EVOLUTION OF THE CLTCL1 GENE ENCODING CHC22 CLATHRIN REVEALS SELECTION INFLUENCING CHC22\'S ROLE IN HUMAN GLUCOSE METABOLISM

CHC22 clathrin plays a key role in intracellular membrane trafficking of the insulin-responsive GLUT4 glucose transporter, and so in post-prandial clearance of glucose from human blood. We performed population genetic and phylogenetic analyses of the CLTCL1 gene, encoding CHC22, to understand its variable presence in vertebrates and gain insight into its functional evolution. Analysis of ~50 complete vertebrate genomes showed independent loss of CLTCL1 in nine lineages after it arose from a gene duplication during the emergence of jawed vertebrates. All vertebrate and non-vertebrate eukaryotes considered here have retained the parent CLTC gene encoding CHC17 clathrin, which mediates endocytosis and other housekeeping membrane traffic pathways. Statistical analysis provides evidence of strong purifying selection over phylogenetic timescales for CLTCL1, as well as for CLTC, supporting preserved functionality of CHC22 in those species that have retained CLTCL1. In population genetic analyses of humans and chimpanzees, extensive allelic diversity was observed for CLTCL1 compared to CLTC. In all human populations, two variants of CLTCL1 segregate at high frequency, resulting in CHC22 protein with either methionine or valine at position 1316. The V1316 variant occurs only in humans, but the same site is polymorphic in non-human primates as well. Analysis of archaic and ancient humans bounded the appearance of the derived V1316 allele to 500-50 KYA. Balancing selection on the two high-frequency CHC22 variants is inferred, with V1316 being more frequent in farming, as compared to hunter-gatherer populations. Together these analyses suggest that CHC22 clathrin is undergoing selection in humans related to its role in nutrient metabolism. Consistent with this conclusion, we observed functional differences between the two CHC22 variants in their ability to control GLUT4 membrane traffic, as predicted by structural modeling and differences in cellular dynamics of the two variants.