title: Folding of the SAM aptamer is determined by the formation of a K-turn-dependent pseudoknot.
abstract: The S-adenosylmethionine (SAM) riboswitch is one of the most recurrent riboswitches found in bacteria and has three known different natural aptamers. The Bacillus subtilis yitJ SAM riboswitch aptamer is organized around a four-way junction which is characterized by the presence of a pseudoknot and a K-turn motif. By replacing the adenine involved in a Watson-Crick base pair at position 138 in the core region of the aptamer with the fluorescent analogue 2-aminopurine (2AP), we show that the ligand-induced reorganization of the aptamer strongly attenuates 2AP fluorescence. The fluorescence quenching process is specific to SAM on the basis of the observation that the structural analogue S-adenosylhomocysteine does not promote a similar effect. We find that the pseudoknot is important for the reorganization of the core domain and that the K-turn motif also has a marked influence on the core domain reorganization, most probably through its important role in pseudoknot formation. Finally, we show that SAM riboswitch ligand binding is facilitated by the L7Ae K-turn binding protein, which suggests that K-turn motifs may be protein anchor sites used by riboswitches to promote RNA folding.
authors.affiliation: Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada J1K 2R1.
authors.forename: Benoit
authors.initials: B
authors.lastname: Heppell
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Lafontaine
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry*; D001483:Base Sequence; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012436:S-Adenosylmethionine / Q000737:chemistry*; D013050:Spectrometry, Fluorescence
chemical_list: D052157:Aptamers, Nucleotide; D012436:S-Adenosylmethionine