Identification of a new bovine MHC class II DRB allele by nucleotide sequencing and an analysis of phylogenetic relationships.

Three overlapping cDNA clones coding for the bovine major histocompatibility complex (MHC) class II DR beta chain were isolated. A clone NR1 encoded a primary translated product of 266 amino acids, 29 of which were deduced to form a signal peptide and 237 to form the mature polypeptide. The protein predicted from this cDNA appeared to have all the features expected of an expressed MHC class II molecule. Comparison of the sequences and construction of a phylogenetic tree revealed that NR1 represents a BoLA-DRB3 gene and not a BoLA-DRB1 or BoLA-DRB2 pseudogene. NR1 and ovine sequences exhibited the greatest overall similarity among sequences from various mammalian species, followed by the equivalent human sequences. Indeed, the bovine allele was more closely related to certain ovine alleles than to other bovine alleles. A large number of replacement substitutions were identified when beta 1 domains encoded by NR1 and each of the 36 distinct BoLA-DRB3 alleles were compared, and most of the allelic variations were found in regions that are commonly polymorphic in DRB sequences from different species and correspond to the predicted antigen-recognition site. Thus, the predicted structure of the unique NR1 allele for BoLA-DRB3 further confirms the overall conservation of the product of this locus, as previously established from studies in rodent and man.