Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome

Abstract

HIV-1 deleted for the vif accessory gene encapsidates the cellular cytidine deaminase APOBEC3G. Upon infection, the encapsidated APOBEC3G induces G→A mutations in the viral reverse transcripts. The G→A mutations result either from C→U deamination of the minus strand or deamination of both strands followed by repair of the plus strand. We report here that minus-strand deamination occurred over the length of the virus genome, preferentially at CCCA sequences, with a graded frequency in the 5′→3′ direction. APOBEC3G induced previously undetected C→T mutations in the 5′ U3 and the primer-binding site, both of which become transiently single-stranded during reverse transcription. In vitro, APOBEC3G bound and deaminated single-stranded DNA (ssDNA) but not double-stranded DNA (dsDNA) or DNA-RNA hybrids. We propose that the requirement for ssDNA accounts for the minus-strand mutations, the 5′→3′ graded frequency of deamination and the rare C→T mutations.