APOBEC3D and APOBEC3F Potently Promote HIV-1 Diversification and Evolution in Humanized Mouse Model

Several APOBEC3 proteins, particularly APOBEC3D, APOBEC3F, and APOBEC3G, induce G-to-A hypermutations in HIV-1 genome, and abrogate viral replication in experimental systems, but their relative contributions to controlling viral replication and viral genetic variation in vivo have not been elucidated. On the other hand, an HIV-1-encoded protein, Vif, can degrade these APOBEC3 proteins via a ubiquitin/proteasome pathway. Although APOBEC3 proteins have been widely considered as potent restriction factors against HIV-1, it remains unclear which endogenous APOBEC3 protein(s) affect HIV-1 propagation in vivo. Here we use a humanized mouse model and HIV-1 with mutations in Vif motifs that are responsible for specific APOBEC3 interactions, DRMR/AAAA (4A) or YRHHY/AAAAA (5A), and demonstrate that endogenous APOBEC3D/F and APOBEC3G exert strong anti-HIV-1 activity in vivo. We also show that the growth kinetics of 4A HIV-1 negatively correlated with the expression level of APOBEC3F. Moreover, single genome sequencing analyses of viral RNA in plasma of infected mice reveal that 4A HIV-1 is specifically and significantly diversified. Furthermore, a mutated virus that is capable of using both CCR5 and CXCR4 as entry coreceptor is specifically detected in 4A HIV-1-infected mice. Taken together, our results demonstrate that APOBEC3D/F and APOBEC3G fundamentally work as restriction factors against HIV-1 in vivo, but at the same time, that APOBEC3D and APOBEC3F are capable of promoting viral diversification and evolution in vivo.

多种载脂蛋白B mRNA编辑酶催化多肽3（APOBEC3）家族蛋白，尤其是APOBEC3D、APOBEC3F与APOBEC3G，可诱导人类免疫缺陷病毒1型（HIV-1）基因组发生G到A超突变，并在实验体系中阻断病毒复制；然而其在体内对病毒复制调控与病毒遗传变异的相对贡献尚未阐明。另一方面，HIV-1编码的病毒感染因子（Vif）可通过泛素-蛋白酶体途径降解此类APOBEC3蛋白。尽管APOBEC3蛋白已被广泛认为是抗HIV-1的强效宿主限制因子，但目前仍不清楚哪种或哪些内源性APOBEC3蛋白会在体内影响HIV-1的传播。本研究利用人源化小鼠模型，以及携带负责介导与特定APOBEC3蛋白相互作用的Vif基序突变的HIV-1毒株（DRMR/AAAA（4A）或YRHHY/AAAAA（5A）），证实内源性APOBEC3D、APOBEC3F与APOBEC3G在体内发挥强效抗HIV-1活性。研究同时发现，4A突变型HIV-1的生长动力学与APOBEC3F的表达水平呈显著负相关。此外，对感染小鼠血浆中的病毒RNA进行单基因组测序分析显示，4A突变型HIV-1发生了特异性且显著的遗传多样化。进一步研究还在4A突变型HIV-1感染的小鼠中特异性检测到了一种可同时利用CCR5与CXCR4作为病毒进入共受体的突变毒株。综上，本研究结果表明，APOBEC3D、APOBEC3F与APOBEC3G在体内作为抗HIV-1的宿主限制因子发挥核心作用；同时，APOBEC3D与APOBEC3F亦可在体内促进病毒的遗传多样化与进化。