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tRNA–mRNA mimicry drives translation initiation from a viral IRES

Nature Structural & Molecular Biology volume 15, pages 57–64 (2008)Cite this article

Abstract

Internal ribosome entry site (IRES) RNAs initiate protein synthesis in eukaryotic cells by a noncanonical cap-independent mechanism. IRESes are critical for many pathogenic viruses, but efforts to understand their function are complicated by the diversity of IRES sequences as well as by limited high-resolution structural information. The intergenic region (IGR) IRESes of the Dicistroviridae viruses are powerful model systems to begin to understand IRES function. Here we present the crystal structure of a Dicistroviridae IGR IRES domain that interacts with the ribosome's decoding groove. We find that this RNA domain precisely mimics the transfer RNA anticodon–messenger RNA codon interaction, and its modeled orientation on the ribosome helps explain translocation without peptide bond formation. When combined with a previous structure, this work completes the first high-resolution description of an IRES RNA and provides insight into how RNAs can manipulate complex biological machines.

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Figure 1: The P site domain of the Dicistroviridae intergenic region IRESes.
Figure 2: Structural details and comparison to authentic tRNA-mRNA interactions.
Figure 3: Translation initiation assays for mutant CrPV IGR IRES RNAs.
Figure 4: Model and probing of domain 3 in the ribosome P site.
Figure 5: Docking of both IRES domain structures into a cryo-EM reconstruction and hypothesized mimicry mechanism.

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Acknowledgements

We thank K. Bjornsen for obtaining initial crystals and for technical assistance, Q. Vicens, T. Evans, R. Batey, B. Hodges, T. Blumenthal, E. Eisenmesser, R. Zhao, M. Filbin and A. Keel for critically reading this manuscript, R. Batey for useful discussions and for providing the iridium(III) hexammine, P. Sarnow (Stanford University), E. Jan (University of British Columbia) and N. Nakashima (Japanese National Institute of Agrobiological Sciences) for plasmids, and the staffs of beam lines 4.2.2 and 12.3.1 at the Advanced Light Source. This work was supported by grants AI072187 and GM072560 from the US National Institutes of Health (J.S.K.).

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  1. Department of Biochemistry and Molecular Genetics, University of Colorado at Denver and Health Sciences Center, Mail Stop 8101, PO Box 6511, Aurora, 80045, Colorado, USA

    David A Costantino, Jennifer S Pfingsten & Jeffrey S Kieft

  2. Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, 94720, California

    Robert P Rambo

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  1. David A Costantino
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Correspondence to Jeffrey S Kieft.

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Costantino, D., Pfingsten, J., Rambo, R. et al. tRNA–mRNA mimicry drives translation initiation from a viral IRES. Nat Struct Mol Biol 15, 57–64 (2008). https://doi.org/10.1038/nsmb1351

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