Figure 4: Effect of RNA structure on the HIV-1 mutation rate.

(a) Mapping of the shuttle vector spontaneous mutations in the env RNA structure model. Nucleotide substitutions are represented with red squares. Regions encoding gp120 and gp41 are separated with a black line. Short dashed lines delimit the following regions in the structure: SP stem (1), region encoding the gp120 OA domains (2), Rev-responsive element (RRE, 3), and a multi stem-loop structure identified in gp41 (SL, 4). For each, the pie chart indicates the fraction of sites forming base pairs, considering only sites for which the pairing status has >90% chance of being conserved across HIV-1 subtypes. (b) In vitro mutation rate of the HIV-1 RT using a stem-like template RNA obtained from PSTVd (red) versus a randomized sequence (blue). Each dot represents an individual replicate and the horizontal bars the mean rate. A list of mutations and their location is provided in Supplementary Data 5 (PSTVd) and Supplementary Data 6 (randomized).