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Flajnik MF, Stanfield R, Pokidysheva EN, Boudko SP, Wilson I, Ohta Y. An Ancient MHC-Linked Gene Encodes a Nonrearranging Shark Antibody, UrIg, Convergent with IgG. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1042-1051. [PMID: 37540118 PMCID: PMC10530332 DOI: 10.4049/jimmunol.2300361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/12/2023] [Indexed: 08/05/2023]
Abstract
Gnathostome adaptive immunity is defined by the Ag receptors, Igs and TCRs, and the MHC. Cartilaginous fish are the oldest vertebrates with these adaptive hallmarks. We and others have unearthed nonrearranging Ag receptor-like genes in several vertebrates, some of which are encoded in the MHC or in MHC paralogous regions. One of these genes, named UrIg, was detected in the class III region of the shark MHC that encodes a protein with typical V and C domains such as those found in conventional Igs and TCRs. As no transmembrane region was detected in gene models or cDNAs, the protein does not appear to act as a receptor. Unlike some other shark Ig genes, the UrIg V region shows no evidence of RAG-mediated rearrangement, and thus it is likely related to other V genes that predated the invasion of the RAG transposon. The UrIg gene is present in all elasmobranchs and evolves conservatively, unlike Igs and TCRs. Also, unlike Ig/TCR, the gene is not expressed in secondary lymphoid tissues, but mainly in the liver. Recombinant forms of the molecule form disulfide-linked homodimers, which is the form also detected in many shark tissues by Western blotting. mAbs specific for UrIg identify the protein in the extracellular matrix of several shark tissues by immunohistochemistry. We propose that UrIg is related to the V gene invaded by the RAG transposon, consistent with the speculation of emergence of Ig/TCR within the MHC or proto-MHC.
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Affiliation(s)
- Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD
| | - Robyn Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA
| | - Elena N Pokidysheva
- Division of Nephrology and Hypertension, Department of Medicine, Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN
| | - Sergei P Boudko
- Division of Nephrology and Hypertension, Department of Medicine, Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN
- Department of Biochemistry, Vanderbilt University, Nashville, TN
| | - Ian Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD
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Kinlein A, Janes ME, Kincer J, Almeida T, Matz H, Sui J, Criscitiello MF, Flajnik MF, Ohta Y. Analysis of shark NCR3 family genes reveals primordial features of vertebrate NKp30. Immunogenetics 2021; 73:333-348. [PMID: 33742259 DOI: 10.1007/s00251-021-01209-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/07/2021] [Indexed: 11/26/2022]
Abstract
Natural killer (NK) cells play major roles in innate immunity against viruses and cancer. Natural killer receptors (NKR) expressed by NK cells recognize foreign- or self-ligands on infected and transformed cells as well as healthy cells. NKR genes are the most rapidly evolving loci in vertebrates, and it is generally difficult to detect orthologues in different taxa. The unique exception is NKp30, an activating NKR in mammals that binds to the self-ligand B7H6. The NKp30-encoding gene, NCR3, has been found in most vertebrates including sharks, the oldest vertebrates with human-type adaptive immunity. NCR3 has a special, non-rearranging VJ-type immunoglobulin superfamily (IgSF) domain that predates the emergence of the rearranging antigen receptors. Herein we show that NCR3 loci are linked to the shark major histocompatibility complex (MHC), proving NCR3's primordial association with the MHC. We identified eight subtypes of differentially expressed highly divergent shark NCR3 family genes. Using in situ hybridization, we detected one subtype, NS344823, to be expressed by predominantly single cells outside of splenic B cell zones. The expression by non-B cells was also confirmed by PCR in peripheral blood lymphocytes. Surprisingly, high expression of NS344823 was detected in the thymic cortex, demonstrating NS344823 expression in developing T cells. Finally, we show for the first time that shark T cells are found as single cells or in small clusters in the splenic red pulp, also unassociated with the large B cell follicles we previously identified.
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Affiliation(s)
- Allison Kinlein
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Morgan E Janes
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Jacob Kincer
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Tereza Almeida
- Centro de Investigacão Em Biodiversidade E Recursos Genéticos, CIBIO-InBIO, Campus Agrário de Vairão, Universidade Do Porto, Vairão, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade Do Porto, Porto, Portugal
| | - Hanover Matz
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Jianxin Sui
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Michael F Criscitiello
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD, 21201, USA
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD, 21201, USA.
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You L, Chi J, Huang S, Yu T, Huang G, Feng Y, Sang X, Gao X, Li T, Yue Z, Liu A, Chen S, Xu A. LanceletDB: an integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5491331. [PMID: 31106360 PMCID: PMC6526094 DOI: 10.1093/database/baz056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 03/19/2019] [Accepted: 04/08/2019] [Indexed: 12/24/2022]
Abstract
Lancelet (amphioxus) represents the most basally divergent extant chordate (cephalochordates) that diverged from the other two chordate lineages (urochordates and vertebrates) more than half a billion years ago. As it occupies a key position in evolution, it is considered as one of the best proxies for understanding the chordate ancestral state. Thus, the construction of a database with multiple lancelet genomes and gene annotation data, including protein domains, is urgently needed to investigate the loss and gain of domains in orthologues among species, especially ancient domain types (non-vertebrate-specific domains) and novel domain combination, which is helpful for providing new insight into the chordate ancestral state and vertebrate evolution. Here, we present an integrated genome database for lancelet, LanceletDB, which provides reference haploid genome sequence and annotation data for lancelet (Branchiostoma belcheri), including gene models and annotation, protein domain types, gene expression pattern in embryogenesis, different expression sequence tag sets and alternative polyadenylation (APA) sites profiled by the sequencing APA sites method. Especially, LanceletDB allows comparison of domain types and combination in orthologues among type species so as to decode the ancient domain types and novel domain combination during evolution. We also integrated the released diploid lancelet genome annotation data (Branchiostoma floridae) to expand LanceletDB and extend its usefulness. These data are available through the search and analysis page, basic local alignment search tool page and genome browser to provide an integrated display.
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Affiliation(s)
- Leiming You
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China.,State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
| | - Jiaqi Chi
- Department of Oncology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Shengfeng Huang
- State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
| | - Ting Yu
- State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
| | - Guangrui Huang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Yuchao Feng
- State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
| | - Xiaopu Sang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Xinhui Gao
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Ting'an Li
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Zirui Yue
- State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
| | - Aijie Liu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Shangwu Chen
- State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
| | - Anlong Xu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China.,State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
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Findly RC, Niagro FD, Sweeney RP, Camus AC, Dickerson HW. Rearranged T Cell Receptor Sequences in the Germline Genome of Channel Catfish Are Preferentially Expressed in Response to Infection. Front Immunol 2018; 9:2117. [PMID: 30319607 PMCID: PMC6170632 DOI: 10.3389/fimmu.2018.02117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/28/2018] [Indexed: 11/27/2022] Open
Abstract
Rearranged V(D)J genes coding for T cell receptor α and β chains are integrated into the germline genome of channel catfish. Previous analysis of expressed TCR Vβ2 repertoires demonstrated that channel catfish express multiple public clonotypes, which were shared among all the fish, following infection with a common protozoan parasite. In each case a single DNA sequence was predominately used to code for a public clonotype. We show here that the rearranged VDJ genes coding for these expressed public Vβ2 clonotypes can be amplified by PCR from germline DNA isolated from oocytes and erythrocytes. Sequencing of the Vβ2 PCR products confirmed that these expressed public Vβ2 clonotypes are integrated into the germline. Moreover, sequencing of PCR products confirmed that all five Vβ gene families and Vα1 have rearranged V(D)J genes with diverse CDR3 sequences integrated into the germline. Germline rearranged Vβ2 and Vβ4 genes retain the intron between the leader and Vβ sequence. This suggests that the germline rearranged TCR Vβ genes arose through VDJ rearrangement in T cells, and subsequently moved into the germline through DNA transposon mediated transposition. These results reveal a new dimension to the adaptive immune system of vertebrates, namely: the expression of evolutionarily conserved, rearranged V(D)J genes from the germline.
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Affiliation(s)
- Robert Craig Findly
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Frank D Niagro
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Ryan P Sweeney
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Alvin C Camus
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Harry W Dickerson
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
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Abstract
The adaptive immune system arose 500 million years ago in ectothermic (cold-blooded) vertebrates. Classically, the adaptive immune system has been defined by the presence of lymphocytes expressing recombination-activating gene (RAG)-dependent antigen receptors and the MHC. These features are found in all jawed vertebrates, including cartilaginous and bony fish, amphibians and reptiles and are most likely also found in the oldest class of jawed vertebrates, the extinct placoderms. However, with the discovery of an adaptive immune system in jawless fish based on an entirely different set of antigen receptors - the variable lymphocyte receptors - the divergence of T and B cells, and perhaps innate-like lymphocytes, goes back to the origin of all vertebrates. This Review explores how recent developments in comparative immunology have furthered our understanding of the origins and function of the adaptive immune system.
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Affiliation(s)
- Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD, USA.
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Morales Poole JR, Paganini J, Pontarotti P. Convergent evolution of the adaptive immune response in jawed vertebrates and cyclostomes: An evolutionary biology approach based study. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:120-126. [PMID: 28232131 DOI: 10.1016/j.dci.2017.02.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/16/2017] [Accepted: 02/17/2017] [Indexed: 06/06/2023]
Abstract
Two different adaptive immune systems (AIS) are present in the two phyla of vertebrates (jawed vertebrates and cyclostomes). The jawed vertebrate system is based on IG/TCR/RAG/MHC while the cyclostome system is based on VLRCs and AID-like enzymes both systems using homologous Cell types (B-cell and B-cell Like, T-cell and T-cell like). We will present our current view of the evolution of these two AISs and present alternative hypotheses that could explain the apparent convergent evolution of the two systems. We will also discuss why comparative immunology analyses should be based on evolutionary biology approaches and not on the scale of progress one.
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Affiliation(s)
- Jose Ricardo Morales Poole
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, équipe évolution biologique modélisation, 13453, Marseille, France
| | | | - Pierre Pontarotti
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, équipe évolution biologique modélisation, 13453, Marseille, France.
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