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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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Dornburg A, Yoder JA. On the relationship between extant innate immune receptors and the evolutionary origins of jawed vertebrate adaptive immunity. Immunogenetics 2022; 74:111-128. [PMID: 34981186 DOI: 10.1007/s00251-021-01232-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/01/2021] [Indexed: 01/17/2023]
Abstract
For over half a century, deciphering the origins of the genomic loci that form the jawed vertebrate adaptive immune response has been a major topic in comparative immunogenetics. Vertebrate adaptive immunity relies on an extensive and highly diverse repertoire of tandem arrays of variable (V), diversity (D), and joining (J) gene segments that recombine to produce different immunoglobulin (Ig) and T cell receptor (TCR) genes. The current consensus is that a recombination-activating gene (RAG)-like transposon invaded an exon of an ancient innate immune VJ-bearing receptor, giving rise to the extant diversity of Ig and TCR loci across jawed vertebrates. However, a model for the evolutionary relationships between extant non-recombining innate immune receptors and the V(D)J receptors of the jawed vertebrate adaptive immune system has only recently begun to come into focus. In this review, we provide an overview of non-recombining VJ genes, including CD8β, CD79b, natural cytotoxicity receptor 3 (NCR3/NKp30), putative remnants of an antigen receptor precursor (PRARPs), and the multigene family of signal-regulatory proteins (SIRPs), that play a wide range of roles in immune function. We then focus in detail on the VJ-containing novel immune-type receptors (NITRs) from ray-finned fishes, as recent work has indicated that these genes are at least 50 million years older than originally thought. We conclude by providing a conceptual model of the evolutionary origins and phylogenetic distribution of known VJ-containing innate immune receptors, highlighting opportunities for future comparative research that are empowered by this emerging evolutionary perspective.
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Affiliation(s)
- Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA.
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, USA.
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA.
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
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Liu X, Wang S, Ma Q, Liang W, Li J, Zhu T, Li Q, Han Y. A novel ITAM-containing immunoglobulin superfamily receptor involved in lamprey VLRB+ lymphocyte immune response. Acta Biochim Biophys Sin (Shanghai) 2021; 53:800-803. [PMID: 33742672 DOI: 10.1093/abbs/gmab035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Xin Liu
- Lamprey Research Center, College of Life Science, Liaoning Normal University, Dalian 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Sifan Wang
- Lamprey Research Center, College of Life Science, Liaoning Normal University, Dalian 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Qidi Ma
- Lamprey Research Center, College of Life Science, Liaoning Normal University, Dalian 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Wenjing Liang
- Lamprey Research Center, College of Life Science, Liaoning Normal University, Dalian 116081, China
- Fujin No.1 Middle School of Heilongjiang, Fujin 156100, China
| | - Jun Li
- Lamprey Research Center, College of Life Science, Liaoning Normal University, Dalian 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Ting Zhu
- Lamprey Research Center, College of Life Science, Liaoning Normal University, Dalian 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Qingwei Li
- Lamprey Research Center, College of Life Science, Liaoning Normal University, Dalian 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Yinglun Han
- Lamprey Research Center, College of Life Science, Liaoning Normal University, Dalian 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
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The immune system of jawless vertebrates: insights into the prototype of the adaptive immune system. Immunogenetics 2020; 73:5-16. [PMID: 33159554 DOI: 10.1007/s00251-020-01182-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 10/23/2020] [Indexed: 01/23/2023]
Abstract
Jawless vertebrates diverged from an ancestor of jawed vertebrates approximately 550 million years ago. They mount adaptive immune responses to repetitive antigenic challenges, despite lacking major histocompatibility complex molecules, immunoglobulins, T cell receptors, and recombination-activating genes. Instead of B cell and T cell receptors, agnathan lymphocytes express unique antigen receptors named variable lymphocyte receptors (VLRs), which generate diversity through a gene conversion-like mechanism. Although gnathostome antigen receptors and VLRs are structurally unrelated, jawed and jawless vertebrates share essential features of lymphocyte-based adaptive immunity, including the expression of a single type of receptor on each lymphocyte, clonal expansion of antigen-stimulated lymphocytes, and the dichotomy of cellular and humoral immunity, indicating that the backbone of the adaptive immune system was established in a common ancestor of all vertebrates. Furthermore, recent evidence indicates that, unlike previously thought, agnathans have a unique classical pathway of complement activation where VLRB molecules act as antibodies instead of immunoglobulins. It seems likely that the last common ancestor of all vertebrates had an adaptive immune system resembling that of jawless vertebrates, suggesting that, as opposed to jawed vertebrates, agnathans have retained the prototype of vertebrate adaptive immunity.
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Zhao T, Luo K, Liu X, Dong S, Han Y, Gou M, Su P, Li Q, Zhu T. A novel Lyn-like protein tyrosine kinase identified in lamprey and its role in immune response. Acta Biochim Biophys Sin (Shanghai) 2020; 52:573-575. [PMID: 32286610 DOI: 10.1093/abbs/gmaa022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 11/09/2018] [Indexed: 02/06/2023] Open
Affiliation(s)
- Tingting Zhao
- College of Life Science, Liaoning Normal University, Dalian 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116081, China
| | - Kedi Luo
- College of Life Science, Liaoning Normal University, Dalian 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116081, China
| | - Xin Liu
- College of Life Science, Liaoning Normal University, Dalian 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116081, China
| | - Shanshan Dong
- College of Life Science, Liaoning Normal University, Dalian 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116081, China
- Green Biomedical Technology (Tianjin) Co., Ltd., Tianjin 301700, China
| | - Yinglun Han
- College of Life Science, Liaoning Normal University, Dalian 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116081, China
| | - Meng Gou
- College of Life Science, Liaoning Normal University, Dalian 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116081, China
| | - Peng Su
- College of Life Science, Liaoning Normal University, Dalian 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116081, China
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116081, China
| | - Ting Zhu
- College of Life Science, Liaoning Normal University, Dalian 116081, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116081, China
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6
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Flajnik MF. A Convergent Immunological Holy Trinity of Adaptive Immunity in Lampreys: Discovery of the Variable Lymphocyte Receptors. THE JOURNAL OF IMMUNOLOGY 2019; 201:1331-1335. [PMID: 30127062 DOI: 10.4049/jimmunol.1800965] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD 21201
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Fu Y, Yang Z, Huang J, Cheng X, Wang X, Yang S, Ren L, Lian Z, Han H, Zhao Y. Identification of Two Nonrearranging IgSF Genes in Chicken Reveals a Novel Family of Putative Remnants of an Antigen Receptor Precursor. THE JOURNAL OF IMMUNOLOGY 2019; 202:1992-2004. [PMID: 30770416 DOI: 10.4049/jimmunol.1801305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/22/2019] [Indexed: 11/19/2022]
Abstract
In this study, we identified a pair of nonrearranging VJ-joined Ig superfamily genes, termed putative remnants of an Ag receptor precursor (PRARP) genes, in chicken. Both genes encode a single V-set Ig domain consisting of a canonical J-like segment and a potential immunoreceptor tyrosine-based inhibitory or switch motif in the cytoplasmic region. In vitro experiments showed that both genes were expressed at the cell surface as membrane proteins, and their recombinant products formed a monomer and a disulfide-linked homodimer or a heterodimer. These two genes were mainly expressed in B and T cells and were upregulated in response to stimulation with poly(I:C) in vitro and vaccination in vivo. Orthologs of PRARP have been identified in bony fish, amphibians, reptiles, and other birds, and a V-C1 structure similar to that of Ig or TCR chains was found in all these genes, with the exception of those in avian species, which appear to contain degenerated C1 domains or divergent Ig domains. Phylogenetic analyses suggested that the newly discovered genes do not belong to any known immune receptor family and appear to be a novel gene family. Further elucidation of the functions of PRARP and their origin might provide significant insights into the evolution of the immune system of jawed vertebrates.
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Affiliation(s)
- Yanbin Fu
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Zhi Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Jinwei Huang
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Xueqian Cheng
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Xifeng Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Science, Beijing 100101, People's Republic of China; and
| | - Shiping Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Liming Ren
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Zhengxing Lian
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Haitang Han
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China;
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Science, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China;
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Boehm T, Hirano M, Holland SJ, Das S, Schorpp M, Cooper MD. Evolution of Alternative Adaptive Immune Systems in Vertebrates. Annu Rev Immunol 2017; 36:19-42. [PMID: 29144837 DOI: 10.1146/annurev-immunol-042617-053028] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Adaptive immunity in jawless fishes is based on antigen recognition by three types of variable lymphocyte receptors (VLRs) composed of variable leucine-rich repeats, which are differentially expressed by two T-like lymphocyte lineages and one B-like lymphocyte lineage. The T-like cells express either VLRAs or VLRCs of yet undefined antigen specificity, whereas the VLRB antibodies secreted by B-like cells bind proteinaceous and carbohydrate antigens. The incomplete VLR germline genes are assembled into functional units by a gene conversion-like mechanism that employs flanking variable leucine-rich repeat sequences as templates in association with lineage-specific expression of cytidine deaminases. B-like cells develop in the hematopoietic typhlosole and kidneys, whereas T-like cells develop in the thymoid, a thymus-equivalent region at the gill fold tips. Thus, the dichotomy between T-like and B-like cells and the presence of dedicated lymphopoietic tissues emerge as ancestral vertebrate features, whereas the somatic diversification of structurally distinct antigen receptor genes evolved independently in jawless and jawed vertebrates.
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Affiliation(s)
- Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; , ,
| | - Masayuki Hirano
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia 30322, USA; , ,
| | - Stephen J Holland
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; , ,
| | - Sabyasachi Das
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia 30322, USA; , ,
| | - Michael Schorpp
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; , ,
| | - Max D Cooper
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia 30322, USA; , ,
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9
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Wu F, Chen L, Ren Y, Yang X, Yu T, Feng B, Chen S, Xu A. An inhibitory receptor of VLRB in the agnathan lamprey. Sci Rep 2016; 6:33760. [PMID: 27762335 PMCID: PMC5071834 DOI: 10.1038/srep33760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/31/2016] [Indexed: 01/19/2023] Open
Abstract
Lamprey, the primitive jawless vertebrate, uses variable lymphocyte receptor (VLR) as alternative adaptive immune system instead of immunoglobulin (Ig)-based receptors used in jawed vertebrates. In the present study, we characterized a potential inhibitory receptor of VLRB from leucocytes in lamprey. It is a novel ITIM-containing IgSF protein and was therefore named as NICIP. NICIP has two Ig-like domains in extracellular region, a transmembrane domain and two classical ITIM motifs in cytoplasmic domain. It is mainly expressed on the surface of granulocytes and monocytes and can interact with VLRB. In transiently transfected HEK293T cells, it was confirmed again that it could interact with VLRB and the two phosphorylated ITIM motifs could recruit SHP-1 and SHP-2. These results imply that NICIP may play a role as a potential inhibitory receptor of VLRB and involve in negative regulation of immune response mediated by VLRB.
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Affiliation(s)
- Fenfang Wu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, P. R. China
| | - Liyong Chen
- Guangdong Province Key Laboratory for Medical Molecular Diagnostics, China-America Cancer Research Institute, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan 523808, P. R. China
| | - Yong Ren
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, P. R. China
| | - Xiaojing Yang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, P. R. China
| | - Tongzhou Yu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, P. R. China
| | - Bo Feng
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, P. R. China
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, P. R. China
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, P. R. China.,Beijing University of Chinese Medicine, Beijing, 100029, P. R. China
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11
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Zhang Q, Song X, Su P, Li R, Liu C, Gou M, Wang H, Liu X, Li Q. A novel homolog of protein tyrosine kinase Fyn identified in Lampetra japonica with roles in the immune response. Gene 2016; 579:193-200. [DOI: 10.1016/j.gene.2015.12.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/10/2015] [Accepted: 12/27/2015] [Indexed: 11/27/2022]
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12
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Liu C, Su P, Li R, Zhang Q, Zhu T, Liu X, Li Q. Molecular cloning, expression pattern, and molecular evolution of the spleen tyrosine kinase in lamprey, Lampetra japonica. Dev Genes Evol 2015; 225:113-20. [PMID: 25682127 DOI: 10.1007/s00427-015-0492-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 01/26/2015] [Indexed: 01/15/2023]
Abstract
Spleen tyrosine kinase (Syk), a member of Syk family of cytoplasmic non-receptor tyrosine kinases, is a key component of B cell receptor signaling and regulates multiple physiological functions of B lymphocytes in vertebrates. In the current study, a Syk homologue was identified in the lamprey Lampetra japonica (Lj-Syk). The cDNA fragment of Lj-Syk contains a 1953-bp open reading frame which encodes 651 amino acids, a 12-bp fragment of 5'-untranslated region, and a 1029-bp 3'-untranslated region. The same as vertebrate's Syks, Lj-Syk protein also contains a tyrosine kinase catalytic domain which functions as its kinase activity center and two Src homology 2 (SH2) domains which are the targets when Syk is recruited by phosphorylated immunoreceptor tyrosine-based activation motif. It is revealed by multiple sequence alignment that the tyrosine kinase catalytic domain and two SH2 domains are conserved throughout the Syk gene family in vertebrates. The evolutionary dynamics of Syks were analyzed by MEME software using conserved motifs as markers. Among 19 conserved motifs elicited from 22 Syks or Syk-like proteins, 12 motifs that locate at N-terminal, two tandem SH2, Inter SH2, and Tyrkc domains are conserved in Syks from jawless to jawed vertebrates. From the absence and existence of the other seven motifs, it can be concluded that the primary Syk gene evolved to modern functional gene through short insertion and deletion strategy in their gene sequence rather than gene duplication. The expression of lamprey Syk was examined by real-time quantitative PCR and Western blot methods in leukocyte cells, gills, supraneural myeloid bodies, kidneys, and hearts of lampreys before and after the animals were stimulated with lipopolysaccharide (LPS). The transcriptional level of lamprey Syk was upregulated in gill, kidney, heart, and leukocyte cells, and the protein expression level is upregulated in leukocyte cells and supraneural myeloid bodies after stimulated with LPS. It could be deduced that Lj-Syk may play a crucial role in immune response of the jawless vertebrates.
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Affiliation(s)
- Chang Liu
- College of Life Science, Liaoning Normal University, Dalian, 116029, China
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13
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Abstract
Jawless vertebrates represented by lampreys and hagfish mount antigen-specific immune responses using variable lymphocyte receptors. These receptors generate diversity comparable to that of T-cell and B-cell receptors by assembling multiple leucine-rich repeat modules with highly variable sequences. Although it is true that jawed and jawless vertebrates have structurally unrelated antigen receptors, their adaptive immune systems have much in common. Most notable is the conservation of lymphocyte lineages. It appears that specialized lymphocyte lineages emerged in a common vertebrate ancestor and that jawed and jawless vertebrates co-opted different antigen receptors within the context of such lymphocyte lineages.
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Affiliation(s)
- Masanori Kasahara
- Department of Pathology, Hokkaido University Graduate School of Medicine, North 15 West 7, Sapporo, 060-8638, Japan.
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14
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Abstract
Classically the immunological 'Big Bang' of adaptive immunity was believed to have resulted from the insertion of a transposon into an immunoglobulin superfamily gene member, initiating antigen receptor gene rearrangement via the RAG recombinase in an ancestor of jawed vertebrates. However, the discovery of a second, convergent adaptive immune system in jawless fish, focused on the so-called variable lymphocyte receptors (VLRs), was arguably the most exciting finding of the past decade in immunology and has drastically changed the view of immune origins. The recent report of a new lymphocyte lineage in lampreys, defined by the antigen receptor VLRC, suggests that there were three lymphocyte lineages in the common ancestor of jawless and jawed vertebrates that co-opted different antigen receptor supertypes. The transcriptional control of these lineages during development is predicted to be remarkably similar in both the jawless (agnathan) and jawed (gnathostome) vertebrates, suggesting that an early 'division of labor' among lymphocytes was a driving force in the emergence of adaptive immunity. The recent cartilaginous fish genome project suggests that most effector cytokines and chemokines were also present in these fish, and further studies of the lamprey and hagfish genomes will determine just how explosive the Big Bang actually was.
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Affiliation(s)
- Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD 21201, USA.
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Takaba H, Imai T, Miki S, Morishita Y, Miyashita A, Ishikawa N, Nishizumi H, Sakano H. A major allogenic leukocyte antigen in the agnathan hagfish. Sci Rep 2013; 3:1716. [PMID: 23612706 PMCID: PMC3634110 DOI: 10.1038/srep01716] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 04/05/2013] [Indexed: 11/30/2022] Open
Abstract
All vertebrates, from jawless fish to mammals, possess adaptive immune systems that can detect and inactivate non-self-antigens through a vast repertoire of antigen receptors. Unlike jawed vertebrates, the hagfish utilizes variable lymphocyte receptors (VLRs) that are unrelated to immunoglobulin molecules but are diversified by copy-choice gene conversion mechanism. Here, we report that hagfish VLRs react with allogenic leukocyte antigens but not with self-antigens. We found that a highly polymorphic membrane protein, NICIR3, is recognized by VLRs as an allogenic leukocyte antigen (ALA). In a serological cross-reactivity test, a close correlation was observed between the amino acid differences in the protein sequences and the VLR cross-reactivities. This leukocyte antigen was predominantly expressed in phagocytic leukocytes, where it was associated with phagocytosed protein antigens. These findings suggest that a polymorphic leukocyte antigen, NICIR3/ALA, plays a pivotal role in jawless vertebrate adaptive immunity.
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Affiliation(s)
- Hiroyuki Takaba
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Takeshi Imai
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
- PRESTO, Japan Science and Technology Agency, Saitama 332-0012, Japan
- Laboratory for Sensory Circuit Formation, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
| | - Shoji Miki
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Yasuyuki Morishita
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Akihiro Miyashita
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Naoko Ishikawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hirofumi Nishizumi
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Hitoshi Sakano
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
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McCurley N, Hirano M, Das S, Cooper MD. Immune related genes underpin the evolution of adaptive immunity in jawless vertebrates. Curr Genomics 2012; 13:86-94. [PMID: 23024600 PMCID: PMC3308329 DOI: 10.2174/138920212799860670] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 11/30/2011] [Accepted: 12/05/2011] [Indexed: 12/17/2022] Open
Abstract
The study of immune related genes in lampreys and hagfish provides a unique perspective on the evolutionary genetic underpinnings of adaptive immunity and the evolution of vertebrate genomes. Separated from their jawed cousins at the stem of the vertebrate lineage, these jawless vertebrates have many of the gene families and gene regulatory networks associated with the defining morphological and physiological features of vertebrates. These include genes vital for innate immunity, inflammation, wound healing, protein degradation, and the development, signaling and trafficking of lymphocytes. Jawless vertebrates recognize antigen by using leucine-rich repeat (LRR) based variable lymphocyte receptors (VLRs), which are very different from the immunoglobulin (Ig) based T cell receptor (TCR) and B cell receptor (BCR) used for antigen recognition by jawed vertebrates. The somatically constructed VLR genes are expressed in monoallelic fashion by T-like and B-like lymphocytes. Jawless and jawed vertebrates thus share many of the genes that provide the molecular infrastructure and physiological context for adaptive immune responses, yet use entirely different genes and mechanisms of combinatorial assembly to generate diverse repertoires of antigen recognition receptors.
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Affiliation(s)
- Nathanael McCurley
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
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18
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Flajnik MF, Tlapakova T, Criscitiello MF, Krylov V, Ohta Y. Evolution of the B7 family: co-evolution of B7H6 and NKp30, identification of a new B7 family member, B7H7, and of B7's historical relationship with the MHC. Immunogenetics 2012; 64:571-90. [PMID: 22488247 DOI: 10.1007/s00251-012-0616-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 03/20/2012] [Indexed: 12/21/2022]
Abstract
The B7 family of genes is essential in the regulation of the adaptive immune system. Most B7 family members contain both variable (V)- and constant (C)-type domains of the immunoglobulin superfamily (IgSF). Through in silico screening of the Xenopus genome and subsequent phylogenetic analysis, we found novel genes belonging to the B7 family, one of which is the recently discovered B7H6. Humans and rats have a single B7H6 gene; however, many B7H6 genes were detected in a single large cluster in the Xenopus genome. The B7H6 expression patterns also varied in a species-specific manner. Human B7H6 binds to the activating natural killer receptor, NKp30. While the NKp30 gene is single-copy and maps to the MHC in most vertebrates, many Xenopus NKp30 genes were found in a cluster on a separate chromosome that does not harbor the MHC. Indeed, in all species so far analyzed from sharks to mammals, the number of NKp30 and B7H6 genes correlates well, suggestive of receptor-ligand co-evolution. Furthermore, we identified a Xenopus-specific B7 homolog (B7HXen) and revealed its close linkage to B2M, which we have demonstrated previously to have been originally encoded in the MHC. Thus, our study provides further proof that the B7 precursor was included in the proto MHC. Additionally, the comparative analysis revealed a new B7 family member, B7H7, which was previously designated in the literature as an unknown gene, HHLA2.
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Affiliation(s)
- Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201, USA
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Laing KJ, Hansen JD. Fish T cells: recent advances through genomics. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2011; 35:1282-1295. [PMID: 21414347 DOI: 10.1016/j.dci.2011.03.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2010] [Revised: 01/14/2011] [Accepted: 03/06/2011] [Indexed: 05/30/2023]
Abstract
This brief review is intended to provide a concise overview of the current literature concerning T cells, advances in identifying distinct T cell functional subsets, and in distinguishing effector cells from memory cells. We compare and contrast a wealth of recent progress made in T cell immunology of teleost, elasmobranch, and agnathan fish, to knowledge derived from mammalian T cell studies. From genome studies, fish clearly have most components associated with T cell function and we can speculate on the presence of putative T cell subsets, and the ability to detect their differentiation to form memory cells. Some recombinant proteins for T cell associated cytokines and antibodies for T cell surface receptors have been generated that will facilitate studying the functional roles of teleost T cells during immune responses. Although there is still a long way to go, major advances have occurred in recent years for investigating T cell responses, thus phenotypic and functional characterization is on the near horizon.
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Affiliation(s)
- Kerry J Laing
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer, Research Center, Seattle, WA 98109, USA
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20
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Smith JJ, Saha NR, Amemiya CT. Genome biology of the cyclostomes and insights into the evolutionary biology of vertebrate genomes. Integr Comp Biol 2010; 50:130-7. [PMID: 21558194 PMCID: PMC3140258 DOI: 10.1093/icb/icq023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The jawless vertebrates (lamprey and hagfish) are the closest extant outgroups to all jawed vertebrates (gnathostomes) and can therefore provide critical insight into the evolution and basic biology of vertebrate genomes. As such, it is notable that the genomes of lamprey and hagfish possess a capacity for rearrangement that is beyond anything known from the gnathostomes. Like the jawed vertebrates, lamprey and hagfish undergo rearrangement of adaptive immune receptors. However, the receptors and the mechanisms for rearrangement that are utilized by jawless vertebrates clearly evolved independently of the gnathostome system. Unlike the jawed vertebrates, lamprey and hagfish also undergo extensive programmed rearrangements of the genome during embryonic development. By considering these fascinating genome biologies in the context of proposed (albeit contentious) phylogenetic relationships among lamprey, hagfish, and gnathostomes, we can begin to understand the evolutionary history of the vertebrate genome. Specifically, the deep shared ancestry and rapid divergence of lampreys, hagfish and gnathostomes is considered evidence that the two versions of programmed rearrangement present in lamprey and hagfish (embryonic and immune receptor) were present in an ancestral lineage that existed more than 400 million years ago and perhaps included the ancestor of the jawed vertebrates. Validating this premise will require better characterization of the genome sequence and mechanisms of rearrangement in lamprey and hagfish.
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Affiliation(s)
- J J Smith
- Benaroya Research Institute at Virginia Mason, 1201 9th Avenue, Seattle, WA 98101, USA.
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21
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Flajnik MF, Kasahara M. Origin and evolution of the adaptive immune system: genetic events and selective pressures. Nat Rev Genet 2009; 11:47-59. [PMID: 19997068 DOI: 10.1038/nrg2703] [Citation(s) in RCA: 573] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The adaptive immune system (AIS) in mammals, which is centred on lymphocytes bearing antigen receptors that are generated by somatic recombination, arose approximately 500 million years ago in jawed fish. This intricate defence system consists of many molecules, mechanisms and tissues that are not present in jawless vertebrates. Two macroevolutionary events are believed to have contributed to the genesis of the AIS: the emergence of the recombination-activating gene (RAG) transposon, and two rounds of whole-genome duplication. It has recently been discovered that a non-RAG-based AIS with similarities to the jawed vertebrate AIS - including two lymphoid cell lineages - arose in jawless fish by convergent evolution. We offer insights into the latest advances in this field and speculate on the selective pressures that led to the emergence and maintenance of the AIS.
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Affiliation(s)
- Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, Maryland 21201, USA.
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Huang L, Cheng T, Xu P, Duan J, Fang T, Xia Q. Immunoglobulin superfamily is conserved but evolved rapidly and is active in the silkworm, Bombyx mori. INSECT MOLECULAR BIOLOGY 2009; 18:517-530. [PMID: 19604311 DOI: 10.1111/j.1365-2583.2009.00896.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Immunoglobulin superfamily (IgSF) proteins are known for their abilities to specifically recognize and adhere to cells. In this paper, we predicted the presence of 133 IgSF proteins in the silkworm (Bombyx mori) genome. Comparison with similar proteins in other model organisms (Caenorhabditis elegans, Drosophila melanogaster, Anopheles gambiae, Apis mellifera and Homo sapiens) indicated that IgSF proteins are conserved but have rapidly evolved from worms to human beings. However, these proteins are well conserved amongst insects. Silkworm microarray-based expression data showed tissue expression of 57 IgSF genes and microbe-induced differential expression of 37 genes. Based on the expression data, we can conclude that the silkworm IgSF is active.
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Affiliation(s)
- L Huang
- Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China.
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Kasahara M, Kasamatsu J, Sutoh Y. Two types of antigen receptor systems in vertebrates. Zoolog Sci 2009; 25:969-75. [PMID: 19267632 DOI: 10.2108/zsj.25.969] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Extant jawless vertebrates, represented by lampreys and hagfishes, have innate immune receptors with variable domains structurally resembling those of T/B-cell receptors. However, they appear to lack cardinal elements of adaptive immunity shared by all jawed vertebrates: major histocompatibility complex molecules and T/B-cell receptors. Thus, it was widely believed that adaptive immunity is unique to jawed vertebrates. Recently, this belief was overturned by the discovery of agnathan antigen receptors named variable lymphocyte receptors. These receptors generate diversity in their antigen-binding sites through assembling highly diverse leucine-rich repeat modules. The crystal structures of hagfish variable lymphocyte receptor monomers indicate that they adopt a horseshoe-shaped structure and likely bind antigens through the hypervariable concave surface. Secreted variable lymphocyte receptors form pentamers or tetramers of dimers and bind antigens with high specificity and avidity. The fact that variable lymphocyte receptors are structurally unrelated to T/B-cell receptors indicates that jawed and jawless vertebrates have developed antigen receptors independently.
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Affiliation(s)
- Masanori Kasahara
- Department of Pathology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan.
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Yu C, Ehrhardt GRA, Alder MN, Cooper MD, Xu A. Inhibitory signaling potential of a TCR-like molecule in lamprey. Eur J Immunol 2009; 39:571-9. [PMID: 19130486 DOI: 10.1002/eji.200838846] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A TCR-like molecule (TCRL) with two canonical ITIM has been identified in the sea lamprey. We show here that TCRL is preferentially expressed by lymphocytes bearing variable lymphocyte receptors. To examine the potential of the TCRL inhibitory motifs, chimeric proteins comprising the FcgammaRIIb extracellular and transmembrane domains and the TCRL intracellular domain were expressed in a mouse B-cell line. BCR co-ligation with the WT version of the FcgammaRIIb/TCRL chimeric protein resulted in its tyrosine phosphorylation and the inhibition of BCR-induced calcium mobilization, whole-cell protein tyrosine phosphorylation and Erk/Akt/JNK activation. Tyrosine to phenylalanine mutations in either or both ITIM compromised the inhibitory capacity of this receptor chimera. Analysis of receptor-associated proteins indicated that the inhibition is mediated by recruitment of the protein tyrosine kinases, SHP1 and SHP2. These findings demonstrate the inhibitory potential of TCRL and its expression by clonally diverse lymphocytes bearing the variable lymphocyte receptors, thereby implying an immunomodulatory role for this ancestral TCR relative in a jawless vertebrate.
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Affiliation(s)
- Cuiling Yu
- Department of Biochemistry, State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
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25
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Hansen JD, Pasquier LD, Lefranc MP, Lopez V, Benmansour A, Boudinot P. The B7 family of immunoregulatory receptors: A comparative and evolutionary perspective. Mol Immunol 2009; 46:457-72. [DOI: 10.1016/j.molimm.2008.10.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Accepted: 10/09/2008] [Indexed: 01/01/2023]
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Litman GW, Cannon JP, Dishaw LJ, Haire RN, Eason DD, Yoder JA, Prada JH, Ostrov DA. Immunoglobulin variable regions in molecules exhibiting characteristics of innate and adaptive immune receptors. Immunol Res 2008; 38:294-304. [PMID: 17917037 DOI: 10.1007/s12026-007-0014-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 11/25/2022]
Abstract
The antigen combining sites of immunoglobulin (Ig) and T cell antigen receptors (TCRs), which are present in all jawed vertebrates, consist of a paired variable (V) domain heterodimer that exhibits varying degrees of germline- and extraordinarily high levels of somatically-derived variation. The near limitless variation in receptor specificity on the surface of individual lymphocytes is the basis for clonal selection in the adaptive immune response. A basic question arises as to whether or not there are other forms of immune-type receptors in vertebrates as well as in invertebrates that derive immune specificity through sequence differences in V domains. Our laboratory has discovered two such families of molecules, the novel immune-type receptors and the variable region-containing chitin-binding proteins. Both families of molecules encode V domains that share some characteristics of adaptive immune receptors but likely mediate innate functions.
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Affiliation(s)
- Gary W Litman
- Department of Pediatrics, University of South Florida College of Medicine, USF/ACH Children's Research Institute, 830 First Street South, St. Petersburg, FL 33701, USA.
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27
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Abstract
Discovery of a large family of Fc receptor-like (FCRL) molecules, homologous to the well-known receptors for the Fc portion of immunoglobulin (FCR), has uncovered an impressive abundance of immunoglobulin superfamily (IgSF) genes in the human 1q21-23 chromosomal region and revealed significant diversity for these genes between humans and mice. The observation that FCRL representatives are members of an ancient multigene family that share a common ancestor with the classical FCR is underscored by their linked genomic locations, gene structure, shared extracellular domain composition, and utilization of common cytoplasmic tyrosine-based signaling elements. In contrast to the conventional FCR, however, FCRL molecules possess diverse extracellular frameworks, autonomous or dual signaling properties, and preferential B lineage expression. Most importantly, there is no strong evidence thus far to support a role for them as Ig-binding receptors. These characteristics, in addition to their identification in malignancies and autoimmune disorders, predict a fundamental role for these receptors as immunomodulatory agents in normal and subverted B lineage cells.
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Affiliation(s)
- Randall S Davis
- Division of Developmental and Clinical Immunology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294-3300, USA.
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28
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Hernández Prada JA, Haire RN, Allaire M, Jakoncic J, Stojanoff V, Cannon JP, Litman GW, Ostrov DA. Ancient evolutionary origin of diversified variable regions demonstrated by crystal structures of an immune-type receptor in amphioxus. Nat Immunol 2006; 7:875-82. [PMID: 16799561 PMCID: PMC3707131 DOI: 10.1038/ni1359] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Accepted: 05/25/2006] [Indexed: 02/05/2023]
Abstract
Although the origins of genes encoding the rearranging binding receptors remain obscure, it is predicted that their ancestral forms were nonrearranging immunoglobulin-type domains. Variable region-containing chitin-binding proteins (VCBPs) are diversified immune-type molecules found in amphioxus (Branchiostoma floridae), an invertebrate that diverged early in deuterostome phylogeny. To study the potential evolutionary relationships between VCBPs and vertebrate adaptive immune receptors, we solved the structures of both a single V-type domain (to 1.15 A) and a pair of V-type domains (to 1.85 A) from VCBP3. The deduced structures show integral features of the ancestral variable-region fold as well as unique features of variable-region pairing in molecules that may reflect characteristics of ancestral forms of diversified immune receptors found in modern-day vertebrates.
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Affiliation(s)
- José A Hernández Prada
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida 32610, USA
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