The molecular origins of the recombining immune system.

Abstract

This dissertation examines the molecular origins of the recombining immune system. Two strategies were adopted involving the examination of the immune system of the most ancient extant organism possessing the vertebrate type immune response, the Carcharhine shark. First, the structural components of a primordial immunoglobulin (Ig) were examined on a molecular level. This revealed a new class of Ig termed IgW. Although IgW is the largest Ig yet described, with 7 bona fide Ig domains, it maintains the canonical residues typified by heavy chain V and C-regions. Because of these canonical residues, IgW is thought to both dimerise with light chains and associate with antigen as a typical heavy chain. IgW also possesses V-regions which are more similar to its own C-regions than any Ig yet described. In phylogenetic tree analysis, the IgW molecule is continually found to be the "root" of the Ig V and C-region trees constructed from the known V and C-region genes. This, and IgW's V and C-region similarities support the contention that IgW is the most ancient Ig yet cloned, possibly being most closely related to the primordiallg gene. The second strategy adopted was the examination of the shark's V(O)J rearrangement machinery. The recombinase activating gene I (RAG I) is responsible for creating diversity in all extant gnathastomes, which is the hallmark of the recombining immune system. The shark RAG I was found to be extremely homologous to the known vertebrate RAG I genes, both at the nucleotide and amino acid levels (∼64 % identical at both levels). Homology domains identified by the comparison of the vertebrate RAG I's and the shark RAG I prompted sequence comparison analyses which suggested similarity of the RAG I and II genes to the integrase family and the integration host factor genes, respectively, of the bacterial site specific recombination system. This was used in conjunction with several shark VH "hairpin" detecting rearrangement intermediate experiments to propose a new and more complete model of V(D)J recombination.