A highly diverged beta 1 exon in the DR region of the human MHC: sequence and evolutionary implications

The DR subregion of the human major histocompatibility complex from a DR4 haplotype includes the well-characterized DR alpha, DR4 beta, DR(MT3)beta psi genes. In addition, the region between the DR alpha and the proximal DR(MT3)beta contains several copies of conserved DR beta-related sequences. These repeated elements, numbered II, III, and IV, include the DR beta signal sequence and a region located further upstream. Further examination of these conserved sequences showed that DR beta first intron sequences are present at the 3' ends of these repeats. Progressively longer portions of the DR beta first intron are conserved from repeat II to repeat IV, producing a gradient of conservation. The most complete repeat element of repeats II, III, and IV is associated with a lone beta 1 exon (DR beta 1). Upon sequencing, DR beta 1 was found to contain several deleterious mutations, indicating that it is nonfunctional. DR beta 1 has accumulated a large number of replacement substitutions and mutations at positions which are invariant in beta 1 domains from expressed DR beta genes: 77.8% of the nucleotide substitutions were replacement substitutions, and 41.5% of the amino acids at invariant positions have been altered. Calculations based on these figures suggest that DR beta 1 may have become inactive approximately 25 million years ago. There are, however, two histidine residues within a variable region which are unique to DR beta 1 and the DR4 beta gene, suggesting that they represent a gene pair which probably evolved by duplication of a single DR beta chain gene.