The origins of the Rag genes--from transposition to V(D)J recombination

Abstract

The recombination activating genes 1 and 2 (Rag1 and Rag2) encode the key enzyme that is required for the generation of the highly diversified antigen receptor repertoire central to adaptive immunity. The longstanding model proposed that this gene pair was acquired by horizontal gene transfer to explain its abrupt appearance in the vertebrate lineage. The analyses of the enormous amount of sequence data created by many genome sequencing projects now provide the basis for a more refined model as to how this unique gene pair evolved from a selfish DNA transposon into a sophisticated DNA recombinase essential for immunity.

Figure 1. The enzymatic activities of Rag1/Rag2

This is a schematic representation of the reactions catalyzed by the Rag recombinase in vivo and in vitro. Gene segments are indicated as boxes on the double-stranded DNA, and the flanking RSSs are shown as triangles. The initial hydrolysis step, creating single strand breaks, occurs at the RSS-gene segment borders, and is followed by a direct transesterification process, giving rise to hairpin-sealed “coding ends” at the gene segments and “signal ends” at the RSSs. In vivo, the DNA ends get rejoined leading to precise “signal joints”, and imprecise “coding joints” (hatched box) as this ligation step requires additional processing of the DNA ends. Note that the joining steps involve the Rag1/Rag2 complex but also require non-homologous end joining DNA repair factors. The alternative fate of the RSS-flanked DNA segment in vitro (and to a limited extend in vivo) is the result of a second transesterification that integrates this fragment into a target DNA location. This pathway represents a bona fide transposition reaction, and does not require any additional enzymes besides the Rag1/Rag2 complex.

Figure 2. Current model of the origins of the Rag1/Rag2 gene cluster

This is a schematic representation of the “Rag1-only” transposon concept, and also illustrates the “two step” concept of the evolution of V(D)J recombination (see section Open Questions). Coding regions are drawn as open boxes with the name of the gene inside, RSS-like TIRs and RSSs of flanking mobile elements as triangles, and directions of transcription are shown by arrows. In a common ancestor of all living deuterostomes, a Rag1-like transposable element integrates next to a Rag2-like gene. The box with “?” indicates that the N-terminus of Rag1 may have either been part of the original transposon or of a gene into which it integrated. The TIRs flanking the transposon are lost, and a functional interaction of the prototypical Rag1 and Rag2 (prot-Rag1 and prot-Rag2) proteins emerged, serving an unknown primitive function. As the lineages that led to sea urchins and jawed vertebrates diverged, the sea urchin gene cluster (SpRag1L/SpRag2L) may have retained this original function, while the vertebrate genes (Rag1/Rag2) evolved into the V(D)J recombinase. The disruption of a V-type Ig-like receptor gene by an RSS-flanked mobile element, an event that is predicted to have occurred in a common ancestor of all jawed vertebrates, represents a critical step in this process.