Juxtacap Nucleotide Sequence Modulates eIF4E Binding and Translation

Abstract

ABSTRACTmRNA translation is an energetically costly activity required for almost all biological processes. The multiprotein complex eIF4F, which bridges the 5’ cap and the polyA tail through eIF4E and eIF4G, respectively, is necessary for efficient translation initiation of most mRNAs and is an important target of translational control. Previous work suggests that cap-proximal nucleotides can modulate eIF4E binding to mRNAs, but the effect of specific cap-proximal nucleotide sequences on eIF4E recruitment and the ultimate consequences for translation remain unknown. Using RNA Bind-n-Seq on a model 5’ UTR, we systematically identify eIF4E-intrinsic cap-proximal nucleotide binding preferences. mRNAs with highly-bound motifs are translated well in a cell-free system, whereas those with low-eIF4E-binding motifs are not. However, eIF4E juxtacap motif preferences do not dictate the ribosome occupancy of endogenous mRNAs in cells, suggesting that the effect of juxtacap sequence on eIF4E binding and translation is mRNA-context-dependent. Accordingly, a single downstream point mutation that disrupts a predicted base pair with a preferred juxtacap nucleotide increases translation. The juxtacap sequence is a previously unappreciated determinant of eIF4E recruitment to mRNAs, and we propose that differences in mRNA 5’ end accessibility defined by the juxtacap sequence are important for establishing translational efficiency.