The SL-I structural element of the 3′ UTR region of West Nile virus participates in the regulation of viral translation

The genome of West Nile virus (WNV) is a positive, ssRNA molecule, which encodes a single ORF flanked by UTRs (5' and 3' UTRs). These UTRs are enriched with structural RNA elements that play critical roles in the viral cycle, including translation, replication and encapsidation. The 3' UTR is crucial for translation control by the combined enhancer and repressor activities of different structural elements. This manuscript provides new roles for the 3' UTR SL-I element as a translation inhibitor in WNV in cis. This inhibitory effect is primarily observed in a cap-dependent translation context, most likely affecting multi-round translation efficiency. The molecular mechanism underlying this phenomenon appears to involve the recruitment of the 40S ribosomal subunit by the 3' UTR. We have previously demonstrated that the 3' UTR recruits the 40S subunit at two independent sites and influences its proper positioning at the 5' UTR. The present work identifies the SL-I element as a critical regulator of WNV translation at late stages of protein synthesis. This can be due, at least partially, to the modulation of the 40S positioning at the 3' UTR, as detected by selective 2'-hydroxyl acylation analysed by primer extension (SHAPE) analyses. These findings provide new insights into the role of the 3' UTR SL-I element in translation regulation and suggest that WNV translation is a finely tuned process dependent on the coordinated and well-balanced interplay of multiple partners.