Home LiteratureArticle Details
PMID: 23332744 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Review

A decade of riboswitches.

Cell ·Vol. 152 ·No. 1-2 ·2013-01-17 ·Pages 17-24

Serganov A, Nudler E

Abstract

Riboswitches were discovered in 2002 in bacteria as RNA-based intracellular sensors of vitamin derivatives. During the last decade, naturally occurring RNA sensor elements have been found to bind a range of small metabolites and ions and to exert regulatory control of transcription, translation, splicing, and RNA stability. Extensive biochemical, structural, and genetic studies have established the basic principles underpinning riboswitch function in all three kingdoms of life with implications for developing antibiotics, designing new molecular sensors, and integrating riboswitches into synthetic circuits.

MeSH Terms
Alternative Splicing Bacteria/genetics Gene Expression Regulation Nucleic Acid Conformation RNA/chemistry,genetics,metabolism Riboswitch
Chemicals
Riboswitch RNA
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Serganov Alexander
Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA. [email protected]
Nudler Evgeny
References (82)
82 references, click to expand
  1. Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches.
    J Am Chem Soc. 2012 Jan 25;134(3):1404-7 PMID: 22192063
  2. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element.
    Nature. 2006 Jun 29;441(7097):1172-5 PMID: 16810258
  3. Adenosylcobalamin inhibits ribosome binding to btuB RNA.
    Proc Natl Acad Sci U S A. 2000 Jun 20;97(13):7190-5 PMID: 10852957
  4. Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch.
    Nature. 2012 May 13;486(7401):85-9 PMID: 22678284
  5. Riboswitch-dependent gene regulation and its evolution in the plant kingdom.
    Genes Dev. 2007 Nov 15;21(22):2874-9 PMID: 18006684
  6. Tandem riboswitch architectures exhibit complex gene control functions.
    Science. 2006 Oct 13;314(5797):300-4 PMID: 17038623
  7. Crystal structure of the lysine riboswitch regulatory mRNA element.
    J Biol Chem. 2008 Aug 15;283(33):22347-51 PMID: 18593706
  8. Structure of the SAM-II riboswitch bound to S-adenosylmethionine.
    Nat Struct Mol Biol. 2008 Feb;15(2):177-82 PMID: 18204466
  9. Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA.
    Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3083-8 PMID: 12626738
  10. An RNA sensor for intracellular Mg(2+).
    Cell. 2006 Apr 7;125(1):71-84 PMID: 16615891
  11. Convergent evolution of adenosine aptamers spanning bacterial, human, and random sequences revealed by structure-based bioinformatics and genomic SELEX.
    Chem Biol. 2012 Oct 26;19(10):1247-54 PMID: 23102219
  12. Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA.
    Nature. 1990 Mar 29;344(6265):467-8 PMID: 1690861
  13. The riboswitch-mediated control of sulfur metabolism in bacteria.
    Proc Natl Acad Sci U S A. 2003 Apr 29;100(9):5052-6 PMID: 12702767
  14. Structural investigation of the GlmS ribozyme bound to Its catalytic cofactor.
    Chem Biol. 2007 Jan;14(1):97-105 PMID: 17196404
  15. A trans-acting riboswitch controls expression of the virulence regulator PrfA in Listeria monocytogenes.
    Cell. 2009 Nov 13;139(4):770-9 PMID: 19914169
  16. Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch.
    Proc Natl Acad Sci U S A. 2011 Sep 6;108(36):14801-6 PMID: 21873197
  17. The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer.
    Structure. 2011 Oct 12;19(10):1413-23 PMID: 21906956
  18. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine.
    Nature. 2004 Nov 18;432(7015):411-5 PMID: 15549109
  19. Structural basis of glmS ribozyme activation by glucosamine-6-phosphate.
    Science. 2006 Sep 22;313(5794):1752-6 PMID: 16990543
  20. Orthogonal riboswitches for tuneable coexpression in bacteria.
    Angew Chem Int Ed Engl. 2012 Apr 10;51(15):3620-4 PMID: 22383398
  21. An allosteric self-splicing ribozyme triggered by a bacterial second messenger.
    Science. 2010 Aug 13;329(5993):845-848 PMID: 20705859
  22. Control of gene expression by a natural metabolite-responsive ribozyme.
    Nature. 2004 Mar 18;428(6980):281-6 PMID: 15029187
  23. An adenosyl-cobalamin (coenzyme-B12)-repressed translational enhancer in the cob mRNA of Salmonella typhimurium.
    Mol Microbiol. 2001 Mar;39(6):1585-94 PMID: 11260475
  24. Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms.
    PLoS Genet. 2011 Jan 20;7(1):e1001278 PMID: 21283784
  25. A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo.
    Nucleic Acids Res. 2004 Mar 05;32(4):1610-4 PMID: 15004248
  26. A pH-responsive riboregulator.
    Genes Dev. 2009 Nov 15;23(22):2650-62 PMID: 19933154
  27. An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches.
    RNA. 2012 Mar;18(3):496-507 PMID: 22279151
  28. Widespread genetic switches and toxicity resistance proteins for fluoride.
    Science. 2012 Jan 13;335(6065):233-235 PMID: 22194412
  29. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria.
    Cell. 2002 Nov 27;111(5):747-56 PMID: 12464185
  30. A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes.
    Trends Genet. 1999 Nov;15(11):439-42 PMID: 10529804
  31. A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria.
    Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9736-41 PMID: 11470904
  32. Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs.
    Chem Biol. 2004 Dec;11(12):1729-41 PMID: 15610857
  33. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches.
    Nature. 2007 May 24;447(7143):497-500 PMID: 17468745
  34. The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo.
    Nat Struct Mol Biol. 2011 Mar;18(3):359-63 PMID: 21317896
  35. Prospects for riboswitch discovery and analysis.
    Mol Cell. 2011 Sep 16;43(6):867-79 PMID: 21925376
  36. Structural basis of cooperative ligand binding by the glycine riboswitch.
    Chem Biol. 2011 Mar 25;18(3):293-8 PMID: 21439473
  37. Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways.
    PLoS Pathog. 2010 Apr 22;6(4):e1000865 PMID: 20421948
  38. Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria.
    Genome Biol. 2005;6(8):R70 PMID: 16086852
  39. Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition.
    Structure. 2006 Sep;14(9):1459-68 PMID: 16962976
  40. Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes.
    Genome Biol. 2010;11(3):R31 PMID: 20230605
  41. Genetic control by a metabolite binding mRNA.
    Chem Biol. 2002 Sep;9(9):1043 PMID: 12323379
  42. Riboswitch control of Rho-dependent transcription termination.
    Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5376-81 PMID: 22431636
  43. Free state conformational sampling of the SAM-I riboswitch aptamer domain.
    Structure. 2010 Jul 14;18(7):787-97 PMID: 20637415
  44. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.
    Science. 1990 Aug 3;249(4968):505-10 PMID: 2200121
  45. Structural insights into amino acid binding and gene control by a lysine riboswitch.
    Nature. 2008 Oct 30;455(7217):1263-7 PMID: 18784651
  46. Reengineering orthogonally selective riboswitches.
    Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):2830-5 PMID: 20133756
  47. Structure and mechanism of a metal-sensing regulatory RNA.
    Cell. 2007 Sep 7;130(5):878-92 PMID: 17803910
  48. Chemical basis of glycine riboswitch cooperativity.
    RNA. 2008 Jan;14(1):25-34 PMID: 18042658
  49. Mechanism of mRNA destabilization by the glmS ribozyme.
    Genes Dev. 2007 Dec 15;21(24):3356-68 PMID: 18079181
  50. Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand.
    Science. 2006 May 26;312(5777):1208-11 PMID: 16675665
  51. Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in Enterococcus faecalis.
    Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4435-40 PMID: 19246383
  52. tRNA as a positive regulator of transcription antitermination in B. subtilis.
    Cell. 1993 Aug 13;74(3):475-82 PMID: 8348614
  53. The ydaO motif is an ATP-sensing riboswitch in Bacillus subtilis.
    Nat Chem Biol. 2012 Dec;8(12):963-5 PMID: 23086297
  54. Inducible gene expression from the plastid genome by a synthetic riboswitch.
    Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6204-9 PMID: 20308585
  55. Control of a Salmonella virulence locus by an ATP-sensing leader messenger RNA.
    Nature. 2012 Jun 13;486(7402):271-5 PMID: 22699622
  56. Attenuation in the control of expression of bacterial operons.
    Nature. 1981 Feb 26;289(5800):751-8 PMID: 7007895
  57. Coupled changes in translation and transcription during cobalamin-dependent regulation of btuB expression in Escherichia coli.
    J Bacteriol. 1998 Dec;180(24):6719-28 PMID: 9852020
  58. Conformational capture of the SAM-II riboswitch.
    Nat Chem Biol. 2011 Jun;7(6):393-400 PMID: 21532598
  59. In vitro selection of RNA molecules that bind specific ligands.
    Nature. 1990 Aug 30;346(6287):818-22 PMID: 1697402
  60. Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch.
    Nature. 2009 Mar 12;458(7235):233-7 PMID: 19169240
  61. Direct physical evidence for secondary structure in an isolated fragment of R17 bacteriophage mRNA.
    Nature. 1974 Mar 15;248(445):204-8 PMID: 4819414
  62. Reprogramming bacteria to seek and destroy an herbicide.
    Nat Chem Biol. 2010 Jun;6(6):464-70 PMID: 20453864
  63. Mechanism for gene control by a natural allosteric group I ribozyme.
    RNA. 2011 Nov;17(11):1967-72 PMID: 21960486
  64. Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism.
    Nat Struct Mol Biol. 2008 Oct;15(10):1076-83 PMID: 18806797
  65. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression.
    Nature. 2002 Oct 31;419(6910):952-6 PMID: 12410317
  66. Do mRNAs act as direct sensors of small molecules to control their expression?
    Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9465-7 PMID: 11504932
  67. Riboswitches in eubacteria sense the second messenger cyclic di-GMP.
    Science. 2008 Jul 18;321(5887):411-3 PMID: 18635805
  68. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch.
    Nature. 2006 Jun 29;441(7097):1167-71 PMID: 16728979
  69. Thiamine biosynthesis in algae is regulated by riboswitches.
    Proc Natl Acad Sci U S A. 2007 Dec 26;104(52):20770-5 PMID: 18093957
  70. Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline.
    Nucleic Acids Res. 2007;35(14):4809-19 PMID: 17621584
  71. The S(MK) box is a new SAM-binding RNA for translational regulation of SAM synthetase.
    Nat Struct Mol Biol. 2006 Mar;13(3):226-33 PMID: 16491091
  72. An mRNA structure that controls gene expression by binding S-adenosylmethionine.
    Nat Struct Biol. 2003 Sep;10(9):701-7 PMID: 12910260
  73. Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch.
    Mol Cell. 2010 Dec 10;40(5):774-86 PMID: 21145485
  74. Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs.
    Plant Cell. 2007 Nov;19(11):3437-50 PMID: 17993623
  75. A stress-responsive RNA switch regulates VEGFA expression.
    Nature. 2009 Feb 12;457(7231):915-9 PMID: 19098893
  76. B12 cofactors directly stabilize an mRNA regulatory switch.
    Nature. 2012 Dec 6;492(7427):133-7 PMID: 23064232
  77. Structural principles of nucleoside selectivity in a 2'-deoxyguanosine riboswitch.
    Nat Chem Biol. 2011 Aug 14;7(10):748-55 PMID: 21841796
  78. 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. 2008 Feb;190(3):823-33 PMID: 18039762
  79. Structural insights into ligand binding and gene expression control by an adenosylcobalamin riboswitch.
    Nat Struct Mol Biol. 2012 Nov;19(11):1182-4 PMID: 23064646
  80. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch.
    Mol Cell. 2005 Apr 1;18(1):49-60 PMID: 15808508
  81. A glycine-dependent riboswitch that uses cooperative binding to control gene expression.
    Science. 2004 Oct 8;306(5694):275-9 PMID: 15472076
  82. The UA_handle: a versatile submotif in stable RNA architectures.
    Nucleic Acids Res. 2009 Jan;37(1):215-30 PMID: 19036788
Article Info
Journal
Cell
Abbr.
Cell
ISSN
1097-4172
Published
2013-01-17
Pages
17-24
Language
English
Region
United States
NLM ID
0413066
PMCID
PMC4215550
Subset
IM
Grants
NIAID NIH HHS · R01 AI090110 · United States
NIGMS NIH HHS · R01 GM058750 · United States
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]