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A Decade of Riboswitches

Serganov, Alexander, Nudler, Evgeny·2013·Cell

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Crossref · 10.1016/j.cell.2012.12.024

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  • Riboswitches are structured RNAs typically found in the 5'-untranslated regions of bacterial mRNAs where they regulate gene expression in response to binding a small molecule or ion.

    “Riboswitches are structured RNAs that are typically found in the 5′-untranslated regions of bacterial mRNAs where they regulate the expression of genes in response to binding a small molecule or ion (Breaker, 2011; Peselis and Serganov, 2014; Serganov and Nudler, 2013).”

    From Small Molecule Fluoride Toxicity Agonists (2015) · cites this paper as Serganov and Nudler, 2013

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  1. Baker, 2012, Widespread genetic switches and toxicity resistance proteins for fluoride, Science, 335, 233, 10.1126/science.1215063 · DOI · Paper page
  2. Batey, 2004, Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine, Nature, 432, 411, 10.1038/nature03037 · DOI
  3. Bocobza, 2007, Riboswitch-dependent gene regulation and its evolution in the plant kingdom, Genes Dev., 21, 2874, 10.1101/gad.443907 · DOI
  4. Breaker, 2011, Prospects for riboswitch discovery and analysis, Mol. Cell, 43, 867, 10.1016/j.molcel.2011.08.024 · DOI · Paper page
  5. Butler, 2011, Structural basis of cooperative ligand binding by the glycine riboswitch, Chem. Biol., 18, 293, 10.1016/j.chembiol.2011.01.013 · DOI
  6. Cheah, 2007, Control of alternative RNA splicing and gene expression by eukaryotic riboswitches, Nature, 447, 497, 10.1038/nature05769 · DOI
  7. Chen, 2011, Mechanism for gene control by a natural allosteric group I ribozyme, RNA, 17, 1967, 10.1261/rna.2757311 · DOI
  8. Cochrane, 2007, Structural investigation of the GlmS ribozyme bound to its catalytic cofactor, Chem. Biol., 14, 97, 10.1016/j.chembiol.2006.12.005 · DOI
  9. Collins, 2007, Mechanism of mRNA destabilization by the glmS ribozyme, Genes Dev., 21, 3356, 10.1101/gad.1605307 · DOI
  10. 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 · DOI
  11. Croft, 2007, Thiamine biosynthesis in algae is regulated by riboswitches, Proc. Natl. Acad. Sci. USA, 104, 20770, 10.1073/pnas.0705786105 · DOI
  12. Cromie, 2006, An RNA sensor for intracellular Mg(2+), Cell, 125, 71, 10.1016/j.cell.2006.01.043 · DOI
  13. Dixon, 2010, Reengineering orthogonally selective riboswitches, Proc. Natl. Acad. Sci. USA, 107, 2830, 10.1073/pnas.0911209107 · DOI
  14. Dixon, 2012, Orthogonal riboswitches for tuneable coexpression in bacteria, Angew. Chem. Int. Ed. Engl., 51, 3620, 10.1002/anie.201109106 · DOI
  15. 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 · DOI
  16. Ellington, 1990, In vitro selection of RNA molecules that bind specific ligands, Nature, 346, 818, 10.1038/346818a0 · DOI
  17. Epshtein, 2003, The riboswitch-mediated control of sulfur metabolism in bacteria, Proc. Natl. Acad. Sci. USA, 100, 5052, 10.1073/pnas.0531307100 · DOI
  18. 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 · DOI
  19. 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 · DOI
  20. Garst, 2008, Crystal structure of the lysine riboswitch regulatory mRNA element, J. Biol. Chem., 283, 22347, 10.1074/jbc.C800120200 · DOI
  21. 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 · DOI
  22. Gilbert, 1986, Origin of life: the RNA world, Nature, 319, 618, 10.1038/319618a0 · DOI · Paper page
  23. Gilbert, 2008, Structure of the SAM-II riboswitch bound to S-adenosylmethionine, Nat. Struct. Mol. Biol., 15, 177, 10.1038/nsmb.1371 · DOI
  24. Gralla, 1974, Direct physical evidence for secondary structure in an isolated fragment of R17 bacteriophage mRNA, Nature, 248, 204, 10.1038/248204a0 · DOI
  25. Grundy, 1993, tRNA as a positive regulator of transcription antitermination in B. subtilis, Cell, 74, 475, 10.1016/0092-8674(93)80049-K · DOI
  26. Haller, 2011, Conformational capture of the SAM-II riboswitch, Nat. Chem. Biol., 7, 393, 10.1038/nchembio.562 · DOI
  27. Hollands, 2012, Riboswitch control of Rho-dependent transcription termination, Proc. Natl. Acad. Sci. USA, 109, 5376, 10.1073/pnas.1112211109 · DOI
  28. 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 · DOI
  29. 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 · DOI
  30. Jaeger, 2009, The UA_handle: a versatile submotif in stable RNA architectures, Nucleic Acids Res., 37, 215, 10.1093/nar/gkn911 · DOI
  31. Johnson, 2012, B12 cofactors directly stabilize an mRNA regulatory switch, Nature, 492, 133, 10.1038/nature11607 · DOI
  32. Kladwang, 2012, Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches, J. Am. Chem. Soc., 134, 1404, 10.1021/ja2093508 · DOI
  33. Klein, 2006, Structural basis of glmS ribozyme activation by glucosamine-6-phosphate, Science, 313, 1752, 10.1126/science.1129666 · DOI
  34. Kwon, 2008, Chemical basis of glycine riboswitch cooperativity, RNA, 14, 25, 10.1261/rna.771608 · DOI
  35. Lee, 2012, Control of a Salmonella virulence locus by an ATP-sensing leader messenger RNA, Nature, 486, 271, 10.1038/nature11090 · DOI
  36. Lee, 2010, An allosteric self-splicing ribozyme triggered by a bacterial second messenger, Science, 329, 845, 10.1126/science.1190713 · DOI
  37. 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 · DOI
  38. 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 · DOI
  39. 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 · DOI
  40. Mandal, 2004, A glycine-dependent riboswitch that uses cooperative binding to control gene expression, Science, 306, 275, 10.1126/science.1100829 · DOI
  41. 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 · DOI
  42. 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 · DOI
  43. 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 · DOI
  44. Montange, 2006, Structure of the S-adenosylmethionine riboswitch regulatory mRNA element, Nature, 441, 1172, 10.1038/nature04819 · DOI
  45. Mulhbacher, 2010, Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways, PLoS Pathog., 6, e1000865, 10.1371/journal.ppat.1000865 · DOI
  46. Nahvi, 2002, Genetic control by a metabolite binding mRNA, Chem. Biol., 9, 1043, 10.1016/S1074-5521(02)00224-7 · DOI
  47. Nechooshtan, 2009, A pH-responsive riboregulator, Genes Dev., 23, 2650, 10.1101/gad.552209 · DOI
  48. 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 · DOI
  49. Nou, 2000, Adenosylcobalamin inhibits ribosome binding to btuB RNA, Proc. Natl. Acad. Sci. USA, 97, 7190, 10.1073/pnas.130013897 · DOI
  50. 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 · DOI
  51. Pikovskaya, 2011, Structural principles of nucleoside selectivity in a 2′-deoxyguanosine riboswitch, Nat. Chem. Biol., 7, 748, 10.1038/nchembio.631 · DOI
  52. 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 · DOI
  53. Ray, 2009, A stress-responsive RNA switch regulates VEGFA expression, Nature, 457, 915, 10.1038/nature07598 · DOI
  54. Ren, 2012, Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch, Nature, 486, 85, 10.1038/nature11152 · DOI · Paper page
  55. Robertson, 1990, Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA, Nature, 344, 467, 10.1038/344467a0 · DOI
  56. 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 · DOI
  57. Serganov, 2006, Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch, Nature, 441, 1167, 10.1038/nature04740 · DOI
  58. Serganov, 2008, Structural insights into amino acid binding and gene control by a lysine riboswitch, Nature, 455, 1263, 10.1038/nature07326 · DOI
  59. Serganov, 2009, Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch, Nature, 458, 233, 10.1038/nature07642 · DOI
  60. Sherman, 2012, An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches, RNA, 18, 496, 10.1261/rna.031286.111 · DOI
  61. Sinha, 2010, Reprogramming bacteria to seek and destroy an herbicide, Nat. Chem. Biol., 6, 464, 10.1038/nchembio.369 · DOI
  62. Stoddard, 2010, Free state conformational sampling of the SAM-I riboswitch aptamer domain, Structure, 18, 787, 10.1016/j.str.2010.04.006 · DOI
  63. 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 · DOI
  64. Sudarsan, 2006, Tandem riboswitch architectures exhibit complex gene control functions, Science, 314, 300, 10.1126/science.1130716 · DOI
  65. Sudarsan, 2008, Riboswitches in eubacteria sense the second messenger cyclic di-GMP, Science, 321, 411, 10.1126/science.1159519 · DOI
  66. Suess, 2004, A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo, Nucleic Acids Res., 32, 1610, 10.1093/nar/gkh321 · DOI
  67. Thore, 2006, Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand, Science, 312, 1208, 10.1126/science.1128451 · DOI
  68. 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 · DOI
  69. 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 · DOI
  70. Tuerk, 1990, Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase, Science, 249, 505, 10.1126/science.2200121 · DOI
  71. Verhounig, 2010, Inducible gene expression from the plastid genome by a synthetic riboswitch, Proc. Natl. Acad. Sci. USA, 107, 6204, 10.1073/pnas.0914423107 · DOI
  72. 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 · DOI
  73. 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 · DOI
  74. Watson, 2011, The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo, Nat. Struct. Mol. Biol., 18, 359, 10.1038/nsmb.1989 · DOI
  75. Watson, 2012, The ydaO motif is an ATP-sensing riboswitch in Bacillus subtilis, Nat. Chem. Biol., 8, 963, 10.1038/nchembio.1095 · DOI
  76. 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 · DOI
  77. 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 · DOI · Paper page
  78. 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 · DOI
  79. Winkler, 2002, Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression, Nature, 419, 952, 10.1038/nature01145 · DOI
  80. Winkler, 2003, An mRNA structure that controls gene expression by binding S-adenosylmethionine, Nat. Struct. Biol., 10, 701, 10.1038/nsb967 · DOI
  81. Winkler, 2004, Control of gene expression by a natural metabolite-responsive ribozyme, Nature, 428, 281, 10.1038/nature02362 · DOI
  82. Yanofsky, 1981, Attenuation in the control of expression of bacterial operons, Nature, 289, 751, 10.1038/289751a0 · DOI

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Authors
Serganov, A., & Nudler, E.
Venue
Cell
Publisher
Elsevier BV
Published
2013-01
Volume
152
Issue
1-2
Pages
17-24
ISSN
0092-8674
Cited by
1,013
References
1
Language
en

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