Antiretroelement activity of APOBEC3H was lost twice in recent human evolution

Abstract

The primate APOBEC3 gene locus encodes a family of proteins (APOBEC3A-H) with various antiviral and antiretroelement activities. Here, we trace the evolution of APOBEC3H activity in hominoids to identify a human-specific loss of APOBEC3H antiviral activity. Reconstruction of the predicted ancestral human APOBEC3H protein shows that human ancestors encoded a stable form of this protein with potent antiviral activity. Subsequently, the antiviral activity of APOBEC3H was lost via two polymorphisms that are each independently sufficient to destabilize the protein. Nonetheless, an APOBEC3H allele that encodes a stably expressed protein is still maintained at high frequency, primarily in African populations. This stable APOBEC3H protein has potent activity against retroviruses and retrotransposons, including HIV and LINE-1 elements. The surprising finding that APOBEC3H antiviral activity has been lost in the majority of humans may have important consequences for our susceptibility to retroviral infections as well as ongoing retroelement proliferation in the human genome.

Figure 1. Instability and Inactivity of APOBEC3H is Unique to Humans and Shared Among Human APOBEC3H Alleles

(A) Western blot analysis of primate APOBEC3H proteins expressed in transiently transfected 293T cells. Actin is shown as a loading control. (B) Western blot analysis of chimpanzee and two versions of the human APOBEC3H protein cloned from two individuals (human_A and human_B). (C) Inhibition of MusD replication by human APOBEC3G and primate APOBEC3H homologs. Values are shown as the % Retrotransposition relative to the assay without any APOBEC (No Apobec) expression plasmid. Averages of three replicates (+/− SEM) are shown. (D) Pulse-chase analysis of chimpanzee and both human APOBEC3H proteins over a six-hour time-course (0, 0.5, 1, 2 and 6 hours). HA-tagged APOBEC3H proteins were immunoprecipitated and radiolabeled proteins detected at each time point by autoradiography following SDS-PAGE. An untransfected control was included to determine background. This is a representative experiment that was done three times with similar results. (E) Autoradiography was used to quantitate protein levels at each time point. Quantities of radiolabeled proteins are shown as the percent of each protein remaining (% remaining) at that time point relative to time 0 (pulse only). The stability of the chimpanzee APOBEC3H is shown in the grey line and triangles; human_A is shown in the solid line and diamonds; human_B is shown in the solid line and squares. The half-life (t1/2) equal to the time in which 50% of the APOBEC3H protein remaining for human_A and human_B is marked on the graph.

Figure 2. The C-terminal Tail Controls the Sub-cellular Localization but not the Stability or Antiviral Activity of APOBEC3H

(A) Schematic of the primate APOBEC3H protein. Location of the HAE and PC--C motifs of APOBEC3H that are conserved in other APOBEC proteins (Conticello et al., 2005) are shown in black. A Premature Termination Codon (PTC) truncates human and chimpanzee APOBEC3H homologs by 30 amino acid residues (asterisk). The leucine residues making up the core of the putative Nuclear Export Sequence (NES) downstream of the PTC are highlighted in red in an alignment of human, chimpanzee, gorilla, orangutan, gibbon and rhesus macaque APOBEC3H C-terminal tail domains. (B) Western blot analysis of human, macaque and chimeric human/macaque APOBEC3H proteins. Actin is shown as a loading control. (C) Sub-cellular localization of human, macaque and chimeric human/macaque APOBEC3H proteins in HeLa cells. APOBEC3H proteins were detected with an anti-HA antibody (red) and DAPI staining was used to define the nucleus (blue). (D) Inhibition of HIV-1 vif- by human, macaque and chimeric human/macaque APOBEC3H proteins in a single-cycle infectivity assay. Averages of triplicate assays (+/− SEM) are shown as the % Infectivity relative to the infectivity of HIV in the absence of an APOBEC expression plasmid (No Apobec).

Figure 3. Two Independent Mutations Determine the Instability of Human APOBEC3H

(A) Schematic of all non-synonymous differences (change the encoded amino acid) between both human (human_A and human_B) and chimpanzee APOBEC3H proteins relative to the ancestral amino acid at that position as determined using gorilla APOBEC3H as the outgroup. The four non-synonymous mutations specific to chimpanzee APOBEC3H are shown in upside down black flags (K16R, K97Q, A142N and S160C -note that only a single chimpanzee APOBEC3H was analyzed; therefore, these changes may not necessarily be fixed in the chimpanzee lineage). The three changes fixed in the human population are shown in as the short solid flags (K91E, D158N and S160Y). Human APOBEC3H polymorphisms are shown as long flags; open for for human_A (R105G and E121K) and grey for human_B (delN15, R18L and E121D). Position of the breakpoint of the chimeric human/chimpanzee APOBEC3H proteins analyzed in panel B is shown as the dotted line at position 127. (B) Western blot analysis of native and chimeric human (human_A and human_B) and chimpanzee APOBEC3H proteins. APOBEC3H expression was detected with an HA antibody and actin is shown as a control. (C) Western blot analysis of native and mutant APOBEC3H proteins. Four of the five non-synonymous mutations in the N-terminal region that distinguish the human_A protein from the chimpanzee protein were mutated in human_A to match the chimpanzee sequence (x4NS). A single mutation was also analyzed (G105R). Two single mutations (+N15 and L18R) as well as the double-mutant (+N15/L18R) were analyzed for the human_B protein. (D) Western blot analysis of native and single-mutant chimpanzee APOBEC3H proteins (chimp R105G/chimp delN15).

Figure 4. A Stable and Active Human APOBEC3H Protein Blocks the Replication of vif-HIV

(A) Schematic of the four dominant haplotypes of APOBEC3H (hap I, hap II, hap III and hap IV) found in the human population. Polymorphisms present in each haplotype are marked with a flag and shading is maintained based on the original human_A and human_B APOBEC3H alleles described in the legend to Figure 3. Of note, human_A corresponds to haplotype I while human_B corresponds to haplotype IV except that it lacks the E178D polymorphism. (B) Western blot analysis of the four human APOBEC3H haplotypes and chimpanzee APOBEC3H. (C) Inhibition of HIV vif-by human APOBEC3H proteins as well as by human APOBEC3G. Single-cycle infectivity assays were performed for both wild-type (HIV WT) and vif-deficient HIV (HIV vif-) in the presence or absence of APOBEC expression. Averages of triplicate assays (+/− SEM) are shown as % Infectivity of the control infection (No Apobec). Note the log scale on the Y-axis.

Figure 5. Ancestral APOBEC3H Proteins Inhibit Retroviruses and LINE-1 Elements

(A) The evolution of modern A3H alleles is presented as a phylogeny of the human/chimpanzee clade. Four changes (K16R, K97Q, A142N and S160C – purple) occurred during the evolution of modern chimpanzees. Three changes (K91E, D158N and S160Y – solid flags) are fixed among human APOBEC3H alleles. Haplotype I accumulated two further changes (R105G and E121K – open flags) while haplotypes II – IV are the result of sequential accumulation of four additional changes (E121D and E178D for haplotypes II; plus del15N for haplotype III; plus R18L for haplotype IV – grey flags). The nodes representing the human ancestor and the human/chimpanzee ancestor are circled. (B) Western blot analysis of human (haplotype I), human ancestor and human/chimpanzee ancestor APOBEC3H proteins. (C) Inhibition of HIV by chimpanzee and ancestral human APOBEC3H proteins. Averages of triplicate assays (+/− SEM) are shown as the % Infectivity relative to the control assay with no APOBEC expression (No Apobec). The open boxes are infections with HIV that contain a deletion in the Vif gene (HIV vif-) and the solid boxes are infections with wild-type HIV that contains a functional Vif gene (HIV WT). Note the log scale on the Y-axis. (D) Inhibition of a human LINE-1 element (L1.3) by chimpanzee, ancestral human (human ancestor and human/chimp ancestor) and human APOBEC3H proteins. APOBEC3G and APOBEC3A are shown as a negative and positive control, respectively. Averages of triplicate assays (+/− SEM) are shown as the % Infectivity relative to the control assay with no APOBEC expression (No Apobec).

Figure 6. Frequency of the Active APOBEC3H Allele Varies Across World Populations

(A) Genotypes were determined for African American (AA; N=22), European American (EA; N=23) and Han Chinese from Los Angeles (CA; N=23) for both the R105G (black bars) and N15 deletion (gray bars) polymorphisms. A list of all inferred haplotypes and their frequencies is found in Table S1, and a list of the number of individuals with each haplotype is found in Table S2. (B) An F_ST statistic was calculated for both the delN15 and R105G polymorphisms in pairwise comparisons of each subpopulation from Panel A with the other two subpopulations (see Experimental Procedures for details). F_ST values near 0 are indicative of no population differentiation while large F_ST values suggest either local selection or demographic effects. (C) Genotypes from HapMap populations (www.hapmap.org) from Yorubans in Ibadan, Nigeria (YRI; N=90), Utah residents with ancestry from northern and western Europe (CEU; N=90), and combined data from Japanese in Tokyo and Han Chinese in Beijing (JPT/CHB; N=92) for both the R105G (black bars) and delN15 (gray bars) polymorphisms. (D) An F_ST statistic was calculated for both the delN15 and R105G polymorphisms in pairwise comparisons of each subpopulation from Panel C with the other two subpopulations. (E) Predicted frequencies of APOBEC3H alleles predicted to encode stable proteins (black sector; that is, with R105 and without the deletion at N15; R105/N15) and unstable proteins (open sectors; that is either R105G or the deletion at N15; R105G/delN15) among the all six three subpopulations. The % of APOBEC3H alleles predicted to encode stable proteins is marked to the right of each bar graph.