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.

With respect to the non-structural polyprotein, SINV and Aura virus (AURAV) form a separate clade from VEEV, WEEV and EEEV but, again, the conservation analysis revealed striking tandem conservation peaks 3 0 of the RT site ( Figure 1B ) and, again, the conservation peaks corresponded to sequences with the potential to base pair to form an RNA structure-this time comprising an 11 bp stem with a 1 nt asymmetric 3 0 bulge, a 12 nt 'spacer' from the RT stop codon, and a 154 nt 'loop' region ( Figure 2 ). For those alphavirus species where there appears to be a constant flux between presence and absence of the RT stop codon, it is not unreasonable to suspect that the 3 0 structure, if any, will be present whether or not the stop codon is present in any particular sequence. However, although we found the potential for conserved RNA stems to form in a number of these species (e.g. Ross River, getah, Semliki Forest and chikungunya viruses; Figure 3 and Supplementary Data), the range of divergences in the available sequence data proved inadequate to obtain supporting evidence from an analysis of conservation at synonymous sites.