title: Solution structure of the K-turn and Specifier Loop domains from the Bacillus subtilis tyrS T-box leader RNA.
abstract: In Gram-positive bacteria, the RNA transcripts of many amino acid biosynthetic and aminoacyl tRNA synthetase genes contain 5' untranslated regions, or leader RNAs, that function as riboswitches. These T-box riboswitches bind cognate tRNA molecules and regulate gene expression by a transcription attenuation mechanism. The Specifier Loop domain of the leader RNA contains nucleotides that pair with nucleotides in the tRNA anticodon loop and is flanked on one side by a kink-turn (K-turn), or GA, sequence motif. We have determined the solution NMR structure of the K-turn sequence element within the context of the Specifier Loop domain. The K-turn sequence motif has several noncanonical base pairs typical of K-turn structures but adopts an extended conformation. The Specifier Loop domain contains a loop E structural motif, and the single-strand Specifier nucleotides stack with their Watson-Crick edges displaced toward the minor groove. Mg(2+) leads to a significant bending of the helix axis at the base of the Specifier Loop domain, but does not alter the K-turn. Isothermal titration calorimetry indicates that the K-turn sequence causes a small enhancement of the interaction between the tRNA anticodon arm and the Specifier Loop domain. One possibility is that the K-turn structure is formed and stabilized when tRNA binds the T-box riboswitch and interacts with Stem I and the antiterminator helix. This motif in turn anchors the orientation of Stem I relative to the 3' half of the leader RNA, further stabilizing the tRNA-T box complex.
authors.affiliation: Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA.
authors.forename: Jiachen
authors.initials: J
authors.lastname: Wang
authors.forename: Edward P
authors.initials: EP
authors.lastname: Nikonowicz
mesh_terms: D020121:5' Untranslated Regions; D001412:Bacillus subtilis / Q000235:genetics*; D020029:Base Pairing; D001483:Base Sequence; D008274:Magnesium / Q000494:pharmacology; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry* / Q000235:genetics; D012365:RNA, Transfer, Tyr / Q000737:chemistry* / Q000235:genetics; D058928:Riboswitch; D014158:Transcription, Genetic; D014448:Tyrosine-tRNA Ligase / Q000235:genetics*
chemical_list: D020121:5' Untranslated Regions; D012329:RNA, Bacterial; D012365:RNA, Transfer, Tyr; D058928:Riboswitch; D014448:Tyrosine-tRNA Ligase; D008274:Magnesium