DNA-Binding and Complex Formation by RAG Proteins

The defining feature of the vertebrate immune response is the establishment of a repertoire of antibody and T-cell receptor molecules. Individually, each molecule is specific for a single antigen, but an organism generates a tremendous variety of these molecules so that, in aggregate, a broad protection is achieved. Since these receptors are encoded by genes, the question of how such diversity is acquired at the genetic level is crucial. Much of the diversity is now understood to arise from a site-specific DNA recombination process called V(D)J recombination. Coding regions inherited in the germ line of pre- B and pre-T cells are "cut and pasted" in a reaction that assembles the mature gene. The mathematics of the combinatorial joining and additional variation introduced in the product by the deliberate imprecision of the joining mechanism create a degree of diversity that could not be obtained by inheriting preformed genes. Two proteins, RAG1 and RAG2, play an essential role in the reaction. These two proteins have been shown to cut the target DNA at the appropriate site, called the Recombination Signal Sequence (RSS), in an in vitro reaction. V(D)J recombination represents the action of an exquisitely precise machine. We showed that RAG1 and RAG2 form a tetramer without DNA and may form even higher order structures during the reaction. A detailed study of the properties and behavior of the RAG proteins in the absence or presence of DNA and in concert with other proteins in the later steps of the reaction is vital to an understanding of this critical mechanism. We will use chemical crosslinking, biochemical and molecular biological methods to reveal the functions of the RAG proteins in each step in V(D)J recombination. Understanding this mechanism will provide a valuable model for DNA recomb ination and additional highly ordered enzyme systems.