Extreme Population Differences in the Human Zinc Transporter ZIP4 (SLC39A4) Are Explained by Positive Selection in Sub-Saharan Africa

Author Summary Zinc is an essential trace element with many biological functions in the body, whose concentrations are tightly regulated by different membrane transporters. Here we report an unusual case of positive natural selection for an amino acid replacement in the human intestinal zinc uptake transporter ZIP4. This substitution is recognized as one of the most strongly differentiated genome-wide polymorphisms among human populations. However, since the extreme population differentiation of this non-synonymous site was not accompanied by additional signatures of natural selection, it was unclear whether it was the result of genetic adaptation. Using computer simulations we demonstrate that such an unusual pattern can be explained by the effect of local recombination, together with positive selection in Sub-Saharan Africa. Moreover, we provide evidence to suggest functional differences between the two ZIP4 isoforms in terms of the transporter cell surface expression and zinc uptake. This result is the first genetic indication that zinc regulation may differ among modern human populations, a finding that may have implications for health research. Further, we speculate that reduced zinc uptake mediated by the derived variant may have been advantageous in Sub-Saharan Africa, possibly by reducing access of a geographically restricted pathogen to this micronutrient. Extreme differences in allele frequency between West Africans and Eurasians were observed for a leucine-to-valine substitution (Leu372Val) in the human intestinal zinc uptake transporter, ZIP4, yet no further evidence was found for a selective sweep around the ZIP4 gene (SLC39A4). By interrogating allele frequencies in more than 100 diverse human populations and resequencing Neanderthal DNA, we confirmed the ancestral state of this locus and found a strong geographical gradient for the derived allele (Val372), with near fixation in West Africa. In extensive coalescent simulations, we show that the extreme differences in allele frequency, yet absence of a classical sweep signature, can be explained by the effect of a local recombination hotspot, together with directional selection favoring the Val372 allele in Sub-Saharan Africans. The possible functional effect of the Leu372Val substitution, together with two pathological mutations at the same codon (Leu372Pro and Leu372Arg) that cause acrodermatitis enteropathica (a disease phenotype characterized by extreme zinc deficiency), was investigated by transient overexpression of human ZIP4 protein in HeLa cells. Both acrodermatitis mutations cause absence of the ZIP4 transporter cell surface expression and nearly absent zinc uptake, while the Val372 variant displayed significantly reduced surface protein expression, reduced basal levels of intracellular zinc, and reduced zinc uptake in comparison with the Leu372 variant. We speculate that reduced zinc uptake by the ZIP4-derived Val372 isoform may act by starving certain pathogens of zinc, and hence may have been advantageous in Sub-Saharan Africa. Moreover, these functional results may indicate differences in zinc homeostasis among modern human populations with possible relevance for disease risk.