Restriction factors are a branch of the innate immune system that potently inhibit viral replication. A number of viral pathogens encode accessory proteins that can antagonize restriction factors, which allows viral dissemination in host. Over evolutionary time, restriction factors evolve to escape viral antagonists, limiting the host range of viruses. In turn, viruses can adapt to these changes and cross species into new hosts by rapid evolution of accessory proteins. The primate APOBEC3 cytidine deaminases are arguably the most extensively studied family of restriction factors. They block the spread of retroviruses and retroelements by hypermutating their genomes and have the potential to inhibit the AIDS virus, HIV-1. However, the HIV-1 accessory protein Vif potently suppresses APOBEC3 enzymes by targeting them for degradation by the host ubiquitin-proteasome system. Vif is conserved in all existing lentiviruses, including those of primate origin such as SIV. Adaptation in Vif has allowed cross-species transmission of SIV from monkeys to chimpanzees and underlies the ancient origin of HIV-1. Accordingly, the APOBEC3-Vif interaction is an archetypical case of a restriction factor and viral antagonist. In principle, host escape by mutation in APOBEC3 and viral adaptation in Vif could occur through changes in protein binding interfaces, insertion of short-linear interaction motifs by gene loss and overprinting or mutation of allosteric sites. However, there are no co-structures of Vif bound to any APOBEC3 family member to document these phenomena, so the detailed mechanisms are unclear. In this project, we will overlay sequencing and viral infectivity data accumulated at critical points during the evolutionary history of HIV-1 with structures of corresponding Vif-A3 complexes. Cutting edge methods, such as Fab-assisted single-particle cryo-EM, will be used to resolve these structures. The functional significance of the observed interactions will be tested by mutagenesis in conjunction with viral infectivity assays in cells and Vif ubiquitination activity assays in vitro. This project will provide a paradigmatic example of the biochemistry, structure, and molecular mechanisms of molecular arms races that are general phenomena of host-pathogen interactions.
