Rearrangement of Immunoglobulin Genes in Shark Germ Cells

Abstract

The variable (V), (diversity [D]), and joining (J) region recombinases (recombination activating genes [RAGs]) can perform like transposases and are thought to have initiated development of the adaptive immune system in early vertebrates by splitting archaic V genes with transposable elements. In cartilaginous fishes, the immunoglobulin (Ig) light chain genes are organized as multiple VJ-constant (C) clusters; some loci are capable of rearrangement while others contain fused VJ. The latter may be key to understanding the evolutionary role of RAG. Are they relics of the archaic genes, or are they results of rearrangement in germ cells? Our data suggest that some fused VJ genes are not only recently rearranged, but also resulted from RAG-like activity involving hairpin intermediates. Expression studies show that these, like some other germline-joined Ig sequences, are expressed at significant levels only early in ontogeny. We suggest that a rejoined Ig gene may not merely be a sequence restricting antibody diversity, but is potentially a novel receptor no longer tied to somatic RAG expression and rearrangement. From the combined data, we arrived at the unexpected conclusion that, in some vertebrates, RAG is still an active force in changing the genome.

Shark Ig Light Chain Junctions Are as Diverse as in Heavy Chains

“…It is now found that the cDNA sequences are all encoded by a small family consisting of one germline-joined cluster and two clusters capable of rearrangement. Together with the NS4 L chain, this is another instance where clusters with joined as well as split gene organizations of an IgL isotype has been found, supporting the idea of rare VJ recombination taking place in the shark germ cells (10). NS5 is a very small family of genes, and the same genes are carried by several sharks from the wild.…”

“…That is, like the NS4 isotype, some NS5 loci contain split V and J gene segments that rearrange in somatic cells while others carry preassembled VJ sequences. The NS4 V genes are closely related (up to 99% identity), enabling the construction of a molecular clock to estimate dates of the recombination events that produced the six germline-joined genes; they are thought to have occurred over a period of 0 -49 million years ago (10). At 82% identity with NS5-2, the rearranged NS5-16 V gene is a member of the same family and definitely not a translocation from the NS3 or NS4 loci, but it diverged a long time ago from the NS5 split genes.…”

“…1). NS4, the L chain homologue (9), is the largest IgL gene family and consists of ϳ60 loci, 6 of which carry fused VJ but the rest can rearrange (10). In contrast, all six NS3 L chain clusters carry germline-joined VJ (11); we had asked whether these preassembled Ig sequences remain invariant throughout the life of the shark.…”

Four primordial immunoglobulin light chain isotypes, including λ and κ, identified in the most primitive living jawed vertebrates

“…For example, extant cartilaginous fish have two H chain isotypes that are expressed in lineages of B cells rather than by class switch [21,27,[37][38][39]. Thus, both the V and C domains of the L chains may have coevolved with H chains to influence L chain evolution.…”

“…4), suggest that nurse shark r genes are also in the cluster configuration. Another unusual feature of shark Ig genes is the phenomenon of germline joining of V-J or V(D)J via RAG activity in germ cells [21]. In nurse shark some or all of the V-J segments are joined for each previously studied isotype.…”