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Veríssimo A, Castro LFC, Muñoz-Mérida A, Almeida T, Gaigher A, Neves F, Flajnik MF, Ohta Y. An Ancestral Major Histocompatibility Complex Organization in Cartilaginous Fish: Reconstructing MHC Origin and Evolution. Mol Biol Evol 2023; 40:msad262. [PMID: 38059517 PMCID: PMC10751288 DOI: 10.1093/molbev/msad262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023] Open
Abstract
Cartilaginous fish (sharks, rays, and chimeras) comprise the oldest living jawed vertebrates with a mammalian-like adaptive immune system based on immunoglobulins (Ig), T-cell receptors (TCRs), and the major histocompatibility complex (MHC). Here, we show that the cartilaginous fish "adaptive MHC" is highly regimented and compact, containing (i) a classical MHC class Ia (MHC-Ia) region containing antigen processing (antigen peptide transporters and immunoproteasome) and presenting (MHC-Ia) genes, (ii) an MHC class II (MHC-II) region (with alpha and beta genes) with linkage to beta-2-microglobulin (β2m) and bromodomain-containing 2, (iii) nonclassical MHC class Ib (MHC-Ib) regions with 450 million-year-old lineages, and (iv) a complement C4 associated with the MHC-Ia region. No MHC-Ib genes were found outside of the elasmobranch MHC. Our data suggest that both MHC-I and MHC-II genes arose after the second round of whole-genome duplication (2R) on a human chromosome (huchr) 6 precursor. Further analysis of MHC paralogous regions across early branching taxa from all jawed vertebrate lineages revealed that Ig/TCR genes likely arose on a precursor of the huchr9/12/14 MHC paralog. The β2m gene is linked to the Ig/TCR genes in some vertebrates suggesting that it was present at 1R, perhaps as the donor of C1 domain to the primordial MHC gene. In sum, extant cartilaginous fish exhibit a conserved and prototypical MHC genomic organization with features found in various vertebrates, reflecting the ancestral arrangement for the jawed vertebrates.
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Affiliation(s)
- Ana Veríssimo
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - L Filipe C Castro
- Department of Biology, Faculty of Sciences, University of Porto, Porto 4169-007, Portugal
- CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
| | - Antonio Muñoz-Mérida
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - Tereza Almeida
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - Arnaud Gaigher
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Fabiana Neves
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
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Janes ME, Kinlein A, Flajnik MF, Du Pasquier L, Ohta Y. Genomic view of the origins of cell-mediated immunity. Immunogenetics 2023; 75:479-493. [PMID: 37735270 PMCID: PMC11019866 DOI: 10.1007/s00251-023-01319-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/10/2023] [Indexed: 09/23/2023]
Abstract
NKp30 is an activating natural killer cell receptor (NKR) with a single-exon variable (VJ)-type immunoglobulin superfamily (IgSF) domain. Such VJ-IgSF domains predate the emergence of the antigen receptors (immunoglobulin and T cell receptor), which possess the same domain but undergo gene rearrangement. NCR3, the gene encoding NKp30, is present in jawed vertebrates from sharks to mammals; thus, unlike most NKR that are highly divergent among vertebrate taxa, NKp30 is uniquely conserved. We previously hypothesized that an ancestral NCR3 gene was encoded in the proto-major histocompatibility complex (MHC), the region where many immune-related genes have accumulated. Herein, we searched in silico databases to identify NCR3 paralogues and examined their genomic locations. We found a paralogue, NCR3H, in many vertebrates but was lost in mammals. Additionally, we identified a set of voltage-gated sodium channel beta (SCNB) genes as NCR3-distantly-related genes. Like NCR3, both NCR3H and SCNB proteins contain a single VJ-IgSF domain followed by a transmembrane region. These genes map to MHC paralogous regions, originally described in an invertebrate, along with genes encoding cell adhesion molecules involved in NK cell recognition networks. Other genes having no obvious relationship to immunity also map to these paralogous regions. These gene complexes were traced to several invertebrates, suggesting that the foundation of these cellular networks emerged before the genome-wide duplications in early gnathostome history. Here, we propose that this ancestral region was involved in cell-mediated immunity prior to the emergence of adaptive immunity and that NCR3 piggybacked onto this primordial complex, heralding the emergence of vertebrate NK cell/T cells.
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Affiliation(s)
- Morgan E Janes
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, 21201, USA
| | - Allison Kinlein
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, 21201, USA
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, 21201, USA
| | - Louis Du Pasquier
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, 21201, USA.
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3
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Campbell LK, Peery RM, Magor KE. Evolution and expression of the duck TRIM gene repertoire. Front Immunol 2023; 14:1220081. [PMID: 37622121 PMCID: PMC10445537 DOI: 10.3389/fimmu.2023.1220081] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/05/2023] [Indexed: 08/26/2023] Open
Abstract
Tripartite motif (TRIM) proteins are involved in development, innate immunity, and viral restriction. TRIM gene repertoires vary between species, likely due to diversification caused by selective pressures from pathogens; however, this has not been explored in birds. We mined a de novo assembled transcriptome for the TRIM gene repertoire of the domestic mallard duck (Anas platyrhynchos), a reservoir host of influenza A viruses. We found 57 TRIM genes in the duck, which represent all 12 subfamilies based on their C-terminal domains. Members of the C-IV subfamily with C-terminal PRY-SPRY domains are known to augment immune responses in mammals. We compared C-IV TRIM proteins between reptiles, birds, and mammals and show that many C-IV subfamily members have arisen independently in these lineages. A comparison of the MHC-linked C-IV TRIM genes reveals expansions in birds and reptiles. The TRIM25 locus with related innate receptor modifiers is adjacent to the MHC in reptile and marsupial genomes, suggesting the ancestral organization. Within the avian lineage, both the MHC and TRIM25 loci have undergone significant TRIM gene reorganizations and divergence, both hallmarks of pathogen-driven selection. To assess the expression of TRIM genes, we aligned RNA-seq reads from duck tissues. C-IV TRIMs had high relative expression in immune relevant sites such as the lung, spleen, kidney, and intestine, and low expression in immune privileged sites such as in the brain or gonads. Gene loss and gain in the evolution of the TRIM repertoire in birds suggests candidate immune genes and potential targets of viral subversion.
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Affiliation(s)
- Lee K. Campbell
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | - Rhiannon M. Peery
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Katharine E. Magor
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
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Zhang L, Park JJ, Dong MB, Arsala D, Xia S, Chen J, Sosa D, Atlas JE, Long M, Chen S. Human gene age dating reveals an early and rapid evolutionary construction of the adaptive immune system. Genome Biol Evol 2023; 15:evad081. [PMID: 37170918 PMCID: PMC10210621 DOI: 10.1093/gbe/evad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 04/24/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023] Open
Abstract
T cells are a type of white blood cell that play a critical role in the immune response against foreign pathogens through a process called T Cell Adaptive Immunity (TCAI). However, the evolution of the genes and nucleotide sequences involved in TCAI is not well understood. To investigate this, we performed comparative studies of gene annotations and genome assemblies of 28 vertebrate species and identified sets of human genes that are involved in TCAI, carcinogenesis, and ageing. We found that these gene sets share interaction pathways which may have contributed to the evolution of longevity in the vertebrate lineage leading to humans. Our human gene age dating analyses revealed that there was rapid origination of genes with TCAI-related functions prior to the Cretaceous eutherian radiation and these new genes mainly encode negative regulators. We identified no new TCAI-related genes after the divergence of placental mammals, but we did detect an extensive number of amino acid substitutions under strong positive selection in recently evolved human immunity genes suggesting they are co-evolving with adaptive immunity. More specifically, we observed that antigen processing and presentation and checkpoint genes are significantly enriched among new genes evolving under positive selection. These observations reveal an evolutionary process of T Cell Adaptive Immunity that were associated with rapid gene duplication in the early stages of vertebrates and subsequent sequence changes in TCAI-related genes. These processes together suggest an early genetic construction of the vertebrate immune system and subsequent molecular adaptation to diverse antigens.
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Affiliation(s)
- Li Zhang
- System Biology Institute, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Yale M.D.-Ph.D. Program, New Haven, Connecticut, USA
| | - Jonathan J Park
- System Biology Institute, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Yale M.D.-Ph.D. Program, New Haven, Connecticut, USA
| | - Matthew B Dong
- System Biology Institute, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Yale M.D.-Ph.D. Program, New Haven, Connecticut, USA
- Immunobiology Program, The Anlyan Center, New Haven, Connecticut, USA
- Department of Immunobiology, The Anlyan Center, New Haven, Connecticut, USA
| | - Deanna Arsala
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Shengqian Xia
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Jianhai Chen
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Dylan Sosa
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Jared E Atlas
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, USA
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Sidi Chen
- System Biology Institute, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Yale M.D.-Ph.D. Program, New Haven, Connecticut, USA
- Immunobiology Program, The Anlyan Center, New Haven, Connecticut, USA
- Yale Comprehensive Cancer Center, New Haven, Connecticut, USA
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA
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5
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Moreno-Santillán DD, Machain-Williams C, Hernández-Montes G, Ortega J. Transcriptomic analysis elucidates evolution of the major histocompatibility complex class I in neotropical bats. J Mammal 2022. [DOI: 10.1093/jmammal/gyac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
The Order Chiroptera comprises more than 1,400 species, each with its evolutionary history and under unique selective pressures, among which are the host–pathogen interactions. Bats have coped with complex interactions with a broad spectrum of microbes throughout their evolutionary history, prompting the development of unique adaptations that allow them to co-exist with microbes with pathogenic potential more efficiently than other nonadapted species. In this sense, an extraordinary immune system with unique adaptations has been hypothesized in bats. To explore this, we focused on the major histocompatibility complex (MHC), which plays a crucial role in pathogen recognition and presentation to T cells to trigger the adaptive immune response. We analyzed MHC class I transcripts in five species, each from different families of New World bats. From RNA-seq data, we assembled a partial region of the MHC-I comprising the α1 and α2 domains, which are responsible for peptide binding and recognition. We described five putative functional variants, two of which have two independent insertions at the α2 domain. Our results suggest that this insertion appeared after the divergence of the order Chiroptera and may have an adaptive function in the defense against intracellular pathogens, providing evidence of positive selection and trans-specific polymorphism on the peptide-binding sites.
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Affiliation(s)
- Diana D Moreno-Santillán
- Department of Integrative Biology, University of California , Berkeley, California 94720-3200 , USA
| | - Carlos Machain-Williams
- Universidad Autónoma de Yucatán, Laboratorio de Arbovirología , Mérida, Yucatán 97000 , México
| | - Georgina Hernández-Montes
- Universidad Nacional Autónoma de México, Red de apoyo a la Investigación, Coordinación de la Investigación Científica entre Universidad y Red de Apoyo , Ciudad de México 14080 , México
| | - Jorge Ortega
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Departamento de Zoología, Posgrado en Ciencias Quimicobiológicas , Ciudad de México 11350 , México
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Holosteans contextualize the role of the teleost genome duplication in promoting the rise of evolutionary novelties in the ray-finned fish innate immune system. Immunogenetics 2021; 73:479-497. [PMID: 34510270 DOI: 10.1007/s00251-021-01225-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/06/2021] [Indexed: 01/16/2023]
Abstract
Over 99% of ray-finned fishes (Actinopterygii) are teleosts, a clade that comprises half of all living vertebrate species that have diversified across virtually all fresh and saltwater ecosystems. This ecological breadth raises the question of how the immunogenetic diversity required to persist under heterogeneous pathogen pressures evolved. The teleost genome duplication (TGD) has been hypothesized as the evolutionary event that provided the substrate for rapid genomic evolution and innovation. However, studies of putative teleost-specific innate immune receptors have been largely limited to comparisons either among teleosts or between teleosts and distantly related vertebrate clades such as tetrapods. Here we describe and characterize the receptor diversity of two clustered innate immune gene families in the teleost sister lineage: Holostei (bowfin and gars). Using genomic and transcriptomic data, we provide a detailed investigation of the phylogenetic history and conserved synteny of gene clusters encoding diverse immunoglobulin domain-containing proteins (DICPs) and novel immune-type receptors (NITRs). These data demonstrate an ancient linkage of DICPs to the major histocompatibility complex (MHC) and reveal an evolutionary origin of NITR variable-joining (VJ) exons that predate the TGD by at least 50 million years. Further characterizing the receptor diversity of Holostean DICPs and NITRs illuminates a sequence diversity that rivals the diversity of these innate immune receptor families in many teleosts. Taken together, our findings provide important historical context for the evolution of these gene families that challenge prevailing expectations concerning the consequences of the TGD during actinopterygiian evolution.
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Klumplerova M, Splichalova P, Oppelt J, Futas J, Kohutova A, Musilova P, Kubickova S, Vodicka R, Orlando L, Horin P. Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae. BMC Genomics 2020; 21:677. [PMID: 32998693 PMCID: PMC7525986 DOI: 10.1186/s12864-020-07089-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/21/2020] [Indexed: 02/08/2023] Open
Abstract
Background The mammalian Major Histocompatibility Complex (MHC) is a genetic region containing highly polymorphic genes with immunological functions. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. The MHC class II sub-region contains genes expressed in antigen presenting cells. The antigen binding site is encoded by the second exon of genes encoding antigen presenting molecules. The exon 2 sequences of these MHC genes have evolved under the selective pressure of pathogens. Interspecific differences can be observed in the class II sub-region. The family Equidae includes a variety of domesticated, and free-ranging species inhabiting a range of habitats exposed to different pathogens and represents a model for studying this important part of the immunogenome. While equine MHC class II DRA and DQA loci have received attention, the genetic diversity and effects of selection on DRB and DQB loci have been largely overlooked. This study aimed to provide the first in-depth analysis of the MHC class II DRB and DQB loci in the Equidae family. Results Three DRB and two DQB genes were identified in the genomes of all equids. The genes DRB2, DRB3 and DQB3 showed high sequence conservation, while polymorphisms were more frequent at DRB1 and DQB1 across all species analyzed. DQB2 was not found in the genome of the Asiatic asses Equus hemionus kulan and E. h. onager. The bioinformatic analysis of non-zero-coverage-bases of DRB and DQB genes in 14 equine individual genomes revealed differences among individual genes. Evidence for recombination was found for DRB1, DRB2, DQB1 and DQB2 genes. Trans-species allele sharing was identified in all genes except DRB1. Site-specific selection analysis predicted genes evolving under positive selection both at DRB and DQB loci. No selected amino acid sites were identified in DQB3. Conclusions The organization of the MHC class II sub-region of equids is similar across all species of the family. Genomic sequences, along with phylogenetic trees suggesting effects of selection as well as trans-species polymorphism support the contention that pathogen-driven positive selection has shaped the MHC class II DRB/DQB sub-regions in the Equidae.
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Affiliation(s)
- Marie Klumplerova
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic
| | - Petra Splichalova
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic
| | - Jan Oppelt
- Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic.,Ceitec MU, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.,National Centre for Biomolecular research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Jan Futas
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic
| | - Aneta Kohutova
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Petra Musilova
- Department of Genetics and Reproductive Biotechnologies, Veterinary Research Institute, Brno, Czech Republic.,Ceitec VRI, RG Animal Cytogenomics, Brno, Czech Republic
| | - Svatava Kubickova
- Department of Genetics and Reproductive Biotechnologies, Veterinary Research Institute, Brno, Czech Republic.,Ceitec VRI, RG Animal Cytogenomics, Brno, Czech Republic
| | - Roman Vodicka
- Zoo Prague, U Trojského zámku 120/3, 171 00, Praha 7, Czech Republic
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000, Toulouse, France.,Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark
| | - Petr Horin
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic. .,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic.
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Andreani M, Gaspari S, Locatelli F. Human leucocyte antigen diversity: A biological gift to escape infections, no longer a barrier for haploidentical Hemopoietic Stem Cell Transplantation. Int J Immunogenet 2019; 47:34-40. [PMID: 31657118 DOI: 10.1111/iji.12459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/10/2019] [Accepted: 10/05/2019] [Indexed: 11/29/2022]
Abstract
Since the beginning of life, every multicellular organism appeared to have a complex innate immune system although the adaptive immune system, centred on lymphocytes bearing antigen receptors generated by somatic recombination, arose in jawed fish approximately 500 million years ago. The major histocompatibility complex MHC, named the Human leucocyte antigen (HLA) system in humans, represents a vital function structure in the organism by presenting pathogen-derived peptides to T cells as the main initial step of the adaptive immune response. The huge level of polymorphism observed in HLA genes definitely reflects selection, favouring heterozygosity at the individual or population level, in a pathogen-rich environment, although many are located in introns or in exons that do not code for the antigen-biding site of the HLA. Over the past three decades, the extent of allelic diversity at HLA loci has been well characterized using high-resolution HLA-DNA typing and the number of new HLA alleles, produced through next-generation sequencing methods, is even more rapidly increasing. The level of the HLA system polymorphism represents an obstacle to the search of potential compatible donors for patients affected by haematological disease proposed for a hematopoietic stem cell transplant (HSCT). Data reported in literature clearly show that antigenic and/or allelic mismatches between related or unrelated donors and patients influences the successful HSCT outcome. However, the recent development of the new transplant strategy based on the choice of haploidentical donors for HSCT is questioning the role of HLA compatibility, since the great HLA disparities present do not worsen the overall clinical outcome. Nowadays, NGS has contributed to define at allelic levels the HLA polymorphism and solve potential ambiguities. However, HLA functions and tissue typing probably need to be further investigated in the next future, to understand the reasons why in haploidentical transplants the presence of a whole mismatch haplotype between donors and recipients, both the survival rate and the incidence of acute GvHD or graft rejection are similar to those reported for unrelated HSCTs.
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Affiliation(s)
- Marco Andreani
- Laboratorio d'Immunogenetica dei Trapianti, Polo di Ricerca di San Paolo, Dipartimento di Onco-Ematologia e Terapia Cellulare e Genica, IRCCS Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Stefania Gaspari
- Dipartimento di Onco-Ematologia e Terapia Cellulare e Genica, IRCCS Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Franco Locatelli
- Dipartimento di Onco-Ematologia e Terapia Cellulare e Genica, IRCCS Ospedale Pediatrico Bambino Gesù, Roma, Italy
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9
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Ohta Y, Kasahara M, O'Connor TD, Flajnik MF. Inferring the "Primordial Immune Complex": Origins of MHC Class I and Antigen Receptors Revealed by Comparative Genomics. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 203:1882-1896. [PMID: 31492741 PMCID: PMC6761025 DOI: 10.4049/jimmunol.1900597] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/02/2019] [Indexed: 02/07/2023]
Abstract
Comparative analyses suggest that the MHC was derived from a prevertebrate "primordial immune complex" (PIC). PIC duplicated twice in the well-studied two rounds of genome-wide duplications (2R) early in vertebrate evolution, generating four MHC paralogous regions (predominantly on human chromosomes [chr] 1, 6, 9, 19). Examining chiefly the amphibian Xenopus laevis, but also other vertebrates, we identified their MHC paralogues and mapped MHC class I, AgR, and "framework" genes. Most class I genes mapped to MHC paralogues, but a cluster of Xenopus MHC class Ib genes (xnc), which previously was mapped outside of the MHC paralogues, was surrounded by genes syntenic to mammalian CD1 genes, a region previously proposed as an MHC paralogue on human chr 1. Thus, this gene block is instead the result of a translocation that we call the translocated part of the MHC paralogous region (MHCtrans) Analyses of Xenopus class I genes, as well as MHCtrans, suggest that class I arose at 1R on the chr 6/19 ancestor. Of great interest are nonrearranging AgR-like genes mapping to three MHC paralogues; thus, PIC clearly contained several AgR precursor loci, predating MHC class I/II. However, all rearranging AgR genes were found on paralogues derived from the chr 19 precursor, suggesting that invasion of a variable (V) exon by the RAG transposon occurred after 2R. We propose models for the evolutionary history of MHC/TCR/Ig and speculate on the dichotomy between the jawless (lamprey and hagfish) and jawed vertebrate adaptive immune systems, as we found genes related to variable lymphocyte receptors also map to MHC paralogues.
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Affiliation(s)
- Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Masanori Kasahara
- Department of Pathology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo 060-8638, Japan
| | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, 21201; and
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 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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11
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Dib L, Salamin N, Gfeller D. Polymorphic sites preferentially avoid co-evolving residues in MHC class I proteins. PLoS Comput Biol 2018; 14:e1006188. [PMID: 29782520 PMCID: PMC5983860 DOI: 10.1371/journal.pcbi.1006188] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 06/01/2018] [Accepted: 05/09/2018] [Indexed: 01/11/2023] Open
Abstract
Major histocompatibility complex class I (MHC-I) molecules are critical to adaptive immune defence mechanisms in vertebrate species and are encoded by highly polymorphic genes. Polymorphic sites are located close to the ligand-binding groove and entail MHC-I alleles with distinct binding specificities. Some efforts have been made to investigate the relationship between polymorphism and protein stability. However, less is known about the relationship between polymorphism and MHC-I co-evolutionary constraints. Using Direct Coupling Analysis (DCA) we found that co-evolution analysis accurately pinpoints structural contacts, although the protein family is restricted to vertebrates and comprises less than five hundred species, and that the co-evolutionary signal is mainly driven by inter-species changes, and not intra-species polymorphism. Moreover, we show that polymorphic sites in human preferentially avoid co-evolving residues, as well as residues involved in protein stability. These results suggest that sites displaying high polymorphism may have been selected during vertebrates’ evolution to avoid co-evolutionary constraints and thereby maximize their mutability. Amino acid co-evolution represents cases of simultaneous substitution of amino acids at distinct positions in protein sequences. In the MHC-I protein family, such co-evolution could result from either amino acid changes across species or changes within species due to the high polymorphism of MHC-I molecules. Here we show that signals captured by global methods such as Direct Coupling Analysis (DCA) to estimate co-evolution primarily result from changes across species. Moreover, our results indicate that polymorphic sites in MHC-I molecules tend to be decoupled from co-evolving ones. This could suggest that they have been selected to maximize their mutability, which is known to be functionally important to entail MHC-I molecules with a wide repertoire of binding specificities for antigen presentation.
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Affiliation(s)
- Linda Dib
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Switzerland
- Swiss Institutes of Bioinformatics, Quartier Sorge, Lausanne, Switzerland
| | - Nicolas Salamin
- Swiss Institutes of Bioinformatics, Quartier Sorge, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - David Gfeller
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Switzerland
- Swiss Institutes of Bioinformatics, Quartier Sorge, Lausanne, Switzerland
- * E-mail:
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12
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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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13
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Wcisel DJ, Yoder JA. The confounding complexity of innate immune receptors within and between teleost species. FISH & SHELLFISH IMMUNOLOGY 2016; 53:24-34. [PMID: 26997203 DOI: 10.1016/j.fsi.2016.03.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 03/03/2016] [Accepted: 03/15/2016] [Indexed: 06/05/2023]
Abstract
Teleost genomes encode multiple multigene families of immunoglobulin domain-containing innate immune receptors (IIIRs) with unknown function and no clear mammalian orthologs. However, the genomic organization of IIIR gene clusters and the structure and signaling motifs of the proteins they encode are similar to those of mammalian innate immune receptor families such as the killer cell immunoglobulin-like receptors (KIRs), leukocyte immunoglobulin-like receptors (LILRs), Fc receptors, triggering receptors expressed on myeloid cells (TREMs) and CD300s. Teleost IIIRs include novel immune-type receptors (NITRs); diverse immunoglobulin domain containing proteins (DICPs); polymeric immunoglobulin receptor-like proteins (PIGRLs); novel immunoglobulin-like transcripts (NILTs) and leukocyte immune-type receptors (LITRs). The accumulation of genomic sequence data has revealed that IIIR gene clusters in zebrafish display haplotypic and gene content variation. This intraspecific genetic variation, as well as significant interspecific variation, frequently confounds the identification of definitive orthologous IIIR sequences between teleost species. Nevertheless, by defining which teleost lineages encode (and do not encode) different IIIR families, predictions can be made about the presence (or absence) of specific IIIR families in each teleost lineage. It is anticipated that further investigations into available genomic resources and the sequencing of a variety of multiple teleost genomes will identify additional IIIR families and permit the modeling of the evolutionary origins of IIIRs.
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Affiliation(s)
- Dustin J Wcisel
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA; Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27607, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27607, USA.
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14
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Rodriguez-Nunez I, Wcisel DJ, Litman RT, Litman GW, Yoder JA. The identification of additional zebrafish DICP genes reveals haplotype variation and linkage to MHC class I genes. Immunogenetics 2016; 68:295-312. [PMID: 26801775 DOI: 10.1007/s00251-016-0901-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 01/07/2016] [Indexed: 10/22/2022]
Abstract
Bony fish encode multiple multi-gene families of membrane receptors that are comprised of immunoglobulin (Ig) domains and are predicted to function in innate immunity. One of these families, the diverse immunoglobulin (Ig) domain-containing protein (DICP) genes, maps to three chromosomal loci in zebrafish. Most DICPs possess one or two Ig ectodomains and include membrane-bound and secreted forms. Membrane-bound DICPs include putative inhibitory and activating receptors. Recombinant DICP Ig domains bind lipids with varying specificity, a characteristic shared with mammalian CD300 and TREM family members. Numerous DICP transcripts amplified from different lines of zebrafish did not match the zebrafish reference genome sequence suggesting polymorphic and haplotypic variation. The expression of DICPs in three different lines of zebrafish has been characterized employing PCR-based strategies. Certain DICPs exhibit restricted expression in adult tissues whereas others are expressed ubiquitously. Transcripts of a subset of DICPs can be detected during embryonic development suggesting roles in embryonic immunity or other developmental processes. Transcripts representing 11 previously uncharacterized DICP sequences were identified. The assignment of two of these sequences to an unplaced genomic scaffold resulted in the identification of an alternative DICP haplotype that is linked to a MHC class I Z lineage haplotype on zebrafish chromosome 3. The linkage of DICP and MHC class I genes also is observable in the genomes of the related grass carp (Ctenopharyngodon idellus) and common carp (Cyprinus carpio) suggesting that this is a shared character with the last common Cyprinidae ancestor.
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Affiliation(s)
- Ivan Rodriguez-Nunez
- Department of Molecular Biomedical Sciences and Center for Comparative Medicine and Translational Research, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - Dustin J Wcisel
- Department of Molecular Biomedical Sciences and Center for Comparative Medicine and Translational Research, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - Ronda T Litman
- Department of Pediatrics, University of South Florida Morsani College of Medicine, USF/ACH Children's Research Institute, 140 7th Avenue South, St. Petersburg, FL, 33701, USA
| | - Gary W Litman
- Department of Pediatrics, University of South Florida Morsani College of Medicine, USF/ACH Children's Research Institute, 140 7th Avenue South, St. Petersburg, FL, 33701, USA.,Department of Molecular Genetics, All Children's Hospital Johns Hopkins Medicine, 501 6th Avenue South, St. Petersburg, FL, 33701, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences and Center for Comparative Medicine and Translational Research, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA.
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15
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Profaizer T, Coonrod E, Delgado J, Kumánovics A. Report on the effects of fragment size, indexing, and read length on HLA sequencing on the Illumina MiSeq. Hum Immunol 2015; 76:897-902. [DOI: 10.1016/j.humimm.2015.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 05/27/2015] [Accepted: 08/06/2015] [Indexed: 10/23/2022]
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16
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Cheng Y, Prickett MD, Gutowska W, Kuo R, Belov K, Burt DW. Evolution of the avian β-defensin and cathelicidin genes. BMC Evol Biol 2015; 15:188. [PMID: 26373713 PMCID: PMC4571063 DOI: 10.1186/s12862-015-0465-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/21/2015] [Indexed: 11/10/2022] Open
Abstract
Background β-defensins and cathelicidins are two families of cationic antimicrobial peptides (AMPs) with a broad range of antimicrobial activities that are key components of the innate immune system. Due to their important roles in host defense against rapidly evolving pathogens, the two gene families provide an ideal system for studying adaptive gene evolution. In this study we performed phylogenetic and selection analyses on β-defensins and cathelicidins from 53 avian species representing 32 orders to examine the evolutionary dynamics of these peptides in birds. Results and conclusions Avian β-defensins are found in a gene cluster consisting of 13 subfamiles. Nine of these are conserved as one to one orthologs in all birds, while the others (AvBD1, AvBD3, AvBD7 and AvBD14) are more subject to gene duplication or pseudogenisation events in specific avian lineages. Avian cathelicidins are found in a gene cluster consisting of three subfamilies with species-specific duplications and gene loss. Evidence suggested that the propiece and mature peptide domains of avian cathelicidins are possibly co-evolving in such a way that the cationicity of the mature peptide is partially neutralised by the negative charge of the propiece prior to peptide secretion (further evidence obtained by repeating the analyses on primate cathelicidins). Negative selection (overall mean dN < dS) was detected in most of the gene domains examined, conserving certain amino acid residues that may be functionally crucial for the avian β-defensins and cathelicidins, while episodic positive selection was also involved in driving the diversification of specific codon sites of certain AMPs in avian evolutionary history. These findings have greatly improved our understanding of the molecular evolution of avian AMPs and will be useful to understand their role in the avian innate immune response. Additionally, the large dataset of β-defensin and cathelicidin peptides may also provide a valuable resource for translational research and development of novel antimicrobial agents in the future. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0465-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuanyuan Cheng
- RMC Gunn Building B19, Faculty of Veterinary Science, University of Sydney, Camperdown, 2006, NSW, Australia.
| | - Michael Dennis Prickett
- Dipartimento di Scienze della Vita-Edif. C11, Università di Trieste, Via Licio Giorgieri 1, 34127, Trieste, Italy.
| | - Weronika Gutowska
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Richard Kuo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Katherine Belov
- RMC Gunn Building B19, Faculty of Veterinary Science, University of Sydney, Camperdown, 2006, NSW, Australia.
| | - David W Burt
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
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17
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Huang S, Chen Z, Yan X, Yu T, Huang G, Yan Q, Pontarotti PA, Zhao H, Li J, Yang P, Wang R, Li R, Tao X, Deng T, Wang Y, Li G, Zhang Q, Zhou S, You L, Yuan S, Fu Y, Wu F, Dong M, Chen S, Xu A. Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes. Nat Commun 2014; 5:5896. [PMID: 25523484 PMCID: PMC4284660 DOI: 10.1038/ncomms6896] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 11/18/2014] [Indexed: 01/19/2023] Open
Abstract
Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution. The lancelet, or amphioxus, is an extant basal chordate that diverged from other chordate lineages about 550 million years ago. Here the authors sequence and assemble the diploid genome of a male adult of the Chinese lancelet, B. belcheri, and highlight genomic features that may have played an important role in the origin and evolution of vertebrates.
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Affiliation(s)
- Shengfeng Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zelin Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xinyu Yan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ting Yu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Guangrui Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Qingyu Yan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Pierre Antoine Pontarotti
- Evolution Biologique et Modélisation UMR 7353 Aix Marseille Université/CNRS, 3 Place Victor Hugo, 13331 Marseille, France
| | - Hongchen Zhao
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jie Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ping Yang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ruihua Wang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Rui Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xin Tao
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ting Deng
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yiquan Wang
- 1] School of Life Sciences, Xiamen University, Xiamen 361005, China [2] Shenzhen Research Institute of Xiamen University, Shenzhen 518058, China
| | - Guang Li
- 1] School of Life Sciences, Xiamen University, Xiamen 361005, China [2] Shenzhen Research Institute of Xiamen University, Shenzhen 518058, China
| | - Qiujin Zhang
- Fujian Key Laboratory of Developmental and Neuron Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350108, China
| | - Sisi Zhou
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Leiming You
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Shaochun Yuan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yonggui Fu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Fenfang Wu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Meiling Dong
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Anlong Xu
- 1] State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China [2] Beijing University of Chinese Medicine, Dong San Huang Road, Chao-yang District, Beijing 100029, China
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Norman PJ, Hollenbach JA, Nemat-Gorgani N, Guethlein LA, Hilton HG, Pando MJ, Koram KA, Riley EM, Abi-Rached L, Parham P. Co-evolution of human leukocyte antigen (HLA) class I ligands with killer-cell immunoglobulin-like receptors (KIR) in a genetically diverse population of sub-Saharan Africans. PLoS Genet 2013; 9:e1003938. [PMID: 24204327 PMCID: PMC3814319 DOI: 10.1371/journal.pgen.1003938] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 09/16/2013] [Indexed: 02/06/2023] Open
Abstract
Interactions between HLA class I molecules and killer-cell immunoglobulin-like receptors (KIR) control natural killer cell (NK) functions in immunity and reproduction. Encoded by genes on different chromosomes, these polymorphic ligands and receptors correlate highly with disease resistance and susceptibility. Although studied at low-resolution in many populations, high-resolution analysis of combinatorial diversity of HLA class I and KIR is limited to Asian and Amerindian populations with low genetic diversity. At the other end of the spectrum is the West African population investigated here: we studied 235 individuals, including 104 mother-child pairs, from the Ga-Adangbe of Ghana. This population has a rich diversity of 175 KIR variants forming 208 KIR haplotypes, and 81 HLA-A, -B and -C variants forming 190 HLA class I haplotypes. Each individual we studied has a unique compound genotype of HLA class I and KIR, forming 1-14 functional ligand-receptor interactions. Maintaining this exceptionally high polymorphism is balancing selection. The centromeric region of the KIR locus, encoding HLA-C receptors, is highly diverse whereas the telomeric region encoding Bw4-specific KIR3DL1, lacks diversity in Africans. Present in the Ga-Adangbe are high frequencies of Bw4-bearing HLA-B*53:01 and Bw4-lacking HLA-B*35:01, which otherwise are identical. Balancing selection at key residues maintains numerous HLA-B allotypes having and lacking Bw4, and also those of stronger and weaker interaction with LILRB1, a KIR-related receptor. Correspondingly, there is a balance at key residues of KIR3DL1 that modulate its level of cell-surface expression. Thus, capacity to interact with NK cells synergizes with peptide binding diversity to drive HLA-B allele frequency distribution. These features of KIR and HLA are consistent with ongoing co-evolution and selection imposed by a pathogen endemic to West Africa. Because of the prevalence of malaria in the Ga-Adangbe and previous associations of cerebral malaria with HLA-B*53:01 and KIR, Plasmodium falciparum is a candidate pathogen.
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Affiliation(s)
- Paul J. Norman
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
| | - Jill A. Hollenbach
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Neda Nemat-Gorgani
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Lisbeth A. Guethlein
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Hugo G. Hilton
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Marcelo J. Pando
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Kwadwo A. Koram
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Eleanor M. Riley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Laurent Abi-Rached
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Centre National de la Recherche Scientifique, Laboratoire d'Analyse, Topologie, Probabilités - Unité Mixte de Recherche 7353, Equipe ATIP, Aix-Marseille Université, Marseille, France
| | - Peter Parham
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
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Abstract
Over several decades, various forms of genomic analysis of the human major histocompatibility complex (MHC) have been extremely successful in picking up many disease associations. This is to be expected, as the MHC region is one of the most gene-dense and polymorphic stretches of human DNA. It also encodes proteins critical to immunity, including several controlling antigen processing and presentation. Single-nucleotide polymorphism genotyping and human leukocyte antigen (HLA) imputation now permit the screening of large sample sets, a technique further facilitated by high-throughput sequencing. These methods promise to yield more precise contributions of MHC variants to disease. However, interpretation of MHC-disease associations in terms of the functions of variants has been problematic. Most studies confirm the paramount importance of class I and class II molecules, which are key to resistance to infection. Infection is likely driving the extreme variation of these genes across the human population, but this has been difficult to demonstrate. In contrast, many associations with autoimmune conditions have been shown to be specific to certain class I and class II alleles. Interestingly, conditions other than infections and autoimmunity are also associated with the MHC, including some cancers and neuropathies. These associations could be indirect, owing, for example, to the infectious history of a particular individual and selective pressures operating at the population level.
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Affiliation(s)
- John Trowsdale
- Department of Pathology and Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 1QP, United Kingdom;
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20
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Chen H, Kshirsagar S, Jensen I, Lau K, Simonson C, Schluter SF. Characterization of arrangement and expression of the beta-2 microglobulin locus in the sandbar and nurse shark. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2010; 34:189-195. [PMID: 19782101 DOI: 10.1016/j.dci.2009.09.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 09/18/2009] [Indexed: 05/28/2023]
Abstract
Beta 2 microglobulin (beta2m) is an essential subunit of major histocompatibility complex (MHC) type I molecules. In this report, beta2m cDNAs were identified and sequenced from sandbar shark spleen cDNA library. Sandbar shark beta2m gene encodes one amino acid less than most teleost beta2m genes, and 3 amino acids less than mammal beta2m genes. Although sandbar shark beta2m protein contains one beta sheet less than that of human in the predicted protein structure, the overall structure of beta2m proteins is conserved during evolution. Germline gene for the beta2m in sandbar and nurse shark is present as a single locus. It contains three exons and two introns. CpG sites are evenly distributed in the shark beta2m loci. Several DNA repeat elements were also identified in the shark beta2m loci. Sequence analysis suggests that the beta2m locus is not linked to the MHC I loci in the shark genome.
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Affiliation(s)
- Hao Chen
- Department of Immunobiology, College of Medicine, University of Arizona, Tucson, AZ 85719, USA
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21
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Kasahara M. Genome duplication and T cell immunity. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2010; 92:7-36. [PMID: 20800811 DOI: 10.1016/s1877-1173(10)92002-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The adaptive immune system (AIS) mediated by T cells and B cells arose ~450 million years ago in a common ancestor of jawed vertebrates. This system was so successful that, once established, it has been maintained in all classes of jawed vertebrates with only minor modifications. One event thought to have contributed to the emergence of this form of AIS is two rounds of whole-genome duplication. This event enabled jawed vertebrate ancestors to acquire many paralogous genes, known as ohnologs, with essential roles in T cell and B cell immunity. Ohnologs encode the key components of the antigen presentation machinery and signal transduction pathway for lymphocyte activation as well as numerous transcription factors important for lymphocyte development. Recently, it has been discovered that jawless vertebrates have developed an AIS employing antigen receptors unrelated to T/B cell receptors, but with marked overall similarities to the AIS of jawed vertebrates. Emerging evidence suggests that a common ancestor of all vertebrates was equipped with T-lymphoid and B-lymphoid lineages.
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Affiliation(s)
- Masanori Kasahara
- Department of Pathology, Hokkaido, University Graduate School of Medicine, Sapporo, Japan
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22
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Abstract
A novel diversified multigene family of tripartite-motif (TRIM) intracellular receptors with putative antiviral activity has been identified in teleost fish and published in BMC Biology. The history of these receptors involves ancient linkage to paralogs of the major histocompatibility complex, and the family has invertebrate precursors.
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Affiliation(s)
- Louis Du Pasquier
- University of Basel, Institute of Zoology and Evolutionary Biology, Vesalgasse 1, Basel CH-4051, Switzerland.
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23
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Markov AV, Kulikov AM. The hypothesis of immune testing of partners—Friend/foe identification systems in historical perspective. BIOL BULL+ 2006. [DOI: 10.1134/s1062359006040017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Abstract
Charles Darwin proposed that evolution occurs primarily by natural selection, but this view has been controversial from the beginning. Two of the major opposing views have been mutationism and neutralism. Early molecular studies suggested that most amino acid substitutions in proteins are neutral or nearly neutral and the functional change of proteins occurs by a few key amino acid substitutions. This suggestion generated an intense controversy over selectionism and neutralism. This controversy is partially caused by Kimura's definition of neutrality, which was too strict (|2Ns|< or =1). If we define neutral mutations as the mutations that do not change the function of gene products appreciably, many controversies disappear because slightly deleterious and slightly advantageous mutations are engulfed by neutral mutations. The ratio of the rate of nonsynonymous nucleotide substitution to that of synonymous substitution is a useful quantity to study positive Darwinian selection operating at highly variable genetic loci, but it does not necessarily detect adaptively important codons. Previously, multigene families were thought to evolve following the model of concerted evolution, but new evidence indicates that most of them evolve by a birth-and-death process of duplicate genes. It is now clear that most phenotypic characters or genetic systems such as the adaptive immune system in vertebrates are controlled by the interaction of a number of multigene families, which are often evolutionarily related and are subject to birth-and-death evolution. Therefore, it is important to study the mechanisms of gene family interaction for understanding phenotypic evolution. Because gene duplication occurs more or less at random, phenotypic evolution contains some fortuitous elements, though the environmental factors also play an important role. The randomness of phenotypic evolution is qualitatively different from allele frequency changes by random genetic drift. However, there is some similarity between phenotypic and molecular evolution with respect to functional or environmental constraints and evolutionary rate. It appears that mutation (including gene duplication and other DNA changes) is the driving force of evolution at both the genic and the phenotypic levels.
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Affiliation(s)
- Masatoshi Nei
- Department of Biology, Institute of Molecular Evolutionary Genetics, , Pennsylvania State University, USA.
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25
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Herranz R, Mateos J, Mas JA, García-Zaragoza E, Cervera M, Marco R. The Coevolution of Insect Muscle TpnT and TpnI Gene Isoforms. Mol Biol Evol 2005; 22:2231-42. [PMID: 16049195 DOI: 10.1093/molbev/msi223] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In bilaterians, the main regulator of muscle contraction is the troponin (Tpn) complex, comprising three closely interacting subunits (C, T, and I). To understand how evolutionary forces drive molecular change in protein complexes, we have compared the gene structures and expression patterns of Tpn genes in insects. In this class, while TpnC is encoded by multiple genes, TpnT and TpnI are encoded by single genes. Their isoform expression pattern is highly conserved within the Drosophilidae, and single orthologous genes were identified in the sequenced genomes of Drosophila pseudoobscura, Anopheles gambiae, and Apis mellifera. Apis expression patterns also support the equivalence of their exon organization throughout holometabolous insects. All TpnT genes include a previously unidentified indirect flight muscle (IFM)-specific exon (10A) that has evolved an expression pattern similar to that of exon 9 in TpnI. Thus, expression patterns, sequence evolution trends, and structural data indicate that Tpn genes and their isoforms have coevolved, building species- and muscle-specific troponin complexes. Furthermore, a clear case can be made for independent evolution of the IFM-specific isoforms containing alanine/proline-rich sequences. Dipteran genomes contain one tropomyosin gene that encodes one or two high-molecular weight isoforms (TmH) incorporating APPAEGA-rich sequences, specifically expressed in IFM. Corresponding exons do not exist in the Apis tropomyosin gene, but equivalent sequences occur in a high-molecular weight Apis IFM-specific TpnI isoform (TnH). Overall, our approach to comparatively analyze supramolecular complexes reveals coevolutionary trends not only in gene families but in isoforms generated by alternative splicing.
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Affiliation(s)
- Raúl Herranz
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas Alberto Sols UAM-CSIC, Facultad de Medicina, Universidad Autónoma de Madrid, C/Arzobispo Morcillo 4, 28029 Madrid, Spain
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26
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Salomonsen J, Sørensen MR, Marston DA, Rogers SL, Collen T, van Hateren A, Smith AL, Beal RK, Skjødt K, Kaufman J. Two CD1 genes map to the chicken MHC, indicating that CD1 genes are ancient and likely to have been present in the primordial MHC. Proc Natl Acad Sci U S A 2005; 102:8668-73. [PMID: 15939887 PMCID: PMC1150808 DOI: 10.1073/pnas.0409213102] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
CD1 molecules play an important role in the immune system, presenting lipid-containing antigens to T and NKT cells. CD1 genes have long been thought to be as ancient as MHC class I and II genes, based on various arguments, but thus far they have been described only in mammals. Here we describe two CD1 genes in chickens, demonstrating that the CD1 system was present in the last common ancestor of mammals and birds at least 300 million years ago. In phylogenetic analysis, these sequences cluster with CD1 sequences from other species but are not obviously like any particular CD1 isotype. Sequence analysis suggests that the expressed proteins bind hydrophobic molecules and are recycled through intracellular vesicles. RNA expression is strong in lymphoid tissues but weaker to undetectable in some nonlymphoid tissues. Flow cytometry confirms expression from one gene on B cells. Based on Southern blotting and cloning, only two such CD1 genes are detected, located approximately 800 nucleotides apart and in the same transcriptional orientation. The sequence of one gene is nearly identical in six chicken lines. By mapping with a backcross family, this gene could not be separated from the chicken MHC on chromosome 16. Mining the draft chicken genome sequence shows that chicken has only these two CD1 genes located approximately 50 kb from the classical class I genes. The unexpected location of these genes in the chicken MHC suggests the CD1 system was present in the primordial MHC and is thus approximately 600 million years old.
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Affiliation(s)
- Jan Salomonsen
- Department of Pathobiology, Laboratory of Immunology, Royal Veterinary and Agricultural University, Stigbøjlen 7, DK-1870 Frederiksberg C, Denmark
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27
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Ruby T, Bed'Hom B, Wittzell H, Morin V, Oudin A, Zoorob R. Characterisation of a cluster of TRIM-B30.2 genes in the chicken MHC B locus. Immunogenetics 2005; 57:116-28. [PMID: 15744538 DOI: 10.1007/s00251-005-0770-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2004] [Revised: 12/13/2004] [Indexed: 01/01/2023]
Abstract
We have identified and characterised a cluster of six TRIM-B30.2 genes flanking the chicken BF/BL region of the B complex. The TRIM-B30.2 proteins are a subgroup of the TRIM protein family containing the tripartite motif (TRIM), consisting of a RING domain, a B-box and a coiled coil region, and a B30.2-like domain. In humans, a cluster of seven TRIM-B30.2 genes has been characterised within the MHC on Chromosome 6p21.33. Among the six chicken TRIM-B30.2 genes two are orthologous to those of the human MHC, and two (TRIM41 and TRIM7) are orthologous to human genes located on Chromosome 5. In humans, these last two genes are adjacent to GNB2L1, a guanine nucleotide-binding protein gene, the ortholog of the chicken c12.3 gene situated in the vicinity of the TRIM-B30.2 genes. This suggests that breakpoints specific to mammals have occurred and led to the remodelling of their MHC structure. In terms of structure, like their mammalian counterparts, each chicken gene consists of five coding exons; exon 1 encodes the RING domain and the B-box, exons 2, 3 and 4 form the coiled-coil region, and the last exon represents the B30.2-like domain. Phylogenetic analysis led us to assume that this extended BF/BL region may be similar to the human extended class I region, because it contains a cluster of BG genes sharing an Ig-V like domain with the BTN genes (Henry et al. 1997a) and six TRIM-B30.2 genes containing the B30.2-like domain, shared with the TRIM-B30.2 members and the BTN genes.
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Affiliation(s)
- Thomas Ruby
- UPR 1983, CNRS, 7 rue Guy Môquet, 94801, Villejuif Cedex, France
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28
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Klein J, Nikolaidis N. The descent of the antibody-based immune system by gradual evolution. Proc Natl Acad Sci U S A 2004; 102:169-74. [PMID: 15618397 PMCID: PMC544055 DOI: 10.1073/pnas.0408480102] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The antibody-based immune system (AIS) is one of many means by which organisms protect themselves against pathogens and parasites. The AIS is present in jawed vertebrates (gnathostomes) but absent in all other taxa, including jawless vertebrates (agnathans). We argue that the AIS has been assembled from elements that have primarily evolved to serve other functions and incorporated existing molecular cascades, resulting in the appearance of new organs and new types of cells. Some molecules serving other functions have been appropriated by the AIS, whereas others have been modified to serve new functions, either after the duplication of their encoding genes or through the acquisition of an additional function without gene duplication. A few molecules may have been created de novo. The deployment and integration of the ready-made elements gives the impression of a sudden origin of the AIS. In reality, however, the AIS is an example of an organ system that has evolved gradually through a series of small steps over an extended period.
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Affiliation(s)
- Jan Klein
- Department of Biology and Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802, USA.
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29
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Danchin E, Vitiello V, Vienne A, Richard O, Gouret P, McDermott MF, Pontarotti P. The major histocompatibility complex origin. Immunol Rev 2004; 198:216-32. [PMID: 15199965 DOI: 10.1111/j.0105-2896.2004.00132.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The present review focuses on the history of genes involved in the major histocompatibility complex (MHC), with a special emphasis on class I function in peptide presentation. The MHC class II story is covered in less detail, as it does not have a major impact on the general understanding of the MHC evolution. We first redefine the MHC as the definition evolved over time. We then use phylogenetic analysis to investigate the history of genes involved in the MHC class I process. As not all the genes involved in this process have been phylogenetically analyzed and because new sequences have been recently released in biological databases, we have re-investigated this matter. In the light of the phylogenetic analysis, the functions of the orthologs of the genes involved in MHC processes are examined in species not having an MHC system. We then demonstrate that the emergence of this new function is due to various levels of co-option.
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Affiliation(s)
- Etienne Danchin
- Phylogenomics Laboratory, Université d'Aix Marseille I, Marseille, France.
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30
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Abstract
In the urochordate Ciona intestinalis some membrane Immunoglobulin superfamily members with ancestral features of antigen receptors are homologs of vertebrate adhesion molecules acting as virus receptors. They include the following: the junction adhesion molecule (reovirus receptor) (JAM), the Cortical thymocyte marker of Xenopus (CTX family) (Coxsackie's virus receptor) and the poliovirus receptor (PVR). In humans these genes belong to the same linkage group, of which 4 paralogous groups exist. This situation is consistent with the notion that the Ciona set of genes would correspond to a preduplication state. In addition, the human region 3q13 and its paralogs, harbour genes remotely related to the nectin family that can be detected in Protostomes (human CRTAM and CD80-86 related to Drosophila Beat). In addition, this linkage group contains several CDs important for the immune system CD166, CD47 and many members of the tetraspanin family. The VC1-like core of the nectin is homologous to the VCI core of the MHC-linked tapasin and to the VC1 segments of, for example, specific antigen receptors of vertebrates, and could be related to a primitive antigen receptor gene. It is suggested that the virus binding property of the members of this family was exploited, and that they were recruited in the vertebrate immune system following the introduction of the somatic rearrangement machinery. In this way the adaptive immune system could have developed from a set of receptors involved in a primitive local innate immunity involving NF-kappaB-mediated apoptosis.
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Affiliation(s)
- Louis Du Pasquier
- Institute of Zoology, University of Basel, Rheinsprung 9, CH-4051 Basel, Switzerland.
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31
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Kasahara M, Suzuki T, Pasquier LD. On the origins of the adaptive immune system: novel insights from invertebrates and cold-blooded vertebrates. Trends Immunol 2004; 25:105-11. [PMID: 15102370 DOI: 10.1016/j.it.2003.11.005] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
When and how adaptive immunity emerged is one of the fundamental questions in immunology. Accumulated evidence suggests that the key components of adaptive immunity, rearranging receptor genes and the MHC, are unique to jawed vertebrates. Recent studies in protochordates, in particular, the draft genome sequence of the ascidian Ciona intestinalis, are providing important clues for understanding the origin of antigen receptors and the MHC. We discuss a group of newly identified protochordate genes along with some cold-blooded vertebrate genes, the ancestors of which might have provided key elements of antigen receptors. The organization of the proto-MHCs in protochordates provides convincing evidence that the MHC regions of jawed vertebrates emerged as a result of two rounds of chromosomal duplication.
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Affiliation(s)
- Masanori Kasahara
- Department of Biosystems Science, School of Advanced Sciences, The Graduate University for Advanced Studies (Sokendai), Shonan Village, Hayama 240-0193, Japan.
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32
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Du Pasquier L, Zucchetti I, De Santis R. Immunoglobulin superfamily receptors in protochordates: before RAG time. Immunol Rev 2004; 198:233-48. [PMID: 15199966 DOI: 10.1111/j.0105-2896.2004.00122.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Urochordates and cephalochordates do not have an adaptive immune system involving the somatic rearrangement of their antigen receptor genes. They do not have antigen-presenting molecules of the major histocompatibility complex (MHC)-linked class I and II types. In the absence of such a system, the status of their genes reflects perhaps a primitive pre-recombination-activating gene (RAG) stage that could suggest the pathway leading to the genesis of the T-cell receptor (TCR) and antibodies. In the genome of Ciona intestinalis, genes that encode molecules with membrane receptor features have been found among many members of the immunoglobulin superfamily (Igsf). They use the domains typical of vertebrate antigen receptors and class I and II: the V, and C1-like domains. These genes belong to two families with recognizable homologs in vertebrates: the junctional adhesion molecule (JAM)/cortical thymocyte marker of Xenopus (CTX) family and the nectin family. The human homologs of these genes segregate in a single unit of four paralogous segments on chromosomes 1q, 3q, 11p, and 21q. These regions contain nowadays several genes involved in the adaptive immune system, and some related members are present in the MHC paralogs as well. They also contain receptor-like genes without homologs in Ciona but with related members in the protostome Drosophila. It looks as if in Ciona one detects what looks like the 'fossil' of one group of genes bound to duplicate and give rise to many crucial elements of the adaptive immune system. The modern homologs of these JAM, CTX, and nectins are all or almost all virus receptors, and the hypothesis is formulated that this property was taken advantage of during evolution to participate in the elaboration of either or both the somatically generated antigen-recognizing receptors and the antigen-presenting molecules.
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33
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Yu CY, Chung EK, Yang Y, Blanchong CA, Jacobsen N, Saxena K, Yang Z, Miller W, Varga L, Fust G. Dancing with complement C4 and the RP-C4-CYP21-TNX (RCCX) modules of the major histocompatibility complex. ACTA ACUST UNITED AC 2004; 75:217-92. [PMID: 14604014 DOI: 10.1016/s0079-6603(03)75007-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The number of the complement component C4 genes varies from 2 to 8 in a diploid genome among different human individuals. Three quarters of the C4 genes in Caucasian populations have the endogenous retrovirus, HERV-K(C4), in the ninth intron. The remainder does not. The C4 serum proteins are highly polymorphic and their concentrations vary from 100 to approximately 1000 microg/ml. There are two distinct classes of C4 protein, C4A and C4B, which have diversified to fulfill (a) the opsonization/immunoclearance purposes and (b) the well-known complement function in the killing of microbes by lysis and neutralization, respectively. Many infectious and autoimmune diseases are associated with complete or partial deficiency of C4A and/or C4B. The adverse effects of high C4 gene dosages, however, are just emerging, as the concepts of human C4 genetics are revised and accurate techniques are applied to distinguish partial deficiencies from differential expression caused by unequal C4A and C4B gene dosages and gene sizes. This review attempts to dissect the sophisticated genetics of complement C4A and C4B. The emphases are on the qualitative and quantitative diversities of C4 genotypes and phenotypes. The many allotypic variants and the processed products of human and mouse C4 proteins are described. The modular variation of C4 genes together with the serine/threonine nuclear kinase gene RP, the steroid 21-hydroxylase CYP21, and extracellular matrix protein TNX (RCCX modules) are investigated for the effects on homogenization of C4 protein polymorphisms, and on the unequal genetic crossovers that knocked out the functions of CYP21 and/or TNX. Furthermore, the influence of the endogenous retrovirus HERV-K(C4) on C4 gene expression and the dispersal of HERV-K(C4) family members in the human genome are discussed.
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Affiliation(s)
- C Yung Yu
- Center for Molecular and Human Genetics, Columbus Children's Research Institute, 700 Children's Drive, Columbus, OH 43205-2696, USA
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34
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Kulski JK, Shiina T, Anzai T, Kohara S, Inoko H. Comparative genomic analysis of the MHC: the evolution of class I duplication blocks, diversity and complexity from shark to man. Immunol Rev 2002; 190:95-122. [PMID: 12493009 DOI: 10.1034/j.1600-065x.2002.19008.x] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The major histocompatibility complex (MHC) genomic region is composed of a group of linked genes involved functionally with the adaptive and innate immune systems. The class I and class II genes are intrinsic features of the MHC and have been found in all the jawed vertebrates studied so far. The MHC genomic regions of the human and the chicken (B locus) have been fully sequenced and mapped, and the mouse MHC sequence is almost finished. Information on the MHC genomic structures (size, complexity, genic and intergenic composition and organization, gene order and number) of other vertebrates is largely limited or nonexistent. Therefore, we are mapping, sequencing and analyzing the MHC genomic regions of different human haplotypes and at least eight nonhuman species. Here, we review our progress with these sequences and compare the human MHC structure with that of the nonhuman primates (chimpanzee and rhesus macaque), other mammals (pigs, mice and rats) and nonmammalian vertebrates such as birds (chicken and quail), bony fish (medaka, pufferfish and zebrafish) and cartilaginous fish (nurse shark). This comparison reveals a complex MHC structure for mammals and a relatively simpler design for nonmammalian animals with a hypothetical prototypic structure for the shark. In the mammalian MHC, there are two to five different class I duplication blocks embedded within a framework of conserved nonclass I and/or nonclass II genes. With a few exceptions, the class I framework genes are absent from the MHC of birds, bony fish and sharks. Comparative genomics of the MHC reveal a highly plastic region with major structural differences between the mammalian and nonmammalian vertebrates. Additional genomic data are needed on animals of the reptilia, crocodilia and marsupial classes to find the origins of the class I framework genes and examples of structures that may be intermediate between the simple and complex MHC organizations of birds and mammals, respectively.
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Affiliation(s)
- Jerzy K Kulski
- Department of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa, Japan
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35
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Miquelis A, Abi-Rached L, Gilles A, Pontarotti P. Mise en évidence de processus de duplications en bloc dans le génome des vertébrés. Med Sci (Paris) 2002. [DOI: 10.1051/medsci/200218111051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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36
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Nagarajan UM, Bushey A, Boss JM. Modulation of gene expression by the MHC class II transactivator. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2002; 169:5078-88. [PMID: 12391224 DOI: 10.4049/jimmunol.169.9.5078] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The class II transactivator (CIITA) is a master regulator of MHC class II expression. CIITA also modulates the expression of MHC class I genes, suggesting that it may have a more global role in gene expression. To determine whether CIITA regulates genes other than the MHC class II and I family, DNA microarray analysis was used to compare the expression profiles of the CIITA expressing B cell line Raji and its CIITA-negative counterpart RJ2.2.5. The comparison identified a wide variety of genes whose expression was modulated by CIITA. Real time RT-PCR from Raji, RJ2.2.5, an RJ2.2.5 cell line complemented with CIITA, was performed to confirm the results and to further identify CIITA-regulated genes. CIITA-regulated genes were found to have diverse functions, which could impact Ag processing, signaling, and proliferation. Of note was the identification of a set of genes localized to chromosome 1p34-35. The global modulation of genes in a local region suggests that this region may share some regulatory control with the MHC.
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Affiliation(s)
- Uma M Nagarajan
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
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37
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Du Pasquier L. Several MHC-linked Ig superfamily genes have features of ancestral antigen-specific receptor genes. Curr Top Microbiol Immunol 2002; 266:57-71. [PMID: 12014203 DOI: 10.1007/978-3-662-04700-2_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- L Du Pasquier
- Basel Institute for Immunology, Grenzacherstrasse 487, 4005 Basel, Switzerland
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38
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Abstract
TAPASIN, a V-C1 (variable-constant) immunoglobulin superfamily (IgSF) molecule that links MHC class I molecules to the transporter associated with antigen processing (TAP) in the endoplasmic reticulum (ER) is encoded by the TAPBP gene, located near to the MHC at 6p21.3. A related gene was identified at chromosome position 12p13.3 between the CD27 and VAMP1 genes near a group of MHC-paralogous loci. The gene, which we have called TAPBP-R (R for related), also encodes a member of the IgSF, TAPASIN-R. Its putative product contains similar structural motifs to TAPASIN, with some marked differences, especially in the V domain, transmembrane and cytoplasmic regions. By using the mouse ortholog to screen tissue, we revealed that the TAPBP-R gene was broadly expressed. Sub-cellular localization showed that the bulk of TAPASIN-R is located within the ER but biotinylation experiments were consistent with some expression at thecell surface. TAPASIN-R lacks an obvious ER retention signal. The function of TAPASIN-R will be of interest in regards to the evolution of the immune system as well as antigen processing.
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39
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Granger SW, Butrovich KD, Houshmand P, Edwards WR, Ware CF. Genomic characterization of LIGHT reveals linkage to an immune response locus on chromosome 19p13.3 and distinct isoforms generated by alternate splicing or proteolysis. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2001; 167:5122-8. [PMID: 11673523 DOI: 10.4049/jimmunol.167.9.5122] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
LIGHT is a member of the TNF cytokine superfamily that signals through the lymphotoxin (LT)beta receptor and the herpesvirus entry mediator. LIGHT may function as a costimulatory factor for the activation of lymphoid cells and as a deterrent to infection by herpesvirus, which may provide significant selective pressure shaping the evolution of LIGHT. Here, we define the molecular genetics of the human LIGHT locus, revealing its close linkage to the TNF superfamily members CD27 ligand and 4-1BB ligand, and the third complement protein (C3), which positions LIGHT within the MHC paralog on chromosome 19p13.3. An alternately spliced isoform of LIGHT mRNA that encodes a transmembrane-deleted form is detected in activated T cells and gives rise to a nonglycosylated protein that resides in the cytosol. Furthermore, membrane LIGHT is shed from the cell surface of human 293 T cells. These studies reveal new mechanisms involved in regulating the physical forms and cellular compartmentalization of LIGHT that may contribute to the regulation and biological function of this cytokine.
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Affiliation(s)
- S W Granger
- Division of Molecular Immunology, La Jolla Institute for Allergy and Immunology, San Diego, CA 92121, USA
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40
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Flajnik MF, Kasahara M. Comparative genomics of the MHC: glimpses into the evolution of the adaptive immune system. Immunity 2001; 15:351-62. [PMID: 11567626 DOI: 10.1016/s1074-7613(01)00198-4] [Citation(s) in RCA: 224] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
MHC gene organization (size, complexity, gene order) differs markedly among different species, and yet all nonmammalian vertebrates examined to date have a true "class I region" with tight linkage of genes encoding the class I presenting and processing molecules. Three paralogous regions of the human genome contain sets of linked genes homologous to various loci in the MHC class I, class II, and/or class III regions, providing insight into the organization of the "proto MHC" before the emergence of the adaptive immune system in the jawed vertebrates.
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Affiliation(s)
- M F Flajnik
- Department of Microbiology and Immunology, University of Maryland at Baltimore, Room 13-009, 655 West Baltimore Street, Baltimore, MD 21021, USA.
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41
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Shiina T, Ando A, Suto Y, Kasai F, Shigenari A, Takishima N, Kikkawa E, Iwata K, Kuwano Y, Kitamura Y, Matsuzawa Y, Sano K, Nogami M, Kawata H, Li S, Fukuzumi Y, Yamazaki M, Tashiro H, Tamiya G, Kohda A, Okumura K, Ikemura T, Soeda E, Mizuki N, Kimura M, Bahram S, Inoko H. Genomic anatomy of a premier major histocompatibility complex paralogous region on chromosome 1q21-q22. Genome Res 2001; 11:789-802. [PMID: 11337475 PMCID: PMC311078 DOI: 10.1101/gr.175801] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Human chromosomes 1q21-q25, 6p21.3-22.2, 9q33-q34, and 19p13.1-p13.4 carry clusters of paralogous loci, to date best defined by the flagship 6p MHC region. They have presumably been created by two rounds of large-scale genomic duplications around the time of vertebrate emergence. Phylogenetically, the 1q21-25 region seems most closely related to the 6p21.3 MHC region, as it is only the MHC paralogous region that includes bona fide MHC class I genes, the CD1 and MR1 loci. Here, to clarify the genomic structure of this model MHC paralogous region as well as to gain insight into the evolutionary dynamics of the entire quadriplication process, a detailed analysis of a critical 1.7 megabase (Mb) region was performed. To this end, a composite, deep, YAC, BAC, and PAC contig encompassing all five CD1 genes and linking the centromeric +P5 locus to the telomeric KRTC7 locus was constructed. Within this contig a 1.1-Mb BAC and PAC core segment joining CD1D to FCER1A was fully sequenced and thoroughly analyzed. This led to the mapping of a total of 41 genes (12 expressed genes, 12 possibly expressed genes, and 17 pseudogenes), among which 31 were novel. The latter include 20 olfactory receptor (OR) genes, 9 of which are potentially expressed. Importantly, CD1, SPTA1, OR, and FCERIA belong to multigene families, which have paralogues in the other three regions. Furthermore, it is noteworthy that 12 of the 13 expressed genes in the 1q21-q22 region around the CD1 loci are immunologically relevant. In addition to CD1A-E, these include SPTA1, MNDA, IFI-16, AIM2, BL1A, FY and FCERIA. This functional convergence of structurally unrelated genes is reminiscent of the 6p MHC region, and perhaps represents the emergence of yet another antigen presentation gene cluster, in this case dedicated to lipid/glycolipid antigens rather than antigen-derived peptides.
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Affiliation(s)
- Takashi Shiina
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Asako Ando
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Yumiko Suto
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Fumio Kasai
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Atsuko Shigenari
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Nobusada Takishima
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Eri Kikkawa
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Kyoko Iwata
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Yuko Kuwano
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Yuka Kitamura
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Yumiko Matsuzawa
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Kazumi Sano
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Masahiro Nogami
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Hisako Kawata
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Suyun Li
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Yasuhito Fukuzumi
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Masaaki Yamazaki
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Hiroyuki Tashiro
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Gen Tamiya
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Atsushi Kohda
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Katsuzumi Okumura
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Toshimichi Ikemura
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Eiichi Soeda
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Nobuhisa Mizuki
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Minoru Kimura
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Seiamak Bahram
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Hidetoshi Inoko
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
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42
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Affiliation(s)
- L Du Pasquier
- Basel Institute for Immunology, Grenzacherstrasse 487, 4005, Basel, Switzerland.
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Abstract
Homeobox genes encode important developmental control proteins. In vertebrates, those encoding the proteins of the HOX class and their most closely related families, including paraHOX and metaHOX classes, are clustered in paralogous regions (or paralogons). We show that the majority of the other homeobox genes (we called contraHOX) can also be clustered and belong to paralogons in humans. This suggests that they duplicated during vertebrate evolution along the same processes as the HOX genes. We tentatively assembled several paralogons in superparalogons. One of the superparalogons contains the contraHOX genes. These observations were extended to hundreds of genes, and allowed to describe a primary human genome paralogy map.
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Affiliation(s)
- C Popovici
- Laboratoire d'Oncologie Moléculaire, U119 Inserm, Marseille, France
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Sültmann H, Sato A, Murray BW, Takezaki N, Geisler R, Rauch GJ, Klein J. Conservation of Mhc class III region synteny between zebrafish and human as determined by radiation hybrid mapping. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2000; 165:6984-93. [PMID: 11120825 DOI: 10.4049/jimmunol.165.12.6984] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In the HLA, H2, and other mammalian MHC:, the class I and II loci are separated by the so-called class III region comprised of approximately 60 genes that are functionally and evolutionarily unrelated to the class I/II genes. To explore the origin of this island of unrelated loci in the middle of the MHC: 19 homologues of HLA class III genes, we identified 19 homologues of HLA class III genes as well as 21 additional non-class I/II HLA homologues in the zebrafish and mapped them by testing a panel of 94 zebrafish-hamster radiation hybrid cell lines. Six of the HLA class III and eight of the flanking homologues were found to be linked to the zebrafish class I (but not class II) loci in linkage group 19. The remaining homologous loci were found to be scattered over 14 zebrafish linkage groups. The linkage group 19 contains at least 25 genes (not counting the class I loci) that are also syntenic on human chromosome 6. This gene assembly presumably represents the pre-MHC: that existed before the class I/II genes arose. The pre-MHC: may not have contained the complement and other class III genes involved in immune response.
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Affiliation(s)
- H Sültmann
- Max-Planck-Institut für Biologie, Abteilung Immungenetik, Tübingen, Germany
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45
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Clark MS, Pontarotti P, Gilles A, Kelly A, Elgar G. Identification and characterization of a beta proteasome subunit cluster in the Japanese pufferfish (Fugu rubripes). JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2000; 165:4446-52. [PMID: 11035083 DOI: 10.4049/jimmunol.165.8.4446] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The low molecular mass polypeptide (LMP2, LMP7, and MECL-1) genes code for beta-type subunits of the proteasome, a multimeric complex that degrades proteins into peptides as part of the MHC class I-mediated Ag-presenting pathway. These gene products are up-regulated in response to infection by IFN-gamma and replace the corresponding constitutively expressed subunits (X, Y, and Z) during the immune response. In humans, the LMP2 and LMP7 genes both reside within the class II region of the MHC (6p21.3), while MECL-1 is located at 16q22.1. In the present study, we have identified all three IFN-gamma-regulated beta-type proteasome subunits in Fugu, which are present as a cluster within the Fugu MHC class I region. We show that in this species, LMP7, LMP2, and MECL-1 are linked. Also within this cluster is an LMP2-like subunit (which seems specific to all teleosts tested to date) and a closely linked LMP7 pseudogene, indicating that within Fugu and potentially other teleosts, there has been an additional regional duplication involving these genes.
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Affiliation(s)
- M S Clark
- Fugu Genomics, HGMP Resource Centre, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom.
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46
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Ohta Y, Okamura K, McKinney EC, Bartl S, Hashimoto K, Flajnik MF. Primitive synteny of vertebrate major histocompatibility complex class I and class II genes. Proc Natl Acad Sci U S A 2000; 97:4712-7. [PMID: 10781076 PMCID: PMC18298 DOI: 10.1073/pnas.97.9.4712] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Major histocompatibility complex (MHC) class I and class II molecules bind to and display peptidic antigens acquired from pathogens that are recognized by lymphocytes coordinating and executing adaptive immune responses. The two classes of MHC proteins have nearly identical tertiary structures and were derived from a common ancestor that probably existed not long before the emergence of the cartilaginous fish. Class I and class II genes are genetically linked in tetrapods but are not syntenic in teleost fish, a phylogenetic taxon derived from the oldest vertebrate ancestor examined to date. Cartilaginous fish (sharks, skates, and rays) are in the oldest taxon of extant jawed vertebrates; we have carried out segregation analyses in two families of nurse sharks and one family of the banded houndshark that revealed a close linkage of class IIalpha and beta genes both with each other and with the classical class I (class Ia) gene. These results strongly suggest that the primordial duplication giving rise to classical class I and class II occurred in cis, and the close linkage between these two classes of genes has been maintained for at least 460 million years in representatives of most vertebrate taxa.
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Affiliation(s)
- Y Ohta
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201, USA
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