title: Functional evidence for D- and T-loop interactions in tmRNA.
abstract: During bacterial protein synthesis, stalled ribosomes can be rescued by tmRNA, a molecule with both tRNA and mRNA features. The tRNA region of tmRNA has sequence similarity with tRNA(Ala) and also has a clover-leaf structure folded similarly as in canonical tRNAs. Here we propose the L-shape of tmRNA to be stabilized by two tertiary interactions between its D- and T-loop on the basis of phylogenetic and experimental evidence. Mutational analysis clearly demonstrates a tertiary interaction between G(13) and U(342). Strikingly, this in evolution conserved interaction is not primarily important for tmRNA alanylation and for binding to elongation factor Tu, but especially for a proper functioning of SmpB.
authors.affiliation: Department of Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands.
authors.forename: Sharief
authors.initials: S
authors.lastname: Barends
authors.forename: Karl
authors.initials: K
authors.lastname: Björk
authors.forename: Alexander P
authors.initials: AP
authors.lastname: Gultyaev
authors.forename: Maarten H
authors.initials: MH
authors.lastname: de Smit
authors.forename: Cornelis W A
authors.initials: CW
authors.lastname: Pleij
authors.forename: Barend
authors.initials: B
authors.lastname: Kraal
mesh_terms: D000409:Alanine / Q000378:metabolism; D001483:Base Sequence; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D010444:Peptide Elongation Factor Tu / Q000378:metabolism; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012344:RNA, Transfer, Ala / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000378:metabolism; D012689:Sequence Homology, Nucleic Acid
chemical_list: D012329:RNA, Bacterial; D012344:RNA, Transfer, Ala; D016601:RNA-Binding Proteins; C430328:small protein B; C096222:tmRNA; D010444:Peptide Elongation Factor Tu; D000409:Alanine