Transspecies dimorphic allelic lineages of the proteasome subunit beta-type 8 gene (PSMB8) in the teleost genus Oryzias

Abstract

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.

Fig. 1.

Map showing collection sites of wild populations of Oryzias species and allelic frequencies of the PSMB8d and PSMB8N lineages in wild populations. Dots indicate the collection site of each wild population of Oryzias species. Allelic frequencies of the PSMB8d and PSMB8N lineages in each wild population are shown in black and white, respectively, in the circle diagrams. Actual frequencies of the d allele (number of d alleles/number of total alleles) for each species are O. curvinotus, 0.862 (119/138); O. celebensis, 0.600 (228/380); O. matanensis, 0.764 (162/212); O. marmoratus, 0.816 (173/212); O. dancena, 1.00 (300/300); O. minutillus, 1.00 (488/488); and O. javanicus, 0.778 (277/356).

Fig. 2.

Comparison of the amino acid sequences of the mature peptides of PSMB8. PSMB8 mature peptides of Oryzias species and two allelic lineages of O. latipes (NCBI accession nos. AB183488 and BA000027) were aligned with ClustalX 2.0. All Oryzias PSMB8 sequences were determined in this study, except for two O. latipes PSMB8N and PSMB8d(V) sequences and the O. dancena PSMB8N sequence (NCBI accession no. FJ481084). Of the 204 positions of the mature peptides, only the 48 positions where amino acid substitutions were observed are shown. Dots indicate identity with the residues in the uppermost sequence.

Fig. 3.

Phylogenetic tree of Oryzias PSMB8 alleles. The nucleotide sequences of mature peptides of 612 residues were aligned by ClustalX 2.0(37), and the phylogenetic tree was constructed by the NJ method (33). The numbers on each branch represent bootstrap probabilities (>50%) based on 1,000 bootstrap trials. The sequences of TeniPSMB8 (Tetraodon nigroviridis, NCBI accession no. CR697191), HosaPSMB8 (Homo sapiens, NCBI CR541661), and MumuPSMB8 (Mus musculus, NCBI BC013785) were used as an outgroup.