Multiple APOBEC3 restriction factors for HIV-1 and one Vif to rule them all

Abstract

Several members of the APOBEC3 family of cellular restriction factors provide intrinsic immunity to the host against viral infection. Specifically, APOBEC3DE, APOBEC3F, APOBEC3G, and APOBEC3H haplotypes II, V, and VII provide protection against HIV-1Δvif through hypermutation of the viral genome, inhibition of reverse transcription, and inhibition of viral DNA integration into the host genome. HIV-1 counteracts APOBEC3 proteins by encoding the viral protein Vif, which contains distinct domains that specifically interact with these APOBEC3 proteins to ensure their proteasomal degradation, allowing virus replication to proceed. Here, we review our current understanding of APOBEC3 structure, editing and non-editing mechanisms of APOBEC3-mediated restriction, Vif-APOBEC3 interactions that trigger APOBEC3 degradation, and the contribution of APOBEC3 proteins to restriction and control of HIV-1 replication in infected patients.

Keywords: APOBEC3F; APOBEC3G; APOBEC3H; Vif; restriction factor.

Figure 1. Functional roles of the APOBEC family of proteins

Each APOBEC protein is shown, containing one or two conserved Zn²⁺ coordinating catalytic domains (green); active catalytic domains (red star). Numbers correspond to length of amino acid sequence. Both the catalytically active and non-active domains contain a conserved sequence His-X-Glu-X_23-28-Pro-Cys-X_2-4Cys, in which X represents any amino acid. Ch. 1, 6, 12, and 22 refer to human chromosome numbers.

Figure 2. Mechanism of action of A3G during infection with HIV-1Δvif virions

In virus producer cells, in the absence of a functional Vif protein, A3G (purple hexagon) is packaged into the viral particles. In the target cell, A3G exerts its antiviral activity by inhibiting reverse transcription, blocking integration, and inducing G-to-A hypermutation. In the hypermutation process, A3G mainly deaminates deoxycytidines in minus-strand DNA to deoxyuridines, which ultimately results in G-to-A hypermutation in the plus-strand DNA. Although hypermutated viral DNA may integrate into the host chromosomal DNA to form proviruses, they are largely defective.

Figure 3. Structural comparison of APOBEC family members' crystal structures

(A) The APOBEC proteins have a canonical deaminase core composed of five β strands and six α helices. As a prototype, the wild-type A3G-CTD monomer structure (PDB entry 3IQS) with the indicated α-helices, β-strands and loops is shown in a ribbon representation. Loop 3, 5, and 7 (L3, L5, and L7, respectively) are shown in blue, orange, and magenta colors, respectively. (B) The active site of A3G-CTD. A zinc atom is coordinated by the three residues H257, C288 and C291, and indirectly via a water molecule (view occluded by zinc atom) with E259. (C) Comparison of ribbon representations of A2 (PDB entry 2NYT), A3A (PDB entry 2M65), A3C (PDB entry 3VOW), A3F-CTD (PDB entry 4IOU), A3G-CTD (PDB entry 3ISQ) and A3G-CTD-2K3A (PDB entry 3IR2) crystal structures. The β1/β2 region is highlighted (blue oval) to emphasize similarities and the conformational plasticity in the β1-β2 loop region across all A3 proteins. The α1 helix (red box) exhibits a similar orientation across all A3 proteins but differs in A2 crystal structure. The corresponding loops (L3, L5, and L7) in Fig. 3A are also labeled in A3A and A3G structures.

Figure 4. Ribbon diagrams and surface representations of the A3C, A3F-CTD and A3G-NTD model structures

(A) Ribbon diagrams of the structure of A3C (PDB entry 3VOW), A3F-CTD (PDB entry 4IOU) and A3G-NTD, a possible model generated through homology modeling based on the A3C structure (PDB entry 3VOW) by using SwissModel Worksplace (http://swissmodel.expasy.org/), ^; showing the known Vif-binding residues labeled in red (critical) and in pink (less critical). The equivalent critical residues in A3G are shown in yellow in A3C and A3F-CTD. The designations of critical and less critical residues are based on mutational analyses. ^{; ; ; ;} (B) Surface representation of the Vif-binding groove delineated by the dashed line in A3C (PDB entry 3VOW), A3F-CTD (PDB entry 4IOU), and A3G-NTD depicted with the same colors used as in (A).

Figure 5. The role of CBF-β in Vif-mediated polyubiquitination and degradation of A3G

Schematic depiction of different components of the A3G polyubiquitination and degradation pathway. CUL5 (scaffold) directly interacts with EloC (a component of the EloB/C adaptors) and RING finger protein 2 (RBX2; regulator of the stepwise cascade of substrate polyubiquitination), which also associates with E2 (ubiquitin conjugating enzyme). Vif (a substrate receptor for A3G) associates with the CUL5-EloB/C-RBX2-E2 complex by binding directly to CUL5 via a conserved Zinc ion coordinating HCCH motif and to EloC via its SOCS box motif. A3G is recruited by Vif to this complex. Subsequently, A3G is polyubiquitinated and is targeted for 26S proteasomal degradation. CBF-β, a recently discovered cofactor of Vif, has been proposed to be required to facilitate the Vif-CUL5 interaction and to suppress the antiviral activity of A3G in HIV-1 infection. ^;