The proteasome subunit β-type 8 (PSMB8) gene in the jawed vertebrate MHC genomic region encodes a catalytic subunit of the immunoproteasome involved in the generation of peptides to be presented by the MHC class I molecules. A teleost, the medaka (Oryzias latipes), has highly diverged dimorphic allelic lineages of the PSMB8 gene with only about 80% amino acid identity, termed "PSMB8d" and "PSMB8N," which have been retained by most wild populations analyzed. To elucidate the evolutionary origin of these two allelic lineages, seven species of the genus Oryzias were analyzed for their PSMB8 allelic sequences using a large number of individuals from wild populations. All the PSMB8 alleles of these species were classified into one of these two allelic lineages based on their nucleotide sequences of exons and introns, indicating that the Oryzias PSMB8 gene has a truly dichotomous allelic lineage. Retention of both allelic lineages was confirmed except for one species. The PSMB8d lineage showed a higher frequency than the PSMB8N lineage in all seven species. The two allelic lineages showed curious substitutions at the 31st and 53rd residues of the mature peptide, probably involved in formation of the S1 pocket, suggesting that these allelic lineages show a functional difference in cleavage specificity. These results indicate that the PSMB8 dimorphism was established before speciation within the genus Oryzias and has been maintained for more than 30-60 million years under a strict and asymmetric balancing selection through several speciation events.long-term balancing selection | antigen processing | transspecies polymorphism T ransspecies polymorphism (TSP) is the passage of allelic lineages from ancestral to descendent species (1), and the underlying selective mechanism is referred to as balancing selection caused by "overdominant selection," "frequency-dependent selection," or "selection that varies in time and space" (2). The vertebrate MHC class I and II genes with a large number of alleles and wide allelic differences provide a classical example of TSP (3, 4), most probably arising by overdominant selection (5). TSP of the MHC genes sometimes persists for very long periods. Certain HLA-DRB alleles are reported to have persisted for 50-60 million years (6). Another well-characterized TSP has been reported for the rabbit Ig heavy-chain variable-region genes; its persistence has been estimated at 50 million years based on molecular phylogenetic analysis (7,8). Except for these genes encoding molecules showing high degree of binding specificity, information for long-term balancing selection resulting in TSP is limited (9-11). Moreover, all TSP reported thus far involve only a few species, and the possible presence of a long-lasting TSP surviving through many speciation events is still to be clarified by systematic phylogenetic analysis.The MHC class I molecules deliver the peptides derived from cytosolic proteins to the cell surface for recognition by cytotoxic T cells. The proteins are degraded proteolytically into s...

The major histocompatibility complex (MHC) class I region of teleosts harbors a tight cluster of the class IA genes and several other genes directly involved in class I antigen presentation. Moreover, the dichotomous haplotypic lineages (termed d- and N- lineages) of the proteasome subunit beta genes, PSMB8 and PSMB10, are present in this region of the medaka, Oryzias latipes. To understand the evolution of the Oryzias MHC class I region at the nucleotide sequence level, we analyzed bacterial artificial chromosome clones covering the MHC class I region containing the d- lineage of Oryzias luzonensis and the d- and N- lineages of Oryzias dancena. Comparison among these three elucidated sequences and the published sequences of the d- and N- lineages of O. latipes indicated that the order and orientation of the encoded genes were completely conserved among these five genomic regions, except for the class IA genes, which showed species-specific variation in copy number. The PSMB8 and PSMB10 genes showed trans-species dimorphism. The remaining regions flanking the PSMB10, PSMB8, and class IA genes showed high degrees of sequence conservation at interspecies as well as intraspecies levels. Thus, the three independent evolutionary patterns under apparently distinctive selective pressures are recognized in the Oryzias MHC class I region.