The Evolution of Rag Gene Enhancers and Transcription Factor E and Id Proteins in the Adaptive Immune System

Abstract

Adaptive immunity relies on the V(D)J DNA recombination of immunoglobulin (Ig) and T cell receptor (TCR) genes, which enables the recognition of highly diverse antigens and the elicitation of antigen-specific immune responses. This process is mediated by recombination-activating gene (Rag) 1 and Rag2 (Rag1/2), whose expression is strictly controlled in a cell type-specific manner; the expression of Rag1/2 genes represents a hallmark of lymphoid lineage commitment. Although Rag genes are known to be evolutionally conserved among jawed vertebrates, how Rag genes are regulated by lineage-specific transcription factors (TFs) and how their regulatory system evolved among vertebrates have not been fully elucidated. Here, we reviewed the current body of knowledge concerning the cis-regulatory elements (CREs) of Rag genes and the evolution of the basic helix-loop-helix TF E protein regulating Rag gene CREs, as well as the evolution of the antagonist of this protein, the Id protein. This may help to understand how the adaptive immune system develops along with the evolution of responsible TFs and enhancers.

Keywords: E protein; Id protein; Rag1/2 gene enhancers; T and B cell development; adaptive immune system; bHLH transcription factors.

Figure 1

Rag gene enhancers in developing T and B cells. A schematic diagram of Rag gene locus and enhancers in developing T and B cells. The blue box indicates T cell-specific enhancer (R-TEn) and TF binding in pro-T and DP cells. The green boxes indicate B cell-specific enhancers (R1B and R2B) and TF binding in pro-/pre-B cells. The red lines indicate the Rag1-promoter region (R1pro) and silencer (Silencer) of Rag gene, respectively.

Figure 2

Schematic summary of the conservation of R-TEn, R1B, and R2B among vertebrates. Black, dotted lines indicate the border between placentaria and maruspialia, reptile and amphibia, and fish and agnathans. The conserved motifs in each enhancer region are shown in the box [21].

Figure 3

Maximum likelihood phylogenetic trees of homologs of E proteins (A) and Id proteins (B). Sequences were aligned using MAFFT (v7.453) [68] with default parameters. Tree reconstruction was performed using RAxML (version 8.2.12) [69] with the JTT + F substitution model and PROTGAMMA parameter with 100 bootstrap replicates. Phylogenetic trees were visualized using MEGA-X (version 10.2.4) [70]. Bootstrap values are given along the branches.