Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase

Abstract

The variable lymphocyte receptors (VLRs) of jawless vertebrates such as lamprey and hagfish are composed of highly diverse modular leucine-rich repeats. Each lymphocyte assembles a unique VLR by rearrangement of the germline gene. In the lamprey genome, we identify here about 850 distinct cassettes encoding leucine-rich repeat modules that serve as sequence templates for the hypervariable VLR repertoires. The data indicate a gene conversion-like process in VLR diversification. Genomic analysis suggested a link between the VLR and platelet glycoprotein receptors. Lamprey lymphocytes express two putative deaminases of the AID-APOBEC family that may be involved in VLR diversification, as indicated by in vitro mutagenesis and recombination assays. Vertebrate acquired immunity could have therefore originated from lymphocyte receptor diversification by an ancestral AID-like DNA cytosine deaminase.

A structural basis for antigen recognition by the T cell-like lymphocytes of sea lamprey

“…1A). Additional contacts are mediated by a protruding loop of LRRCT (residues 211-220), which corresponds to the highly variable insert of VLRs (9). This insert is absent from the LRRCTs of all other LRR-containing proteins except platelet receptor glycoprotein Ibα (GpIbα) (18).…”

“…All VLR sequences used here were derived from previous studies (1,2,9). Protein sequence searches were performed using the BLASTPGP and PSI-BLAST programs (31), with a profile threshold of 0.01.…”

“…However, antibodies and TCRs are assembled from V, D, and J gene segments, and VLRs are assembled from multiple LRR-encoding cassettes selected from several hundred that flank each germline VLR gene (2,6,7). This process can generate a vast repertoire of receptors, estimated to comprise more than 10 14 unique VLRs, which is sufficiently diverse to recognize most, if not all, pathogens (7)(8)(9).…”

Structure and specificity of lamprey monoclonal antibodies

“…Two VLR genes, VLR-A and VLR-B, have been identified in both lamprey and hagfish (1)(2)(3). The germline VLR genes are incomplete in that they have coding regions only for the invariant N-terminal and C-terminal sequences, which are separated by intervening sequences, lacking canonical splice sites (1,2).…”

“…During development of lymphocyte lineage cells, components of the flanking LRR modular units are sequentially inserted into the incomplete VLR gene with a concomitant deletion of the intervening sequences (4,5). The stepwise assembly of a mature VLR gene is mediated via a gene conversion mechanism in which AID-APOBEC family members with lymphocyte-restricted expression may serve a catalytic role (3,5). This somatic gene rearrangement process has been estimated to produce a potential repertoire of Ͼ10 14 distinct VLR-B receptors (4).…”