title: The cap-binding translation initiation factor, eIF4E, binds a pseudoknot in a viral cap-independent translation element.
abstract: Eukaryotic initiation factor eIF4E performs a key early step in translation by specifically recognizing the m⁷GpppN cap structure at the 5' end of cellular mRNAs. Many viral mRNAs lack a 5' cap and thus bypass eIF4E. In contrast, we reported a cap-independent translation element (PTE) in Pea enation mosaic virus RNA2 that binds and requires eIF4E for translation initiation. To understand how this uncapped RNA is bound tightly by eIF4E, we employ SHAPE probing, phylogenetic comparisons with new PTEs discovered in panico- and carmoviruses, footprinting of the eIF4E binding site, and 3D RNA modeling using NAST, MC-Fold, and MC-Sym to predict a compact, 3D structure of the RNA. We propose that the cap-binding pocket of eIF4E clamps around a pseudoknot, placing a highly SHAPE-reactive guanosine in the pocket in place of the normal m⁷GpppN cap. This reveals a new mechanism of mRNA recognition by eIF4E.
authors.affiliation: Plant Pathology Department, and Biochemistry, Biophysics, and Molecular Biology Department, Iowa State University, Ames, IA 50011, USA.
authors.forename: Zhaohui
authors.initials: Z
authors.lastname: Wang
authors.forename: Marc
authors.initials: M
authors.lastname: Parisien
authors.forename: Kay
authors.initials: K
authors.lastname: Scheets
authors.forename: W Allen
authors.initials: WA
authors.lastname: Miller
mesh_terms: D020413:3' Untranslated Regions; D001483:Base Sequence; D001665:Binding Sites; D002474:Cell-Free System; D003198:Computer Simulation; D039561:Eukaryotic Initiation Factor-4E / Q000737:chemistry*; D017930:Genes, Reporter; D049409:Luciferases, Firefly / Q000235:genetics / Q000378:metabolism; D008274:Magnesium / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010940:Plant Proteins / Q000737:chemistry*; D011485:Protein Binding; D014176:Protein Biosynthesis; D012328:RNA Viruses / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry*; D011994:Recombinant Proteins / Q000737:chemistry*; D014908:Triticum
chemical_list: D020413:3' Untranslated Regions; D039561:Eukaryotic Initiation Factor-4E; D010940:Plant Proteins; D012333:RNA, Messenger; D011994:Recombinant Proteins; D049409:Luciferases, Firefly; D008274:Magnesium