Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity

Abstract

SUMMARY HIV-1 encodes the accessory protein Vif, which hijacks a host Cullin-RING ubiquitin ligase (CRL) complex as well as the non-canonical cofactor CBFβ, to antagonize APOBEC3 antiviral proteins. Non-canonical cofactor recruitment to CRL complexes by viral factors, to date, has only been attributed to HIV-1 Vif. To further study this phenomenon, we employed a comparative approach combining proteomic, biochemical, structural, and virological techniques to investigate Vif complexes across the lentivirus genus, including primate (HIV-1, SIVmac) and non-primate (FIV, BIV, and MVV) viruses. We find that CBFβ is completely dispensable for the activity of non-primate lentiviral Vif proteins. Furthermore, we find that BIV Vif requires no cofactor, and that MVV Vif requires a novel cofactor, Cyclophilin A (CYPA), for stable CRL complex formation and anti-APOBEC3 activity. We propose modular conservation of Vif complexes allows for potential exaptation of novel functions through the acquisition of non-CRL associated host cofactors while preserving anti-APOBEC3 activity.

Feline Immunodeficiency Virus Vif N-Terminal Residues Selectively Counteract Feline APOBEC3s

“…However, HIV-1 and SIV Vifs need the cofactor CBF-␤ to stabilize and form this complex (51,52), whereas FIV and other nonprimate lentiviruses (e.g., maedi-visna virus [MVV], caprine arthritis encephalitis virus, and bovine immunodeficiency virus [BIV]) Vifs do not require CBF-␤ to induce A3 degradation (53)(54)(55)(56). A recent study demonstrated that BIV Vif appears to operate independently of any cofactors, whereas MVV Vif hijacks cellular cyclophilin A as a cofactor in reconstituting the E3 ligase complex (53). Whether FIV Vif recruits any additional protein is unclear.…”

Conserved Interaction of Lentiviral Vif Molecules with HIV-1 Gag and Differential Effects of Species-Specific Vif on Virus Production

“…The Vif molecules of lentiviruses are important for viral replication, inactivating host antiviral factors of cytidine deaminases (APOBEC3) (32,(72)(73)(74). These lentiviral Vif proteins have evolved to use different strategies for overcoming their host's APOBEC3 (7,38,39,75). HIV-1 Vif assembles the CRL5 E3 ubiquitin ligase to induce the polyubiquitination and proteasome-mediated degradation of APOBEC3 (17,30,(76)(77)(78)(79)(80); this assembly is regulated by CBF␤ (14,(23)(24)(25)(26)(27)(28)39).…”

“…HIV-1 Vif assembles the CRL5 E3 ubiquitin ligase to induce the polyubiquitination and proteasome-mediated degradation of APOBEC3 (17,30,(76)(77)(78)(79)(80); this assembly is regulated by CBF␤ (14,(23)(24)(25)(26)(27)(28)39). In contrast, BIV Vif assembles with the CRL2 E3 ubiquitin ligase to induce the polyubiquitination and proteasome-mediated degradation of bovine APOBEC3, and BIV Vif activity is not regulated by CBF␤ (7,38,39). Surprisingly, we have discovered that BIV Vif is a potent inhibitor of HIV-1 replication, and this inhibition was manifested even in the absence of the antiviral factor APOBEC3.…”

“…This lentivirus also encodes a Vif protein of 198 amino acids (37). BIV Vif is required to overcome the antiviral activity of bovine APOBEC3 proteins (38,39). Although the general strategy for inhibiting APOBEC3 proteins through ubiquitination is conserved between HIV-1/simian immunodeficiency virus (SIV) and BIV, the cellular requirements and molecular mechanisms involved differ substantially (7,38,39).…”

“…For example, BIV Vif recruits Cul2-CRL2 rather than Cul5-CRL5 E3 ubiquitin ligase (7,40). Furthermore, unlike regulation of HIV-1 Vif, the regulation of BIV Vif function does not involve CBF␤ (7,38,39). During lentiviral evolution, the Vif-APOBEC3 interaction has been mainly been species specific: BIV Vif cannot induce the degradation of human APOBEC3 proteins, and HIV-1 Vif cannot overcome bovine APOBEC3 proteins (39,41).…”