Abstract
Riboswitches are one of the most compact and efficient gene regulatory elements. These structured RNAs bind small molecule ligands to regulate gene expression and have been discovered in all three domains of life. The study of natural riboswitches has given many fundamental insights into molecular recognition by RNA, RNA structure and conformational dynamics, and mechanisms of gene regulation at the RNA level.
References
Ames TD, Breaker RR (2011) Bacterial aptamers that selectively bind glutamine. RNA Biol 8:82–89. https://doi.org/10.4161/rna.8.1.13864
Ames TD, Rodionov DA, Weinberg Z, Breaker RR (2010) A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate. Chem Biol 17:681–685. https://doi.org/10.1016/j.chembiol.2010.05.020
Atilho RM, Mirihana Arachchilage G, Greenlee EB et al (2019) A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer. eLife 8:e45210. https://doi.org/10.7554/eLife.45210
Baker JL, Sudarsan N, Weinberg Z et al (2012) Widespread genetic switches and toxicity resistance proteins for fluoride. Science 335:233–235. https://doi.org/10.1126/science.1215063
Blount KF, Wang JX, Lim J et al (2007) Antibacterial lysine analogs that target lysine riboswitches. Nat Chem Biol 3:44–49. https://doi.org/10.1038/nchembio842
Breaker RR (2022) The biochemical landscape of riboswitch ligands. Biochemistry 61:137–149. https://doi.org/10.1021/acs.biochem.1c00765
Cheah MT, Wachter A, Sudarsan N, Breaker RR (2007) Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 447:497–500. https://doi.org/10.1038/nature05769
Chen X, Arachchilage GM, Breaker RR (2019) Biochemical validation of a second class of tetrahydrofolate riboswitches in bacteria. RNA 25:1091–1097. https://doi.org/10.1261/rna.071829.119
Corbino KA, Barrick JE, Lim J et al (2005) Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. Genome Biol 6:R70. https://doi.org/10.1186/gb-2005-6-8-r70
Croft MT, Moulin M, Webb ME, Smith AG (2007) Thiamine biosynthesis in algae is regulated by riboswitches. Proc Natl Acad Sci U S A 104:20770–20775. https://doi.org/10.1073/pnas.0705786105
Cromie MJ, Shi Y, Latifi T, Groisman EA (2006) An RNA sensor for intracellular Mg2+. Cell 125:71–84. https://doi.org/10.1016/j.cell.2006.01.043
Dambach M, Sandoval M, Updegrove TB et al (2015) The ubiquitous yybP-ykoY riboswitch is a manganese-responsive regulatory element. Mol Cell 57:1099–1109. https://doi.org/10.1016/j.molcel.2015.01.035
Dann CE, Wakeman CA, Sieling CL et al (2007) Structure and mechanism of a metal-sensing regulatory RNA. Cell 130:878–892. https://doi.org/10.1016/j.cell.2007.06.051
Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818–822. https://doi.org/10.1038/346818a0
Fuchs RT, Grundy FJ, Henkin TM (2006) The SMK box is a new SAM-binding RNA for translational regulation of SAM synthetase. Nat Struct Mol Biol 13:226–233. https://doi.org/10.1038/nsmb1059
Furukawa K, Ramesh A, Zhou Z et al (2015) Bacterial riboswitches cooperatively bind Ni2+ or Co2+ ions and control expression of heavy metal transporters. Mol Cell 57:1088–1098. https://doi.org/10.1016/j.molcel.2015.02.009
Grundy FJ, Lehman SC, Henkin TM (2003) The L box regulon: lysine sensing by leader RNAs of bacterial lysine biosynthesis genes. Proc Natl Acad Sci U S A 100:12057–12062. https://doi.org/10.1073/pnas.2133705100
Hallberg ZF, Su Y, Kitto RZ, Hammond MC (2017) Engineering and in vivo applications of riboswitches. Annu Rev Biochem 86:515–539. https://doi.org/10.1146/annurev-biochem-060815-014628
Haller A, Rieder U, Aigner M et al (2011) Conformational capture of the SAM-II riboswitch. Nat Chem Biol 7:393–400. https://doi.org/10.1038/nchembio.562
Hollands K, Proshkin S, Sklyarova S et al (2012) Riboswitch control of Rho-dependent transcription termination. Proc Natl Acad Sci U S A 109:5376–5381. https://doi.org/10.1073/pnas.1112211109
Howe JA, Wang H, Fischmann TO et al (2015) Selective small-molecule inhibition of an RNA structural element. Nature 526:672–677. https://doi.org/10.1038/nature15542
Johnson Jr JE, Reyes FE, Polaski JT, Batey RT (2012) B12 cofactors directly stabilize an mRNA regulatory switch. Nature 492:133–137. https://doi.org/10.1038/nature11607
Kang M, Peterson R, Feigon J (2009) Structural insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of tRNA. Mol Cell 33:784–790. https://doi.org/10.1016/j.molcel.2009.02.019
Kellenberger CA, Wilson SC, Hickey SF et al (2015) GEMM-I riboswitches from Geobacter sense the bacterial second messenger cyclic AMP-GMP. Proc Natl Acad Sci U S A 112:5383–5388. https://doi.org/10.1073/pnas.1419328112
Kim JN, Roth A, Breaker RR (2007) Guanine riboswitch variants from Mesoplasma florum selectively recognize 2′-deoxyguanosine. Proc Natl Acad Sci U S A 104:16092–16097. https://doi.org/10.1073/pnas.0705884104
Kim PB, Nelson JW, Breaker RR (2015) An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism. Mol Cell 57:317–328. https://doi.org/10.1016/j.molcel.2015.01.001
Klähn S, Bolay P, Wright PR et al (2018) A glutamine riboswitch is a key element for the regulation of glutamine synthetase in Cyanobacteria. Nucleic Acids Res 46:10082–10094. https://doi.org/10.1093/nar/gky709
Lee ER, Blount KF, Breaker RR (2009) Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression. RNA Biol 6:187–194. https://doi.org/10.4161/rna.6.2.7727
Lee ER, Baker JL, Weinberg Z et al (2010) An allosteric self-splicing ribozyme triggered by a bacterial second messenger. Science 329:845–848. https://doi.org/10.1126/science.1190713
Li S, Hwang XY, Stav S, Breaker RR (2016) The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds. RNA 22:530–541. https://doi.org/10.1261/rna.054890.115
Loh E, Dussurget O, Gripenland J et al (2009) A trans-acting riboswitch controls expression of the virulence regulator PrfA in Listeria monocytogenes. Cell 139:770–779. https://doi.org/10.1016/j.cell.2009.08.046
Lünse CE, Schmidt MS, Wittmann V, Mayer G (2011) Carba-sugars activate the glmS-riboswitch of Staphylococcus aureus. ACS Chem Biol 6:675–678. https://doi.org/10.1021/cb200016d
Malkowski SN, Spencer TCJ, Breaker RR (2019) Evidence that the nadA motif is a bacterial riboswitch for the ubiquitous enzyme cofactor NAD+. RNA 25:1616–1627. https://doi.org/10.1261/rna.072538.119
Malkowski SN, Atilho RM, Greenlee EB et al (2020) A rare bacterial RNA motif is implicated in the regulation of the purF gene whose encoded enzyme synthesizes phosphoribosylamine. RNA 26:1838–1846. https://doi.org/10.1261/rna.077313.120
Mandal M, Breaker RR (2004) Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat Struct Mol Biol 11:29–35. https://doi.org/10.1038/nsmb710
Mandal M, Boese B, Barrick JE et al (2003) Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113:577–586. https://doi.org/10.1016/S0092-8674(03)00391-X
Mandal M, Lee M, Barrick JE et al (2004) A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306:275–279. https://doi.org/10.1126/science.1100829
McCown PJ, Liang JJ, Weinberg Z, Breaker RR (2014) Structural, functional, and taxonomic diversity of three PreQ1 riboswitch classes. Chem Biol 21:880–889. https://doi.org/10.1016/j.chembiol.2014.05.015
McDaniel BAM, Grundy FJ, Artsimovitch I, Henkin TM (2003) Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA. Proc Natl Acad Sci U S A 100:3083–3088. https://doi.org/10.1073/pnas.0630422100
Meyer MM, Roth A, Chervin SM et al (2008) Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria. RNA 14:685–695. https://doi.org/10.1261/rna.937308
Mirihana Arachchilage G, Sherlock ME, Weinberg Z, Breaker RR (2018) SAM-VI RNAs selectively bind S-adenosylmethionine and exhibit similarities to SAM-III riboswitches. RNA Biol 15:371–378. https://doi.org/10.1080/15476286.2017.1399232
Motika SE, Ulrich RJ, Geddes EJ et al (2020) Gram-negative antibiotic active through inhibition of an essential riboswitch. J Am Chem Soc 142:10856–10862. https://doi.org/10.1021/jacs.0c04427
Mulhbacher J, Brouillette E, Allard M et al (2010) Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways. PLoS Pathog 6:e1000865. https://doi.org/10.1371/journal.ppat.1000865
Nahvi A, Green R (2013) Chapter 22. -Structural analysis of RNA backbone using in-line probing. In: Lorsch J (ed) Methods in enzymology. Academic Press, London, pp 381–397
Nahvi A, Sudarsan N, Ebert MS et al (2002) Genetic control by a metabolite binding mRNA. Chem Biol 9:1043–1049. https://doi.org/10.1016/S1074-5521(02)00224-7
Nelson JW, Sudarsan N, Furukawa K et al (2013) Riboswitches in eubacteria sense the second messenger c-di-AMP. Nat Chem Biol 9:834–839. https://doi.org/10.1038/nchembio.1363
Nelson JW, Sudarsan N, Phillips GE et al (2015) Control of bacterial exoelectrogenesis by c-AMP-GMP. Proc Natl Acad Sci U S A 112:5389–5394. https://doi.org/10.1073/pnas.1419264112
Nelson JW, Atilho RM, Sherlock ME et al (2017) Metabolism of free guanidine in bacteria is regulated by a widespread riboswitch class. Mol Cell 65:220–230. https://doi.org/10.1016/j.molcel.2016.11.019
Nou X, Kadner RJ (2000) Adenosylcobalamin inhibits ribosome binding to btuB RNA. Proc Natl Acad Sci U S A 97:7190–7195. https://doi.org/10.1073/pnas.130013897
Panchal V, Brenk R (2021) Riboswitches as drug targets for antibiotics. Antibiotics 10:45. https://doi.org/10.3390/antibiotics10010045
Panchapakesan SSS, Corey L, Malkowski SN et al (2021) A second riboswitch class for the enzyme cofactor NAD+. RNA 27:99–105. https://doi.org/10.1261/rna.077891.120
Pedrolli DB, Matern A, Wang J et al (2012) A highly specialized flavin mononucleotide riboswitch responds differently to similar ligands and confers roseoflavin resistance to Streptomyces davawensis. Nucleic Acids Res 40:8662–8673. https://doi.org/10.1093/nar/gks616
Poiata E, Meyer MM, Ames TD, Breaker RR (2009) A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria. RNA 15:2046–2056. https://doi.org/10.1261/rna.1824209
Regulski EE, Moy RH, Weinberg Z et al (2008) A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. Mol Microbiol 68:918–932. https://doi.org/10.1111/j.1365-2958.2008.06208.x
Rode AB, Endoh T, Sugimoto N (2018) Crowding shifts the FMN recognition mechanism of riboswitch aptamer from conformational selection to induced fit. Angew Chem Int Ed 57:6868–6872. https://doi.org/10.1002/anie.201803052
Roth A, Winkler WC, Regulski EE et al (2007) A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain. Nat Struct Mol Biol 14:308–317. https://doi.org/10.1038/nsmb1224
Salvail H, Balaji A, Yu D et al (2020) Biochemical validation of a fourth guanidine riboswitch class in bacteria. Biochemistry 59:4654–4662. https://doi.org/10.1021/acs.biochem.0c00793
Sherlock ME, Breaker RR (2017) Biochemical validation of a third guanidine riboswitch class in bacteria. Biochemistry 56:359–363. https://doi.org/10.1021/acs.biochem.6b01271
Sherlock ME, Malkowski SN, Breaker RR (2017) Biochemical validation of a second guanidine riboswitch class in bacteria. Biochemistry 56:352–358. https://doi.org/10.1021/acs.biochem.6b01270
Sherlock ME, Sudarsan N, Breaker RR (2018a) Riboswitches for the alarmone ppGpp expand the collection of RNA-based signaling systems. Proc Natl Acad Sci U S A 115:6052–6057. https://doi.org/10.1073/pnas.1720406115
Sherlock ME, Sudarsan N, Stav S, Breaker RR (2018b) Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria. eLife 7:e33908. https://doi.org/10.7554/eLife.33908
Sherlock ME, Sadeeshkumar H, Breaker RR (2019) Variant bacterial riboswitches associated with nucleotide hydrolase genes sense nucleoside diphosphates. Biochemistry 58:401–410. https://doi.org/10.1021/acs.biochem.8b00617
Sherwood AV, Henkin TM (2016) Riboswitch-mediated gene regulation: novel RNA architectures dictate gene expression responses. Annu Rev Microbiol 70:361–374. https://doi.org/10.1146/annurev-micro-091014-104306
Speed MC, Burkhart BW, Picking JW, Santangelo TJ (2018) An archaeal fluoride-responsive riboswitch provides an inducible expression system for hyperthermophiles. Appl Environ Microbiol 84:e02306–e02317. https://doi.org/10.1128/AEM.02306-17
Stoddard CD, Montange RK, Hennelly SP et al (2010) Free state conformational sampling of the SAM-I riboswitch aptamer domain. Structure 18:787–797. https://doi.org/10.1016/j.str.2010.04.006
Sudarsan N, Wickiser JK, Nakamura S et al (2003) An mRNA structure in bacteria that controls gene expression by binding lysine. Genes Dev 17:2688–2697. https://doi.org/10.1101/gad.1140003
Sudarsan N, Cohen-Chalamish S, Nakamura S et al (2005) Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine. Chem Biol 12:1325–1335. https://doi.org/10.1016/j.chembiol.2005.10.007
Sudarsan N, Hammond MC, Block KF et al (2006) Tandem riboswitch architectures exhibit complex gene control functions. Science 314:300–304. https://doi.org/10.1126/science.1130716
Sudarsan N, Lee ER, Weinberg Z et al (2008) Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321:411–413. https://doi.org/10.1126/science.1159519
Suddala KC, Wang J, Hou Q, Walter NG (2015) Mg2+ shifts ligand-mediated folding of a riboswitch from induced-fit to conformational selection. J Am Chem Soc 137:14075–14083. https://doi.org/10.1021/jacs.5b09740
Viladoms J, Fedor MJ (2012) The glmS ribozyme cofactor is a general acid–base catalyst. J Am Chem Soc 134:19043–19049. https://doi.org/10.1021/ja307021f
Wachter A, Tunc-Ozdemir M, Grove BC et al (2007) Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mRNAs. Plant Cell 19:3437–3450. https://doi.org/10.1105/tpc.107.053645
Wang JX, Lee ER, Morales DR et al (2008) Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling. Mol Cell 29:691–702. https://doi.org/10.1016/j.molcel.2008.01.012
Watson PY, Fedor MJ (2011) The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo. Nat Struct Mol Biol 18:359–363. https://doi.org/10.1038/nsmb.1989
Weinberg Z, Regulski EE, Hammond MC et al (2008) The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. RNA 14:822–828. https://doi.org/10.1261/rna.988608
Weinberg Z, Nelson JW, Lünse CE et al (2017) Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity. Proc Natl Acad Sci U S A 114:E2077–E2085. https://doi.org/10.1073/pnas.1619581114
White N, Sadeeshkumar H, Sun A et al (2022a) Lithium-sensing riboswitch classes regulate expression of bacterial cation transporter genes. Sci Rep 12:19145. https://doi.org/10.1038/s41598-022-20695-6
White N, Sadeeshkumar H, Sun A et al (2022b) Na+ riboswitches regulate genes for diverse physiological processes in bacteria. Nat Chem Biol 18:878–885. https://doi.org/10.1038/s41589-022-01086-4
Winkler W, Nahvi A, Breaker RR (2002a) Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419:952–956. https://doi.org/10.1038/nature01145
Winkler WC, Cohen-Chalamish S, Breaker RR (2002b) An mRNA structure that controls gene expression by binding FMN. Proc Natl Acad Sci U S A 99:15908–15913. https://doi.org/10.1073/pnas.212628899
Winkler WC, Nahvi A, Sudarsan N et al (2003) An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat Struct Mol Biol 10:701–707. https://doi.org/10.1038/nsb967
Winkler WC, Nahvi A, Roth A et al (2004) Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428:281–286. https://doi.org/10.1038/nature02362
Xu J, Cotruvo Jr JA (2022) Reconsidering the czcD (NiCo) riboswitch as an iron riboswitch. ACS Bio Med Chem Au 2:376–385. https://doi.org/10.1021/acsbiomedchemau.1c00069
Yu D, Breaker RR (2020) A bacterial riboswitch class senses xanthine and uric acid to regulate genes associated with purine oxidation. RNA 26:960–968. https://doi.org/10.1261/rna.075218.120
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Banuelos Jara, B., Hammond, M.C. (2023). Natural Riboswitches. In: Sugimoto, N. (eds) Handbook of Chemical Biology of Nucleic Acids. Springer, Singapore. https://doi.org/10.1007/978-981-16-1313-5_91-1
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