title: Sequence, structure, and stacking: specifics of tRNA anchoring to the T box riboswitch.
abstract: The term riboswitch usually refers to small molecule sensing regulatory modules in the 5' untranslated regions of a mRNA. They are typically comprised of separate ligand binding and regulatory domains. The T box riboswitch is unique from other identified riboswitches because its effector is an essential macromolecule, tRNA. It senses the aminoacylation state of tRNA to regulate genes involved in a variety of functions relating to amino acid metabolism and tRNA aminoacylation. T box riboswitches performs an intuitively simple process using a complex structured RNA element and, until recently, the underlying mechanisms were poorly understood. Only two sequence-specific contacts had been previously identified: (1) between the specifier sequence (codon) and the tRNA anticodon and (2) between an anti-terminator stem loop and the tRNA acceptor arm CCA tail. tRNA aminoacylation blocks the latter interaction and therefore serves as the switch between termination and anti-termination. Outside of these two contacts, the structure and functions of T box riboswitches have come to light in some recent studies. We recently described the X-ray crystal structure of the highly conserved T box riboswitch distal Stem I region and demonstrated that this region interacts with the tRNA elbow to anchor it to the riboswitch. Independently, Lehmann et al. used sequence homology search to arrive at a similar model for Stem I-tRNA interactions. The model was further supported by two recent structures of the Stem I-tRNA complex, determined independently by our group and by Zhang and Ferré-D'Amaré. This article highlights some of these contributions to synthesize an updated model for tRNA recognition by the T box riboswitch.
authors.affiliation: The Department of Molecular Biology and Genetics; Cornell University; Ithaca, NY USA.
authors.forename: Jason C
authors.initials: JC
authors.lastname: Grigg
authors.affiliation: The Department of Molecular Biology and Genetics; Cornell University; Ithaca, NY USA.
authors.forename: Ailong
authors.initials: A
authors.lastname: Ke
mesh_terms: D001665:Binding Sites; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012343:RNA, Transfer / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D058928:Riboswitch
chemical_list: D058928:Riboswitch; D012343:RNA, Transfer
keywords: RNA; RNA-RNA complex; T-loop; interlocking T-loop; structure