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Structural aspects of messenger RNA reading frame maintenance by the ribosome

Nature Structural & Molecular Biology volume 17, pages 555–560 (2010)Cite this article

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Abstract

One key question in protein biosynthesis is how the ribosome couples mRNA and tRNA movements to prevent disruption of weak codon-anticodon interactions and loss of the translational reading frame during translocation. Here we report the complete path of mRNA on the 70S ribosome at the atomic level (3.1-Å resolution), and we show that one of the conformational rearrangements that occurs upon transition from initiation to elongation is a narrowing of the downstream mRNA tunnel. This rearrangement triggers formation of a network of interactions between the mRNA downstream of the A-site codon and the elongating ribosome. Our data elucidate the mechanism by which hypermodified nucleoside 2-methylthio-N6 isopentenyl adenosine at position 37 (ms2i6A37) in tRNAPheGAA stabilizes mRNA-tRNA interactions in all three tRNA binding sites. Another network of contacts is formed between this tRNA modification and ribosomal elements surrounding the mRNA E/P kink, resulting in the anchoring of P-site tRNA. These data allow rationalization of how modification deficiencies of ms2i6A37 in tRNAs may lead to shifts of the translational reading frame.

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Figure 1: Comparison of the ribosome in the elongation and initiation states.
Figure 2: mRNA-ribosome interactions downstream of the A codon.
Figure 3: Stabilization of codon-anticodon interactions by cross-strand stacking of hypermodified nucleotide 37 (ms2i6A37) in the A, P and E sites.
Figure 4: Overview of mRNA and tRNA interactions with the ribosome.

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Acknowledgements

We thank C. Schulze-Briese and the staff at the Swiss Light Source, Switzerland, for help during synchrotron X-ray data collection, D. Moras for discussions and scientific support, M. Iskakova for assisting during X-ray data collection, S. Duclaud for technical assistance in ribosome preparation and crystallization as well as the staff of the Structural Biology Department core facility at IGBMC and S. Melnikov for helpful discussions. This work was supported by ANR BLANC07-3_190451 (M.Y.), ANR-07-PCVI-0015-01 (G.Y.) and by the European Commission SPINE2.

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Authors and Affiliations

  1. Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France

    Lasse B Jenner, Natalia Demeshkina, Gulnara Yusupova & Marat Yusupov

  2. Institut National de la Santé et de la Recherche Médicale, Unité 964, Illkirch, France

    Lasse B Jenner

  3. Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7104, Illkirch, France

    Natalia Demeshkina, Gulnara Yusupova & Marat Yusupov

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  1. Lasse B Jenner
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Contributions

L.B.J. performed ribosome purification, data collection, model building, refinement, data analysis and writing of the manuscript; N.D. performed data collection and model building; G.Y. performed crystallization; G.Y. and M.Y. initiated the project, performed model building and writing of the manuscript and acted as project leaders.

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Correspondence to Gulnara Yusupova or Marat Yusupov.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–3 and Supplementary Methods (PDF 1681 kb)

Supplementary Movie 1

30S domain closure. This animation shows the 30S subunit domain closure upon transition from the initiation to elongation state. (GIF 2578 kb)

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Jenner, L., Demeshkina, N., Yusupova, G. et al. Structural aspects of messenger RNA reading frame maintenance by the ribosome. Nat Struct Mol Biol 17, 555–560 (2010). https://doi.org/10.1038/nsmb.1790

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