Characterization of two distinct DR beta chain alleles at the beta III locus of the DR5 haplotype: beta III alleles are highly conserved.

The HLA-DR beta region of at least two members of the DRw52 (MT2) supertypic group (DR3, DR5, DRw6, and DRw8) has recently been shown to contain three beta-chain genes--beta I, beta II, and beta III, ordered in the direction of transcription. beta III is apparently a duplication of beta I. Both beta I and beta III are expressed, whereas beta II is a pseudogene. We previously reported the sequence of the DR5 beta I cDNA from the homozygous DR5 cell line Swei. We report here the sequence of two different DR5 beta III cDNA from the same cell line. The assignment of the genes of this and other members of the DRw52 supertypic group to specific loci allow comparisons between products of known alleles and between products of distinct loci. beta I allelic products showed approximately 11% divergence in the first domain, whereas beta I and beta III products showed 17% difference. These differences were clustered and found predominantly in the previously described variable regions (amino acid residues 9 through 13, 26 through 38, and 67 through 74). These data, coupled with the finding of shared variable regions among different DR beta chains, suggest gene conversion as a means of generating polymorphism in the beta I alleles. In contrast, the beta III allelic products showed less than 1% amino acid and nucleotide divergence in the first domain. These differences were outside the variable regions, and attributable to single nucleotide changes. The polymorphism at the beta I locus and the conservation at the beta III locus suggest selective pressure conserving the beta III locus and/or generating polymorphism at the beta I locus, and further suggest that gene conversion may be acting unidirectionally from beta III to beta I.