A novel multigene family encodes diversified variable regions

Abstract

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 ...

Reconstructing immune phylogeny: new perspectives

“…The germline-diversified V domains in NITRs are an example of an adaptive immune feature in an innate immune receptor 73,74 , whereas germline joining of immunoglobulin-gene clusters in cartilaginous fish is an example of an innate immune feature in an adaptive immune receptor 18 . The Dscam variants in insects 10 , the FREPs in snails 8,126 , the VLRs in the jawless vertebrates lampreys 9 and hagfish 99 , and Our historical considerations of the evolution of adaptive immunity have centred on the origins of the adaptive antigen-binding immune receptors themselves, as well as the MHC class I and class II molecules on which T-cell function depends so closely and the origins in phylogeny of which seem to coincide with the emergence of the antigen-binding receptors.…”

“…The germline-diversified V domains in NITRs are an example of an adaptive immune feature in an innate immune receptor 73,74 , whereas germline joining of immunoglobulin-gene clusters in cartilaginous fish is an example of an innate immune feature in an adaptive immune receptor 18 . The Dscam variants in insects 10 , the FREPs in snails 8,126 , the VLRs in the jawless vertebrates lampreys 9 and hagfish 99 , and the VCBPs in the protochordate amphioxus 7,113 all share certain fundamental characteristics with the adaptive antigen-binding immune receptors of jawed vertebrates.…”

“…However, given the diversity of NK-cell receptors that have already been identified in mammals, this could prove daunting. The NITRs (novel immune-type receptors) -a large multigene family of NK-cell-like activating and inhibitory cell-surface receptors in bony fish -show an intriguing link between conventional adaptive immune receptors and innate immune receptors 73 (TABLE 1) 74 . Some NITRs have amino-acid motifs that are related to the IMMUNORECEPTOR TYROSINE-BASED SWITCH MOTIF (ITSM) that has been described in members of the mammalian CD2, SIRP (signal-regulatory protein), SIGLEC (sialic-acidbinding immunoglobulin-like lectin), CEA (carcinoembryonic antigen) and PIR (paired immunoglobulin-like receptor) families, potentially allowing the modulation of signalling by differential interaction with SRC homology 2 (SH2)-domain-containing adaptor proteins (thereby allowing either activating or inhibitory function) 75 .…”

“…In pufferfish, 13 main families of NITR V regions are encoded at a single compact locus 73 . In zebrafish, 12 families of NITR V domains are encoded at a single locus on chromosome 7 (REF.…”

Evidence for a transposition event in a second NITR gene cluster in zebrafish

“…The novel immune-type receptors (NITRs) are a large family of cell surface receptors that have been identified in bony fish species (Strong et al 1999;Yoder et al 2001;Hawke et al 2001;Yoder et al 2002;Piyaviriyakul et al 2006;Evenhuis et al 2007). NITRs share structural and signaling similarities with the mammalian natural killer (NK) receptors encoded by the leukocyte receptor complex (e.g.…”