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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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Wang X, Wang P, Wang R, Wang C, Bai J, Ke C, Yu D, Li K, Ma Y, Han H, Zhao Y, Zhou X, Ren L. Analysis of TCRβ and TCRγ genes in Chinese alligator provides insights into the evolution of TCR genes in jawed vertebrates. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 85:31-43. [PMID: 29574022 DOI: 10.1016/j.dci.2018.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/12/2018] [Accepted: 01/12/2018] [Indexed: 06/08/2023]
Abstract
All jawed vertebrates have four T cell receptor (TCR) chains that are expressed by thymus-derived lymphocytes and play a major role in animal immune defence. However, few studies have investigated the TCR chains of crocodilians compared with those of birds and mammals, despite their key evolutionary position linking amphibians, reptiles, birds and mammals. Here, employing an Alligator sinensis genomic bacterial artificial chromosome (BAC) library and available genome data, we characterized the genomic organization, evolution and expression of TRB and TRG loci in Alligator sinensis. According to the sequencing data, the Alligator sinensis TRB locus spans approximately 500 Kb of genomic DNA containing two D-J-C clusters and 43 V gene segments and is organized as Vβ(39)-pJβ1-pCβ1-pDβ1-Dβ2- Jβ2(12)-Cβ2-Vβ(4), whereas the TRG locus spans 115 Kb of DNA genomic sequence consisting of 18 V gene segments, nine J gene segments and one C gene segment and is organized in a classical translocon pattern as Vγ(18)-Jγ(9)-Cγ. Moreover, syntenic analysis of TRB and TRG chain loci suggested a high degree of conserved synteny in the genomic regions across mammals, birds and Alligator sinensis. By analysing the cloned TRB/TRG cDNA, we identified the usage pattern of V families in the expressed TRB and TRG. An analysis of the junctions of the recombined VJ revealed the presence of N and P nucleotides in both expressed TRB and TRG sequences. Phylogenetic analysis revealed that TRB and TRG loci possess distinct evolutionary patterns. Most Alligator sinensis V subgroups have closely related orthologues in chicken and duck, and a small number of Alligator sinensis V subgroups have orthologues in mammals, which supports the hypothesis that crocodiles are the closest relatives of birds and mammals. Collectively, these data provide insights into TCR gene evolution in vertebrates and improve our understanding of the Alligator sinensis immune system.
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Affiliation(s)
- Xifeng Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Peng Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Renping Wang
- Administration Bureau of Chinese Alligator National Nature Reserve Protection, Anhui, People's Republic of China
| | - Chaolin Wang
- Administration Bureau of Chinese Alligator National Nature Reserve Protection, Anhui, People's Republic of China
| | - Jianhui Bai
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Cuncun Ke
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Di Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Kongpan Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Yonghe Ma
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Haitang Han
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100193, People's Republic of China; College of Plant Protection, China Agricultural University, Beijing, People's Republic of China.
| | - Liming Ren
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China.
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Husbandry of Monodelphis domestica in the study of mammalian embryogenesis. Lab Anim (NY) 2010; 39:219-26. [DOI: 10.1038/laban0710-219] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Accepted: 03/08/2010] [Indexed: 01/23/2023]
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Miller RD. Those other mammals: the immunoglobulins and T cell receptors of marsupials and monotremes. Semin Immunol 2010; 22:3-9. [PMID: 20004116 PMCID: PMC2880534 DOI: 10.1016/j.smim.2009.11.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2009] [Accepted: 11/12/2009] [Indexed: 01/15/2023]
Abstract
This review summarizes analyses of marsupial and monotreme immunoglobulin and T cell receptor genetics and expression published over the past decade. Analyses of recently completed whole genome sequences from the opossum and the platypus have yielded insight into the evolution of the common antigen receptor systems, as well as discovery of novel receptors that appear to have been lost in eutherian mammals. These species are also useful for investigation of the development of the immune system in organisms notable for giving birth to highly altricial young, as well as the evolution of maternal immunity through comparison of oviparous and viviparous mammals.
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Affiliation(s)
- Robert D Miller
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM 87110, USA.
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Parra ZE, Baker ML, Hathaway J, Lopez AM, Trujillo J, Sharp A, Miller RD. Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica. BMC Genomics 2008; 9:111. [PMID: 18312668 PMCID: PMC2275272 DOI: 10.1186/1471-2164-9-111] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 02/29/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND All jawed-vertebrates have four T cell receptor (TCR) chains: alpha (TRA), beta (TRB), gamma (TRG) and delta (TRD). Marsupials appear unique by having an additional TCR: mu (TRM). The evolutionary origin of TRM and its relationship to other TCR remain obscure, and is confounded by previous results that support TRM being a hybrid between a TCR and immunoglobulin locus. The availability of the first marsupial genome sequence allows investigation of these evolutionary relationships. RESULTS The organization of the conventional TCR loci, encoding the TRA, TRB, TRG and TRD chains, in the opossum Monodelphis domestica are highly conserved with and of similar complexity to that of eutherians (placental mammals). There is a high degree of conserved synteny in the genomic regions encoding the conventional TCR across mammals and birds. In contrast the chromosomal region containing TRM is not well conserved across mammals. None of the conventional TCR loci contain variable region gene segments with homology to those found in TRM; rather TRM variable genes are most similar to that of immunoglobulin heavy chain genes. CONCLUSION Complete genomic analyses of the opossum TCR loci continue to support an origin of TRM as a hybrid between a TCR and immunoglobulin locus. None of the conventional TCR loci contain evidence that such a recombination event occurred, rather they demonstrate a high degree of stability across distantly related mammals. TRM, therefore, appears to be derived from receptor genes no longer extant in placental mammals. These analyses provide the first genomic scale structural detail of marsupial TCR genes, a lineage of mammals used as models of early development and human disease.
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Affiliation(s)
- Zuly E Parra
- Center for Evolutionary and Theoretical Immunology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA.
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Parra ZE, Baker ML, Schwarz RS, Deakin JE, Lindblad-Toh K, Miller RD. A unique T cell receptor discovered in marsupials. Proc Natl Acad Sci U S A 2007; 104:9776-81. [PMID: 17535902 PMCID: PMC1887558 DOI: 10.1073/pnas.0609106104] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2006] [Indexed: 11/18/2022] Open
Abstract
T cells recognize antigens by using T cell receptors (TCRs) encoded by gene segments, called variable (V), diversity (D), and joining (J), that undergo somatic recombination to create diverse binding specificities. Four TCR chains (alpha, beta, gamma, and delta) have been identified to date, and, as T cells develop in the thymus, they express exclusively either an alphabetaTCR or a gammadeltaTCR heterodimer. Here, we show that marsupials have an additional TCR (TCRmu) that has V, D, and J that are either somatically recombined, as in conventional TCRs, or are already prejoined in the germ-line DNA in a manner consistent with their creation by retrotransposition. TCRmu does not have a known homolog in eutherian mammals but has features analogous to a recently described TCRdelta isoform in sharks. TCRmu is expressed in at least two mRNA isoforms that appear capable of encoding a full-length protein, both of which are transcribed in the thymus and spleen. One contains two variable domains: a somatically recombined V and a prejoined V. This appears to be the dominant isoform in peripheral lymphoid tissue. The other isoform contains only the prejoined V and is structurally more similar to conventional TCR chains, however invariant. Unlike other TCRs, TCRmu uses prejoined gene segments and is likely present in all marsupials. Its similarity to a TCR isoform in sharks suggests that it, or something similar, may be present in other vertebrate lineages and, therefore, may represent an ancient receptor system.
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Affiliation(s)
- Zuly E. Parra
- *Center for Evolutionary and Theoretical Immunology and Department of Biology, University of New Mexico, Albuquerque, NM 87131
| | - Michelle L. Baker
- *Center for Evolutionary and Theoretical Immunology and Department of Biology, University of New Mexico, Albuquerque, NM 87131
| | - Ryan S. Schwarz
- *Center for Evolutionary and Theoretical Immunology and Department of Biology, University of New Mexico, Albuquerque, NM 87131
| | - Janine E. Deakin
- Australian Research Council Centre for Kangaroo Genomics, Research School of Biological Sciences, Australian National University, Canberra, ACT 0200, Australia; and
| | | | - Robert D. Miller
- *Center for Evolutionary and Theoretical Immunology and Department of Biology, University of New Mexico, Albuquerque, NM 87131
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Samollow PB. Status and applications of genomic resources for the gray, short-tailed opossum, Monodelphis domestica, an American marsupial model for comparative biology. AUST J ZOOL 2006. [DOI: 10.1071/zo05059] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Owing to its small size, favourable reproductive characteristics, and simple husbandry, the gray, short-tailed opossum, Monodelphis domestica, has become the most widely distributed and intensively utilised laboratory-bred research marsupial in the world today. This article provides an overview of the current state and future projections of genomic resources for this species and discusses the potential impact of this growing resource base on active research areas that use M. domestica as a model system. The resources discussed include: fully arrayed, bacterial artificial chromosome (BAC) libraries; an expanding linkage map; developing full-genome BAC-contig and chromosomal fluorescence in situ hybridisation maps; public websites providing access to the M. domestica whole-genome-shotgun sequence trace database and the whole-genome sequence assembly; and a new project underway to create an expressed-sequence database and microchip expression arrays for functional genomics applications. Major research areas discussed span a variety of genetic, evolutionary, physiologic, reproductive, developmental, and behavioural topics, including: comparative immunogenetics; genomic imprinting; reproductive biology; neurobiology; photobiology and carcinogenesis; genetics of lipoprotein metabolism; developmental and behavioural endocrinology; sexual differentiation and development; embryonic and fetal development; meiotic recombination; genome evolution; molecular evolution and phylogenetics; and more.
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