is a new SAM-binding RNA for translational regulation of SAM synthetase, Nat. Struct. Mol. Biol., 13, 226, 10.1038/nsmb1059

Garst, 2008, Crystal structure of the lysine riboswitch regulatory mRNA element, J. Biol. Chem., 283, 22347, 10.1074/jbc.C800120200

Gelfand, 1999, A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes, Trends Genet., 15, 439, 10.1016/S0168-9525(99)01856-9

Gilbert, 1986, Origin of life: the RNA world, Nature, 319, 618, 10.1038/319618a0

Gilbert, 2008, Structure of the SAM-II riboswitch bound to S-adenosylmethionine, Nat. Struct. Mol. Biol., 15, 177, 10.1038/nsmb.1371

Gralla, 1974, Direct physical evidence for secondary structure in an isolated fragment of R17 bacteriophage mRNA, Nature, 248, 204, 10.1038/248204a0

Grundy, 1993, tRNA as a positive regulator of transcription antitermination in B. subtilis, Cell, 74, 475, 10.1016/0092-8674(93)80049-K

Haller, 2011, Conformational capture of the SAM-II riboswitch, Nat. Chem. Biol., 7, 393, 10.1038/nchembio.562

Hollands, 2012, Riboswitch control of Rho-dependent transcription termination, Proc. Natl. Acad. Sci. USA, 109, 5376, 10.1073/pnas.1112211109

Huang, 2010, Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch, Mol. Cell, 40, 774, 10.1016/j.molcel.2010.11.026

Huang, 2011, Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch, Proc. Natl. Acad. Sci. USA, 108, 14801, 10.1073/pnas.1111701108

Jaeger, 2009, The UA_handle: a versatile submotif in stable RNA architectures, Nucleic Acids Res., 37, 215, 10.1093/nar/gkn911

Johnson, 2012, B12 cofactors directly stabilize an mRNA regulatory switch, Nature, 492, 133, 10.1038/nature11607

Kladwang, 2012, Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches, J. Am. Chem. Soc., 134, 1404, 10.1021/ja2093508

Klein, 2006, Structural basis of glmS ribozyme activation by glucosamine-6-phosphate, Science, 313, 1752, 10.1126/science.1129666

Kwon, 2008, Chemical basis of glycine riboswitch cooperativity, RNA, 14, 25, 10.1261/rna.771608

Lee, 2012, Control of a Salmonella virulence locus by an ATP-sensing leader messenger RNA, Nature, 486, 271, 10.1038/nature11090

Lee, 2010, An allosteric self-splicing ribozyme triggered by a bacterial second messenger, Science, 329, 845, 10.1126/science.1190713

Lemay, 2011, Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms, PLoS Genet., 7, e1001278, 10.1371/journal.pgen.1001278

Lilley, 2008, Ribozymes and RNA catalysis: introduction and primer, 1

Loh, 2009, A trans-acting riboswitch controls expression of the virulence regulator PrfA in Listeria monocytogenes, Cell, 139, 770, 10.1016/j.cell.2009.08.046

Lu, 2008, Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism, Nat. Struct. Mol. Biol., 15, 1076, 10.1038/nsmb.1494

Mandal, 2004, A glycine-dependent riboswitch that uses cooperative binding to control gene expression, Science, 306, 275, 10.1126/science.1100829

McDaniel, 2003, Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA, Proc. Natl. Acad. Sci. USA, 100, 3083, 10.1073/pnas.0630422100

Miranda-Ríos, 2001, A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria, Proc. Natl. Acad. Sci. USA, 98, 9736, 10.1073/pnas.161168098

Mironov, 2002, Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria, Cell, 111, 747, 10.1016/S0092-8674(02)01134-0

Montange, 2006, Structure of the S-adenosylmethionine riboswitch regulatory mRNA element, Nature, 441, 1172, 10.1038/nature04819

Mulhbacher, 2010, Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways, PLoS Pathog., 6, e1000865, 10.1371/journal.ppat.1000865

Nahvi, 2002, Genetic control by a metabolite binding mRNA, Chem. Biol., 9, 1043, 10.1016/S1074-5521(02)00224-7

Nechooshtan, 2009, A pH-responsive riboregulator, Genes Dev., 23, 2650, 10.1101/gad.552209

Nou, 1998, Coupled changes in translation and transcription during cobalamin-dependent regulation of btuB expression in Escherichia coli, J. Bacteriol., 180, 6719, 10.1128/JB.180.24.6719-6728.1998

Nou, 2000, Adenosylcobalamin inhibits ribosome binding to btuB RNA, Proc. Natl. Acad. Sci. USA, 97, 7190, 10.1073/pnas.130013897

Perkins, 2002, Biosynthesis of riboflavin, biotin, folic acid, and cobalamin, 271

Peselis, 2012, Structural insights into ligand binding and gene expression control by an adenosylcobalamin riboswitch, Nat. Struct. Mol. Biol., 19, 1182, 10.1038/nsmb.2405

Pikovskaya, 2011, Structural principles of nucleoside selectivity in a 2′-deoxyguanosine riboswitch, Nat. Chem. Biol., 7, 748, 10.1038/nchembio.631

Ravnum, 2001, An adenosyl-cobalamin (coenzyme-B12)-repressed translational enhancer in the cob mRNA of Salmonella typhimurium, Mol. Microbiol., 39, 1585, 10.1046/j.1365-2958.2001.02346.x

Ray, 2009, A stress-responsive RNA switch regulates VEGFA expression, Nature, 457, 915, 10.1038/nature07598

Ren, 2012, Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch, Nature, 486, 85, 10.1038/nature11152

Robertson, 1990, Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA, Nature, 344, 467, 10.1038/344467a0

Serganov, 2004, Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs, Chem. Biol., 11, 1729, 10.1016/j.chembiol.2004.11.018

Serganov, 2006, Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch, Nature, 441, 1167, 10.1038/nature04740

Serganov, 2008, Structural insights into amino acid binding and gene control by a lysine riboswitch, Nature, 455, 1263, 10.1038/nature07326

Serganov, 2009, Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch, Nature, 458, 233, 10.1038/nature07642

Sherman, 2012, An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches, RNA, 18, 496, 10.1261/rna.031286.111

Sinha, 2010, Reprogramming bacteria to seek and destroy an herbicide, Nat. Chem. Biol., 6, 464, 10.1038/nchembio.369

Stoddard, 2010, Free state conformational sampling of the SAM-I riboswitch aptamer domain, Structure, 18, 787, 10.1016/j.str.2010.04.006

Stormo, 2001, Do mRNAs act as direct sensors of small molecules to control their expression?, Proc. Natl. Acad. Sci. USA, 98, 9465, 10.1073/pnas.181334498

Sudarsan, 2006, Tandem riboswitch architectures exhibit complex gene control functions, Science, 314, 300, 10.1126/science.1130716

Sudarsan, 2008, Riboswitches in eubacteria sense the second messenger cyclic di-GMP, Science, 321, 411, 10.1126/science.1159519

Suess, 2004, A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo, Nucleic Acids Res., 32, 1610, 10.1093/nar/gkh321

Thore, 2006, Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand, Science, 312, 1208, 10.1126/science.1128451

Tomsic, 2008, 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, 823, 10.1128/JB.01034-07

Trausch, 2011, The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer, Structure, 19, 1413, 10.1016/j.str.2011.06.019

Tuerk, 1990, Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase, Science, 249, 505, 10.1126/science.2200121

Verhounig, 2010, Inducible gene expression from the plastid genome by a synthetic riboswitch, Proc. Natl. Acad. Sci. USA, 107, 6204, 10.1073/pnas.0914423107

Vu, 2012, Convergent evolution of adenosine aptamers spanning bacterial, human, and random sequences revealed by structure-based bioinformatics and genomic SELEX, Chem. Biol., 19, 1247, 10.1016/j.chembiol.2012.08.010

Wachter, 2007, Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mRNAs, Plant Cell, 19, 3437, 10.1105/tpc.107.053645

Watson, 2011, The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo, Nat. Struct. Mol. Biol., 18, 359, 10.1038/nsmb.1989

Watson, 2012, The ydaO motif is an ATP-sensing riboswitch in Bacillus subtilis, Nat. Chem. Biol., 8, 963, 10.1038/nchembio.1095

Weinberg, 2007, Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline, Nucleic Acids Res., 35, 4809, 10.1093/nar/gkm487

Weinberg, 2010, Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes, Genome Biol., 11, R31, 10.1186/gb-2010-11-3-r31

Wickiser, 2005, The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch, Mol. Cell, 18, 49, 10.1016/j.molcel.2005.02.032

Winkler, 2002, Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression, Nature, 419, 952, 10.1038/nature01145

Winkler, 2003, An mRNA structure that controls gene expression by binding S-adenosylmethionine, Nat. Struct. Biol., 10, 701, 10.1038/nsb967

Winkler, 2004, Control of gene expression by a natural metabolite-responsive ribozyme, Nature, 428, 281, 10.1038/nature02362

Yanofsky, 1981, Attenuation in the control of expression of bacterial operons, Nature, 289, 751, 10.1038/289751a0