Stimulation of stop codon readthrough: frequent presence of an extended 3' RNA structural element

Firth, Andrew E.; Wills, Norma M.; Gesteland, Raymond F.; Atkins, John F.

In the benyviruses-which generally have a tobamovirus-like stop codon context (i.e. UAG-CAA-UUA; however, highly divergent rice stripe necrosis virus, EU099845, has UAG-GGG-UAC), the potential was observed for a local stem-loop structure (e.g. 9 nt spacer, 12 nt stem, 8 nt loop in beet necrotic yellow vein virus, D84411; Figure 3 ), but there was insufficient sequence data to obtain strong support from the synonymous site conservation analysis ( Figure 4 ). Previous deletion experiments in beet necrotic yellow vein benyvirus have shown, incidentally, that RT efficiency is considerably reduced when sequence corresponding to codons +3 to +34 from the RT codon is deleted, even though the immediately 3 0 -adjacent nucleotide context UAG-CAA-UUA is left intact (66) . In contrast, deletion of codons +28 to +61 had little effect on RT. These results indicate that there is an additional stimulatory element within the region defined by codons +3 to +27, consistent with the predicted stem-loop structure (codons +4 to +14).