Riboswitch structure in the ligand-free state

Wiley Interdisciplinary Reviews: RNA

Volumn 3, Issue 3, 2012, Pages 369-384

  Liberman, Joseph A ^a   Wedekind, Joseph E ^a  

^a UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; BACTERIAL RNA; GLYCINE; GUANINE; LYSINE;

BACTERIUM; COMPUTER SIMULATION; CRYSTAL STRUCTURE; ENERGY TRANSFER; FORSTER RESONANCE ENERGY TRANSFER; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; REVIEW; RIBOSWITCH; RNA CONFORMATION; RNA FOLDING; SMALL ANGLE SCATTERING;

AMINO ACIDS; BINDING SITES; LIGANDS; NUCLEIC ACID CONFORMATION; PURINES; PYRIMIDINONES; PYRROLES; RIBOSWITCH; RNA FOLDING; S-ADENOSYLMETHIONINE;

EID: 84865243362     PISSN: 17577004     EISSN: 17577012     Source Type: Journal    
DOI: 10.1002/wrna.114     Document Type: Review

References (79)

1. Mironov AS, Gusarov I, Rafikov R, Lopez LE, Shatalin K, Kreneva RA, Perumov DA, Nudler E. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell 2002, 111:747-756.
2. Winkler W, Nahvi A, Breaker RR. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 2002, 419:952-956.
3. Barrick JE, Breaker RR. The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol 2007, 8:R239.
4. Wachter A. Riboswitch-mediated control of gene expression in eukaryotes. RNA Biol 2010, 7:67-76.
5. Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR. Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol 2010, 11:R31.
6. Cheah MT, Wachter A, Sudarsan N, Breaker RR. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 2007, 447:497-500.
7. Sudarsan N, Barrick JE, Breaker RR. Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA 2003, 9:644-647.
8. Wachter A, Tunc-Ozdemir M, Grove BC, Green PJ, Shintani DK, Breaker RR. Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs. Plant Cell 2007, 19:3437-3450.
9. Bocobza S, Adato A, Mandel T, Shapira M, Nudler E, Aharoni A. Riboswitch-dependent gene regulation and its evolution in the plant kingdom. Genes Dev 2007, 21:2874-2879.
10. Croft MT, Moulin M, Webb ME, Smith AG. Thiamine biosynthesis in algae is regulated by riboswitches. Proc Natl Acad Sci U S A 2007, 104:20770-20775.
11. Garst AD, Batey RT. A switch in time: detailing the life of a riboswitch. Biochim Biophys Acta 2009, 1789:584-591.
12. Henkin TM. Riboswitch RNAs: using RNA to sense cellular metabolism. Genes Dev 2008, 22:3383-3390.
13. Smith KD, Lipchock SV, Livingston AL, Shanahan CA, Strobel SA. Structural and biochemical determinants of ligand binding by the c-di-GMP riboswitch. Biochemistry 2010, 49:7351-7359.
14. Wickiser JK, Winkler WC, Breaker RR, Crothers DM. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol Cell 2005, 18:49-60.
15. Smith KD, Lipchock SV, Ames TD, Wang J, Breaker RR, Strobel SA. Structural basis of ligand binding by a c-di-GMP riboswitch. Nat Struct Mol Biol 2009, 16:1218-1223.
16. Tomsic J, McDaniel BA, Grundy FJ, Henkin TM. 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, 190:823-833.
17. Batey RT, Gilbert SD, Montange RK. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 2004, 432:411-415.
18. Serganov A, Yuan YR, Pikovskaya O, Polonskaia A, Malinina L, Phan AT, Hobartner C, Micura R, Breaker RR, Patel DJ. Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem Biol 2004, 11:1729-1741.
19. Spitale RC, Torelli AT, Krucinska J, Bandarian V, Wedekind JE. The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain. J Biol Chem 2009, 284:11012-11016.
20. Jenkins JL, Krucinska J, McCarty RM, Bandarian V, Wedekind JE. Comparison of a PreQ1 riboswitch aptamer in metabolite-bound and free states with implications for gene regulation. J Biol Chem 2011, 286:24626-24637.
21. Klein DJ, Edwards TE, Ferre-D'Amare AR. Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase. Nat Struct Mol Biol 2009, 16:343-344.
22. Kang M, Peterson R, Feigon J. Structural insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of tRNA. Mol Cell 2009, 33:784-790.
23. Montange RK, Batey RT. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 2006, 441:1172-1175.
24. Stoddard CD, Montange RK, Hennelly SP, Rambo RP, Sanbonmatsu KY, Batey RT. Free state conformational sampling of the SAM-I riboswitch aptamer domain. Structure 2010, 18:787-797.
25. Lu C, Ding F, Chowdhury A, Pradhan V, Tomsic J, Holmes WM, Henkin TM, Ke A. SAM recognition and conformational switching mechanism in the Bacillus subtilis yitJ S box/SAM-I riboswitch. J Mol Biol 2010, 404:803-818.
26. Gilbert SD, Rambo RP, Van Tyne D, Batey RT. Structure of the SAM-II riboswitch bound to S-adenosylmethionine. Nat Struct Mol Biol 2008, 15:177-182.
27. Lu C, Smith AM, Fuchs RT, Ding F, Rajashankar K, Henkin TM, Ke A. Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism. Nat Struct Mol Biol 2008, 15:1076-1083.
28. Garst AD, Heroux A, Rambo RP, Batey RT. Crystal structure of the lysine riboswitch regulatory mRNA element. J Biol Chem 2008, 283:22347-22351.
29. Serganov A, Huang L, Patel DJ. Structural insights into amino acid binding and gene control by a lysine riboswitch. Nature 2008, 455:1263-1267.
30. Huang L, Serganov A, Patel DJ. Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch. Mol Cell 2010, 40:774-786.
31. Shine J, Dalgarno L. Terminal-sequence analysis of bacterial ribosomal RNA. Correlation between the 3'-terminal-polypyrimidine sequence of 16-S RNA and translational specificity of the ribosome. Eur J Biochem 1975, 57:221-230.
32. Irnov I, Kertsburg A, Winkler WC. Genetic control by cis-acting regulatory RNAs in Bacillus subtilis: general principles and prospects for discovery. Cold Spring Harb Symp Quant Biol 2006, 71:239-249.
33. Sudarsan N, Wickiser JK, Nakamura S, Ebert MS, Breaker RR. An mRNA structure in bacteria that controls gene expression by binding lysine. Genes Dev 2003, 17:2688-2697.
34. Sudarsan N, Cohen-Chalamish S, Nakamura S, Emilsson GM, Breaker RR. Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine. Chem Biol 2005, 12:1325-1335.
35. Serganov A, Polonskaia A, Phan AT, Breaker RR, Patel DJ. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature 2006, 441:1167-1171.
36. Edwards TE, Ferre-D'Amare AR. Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. Structure 2006, 14:1459-1468.
37. Blount KF, Wang JX, Lim J, Sudarsan N, Breaker RR. Antibacterial lysine analogs that target lysine riboswitches. Nat Chem Biol 2007, 3:44-49.
38. Lee ER, Blount KF, Breaker RR. Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression. RNA Biol 2009, 6:187-194.
39. Ataide SF, Wilson SN, Dang S, Rogers TE, Roy B, Banerjee R, Henkin TM, Ibba M. Mechanisms of resistance to an amino acid antibiotic that targets translation. ACS Chem Biol 2007, 2:819-827.
40. Serganov A, Patel DJ. Amino acid recognition and gene regulation by riboswitches. Biochim Biophys Acta 2009, 1789:592-611.
41. Du Q, Wang H, Xie J. Thiamin (vitamin B1) biosynthesis and regulation: a rich source of antimicrobial drug targets? Int J Biol Sci 2011, 7:41-52.
42. Thore S, Frick C, Ban N. Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch. J Am Chem Soc 2008, 130:8116-8117.
43. Mulhbacher J, Brouillette E, Allard M, Fortier LC, Malouin F, Lafontaine DA. Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways. PLoS Pathog 2010, 6:e1000865.
44. Kim JN, Blount KF, Puskarz I, Lim J, Link KH, Breaker RR. Design and antimicrobial action of purine analogues that bind Guanine riboswitches. ACS Chem Biol 2009, 4:915-927.
45. Serganov A. Determination of riboswitch structures: light at the end of the tunnel? RNA Biol 2010, 7:98-103.
46. Winkler WC, Nahvi A, Sudarsan N, Barrick JE, Breaker RR. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat Struct Biol 2003, 10:701-707.
47. Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick ND, Breaker RR. Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. Genome Biol 2005, 6:R70.
48. Fuchs RT, Grundy FJ, Henkin TM. The S(MK) box is a new SAM-binding RNA for translational regulation of SAM synthetase. Nat Struct Mol Biol 2006, 13:226-233.
49. Poiata E, Meyer MM, Ames TD, Breaker RR. A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria. RNA 2009, 15: 2046-2056.
50. Batey RT. Recognition of S-adenosylmethionine by riboswitches. In: Wiley Interdisciplinary Reviews: RNA, vol 2. John Wiley and Sons; 2011, 199-311.
51. Roth A, Winkler WC, Regulski EE, Lee BW, Lim J, Jona I, Barrick JE, Ritwik A, Kim JN, Welz R, et al. A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain. Nat Struct Mol Biol 2007, 14:308-317.
52. Meyer MM, Roth A, Chervin SM, Garcia GA, Breaker RR. Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria. RNA 2008, 14:685-695.
53. Sudarsan N, Lee ER, Weinberg Z, Moy RH, Kim JN, Link KH, Breaker RR. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 2008, 321:411-413.
54. Lee ER, Baker JL, Weinberg Z, Sudarsan N, Breaker RR. An allosteric self-splicing ribozyme triggered by a bacterial second messenger. Science 2010, 329:845-848.
55. Edwards AL, Reyes FE, Heroux A, Batey RT. Structural basis for recognition of S-adenosylhomocysteine by riboswitches. RNA 2010, 16:2144-2155.
56. Wilkinson KA, Merino EJ, Weeks KM. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat Protoc 2006, 1:1610-1616.
57. Boehr DD, Nussinov R, Wright PE. The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 2009, 5:789-796.
58. Haller A, Rieder U, Aigner M, Blanchard SC, Micura R. Conformational capture of the SAM-II riboswitch. Nat Chem Biol 2011, 7:393-400.
59. Smith AM, Fuchs RT, Grundy FJ, Henkin TM. The SAM-responsive S(MK) box is a reversible riboswitch. Mol Microbiol 2010, 78:1393-1402.
60. Wilson RC, Smith AM, Fuchs RT, Kleckner IR, Henkin TM, Foster MP. Tuning riboswitch regulation through conformational selection. J Mol Biol 2011, 405:926-938.
61. Lu C, Smith AM, Ding F, Chowdhury A, Henkin TM, Ke A. Variable sequences outside the Sam-binding core critically influence the conformational dynamics of the SAM-III/SMK box riboswitch. J Mol Biol 2011, 409:786-799.
62. Kim JN, Roth A, Breaker RR. Guanine riboswitch variants from mesoplasma florum selectively recognize 2'-deoxyguanosine. Proc Natl Acad Sci U S A 2007, 104:16092-16097.
63. Kim JN, Breaker RR. Purine sensing by riboswitches. Biol Cell 2008, 100:1-11.
64. Lemay JF, Penedo JC, Tremblay R, Lilley DM, Lafontaine DA. Folding of the adenine riboswitch. Chem Biol 2006, 13:857-868.
65. Brenner MD, Scanlan MS, Nahas MK, Ha T, Silverman SK. Multivector fluorescence analysis of the xpt guanine riboswitch aptamer domain and the conformational role of guanine. Biochemistry 2010, 49:1596-1605.
66. Noeske J, Buck J, Furtig B, Nasiri HR, Schwalbe H, Wohnert J. Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch. Nucleic Acids Res 2007, 35:572-583.
67. Liberman JA, Wedekind JE. Base ionization and ligand binding: how small ribozymes and riboswitches gain a foothold in a protein world. Curr Opin Struct Biol 2011, 21:327-334.
68. Rieder U, Lang K, Kreutz C, Polacek N, Micura R. Evidence for pseudoknot formation of class I preQ1 riboswitch aptamers. Chembiochem 2009, 10:1141-1144.
69. Rieder U, Kreutz C, Micura R. Folding of a transcriptionally acting preQ1 riboswitch. Proc Natl Acad Sci U S A 2010, 107:10804-10809.
70. Grundy FJ, Lehman SC, Henkin TM. The L box regulon: lysine sensing by leader RNAs of bacterial lysine biosynthesis genes. Proc Natl Acad Sci U S A 2003, 100:12057-12062.
71. Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch? Nucleic Acids Res 2003, 31:6748-6757.
72. Blouin S, Chinnappan R, Lafontaine DA. Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation. Nucleic Acids Res 2011, 39:3373-3387.
73. Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, et al. New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc Natl Acad Sci U S A 2004, 101:6421-6426.
74. Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 2004, 306:275-279.
75. Lipfert J, Das R, Chu VB, Kudaravalli M, Boyd N, Herschlag D, Doniach S. Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. J Mol Biol 2007, 365:1393-1406.
76. Mulhbacher J, St-Pierre P, Lafontaine DA. Therapeutic applications of ribozymes and riboswitches. Curr Opin Pharmacol 2010, 10:551-556.
77. Rfam rfam.sanger.ac.uk (A database comprising a collection of RNA families derived from multiple sequence alignments, consensus secondary structures and covariance analysis).
78. Protein Data Bank (A database comprising experimentally derived atomic coordinates and structure-factor amplitudes that includes riboswitch structures).
79. Recognition of S-adenosylmethionine by riboswitches.