Insights into RAG evolution from the identification of “missing link” family ARAGLtransposons

Abstract

ABSTRACTA series of “molecular domestication” events are thought to have converted an invertebrate RAG-like (RAGL) transposase into the RAG1-RAG2 (RAG) recombinase, a critical enzyme for adaptive immunity in jawed vertebrates. The timing and order of these events is not well understood, in part because of a dearth of information regarding the invertebrateRAGL-Atransposon family. In contrast to the abundant and divergentRAGL-Btransposon family,RAGL-Amost closely resemblesRAGand is represented by a single orphanRAG1-like(RAG1L) gene in the genome of the hemichordatePtychodera flava(PflRAG1L-A). Here, we provide evidence for the existence of completeRAGL-Atransposons in the genomes ofP. flavaand several echinoderms. The predicted RAG1L-A and RAG2L-A proteins encoded by these transposons intermingle sequence features of jawed vertebrate RAG and RAGL-B transposases, leading to a prediction of DNA binding, catalytic, and transposition activities that are a hybrid of RAG and RAGL-B. Similarly, the terminal inverted repeats (TIRs) of theRAGL-Atransposons combine features of bothRAGL-Btransposon TIRs and RAG recombination signal sequences. Unlike all previously described RAG2L proteins, PflRAG2L-A and echinoderm RAG2L-A contain an acidic hinge region, which we demonstrate is capable of efficiently inhibiting RAG-mediated transposition. Our findings provide evidence for a critical intermediate in RAG evolution and argue that certain adaptations thought to be specific to jawed vertebrates (e.g., the RAG2 acidic hinge) actually arose in invertebrates, thereby focusing attention on other adaptations as the pivotal steps in the completion of RAG domestication in jawed vertebrates.