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Lefranc MP, Lefranc G. IMGT®Homo sapiens IG and TR Loci, Gene Order, CNV and Haplotypes: New Concepts as a Paradigm for Jawed Vertebrates Genome Assemblies. Biomolecules 2022; 12:biom12030381. [PMID: 35327572 PMCID: PMC8945572 DOI: 10.3390/biom12030381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 02/04/2023] Open
Abstract
IMGT®, the international ImMunoGeneTics information system®, created in 1989, by Marie-Paule Lefranc (Université de Montpellier and CNRS), marked the advent of immunoinformatics, a new science which emerged at the interface between immunogenetics and bioinformatics for the study of the adaptive immune responses. IMGT® is based on a standardized nomenclature of the immunoglobulin (IG) and T cell receptor (TR) genes and alleles from fish to humans and on the IMGT unique numbering for the variable (V) and constant (C) domains of the immunoglobulin superfamily (IgSF) of vertebrates and invertebrates, and for the groove (G) domain of the major histocompatibility (MH) and MH superfamily (MhSF) proteins. IMGT® comprises 7 databases, 17 tools and more than 25,000 pages of web resources for sequences, genes and structures, based on the IMGT Scientific chart rules generated from the IMGT-ONTOLOGY axioms and concepts. IMGT® reference directories are used for the analysis of the NGS high-throughput expressed IG and TR repertoires (natural, synthetic and/or bioengineered) and for bridging sequences, two-dimensional (2D) and three-dimensional (3D) structures. This manuscript focuses on the IMGT®Homo sapiens IG and TR loci, gene order, copy number variation (CNV) and haplotypes new concepts, as a paradigm for jawed vertebrates genome assemblies.
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Le Page L, Gillespie A, Schwartz JC, Prawits LM, Schlerka A, Farrell CP, Hammond JA, Baldwin CL, Telfer JC, Hammer SE. Subpopulations of swine γδ T cells defined by TCRγ and WC1 gene expression. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 125:104214. [PMID: 34329647 DOI: 10.1016/j.dci.2021.104214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/24/2021] [Accepted: 07/24/2021] [Indexed: 06/13/2023]
Abstract
γδ T cells constitute a major portion of lymphocytes in the blood of both ruminants and swine. Subpopulations of swine γδ T cells have been distinguished by CD2 and CD8α expression. However, it was not clear if they have distinct expression profiles of their T-cell receptor (TCR) or WC1 genes. Identifying receptor expression will contribute to understanding the functional differences between these subpopulations and their contributions to immune protection. Here, we annotated three genomic assemblies of the swine TCRγ gene locus finding four gene cassettes containing C, J and V genes, although some haplotypes carried a null TRGC gene (TRGC4). Genes in the TRGC1 cassette were homologs of bovine TRGC5 cassette while the others were not homologous to bovine genes. Here we evaluated three principal populations of γδ T cells (CD2+/SWC5-, CD2-/SWC5+, and CD2-/SWC5-). Both CD2- subpopulations transcribed WC1 co-receptor genes, albeit with different patterns of gene expression but CD2+ cells did not. All subpopulations transcribed TCR genes from all four cassettes, although there were differences in expression levels. Finally, the CD2+ and CD2- γδ T-cell populations differed in their representation in various organs and tissues, presumably at least partially reflective of different ligand specificities for their receptors.
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Affiliation(s)
- Lauren Le Page
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Alexandria Gillespie
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | | | - Lisa-Maria Prawits
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Angela Schlerka
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Colin P Farrell
- Division of Hematology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Cynthia L Baldwin
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Janice C Telfer
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Sabine E Hammer
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria.
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Edholm ES, Fenton CG, Mondot S, Paulssen RH, Lefranc MP, Boudinot P, Magadan S. Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids. Front Immunol 2021; 12:753960. [PMID: 34733285 PMCID: PMC8559430 DOI: 10.3389/fimmu.2021.753960] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/28/2021] [Indexed: 12/17/2022] Open
Abstract
In jawed vertebrates, two major T cell populations have been characterized. They are defined as α/β or γ/δ T cells, based on the expressed T cell receptor. Salmonids (family Salmonidae) include two key teleost species for aquaculture, rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) which constitute important models for fish immunology and important targets for vaccine development. The growing interest to decipher the dynamics of adaptive immune responses against pathogens or vaccines has resulted in recent efforts to sequence the immunoglobulin (IG) or antibodies and T cell receptor (TR) repertoire in these species. In this context, establishing a comprehensive and coherent locus annotation is the fundamental basis for the analysis of high-throughput repertoire sequencing data. We therefore decided to revisit the description and annotation of TRA/TRD locus in Atlantic salmon and two strains of rainbow trout (Swanson and Arlee) using the now available high-quality genome assemblies. Phylogenetic analysis of functional TRA/TRD V genes from these three genomes led to the definition of 25 subgroups shared by both species, some with particular feature. A total of 128 TRAJ genes were identified in Salmo, the majority with a close counterpart in Oncorhynchus. Analysis of expressed TRA repertoire indicates that most TRAV gene subgroups are expressed at mucosal and systemic level. The present work on TRA/TRD locus annotation along with the analysis of TRA repertoire sequencing data show the feasibility and advantages of a common salmonid TRA/TRD nomenclature that allows an accurate annotation and analysis of high-throughput sequencing results, across salmonid T cell subsets.
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Affiliation(s)
- Eva-Stina Edholm
- Faculty of Biosciences, Fisheries & Economics, Norwegian College of Fishery Science, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Christopher Graham Fenton
- Clinical Bioinformatics Research Group, Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, Faculty of Health Sciences, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Stanislas Mondot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.,GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Ruth H Paulssen
- Clinical Bioinformatics Research Group, Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, Faculty of Health Sciences, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Marie-Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System (IMGT), Laboratoire d´ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier Cedex, France
| | - Pierre Boudinot
- Université Paris Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Susana Magadan
- Immunology Laboratory, Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain.,Galicia Sur Health Research Institute (IIS-GS), Hospital Alvaro Cunqueiro, Vigo, Spain
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Zhou H, Ma L, Liu L, Yao X. TR Locus Annotation and Characteristics of Rhinolophus ferrumequinum. Front Immunol 2021; 12:741408. [PMID: 34659234 PMCID: PMC8514952 DOI: 10.3389/fimmu.2021.741408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
T-cell antigen receptors (TRs) in vertebrates can be divided into αβ or γδ, encoded by TRA/D, TRG, or TRB loci. TRs play a central role in mammal cellular immunity, which occurs by rearrangement of V, D, J, and C genes in the loci. The bat is the only mammal with flying ability and is considered the main host of zoonotic viruses, an important public health concern. However, at present, little is known about the composition of bat TR genes. Based on the whole genome sequence of the greater horseshoe bat (Rhinolophus ferrumequinum) and referring to the TR/IG annotation rules formulated by the international ImMunoGeneTics information system (IMGT), we present a complete annotation of TRA/D, TRG, and TRB loci of R. ferrumequinum. A total of 128 V segments, three D segments, 85 J segments, and 6 C segments were annotated and compared with other known mammalian data. The characteristics of the TR locus and germline genes of R. ferrumequinum are analyzed.
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Affiliation(s)
- Hao Zhou
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Long Ma
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Longyu Liu
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Xinsheng Yao
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
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The T Cell Receptor (TRB) Locus in Tursiops truncatus: From Sequence to Structure of the Alpha/Beta Heterodimer in the Human/Dolphin Comparison. Genes (Basel) 2021; 12:genes12040571. [PMID: 33919966 PMCID: PMC8070946 DOI: 10.3390/genes12040571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/27/2021] [Accepted: 04/12/2021] [Indexed: 01/25/2023] Open
Abstract
The bottlenose dolphin (Tursiops truncatus) belongs to the Cetartiodactyla and, similarly to other cetaceans, represents the most successful mammalian colonization of the aquatic environment. Here we report a genomic, evolutionary, and expression study of T. truncatus T cell receptor beta (TRB) genes. Although the organization of the dolphin TRB locus is similar to that of the other artiodactyl species, with three in tandem D-J-C clusters located at its 3' end, its uniqueness is given by the reduction of the total length due essentially to the absence of duplications and to the deletions that have drastically reduced the number of the germline TRBV genes. We have analyzed the relevant mature transcripts from two subjects. The simultaneous availability of rearranged T cell receptor α (TRA) and TRB cDNA from the peripheral blood of one of the two specimens, and the human/dolphin amino acids multi-sequence alignments, allowed us to calculate the most likely interactions at the protein interface between the alpha/beta heterodimer in complex with major histocompatibility class I (MH1) protein. Interacting amino acids located in the complementarity-determining region according to IMGT numbering (CDR-IMGT) of the dolphin variable V-alpha and beta domains were identified. According to comparative modelization, the atom pair contact sites analysis between the human MH1 grove (G) domains and the T cell receptor (TR) V domains confirms conservation of the structure of the dolphin TR/pMH.
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Massari S, Linguiti G, Giannico F, D’Addabbo P, Ciccarese S, Antonacci R. The Genomic Organisation of the TRA/TRD Locus Validates the Peculiar Characteristics of Dromedary δ-Chain Expression. Genes (Basel) 2021; 12:genes12040544. [PMID: 33918850 PMCID: PMC8069558 DOI: 10.3390/genes12040544] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 03/31/2021] [Accepted: 04/07/2021] [Indexed: 12/24/2022] Open
Abstract
The role of γδ T cells in vertebrate immunity is still an unsolved puzzle. Species such as humans and mice display a low percentage of these T lymphocytes (i.e., “γδ low species”) with a restricted diversity of γδ T cell receptors (TR). Conversely, artiodactyl species (i.e., “γδ high species”) account for a high proportion of γδ T cells with large γ and δ chain repertoires. The genomic organisation of the TR γ (TRG) and δ (TRD) loci has been determined in sheep and cattle, noting that a wide number of germline genes that encode for γ and δ chains characterise their genomes. Taking advantage of the current improved version of the genome assembly, we have investigated the genomic structure and gene content of the dromedary TRD locus, which, as in the other mammalian species, is nested within the TR α (TRA) genes. The most remarkable finding was the identification of a very limited number of variable germline genes (TRDV) compared to sheep and cattle, which supports our previous expression analyses for which the somatic hypermutation mechanism is able to enlarge and diversify the primary repertoire of dromedary δ chains. Furthermore, the comparison between genomic and expressed sequences reveals that D genes, up to four incorporated in a transcript, greatly contribute to the increased diversity of the dromedary δ chain antigen binding-site.
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MESH Headings
- Animals
- Camelus/genetics
- Computational Biology/methods
- Genetic Loci
- Genome
- Phylogeny
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
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Affiliation(s)
- Serafina Massari
- Department of Biological and Environmental Science and Technologies, University of Salento, 73100 Lecce, Italy
- Correspondence:
| | - Giovanna Linguiti
- Department of Biology, University of Bari “Aldo Moro”, 70125 Bari, Italy; (G.L.); (P.D.); (S.C.); (R.A.)
| | - Francesco Giannico
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, 70010 Bari, Italy;
| | - Pietro D’Addabbo
- Department of Biology, University of Bari “Aldo Moro”, 70125 Bari, Italy; (G.L.); (P.D.); (S.C.); (R.A.)
| | - Salvatrice Ciccarese
- Department of Biology, University of Bari “Aldo Moro”, 70125 Bari, Italy; (G.L.); (P.D.); (S.C.); (R.A.)
| | - Rachele Antonacci
- Department of Biology, University of Bari “Aldo Moro”, 70125 Bari, Italy; (G.L.); (P.D.); (S.C.); (R.A.)
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Gillespie A, Yirsaw A, Gunasekaran KP, Smith TP, Bickhart DM, Turley M, Connelley T, Telfer JC, Baldwin CL. Characterization of the domestic goat γδ T cell receptor gene loci and gene usage. Immunogenetics 2021; 73:187-201. [PMID: 33479855 DOI: 10.1007/s00251-021-01203-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/02/2021] [Indexed: 11/28/2022]
Abstract
Goats and cattle diverged 30 million years ago but retain similarities in immune system genes. Here, the caprine T cell receptor (TCR) gene loci and transcription of its genes were examined and compared to cattle. We annotated the TCR loci using an improved genome assembly (ARS1) of a highly homozygous San Clemente goat. This assembly has already proven useful for describing other immune system genes including antibody and leucocyte receptors. Both the TCRγ (TRG) and TCRδ (TRD) loci were similarly organized in goats as in cattle and the gene sequences were highly conserved. However, the number of genes varied slightly as a result of duplications and differences occurred in mutations resulting in pseudogenes. WC1+ γδ T cells in cattle have been shown to use TCRγ genes from only one of the six available cassettes. The structure of that Cγ gene product is unique and may be necessary to interact with WC1 for signal transduction following antigen ligation. Using RT-PCR and PacBio sequencing, we observed the same restriction for goat WC1+ γδ T cells. In contrast, caprine WC1+ and WC1- γδ T cell populations had a diverse TCRδ gene usage although the propensity for particular gene usage differed between the two cell populations. Noncanonical recombination signal sequences (RSS) largely correlated with restricted expression of TCRγ and δ genes. Finally, caprine γδ T cells were found to incorporate multiple TRD diversity gene sequences in a single transcript, an unusual feature among mammals but also previously observed in cattle.
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Affiliation(s)
- Alexandria Gillespie
- Integrated Sciences Building, Department of Veterinary and Animal Sciences, University of Massachusetts, 661 N. Pleasant St, Amherst, MA, 01003, USA
| | - Al Yirsaw
- Integrated Sciences Building, Department of Veterinary and Animal Sciences, University of Massachusetts, 661 N. Pleasant St, Amherst, MA, 01003, USA
| | - Karthick P Gunasekaran
- College of Information and Computer Sciences, University of Massachusetts, 140 Governors Drive, Amherst, MA, 01003, USA
| | - Timothy P Smith
- United States Department of Agriculture, Agricultural Research Service, United States Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Derek M Bickhart
- United States Department of Agriculture, Agricultural Research Service, United States Dairy Forage Research Center, Madison, WI, 53706, USA
| | - Michael Turley
- Integrated Sciences Building, Department of Veterinary and Animal Sciences, University of Massachusetts, 661 N. Pleasant St, Amherst, MA, 01003, USA
| | | | - Janice C Telfer
- Integrated Sciences Building, Department of Veterinary and Animal Sciences, University of Massachusetts, 661 N. Pleasant St, Amherst, MA, 01003, USA
| | - Cynthia L Baldwin
- Integrated Sciences Building, Department of Veterinary and Animal Sciences, University of Massachusetts, 661 N. Pleasant St, Amherst, MA, 01003, USA.
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IMGT ® Biocuration and Comparative Analysis of Bos taurus and Ovis aries TRA/TRD Loci. Genes (Basel) 2020; 12:genes12010030. [PMID: 33379283 PMCID: PMC7824213 DOI: 10.3390/genes12010030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/17/2020] [Accepted: 12/22/2020] [Indexed: 12/20/2022] Open
Abstract
The adaptive immune response provides the vertebrate immune system with the ability to recognize and remember specific pathogens to generate immunity, and mount stronger attacks each time the pathogen is encountered. T cell receptors are the antigen receptors of the adaptive immune response expressed by T cells, which specifically recognize processed antigens, presented as peptides by the highly polymorphic major histocompatibility (MH) proteins. T cell receptors (TR) are divided into two groups, αβ and γδ, which express distinct TR containing either α and β, or γ and δ chains, respectively. The TRα locus (TRA) and TRδ locus (TRD) of bovine (Bos taurus) and the sheep (Ovis aries) have recently been described and annotated by IMGT® biocurators. The aim of the present study is to present the results of the biocuration and to compare the genes of the TRA/TRD loci among these ruminant species based on the Homo sapiens repertoire. The comparative analysis shows similarities but also differences, including the fact that these two species have a TRA/TRD locus about three times larger than that of humans and therefore have many more genes which may demonstrate duplications and/or deletions during evolution.
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Giannico F, Massari S, Caputi Jambrenghi A, Soriano A, Pala A, Linguiti G, Ciccarese S, Antonacci R. The expansion of the TRB and TRG genes in domestic goats (Capra hircus) is characteristic of the ruminant species. BMC Genomics 2020; 21:623. [PMID: 32912163 PMCID: PMC7488459 DOI: 10.1186/s12864-020-07022-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/24/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Goats (Capra hircus), one of the first domesticated species, are economically important for milk and meat production, and their broad geographical distribution reflects their successful adaptation to diverse environmental conditions. Despite the relevance of this species, the genetic research on the goat traits is limited compared to other domestic species. Thanks to the latest goat reference genomic sequence (ARS1), which is considered to be one of the most continuous assemblies in livestock, we deduced the genomic structure of the T cell receptor beta (TRB) and gamma (TRG) loci in this ruminant species. RESULTS Our analyses revealed that although the organization of the goat TRB locus is broadly similar to that of the other artiodactyl species, with three in-tandem D-J-C clusters located at the 3' end, a complex and extensive series of duplications have occurred in the V genes at the 5' end, leading to a marked expansion in the number of the TRBV genes. This phenomenon appears to be a feature of the ruminant lineage since similar gene expansions have also occurred in sheep and cattle. Likewise, the general organization of the goat TRG genes is typical of ruminant species studied so far, with two paralogous TRG loci, TRG1 and TRG2, located in two distinct and distant positions on the same chromosome as result of a split in the ancestral locus. Each TRG locus consists of reiterated V-J-J-C cassettes, with the goat TRG2 containing an additional cassette relative to the corresponding sheep and cattle loci. CONCLUSIONS Taken together, these findings demonstrate that strong evolutionary pressures in the ruminant lineage have selected for the development of enlarged sets of TRB and TRG genes that contribute to a diverse T cell receptor repertoire. However, differences observed among the goat, sheep and cattle TRB and TRG genes indicate that distinct evolutionary histories, with independent expansions and/or contractions, have also affected each ruminant species.
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Affiliation(s)
- Francesco Giannico
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Serafina Massari
- Department of Biological and Environmental Science and Technologies, University of Salento, Lecce, Italy
| | - Anna Caputi Jambrenghi
- Department of Agricultural and Environmental Science, University of Bari "Aldo Moro", Bari, Italy
| | - Adriano Soriano
- Department of Biology, University of Bari "Aldo Moro", 70124, Bari, Italy
| | - Angela Pala
- Department of Biology, University of Bari "Aldo Moro", 70124, Bari, Italy
| | - Giovanna Linguiti
- Department of Biology, University of Bari "Aldo Moro", 70124, Bari, Italy
| | | | - Rachele Antonacci
- Department of Biology, University of Bari "Aldo Moro", 70124, Bari, Italy.
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Lefranc MP, Lefranc G. Immunoglobulins or Antibodies: IMGT ® Bridging Genes, Structures and Functions. Biomedicines 2020; 8:E319. [PMID: 32878258 PMCID: PMC7555362 DOI: 10.3390/biomedicines8090319] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
IMGT®, the international ImMunoGeneTics® information system founded in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), marked the advent of immunoinformatics, a new science at the interface between immunogenetics and bioinformatics. For the first time, the immunoglobulin (IG) or antibody and T cell receptor (TR) genes were officially recognized as 'genes' as well as were conventional genes. This major breakthrough has allowed the entry, in genomic databases, of the IG and TR variable (V), diversity (D) and joining (J) genes and alleles of Homo sapiens and of other jawed vertebrate species, based on the CLASSIFICATION axiom. The second major breakthrough has been the IMGT unique numbering and the IMGT Collier de Perles for the V and constant (C) domains of the IG and TR and other proteins of the IG superfamily (IgSF), based on the NUMEROTATION axiom. IMGT-ONTOLOGY axioms and concepts bridge genes, sequences, structures and functions, between biological and computational spheres in the IMGT® system (Web resources, databases and tools). They provide the IMGT Scientific chart rules to identify, to describe and to analyse the IG complex molecular data, the huge diversity of repertoires, the genetic (alleles, allotypes, CNV) polymorphisms, the IG dual function (paratope/epitope, effector properties), the antibody humanization and engineering.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT, The International ImMunoGeneTics Information System, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, Université de Montpellier UM, Centre National de la Recherche Scientifique CNRS, UMR 9002 CNRS-UM, 141 Rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
| | - Gérard Lefranc
- IMGT, The International ImMunoGeneTics Information System, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, Université de Montpellier UM, Centre National de la Recherche Scientifique CNRS, UMR 9002 CNRS-UM, 141 Rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
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Antonacci R, Massari S, Linguiti G, Caputi Jambrenghi A, Giannico F, Lefranc MP, Ciccarese S. Evolution of the T-Cell Receptor (TR) Loci in the Adaptive Immune Response: The Tale of the TRG Locus in Mammals. Genes (Basel) 2020; 11:E624. [PMID: 32517024 PMCID: PMC7349638 DOI: 10.3390/genes11060624] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 12/16/2022] Open
Abstract
T lymphocytes are the principal actors of vertebrates' cell-mediated immunity. Like B cells, they can recognize an unlimited number of foreign molecules through their antigen-specific heterodimer receptors (TRs), which consist of αβ or γδ chains. The diversity of the TRs is mainly due to the unique organization of the genes encoding the α, β, γ, and δ chains. For each chain, multi-gene families are arranged in a TR locus, and their expression is guaranteed by the somatic recombination process. A great plasticity of the gene organization within the TR loci exists among species. Marked structural differences affect the TR γ (TRG) locus. The recent sequencing of multiple whole genome provides an opportunity to examine the TR gene repertoire in a systematic and consistent fashion. In this review, we report the most recent findings on the genomic organization of TRG loci in mammalian species in order to show differences and similarities. The comparison revealed remarkable diversification of both the genomic organization and gene repertoire across species, but also unexpected evolutionary conservation, which highlights the important role of the T cells in the immune response.
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Affiliation(s)
- Rachele Antonacci
- Department of Biology, University of Bari “Aldo Moro”, 70124 Bari, Italy; (G.L.); (S.C.)
| | - Serafina Massari
- Department of Biological and Environmental Science and Technologies, University of Salento, 73100 Lecce, Italy;
| | - Giovanna Linguiti
- Department of Biology, University of Bari “Aldo Moro”, 70124 Bari, Italy; (G.L.); (S.C.)
| | - Anna Caputi Jambrenghi
- Department of Agricultural and Environmental Science, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.C.J.); (F.G.)
| | - Francesco Giannico
- Department of Agricultural and Environmental Science, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.C.J.); (F.G.)
| | - Marie-Paule Lefranc
- IMGT, the International ImMunoGeneTics Information System, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR9002 CNRS, Université de Montpellier, CEDEX 5, 34396 Montpellier, France;
| | - Salvatrice Ciccarese
- Department of Biology, University of Bari “Aldo Moro”, 70124 Bari, Italy; (G.L.); (S.C.)
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Ming L, Wang Z, Yi L, Batmunkh M, Liu T, Siren D, He J, Juramt N, Jambl T, Li Y, Jirimutu. Chromosome-level assembly of wild Bactrian camel genome reveals organization of immune gene loci. Mol Ecol Resour 2020; 20. [PMID: 32012460 DOI: 10.1111/1755-0998.13141] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/09/2020] [Accepted: 01/30/2020] [Indexed: 01/22/2023]
Abstract
Camelids are characterized by their unique adaptive immune system that exhibits the generation of homodimeric heavy-chain immunoglobulins, somatic hypermutation of T-cell receptors, and low genetic diversity of major histocompatibility complex (MHC) genes. However, short-read assemblies are typically highly fragmented in these gene loci owing to their repetitive and polymorphic nature. Here, we constructed a chromosome-level assembly of wild Bactrian camel genome based on high-coverage long-read sequencing and chromatin interaction mapping. The assembly with a contig N50 of 5.37 Mb and a scaffold N50 of 76.03 Mb, represents the most contiguous camelid genome to date. The genomic organization of immunoglobulin heavy-chain locus was similar between the wild Bactrian camel and alpaca, and genes encoding for conventional and heavy-chain antibodies were intermixed. The organizations of two immunoglobulin light-chain loci and four T cell receptor loci were also fully deciphered using the new assembly. Additionally, the complete classical MHC region was resolved into a single contig. The high-quality assembly presented here provides an essential reference for future investigations examining the camelid immune system.
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Affiliation(s)
- Liang Ming
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China.,Inner Mongolia Institute of Camel Research, West Alax, Inner Mongolia, China
| | - Zhen Wang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Li Yi
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China
| | - Mijiddorj Batmunkh
- Mongolian Wild Camel Protection Area, Ministry of Nature and Environment, Ulaanbaatar, Mongolia
| | - Tao Liu
- Annoroad Gene Technology (Beijing) Co. Ltd, Beijing, China
| | - Dalai Siren
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China.,Inner Mongolia Institute of Camel Research, West Alax, Inner Mongolia, China
| | - Jing He
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China
| | | | - Tuyatsetseg Jambl
- College of Industrial Technology, Mongolian University of Science and Technology, Ulaanbaater, Mongolia
| | - Yixue Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Bio-Med Big Data Center, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, China.,Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Jirimutu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, China.,Inner Mongolia Institute of Camel Research, West Alax, Inner Mongolia, China
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13
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Mondot S, Lantz O, Lefranc MP, Boudinot P. The T cell receptor (TRA) locus in the rabbit (Oryctolagus cuniculus): Genomic features and consequences for invariant T cells. Eur J Immunol 2019; 49:2146-2158. [PMID: 31355919 DOI: 10.1002/eji.201948228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/14/2019] [Indexed: 11/07/2022]
Abstract
The rabbit has been widely used in immunology and infectiology. Rabbit immunoglobulins have been extensively studied, leading to the discovery of their idiotypes, allotypic diversity, and of the diversification of the primary repertoire by hyperconversion. Much less is known about rabbit T cell receptors (TR), especially TRA. This isotype is particularly important for innate-like T cells, which typically express invariant TRA (iTRA). The presence of such cells in the rabbit remains an enigma. Rabbit NKT cells seem to be very rare, and lagomorphs lack MAIT cells. TRAV1, the variable gene expressed in the iTRA of these cells across most mammals, and MR1, the MH1-like receptor that present riboflavin derivatives to MAIT cells, are missing in rabbit. An alternative iTRA has been identified, that may be expressed by new innate-like T cells. To facilitate TRA repertoire analyses in rabbit, we report here a full description of TRA and TRD loci and a subgroup definition based on IMGT® classification. Rabbit TRA rearrangements follow the same temporal pattern that is observed in mouse and human. Rare transcripts expressing TRDV/TRDD/TRDJ rearrangements spliced to TRAC were detected. TRA and TRD genes have been made available in IMGT and IMGT/HighV-QUEST, allowing easy analysis of TRA/TRD RepSeq.
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Affiliation(s)
- Stanislas Mondot
- MICALIS, Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Jouy-en-Josas, France
| | - Olivier Lantz
- INSERM U932, Institut Curie, Paris Sciences et Lettres Research University, Paris, France.,Center of Clinical Investigation in Biotherapy 1428, Gustave-Roussy/Curie, Paris, France.,Laboratoire d'Immunologie Clinique, Institut Curie, Paris, France
| | - Marie-Paule Lefranc
- IMGT®, the International ImMunoGeneTics Information System® (IMGT), Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Pierre Boudinot
- Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Jouy-en-Josas, France
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14
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Antonacci R, Bellini M, Linguiti G, Ciccarese S, Massari S. Comparative Analysis of the TRB Locus in the Camelus Genus. Front Genet 2019; 10:482. [PMID: 31231418 PMCID: PMC6558370 DOI: 10.3389/fgene.2019.00482] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 05/06/2019] [Indexed: 11/26/2022] Open
Abstract
T cells can be separated into two major subsets based on the heterodimer that forms their T cell receptors. αβ T cells have receptors consisting of α and β chains, while γδ T cells are composed of γ and δ chains. αβ T cells play an essential role within the adaptive immune responses against pathogens. The recent genomic characterization of the Camelus dromedarius T cell receptor β (TRB) locus has allowed us to infer the structure of this locus from the draft genome sequences of its wild and domestic Bactrian congeners, Camelus ferus and Camelus bactrianus. The general structural organization of the wild and domestic Bactrian TRB locus is similar to that of the dromedary, with a pool of TRBV genes positioned at the 5′ end of D-J-C clusters, followed by a single TRBV gene located at the 3′ end with an inverted transcriptional orientation. Despite the fragmented nature of the assemblies, comparative genomics reveals the existence of a perfect co-linearity between the three Old World camel TRB genomic sequences, which enables the transfer of information from one sequence to another and the filling of gaps in the genomic sequences. A virtual camelid TRB locus is hypothesized with the presence of 33 TRBV genes distributed in 26 subgroups. Likewise, in the artiodactyl species, three in-tandem D-J-C clusters, each composed of one TRBD gene, six or seven TRBJ genes, and one TRBC gene, are placed at the 3′ end of the locus. As reported in the ruminant species, a group of four functional TRY genes at the 5′ end and only one gene at the 3′ end, complete the camelid TRB locus. Although the gene content is similar, differences are observed in the TRBV functional repertoire, and genes that are functional in one species are pseudogenes in the other species. Hence, variations in the functional repertoire between dromedary, wild and domestic Bactrian camels, rather than differences in the gene content, may represent the molecular basis explaining the disparity in the TRB repertoire between the Camelus species. Finally, our data contribute to the knowledge about the evolutionary history of Old World camelids.
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Affiliation(s)
| | | | | | | | - Serafina Massari
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
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15
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Zhang Z, Mu Y, Shan L, Sun D, Guo W, Yu Z, Tian R, Xu S, Yang G. Divergent Evolution of TRC Genes in Mammalian Niche Adaptation. Front Immunol 2019; 10:871. [PMID: 31068942 PMCID: PMC6491686 DOI: 10.3389/fimmu.2019.00871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/04/2019] [Indexed: 12/01/2022] Open
Abstract
Mammals inhabit a wide variety of ecological niches, which in turn can be affected by various ecological factors, especially in relation to immunity. The canonical TRC repertoire (TRAC, TRBC, TRGC, and TRDC) codes C regions of T cell receptor chains that form the primary antigen receptors involved in the activation of cellular immunity. At present, little is known about the correlation between the evolution of mammalian TRC genes and ecological factors. In this study, four types canonical of TRC genes were identified from 37 mammalian species. Phylogenetic comparative methods (phyANOVA and PGLS) and selective pressure analyses among different groups of ecological factors (habitat, diet, and sociality) were carried out. The results showed that habitat was the major ecological factor shaping mammalian TRC repertoires. Specifically, trade-off between TRGC numbers and positive selection of TRAC and the balanced evolutionary rates between TRAC and TRDC genes were speculated as two main mechanisms in adaption to habitat and sociality. Overall, our study suggested divergent mechanisms for the evolution of TRCs, prompting mammalian immunity adaptions within diverse niches.
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Affiliation(s)
- Zepeng Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yuan Mu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Lei Shan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Di Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Weijian Guo
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhenpeng Yu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ran Tian
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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16
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Powers JM, Ioachim G, Stroman PW. Ten Key Insights into the Use of Spinal Cord fMRI. Brain Sci 2018; 8:E173. [PMID: 30201938 PMCID: PMC6162663 DOI: 10.3390/brainsci8090173] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 08/29/2018] [Accepted: 09/06/2018] [Indexed: 01/27/2023] Open
Abstract
A comprehensive review of the literature-to-date on functional magnetic resonance imaging (fMRI) of the spinal cord is presented. Spinal fMRI has been shown, over more than two decades of work, to be a reliable tool for detecting neural activity. We discuss 10 key points regarding the history, development, methods, and applications of spinal fMRI. Animal models have served a key purpose for the development of spinal fMRI protocols and for experimental spinal cord injury studies. Applications of spinal fMRI span from animal models across healthy and patient populations in humans using both task-based and resting-state paradigms. The literature also demonstrates clear trends in study design and acquisition methods, as the majority of studies follow a task-based, block design paradigm, and utilize variations of single-shot fast spin-echo imaging methods. We, therefore, discuss the similarities and differences of these to resting-state fMRI and gradient-echo EPI protocols. Although it is newly emerging, complex connectivity and network analysis is not only possible, but has also been shown to be reliable and reproducible in the spinal cord for both task-based and resting-state studies. Despite the technical challenges associated with spinal fMRI, this review identifies reliable solutions that have been developed to overcome these challenges.
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Affiliation(s)
- Jocelyn M Powers
- Centre for Neuroscience Studies, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Gabriela Ioachim
- Centre for Neuroscience Studies, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Patrick W Stroman
- Centre for Neuroscience Studies, Queen's University, Kingston, ON K7L 3N6, Canada.
- Department of Biomedical Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
- Department of Physics, Queen's University, Kingston, ON K7L 3N6, Canada.
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17
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Breaux B, Hunter ME, Cruz-Schneider MP, Sena L, Bonde RK, Criscitiello MF. The Florida manatee (Trichechus manatus latirostris) T cell receptor loci exhibit V subgroup synteny and chain-specific evolution. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 85:71-85. [PMID: 29649552 DOI: 10.1016/j.dci.2018.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/06/2018] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
The Florida manatee (Trichechus manatus latirostris) has limited diversity in the immunoglobulin heavy chain. We therefore investigated the antigen receptor loci of the other arm of the adaptive immune system: the T cell receptor. Manatees are the first species from Afrotheria, a basal eutherian superorder, to have an in-depth characterization of all T cell receptor loci. By annotating the genome and expressed transcripts, we found that each chain has distinct features that correlates to their individual functions. The genomic organization also plays a role in modulating sequence conservation between species. There were extensive V subgroup synteny blocks in the TRA and TRB loci between T. m. latirostris and human. Increased genomic locus complexity correlated to increased locus synteny. We also identified evidence for a VHD pseudogene for the first time in a eutherian mammal. These findings emphasize the value of including species within this basal eutherian radiation in comparative studies.
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Affiliation(s)
- Breanna Breaux
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Margaret E Hunter
- Sirenia Project, Wetland and Aquatic Research Center, U.S. Geological Survey, 7920 NW 71st Street, Gainesville, FL 32653, USA.
| | | | - Leonardo Sena
- Laboratory of Medical and Human Genetics, Federal University of Pará, Belém, Pará, Brazil.
| | - Robert K Bonde
- Sirenia Project, Wetland and Aquatic Research Center, U.S. Geological Survey, 7920 NW 71st Street, Gainesville, FL 32653, USA.
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA; Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX 77843, USA.
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18
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Antonacci R, Bellini M, Pala A, Mineccia M, Hassanane MS, Ciccarese S, Massari S. The occurrence of three D-J-C clusters within the dromedary TRB locus highlights a shared evolution in Tylopoda, Ruminantia and Suina. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 76:105-119. [PMID: 28577760 DOI: 10.1016/j.dci.2017.05.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/26/2017] [Accepted: 05/26/2017] [Indexed: 06/07/2023]
Abstract
The αβ T cells are important components of the adaptive immune system and can recognize a vast array of peptides presented by MHC molecules. The ability of these T cells to recognize the complex depends on the diversity of the αβ TR, which is generated by a recombination of specific Variable, Diversity and Joining genes for the β chain, and Variable and Joining genes for the α chain. In this study, we analysed the genomic structure and the gene content of the TRB locus in Camelus dromedarius, which is a species belonging to the Tylopoda suborder. The most noteworthy result is the presence of three in tandem TRBD-J-C clusters in the dromedary TRB locus, which is similar to clusters found in sheep, cattle and pigs and suggests a common duplication event occurred prior to the Tylopoda/Ruminantia/Suina divergence. Conversely, a significant contraction of the dromedary TRBV genes, which was previously found in the TRG and TRD loci, was observed with respect to the other artiodactyl species.
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Affiliation(s)
| | | | - Angela Pala
- Department of Biology, University "Aldo Moro" of Bari, Bari, Italy.
| | - Micaela Mineccia
- Department of Biology, University "Aldo Moro" of Bari, Bari, Italy.
| | | | | | - Serafina Massari
- Department of Biological and Environmental Science e Technologies, University of Salento, Lecce, Italy.
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19
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Linguiti G, Antonacci R, Tasco G, Grande F, Casadio R, Massari S, Castelli V, Consiglio A, Lefranc MP, Ciccarese S. Genomic and expression analyses of Tursiops truncatus T cell receptor gamma (TRG) and alpha/delta (TRA/TRD) loci reveal a similar basic public γδ repertoire in dolphin and human. BMC Genomics 2016; 17:634. [PMID: 27528257 PMCID: PMC4986337 DOI: 10.1186/s12864-016-2841-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 06/15/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The bottlenose dolphin (Tursiops truncatus) is a mammal that belongs to the Cetartiodactyla and have lived in marine ecosystems for nearly 60 millions years. Despite its popularity, our knowledge about its adaptive immunity and evolution is very limited. Furthermore, nothing is known about the genomics and evolution of dolphin antigen receptor immunity. RESULTS Here we report a evolutionary and expression study of Tursiops truncatus T cell receptor gamma (TRG) and alpha/delta (TRA/TRD) genes. We have identified in silico the TRG and TRA/TRD genes and analyzed the relevant mature transcripts in blood and in skin from four subjects. The dolphin TRG locus is the smallest and simplest of all mammalian loci as yet studied. It shows a genomic organization comprising two variable (V1 and V2), three joining (J1, J2 and J3) and a single constant (C), genes. Despite the fragmented nature of the genome assemblies, we deduced the TRA/TRD locus organization, with the recent TRDV1 subgroup genes duplications, as it is expected in artiodactyls. Expression analysis from blood of a subject allowed us to assign unambiguously eight TRAV genes to those annotated in the genomic sequence and to twelve new genes, belonging to five different subgroups. All transcripts were productive and no relevant biases towards TRAV-J rearrangements are observed. Blood and skin from four unrelated subjects expression data provide evidence for an unusual ratio of productive/unproductive transcripts which arise from the TRG V-J gene rearrangement and for a "public" gamma delta TR repertoire. The productive cDNA sequences, shared both in the same and in different individuals, include biases of the TRGV1 and TRGJ2 genes. The high frequency of TRGV1-J2/TRDV1- D1-J4 productive rearrangements in dolphins may represent an interesting oligo-clonal population comparable to that found in human with the TRGV9- JP/TRDV2-D-J T cells and in primates. CONCLUSIONS Although the features of the TRG and TRA/TRD loci organization reflect those of the so far examined artiodactyls, genomic results highlight in dolphin an unusually simple TRG locus. The cDNA analysis reveal productive TRA/TRD transcripts and unusual ratios of productive/unproductive TRG transcripts. Comparing multiple different individuals, evidence is found for a "public" gamma delta TCR repertoire thus suggesting that in dolphins as in human the gamma delta TCR repertoire is accompanied by selection for public gamma chain.
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MESH Headings
- Amino Acid Sequence
- Animals
- Bottle-Nosed Dolphin/genetics
- Bottle-Nosed Dolphin/metabolism
- Gene Expression Profiling
- Gene Expression Regulation
- Genetic Loci
- Humans
- Molecular Sequence Data
- Phylogeny
- Protein Structure, Secondary
- RNA/blood
- RNA/isolation & purification
- RNA/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/classification
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Receptors, Antigen, T-Cell, gamma-delta/classification
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- Sequence Alignment
- Skin/metabolism
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Affiliation(s)
- Giovanna Linguiti
- Department of Biology, University of Bari, via E. Orabona 4, 70125 Bari, Italy
| | - Rachele Antonacci
- Department of Biology, University of Bari, via E. Orabona 4, 70125 Bari, Italy
| | - Gianluca Tasco
- Biocomputing Group, CIRI-Health Science and Technologies/Department of Biology, University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Francesco Grande
- Zoomarine Italia SpA, via Casablanca 61, 00071 Pomezia, RM Italy
| | - Rita Casadio
- Biocomputing Group, CIRI-Health Science and Technologies/Department of Biology, University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Serafina Massari
- Department of Biological and Environmental Science e Technologies, University of Salento, via per Monteroni, 73100 Lecce, Italy
| | - Vito Castelli
- Department of Biology, University of Bari, via E. Orabona 4, 70125 Bari, Italy
| | - Arianna Consiglio
- CNR, Institute for Biomedical Technologies of Bari, via Amendola, 70125 Bari, Italy
| | - Marie-Paule Lefranc
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d’ImmunoGénétique Moléculaire, Institut de Génétique Humaine, UPR CNRS 1142, University of Montpellier, 34396 Montpellier Cedex 5, France
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