A dynamic RNA loop in an IRES affects multiple steps of elongation factor-mediated translation initiation
Marisa D Ruehle,
Haibo Zhang,
Ryan M Sheridan,
Somdeb Mitra,
Yuanwei Chen,
Ruben L Gonzalez Jr,
Barry S Cooperman,
Jeffrey S Kieft
Affiliations
Marisa D Ruehle
Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, United States
Haibo Zhang
Department of Chemistry, University of Pennsylvania, Pennsylvania, United States
Ryan M Sheridan
Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, United States
Somdeb Mitra
Department of Chemistry, Columbia University, New York, United States
Yuanwei Chen
Department of Chemistry, University of Pennsylvania, Pennsylvania, United States
Ruben L Gonzalez Jr
Department of Chemistry, Columbia University, New York, United States
Barry S Cooperman
Department of Chemistry, University of Pennsylvania, Pennsylvania, United States
Jeffrey S Kieft
Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, United States; Howard Hughes Medical Institute, University of Colorado Denver School of Medicine, Aurora, United States
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.
