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.

The genus Alphavirus encompasses approximately 30 described species, many of which infect humans and livestock, causing rashes, painful arthritis, fever and potentially fatal encephalitis (reviewed in reference 47; see reference 48 for a phylogeny). Transmission is generally via arthropods such as mosquitoes. The single-stranded positive sense genomic RNA is about 11-12 kb long and contains two long ORFs separated by a short non-coding sequence ( Figure 1A ). The 5 0 -proximal ORF codes for the non-structural proteins nsP1-nsP2-nsP3-nsP4 while the 3 0 -proximal ORF, which is translated from a subgenomic RNA, codes for the structural polyprotein C-E3-E2-6K-E1 and, via programmed ribosomal frameshifting, C-E3-E2-TF (49) . In SINV, Venezuelan equine encephalitis (VEEV), eastern equine encephalitis (EEEV), western equine encephalitis (WEEV) and related alphaviruses, a UGA stop codon separates the coding sequence for nsP4 (RNA-dependent RNA polymerase, RdRp) from the coding sequence for nsP123 (30, 50) . In contrast, the salmonid alphaviruses lack the UGA stop codon while, for alphaviruses in the Semliki Forest complex, the stop codon tends to be present in some but not all strains even within a single species, possibly as a result of conflicting selective forces in alternating arthropod and vertebrate hosts (passaging in cell culture may also drive selection for or against a stop codon at this location; see ref. 51 and references therein).