The Cap-Binding Translation Initiation Factor, elF4E, Binds a Pseudoknot in a Viral Cap-Independent Translation Element

Eukaryotic initiation factor elF4E performs a key early step in translation by specifically recognizing the m 7 GpppN cap structure at the 5' end of cellular mRNAs. Many viral mRNAs lack a 5' cap and thus bypass elF4E. In contrast, we reported a cap-independent translation element (PTE) in Pea enation mosaic virus RNA2 that binds and requires elF4E for translation initiation. To understand how this uncapped RNA is bound tightly by elF4E, we employ SHAPE probing, phylogenetic comparisons with new PTEs discovered in panico- and carmoviruses, footprinting of the elF4E 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 elF4E clamps around a pseudoknot, placing a highly SHAPE-reactive guanosine in the pocket in place of the normal m 7 GpppN cap. This reveals a new mechanism of mRNA recognition by elF4E.