title: A dynamic RNA loop in an IRES affects multiple steps of elongation factor-mediated translation initiation.
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.
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, United States.
authors.forename: Marisa D
authors.initials: MD
authors.lastname: Ruehle
authors.affiliation: Department of Chemistry, University of Pennsylvania, Pennsylvania, United States.
authors.forename: Haibo
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, United States.
authors.forename: Ryan M
authors.initials: RM
authors.lastname: Sheridan
authors.affiliation: Department of Chemistry, Columbia University, New York, United States.
authors.forename: Somdeb
authors.initials: S
authors.lastname: Mitra
authors.affiliation: Department of Chemistry, University of Pennsylvania, Pennsylvania, United States.
authors.forename: Yuanwei
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Department of Chemistry, Columbia University, New York, United States.
authors.forename: Ruben L
authors.initials: RL
authors.lastname: Gonzalez
authors.affiliation: Department of Chemistry, University of Pennsylvania, Pennsylvania, United States.
authors.forename: Barry S
authors.initials: BS
authors.lastname: Cooperman
authors.affiliation: 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.
authors.forename: Jeffrey S
authors.initials: JS
authors.lastname: Kieft
mesh_terms: D056629:Dicistroviridae / Q000235:genetics* / Q000502:physiology; D000067556:Internal Ribosome Entry Sites; D009690:Nucleic Acid Conformation; D010445:Peptide Elongation Factors / Q000378:metabolism*; D014176:Protein Biosynthesis; D012367:RNA, Viral / Q000737:chemistry / Q000378:metabolism*; D012270:Ribosomes / Q000378:metabolism*
chemical_list: D000067556:Internal Ribosome Entry Sites; D010445:Peptide Elongation Factors; D012367:RNA, Viral
keywords: IGR IRES RNA; biochemistry; pseudoknot; pseudotranslocation; translation initiation; viruses