UBC Theses and Dissertations
The DNA sequence of a rat RT1 Esub β DNA : assessment of homology within class 11β chains Robertson, Katherine Anne
The Major Histocompatibility Complex (MHC) is a group of loci encoding cell surface glycoproteins involved in the regulation of the immune response. The loci within the complex display an unusually high degree of polymorphism in the two species studied to date; mice and humans. In order to determine if this polymorphism is found across other species, and if the encoded molecules show consistent similarities across the species, the MHC of a third mammal, the rat, was studied. The MHC of the rat, the RT1 Complex, codes for two types of Class II molecules, A and E, each composed of an α and β chain. A cDNA library made from Wistar rat spleen poly(A) RNA was screened with a DNA fragment from an RT1 Aβ gene to determine the coded message of a Class II β gene. A single cDNA clone was isolated and when sequenced was found to encode the complete RT1 Eg chain on the basis of comparison to the sequence of the Class II β chains of mice, as this chain had not been previously sequenced in the rat. The predicted protein sequence of the RT1 Eβ chain was found to contain greater amino acid sequence identity to the equivalent genes in mice and humans (82% and 73%) than to the RT1 Aβ gene (58%). Comparison of the predicted proteins of the A and Eβ genes of rats, mice and humans showed 105 out of 278 residues were identical across all six chains. In all six chains a number of regions containing stretches of identical residues were found which may be residues involved in structure and function. The divergence of the Aβ and Eβ chains across three species was examined by comparing the number of replacement and silent nucleotide changes between the protein coding sequences. This comparison showed that whereas the number of silent site substitutions increased with increasing species divergence, the number of replacement site substitutions did not, suggesting that these substitutions are under selective pressure.