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Structural insights into the evolution of the RAG recombinase

Nature Reviews Immunology volume 22, pages 353–370 (2022)Cite this article

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Abstract

Adaptive immunity in jawed vertebrates relies on the assembly of antigen receptor genes by the recombination activating gene 1 (RAG1)–RAG2 (collectively RAG) recombinase in a reaction known as V(D)J recombination. Extensive biochemical and structural evidence indicates that RAG and V(D)J recombination evolved from the components of a RAG-like (RAGL) transposable element through a process known as transposon molecular domestication. This Review describes recent advances in our understanding of the functional and structural transitions that occurred during RAG evolution. We use the structures of RAG and RAGL enzymes to trace the evolutionary adaptations that yielded a RAG recombinase with exquisitely regulated cleavage activity and a multilayered array of mechanisms to suppress transposition. We describe how changes in modes of DNA binding, alterations in the dynamics of protein–DNA complexes, single amino acid mutations and a modular design likely enabled RAG family enzymes to survive and spread in the genomes of eukaryotes. These advances highlight the insight that can be gained from viewing evolution of vertebrate immunity through the lens of comparative genome analyses coupled with structural biology and biochemistry.

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Fig. 1: Overview of V(D)J recombination, RAG and RAGL transposases.
Fig. 2: Transposition, recombination and evolution of the RAG recombinase.
Fig. 3: Structural comparison of HzTransib and RAG illustrating functional implications of RAG2 acquisition.
Fig. 4: Regulation of transposition in RAG and RAGL proteins.
Fig. 5: Domains and residues regulating RAG binding and cleavage activity.
Fig. 6: Distribution of modules in RAG and RAGL proteins in metazoans.

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Acknowledgements

The authors thank E. Martin and A. Petrescu for sequence and structural analyses that contributed to developing the conceptual framework for this Review, and A. Roger and D. Pisani for advice on the timing of divergence of metazoan lineages. This work was supported by US National Institutes of Health (NIH) grants AI137079 and AI32524 (to D.G.S.).

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Author notes

  1. These authors contributed equally: Chang Liu, Yuhang Zhang.

Authors and Affiliations

  1. Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA

    Chang Liu & David G. Schatz

  2. School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China

    Yuhang Zhang

  3. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA

    Catherine C. Liu

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  1. Chang Liu
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  2. Yuhang Zhang
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  3. Catherine C. Liu
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All authors contributed substantially to the design of the figures, discussion of content and writing of the manuscript.

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Correspondence to David G. Schatz.

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Nature Reviews Immunology thanks T. Boehm; M. Criscitiello, who co-reviewed with J. Ott; and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Related links

RCSB Protein Data Bank (PDB): https://www.rcsb.org/

Glossary

Selfish DNA

A genetic element that can make additional copies of itself in the genome of a host and that provides no specific benefit to the host.

Terminal inverted repeats

(TIRs). Inverted repeat sequences found at the extreme termini of transposons that are recognized and cleaved by the transposase during transposition.

Target capture complex

(TCC). A complex formed after DNA cleavage that contains transposase, terminal inverted repeats (TIRs) flanking the transposon and captured target DNA, and in which TIRs and target DNA have yet to be covalently linked.

Strand transfer complex

(STC). A complex formed from the target capture complex that contains transposase, terminal inverted repeats (TIRs) and captured target DNA, in which covalent links connect the TIRs to the target DNA.

Coding joints

The products that result from joining of the two coding segments after DNA cleavage during V(D)J recombination.

Signal joints

The products that result from joining of the two recombination signal sequences after DNA cleavage during V(D)J recombination.

Transposon molecular domestication

An evolutionary process in which components of a transposon are repurposed to carry out a function that is useful to the host organism.

Pre-reaction complex

A protein–DNA complex in which RAG or RAG-like (RAGL) protein is bound to its DNA substrates but DNA cleavage has not yet been initiated.

Hairpin-forming complex

(HFC). An intermediate in the DNA cleavage reaction in which RAG or RAG-like (RAGL) protein is bound to its DNA substrates and DNA nicking, but not hairpin formation, has occurred.

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Liu, C., Zhang, Y., Liu, C.C. et al. Structural insights into the evolution of the RAG recombinase. Nat Rev Immunol 22, 353–370 (2022). https://doi.org/10.1038/s41577-021-00628-6

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