title: Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch.
abstract: Riboswitches are highly structured elements in the 5'-untranslated regions (5'-UTRs) of messenger RNA that control gene expression by specifically binding to small metabolite molecules. They consist of an aptamer domain responsible for ligand binding and an expression platform. Ligand binding in the aptamer domain leads to conformational changes in the expression platform that result in transcription termination or abolish ribosome binding. The guanine riboswitch binds with high-specificity to guanine and hypoxanthine and is among the smallest riboswitches described so far. The X-ray-structure of its aptamer domain in complex with guanine/hypoxanthine reveals an intricate RNA-fold consisting of a three-helix junction stabilized by long-range base pairing interactions. We analyzed the conformational transitions of the aptamer domain induced by binding of hypoxanthine using high-resolution NMR-spectroscopy in solution. We found that the long-range base pairing interactions are already present in the free RNA and preorganize its global fold. The ligand binding core region is lacking hydrogen bonding interactions and therefore likely to be unstructured in the absence of ligand. Mg2+-ions are not essential for ligand binding and do not change the structure of the RNA-ligand complex but stabilize the structure at elevated temperatures. We identified a mutant RNA where the long-range base pairing interactions are disrupted in the free form of the RNA but form upon ligand binding in an Mg2+-dependent fashion. The tertiary interaction motif is stable outside the riboswitch context.
authors.affiliation: Institute of Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance, Johann-Wolfgang-Goethe-University, 60438 Frankfurt/M., Germany.
authors.forename: Jonas
authors.initials: J
authors.lastname: Noeske
authors.forename: Janina
authors.initials: J
authors.lastname: Buck
authors.forename: Boris
authors.initials: B
authors.lastname: Fürtig
authors.forename: Hamid R
authors.initials: HR
authors.lastname: Nasiri
authors.forename: Harald
authors.initials: H
authors.lastname: Schwalbe
authors.forename: Jens
authors.initials: J
authors.lastname: Wöhnert
mesh_terms: D020121:5' Untranslated Regions / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D000494:Allosteric Regulation; D052157:Aptamers, Nucleotide / Q000737:chemistry; D001412:Bacillus subtilis / Q000235:genetics; D001483:Base Sequence; D006147:Guanine / Q000737:chemistry / Q000378:metabolism; D019271:Hypoxanthine / Q000737:chemistry* / Q000378:metabolism; D008024:Ligands; D008274:Magnesium / Q000737:chemistry; D008969:Molecular Sequence Data; D009154:Mutation; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry / Q000378:metabolism; D038621:Regulatory Sequences, Ribonucleic Acid
chemical_list: D020121:5' Untranslated Regions; D052157:Aptamers, Nucleotide; D008024:Ligands; D012329:RNA, Bacterial; D038621:Regulatory Sequences, Ribonucleic Acid; D019271:Hypoxanthine; D006147:Guanine; D008274:Magnesium