The apolipoprotein E (APOE) gene appears functionally monomorphic in chimpanzees (Pan troglodytes)

Abstract

Background: The human apolipoprotein E (APOE) gene is polymorphic, with three primary alleles (E2, E3, E4) that differ at two key non-synonymous sites. These alleles are functionally different in how they bind to lipoproteins, and this genetic variation is associated with phenotypic variation for several medical traits, including cholesterol levels, cardiovascular health, Alzheimer's disease risk, and longevity. The relative frequencies of these alleles vary across human populations, and the evolution and maintenance of this diversity is much debated. Previous studies comparing human and chimpanzee APOE sequences found that the chimpanzee sequence is most similar to the human E4 allele, although the resulting chimpanzee protein might function like the protein coded for by the human E3 allele. However, these studies have used sequence data from a single chimpanzee and do not consider whether chimpanzees, like humans, show intra-specific and subspecific variation at this locus.

Methodology and principal findings: To examine potential intraspecific variation, we sequenced the APOE gene of 32 chimpanzees. This sample included 20 captive individuals representing the western subspecies (P. troglodytes verus) and 12 wild individuals representing the eastern subspecies (P. t. schweinfurthii). Variation in our resulting sequences was limited to one non-coding, intronic SNP, which showed fixed differences between the two subspecies. We also compared APOE sequences for all available ape genera and fossil hominins. The bonobo APOE protein is identical to that of the chimpanzee, and the Denisovan APOE exhibits all four human-specific, non-synonymous changes and appears functionally similar to the human E4 allele.

Conclusions: We found no coding variation within and between chimpanzee populations, suggesting that the maintenance of functionally diverse APOE polymorphisms is a unique feature of human evolution.

Figure 1. A schematic of the APOE gene.

Structure and nucleotide position numbers follow Fullerton et al. and Ensembl (ENSG00000130203). The location of primers used in this study are given above (forward primers) and below (reverse primers) the labeled exons. See Table S1 for primer and PCR-cycling information. An intronic SNP differentiating the two chimpanzee populations is highlighted in orange (position 2098*). SNP locations in red (3071 and 3073) represent putative APOE non-synonymous changes based on the chimpanzee genome assembly (Pan_troglodytes-2.1.4). Positions in blue (3205, 3937 and 4075) correspond to the amino acids (61, 112 and 158, respectively) that define the three human APOE alleles (E2, E3, E4). Position 4219^† (in green) represents the single, synonymous difference between the P. t. verus sequences generated in this study and that of Fullerton et al. (2000) . *corresponds to Ensembl coordinates 19∶45411002 for the human genome and 19∶50097633 for the chimpanzee genome. ^†corresponds to Ensembl coordinates 19∶45412223 for the human genome.

Figure 2. Lineage-specific mutations mapped onto a schematic of the APOE protein (A) and primate phylogeny (B).

Protein structure is modeled after Bu 2009 , and tree topology represents known evolutionary relationships based on genome-wide data . Human mutations at key residues 61, 112 and 158 are in red. Including residue 61, the human APOE protein has four fixed, Homo-specific, non-synonymous mutations, all of which seem to be shared with the Denisovan hominin (inferred from reads mapped to the human genome at http://www.genome.ucsc.edu). The chimpanzee APOE protein is monomorphic within and between subspecies, and is identical to the bonobo APOE protein. Mutation R15H (dotted arrow) is shared by gorillas, chimpanzees and bonobos likely as a result of incomplete lineage sorting rather than independent evolution .