HIV-1 evolution driven by intracellular defenses

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Retroviruses have devised a number of strategies to evade cellular mechanisms aimed at preventing retroviral infection. HIV-1 expressesVif, a protein that counteracts the antiviral activity of the cytidine deaminases APOBEC3G and APOBEC3F. The nucleotide composition of the HIV-1 genome suggests, however, that protection from host-mediated viral cDNA deamination may not be absolute. In preliminary studies, we showed that vif genes encoding proteins that fail to degrade APOBEC3G, APOBEC3F or both can be detected in vivo. The loss of Vif function was mapped to single nucleotide substitutions. These studies indicate that natural variation in Vif function may profoundly impact the extent and direction of viral sequence evolution within HIV-1 infected individuals. The experiments proposed herein will determine the extent to which host mechanisms aimed to prevent retroviral infection, in fact, contribute to viral diversification and pathogenesis. We will analyze the fitness of viruses expressing Vif proteins that are closely related but differ in their ability to neutralize APOBEC3G or APOBEC3F activities. We will also test if variation in Vif function may be beneficial for viral adaptation under certain circumstances (e.g., in the presence of antiretroviral drugs) by determining whether cytidine deamination by APOBEC3G or APOBEC3F selects for certain drug resistance mutations. The pattern of hypermutations associated with partial protection from cytidine deamination will be correlated to HIV fitness. Since APOBEC3 enzymes induce hypermutations in different dinucleotide contexts the understanding of how activity against one enzyme but not the other is maintained is relevant for viral evolution. We will conduct structure function studies to determine whether domains other than the Vif SOCS box motif are necessary and essential for Vif mediated specific neutralization of APOBEC3 enzymes. Finally, we will assess the impact of reverse transcription and APOBECS-driven mutagenesis on loss of Vif function. We will determine the rate of Vif inactivation as result of either reverse transcriptase or cytidine deamination induced mutations on a single cell level using assays based on fluorescence tagged APOBEC3G degradation. Variation in Vif function may influence the pathogenicity of HIV-1 by rendering its genome more or less resistant to deaminase activity and these studies have the potential to reveal how Vif mediated protection from cytidine deamination is modulated in vivo.