Two new back-to-back articles in the EMBO Journal describe atomic models of ribosomes in complex with tmRNA, a molecule that rescues the ribosomes stalled at truncated messages. MDFF was employed in both studies to aid the interpretation of the cryo-EM reconstructions.
tmRNA–SmpB: a journey to the centre of the bacterial ribosome.
Félix Weis, Patrick Bron, Emmanuel Giudice, Jean-Paul Rolland, Daniel Thomas, Brice Felden, and Reynald Gillet. EMBO J., 29, 3810-3818, 2010.
Ribosomes mediate protein synthesis by decoding the information carried by messenger RNAs (mRNAs) and catalysing peptide bond formation between amino acids. When bacterial ribosomes stall on incomplete messages, the trans-translation quality control mechanism is activated by the transfer-messenger RNA bound to small protein B (tmRNA–SmpB ribonucleoprotein complex). Trans-translation liberates the stalled ribosomes and triggers degradation of the incomplete proteins. Here, we present the cryo-electron microscopy structures of tmRNA–SmpB accommodated or translocated into stalled ribosomes. Two atomic models for each state are proposed. This study reveals how tmRNA–SmpB crosses the ribosome and how, as the problematic mRNA is ejected, the tmRNA resume codon is placed onto the ribosomal decoding site by new contacts between SmpB and the nucleotides upstream of the tag-encoding sequence. This provides a structural basis for the transit of the large tmRNA–SmpB complex through the ribosome and for the means by which the tmRNA internal frame is set for translation to resume.
Visualizing the transfer-messenger RNA as the ribosome resumes translation.
Jie Fu, Yaser Hashem, Iwona Wower, Jianlin Lei, Hstau Y Liao, Christian Zwieb, Jacek Wower, and Joachim Frank. EMBO J., 29, 3819-3825, 2010.
Bacterial ribosomes stalled by truncated mRNAs are rescued by transfer-messenger RNA (tmRNA), a dual-function molecule that contains a tRNA-like domain (TLD) and an internal open reading frame (ORF). Occupying the empty A site with its TLD, the tmRNA enters the ribosome with the help of elongation factor Tu and a protein factor called small protein B (SmpB), and switches the translation to its own ORF. In this study, using cryo-electron microscopy, we obtained the first structure of an in vivo-formed complex containing ribosome and the tmRNA at the point where the TLD is accommodated into the ribosomal P site. We show that tmRNA maintains a stable ‘arc and fork’ structure on the ribosome when its TLD moves to the ribosomal P site and translation resumes on its ORF. Based on the density map, we built an atomic model, which suggests that SmpB interacts with the five nucleotides immediately upstream of the resume codon, thereby determining the correct selection of the reading frame on the ORF of tmRNA.