Taura syndrome virus IRES initiates translation by binding its tRNA-mRNA–like structural element in the ribosomal decoding center
Edited by Jennifer A. Doudna, University of California, Berkeley, CA, and approved May 13, 2014 (received for review April 6, 2014)
Significance
Ribosomes decode genetic information encoded in mRNAs to synthesize cellular proteins. Initiation of translation is a key step, during which the ORF coding for a protein gets properly positioned on the ribosome with the AUG start codon and its cognate tRNA located in the ribosomal peptidyl site. Here, we report molecular structures of a eukaryotic ribosome complexed with viral mRNA, which uncover an unusual mechanism of initiation. The structures reveal that viral mRNAs carrying an intergenic RNA structure known as the internal ribosome entry site (IRES) initiate translation by binding a tRNA-mRNA–like element in the aminoacyl site of the ribosome. A structural mechanism of how viral mRNAs with intergenic IRESs hijack host ribosomes is proposed.
Abstract
In cap-dependent translation initiation, the open reading frame (ORF) of mRNA is established by the placement of the AUG start codon and initiator tRNA in the ribosomal peptidyl (P) site. Internal ribosome entry sites (IRESs) promote translation of mRNAs in a cap-independent manner. We report two structures of the ribosome-bound Taura syndrome virus (TSV) IRES belonging to the family of Dicistroviridae intergenic IRESs. Intersubunit rotational states differ in these structures, suggesting that ribosome dynamics play a role in IRES translocation. Pseudoknot I of the IRES occupies the ribosomal decoding center at the aminoacyl (A) site in a manner resembling that of the tRNA anticodon-mRNA codon. The structures reveal that the TSV IRES initiates translation by a previously unseen mechanism, which is conceptually distinct from initiator tRNA-dependent mechanisms. Specifically, the ORF of the IRES-driven mRNA is established by the placement of the preceding tRNA-mRNA–like structure in the A site, whereas the 40S P site remains unoccupied during this initial step.
Data Availability
Data deposition: Electron cryomicroscopy maps and structural models have been deposited in the EMDataBank (EMDB), www.emdatabank.org (EMDB ID codes EMD-5942 and EMD-5943), and the Protein Data Bank (PDB), www.pdb.org (PDB ID codes 3J6X and 3J6Y), respectively.
Acknowledgments
We thank A. Jacobson, R. Madireddy, and E. Mandon for providing reagents; A. Arif for initial work; Z. H. Yu and J. de la Cruz for help with collecting data; Y. X. Liao for help in picking particles; P. D. Zamore, R. Fukunaga, and E. Ricci for useful discussions; and D. N. Ermolenko, J. Kieft, and A. Korennykh for comments on the manuscript. The study was supported by grants from the Worcester Foundation for Biomedical Research, the University of Massachusetts Medical School Center for AIDS Research (to A.A.K.), and the Natural Sciences and Engineering Research Council (to A.F.B.) and by National Institutes of Health Grants R01 GM106105 (to A.A.K.) and P01 GM62580 (to N.G.).
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Data Availability
Data deposition: Electron cryomicroscopy maps and structural models have been deposited in the EMDataBank (EMDB), www.emdatabank.org (EMDB ID codes EMD-5942 and EMD-5943), and the Protein Data Bank (PDB), www.pdb.org (PDB ID codes 3J6X and 3J6Y), respectively.
Submission history
Published online: June 9, 2014
Published in issue: June 24, 2014
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Acknowledgments
We thank A. Jacobson, R. Madireddy, and E. Mandon for providing reagents; A. Arif for initial work; Z. H. Yu and J. de la Cruz for help with collecting data; Y. X. Liao for help in picking particles; P. D. Zamore, R. Fukunaga, and E. Ricci for useful discussions; and D. N. Ermolenko, J. Kieft, and A. Korennykh for comments on the manuscript. The study was supported by grants from the Worcester Foundation for Biomedical Research, the University of Massachusetts Medical School Center for AIDS Research (to A.A.K.), and the Natural Sciences and Engineering Research Council (to A.F.B.) and by National Institutes of Health Grants R01 GM106105 (to A.A.K.) and P01 GM62580 (to N.G.).
Notes
*This Direct Submission article had a prearranged editor.
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The authors declare no conflict of interest.
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