The Major Histocompatibility Complex Class I Genes of Zebrafish

While the genes of the major histocompatibility complex (MHC) were named after the discovery that they encode the primary antigens responsible for determining transplant compatibility, MHC molecules also play a central role in adaptive immunity through presenting antigens to T cells. Mammalian MHC class I molecules present cytosolic antigens to CD8+ cytotoxic T cells and serve as inhibitory ligands to natural killer (NK) cells. MHC class I genes can be classified as classical or nonclassical where the classical MHC class I genes encode molecules that present antigens to T cells, are highly polymorphic, and are ubiquitously expressed. The nonclassical MHC class I genes encode molecules that are structurally similar to classical molecules but exhibit different functions, have low-level polymorphism, and display tissue-specific expression.;Genes encoding MHC class I molecules have been identified in all jawed vertebrate species examined, including cartilaginous fish, but are absent from jawless fish. After the MHC had been described in several mammalian species, researchers became interested in identifying orthologous genes in bony fish, or teleosts, in order to gain perspective on the evolutionary origins of adaptive immunity. Zebrafish provide an ideal animal model in which to study the MHC class I genes as they have a complete reference genome, though the description of all the zebrafish MHC class I genes is incomplete. The goal of this research was to characterize the sequence diversity of the zebrafish MHC class I genes and hypothesize about the functional consequences of this diversity.;Five phylogenetic lineages of MHC class I genes, termed U, Z, L, S, and P, have been identified from multiple bony fish, though zebrafish possess only the U, Z, and L lineages. U lineage proteins are predicted to bind peptides in a manner similar to mammalian classical MHC class I. Zebrafish encode a U lineage locus on chromosome 19 that displays significant haplotypic variation and is the only zebrafish locus that shares conserved synteny with the mammalian MHC core locus. In chapter 3, two additional MHC class I U lineage genes encoded on chromosome 22 are characterized that differ from the other genes in the U lineage in that they do not exhibit many of the characteristics of classical MHC class I genes. A second, alternate haplotype at this locus is also described with a ~30 kb deletion that completely removes the MHC class I genes. In chapter 2 twelve unique MHC class I genes of the Z lineage are introduced that are encoded on zebrafish chromosomes 1 and 3. This chapter provides genomic and experimental evidence that these twelve Z genes represent at least two different haplotypes for each locus. The functional significance of the Z lineage MHC class I genes remains unclear as they exhibit features of both classical and nonclassical molecules. In chapter 4 a preliminary analysis of the zebrafish L lineage is provided identifying 14 unique genes in the latest draft of the reference genome encoded on chromosomes 3, 8, and 25. The L genes appear to encode nonclassical MHC class I proteins that lack the residues thought to be necessary for peptide binding. The only in vitro analysis of this lineage in zebrafish to date is described, providing evidence of L gene expression through RNAseq and RT-PCR. It is observed that the L lineage may be subject to haplotypic variation and suggested that the linkage of L genes on chromosome 8 with MHC class II genes may be a remnant of the ancestral MHC organization that has been maintained in tetrapods and cartilaginous fishes but not in the bony fishes.