Figure 3.

Secondary structure model of the SIVmac239 5′ end of gag coding region, accordingly the model described by Weill et al., (2010). (A) The conserved structural elements forming pairings are designated P1 through P8. The three AUG in frame, initiation codons yielding three isoforms of the Gag, are indicated by red zones. Highlighted in a green box are indicated the elements P6 and P7 that were mutated in this work. The corresponding 5′ end of gag 45-269 and gag 76-123 minigenes are indicated by green arrows and boxes. (B) Schematic drawing of the secondary structure of P6 and P7 RNA elements showing the nucleotides involved in pairing (green) as well as the AUG initiation code location (red) as illustrated by the VARNA program (Darty et al., 2009). (C) Alignment of SIVmac239 gag sequence containing the P6 and P7 elements with the corresponding sequence of SIVmac251 gag (GenBank AY588946) that was used to establish the structural model described elsewhere (Weill et al., 2010). (D) Alignment of the same gag regions present in YF17D/SIV Gag_45-269 and the mutated version virus YF17D/SIV GagΔIRES. The mutated nucleotides in YF infectious clone are shown in red. Nucleotide differences between the original SIV virus and recombinant YF17D/SIV viruses due to codon optimization are indicated in blue.