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Peptide bond formation destabilizes Shine–Dalgarno interaction on the ribosome

Nature volume 446, pages 454–457 (2007)Cite this article

Abstract

The ribosome is a molecular machine that translates the genetic code contained in the messenger RNA into an amino acid sequence through repetitive cycles of transfer RNA selection, peptide bond formation and translocation1,2,3. Here we demonstrate an optical tweezer assay to measure the rupture force between a single ribosome complex and mRNA. The rupture force was compared between ribosome complexes assembled on an mRNA with and without a strong Shine–Dalgarno (SD) sequence—a sequence found just upstream of the coding region of bacterial mRNAs, involved in translation initiation4,5. The removal of the SD sequence significantly reduced the rupture force in complexes carrying an aminoacyl tRNA, Phe-tRNAPhe, in the A site, indicating that the SD interactions contribute significantly to the stability of the ribosomal complex on the mRNA before peptide bond formation. In contrast, the presence of a peptidyl tRNA analogue, N-acetyl-Phe-tRNAPhe, in the A site, which mimicked the post-peptidyl transfer state, weakened the rupture force as compared to the complex with Phe-tRNAPhe, and the resultant force was the same for both the SD-containing and SD-deficient mRNAs. These results suggest that formation of the first peptide bond destabilizes the SD interaction, resulting in the weakening of the force with which the ribosome grips an mRNA. This might be an important requirement to facilitate movement of the ribosome along mRNA during the first translocation step.

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Figure 1: Experimental design for rupture force measurements on the ribosome.
Figure 2: Examples of displacement–time traces, showing the behaviour of the bead.
Figure 3: Rupture force distributions for ribosome complexes assembled on mRNAs containing (left panels) or lacking (middle panels) the SD sequence.

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Acknowledgements

We thank C. Squires for the SQ380 strain that was used to engineer the ribosomes. We are grateful to colleagues in the S. Chu and J. Puglisi groups at Stanford University for encouragement and discussions. S.U. is a recipient of JSPS Postdoctoral Fellowships for Research Abroad. M.D. was supported by the HHMI Predoctoral Fellowship. This work was funded by grants to J.D.P. from the NIH and the Packard Foundation, to S.C. from the NSF and NASA, and to J.D.P. and S.C. from the Packard Foundation.

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Authors and Affiliations

  1. Department of Physics,,

    Sotaro Uemura, Tae-Hee Lee, Harold D. Kim & Steven Chu

  2. Department of Structural Biology, Stanford University, Stanford, California 94305, USA,

    Magdalena Dorywalska & Joseph D. Puglisi

  3. Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA,

    Steven Chu

  4. Departments of Physics, Molecular and Cellular Biology, University of California, Berkeley, California 94720, USA,

    Steven Chu

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  1. Sotaro Uemura
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Correspondence to Joseph D. Puglisi or Steven Chu.

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Uemura, S., Dorywalska, M., Lee, TH. et al. Peptide bond formation destabilizes Shine–Dalgarno interaction on the ribosome. Nature 446, 454–457 (2007). https://doi.org/10.1038/nature05625

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