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 various motifs that stimulate RT in eukaryotic cells have been previously classified by Beier and Grimm and by Harrell et al. (34, 81) . Beier and Grimm define the classes Type I (generally UAG-CAA-UYA; includes tobamovirus replicase, and benyvirus and pomovirus CP extension), Type II (generally UGA-CGG or UGA-CUA; includes alphavirus replicase, tobravirus, pecluvirus, furovirus and pomovirus replicase, and furovirus CP extension), and Type III (generally UAG-G, plus a compact pseudoknot in gammaretroviruses and possible but as yet relatively uncharacterized structures in the luteoviruses and tombusviruses). There are exceptions to the rule (e.g. enamovirus UGA-G, various pomovirus cases with atypical stop codons, and so on). One reason for this may be that the required level of RT may vary between different viruses, and may also be modulated by other sequence elements (e.g. 5 0 nucleotide and/or amino acid context) so that, in certain cases, deviations from one of the 'canonical' RT motifs may be tolerated. With this proviso, our results suggest that the definition of the Type II motif should, in general though perhaps not ubiquitously, be modified to include a 3 0 RNA structure component. Our discovery in alphaviruses and phylogenetically supported predictions for many plant viruses and the Drosophila gene kelch, together with the small number of previously identified cases of structure-stimulated RT, now suggest that 3 0 RNA structures as a component of efficient RT cassettes in eukaryotes (especially those that lack a CAR-YYA tobamovirus-like stimulator), rather than being exceptional, may in fact be the norm.