A dynamic RNA loop in an IRES affects multiple steps of elongation factor-mediated translation initiation

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Abstract

Internal ribosome entry sites (IRESs) are powerful model systems to understand how the translation machinery can be manipulated by structured RNAs and for exploring inherent features of ribosome function. The intergenic region (IGR) IRESs from the Dicistroviridae family of viruses are structured RNAs that bind directly to the ribosome and initiate translation by co-opting the translation elongation cycle. These IRESs require an RNA pseudoknot that mimics a codon-anticodon interaction and contains a conformationally dynamic loop. We explored the role of this loop and found that both the length and sequence are essential for translation in different types of IGR IRESs and from diverse viruses. We found that loop 3 affects two discrete elongation factor-dependent steps in the IRES initiation mechanism. Our results show how the IRES directs multiple steps after 80S ribosome placement and highlights the often underappreciated significance of discrete conformationally dynamic elements within the context of structured RNAs.

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Marisa Ruehle

Department of Biochemistry and Molecular Genetics, Howard Hughes Medical Institute, University of Colorado Denver School of Medicine, Aurora, United States

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The authors declare that no competing interests exist.
Haibo Zhang

Department of Chemistry, University of Pennsylvania, Philadelphia, United States

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The authors declare that no competing interests exist.
Ryan M Sheridan

Department of Biochemistry and Molecular Genetics, Howard Hughes Medical Institute, University of Colorado Denver School of Medicine, Aurora, United States

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The authors declare that no competing interests exist.
Somdeb Mitra

Department of Chemistry, Columbia University, New York, United States

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The authors declare that no competing interests exist.
Yuanwei Chen

Department of Chemistry, University of Pennsylvania, Philadelphia, United States

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The authors declare that no competing interests exist.
Ruben L Gonzalez

Department of Chemistry, Columbia University, New York, United States

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The authors declare that no competing interests exist.
Barry S Cooperman

Department of Chemistry, University of Pennsylvania, Philadelphia, United States

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The authors declare that no competing interests exist.
Jeffrey S Kieft

Department of Biochemistry and Molecular Genetics, Howard Hughes Medical Institute, University of Colorado Denver School of Medicine, Aurora, United States

For correspondence
jeffrey.kieft@ucdenver.edu

Competing interests
The authors declare that no competing interests exist.

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