HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome

Mouzakis, Kathryn D.; Lang, Andrew L.; Vander Meulen, Kirk A.; Easterday, Preston D.; Butcher, Samuel E.

In light of the local stability hypothesis, we can re-examine data from prior studies that investigated trends between thermodynamic stability of the HIV-1 stem-loop and frameshift efficiency (30, 44, 45) . Indeed, we find that these results are generally consistent with local stability being the primary determinant in frameshift efficiency. For example, Bidou et al. Mutations in the frameshift site that arise in response to cytotoxic T-cell escape (74) and protease inhibitor resistance (75, 76) are also consistent with our results. Prado et al. (74) investigated the frameshift efficiency of four HIV-1 strains with mutations in the frameshift site. In this study, the only mutation that produced a significant change (decrease) in frameshift efficiency was one with a decreased local stability due to disruption of the first base pair in the stem-loop. Nijhuis et al. If the local stability of 3-4 bp is sufficient to determine frameshift efficiency, why does the HIV-1 frameshift site stem-loop contain 11 Watson-Crick base pairs? We can see two possible explanations for this. First, the additional base pairs ensure that the stem-loop has a high probability of folding and cannot be out-competed by suboptimal folds, which can severely impact HIV replication (77) . In the >9100-nt genome, there are a total of only 11 helices that are equal or larger in size (54) . Second, the additional base pairs serve to cooperatively stabilize the base pairs at the base of the stem. These effects may explain why severely truncated constructs produce lower frameshift efficiencies compared to stem-loops with identical local stability (MS9 versus WT, MS16 versus MS17). Cooperative stabilization of local stability may also explain why severe truncations of a hairpin downstream of the Simian retrovirus type-1 (SRV-1) slippery site result in lower frameshift efficiency (78) .