Letter | Published:

A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting

Nature volume 441, pages 244247 (11 May 2006) | Download Citation

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Abstract

The triplet-based genetic code requires that translating ribosomes maintain the reading frame of a messenger RNA faithfully to ensure correct protein synthesis1. However, in programmed -1 ribosomal frameshifting2, a specific subversion of frame maintenance takes place, wherein the ribosome is forced to shift one nucleotide backwards into an overlapping reading frame and to translate an entirely new sequence of amino acids. This process is indispensable in the replication of numerous viral pathogens, including HIV and the coronavirus associated with severe acute respiratory syndrome3, and is also exploited in the expression of several cellular genes4. Frameshifting is promoted by an mRNA signal composed of two essential elements: a heptanucleotide ‘slippery’ sequence5 and an adjacent mRNA secondary structure, most often an mRNA pseudoknot6. How these components operate together to manipulate the ribosome is unknown. Here we describe the observation of a ribosome–mRNA pseudoknot complex that is stalled in the process of -1 frameshifting. Cryoelectron microscopic imaging of purified mammalian 80S ribosomes from rabbit reticulocytes paused at a coronavirus pseudoknot reveals an intermediate of the frameshifting process. From this it can be seen how the pseudoknot interacts with the ribosome to block the mRNA entrance channel, compromising the translocation process and leading to a spring-like deformation of the P-site transfer RNA. In addition, we identify movements of the likely eukaryotic ribosomal helicase and confirm a direct interaction between the translocase eEF2 and the P-site tRNA. Together, the structural changes provide a mechanical explanation of how the pseudoknot manipulates the ribosome into a different reading frame.

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Acknowledgements

I.B. thanks P. Farabaugh for helpful discussions. This work was supported by grants from the Biotechnology and Biological Sciences Research Council, UK, and the Medical Research Council, UK. S.J.M. holds a Wellcome Trust Structural Biology Studentship, D.I.S. is an MRC Research Professor, and R.J.C.G. is a Royal Society University Research Fellow. Author Contributions O.N. and S.J.M. contributed equally to this work. O.N. and I.B. purified the stalled ribosome complexes; S.J.M., D.I.S. and R.J.C.G. solved the structures. All authors discussed the results and contributed to writing of the manuscript.

Author information

Author notes

    • Olivier Namy

    †Present address: Institut de Génétique et Microbiologie, UMR8621, Université Paris-Sud, 91405 Orsay, France

    • Olivier Namy
    •  & Stephen J. Moran

    *These authors contributed equally to this work

Affiliations

  1. Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK

    • Olivier Namy
    •  & Ian Brierley
  2. Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

    • Stephen J. Moran
    • , David I. Stuart
    •  & Robert J. C. Gilbert
  3. Oxford Centre for Molecular Sciences, Central Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QH, UK

    • David I. Stuart
    •  & Robert J. C. Gilbert

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Competing interests

Electron-density maps have been deposited in the European Bioinformatics Institute Electron Microscopy database, accession numbers EMD-1197, EMD-1198 and EMD-1199 (www.ebi.ac.uk/msd/iims/3D_EMdep.html). Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Corresponding authors

Correspondence to Robert J. C. Gilbert or Ian Brierley.

Supplementary information

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  1. 1.

    Supplementary Notes

    This file contains Supplementary Figures 1 and 2, Supplementary Methods and Supplementary Notes. Of the two supplementary figures, one illustrates the purification of stalled ribosomes, the other a stereoview of the small subunit of the pseudoknot-stalled complex.

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https://doi.org/10.1038/nature04735

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