Zebrafish Mhc class II ? chain-encoding genes: polymorphism, expression, and function

Abstract

Its small size and short generation time renders the zebrafish (Brachydanio rerio) an ideal vertebrate for immunological research involving large populations. A prerequisite for this is the identification of the molecules critical for an immune response in this species. In earlier studies, we cloned the zebrafish genes coding for the beta chains of the class I and class II major histocompatibility complex (Mhc) molecules. Here, we describe the cloning of the zebrafish alpha chain-encoding class II gene, which represents the first identification of a class II A gene in teleost fishes. The gene, which is less than 3 kilobases (kb) distant from one of the beta chain-encoding genes, is approximately 1.2 kb long and consists of four exons interrupted by very short (< 200 base pairs) introns. Its organization is similar to that of the mammalian class II A genes, but its sequence differs greatly from the sequence of the latter (36% sequence similarity). Among the most conserved parts is the promoter region, which contains X, Y, and TATA boxes with high sequence similarity to the corresponding mammalian boxes. The observed striking conservation of the promoter region suggests that the regulatory system of the class II genes was established more than 400 million years ago and has, principally, remained the same ever since. Like the DMA, but unlike all other mammalian class II A genes, the zebrafish gene codes for two cysteine residues which might potentially be involved in the formation of a disulfide bond in the alpha 1 domain. The primary transcript of the gene is 1196 nucleotides long and contains 708 nucleotides of coding sequence. The gene is expressed in tissues with a high content of lymphoid/myeloid cells (spleen, pronephros, hepatopancreas, and intestine). The analyzed genomic and cDNA sequences are probably derived from different loci (their overall sequence similarity in the coding region is 73% and their 3' untranslated regions are highly divergent from each other). The genes are apparently functional. Comparison of genes from different zebrafish populations reveals high exon 2 variability concentrated in positions coding for the putative peptide-binding region. Phylogenetic analysis suggests that the zebrafish class II A genes stem from a different ancestor than the mammalian class II A genes and the recently cloned shark class II A gene.

Trans-species polymorphism of class II Mhc loci in danio fishes

“…In our earlier studies (Ono et al 1992;Sültmann et al 1993, we demonstrated the existence of four class II A and six class II B loci in the zebrafish. Of the four class II A loci, Dare-DAA is linked to Dare-DAB, Dare-DCA is linked to Dare-DCB, and Dare-DEA is linked to Dare-DEB (Sültmann et al 1993J.…”

“…Of the four class II A loci, Dare-DAA is linked to Dare-DAB, Dare-DCA is linked to Dare-DCB, and Dare-DEA is linked to Dare-DEB (Sültmann et al 1993J. BingulacPopovic, F. Figueroa, J. Postlethwait, and J. Klein, unpublished data); the location of the Dare-DBA locus is not known.…”

“…The designation Danio rerio for the zebrafish is now used almost uniformly by developmental biologists. Hence to avoid further confusion, here we introduce the designation Dare for the Mhc of the zebrafish to replace the former designation Brre (Ono et al 1992Sültmann et al 1993. We retain, however, the name D. malabaricus for the giant danio because most recent studies (Meyer et al 1995) suggest that it might be a distinct species from D. aequipinnatus after all.…”

“…Another possibility is that all the sequences, in fact, belong to a single locus. Linkage data for the putative DBA locus are not available and the locus assignments were made on the basis of genetic distance and differences in the 39 untranslated regions (Sültmann et al 1993. If we take the most conservative stand and consider only the sequences that belong clearly to either the DAA locus group or to the DBA group, we find unambig- Fig.…”

“…The final extension at 72°C was for 10 min. Exon 2 of class II A genes was amplified using the primer pair A20290 and A20291 based on known D. rerio cDNA and genomic sequences (Sültmann et al 1993).…”