HIV-1 evolution driven by intracellular defenses

描述（由申请人提供）：逆转录病毒设计了许多策略来逃避旨在预防逆转录病毒感染的细胞机制。HIV-1表达Vif，一种抵消胞苷脱氨酶APOBEC3G和APOBEC3F抗病毒活性的蛋白质。然而，HIV-1基因组的核苷酸组成表明，对宿主介导的病毒cDNA脱胺的保护可能不是绝对的。在初步研究中，我们发现在体内可以检测到编码不能降解APOBEC3G、APOBEC3F或两者的蛋白的vif基因。Vif功能的丧失被定位为单核苷酸取代。这些研究表明，Vif功能的自然变异可能深刻影响HIV-1感染个体内病毒序列进化的程度和方向。

DESCRIPTION (provided by applicant): Retroviruses have devised a number of strategies to evade cellular mechanisms aimed at preventing retroviral infection. HIV-1 expresses Vif, 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.