Protein binding in an mRNA 5′-UTR sterically hinders translation

Structures in the 5' untranslated regions (UTRs) of mRNAs can physically modulate translation efficiency by impeding the scanning ribosome or by sequestering the translational start site. We assessed the impact of stable protein binding in 5'- and 3'-UTRs on translation efficiency by targeting the MS2 coat protein to a reporter RNA via its hairpin recognition site. Translation was assessed from the reporter RNA when coexpressed with MS2 coat proteins of varying affinities for the RNA, and at different expression levels. Binding of high-affinity proteins in the 5'-UTR hindered translation, whereas no effect was observed when the coat protein was targeted to the 3'-UTR. Inhibition of translation increased with coat protein concentration and affinity, reaching a maximum of 50%-70%. MS2 proteins engineered to bind two reporter mRNA sites had a stronger effect than those binding a single site. Our findings demonstrate that protein binding in an mRNA 5'-UTR physically impedes translation, with the effect governed by affinity, concentration, and sterics.