Functional evidence for D- and T-loop interactions in tmRNA.
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.
Barends
Sharief
S
Department of Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands.
Björk
Karl
K
Gultyaev
Alexander P
AP
de Smit
Maarten H
MH
Pleij
Cornelis W A
CW
Kraal
Barend
B
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
D012329:RNA, Bacterial; D012344:RNA, Transfer, Ala; D016601:RNA-Binding Proteins; C430328:small protein B; C096222:tmRNA; D010444:Peptide Elongation Factor Tu; D000409:Alanine