Edwards et al., Curr Opin Struct Biol 2007

Metabolite recognition by riboswitches Edwards, Klein and Ferré-D’Amaré 279
16. Klein DJ, Schmeing TM, Moore PB, Steitz TA: The kink-turn:
a new RNA secondary structure motif. EMBO J 2001,
20:4214-4221.
17. Winkler WC, Nahvi A, Roth A, Collins JA, Breaker RR: Control of
gene expression by a natural metabolite-responsive ribozyme.
Nature 2004, 428:281-286.
18.
Klein DJ, Ferré-D’Amaré AR: Structural basis of glmS ribozyme
activation by glucosamine-6-phosphate. Science 2006,
313:1752-1756.
Crystal structures of the glmS ribozyme in pre- and post-cleavage states,
together with the demonstration of ribozyme activity in the crystalline
state, indicate that this riboswitch is remarkably rigid and folds in the
absence of effector. The structure of the ribozyme bound to the antagonist
Glc6P suggests how the activator functions as a coenzyme.
19.
Cochrane JC, Lipchock SV, Strobel SA: Structural investigation
of the glmS ribozyme bound to its catalytic cofactor.
Chem Biol 2007, 14:97-105.
The structure of the glmS ribozyme bound to the activator GlcN6P
confirms that its mode of binding is similar to that of the antagonist
Glc6P. Kinetic analyses show that the K m but not the k cat of the reaction is
pH dependent.
20.
Hampel KJ, Tinsley MM: Evidence for preorganization of the
glmS ribozyme ligand binding pocket. Biochemistry 2006,
45:7861-7871.
Biochemical analysis of the glmS ribozyme-riboswitch provides evidence
that the activator-binding site is largely pre-organized.
21. Rupert PB, Ferré-D’Amaré AR: Crystal structure of a hairpin
ribozyme-inhibitor complex with implications for catalysis.
Nature 2001, 410:780-786.
22. Rupert PB, Massey AP, Sigurdsson ST, Ferré-D’Amaré AR:
Transition state stabilization by a catalytic RNA. Science 2002,
298:1421-1424.
23. Serganov A, Keiper S, Malinina L, Tereshko V, Skripkin E,
Hobartner C, Polonskaia A, Phan AT, Wombacher R, Micura R
et al.: Structural basis for Diels-Alder ribozyme-catalyzed
carbon-carbon bond formation. Nat Struct Mol Biol 2005,
12:218-224.
24.
Gilbert SD, Stoddard CD, Wise SJ, Batey RT: Thermodynamic
and kinetic characterization of ligand binding to the purine
riboswitch aptamer domain. J Mol Biol 2006, 359:754-768.
The authors present a biophysical and structural analysis of the specificity
of the purine riboswitch, in particular, the importance of Watson–Crick
pairing of the effector with pyrimidine 74.
25. Gilbert SD, Mediatore SJ, Batey RT: Modified pyrimidines
specifically bind the purine riboswitch. J Am Chem Soc 2006,
128:14214-14215.
26. Noeske J, Richter C, Grundl MA, Nasiri HR, Schwalbe H,
Wöhnert 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 2005, 102:1372-1377.
27. Dieckmann T, Suzuki E, Nakamura GK, Feigon J: Solution
structure of an ATP-binding RNA aptamer reveals a novel fold.
RNA 1996, 2:628-640.
28. Jiang F, Kumar RA, Jones RA, Patel DJ: Structural basis of RNA
folding and recognition in an AMP-RNA aptamer complex.
Nature 1996, 382:183-186.
29. Noeske J, Richter C, Stirnal E, Schwalbe H, Wöhnert J:
Phosphate-group recognition by the aptamer domain of the
thiamine pyrophosphate sensing riboswitch. ChemBioChem
2006, 7:1451-1456.
30. Lim J, Winkler WC, Nakamura S, Scott V, Breaker RR: Molecularrecognition
characteristics of SAM-binding riboswitches.
Angew Chem Int Ed Engl 2006, 45:964-968.
31. Auffinger P, Bielecki L, Westhof E: Anion binding to nucleic
acids. Structure 2004, 12:379-388.
32. Wilson DS, Szostak JW: In vitro selection of functional nucleic
acids. Annu Rev Biochem 1999, 68:611-647.
33. Hermann T, Patel DJ: Adaptive recognition by nucleic acid
aptamers. Science 2000, 287:820-825.
34. Ferré-D’Amaré AR, Doudna JA: RNA folds: insights from
recent crystal structures. Annu Rev Biophys Biomol Struct 1999,
28:57-73.
35. Eisenberg D, McLachlan AD: Solvation energy in protein folding
and binding. Nature 1986, 319:199-203.
36. Nahvi A, Sudarsan N, Ebert MS, Zou X, Brown KL, Breaker RR:
Genetic control by a metabolite binding mRNA. Chem Biol
2002, 9:1043.
37. Müller M, Weigand JE, Weichenrieder O, Suess B:
Thermodynamic characterization of an engineered
tetracycline-binding riboswitch. Nucleic Acids Res 2006,
34:2607-2617.
38. 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.
39. Carothers JM, Oestreich SC, Davis JH, Szostak JW:
Informational complexity and functional activity of RNA
structures. J Am Chem Soc 2004, 126:5130-5137.
40.
Carothers JM, Oestreich SC, Szostak JW: Aptamers selected for
higher-affinity binding are not more specific for the target
ligand. J Am Chem Soc 2006, 128:7929-7937.
The authors analyzed the effect of structural complexity on affinity and
selectivity for 11 distinct classes of GTP aptamers.
41. Lemay JF, Penedo JC, Tremblay R, Lilley DM, Lafontaine DA:
Folding of the adenine riboswitch. Chem Biol 2006, 13:857-868.
Ensemble and single-molecule FRET measurements demonstrated multiple
Mg 2+ -dependent folded states of the adenine riboswitch in the
absence of ligand.
42.
Noeske J, Buck J, Furtig B, Nasiri HR, Schwalbe H, Wöhnert 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, 35:101-112.
Solution NMR analysis of a guanine riboswitch reveals pre-organization of
the global fold, including the terminal loop–loop interaction, in the
absence of effector.
43. 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.
44. 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.
45. Wickiser JK, Cheah MT, Breaker RR, Crothers DM: The kinetics
of ligand binding by an adenine-sensing riboswitch.
Biochemistry 2005, 44:13404-13414.
46.
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.
The rates of riboswitch transcription, the influence of transcriptional
pause sites and the association rates of FMN are studied, showing that
the FMN riboswitch is under kinetic rather than thermodynamic control.
47. Grundy FJ, Henkin TM: Regulation of gene expression by
effectors that bind to RNA. Curr Opin Microbiol 2004,
7:126-131.
48. Cromie MJ, Shi Y, Latifi T, Groisman EA: An RNA sensor for
intracellular Mg(2+). Cell 2006, 125:71-84.
49. Chowdhury S, Maris C, Allain FH, Narberhaus F: Molecular
basis for temperature sensing by an RNA thermometer.
EMBO J 2006, 25:2487-2497.
50. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-
Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS et al.:
Crystallography & NMR system: a new software suite for
macromolecular structure determination. Acta Crystallogr D
Biol Crystallogr 1998, 54:905-921.
51. DeLano WL: The PyMOL Molecular Graphics System. San Carlos,
CA: DeLano Scientific; 2002.
www.sciencedirect.com Current Opinion in Structural Biology 2007, 17:273–279