Structural characterization of the caprine major histocompatibility complex class II DQB1 (Cahi-DQB1) gene

The major histocompatibility class II genes have been extensively characterized in sheep and cattle, whereas in goats the only class II genes that have been completely sequenced are DRA and DRB. Herewith, we report the complete coding sequence of the goat DQB1 gene. This gene has a single open reading frame of 786bp, being organized in five exons and displaying 95-97% nucleotide identity with its bovine and ovine cDNA orthologous sequences. The structural features of the goat DQB1 molecule are well conserved with regard to its mammalian orthologues. Conserved glycosilation sites (beta19) and cysteine residues (beta15, beta79, beta117, beta173) forming disulfide bridges have been identified in the goat DQB1 molecule. The alignment of several Cahi-DQB1 exon 2 sequences has allowed to identify five different allelic variants Neighbor-joining phylogenetic analysis of caprine, ovine and bovine DQB sequences has allowed to ascertain that the five Cahi-DQB1 alleles we have found correspond to three different allelic lineages. We have identified fifteen polymorphic positions in the Cahi-DQB1 molecule, but only six of them are located in the peptide binding region. The high degree of conservation of these polymorphic sites located outside the peptide binding region in cattle and sheep suggests that they might play a functional role in antigen-presentation to CD4+ T cells.