Folding of the Adenine Riboswitch

Chemistry and Biology

Volumn 13, Issue 8, 2006, Pages 857-868

  Lemay, Jean François ^a   Penedo, J Carlos ^b   Tremblay, Renaud ^a   Lilley, David M J ^b   Lafontaine, Daniel A ^a  

^a UNIVERSITÉ DE SHERBROOKE   (Canada)

^b UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

2 AMINOPURINE; ADENINE; APTAMER; DRUG DERIVATIVE; LIGAND; MAGNESIUM; RNA;

ARTICLE; BACILLUS SUBTILIS; BINDING SITE; CHEMISTRY; CONFORMATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; METHODOLOGY;

2-AMINOPURINE; ADENINE; APTAMERS, NUCLEOTIDE; BACILLUS SUBTILIS; BINDING SITES; FLUORESCENCE RESONANCE ENERGY TRANSFER; LIGANDS; MAGNESIUM; NUCLEIC ACID CONFORMATION; RNA;

EID: 33747345020     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2006.06.010     Document Type: Article

References (64)

1. Sudarsan N., Barrick J.E., and Breaker R.R. Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA 9 (2003) 644-647
2. Kubodera T., Watanabe M., Yoshiuchi K., Yamashita N., Nishimura A., Nakai S., Gomi K., and Hanamoto H. Thiamine-regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5′-UTR. FEBS Lett. 555 (2003) 516-520
3. Mandal M., and Breaker R.R. Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat. Struct. Mol. Biol. 11 (2004) 29-35
4. Soukup J.K., and Soukup G.A. Riboswitches exert genetic control through metabolite-induced conformational change. Curr. Opin. Struct. Biol. 14 (2004) 344-349
5. Mandal M., Boese B., Barrick J.E., Winkler W.C., and Breaker R.R. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113 (2003) 577-586
6. Johansen L.E., Nygaard P., Lassen C., Agerso Y., and Saxild H.H. Definition of a second Bacillus subtilis pur regulon comprising the pur and xpt-pbuX operons plus pbuG, nupG (yxjA), and pbuE (ydhL). J. Bacteriol. 185 (2003) 5200-5209
7. Nygaard P., and Saxild H.H. The purine efflux pump PbuE in Bacillus subtilis modulates expression of the PurR and G-box (XptR) regulons by adjusting the purine base pool size. J. Bacteriol. 187 (2005) 791-794
8. Serganov A., Yuan Y.R., Pikovskaya O., Polonskaia A., Malinina L., Phan A.T., Hobartner C., Micura R., Breaker R.R., and Patel D.J. Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem. Biol. 11 (2004) 1729-1741
9. Batey R.T., Gilbert S.D., and Montange R.K. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432 (2004) 411-415
10. Lafontaine D.A., Norman D.G., and Lilley D.M. The global structure of the VS ribozyme. EMBO J. 21 (2002) 2461-2471
11. Lafontaine D.A., Norman D.G., and Lilley D.M. Structure, folding and activity of the VS ribozyme: importance of the 2-3-6 helical junction. EMBO J. 20 (2001) 1415-1424
12. Lescoute A., and Westhof E. Topology of three-way junctions in folded RNAs. RNA 12 (2006) 83-93
13. 2+-induced conformational changes in the S15 binding site of 16 S ribosomal RNA. J. Mol. Biol. 275 (1998) 453-464
14. Noeske J., Richter C., Grundl M.A., Nasiri H.R., Schwalbe H., and Wohnert J. An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs. Proc. Natl. Acad. Sci. USA 102 (2005) 1372-1377
15. Wickiser J.K., Cheah M.T., Breaker R.R., and Crothers D.M. The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry 44 (2005) 13404-13414
16. Ward D.C., Reich E., and Stryer L. Fluorescence studies of nucleotides and polynucleotides. I. Formycin, 2-aminopurine riboside, 2,6-diaminopurine riboside, and their derivatives. J. Biol. Chem. 244 (1969) 1228-1237
17. Xu D., Evans K.O., and Nordlund T.M. Melting and premelting transitions of an oligomer measured by DNA base fluorescence and absorption. Biochemistry 33 (1994) 9592-9599
18. Stivers J.T. 2-Aminopurine fluorescence studies of base stacking interactions at abasic sites in DNA: metal-ion and base sequence effects. Nucleic Acids Res. 26 (1998) 3837-3844
19. Jean J.M., and Hall K.B. 2-Aminopurine fluorescence quenching and lifetimes: role of base stacking. Proc. Natl. Acad. Sci. USA 98 (2001) 37-41
20. Lafontaine D.A., Wilson T.J., Zhao Z.Y., and Lilley D.M. Functional group requirements in the probable active site of the VS ribozyme. J. Mol. Biol. 323 (2002) 23-34
21. Déclais A.C., and Lilley D.M. Extensive central disruption of a four-way junction on binding CCE1 resolving enzyme. J. Mol. Biol. 296 (2000) 421-433
22. Soukup G.A., and Breaker R.R. Relationship between internucleotide linkage geometry and the stability of RNA. RNA 5 (1999) 1308-1325
23. Nahvi A., Sudarsan N., Ebert M.S., Zou X., Brown K.L., and Breaker R.R. Genetic control by a metabolite binding mRNA. Chem. Biol. 9 (2002) 1043
24. Winkler W., Nahvi A., and Breaker R.R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419 (2002) 952-956
25. Winkler W.C., and Breaker R.R. Genetic control by metabolite-binding riboswitches. ChemBioChem 4 (2003) 1024-1032
26. Winkler W.C., Cohen-Chalamish S., and Breaker R.R. An mRNA structure that controls gene expression by binding FMN. Proc. Natl. Acad. Sci. USA 99 (2002) 15908-15913
27. Winkler W.C., Nahvi A., Roth A., Collins J.A., and Breaker R.R. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428 (2004) 281-286
28. Mandal M., Lee M., Barrick J.E., Weinberg Z., Emilsson G.M., Ruzzo W.L., and Breaker R.R. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306 (2004) 275-279
29. Law S.M., Eritja R., Goodman M.F., and Breslauer K.J. Spectroscopic and calorimetric characterizations of DNA duplexes containing 2-aminopurine. Biochemistry 35 (1996) 12329-12337
30. Khvorova A., Lescoute A., Westhof E., and Jayasena S.D. Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat. Struct. Biol. 10 (2003) 708-712
31. Penedo J.C., Wilson T.J., Jayasena S.D., Khvorova A., and Lilley D.M. Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements. RNA 10 (2004) 880-888
32. Murchie A.I., Thomson J.B., Walter F., and Lilley D.M. Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops. Mol. Cell 1 (1998) 873-881
33. Walter N.G., Burke J.M., and Millar D.P. Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction. Nat. Struct. Biol. 6 (1999) 544-549
34. Lilley D.M. Folding of branched RNA species. Biopolymers 48 (1998) 101-112
35. Silverman S.K., and Cech T.R. Energetics and cooperativity of tertiary hydrogen bonds in RNA structure. Biochemistry 38 (1999) 8691-8702
36. Silverman S.K., Zheng M., Wu M., Tinoco Jr. I., and Cech T.R. Quantifying the energetic interplay of RNA tertiary and secondary structure interactions. RNA 5 (1999) 1665-1674
37. 2+ in TPP-dependent riboswitch. FEBS Lett. 579 (2005) 2583-2588
38. Lilley D.M., and Wilson T.J. Fluorescence resonance energy transfer as a structural tool for nucleic acids. Curr. Opin. Chem. Biol. 4 (2000) 507-517
39. Förster T. Zwischenmolekulare Energiewanderung und Fluoreszenz. Ann. Phys. 2 (1948) 55-75
40. Norman D.G., Grainger R.J., Uhrin D., and Lilley D.M. Location of cyanine-3 on double-stranded DNA: importance for fluorescence resonance energy transfer studies. Biochemistry 39 (2000) 6317-6324
41. Hobartner C., Rieder R., Kreutz C., Puffer B., Lang K., Polonskaia A., Serganov A., and Micura R. Syntheses of RNAs with up to 100 nucleotides containing site-specific 2′-methylseleno labels for use in X-ray crystallography. J. Am. Chem. Soc. 127 (2005) 12035-12045
42. Sherlin L.D., Bullock T.L., Nissan T.A., Perona J.J., Lariviere F.J., Uhlenbeck O.C., and Scaringe S.A. Chemical and enzymatic synthesis of tRNAs for high-throughput crystallization. RNA 7 (2001) 1671-1678
43. Lescoute A., and Westhof E. Riboswitch structures: purine ligands replace tertiary contacts. Chem. Biol. 12 (2005) 10-13
44. Mehta A.D., Rief M., Spudich J.A., Smith D.A., and Simmons R.M. Single-molecule biomechanics with optical methods. Science 283 (1999) 1689-1695
45. Weiss S. Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy. Nat. Struct. Biol. 7 (2000) 724-729
46. Zhuang X., Bartley L.E., Babcock H.P., Russell R., Ha T., Herschlag D., and Chu S. A single-molecule study of RNA catalysis and folding. Science 288 (2000) 2048-2051
47. Zhuang X., Kim H., Pereira M.J., Babcock H.P., Walter N.G., and Chu S. Correlating structural dynamics and function in single ribozyme molecules. Science 296 (2002) 1473-1476
48. McKinney S.A., Declais A.C., Lilley D.M., and Ha T. Structural dynamics of individual Holliday junctions. Nat. Struct. Biol. 10 (2003) 93-97
49. Deniz A.A., Laurence T.A., Beligere G.S., Dahan M., Martin A.B., Chemla D.S., Dawson P.E., Schultz P.G., and Weiss S. Single-molecule protein folding: diffusion fluorescence resonance energy transfer studies of the denaturation of chymotrypsin inhibitor 2. Proc. Natl. Acad. Sci. USA 97 (2000) 5179-5184
50. Schuler B., Lipman E.A., and Eaton W.A. Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature 419 (2002) 743-747
51. Rothwell P.J., Berger S., Kensch O., Felekyan S., Antonik M., Wohrl B.M., Restle T., Goody R.S., and Seidel C.A. Multiparameter single-molecule fluorescence spectroscopy reveals heterogeneity of HIV-1 reverse transcriptase:primer/template complexes. Proc. Natl. Acad. Sci. USA 100 (2003) 1655-1660
52. Tan E., Wilson T.J., Nahas M.K., Clegg R.M., Lilley D.M., and Ha T. A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate. Proc. Natl. Acad. Sci. USA 100 (2003) 9308-9313
53. Xie Z., Srividya N., Sosnick T.R., Pan T., and Scherer N.F. Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme. Proc. Natl. Acad. Sci. USA 101 (2004) 534-539
54. Wickiser J.K., Winkler W.C., Breaker R.R., and Crothers D.M. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol. Cell 18 (2005) 49-60
55. Gusarov I., and Nudler E. The mechanism of intrinsic transcription termination. Mol. Cell 3 (1999) 495-504
56. Yakhnin A.V., and Babitzke P. NusA-stimulated RNA polymerase pausing and termination participates in the Bacillus subtilis trp operon attenuation mechanism in vitro. Proc. Natl. Acad. Sci. USA 99 (2002) 11067-11072
57. Milligan J.F., Groebe D.R., Witherell G.W., and Uhlenbeck O.C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15 (1987) 8783-8798
58. Pleiss J.A., Derrick M.L., and Uhlenbeck O.C. T7 RNA polymerase produces 5′ end heterogeneity during in vitro transcription from certain templates. RNA 4 (1998) 1313-1317
59. Flannery B.P., Teukolsky S.A., and Vetterling W.T. Numerical Recipes in Fortran. Second Edition (1992), Cambridge University Press, Cambridge, UK
60. Rist M., and Marino J. Association of an RNA kissing complex analyzed using 2-aminopurine fluorescence. Nucleic Acids Res. 29 (2001) 2401-2408
61. Wilson T.J., and Lilley D.M. Metal ion binding and the folding of the hairpin ribozyme. RNA 8 (2002) 587-600
62. Bassi G.S., Murchie A.I., Walter F., Clegg R.M., and Lilley D.M. Ion-induced folding of the hammerhead ribozyme: a fluorescence resonance energy transfer study. EMBO J. 16 (1997) 7481-7489
63. Clegg R.M., Murchie A.I., Zechel A., Carlberg C., Diekmann S., and Lilley D.M. Fluorescence resonance energy transfer analysis of the structure of the four-way DNA junction. Biochemistry 31 (1992) 4846-4856
64. Murchie A.I., Clegg R.M., von Kitzing E., Duckett D.R., Diekmann S., and Lilley D.M. Fluorescence energy transfer shows that the four-way DNA junction is a right-handed cross of antiparallel molecules. Nature 341 (1989) 763-766