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 long 'loop' length of the predicted structures is noteworthy. While long-distance base pairings have been demonstrated to play important regulatory roles in RNA viruses (reviewed in ref. 75) , the distances involved in the RT base pairings identified here are very much smaller and a genome-scale regulatory role seems unlikely. Furthermore, our loop-deletion mutant promoted even higher RT than the WT construct, suggesting that the presence of a long loop region, or any sequence motifs therein, play little if any role in stimulating efficient RT. Thus, we hypothesize that evolutionary selection simply acts to place the 3 0 component of the stem in a convenient location (e.g. with regards to minimizing interference with the encoded amino acid sequence). Although we refer to the region between the two components of the stem as a 'loop', it should not be taken to imply that this region does not fold. In fact the region generally is predicted to fold, and the fact that it can fold may indeed be functionally important-perhaps just to provide stability to the basal stem. However, in most cases, the nature of the fold seems to be relatively unimportant as it is not well-conserved between related sequences.