Characterization of Maize Necrotic Streak Virus (MNeSV) mRNA 3′ Cap Independent Translation Enhancers (3′ CITE) Binding with Eukaryotic Initiation Factors

Abstract

5′ m7GpppN cap and the 3′ poly adenosine (A) tail of eukaryotic mRNAs are key elements for recruiting translation initiation machinery. Unlike host mRNAs, many viruses lack those elements and yet they are translated efficiently. Plant viruses, in particular, have complex structures within their untranslated regions (UTR) that allow them to bypass some cellular translation control steps. In Maize necrotic streak virus (MNeSV) 3′ UTR, an I‐Shaped RNA Structure (ISS) has been reported to mediate the virus translation initiation progress. The details of how these structures mediate translation are not well understood. Biophysical methods were applied to study the binding of 3′ ISS with eIFs. With fluorescence quenching and anisotropy techniques, it was found that eIF4A‐eIF4B complex increased binding affinity of eIF4F with 3′ISS four fold (from Kd =~173±34 nM to Kd =~48±11 nM). The enhanced binding affinity was not caused by the helicase activity of the eIF4A‐eIF4B complex. Using mutants of the ISS, translational efficiency was found not to correlate with binding affinity to eIF4F. ISS‐iA/B is a single nucleotide mutant of ISS but has a different predicted secondary structure with ISS. ISS‐iA/B′s binding affinity to eIF4F was similar with wild‐type, whereas translation efficiency was lower. Binding of wild‐type ISS with eIF4F was both enthalpically and entropically favorable, while ISS‐iA/B binding with eIF4F was only enthalpically favorable. Kinetics association rate, k1, for ISS binding to eIF4F was found to be 30.08 s−1μm−1 and the dissociation rate, k−1, was found to be 5.08 s−1. These rates are comparable to binding of m7GTP‐capped RNA with eIF4F. Both thermodynamics and kinetics indicate that factors in addition to eIF4F are necessary for MNeSV to outcompete host cell mRNA for translation.Support or Funding InformationGrant Fund NSF MCB1513737