Evolutionarily conserved TCR binding sites, identification of T cells in primary lymphoid tissues, and surprising trans-rearrangements in nurse shark.

Cartilaginous fish are the oldest animals that generate RAG-based Ag receptor diversity. We have analyzed the genes and expressed transcripts of the four TCR chains for the first time in a cartilaginous fish, the nurse shark (Ginglymostoma cirratum). Northern blotting found TCR mRNA expression predominantly in lymphoid and mucosal tissues. Southern blotting suggested translocon-type loci encoding all four chains. Based on diversity of V and J segments, the expressed combinatorial diversity for gamma is similar to that of human, alpha and beta may be slightly lower, and delta diversity is the highest of any organism studied to date. Nurse shark TCRdelta have long CDR3 loops compared with the other three chains, creating binding site topologies comparable to those of mammalian TCR in basic paratope structure; additionally, nurse shark TCRdelta CDR3 are more similar to IgH CDR3 in length and heterogeneity than to other TCR chains. Most interestingly, several cDNAs were isolated that contained IgM or IgW V segments rearranged to other gene segments of TCRdelta and alpha. Finally, in situ hybridization experiments demonstrate a conservation of both alpha/beta and gamma/delta T cell localization in the thymus across 450 million years of vertebrate evolution, with gamma/delta TCR expression especially high in the subcapsular region. Collectively, these data make the first cellular identification of TCR-expressing lymphocytes in a cartilaginous fish.

Allelic polymorphism of TCRalpha chain constant domain genes in the bicolor damselfish.

T cell receptor (TCR) chains are composed of two extracellular domains, the membrane-distal variable domain and the membrane-proximal constant domain. Data presented here show that the TCRA 'constant' (C) domain of damselfish exhibits considerable allelic polymorphisms that appear to be positively selected. Each of 32 damselfish TCRAC clones showed different patterns of atypical polymorphism in the constant region. Twenty-three of the 121 TCRalpha constant region amino acid residues show substitutions, clustered mainly in the loops between the beta strands. Coding regions of the TCRAC genes differ by up to 8% at the nucleotide level and 20% at the amino acid level. Southern hybridization, polymorphism segregation, and genomic cloning data suggest allelic polymorphism at two TCRAC genes, distinguished by a single amino acid. KA/KS ratios suggest that balancing selection is acting to maintain polymorphisms at the variable sites of one of these genes, but not the other, in a manner comparable to the peptide binding regions of MHC. Nonetheless, each TCRAC gene is spliced to variable and joining segments similar to those described in other species. These data suggest that our understanding of the function of the TCR constant domains of these vertebrates is incomplete.

Allelic polymorphism of T-cell receptor constant domains is widespread in fishes.

T-cell receptor chains contain membrane-proximal constant domains of the immunoglobulin superfamily that are relatively invariant in mammalian species. In contrast, recent studies in the bicolor damselfish have demonstrated surprising allelic polymorphism in the TCR alpha ( A) and TCR beta ( B) "constant" (C) domain genes. This report extends these initial observations beyond Perciformes to two other orders of teleost fishes. Studies in both the Atlantic cod and zebrafish show high levels of polymorphism in the TCRA constant genes. Levels of 13% and 15% amino acid nonidentity were found within cod and zebrafish, respectively. Evolutionary analysis of codon usage suggests that positive selection maintains the high number of TCRAC alleles in these fish populations. Additionally, investigation of a TCRB constant gene from the Beau Gregory, a sister species of the bicolor damselfish, shows no evidence of transpecies maintenance of constant region alleles. These data argue that the T-cell receptor constant domain is being employed by many vertebrates in a manner inconsistent with our current understanding, and may indicate unheralded complexity in signal transduction through the TCR/CD3 complex.

Proteasome, transporter associated with antigen processing, and class I genes in the nurse shark Ginglymostoma cirratum: evidence for a stable class I region and MHC haplotype lineages.

Cartilaginous fish (e.g., sharks) are derived from the oldest vertebrate ancestor having an adaptive immune system, and thus are key models for examining MHC evolution. Previously, family studies in two shark species showed that classical class I (UAA) and class II genes are genetically linked. In this study, we show that proteasome genes LMP2 and LMP7, shark-specific LMP7-like, and the TAP1/2 genes are linked to class I/II. Functional LMP7 and LMP7-like genes, as well as multiple LMP2 genes or gene fragments, are found only in some sharks, suggesting that different sets of peptides might be generated depending upon inherited MHC haplotypes. Cosmid clones bearing the MHC-linked classical class I genes were isolated and shown to contain proteasome gene fragments. A non-MHC-linked LMP7 gene also was identified on another cosmid, but only two exons of this gene were detected, closely linked to a class I pseudogene (UAA-NC2); this region probably resulted from a recent duplication and translocation from the functional MHC. Tight linkage of proteasome and class I genes, in comparison with gene organizations of other vertebrates, suggests a primordial MHC organization. Another nonclassical class I gene (UAA-NC1) was detected that is linked neither to MHC nor to UAA-NC2; its high level of sequence similarity to UAA suggests that UAA-NC1 also was recently derived from UAA and translocated from MHC. These data further support the principle of a primordial class I region with few class I genes. Finally, multiple paternities in one family were demonstrated, with potential segregation distortions.