Crystal Structure of the Lamprey Variable Lymphocyte Receptor C Reveals an Unusual Feature in Its N-Terminal Capping Module

Abstract

Jawless vertebrates represented by lampreys and hagfish use variable lymphocyte receptors (VLRs) as antigen receptors to mount adaptive immune responses. VLRs generate diversity that is comparable to immunoglobulins and T-cell receptors by a gene conversion-like mechanism, which is mediated by cytosine deaminases. Currently, three types of VLRs, VLRA, VLRB, and VLRC, have been identified in lampreys. Crystal structures of VLRA and VLRB in complex with antigens have been reported recently, but no structural information is available for VLRC. Here, we present the first crystal structure of VLRC from the Japanese lamprey (Lethenteron japonicum). Similar to VLRA and VLRB, VLRC forms a typical horseshoe-like solenoid structure with a variable concave surface. Strikingly, its N-terminal cap has a long loop with limited sequence variability that protrudes toward the concave surface, which is the putative antigen-binding surface. Furthermore, as predicted previously, its C-terminal cap lacks a highly variable protruding loop that plays an important role in antigen recognition by lamprey VLRA and VLRB. Recent work suggests that VLRC+ lymphocytes in jawless vertebrates might be akin to γδ T cells in jawed vertebrates. Structural features of lamprey VLRC described here suggest that it may recognize antigens in a unique manner.

Selection of the lamprey VLRC antigen receptor repertoire

“…This, together with the spatial distributions of the high entropy sites in the LRRV modules suggests that the general mode of antigen engagement by the central concave region is conserved across the VLRs. As noted previously (27), VLRC molecules exhibit several high entropy sites on the convex side of the molecule, in addition to those on the concave, presumably antigen-binding surface (Fig. 4 A-C and Fig.…”

“…In the VLRC.1MP structure, the LRRCT insert comprises only 2 residues and does not protrude from LRRCT or extend across the concave surface of the VLR. This structural feature is characteristic of both lamprey and hagfish VLRCs (26,27) and distinguishes them from VLRAs and VLRBs.…”

“…Assemblies in blood minus assemblies in thymoid from Japanese lamprey (Lethenteron japonicum) (3WO9) (78% sequence identity) (27), gave rms differences in Cα positions of 1.4 and 0.9 Å, respectively. Compared with VLRAs and VLRBs, VLRC.1MP contains a loop insert of eight amino acids (residues 15-22) in LRRNT (Fig.…”

“…Compared with VLRAs and VLRBs, VLRC.1MP contains a loop insert of eight amino acids (residues 15-22) in LRRNT (Fig. S1C) that was also present in Japanese lamprey VLRC (27). This loop, which connects two antiparallel β-strands in LRRNT (β1 and β2), projects toward the concave surface of VLRC.1MP and could therefore potentially contact antigen or an antigenpresenting molecule (Fig.…”

Genomic donor cassette sharing duringVLRAandVLRCassembly in jawless vertebrates

“…A phylogenetic analysis of modules found in mature hagfish VLR assemblies supports the notion that LRRNT and LRRCT modules form distinct clades, with VLRA and VLRC forming sister branches; notable exceptions are the LRRNTs of lamprey VLRC molecules, which did not group with LRRNTs of hagfishes (SI Appendix, Fig. S1A), consistent with the unusual divergence of the lamprey VLRCs with the acquisition of a neomorphic insert in LRRNT modules (18). Like lamprey modules, hagfish LRR1, LRRV, and CP modules tend to be mixed together in the trees (SI Appendix, Figs.…”