Evolution of HLA class II through diversification in protein stability levels (P5009)

Abstract

Abstract Allelic diversity in human leukocyte antigens (HLA) have been explained by balancing selection acting on polymorphic residues in the peptide binding groove of HLA that diversify binding spectrum for pathogenic epitopes. Here we show that HLA class II (HLA-DQ) allele products are extremely diverse in protein stability levels. We have profiled the relative stability of DQ proteins by a cell-based assay that measures cell surface MHC protein density (surface density index; SDI). The SDI varies over 100-fold among DQ allele products, indicating large stability differences. Through mutagenesis, we identified polymorphic residues that regulate the intrinsic stability of DQ protein, which includes variations on the exterior of the peptide-binding groove that mediate interdomain hydrogen bonds. One of the major stability regulator in DQA1 achieves high ratio of synonymous to non-sysnonymous substitutions per site (ds/dn), suggesting that variations at this site have been maintained through balancing selection. DQ genes of non-human primates and mammals also maintain these variatns. These data suggest that HLA and MHC have been evolving through diversifications in protein stability levels. Our study provides new functional insights into the mechanism of HLA evolution.