Eukaryotic Initiation Factor 3 Interactions with 5′ and 3′ RNA structures of the Barley Yellow Dwarf Virus Facilitate a Non‐Canonical Translation Mechanism

Abstract

Barley Yellow Dwarf Virus (BYDV) is a positive strand RNA plant virus that translates without using a 5′ 7‐methylguanosine cap or a 3′ poly‐adenosine tail that are required for the canonical translation mechanism used by most mRNA. BYDV’s non‐canonical translation relies on RNA structures in the 5′ and 3′ untranslated regions (UTRs) that recruit eukaryotic initiation factors (eIFs) and ribosomes. Using a combination of biophysical, biochemical and chemical probing techniques, we have measured direct binding of eukaryotic initiation factors (eIFs) to BYVD 5′ and 3′ UTRs and probed binding sites. Our data show that one of the initiation factors, eIF3, can bind tightly, specifically, and simultaneously to structures in both 5′ and 3′ UTRs. This suggests that eIF3’s mechanistic role includes stabilization of the long‐distance RNA‐RNA interaction and the transfer of 3′‐bound factors/complexes to the 5′ UTR. Further work with RNA chemical probing has identified regions of the BYDV UTRs that interact with eIF3. This data highlights commonalities between BYDV structures and structures found in other viruses (e.g. Hepatitis C virus) and cellular mRNAs (e.g. c_JUN mRNA).Support or Funding InformationNSF MCB‐1902054 to Dixie J. Goss, NSF IGERT‐0965983 to Hunter College