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Structural basis for messenger RNA movement on the ribosome

Abstract

Translation initiation is a major determinant of the overall expression level of a gene1,2,3. The translation of functionally active protein requires the messenger RNA to be positioned on the ribosome such that the start/initiation codon will be read first and in the correct frame. Little is known about the molecular basis for the interaction of mRNA with the ribosome at different states of translation. Recent crystal structures of the ribosomal subunits4,5,6,7,8, the empty 70S ribosome9 and the 70S ribosome containing functional ligands10,11,12,13 have provided information about the general organization of the ribosome and its functional centres. Here we compare the X-ray structures of eight ribosome complexes modelling the translation initiation, post-initiation and elongation states. In the initiation and post-initiation complexes, the presence of the Shine–Dalgarno (SD) duplex causes strong anchoring of the 5′-end of mRNA onto the platform of the 30S subunit, with numerous interactions between mRNA and the ribosome. Conversely, the 5′ end of the ‘elongator’ mRNA lacking SD interactions is flexible, suggesting a different exit path for mRNA during elongation. After the initiation of translation, but while an SD interaction is still present, mRNA moves in the 3′→5′ direction with simultaneous clockwise rotation and lengthening of the SD duplex, bringing it into contact with ribosomal protein S2.

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Figure 1: Movement of mRNA on the ribosome.
Figure 2: Path of mRNA with a 5′-terminal extension through the ribosome.
Figure 3: mRNA path at the elongation step.

References

  1. Gold, L. Posttranscriptional regulatory mechanisms in Escherichia coli.. Annu. Rev. Biochem. 57, 199–233 (1988)

    CAS  Article  PubMed  Google Scholar 

  2. Draper, D. E. in Escherichia coli and Salmonella: Cellular and Molecular Biology 2nd edn (eds Neidhardt, F. C. et al.) 902–908 (ASM Press, Washington, DC, 1996)

  3. Kozak, M. Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene 361, 13–37 (2005)

    CAS  Article  PubMed  Google Scholar 

  4. Wimberly, B. T. et al. Structure of the 30S ribosomal subunit. Nature 407, 327–339 (2000)

    ADS  CAS  Article  PubMed  Google Scholar 

  5. Ogle, J. M. et al. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292, 897–902 (2001)

    ADS  CAS  Article  PubMed  Google Scholar 

  6. Ban, N. et al. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289, 905–920 (2000)

    ADS  CAS  Article  PubMed  Google Scholar 

  7. Schluenzen, F. et al. Structure of functionally activated small ribosomal subunit at 3.3 Å resolution. Cell 102, 615–623 (2000)

    CAS  Article  PubMed  Google Scholar 

  8. Harms, J. et al. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell 107, 679–688 (2001)

    CAS  Article  PubMed  Google Scholar 

  9. Schuwirth, B. S. et al. Structures of the bacterial ribosome at 3.5 Å resolution. Science 310, 827–834 (2005)

    ADS  CAS  Article  PubMed  Google Scholar 

  10. Yusupov, M. M. et al. Crystal structure of the ribosome at 5.5 Å resolution. Science 292, 883–896 (2001)

    ADS  CAS  Article  PubMed  Google Scholar 

  11. Yusupova, G. Z. et al. The path of messenger RNA through the ribosome. Cell 106, 233–241 (2001)

    CAS  Article  PubMed  Google Scholar 

  12. Jenner, L. et al. Translational operator of mRNA on the ribosome: how repressor proteins exclude ribosome binding. Science 308, 120–123 (2005)

    ADS  CAS  Article  PubMed  Google Scholar 

  13. Petry, S. et al. Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon. Cell 123, 1255–1266 (2005)

    CAS  Article  PubMed  Google Scholar 

  14. Schurr, T., Nadir, E. & Margalit, H. Identification and characterization of E. coli ribosomal binding sites by free energy computation. Nucleic Acids Res. 21, 4019–4023 (1993)

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  15. Ringquist, S. et al. Translation initiation in Escherichia coli: sequences within the ribosome-binding site. Mol. Microbiol. 6, 1219–1229 (1992)

    CAS  Article  PubMed  Google Scholar 

  16. Ma, J., Campbell, A. & Karlin, S. Correlations between Shine–Dalgarno sequences and gene features such as predicted expression levels and operon structures. J. Bacteriol. 184, 5733–5745 (2002)

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  17. La Teana, A., Gualerzi, C. O. & Brimacombe, R. From stand-by to decoding site. Adjustment of the mRNA on the 30S ribosomal subunit under the influence of the initiation factors. RNA 1, 772–782 (1995)

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Rinke-Appel, J. et al. Contacts between 16S ribosomal RNA and mRNA, within the spacer region separating the AUG initiator codon and the Shine–Dalgarno sequence; a site-directed cross-linking study. Nucleic Acids Res. 22, 3018–3025 (1994)

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  19. Canonaco, M. A., Gualerzi, C. O. & Pon, C. L. Alternative occupancy of a dual ribosomal binding site by mRNA affected by translation initiation factors. Eur. J. Biochem. 182, 501–506 (1989)

    CAS  Article  PubMed  Google Scholar 

  20. Cate, J., Yusupov, M., Yusupova, G., Earnest, T. & Noller, H. X-ray crystal structures of 70S ribosome functional complexes. Science 285, 2095–2104 (1999)

    CAS  Article  PubMed  Google Scholar 

  21. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)

    CAS  Article  PubMed  Google Scholar 

  22. Brünger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)

    Article  PubMed  Google Scholar 

  23. Rees, B., Jenner, L. & Yusupov, M. Bulk-solvent correction in large macromolecular structures. Acta Crystallogr. D 61, 1299–1301 (2005)

    Article  PubMed  Google Scholar 

  24. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991)

    Article  PubMed  Google Scholar 

  25. DeLano, W. L. The PyMOL Molecular Graphics System (DeLano Scientific, San Carlos, California, 2002)

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Acknowledgements

We thank C. Schulze-Briese and the SLS staff for help with X-ray data collection. This work was funded by CNRS and INSERM. Author Contributions G.Y. and L.J. contributed equally to this work. G.Y. performed the biochemical experiments and crystallized the ribosome complexes. L.J. solved the structures. All authors participated in discussing the results and writing the manuscript.

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Correspondence to Marat Yusupov.

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Coordinates and structure factors have been deposited in the Protein Data Bank under accession numbers 2HGR and 2HGU (initiation complex 30S and 50S subunits), 2HGP and 2HGQ (post-initiation complex) and 2HGI and 2HGJ (mRNA-free complex). Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

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Yusupova, G., Jenner, L., Rees, B. et al. Structural basis for messenger RNA movement on the ribosome. Nature 444, 391–394 (2006). https://doi.org/10.1038/nature05281

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