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Wu M, Zhao H, Tang X, Zhao W, Yi X, Li Q, Sun X. Organization and Complexity of the Yak (Bos Grunniens) Immunoglobulin Loci. Front Immunol 2022; 13:876509. [PMID: 35615368 PMCID: PMC9124968 DOI: 10.3389/fimmu.2022.876509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/11/2022] [Indexed: 12/03/2022] Open
Abstract
As important livestock in Qinghai-Tibet Plateau, yak provides meat and other necessities for Tibetans living. Plateau yak has resistance to diseases and stress, yet is nearly unknown in the structure and expression mechanism of yak immunoglobulin loci. Based on the published immunoglobulin genes of bovids (cattle, sheep and goat), the genomic organization of the yak immunoglobulin heavy chain (IgH) and immunoglobulin light chain (IgL) were described. The assemblage diversity of IgH, Igλ and Igκ in yak was similar to that in bovids, and contributes little to the antibody lineage compared with that in humans and mice. Somatic hypermutation (SHM) had a greater effect on immunoglobulin diversity in yak than in goat and sheep, and in addition to the complementarity-determining region (CDR), some loci in the framework region (FR) also showed high frequency mutations. CDR3 diversity showed that immunological lineages in yak were overwhelmingly generated through linkage diversity in IgH rearrangements. The emergence of new high-throughput sequencing technologies and the yak whole genome (2019) publication have greatly improved our understanding of the immune response in yaks. We had a more comprehensive analysis of yak immunoglobulin expression diversity by PE300, which avoided the disadvantage of missing low-frequency recombination in traditional Sanger sequencing. In summary, we described the schematic structure of the genomic organization of yak IgH loci and IgL loci. The analysis of immunoglobulin expression diversity showed that yak made up for the deficiency of V(D)J recombinant diversity by junctional diversity and CDR3 diversity. In addition, yak, like cattle, also had the same ultra-long IgH CDR3 (CDR3H), which provided more contribution to the diverse expression of yak immunoglobulin. These findings might provide a theoretical basis for disease resistance breeding and vaccine development in yak.
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Affiliation(s)
- Mingli Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Haidong Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoqin Tang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wanxia Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaohua Yi
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qi Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiuzhu Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
- *Correspondence: Xiuzhu Sun,
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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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Guselnikov SV, Baranov KO, Najakshin AM, Mechetina LV, Chikaev NA, Makunin AI, Kulemzin SV, Andreyushkova DA, Stöck M, Wuertz S, Gessner J, Warren WC, Schartl M, Trifonov VA, Taranin AV. Diversity of Immunoglobulin Light Chain Genes in Non-Teleost Ray-Finned Fish Uncovers IgL Subdivision into Five Ancient Isotypes. Front Immunol 2018; 9:1079. [PMID: 29892283 PMCID: PMC5985310 DOI: 10.3389/fimmu.2018.01079] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/30/2018] [Indexed: 01/02/2023] Open
Abstract
The aim of this study was to fill important gaps in the evolutionary history of immunoglobulins by examining the structure and diversity of IgL genes in non-teleost ray-finned fish. First, based on the bioinformatic analysis of recent transcriptomic and genomic resources, we experimentally characterized the IgL genes in the chondrostean fish, Acipenser ruthenus (sterlet). We show that this species has three loci encoding IgL kappa-like chains with a translocon-type gene organization and a single VJC cluster, encoding homogeneous lambda-like light chain. In addition, sterlet possesses sigma-like VL and J-CL genes, which are transcribed separately and both encode protein products with cleavable leader peptides. The Acipenseriformes IgL dataset was extended by the sequences mined in the databases of species belonging to other non-teleost lineages of ray-finned fish: Holostei and Polypteriformes. Inclusion of these new data into phylogenetic analysis showed a clear subdivision of IgL chains into five groups. The isotype described previously as the teleostean IgL lambda turned out to be a kappa and lambda chain paralog that emerged before the radiation of ray-finned fish. We designate this isotype as lambda-2. The phylogeny also showed that sigma-2 IgL chains initially regarded as specific for cartilaginous fish are present in holosteans, polypterids, and even in turtles. We conclude that there were five ancient IgL isotypes, which evolved differentially in various lineages of jawed vertebrates.
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Affiliation(s)
- Sergey V. Guselnikov
- Laboratory of Immunogenetics, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Konstantin O. Baranov
- Laboratory of Immunogenetics, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Alexander M. Najakshin
- Laboratory of Immunogenetics, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Ludmila V. Mechetina
- Laboratory of Immunogenetics, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Nikolai A. Chikaev
- Laboratory of Immunogenetics, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Alexey I. Makunin
- Laboratory of Comparative Genomics, Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Sergey V. Kulemzin
- Laboratory of Immunogenetics, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Daria A. Andreyushkova
- Laboratory of Comparative Genomics, Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Sven Wuertz
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Jörn Gessner
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Wesley C. Warren
- School of Medicine, McDonnell Genome Institute, Washington University, St. Louis, MO, United States
| | - Manfred Schartl
- Department of Physiological Chemistry, Biocenter, University of Würzburg, Würzburg, Germany
- Department of Biology, Hagler Institute for Advanced Study, Texas A&M University, College Station, TX, United States
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, Würzburg, Germany
| | - Vladimir A. Trifonov
- Novosibirsk State University, Novosibirsk, Russia
- Laboratory of Comparative Genomics, Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Alexander V. Taranin
- Laboratory of Immunogenetics, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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Olivieri DN, Garet E, Estevez O, Sánchez-Espinel C, Gambón-Deza F. Genomic structure and expression of immunoglobulins in Squamata. Mol Immunol 2016; 72:81-91. [DOI: 10.1016/j.molimm.2016.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 02/24/2016] [Accepted: 03/02/2016] [Indexed: 11/24/2022]
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5
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A Comprehensive Analysis of the Phylogeny, Genomic Organization and Expression of Immunoglobulin Light Chain Genes in Alligator sinensis, an Endangered Reptile Species. PLoS One 2016; 11:e0147704. [PMID: 26901135 PMCID: PMC4762898 DOI: 10.1371/journal.pone.0147704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/07/2016] [Indexed: 12/02/2022] Open
Abstract
Crocodilians are evolutionarily distinct reptiles that are distantly related to lizards and are thought to be the closest relatives of birds. Compared with birds and mammals, few studies have investigated the Ig light chain of crocodilians. Here, employing an Alligator sinensis genomic bacterial artificial chromosome (BAC) library and available genome data, we characterized the genomic organization of the Alligator sinensis IgL gene loci. The Alligator sinensis has two IgL isotypes, λ and κ, the same as Anolis carolinensis. The Igλ locus contains 6 Cλ genes, each preceded by a Jλ gene, and 86 potentially functional Vλ genes upstream of (Jλ-Cλ)n. The Igκ locus contains a single Cκ gene, 6 Jκs and 62 functional Vκs. All VL genes are classified into a total of 31 families: 19 Vλ families and 12 Vκ families. Based on an analysis of the chromosomal location of the light chain genes among mammals, birds, lizards and frogs, the data further confirm that there are two IgL isotypes in the Alligator sinensis: Igλ and Igκ. By analyzing the cloned Igλ/κ cDNA, we identified a biased usage pattern of V families in the expressed Vλ and Vκ. An analysis of the junctions of the recombined VJ revealed the presence of N and P nucleotides in both expressed λ and κ sequences. Phylogenetic analysis of the V genes revealed V families shared by mammals, birds, reptiles and Xenopus, suggesting that these conserved V families are orthologous and have been retained during the evolution of IgL. Our data suggest that the Alligator sinensis IgL gene repertoire is highly diverse and complex and provide insight into immunoglobulin gene evolution in vertebrates.
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6
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Qin T, Liu Z, Zhao H. Organization and genomic complexity of sheep immunoglobulin light chain gene loci. Immunol Lett 2015; 168:313-8. [DOI: 10.1016/j.imlet.2015.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Revised: 10/09/2015] [Accepted: 10/15/2015] [Indexed: 01/06/2023]
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7
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Characterization of antibody V segment diversity in the Tasmanian devil (Sarcophilus harrisii). Vet Immunol Immunopathol 2015; 167:156-65. [DOI: 10.1016/j.vetimm.2015.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/25/2015] [Accepted: 08/06/2015] [Indexed: 10/23/2022]
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Abstract
Two types of adaptive immune strategies are known to have evolved in vertebrates: the VLR-based system, which is present in jawless organisms and is mediated by VLRA and VLRB lymphocytes, and the BCR/TCR-based system, which is present in jawed species and is provided by B and T cell receptors expressed on B and T cells, respectively. Here we summarize features of B cells and their predecessors in the different animal phyla, focusing the review on B cells from jawed vertebrates. We point out the critical role of nonclassical species and comparative immunology studies in the understanding of B cell immunity. Because nonclassical models include species relevant to veterinary medicine, basic science research performed in these animals contributes to the knowledge required for the development of more efficacious vaccines against emerging pathogens.
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Affiliation(s)
- David Parra
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Fumio Takizawa
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - J Oriol Sunyer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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9
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Pettinello R, Dooley H. The immunoglobulins of cold-blooded vertebrates. Biomolecules 2014; 4:1045-69. [PMID: 25427250 PMCID: PMC4279169 DOI: 10.3390/biom4041045] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 11/10/2014] [Accepted: 11/13/2014] [Indexed: 12/27/2022] Open
Abstract
Although lymphocyte-like cells secreting somatically-recombining receptors have been identified in the jawless fishes (hagfish and lamprey), the cartilaginous fishes (sharks, skates, rays and chimaera) are the most phylogenetically distant group relative to mammals in which bona fide immunoglobulins (Igs) have been found. Studies of the antibodies and humoral immune responses of cartilaginous fishes and other cold-blooded vertebrates (bony fishes, amphibians and reptiles) are not only revealing information about the emergence and roles of the different Ig heavy and light chain isotypes, but also the evolution of specialised adaptive features such as isotype switching, somatic hypermutation and affinity maturation. It is becoming increasingly apparent that while the adaptive immune response in these vertebrate lineages arose a long time ago, it is most definitely not primitive and has evolved to become complex and sophisticated. This review will summarise what is currently known about the immunoglobulins of cold-blooded vertebrates and highlight the differences, and commonalities, between these and more “conventional” mammalian species.
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Affiliation(s)
- Rita Pettinello
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK.
| | - Helen Dooley
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK.
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10
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Novel X-linked genes revealed by quantitative polymerase chain reaction in the green anole, Anolis carolinensis. G3-GENES GENOMES GENETICS 2014; 4:2107-13. [PMID: 25172916 PMCID: PMC4232536 DOI: 10.1534/g3.114.014084] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The green anole, Anolis carolinensis (ACA), is the model reptile for a vast array of biological disciplines. It was the first nonavian reptile to have its genome fully sequenced. During the genome project, the XX/XY system of sex chromosomes homologous to chicken chromosome 15 (GGA15) was revealed, and 106 X-linked genes were identified. We selected 38 genes located on eight scaffolds in ACA and having orthologs located on GGA15, then tested their linkage to ACA X chromosome by using comparative quantitative fluorescent real-time polymerase chain reaction applied to male and female genomic DNA. All tested genes appeared to be X-specific and not present on the Y chromosome. Assuming that all genes located on these scaffolds should be localized to the ACA X chromosome, we more than doubled the number of known X-linked genes in ACA, from 106 to 250. While demonstrating that the gene content of chromosome X in ACA and GGA15 is largely conserved, we nevertheless showed that numerous interchromosomal rearrangements had occurred since the splitting of the chicken and anole evolutionary lineages. The presence of many ACA X-specific genes localized to distinct contigs indicates that the ACA Y chromosome should be highly degenerated, having lost a large amount of its original gene content during evolution. The identification of novel genes linked to the X chromosome and absent on the Y chromosome in the model lizard species contributes to ongoing research as to the evolution of sex determination in reptiles and provides important information for future comparative and functional genomics.
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Olivieri DN, von Haeften B, Sánchez-Espinel C, Faro J, Gambón-Deza F. Genomic V exons from whole genome shotgun data in reptiles. Immunogenetics 2014; 66:479-92. [DOI: 10.1007/s00251-014-0784-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 05/23/2014] [Indexed: 10/25/2022]
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12
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Extensive diversification of IgH subclass-encoding genes and IgM subclass switching in crocodilians. Nat Commun 2013; 4:1337. [PMID: 23299887 DOI: 10.1038/ncomms2317] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 11/22/2012] [Indexed: 01/01/2023] Open
Abstract
Crocodilians are a group of reptiles that are closely related to birds and are thought to possess a strong immune system. Here we report that the IgH locus in the Siamese crocodile and the Chinese alligator contains multiple μ genes, in contrast to other tetrapods. Both the μ2 and μ3 genes are expressed through class-switch recombination involving the switch region and germline transcription. Both IgM1 and IgM2 are present in the serum as polymers, which implies that IgM class switching may have significant roles in humoural immunity. The crocodilian α genes are the first IgA-encoding genes identified in reptiles, and these genes show an inverted transcriptional orientation similar to that of birds. The identification of both α and δ genes in crocodilians suggests that the IgH loci of modern living mammals, reptiles and birds share a common ancestral organization.
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13
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Sun Y, Wei Z, Li N, Zhao Y. A comparative overview of immunoglobulin genes and the generation of their diversity in tetrapods. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 39:103-109. [PMID: 22366185 DOI: 10.1016/j.dci.2012.02.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 02/17/2012] [Accepted: 02/17/2012] [Indexed: 05/31/2023]
Abstract
In the past several decades, immunoglobulin (Ig) genes have been extensively characterized in many tetrapod species. This review focuses on the expressed Ig isotypes and the diversity of Ig genes in mammals, birds, reptiles, and amphibians. With regard to heavy chains, five Ig isotypes - IgM, IgD, IgG, IgA, and IgE - have been reported in mammals. Among these isotypes, IgM, IgD, and IgA (or its analog, IgX) are also found in non-mammalian tetrapods. Birds, reptiles, and amphibians express IgY, which is considered the precursor of IgG and IgE. Some species have developed unique isotypes of Ig, such as IgO in the platypus, IgF in Xenopus, and IgY (ΔFc) in ducks and turtles. The κ and λ light chains are both utilized in tetrapods, but the usage frequencies of κ and λ chains differ greatly among species. The diversity of Ig genes depends on several factors, including the germline repertoire and recombinatorial and post-recombinatorial diversity, and different species have evolved distinct mechanisms to generate antibody diversity.
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Affiliation(s)
- Yi Sun
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, PR China.
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Das S, Hirano M, Tako R, McCallister C, Nikolaidis N. Evolutionary genomics of immunoglobulin-encoding Loci in vertebrates. Curr Genomics 2012; 13:95-102. [PMID: 23024601 PMCID: PMC3308330 DOI: 10.2174/138920212799860652] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 12/13/2011] [Accepted: 01/14/2012] [Indexed: 11/22/2022] Open
Abstract
Immunoglobulins (or antibodies) are an essential element of the jawed vertebrate adaptive immune response system. These molecules have evolved over the past 500 million years and generated highly specialized proteins that recognize an extraordinarily large number of diverse substances, collectively known as antigens. During vertebrate evolution the diversification of the immunoglobulin-encoding loci resulted in differences in the genomic organization, gene content, and ratio of functional genes and pseudogenes. The tinkering process in the immunoglobulin-encoding loci often gave rise to lineage-specific characteristics that were formed by selection to increase species adaptation and fitness. Immunoglobulin loci and their encoded antibodies have been shaped repeatedly by contrasting evolutionary forces, either to conserve the prototypic structure and mechanism of action or to generate alternative and diversified structures and modes of function. Moreover, evolution favored the development of multiple mechanisms of primary and secondary antibody diversification, which are used by different species to effectively generate an almost infinite collection of diverse antibody types. This review summarizes our current knowledge on the genomics and evolution of the immunoglobulin-encoding loci and their protein products in jawed vertebrates.
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Affiliation(s)
- Sabyasachi Das
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, School of Medicine, Emory University, USA
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Gambón-Deza F, Sánchez-Espinel C, Mirete-Bachiller S, Magadán-Mompó S. Snakes antibodies. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2012; 38:1-9. [PMID: 22426516 DOI: 10.1016/j.dci.2012.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 02/28/2012] [Accepted: 03/01/2012] [Indexed: 05/31/2023]
Abstract
Immunoglobulins are basic molecules of the immune system of vertebrates. In previous studies we described the immunoglobulins found in two squamata reptiles, Anolis carolinensis and Eublepharis macularius. Snakes are squamata reptiles too but they have undergone an extreme evolutionary process. We therefore wanted to know how these changes affected their immunoglobulin coding genes. To perform this analysis we studied five snake transcriptomes and two genome draft sequences. Sequences coding for immunoglobulin M (IgM), immunoglobulin D (IgD) and two classes of immunoglobulin Y (IgY - named IgYa and IgYb-) were found in all of them. Moreover, the Thamnophis elegans transcriptome and Python molurus genome draft sequences showed a third class of IgY, the IgYc, whose constant region only presents three domains and lacks the CH2. All data suggest that the IgYb is the evolutionary origin of this IgYc. An exhaustive search of the light chains were carried out, being lambda the only light chain found in snakes. The results provide a clear picture of the immunoglobulins present in the suborder Serpentes.
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Affiliation(s)
- Francisco Gambón-Deza
- Servicio Gallego de Salud (SERGAS) Unidad de Inmunología, Hospital do Meixoeiro, Carretera de Madrid s/n, Vigo, Pontevedra, Spain.
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Wang T, Sun Y, Shao W, Cheng G, Li L, Cao Z, Yang Z, Zou H, Zhang W, Han B, Hu Y, Ren L, Hu X, Guo Y, Fei J, Hammarström L, Li N, Zhao Y. Evidence of IgY subclass diversification in snakes: evolutionary implications. THE JOURNAL OF IMMUNOLOGY 2012; 189:3557-65. [PMID: 22933626 DOI: 10.4049/jimmunol.1200212] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mammalian IgG and IgE are thought to have evolved from IgY of nonmammalian tetrapods; however, no diversification of IgY subclasses has been reported in reptiles or birds, which are phylogenetically close to mammals. To our knowledge, we report the first evidence of the presence of multiple IgY-encoding (υ) genes in snakes. Two υ genes were identified in the snake Elaphe taeniura, and three υ genes were identified in the Burmese python (Python molurus bivittatus). Although four of the υ genes displayed a conventional four-H chain C region exon structure, one of the υ genes in the Burmese python lacked the H chain C region 2 exon, thus exhibiting a structure similar to that of the mammalian γ genes. We developed mouse mAbs specific for the IgY1 and IgY2 of E. taeniura and showed that both were expressed in serum; each had two isoforms: one full-length and one truncated at the C terminus. The truncation was not caused by alternative splicing or transcriptional termination. We also identified the μ and δ genes, but no α gene, in both snakes. This study provides valuable clues for our understanding of Ig gene evolution in tetrapods.
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Affiliation(s)
- Tao Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100094, People's Republic of China
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17
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Huang T, Zhang M, Wei Z, Wang P, Sun Y, Hu X, Ren L, Meng Q, Zhang R, Guo Y, Hammarstrom L, Li N, Zhao Y. Analysis of immunoglobulin transcripts in the ostrich Struthio camelus, a primitive avian species. PLoS One 2012; 7:e34346. [PMID: 22479606 PMCID: PMC3315531 DOI: 10.1371/journal.pone.0034346] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 02/26/2012] [Indexed: 11/21/2022] Open
Abstract
Previous studies on the immunoglobulin (Ig) genes in avian species are limited (mainly to galliformes and anseriformes) but have revealed several interesting features, including the absence of the IgD and Igκ encoding genes, inversion of the IgA encoding gene and the use of gene conversion as the primary mechanism to generate an antibody repertoire. To better understand the Ig genes and their evolutionary development in birds, we analyzed the Ig genes in the ostrich (Struthio camelus), which is one of the most primitive birds. Similar to the chicken and duck, the ostrich expressed only three IgH chain isotypes (IgM, IgA and IgY) and λ light chains. The IgM and IgY constant domains are similar to their counterparts described in other vertebrates. Although conventional IgM, IgA and IgY cDNAs were identified in the ostrich, we also detected a transcript encoding a short membrane-bound form of IgA (lacking the last two CH exons) that was undetectable at the protein level. No IgD or κ encoding genes were identified. The presence of a single leader peptide in the expressed heavy chain and light chain V regions indicates that gene conversion also plays a major role in the generation of antibody diversity in the ostrich. Because the ostrich is one of the most primitive living aves, this study suggests that the distinct features of the bird Ig genes appeared very early during the divergence of the avian species and are thus shared by most, if not all, avian species.
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Affiliation(s)
- Tian Huang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Min Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Zhiguo Wei
- College of Animal Science and Technology, Henan University of Science and Technology, Henan, People's Republic of China
| | - Ping Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Yi Sun
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Liming Ren
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Qingyong Meng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Ran Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Ying Guo
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Lennart Hammarstrom
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Ning Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
- Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, People's Republic of China
- * E-mail:
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Edholm ES, Wilson M, Bengten E. Immunoglobulin light (IgL) chains in ectothermic vertebrates. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2011; 35:906-915. [PMID: 21256861 DOI: 10.1016/j.dci.2011.01.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 01/16/2011] [Accepted: 01/16/2011] [Indexed: 05/30/2023]
Abstract
Four major ancesteral IgL isotypes have been identified κ, λ, σ and σ-cart. However, depending on the vertebrate class the genomic representation of these isotypes differs in regards to what is encoded in the germline and how these genes are organized. Also, the relative contribution of each isotype in immune responses varies. This review focuses on the IgL chains of ectothermic vertebrates, specifically the number of different isotypes, their phylogenetic relationship, genomic organizations and expression.
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Affiliation(s)
- Eva-Stina Edholm
- Department of Microbiology, University of Mississippi Medical Center, Jackson, MS 39216, United States
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19
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Qin T, Ren LM, Meng QY. Junctional Diversity in <I>Xenopus tropicalis</I> Immunoglobulin Light Chains. PROG BIOCHEM BIOPHYS 2011. [DOI: 10.3724/sp.j.1206.2010.00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Das S, Hirano M, McCallister C, Tako R, Nikolaidis N. Comparative genomics and evolution of immunoglobulin-encoding loci in tetrapods. Adv Immunol 2011; 111:143-78. [PMID: 21970954 DOI: 10.1016/b978-0-12-385991-4.00004-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The immunoglobulins (Igs or antibodies) as an integral part of the tetrapod adaptive immune response system have evolved toward producing highly diversified molecules that recognize a remarkably large number of different antigens. Antibodies and their respective encoding loci have been shaped by different and often contrasting evolutionary forces, some of which aim to conserve an established pattern or mechanism and others to generate alternative and diversified structural and functional configurations. The genomic organization, gene content, ratio between functional genes and pseudogenes, number and position of recombining genetic elements, and the different levels of divergence present at the germline of the Ig-encoding loci have been evolutionarily shaped and optimized in a lineage- and, in some cases, species-specific mode aiming to increase organismal fitness. Further, evolution favored the development of multiple mechanisms of primary and secondary antibody diversification, such as V(D)J recombination, class switch recombination, isotype exclusion, somatic hypermutation, and gene conversion. Diverse tetrapod species, based on their specific germline configurations, use these mechanisms in several different combinations to effectively generate a vast array of distinct antibody types and structures. This chapter summarizes our current knowledge on the Ig-encoding loci in tetrapods and discusses the different evolutionary mechanisms that shaped their diversification.
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Affiliation(s)
- Sabyasachi Das
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, School of Medicine, Emory University, Atlanta, Georgia, USA
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21
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Janes DE, Organ CL, Fujita MK, Shedlock AM, Edwards SV. Genome evolution in Reptilia, the sister group of mammals. Annu Rev Genomics Hum Genet 2010; 11:239-64. [PMID: 20590429 DOI: 10.1146/annurev-genom-082509-141646] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genomes of birds and nonavian reptiles (Reptilia) are critical for understanding genome evolution in mammals and amniotes generally. Despite decades of study at the chromosomal and single-gene levels, and the evidence for great diversity in genome size, karyotype, and sex chromosome diversity, reptile genomes are virtually unknown in the comparative genomics era. The recent sequencing of the chicken and zebra finch genomes, in conjunction with genome scans and the online publication of the Anolis lizard genome, has begun to clarify the events leading from an ancestral amniote genome--predicted to be large and to possess a diverse repeat landscape on par with mammals and a birdlike sex chromosome system--to the small and highly streamlined genomes of birds. Reptilia exhibit a wide range of evolutionary rates of different subgenomes and, from isochores to mitochondrial DNA, provide a critical contrast to the genomic paradigms established in mammals.
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Affiliation(s)
- Daniel E Janes
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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