The Highly Conserved Codon following the Slippery Sequence Supports -1 Frameshift Efficiency at the HIV-1 Frameshift Site

Mathew, Suneeth F.; Crowe-McAuliffe, Caillan; Graves, Ryan; Cardno, Tony S.; McKinney, Cushla; Poole, Elizabeth S.; Tate, Warren P.

Changing the intercodon to a UGA stop codon reduced apparent frameshift efficiency by *70% (P < 0.001), irrespective of whether the lower stem was disrupted (UGA), or restored by further substitutions in the opposing strand (UGA_U). Substituting a different stop codon (UAG for UGA) in the same position, which maintains the native structure of the lower stem, also reduced frameshifting by the same extent. Caution is warranted in interpreting these results, as the (non-frameshifted) short-form Renilla luciferase generated by this reporter, terminated at the intercodon, is truncated by 15 amino acids compared to the other constructs. The same relative results between these constructs were observed in a different bicistronic reporter system using the fluorophores EGFP and DsRed.T4 (S1 File), however [29] . Collectively, these data suggest that the GGG intercodon of the HIV-1 frameshift element influences frameshifting in at least two ways: in a minor fashion by promoting the lower stem structure and increasing the chance for −1 PRF to occur, but also more markedly by exerting another major influence that is not explained by current models of −1 PRF.