Variability in HIV-1 Transmitted/Founder Virus Susceptibility to Combined APOBEC3F and APOBEC3G Host Restriction
Authors: Gaba Amit , Yousefi Maria , Bhattacharjee Shreoshri , Chelico Linda 
Published: January 2024

Several APOBEC3 enzymes restrict HIV-1 replication by deaminating cytosine to form uracil in single-stranded proviral (-)DNA. However, HIV-1 Vif binds to APOBEC3 enzymes and counteracts their activity by inducing their proteosomal degradation. This counteraction by Vif is not complete as evidenced by footprints of APOBEC3-mediated mutations within integrated proviral genomes of people living with HIV-1. The APOBEC3 enzymes are co-ordinately expressed in CD4+T cells and relative contributions of APOBEC3s in HIV-1 restriction is not fully understood. In this study, we investigated the activity of co-expressed APOBEC3F and APOBEC3G against HIV-1 Subtype B and Subtype C Transmitted/Founder viruses. APOBEC3F and APOBEC3G when co-expressed were previously determined to form a hetero-oligomer that enables partial resistance of APOBEC3F to Vif-mediated degradation. Here, we determined that that APOBEC3F interacts with APOBEC3G through its N-terminal domain. We provide evidence that this results in protection from Vif-mediated degradation because the APOBEC3F N-terminal domain contains residues required for recognition by Vif. We also found subtype specific differences in activity of Transmitted/Founder Vifs against APOBEC3G and the APOBEC3F/APOBEC3G hetero-oligomer. HIV-1 Subtype C Vifs were more active in counteracting APOBEC3G compared to HIV-1 Subtype B Vifs when APOBEC3G was expressed alone. However, HIV-1 Subtype C Vifs were less active against APOBEC3G when APOBEC3F and APOBEC3G were co-expressed. Consequently, when APOBEC3F and APOBEC3G were expressed together HIV-1 Subtype C viruses showed a decrease in relative infectivity compared to that when APOBEC3G was expressed alone. Inspection of Vif amino acid sequences revealed that that differences in amino acids adjacent to conserved sequences influenced the Vif-mediated APOBEC3 degradation ability. Altogether, the data provide a possible mechanism for how combined expression of APOBEC3F and APOBEC3G could contribute to mutagenesis of HIV-1 proviral genomes in the presence of Vif and provide evidence for variability in the Vif-mediated degradation ability of Transmitted/Founder viruses.

Author Summary

APOBEC3 enzymes act as barriers to HIV infection by inducing cytosine deamination in proviral DNA, but their effectiveness is hindered by their counteraction by HIV Vif, which leads to APOBEC3 proteasomal degradation. The APOBEC3-Vif interaction has largely been determined using lab adapted HIV-1 Subtype B viruses and with singular APOBEC3 enzymes. Here we examined how primary isolates of HIV-1 replicated in the presence of APOBEC3F and APOBEC3G. APOBEC3F and APOBEC3G interact and this imparts partial resistance to Vif-mediated degradation. We determined that APOBEC3F interacts with APOBEC3G through its N terminal domain, and that APOBEC3F, like APOBEC3G has Vif-mediated degradation determinants in the N-terminal domain, providing a rational for protection from Vif-mediated degradation. We also demonstrate subtype-specific differences in the activity of Transmitted/Founder Vifs against APOBEC3G and the APOBEC3F/APOBEC3G hetero-oligomer. Through an analysis of Vif amino acid sequences, we identified variations influencing the Vif-mediated APOBEC3 degradation ability. This research uncovers previously unidentified mechanisms by which combined expression of APOBEC3F and APOBEC3G may contribute to HIV-1 proviral genome mutagenesis in the presence of Vif and emphasizes the contribution of amino acid variation outside of previously identified conserved regions in Vif-mediating APOBEC3 degradation.