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.

Interestingly, although RT for the VEEV and SINV cassettes was much more efficient in cell culture than in vitro, there was little difference between the two systems for the MuLV RT cassette ( Figure 6 ). While the action of some cellular trans-acting stimulatory factor cannot be ruled out (albeit presumably not interacting with the loop region, given the increased RT observed when the loop was deleted), other possible explanations include: (i) the different stop codons and nucleotide contexts involved (UGA-C in VEEV and SINV; UAG-G in MuLV) and hence the different pools of potential stop codon-decoding tRNAs and (ii) the nature of the 3 0 structure (a compact pseudoknot in MuLV but an extended stem-loop in VEEV and SINV) with possible consequences for the ease with which the structure may fold in different environments. Similar differences in RT efficiency between in vitro and cell culture systems were noted for Colorado tick fever coltivirus which, like SINV and VEEV, utilizes a UGA RT codon with a predicted 3 0 -adjacent stem-loop structure (65) .