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Structural rearrangements of the ribosome at the tRNA proofreading step

Nature Structural & Molecular Biology volume 17, pages 1072–1078 (2010)Cite this article

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Abstract

Discrimination of tRNA on the ribosome occurs in two consecutive steps: initial selection and proofreading. Here we propose a proofreading mechanism based on comparison of crystal structures of the 70S ribosome with an empty A site or with the A site occupied by uncharged cognate or near-cognate tRNA. We observe that ribosomal proteins S13, S19, L16, L25, L27 and L31 are actively involved in the proofreading of tRNA. We suggest that proofreading begins with the monitoring of the entire anticodon loop of tRNA by nucleotides from 16S rRNA (helices 18 and 44) of the small subunit and 23S rRNA (helix 69) of the large subunit with involvement of magnesium ions. Subsequently, the elbow region is scanned by rRNA (helices 38 and 89) and proteins from the large subunit determining whether to accommodate the acceptor end of tRNA in the peptidyl transferase center or not.

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Figure 1: The A site of the 70S ribosome.
Figure 2: Conformational changes in the decoding center in respond to cognate or near-cognate tRNA.
Figure 3: Protein environment around the A-site tRNA.
Figure 4: The ribosomal environment of the elbow region of cognate A-site tRNA.
Figure 5: Rearrangements in the PTC induced by cognate or near-cognate tRNA.
Figure 6: Proposed scheme of the tRNA proofreading mechanism.

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Acknowledgements

We thank C. Schulze-Briese and the staff at the Swiss Light Source for help during synchrotron X-ray data collection, M. Rodnina and R. Green for the critical reading of the manuscript and advice, S. Duclaud for assistance in ribosome preparation, S. Melnikov for helpful discussions and the staff of the Structural Biology Department core facility at the Institut de Génétique et de Biologie Moléculaire et Cellulaire. This work was supported by the Agence Nationale de la Recherche BLAN07-3_190451 (M.Y.), ANR-07-PCVI-0015-01 (G.Y.) and by the European Commission SPINE2.

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  1. Lasse Jenner and Natalia Demeshkina: These authors contributed equally to this work.

Authors and Affiliations

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

    Lasse Jenner, Natalia Demeshkina, Gulnara Yusupova & Marat Yusupov

  2. Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France

    Lasse Jenner

  3. Centre National de la Recherche Scientifique, UMR7104, Illkirch, France

    Natalia Demeshkina, Gulnara Yusupova & Marat Yusupov

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  1. Lasse Jenner
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Contributions

L.J. and N.D. contributed equally to the study; L.J. purified the ribosomes, collected, processed and refined X-ray data and performed model building; N.D. collected X-ray data, performed model building and wrote the manuscript; G.Y. designed the study, and crystallized and performed model building; M.Y. designed the study; L.J., G.Y. and M.Y. corrected the manuscript; all authors discussed the results.

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Correspondence to Gulnara Yusupova or Marat Yusupov.

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Jenner, L., Demeshkina, N., Yusupova, G. et al. Structural rearrangements of the ribosome at the tRNA proofreading step. Nat Struct Mol Biol 17, 1072–1078 (2010). https://doi.org/10.1038/nsmb.1880

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