Structural and functional evolution of the extracellular regions of T cell receptors

Structure of a fully assembled γδ T cell antigen receptor

T cells in jawed vertebrates comprise two lineages, αβ T cells and γδ T cells, defined by the antigen receptors they express-that is, αβ and γδ T cell receptors (TCRs), respectively. The two lineages have different immunological roles, requiring that γδ TCRs recognize more structurally diverse ligands1. Nevertheless, the receptors use shared CD3 subunits to initiate signalling. Whereas the structural organization of αβ TCRs is understood2,3, the architecture of γδ TCRs is unknown. Here, we used cryogenic electron microscopy to determine the structure of a fully assembled, MR1-reactive, human Vγ8Vδ3 TCR-CD3δγε2ζ2 complex bound by anti-CD3ε antibody Fab fragments4,5. The arrangement of CD3 subunits in γδ and αβ TCRs is conserved and, although the transmembrane α-helices of the TCR-γδ and -αβ subunits differ markedly in sequence, packing of the eight transmembrane-helix bundles is similar. However, in contrast to the apparently rigid αβ TCR2,3,6, the γδ TCR exhibits considerable conformational heterogeneity owing to the ligand-binding TCR-γδ subunits being tethered to the CD3 subunits by their transmembrane regions only. Reducing this conformational heterogeneity by transfer of the Vγ8Vδ3 TCR variable domains to an αβ TCR enhanced receptor signalling, suggesting that γδ TCR organization reflects a compromise between efficient signalling and the ability to engage structurally diverse ligands. Our findings reveal the marked structural plasticity of the TCR on evolutionary timescales, and recast it as a highly versatile receptor capable of initiating signalling as either a rigid or flexible structure.

The Vγ9Vδ2 T Cell Antigen Receptor and Butyrophilin-3 A1: Models of Interaction, the Possibility of Co-Evolution, and the Case of Dendritic Epidermal T Cells

Most circulating human gamma delta T cells are Vγ9Vδ2 T cells. Their hallmark is the expression of T cell antigen receptors (TCR) whose γ-chains show a Vγ9-JP (Vγ2-Jγ1.2) rearrangement and are paired with Vδ2-containing δ-chains, a dominant TCR configuration, which until recently seemed to occur in primates only. Vγ9Vδ2 T cells respond to phosphoantigens (PAg) such as (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), which is produced by many pathogens and isopentenyl pyrophosphate (IPP), which accumulates in certain tumors or cells treated with aminobisphosphonates such as zoledronate. A prerequisite for PAg-induced activation is the contact of Vγ9Vδ2 T cells with cells expressing butyrophilin-3 A1 (BTN3A1). We will first critically review models of how BTN3 might act in PAg-mediated Vγ9Vδ2 T cell activation and then address putative co-evolution of Vγ9, Vδ2, and BTN3 genes. In those rodent and lagomorphs used as animal models, all three genes are lost but a data-base analysis showed that they emerged together with placental mammals. A strong concomitant conservation of functional Vγ9, Vδ2, and BTN3 genes in other species suggests co-evolution of these three genes. A detailed analysis was performed for the new world camelid alpaca (Vicugna pacos). It provides an excellent candidate for a non-primate species with presumably functional Vγ9Vδ2 T cells since TCR rearrangements share features characteristic for PAg-reactive primate Vγ9Vδ2 TCR and proposed PAg-binding sites of BTN3A1 have been conserved. Finally, we analyze the possible functional relationship between the butyrophilin-family member Skint1 and the γδ TCR-V genes used by murine dendritic epithelial T cells (DETC). Among placental mammals, we identify five rodents, the cow, a bat, and the cape golden mole as the only species concomitantly possessing potentially functional homologs of murine Vγ3, Vδ4 genes, and Skint1 gene and suggest to search for DETC like cells in these species.

Complementary DNA sequences of the constant regions of T-cell antigen receptors α, β and γ in mandarin fish, Siniperca chuatsi Basilewsky, and their transcriptional changes after stimulation with Flavobacterium columnare

In this study, the constant-region genes (Cα, Cβ and Cγ) that encode the T-cell antigen receptor (TCR) α, β and γ chains were cloned from mandarin fish, Siniperca chuatsi Basilewsky, an important freshwater fish species in China. The complementary DNA sequences of Cα, Cβ and Cγ were 843, 716 and 906 base pairs (bp) in length and had a 465-, 289- and 360-bp 3' untranslated region, encoding 125, 142 and 182 amino acids, respectively. The amino-acid sequences of the constant regions of mandarin fish TCR α, β and γ chains (encoded by Cα, Cβ and Cγ, respectively) were most similar to those of their teleost counterparts, showing 60% similarity with pufferfish, 48% similarity with Atlantic salmon and 57% similarity with flounder, respectively. The phylogenetic analysis revealed that the mandarin fish Cα, Cβ and Cγ were clustered, respectively, with their vertebrate counterparts. The mandarin fish Cα, Cβ and Cγ could also be separated into four domains: immunoglobulin; connecting peptide (CP); transmembrane (TM); and cytoplasmic tail. Several conserved features in mammalian TCRs were also found in those of mandarin fish, such as a conserved cysteine residue in the CP domain of Cα, necessary for creating an interchain disulphide bond with the TCR β chain, and a conserved antigen receptor TM motif in Cα and Cβ. Meanwhile, transcripts of Cα, Cβ and Cγ were detectable in all examined organs, with a stronger signal observed in lymphoid organs. In addition, the temporal transcriptional changes for Cα and Cγ were investigated, 1, 2, 3, 4, 5, 6 and 8 weeks after stimulation with Flavobacterium columnare, in head kidney, spleen, blood, thymus, gill and intestine, using real-time polymerase chain reaction. The results demonstrated stimulation-dependent up-regulations in almost all tissues examined, which indicates that T cells may play important roles in preventing mandarin fish from bacterial invasion. In particular, apart from thymus, T cells were distributed mainly in gill and intestine, where striking up-regulation of Cγ was also observed. These results will facilitate functional studies of teleost TCRs and T cells.

Molecular characterization and increased expression of the Nile tilapia, Oreochromis niloticus (L.), T-cell receptor beta chain in response to Streptococcus agalactiae infection

The complete cDNA sequence of the Nile tilapia T-cell receptor (TCR) β chain was cloned using 5' RACE. The full-length, 1263-bp cDNA contained a 942-bp open reading frame (ORF) encoding a 314-amino-acid protein. Sequence analyses revealed that the Nile tilapia TCR β chain contains four conserved cysteine residues involved in the formation of disulphide bridges and a conserved amino acid motif believed to be important for assembly and signalling of the TCR αβ/CD3 complex, both of which are normally found in the TCR β chain of other vertebrates. As detected using semi-quantitative and quantitative RT-PCR, the highest expression level of TCR β was detected in the thymus. Interestingly, Streptococcus agalactiae significantly induced the up-regulation of the TCR β chain, and the strongest up-regulation was detected in the brain and peripheral blood leucocytes (PBLs). In in vitro experiments, concanavalin A and Aeromonas hydrophila were found to significantly increase the expression of the TCR β chain in PBLs after 48 h (P < 0.01) and 72 h (P < 0.05), respectively. Furthermore, real-time PCR analysis showed that intraperitoneal injection (IP) of 10(7) cfu mL(-1) of S. agalactiae could induce TCR β expression that was greater than the expression observed following administration of 10(9) cfu mL(-1). The presence of the TCR β chain in fish detected in this study suggests the presence of T-cell populations that have been found in higher vertebrates, which may play a crucial functional role in the response to fish pathogens.

Divergent T-cell receptor delta chains from marsupials

Complementary DNAs (cDNAs) encoding T-cell receptor delta (TRD) chains from the northern brown bandicoot, Isoodon macrourus, were identified while sequencing expressed sequence tags (ESTs) from a thymus cDNA library. Surprisingly, the I. macrourus TRD sequences were not orthologous to previously published TRD sequences from another Australian marsupial, the tammar wallaby, Macropus eugenii. Identification of TRD genes in the recently completed whole genome sequence of the South American opossum, Monodelphis domestica, revealed the presence of two highly divergent TRD loci. To determine whether the presence of multiple TRD loci accounts for the lack of orthology between the I. macrourus and M. eugenii cDNAs, additional TRD sequences were obtained from both species of marsupials. The results of this analysis revealed that, unlike eutherian mammals, all three species of marsupials have multiple, highly divergent TRD loci. One group of marsupial TRD sequences was closely related to TR sequences from eutherian mammals. A second group of TRD sequences formed a unique marsupial-specific clade, separate from TR sequences from eutherians. An interesting expression pattern of TRD variable (TRDV) and constant (TRDC) segments was evident in cDNAs from I. macrourus and M. eugenii. TRDV and TRDC sequences that were closely related to TRD genes from eutherian mammals were only found in association with each other in cDNAs from both marsupial species. A similar pattern was seen between TRDV and TRDC sequences that were most closely related to other marsupial TRD genes.

The four TCR genes of teleost fish: the cDNA and genomic DNA analysis of Japanese flounder (Paralichthys olivaceus) TCR alpha-, beta-, gamma-, and delta-chains

We have isolated and identified all four TCR alpha, beta, gamma, and delta cDNAs and genomic clones from a Japanese flounder leukocyte cDNA library and bacterial artificial chromosomal genomic library. Numerous TCR transcripts were sequenced to examine the variability against antigenic peptide, and were shown hypervariability on their complementarity-determining region 3 (CDR3) loops. Among CDR3s, CDR3 delta showed a long and broad length distribution, indicating greater similarity to that of Ig. From cDNA sequences and genomic gene analysis of each chain, we found that flounder TCR beta, gamma, and delta have two different C gene segments, while the TCR alpha C region exists as a single segment. The flounder C gammas and C deltas showed different lengths in the connecting peptide (CP) region between the different types of polypeptides. The C delta 1 gene consists of two exons, one that encodes an extracellular Ig-like domain (exon 1) and the other that encodes either a very short or possibly a lacking CP region, a transmembrane region, and a cytoplasmic tail (exon 2); these are located within TCR alpha gene locus. Southern blot analysis, using the bacterial artificial chromosomal genomic DNA clones, revealed that the C delta 2 gene segment, which has a long CP region and different genomic organization to the C delta 1 gene, exists on same gene locus as the TCR gamma-chain. This suggests that the flounder possesses very unique genomic DNA organization and gene loci for TCR, C alpha/C delta 1, and C gamma/C delta 2.

On the role of CD3delta chains in TCRgammadelta/CD3 complexes during assembly and membrane expression

The present study was performed in order to analyze whether T-cell receptor (TCR)/CD3 assembly, intracellular transport and surface expression are carried in a similar way in alphabeta-and gammadelta-T cells. By means of optimal immunoprecipitation conditions with 35S-methionine/cysteine- or biotin-labelled TCR/CD3 proteins from alphabeta- or gammadelta-T-lymphoma-cell lines, as well as TCRgammadelta cDNA transfectants, it was found that CD3delta chains associate less strongly with TCRgammadelta heterodimers compared to TCRalphabeta heterodimers. This preferential reactivity of CD3delta chains appears to be structural and not owing to differences in gammadelta- versus alphabeta-T-cell intracellular environments. Our results are in accordance firstly, with data from CD3delta-deficient mice, which have gammadelta-T cells but no alphabeta-T cells, secondly with the suggested role of CD3delta chains in the positive selection of alphabeta-T cells, a process apparently not followed by gammadelta-T cells, and lastly with the differential roles of CD3delta chains versus CD3gamma chains, explaining the maintenance of two CD3delta and CD3gamma genes after the duplication from a CD3delta/gamma gene present in avians. The impaired reactivity of CD3delta chains with TCRgammadelta heterodimers seems to be owing to a less efficient association with TCRgamma chains. In contrast, CD3delta chains interact as strongly with TCRdelta chains as do CD3gamma chains with both TCRgamma and TCRdelta chains. These data may explain, at the molecular levels, why surface TCR/CD3 expression levels are impaired in gammadelta-T cells from CD3gamma-deficient mice but not from CD3delta-deficient mice.

T-cell antigen receptors in Atlantic cod (Gadus morhua l.): structure, organisation and expression of TCR alpha and beta genes

By using short degenerate primers complementing conserved T-cell antigen receptor (TCR) variable and constant region segments for PCR, we were able to isolate putative TCRalpha and beta chain full length cDNAs in Atlantic cod. The Valpha and Vbeta domains have the canonical features of known teleost and mammalian TCR V domains, including conserved residues in the beginning of FR2 and at the end of FR3. The Jalpha and Jbeta region possess the conserved Phe-Gly-X-Gly motif found in nearly all TCR and immunoglobulin light chain J regions. Similar to other vertebrates, the Atlantic cod Calpha and Cbeta sequences exhibit distinct immunoglobulin, connecting peptide, transmembrane and cytoplasmic regions. The Atlantic cod Cbeta sequence lacks a cysteine in its connecting peptide region, but other motifs proposed to be important for dimerisation and cell surface expression are observed. Four different cod Cbeta sequences were identified, two of which share 3' untranslated regions different from one of the other two sequences, suggesting the existence of isotypic gene variants of Cbeta. Based on Southern blot analyses, the TCRalpha and beta gene loci appear to be arranged in translocon organisation (as opposed to multicluster) with multiple V gene segments, some (D) and J gene segments and a single or few C gene segments. Northern blot analyses show expression of the TCRalpha and beta chains in thymus, spleen and head kidney, expression of the TCRbeta chain was also detected in the ovary. Interestingly, no expression was detected in intestine even though the existence of T-cells in intestine has been proposed in other teleost species.

In search of the origin of the thymus: the thymus and GALT may be evolutionarily related

The thymus is the major primary immune tissue for the production of functional T lymphocytes in vertebrates. However, its evolutionary origin is unknown. It has recently been shown that the generation of local T cells also occurs in gut-associated lymphoid tissues (GALT). This suggests that the thymus and GALT have similar functions and that they might be evolutionarily related. We discuss the possibility that the thymus may have evolved from mucosa-associated lymphoid tissues (MALT) located in the gill region in early vertebrates. Various facts supporting this proposal are summarized.

Expression of functional CD8alpha Beta heterodimer on rat gamma delta T cells does not correlate with the CDR3 length of the TCR delta chain predicted for MHC class I-restricted antigen recognition

In accordance with their lack of MHC restriction, most mouse and human gamma delta T cells express neither the CD4 nor CD8(alpha beta) coreceptor. In striking contrast, up to 80% of splenic rat gamma delta T cells express the CD8alpha beta isoform of CD8, which for the alpha beta T cell subset serves as a marker for MHC class I-restricted cells. We compared CD8 on alpha beta and gamma delta T cells with regard to co-stimulatory function and correlation of CD8 expression with TCRDV usage and CDR3delta length. In both subsets, CD8 acted as a co-stimulatory molecule in vitro and was found to bind the kinase lck efficiently. No differences between the CDR3delta length spectra of CD8+ and CD8- gamma delta T cells or between unselected thymic and peripheral gamma delta T cells were found. As seen in man and mice, CDR3delta were rather long, a structural feature which can be expected to interfere with an alpha beta TCR-like mode of MHC class I binding. In summary, CD8 expressed by rat gamma delta T cells is a molecule with the potential to act as a coreceptor, but its expression gives no indication for antigen recognition analogous to that of MHC class I-restricted alpha beta T cells.

Characterization of an Avian (Gallus gallus domesticus) TCR αδ Gene Locus

Mammalian TCRδ genes are located in the midst of the TCRα gene locus. In the chicken, one large Vδ gene family, two Dδ gene segments, two Jδ gene segments, and one Cδ gene have been identified. The TCRδ genes were deleted on both alleles in αβ T cell lines, thereby indicating conservation of the combined TCRαδ locus in birds. Vα and Vδ gene segments were found to rearrange with one, both or neither of the Dδ segments and either of the two Jδ segments. Exonuclease activity, P-addition, and N-addition during VDJδ rearrangement contributed to TCRδ repertoire diversification in the first embryonic wave of T cells. An unbiased Vδ1 repertoire was observed at all ages, but an acquired Jδ1 usage bias occurred in the TCRδ repertoire. The unrestricted combinatorial diversity of relatively complex TCRγ and δ loci may contribute to the remarkable abundance of γδ T cells in this avian representative.

T-cell receptors in channel catfish: structure and expression of TCR alpha and beta genes

Herein are reported full length cDNA sequences for TCR alpha- and beta-chains of the channel catfish. Included are sequences belonging to four Valpha and six Vbeta families which share hallmarks in common with the Valpha and Vbeta genes of other species. Similar to the situation in other vertebrates, the catfish Calpha and Cbeta sequences exhibit distinct immunoglobulin, connecting peptide, transmembrane and cytoplasmic domains. However, the catfish TCR Calpha and Cbeta regions are shorter than those of mammals and the catfish Cbeta chain lacks a cysteine in its connecting peptide region. Two different catfish Cbeta cDNA sequences were identified, suggesting the existence of either two Cbeta loci or allotypes. Based on Southern blot analyses, each of the catfish TCR gene loci appear to be arranged in a translocon (as opposed to multicluster) organization with multiple V elements and a single or few copies of C region DNA. At the deduced amino acid level, the catfish Cbeta sequence exhibits 42% identity with the Cbeta of Atlantic salmon, 41% identity with the Cbeta of rainbow trout and 26% identity with Cbeta of the horned shark. The catfish Calpha amino acid sequence exhibits 44 and 29% identity with Calpha of the rainbow trout and southern pufferfish, respectively. TCRalpha and beta messages are selectively expressed and rearranged in a catfish clonal cell line that appears to be of the T lineage. This TCR alpha/beta expressing clonal lymphocyte line, designated 28S.1, has T-cell like function in that it constitutively produces a supernatant factor(s) with growth promoting activity. These findings should facilitate functional studies of fish TCRs and T cells in ways not previously possible with other 'lower' vertebrate models.

Characterization of avian T-cell receptor gamma genes

In birds and mammals T cells develop along two discrete pathways characterized by expression of either the alpha beta or the gamma delta T-cell antigen receptors (TCRs). To gain further insight into the evolutionary significance of the gamma delta T-cell lineage, the present studies sought to define the chicken TCR gamma locus. A splenic cDNA library was screened with two polymerase chain reaction products obtained from genomic DNA using primers for highly conserved regions of TCR and immunoglobulin genes. This strategy yielded cDNA clones with characteristics of mammalian TCR gamma chains, including canonical residues considered important for proper folding and stability. Northern blot analysis with the TCR gamma cDNA probe revealed 1.9-kb transcripts in the thymus, spleen, and a gamma delta T-cell line, but not in B or alpha beta T-cell lines. Three multimember V gamma subfamilies, three J gamma gene segments, and a single constant region C gamma gene were identified in the avian TCR gamma locus. Members of each of the three V gamma subfamilies were found to undergo rearrangement in parallel during the first wave of thymocyte development. TCR gamma repertoire diversification was initiated on embryonic day 10 by an apparently random pattern of V-J gamma recombination, nuclease activity, and P-and N-nucleotide additions to generate a diverse repertoire of avian TCR gamma genes early in ontogeny.

Heavy-chain variable regions in carcharhine sharks: development of a comprehensive model for the evolution of VH domains among the gnathanstomes

We determined the sequence of 18 DNA clones encoding VH regions of sandbar shark and bull shark. All of these sequences exhibit key structural coding features characteristic of known VH genes of higher vertebrates. These VH sequences disclosed considerable diversity, and can be divided into six families according to the criterion of 80% DNA sequence identity. The overlapping of some VH gene clones to two or more families is a particular feature found in carcharhine sharks, which suggests that VH diversification is a continuing process. The basic sequence patterns of heavy-chain V regions found in all representative gnathanstomes and in VH of the shark heavy immunoglobulin IgW provides evidence for selection of canonical residues in all VH structures. Elasmobranch VH sequences can be divided into two classes or clans, one comprising the 'classical' VH set and the other comprising VHS related to those of IgW (V omega). Phylogenetic analyses place the VH cluster as the root of all the classic VHS and indicates that the V omega set is most probably that of the primordial heavy chain.