A series of products were amplified using a PCR strategy based on short minimally degenerate primers and R. eglanteria (clearnose skate) spleen cDNA as template. These products were used as probes to select corresponding cDNAs from a spleen cDNA library. The cDNA sequences exhibit significant identity with prototypic (alpha, beta, gamma, and delta T cell antigen receptor (TCR) genes. Characterization of cDNAs reveals extensive variable region diversity, putative diversity segments, and varying degrees of junctional diversification. This demonstrates expression of both alpha/beta and gamma/delta TCR genes at an early level of vertebrate phylogeny and indicates that the three major known classes of rearranging antigen receptors were present in the common ancestor of the present-day jawed vertebrates.

Antigen recognition in the adaptive immune response by Ig and T-cell antigen receptors (TCRs) is effected through patterned differences in the peptide sequence in the V regions. V-region specificity forms through genetically programmed rearrangement of individual, diversified segmental elements in single somatic cells. Other Ig superfamily members, including natural killer receptors that mediate cell-surface recognition, do not undergo segmental reorganization, and contain type-2 C (C2) domains, which are structurally distinct from the C1 domains found in Ig and TCR. Immunoreceptor tyrosine-based inhibitory motifs that transduce negative regulatory signals through the cell membrane are found in certain natural killer and other cell surface inhibitory receptors, but not in Ig and TCR. In this study, we employ a genomic approach by using the pufferfish (Spheroides nephelus) to characterize a nonrearranging novel immune-type receptor gene family. Twentysix different nonrearranging genes, which each encode highly diversified V as well as a V-like C2 extracellular domain, a transmembrane region, and in most instances, an immunoreceptor tyrosine-based inhibitory motif-containing cytoplasmic tail, are identified in an Ϸ113 kb P1 artificial chromosome insert. The presence in novel immune-type receptor genes of V regions that are related closely to those found in Ig and TCR as well as regulatory motifs that are characteristic of inhibitory receptors implies a heretofore unrecognized link between known receptors that mediate adaptive and innate immune functions.V gene diversity ͉ immunoreceptor tyrosine-based inhibitory motif ͉ evolution ͉ adaptive immunity ͉ innate immunity I g and T-cell antigen receptor (TCR) genes are the primary mediators of highly specific adaptive immune responses. Recognition of antigens by these two structurally related but functionally distinct types of antigen-binding receptors is achieved through specific polypeptide folding patterns in N-terminal V regions that are created by both somatic rearrangement of individual segmental elements encoding V, diversity (D), and J regions as well as through nontemplated mechanisms that introduce additional sequence variation (1, 2). Patterns of shared sequence identity, organizational similarities, and a common rearrangement mechanism in Ig and TCR found in jawed vertebrate species are consistent with their origin from a common ancestral form in the distant evolutionary past and diversification in structure and organization throughout vertebrate phylogeny (3). Although V regions have undergone diversification during vertebrate evolution, comparisons of both Ig and TCR, as well as CD8␤, a nonrearranging V region-containing gene expressed on the surface of T cells (4, 5), indicate general conservation of short-sequence motifs in the second and third framework regions (FR2 and FR3) of the V region (6). Sharing of such short-sequence regions forms the basis for a strategy that has been used to identify TCR gene homologs as well as Ig genes and an Ig-like gene ...