Evolution of HIV-1 Isolates that Use a Novel Vif-Independent Mechanism to Resist Restriction by Human APOBEC3G

Hypermutation, the introduction of excessive G-to-A substitutions by host proteins in the APOBEC family, can impair replication of the human immunodeficiency virus (HIV). Because hypermutation represents a potential antiviral strategy, it is important to determine whether greater hypermutation is associated with slower disease progression in natural infection. We examined the level of HIV-1 hypermutation among 28 antiretroviral-naive Kenyan women at two times during infection. By examining single-copy gag sequences from proviral DNA, hypermutation was detected in 16 of 28 individuals. Among individuals with any hypermutation, a median of 15% of gag sequences were hypermutated (range, 5 to 43%). However, there was no association between the level of gag hypermutation and the viral load or CD4 count. Thus, we observed no overall relationship between hypermutation and markers of disease progression among individuals with low to moderate levels of hypermutation. In addition, one individual sustained a typical viral load despite having a high level of hypermutation. This individual had 43% of gag sequences hypermutated and harbored a partially defective Vif, which was found to permit hypermutation in a peripheral blood mononuclear cell culture. Overall, our results suggest that a potential antiviral therapy based on hypermutation may need to achieve a substantially higher level of hypermutation than is naturally seen in most individuals to impair virus replication and subsequent disease progression.Interactions between the human immunodeficiency virus type 1 (HIV-1) protein Vif (for viral infectivity factor) and antiviral host factors in the APOBEC family (for apolipoprotein B mRNA editing enzyme, catalytic polypeptide) have recently attracted interest as potential targets for antiviral therapy (10,13,16,26,28,40). One of the mechanisms by which APOBEC3G, a cytidine deaminase, may impair HIV-1 replication is through the introduction of C-to-U lesions in the negative-sense DNA strand during reverse transcription (RT). This process, known as hypermutation, results in excessive G-to-A changes in the HIV-1 coding strand, leading to premature stop codons and other potentially disruptive mutations (24). APOBEC3G activity is typically counteracted by the HIV-1 protein Vif, which targets it for degradation by the proteasome (38). This prevents APOBEC from being incorporated into nascent virions and causing hypermutation. However, Vif activity in vivo is imperfect, as demonstrated by the observation of hypermutated sequences in HIV-infected individuals (9,17,18,31,42). Because hypermutation is expected to impair virus replication, recent efforts have focused on characterizing hypermutation in HIV-infected individuals and examining its relationship with disease progression.The relationship between hypermutation and markers of disease progression has been addressed in two different ways. In three studies, markers of disease progression were compared between individuals with or without hypermutation detected by population sequen...

Section: Discussionsupporting

confidence: 92%

Analysis of the Percentage of Human Immunodeficiency Virus Type 1 Sequences That Are Hypermutated and Markers of Disease Progression in a Longitudinal Cohort, Including One Individual with a Partially Defective Vif

Piantadosi

Humes

Chohan

et al. 2009

“…HIV may take advantage of 63 K-linked poly-Ub A3H, which can associate with Gag through an RNA intermediate or directly (75), to promote virus release. This may aid in virus budding and titrate out the effect of the A3H during viral adaptation akin to how Vif mutants unable to degrade A3G can acquire mutations that enable the production of more virus particles to minimize A3G packaging (76,77). This may occur for A3H since it binds Alu RNA with an apparent K d that is 3-fold higher than A3G (A3H K d of 717 Ϯ 29 nM; A3G K d of 246 Ϯ 46 nM [data not shown]).…”

Section: Discussionmentioning

confidence: 99%

Determinants of Efficient Degradation of APOBEC3 Restriction Factors by HIV-1 Vif

Baig

Feng

Chelico

2014

The APOBEC3 deoxycytidine deaminases can restrict the replication of HIV-1 in cell culture to differing degrees. The effects of APOBEC3 enzymes are largely suppressed by HIV-1 Vif that interacts with host proteins to form a Cullin5-Ring E3 ubiquitin ligase that induces 48 K-linked polyubiquitination (poly-Ub) and proteasomal degradation of APOBEC3 enzymes. Vif variants have differing abilities to induce degradation of APOBEC3 enzymes and the underlying biochemical mechanisms for these differences is not fully understood. We hypothesized that by characterizing the interaction of multiple APOBEC3 enzymes and Vif variants we could identify common features that resulted in Vif-mediated degradation and further define the determinants required for efficient Vif-mediated degradation of APOBEC3 enzymes. We used Vifs from HIV-1 NL4-3 (IIIB) and HXB2 to characterize their induced degradation of and interaction with APOBEC3G, APOBEC3G D128K, APOBEC3H, and APOBEC3B in 293T cells. We quantified the APOBEC3G-Vif and APOBEC3H-Vif interaction strengths in vitro using rotational anisotropy.

“…These studies yielded viral variants that could spread effectively in the presence of A3G despite retention of these tandem stop codons; rather, all isolates had acquired a pyrimidine at nucleotide 200 and a stop codon in vpr (18). While the effect of the vpr null mutation remains unknown, the substitution of A to T or C at nucleotide 200 (T/C200) functions to optimize viral translation, resulting in increased particle production and a relative decrease in A3G encapsidation to levels tolerable to the viral population (17).…”

mentioning

confidence: 99%

Long-Term Restriction by APOBEC3F Selects Human Immunodeficiency Virus Type 1 Variants with Restored Vif Function

Albin

Haché

Hultquist

et al. 2010

Self Cite

Tandem stop mutations K26X and H27X in human immunodeficiency virus type 1 (HIV-1) vif compromise virus replication in human T-cell lines that stably express APOBEC3F (A3F) or APOBEC3G (A3G). We previously reported that partial resistance to A3G could develop in these Vif-deficient viruses through a nucleotide A200-to-T/C transversion and a vpr null mutation, but these isolates were still susceptible to restriction by A3F. Here, long-term selection experiments were done to determine how these A3G-selected isolates might evolve to spread in the presence of A3F. We found that A3F, like A3G, is capable of potent, long-term restriction that eventually selects for heritable resistance. In all 7 instances, the selected isolates had restored Vif function to cope with A3F activity. In two isolates, Vif Q26-Q27 and Y26-Q27, the resistance phenotype recapitulated in molecular clones, but when the selected vif alleles were analyzed in the context of an otherwise wild-type viral background, a different outcome emerged. Although HIV-1 clones with Vif Q26-Q27 or Y26-Q27 were fully capable of overcoming A3F, they were now susceptible to restriction by A3G. Concordant with prior studies, a lysine at position 26 proved essential for A3G neutralization. These data combine to indicate that A3F and A3G exert at least partly distinct selective pressures and that Vif function may be essential for the virus to replicate in the presence of A3F.