A Highly Defective HIV-1 Group O Provirus: Evidence for the Role of Local Sequence Determinants in G → A Hypermutation during Negative-Strand Viral DNA Synthesis

Abstract

The sequence of 2350 nucleotides in the env and IN regions of a group O HIV-1 genome which is hypermutated throughout its entirety was compared to the equivalent sequence of a nonhypermutated genome from the same isolate. Almost 30% of G residues were affected by G → A transitions. As previously reported, transitions occurred mainly at GpA and GpG dinucleotides, with a marked preference for changes of the 5′-proximal G residues in poly(G) stretches. Inspection of the sequences around the hypermutation sites revealed no bias when the mutation was at the 5′ G residue of a GpG dinucleotide. In contrast, a preferred context for hypermutation at the 3′ G (or at single G residues) could be defined. In addition to a preference for A residues immediately downstream of hypermutated 3′ G residues, C residues were underrepresented in these positions. The observed context fits well with a model whereby G → A mutation occurs by a combination of dislocation mutagenesis at GpA dinucleotides and direct misincorporation of dTTP at the 5′ G of GpG dinucleotides. Furthermore, both runs of six G residues present in the polypurine tracts (PPTs) had escaped hypermutation, despite the fact that 95% of runs of three G residues contained at least one G → A transition. This finding suggests that genomes with hypermutated PPT motifs had been selected against and provides direct evidence that hypermutation occurs during negative-strand DNA synthesis. © 1995 Academic Press. All rights reserved.