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Million KM, Lively CM. Trans‐specific polymorphism and the convergent evolution of supertypes in major histocompatibility complex class II genes in darters (
Etheostoma
). Ecol Evol 2022; 12:e8485. [PMID: 36311547 PMCID: PMC9601779 DOI: 10.1002/ece3.8485] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 12/24/2022] Open
Abstract
Major Histocompatibility Complex (MHC) genes are one of the most polymorphic gene groups known in vertebrates. MHC genes also exhibit allelic variants that are shared among taxa, referred to as trans‐specific polymorphism (TSP). The role that selection plays in maintaining such high diversity within species, as well as TSP, is an ongoing discussion in biology. In this study, we used deep‐sequencing techniques to characterize MHC class IIb gene diversity in three sympatric species of darters. We found at least 5 copies of the MHC gene in darters, with 126 genetic variants encoding 122 unique amino acid sequences. We identified four supertypes based on the binding properties of proteins encoded by the sequences. Although each species had a unique pool of variants, many variants were shared between species pairs and across all three species. Phylogenetic analysis showed that the variants did not group together monophyletically based on species identity or on supertype. An expanded phylogenetic analysis showed that some darter alleles grouped together with alleles from other percid fishes. Our findings show that TSP occurs in darters, which suggests that balancing selection is acting at the genotype level. Supertypes, however, are most likely evolving convergently, as evidenced by the fact that alleles do not form monophyletic groups based on supertype. Our research demonstrates that selection may be acting differently on MHC genes at the genotype and supertype levels, selecting for the maintenance of high genotypic diversity while driving the convergent evolution of similar MHC phenotypes across different species.
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Affiliation(s)
- Kara M. Million
- Department of Biology Indiana University Bloomington Indiana USA
| | - Curtis M. Lively
- Department of Biology Indiana University Bloomington Indiana USA
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2
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Grimholt U, Lukacs M. Fate of MHCII in salmonids following 4WGD. Immunogenetics 2020; 73:79-91. [PMID: 33225379 PMCID: PMC7862078 DOI: 10.1007/s00251-020-01190-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/11/2020] [Indexed: 12/27/2022]
Abstract
Major histocompatibility complex (MHC) genes are key players in the adaptive immunity providing a defense against invading pathogens. Although the basic structures are similar when comparing mammalian and teleost MHC class II (MHCII) molecules, there are also clear-cut differences. Based on structural requirements, the teleosts non-classical MHCII molecules do not comply with a function similar to the human HLA-DM and HLA-DO, i.e., assisting in peptide loading and editing of classical MHCII molecules. We have previously studied the evolution of teleost class II genes identifying various lineages and tracing their phylogenetic occurrence back to ancient ray-finned fishes. We found no syntenic MHCII regions shared between cyprinids, salmonids, and neoteleosts, suggesting regional instabilities. Salmonids have experienced a unique whole genome duplication 94 million years ago, providing them with the opportunity to experiment with gene duplicates. Many salmonid genomes have recently become available, and here we set out to investigate how MHCII has evolved in salmonids using Northern pike as a diploid sister phyla, that split from the salmonid lineage prior to the fourth whole genome duplication (4WGD) event. We identified 120 MHCII genes in pike and salmonids, ranging from 11 to 20 genes per species analyzed where DB-group genes had the most expansions. Comparing the MHC of Northern pike with that of Atlantic salmon and other salmonids species provides a tale of gene loss, translocations, and genome rearrangements.
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Affiliation(s)
- Unni Grimholt
- Norwegian Veterinary Institute, P.O. Box 8146 Dep, 0033, Oslo, Norway.
| | - Morten Lukacs
- Norwegian Veterinary Institute, P.O. Box 8146 Dep, 0033, Oslo, Norway
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3
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Hou J, Chen SN, Gan Z, Li N, Huang L, Huo HJ, Yang YC, Lu Y, Yin Z, Nie P. In Primitive Zebrafish, MHC Class II Expression Is Regulated by IFN-γ, IRF1, and Two Forms of CIITA. THE JOURNAL OF IMMUNOLOGY 2020; 204:2401-2415. [DOI: 10.4049/jimmunol.1801480] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/13/2020] [Indexed: 12/21/2022]
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4
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Sundaram AYM, Garseth ÅH, Maccari G, Grimholt U. An Illumina approach to MHC typing of Atlantic salmon. Immunogenetics 2020; 72:89-100. [PMID: 31713647 PMCID: PMC6970960 DOI: 10.1007/s00251-019-01143-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 01/09/2023]
Abstract
The IPD-MHC Database represents the official repository for non-human major histocompatibility complex (MHC) sequences, overseen and supported by the Comparative MHC Nomenclature Committee, providing access to curated MHC data and associated analysis tools. IPD-MHC gathers allelic MHC class I and class II sequences from classical and non-classical MHC loci from various non-human animals including pets, farmed and experimental model animals. So far, Atlantic salmon and rainbow trout are the only teleost fish species with MHC class I and class II sequences present. For the remaining teleost or ray-finned species, data on alleles originating from given classical locus is scarce hampering their inclusion in the database. However, a fast expansion of sequenced genomes opens for identification of classical loci where high-throughput sequencing (HTS) will enable typing of allelic variants in a variety of new teleost or ray-finned species. HTS also opens for large-scale studies of salmonid MHC diversity challenging the current database nomenclature and analysis tools. Here we establish an Illumina approach to identify allelic MHC diversity in Atlantic salmon, using animals from an endangered wild population, and alter the salmonid MHC nomenclature to accommodate the expected sequence expansions.
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Affiliation(s)
- Arvind Y M Sundaram
- Norwegian Veterinary Institute, P.O. Box 750 Sentrum, 0106, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, 0450, Oslo, Norway
| | - Åse Helen Garseth
- Norwegian Veterinary Institute, P.O. Box 750 Sentrum, 0106, Oslo, Norway
| | - Giuseppe Maccari
- The Pirbright Institute, Woking, UK
- Anthony Nolan Research Institute, London, UK
| | - Unni Grimholt
- Norwegian Veterinary Institute, P.O. Box 750 Sentrum, 0106, Oslo, Norway.
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5
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Major Histocompatibility Complex (MHC) Genes and Disease Resistance in Fish. Cells 2019; 8:cells8040378. [PMID: 31027287 PMCID: PMC6523485 DOI: 10.3390/cells8040378] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/12/2019] [Accepted: 04/23/2019] [Indexed: 12/20/2022] Open
Abstract
Fascinating about classical major histocompatibility complex (MHC) molecules is their polymorphism. The present study is a review and discussion of the fish MHC situation. The basic pattern of MHC variation in fish is similar to mammals, with MHC class I versus class II, and polymorphic classical versus nonpolymorphic nonclassical. However, in many or all teleost fishes, important differences with mammalian or human MHC were observed: (1) The allelic/haplotype diversification levels of classical MHC class I tend to be much higher than in mammals and involve structural positions within but also outside the peptide binding groove; (2) Teleost fish classical MHC class I and class II loci are not linked. The present article summarizes previous studies that performed quantitative trait loci (QTL) analysis for mapping differences in teleost fish disease resistance, and discusses them from MHC point of view. Overall, those QTL studies suggest the possible importance of genomic regions including classical MHC class II and nonclassical MHC class I genes, whereas similar observations were not made for the genomic regions with the highly diversified classical MHC class I alleles. It must be concluded that despite decades of knowing MHC polymorphism in jawed vertebrate species including fish, firm conclusions (as opposed to appealing hypotheses) on the reasons for MHC polymorphism cannot be made, and that the types of polymorphism observed in fish may not be explained by disease-resistance models alone.
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6
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Li Z, Zhang N, Ma L, Qu Z, Wei X, Liu Z, Tang M, Zhang N, Jiang Y, Xia C. Distribution of ancient α1 and α2 domain lineages between two classical MHC class I genes and their alleles in grass carp. Immunogenetics 2019; 71:395-405. [PMID: 30941483 DOI: 10.1007/s00251-019-01111-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/05/2019] [Indexed: 12/13/2022]
Abstract
Major histocompatibility complex (MHC) class I molecules play a crucial role in the immune response by binding and presenting pathogen-derived peptides to specific CD8+ T cells. From cDNA of 20 individuals of wild grass carp (Ctenopharyngodon idellus), we could amplify one or two alleles each of classical MHC class I genes Ctid-UAA and Ctid-UBA. In total, 27 and 22 unique alleles of Ctid-UAA and Ctid-UBA were found. The leader, α1, transmembrane and cytoplasmic regions distinguish between Ctid-UAA and Ctid-UBA, and their encoded α1 domain sequences belong to the ancient lineages α1-V and α1-II, respectively, which separated several hundred million years ago. However, Ctid-UAA and Ctid-UBA share allelic lineage variation in their α2 and α3 sequences, in a pattern suggestive of past interlocus recombination events that transferred α2+α3 fragments. The allelic Ctid-UAA and Ctid-UBA variation involves ancient variation between domain lineages α2-I and α2-II, which in the present study was dated back to before the ancestral separation of teleost fish and spotted gar (> 300 million years ago). This is the first report with compelling evidence that recombination events combining different ancient α1 and α2 domain lineages had a major impact on the allelic variation of two different classical MHC class I genes within the same species.
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Affiliation(s)
- Zibin Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Nan Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lizhen Ma
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zehui Qu
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiaohui Wei
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zixin Liu
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Minghu Tang
- Chinese Carp of Yangtze River System and Primitive Breed Fishery, Guangling, Yangzhou, China
| | - Nianzhi Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yinan Jiang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China.
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7
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Molecular and Structural Characterization of MHC Class II β Genes Reveals High Diversity in the Cold-Adapted Icefish Chionodraco hamatus. Sci Rep 2019; 9:5523. [PMID: 30940855 PMCID: PMC6445107 DOI: 10.1038/s41598-019-42003-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 03/21/2019] [Indexed: 01/04/2023] Open
Abstract
This study reports the presence of two distinct MHC class II β genes in the Antarctic icefish Chionodraco hamatus, belonging to the classical (ChhaDAB) and nonclassical (ChhaDBB) evolutionary lineages. By the application of targeted sequencing approach, a remarkable molecular diversity in the exon 2 sequence of the highly expressed gene ChhaDAB has been observed, resulting in an estimate of 92 different variants translated in 87 different peptides from 54 analysed icefish individuals. A highly conservative estimate, based on a 95% sequence identity threshold clustering, translate this variability in 41 different peptide clusters belonging to four different clades and showing the signature of different kinds of selection. In stark contrast, the poorly expressed ChhaDBB gene displayed a very low level of molecular diversity within exon 2, in agreement with expectations for a nonclassical MHC class II β gene.
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8
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Hurt C, Ellis N, Harman A, Savage C. Genetic Structure at the Major Histocompatibility Complex in the Endangered Barrens Topminnow (Fundulus julisia). SOUTHEAST NAT 2019. [DOI: 10.1656/058.018.0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Carla Hurt
- Department of Biology, Tennessee Technological University, Cookeville, TN 38505
| | - Natalie Ellis
- Department of Biology, Tennessee Technological University, Cookeville, TN 38505
| | - Alexis Harman
- Department of Biology, Tennessee Technological University, Cookeville, TN 38505
| | - Courtney Savage
- Department of Biology, Tennessee Technological University, Cookeville, TN 38505
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9
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Osborne MJ, Pilger TJ, Lusk JD, Turner TF. Spatio-temporal variation in parasite communities maintains diversity at the major histocompatibility complex class IIβ in the endangered Rio Grande silvery minnow. Mol Ecol 2016; 26:471-489. [PMID: 27864911 DOI: 10.1111/mec.13936] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/02/2016] [Accepted: 11/14/2016] [Indexed: 01/30/2023]
Abstract
Climate change will strongly impact aquatic ecosystems particularly in arid and semi-arid regions. Fish-parasite interactions will also be affected by predicted altered flow and temperature regimes, and other environmental stressors. Hence, identifying environmental and genetic factors associated with maintaining diversity at immune genes is critical for understanding species' adaptive capacity. Here, we combine genetic (MHC class IIβ and microsatellites), parasitological and ecological data to explore the relationship between these factors in the remnant wild Rio Grande silvery minnow (Hybognathus amarus) population, an endangered species found in the southwestern United States. Infections with multiple parasites on the gills were observed and there was spatio-temporal variation in parasite communities and patterns of infection among individuals. Despite its highly endangered status and chronically low genetic effective size, Rio Grande silvery minnow had high allelic diversity at MHC class IIβ with more alleles recognized at the presumptive DAB1 locus compared to the DAB3 locus. We identified significant associations between specific parasites and MHC alleles against a backdrop of generalist parasite prevalence. We also found that individuals with higher individual neutral heterozygosity and higher amino acid divergence between MHC alleles had lower parasite abundance and diversity. Taken together, these results suggest a role for fluctuating selection imposed by spatio-temporal variation in pathogen communities and divergent allele advantage in maintenance of high MHC polymorphism. Understanding the complex interaction of habitat, pathogens and immunity in protected species will require integrated experimental, genetic and field studies.
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Affiliation(s)
- Megan J Osborne
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, MSC 03-2020, Albuquerque, NM, 87131, USA
| | - Tyler J Pilger
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, MSC 03-2020, Albuquerque, NM, 87131, USA
| | - Joel D Lusk
- U.S. Fish and Wildlife Service, New Mexico Ecological Services, Albuquerque, NM, 87113, USA
| | - Thomas F Turner
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, MSC 03-2020, Albuquerque, NM, 87131, USA
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10
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Faulks LK, Östman Ö. Adaptive major histocompatibility complex (MHC) and neutral genetic variation in two native Baltic Sea fishes (perch Perca fluviatilis and zander Sander lucioperca) with comparisons to an introduced and disease susceptible population in Australia (P. fluviatilis): assessing the risk of disease epidemics. JOURNAL OF FISH BIOLOGY 2016; 88:1564-1583. [PMID: 26940068 DOI: 10.1111/jfb.12930] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 01/29/2016] [Indexed: 06/05/2023]
Abstract
This study assessed the major histocompatibility complex (MHC) and neutral genetic variation and structure in two percid species, perch Perca fluviatilis and zander Sander lucioperca, in a unique brackish ecosystem, the Baltic Sea. In addition, to assess the importance of MHC diversity to disease susceptibility in these populations, comparisons were made to an introduced, disease susceptible, P. fluviatilis population in Australia. Eighty-three MHC class II B exon 2 variants were amplified: 71 variants from 92 P. fluviatilis samples, and 12 variants from 82 S. lucioperca samples. Microsatellite and MHC data revealed strong spatial genetic structure in S. lucioperca, but not P. fluviatilis, across the Baltic Sea. Both microsatellite and MHC data showed higher levels of genetic diversity in P. fluviatilis from the Baltic Sea compared to Australia, which may have facilitated the spread of an endemic virus, EHNV in the Australian population. The relatively high levels of genetic variation in the Baltic Sea populations, together with spatial genetic structure, however, suggest that there currently seems to be little risk of disease epidemics in this system. To ensure this remains the case in the face of ongoing environmental changes, fisheries and habitat disturbance, the conservation of local-scale genetic variation is recommended.
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Affiliation(s)
- L K Faulks
- Department of Ecology and Genetics - Animal Ecology, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Ö Östman
- Department of Aquatic Resources - Institute of Coastal Research, Swedish University of Agricultural Sciences, Skolvägen 6, 74242, Öregrund, Sweden
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11
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Grimholt U. MHC and Evolution in Teleosts. BIOLOGY 2016; 5:biology5010006. [PMID: 26797646 PMCID: PMC4810163 DOI: 10.3390/biology5010006] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/12/2016] [Accepted: 01/13/2016] [Indexed: 12/18/2022]
Abstract
Major histocompatibility complex (MHC) molecules are key players in initiating immune responses towards invading pathogens. Both MHC class I and class II genes are present in teleosts, and, using phylogenetic clustering, sequences from both classes have been classified into various lineages. The polymorphic and classical MHC class I and class II gene sequences belong to the U and A lineages, respectively. The remaining class I and class II lineages contain nonclassical gene sequences that, despite their non-orthologous nature, may still hold functions similar to their mammalian nonclassical counterparts. However, the fact that several of these nonclassical lineages are only present in some teleost species is puzzling and questions their functional importance. The number of genes within each lineage greatly varies between teleost species. At least some gene expansions seem reasonable, such as the huge MHC class I expansion in Atlantic cod that most likely compensates for the lack of MHC class II and CD4. The evolutionary trigger for similar MHC class I expansions in tilapia, for example, which has a functional MHC class II, is not so apparent. Future studies will provide us with a more detailed understanding in particular of nonclassical MHC gene functions.
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Affiliation(s)
- Unni Grimholt
- Department of Virology, Norwegian Veterinary Institute, Ullevaalsveien 68, Oslo N-0106, Norway.
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12
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Jiang J, Li C, Zhang Q, Wang X. Locus number estimation of MHC class II B in stone flounder and Japanese flounder. Int J Mol Sci 2015; 16:6000-17. [PMID: 25782161 PMCID: PMC4394517 DOI: 10.3390/ijms16036000] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 12/22/2014] [Accepted: 12/25/2014] [Indexed: 01/19/2023] Open
Abstract
Members of major histocompatibility complex (MHC) family are important in immune systems. Great efforts have been made to reveal their complicated gene structures. But many existing studies focus on partial sequences of MHC genes. In this study, by gene cloning and sequencing, we identified cDNA sequences and DNA sequences of the MHC class II B in two flatfishes, stone flounder (Kareius bicoloratus) and homozygous diploid Japanese flounder (Paralichthys olivaceus). Eleven cDNA sequences were acquired from eight stone flounder individuals, and most of the polymorphic sites distributed in exons 2 and 3. Twenty-eight alleles were identified from the DNA fragments in these eight individuals. It could be deduced from their Bayesian inference phylogenetic tree that at least four loci of MHC class II B exist in stone flounder. The detailed whole-length DNA sequences in one individual were analyzed, revealing that the intron length varied among different loci. Four different cDNA sequences were identified from one homozygous diploid Japanese flounder individual, implying the existence of at least four loci. Comparison of the cDNA sequences to the DNA sequence confirmed that six exons existed in this gene of Japanese flounder, which was a common feature shared by Pleuronectiformes fishes. Our results proved the multi-locus feature of MHC class II B. The sequences we obtained would provide detailed and systematic data for further research.
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Affiliation(s)
- Jiajun Jiang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China.
| | - Chunmei Li
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China.
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China.
| | - Xubo Wang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China.
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Grimholt U, Tsukamoto K, Azuma T, Leong J, Koop BF, Dijkstra JM. A comprehensive analysis of teleost MHC class I sequences. BMC Evol Biol 2015; 15:32. [PMID: 25888517 PMCID: PMC4364491 DOI: 10.1186/s12862-015-0309-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/16/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND MHC class I (MHCI) molecules are the key presenters of peptides generated through the intracellular pathway to CD8-positive T-cells. In fish, MHCI genes were first identified in the early 1990's, but we still know little about their functional relevance. The expansion and presumed sub-functionalization of cod MHCI and access to many published fish genome sequences provide us with the incentive to undertake a comprehensive study of deduced teleost fish MHCI molecules. RESULTS We expand the known MHCI lineages in teleosts to five with identification of a new lineage defined as P. The two lineages U and Z, which both include presumed peptide binding classical/typical molecules besides more derived molecules, are present in all teleosts analyzed. The U lineage displays two modes of evolution, most pronouncedly observed in classical-type alpha 1 domains; cod and stickleback have expanded on one of at least eight ancient alpha 1 domain lineages as opposed to many other teleosts that preserved a number of these ancient lineages. The Z lineage comes in a typical format present in all analyzed ray-finned fish species as well as lungfish. The typical Z format displays an unprecedented conservation of almost all 37 residues predicted to make up the peptide binding groove. However, also co-existing atypical Z sub-lineage molecules, which lost the presumed peptide binding motif, are found in some fish like carps and cavefish. The remaining three lineages, L, S and P, are not predicted to bind peptides and are lost in some species. CONCLUSIONS Much like tetrapods, teleosts have polymorphic classical peptide binding MHCI molecules, a number of classical-similar non-classical MHCI molecules, and some members of more diverged MHCI lineages. Different from tetrapods, however, is that in some teleosts the classical MHCI polymorphism incorporates multiple ancient MHCI domain lineages. Also different from tetrapods is that teleosts have typical Z molecules, in which the residues that presumably form the peptide binding groove have been almost completely conserved for over 400 million years. The reasons for the uniquely teleost evolution modes of peptide binding MHCI molecules remain an enigma.
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Affiliation(s)
| | - Kentaro Tsukamoto
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, 470-1192, Japan.
| | - Teruo Azuma
- Fisheries Technology Division, National Research Institute of Fisheries Engineering, 7620-7, Hasaki, Kamisu-shi, Ibaraki, Japan.
| | - Jong Leong
- Centre for Biomedical Research, Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, Canada.
| | - Ben F Koop
- Centre for Biomedical Research, Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, Canada.
| | - Johannes M Dijkstra
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, 470-1192, Japan.
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14
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Yu H, Yan QG, Wang ZB, Lu YJ, Xu MJ, Li H, Zhu XQ. MH II-DAB gene expression in grass carp Ctenopharyngodon idella (Valenciennes) after infection with the ciliate parasite, Ichthyophthirius multifiliis. JOURNAL OF FISH DISEASES 2014; 37:43-50. [PMID: 24131264 DOI: 10.1111/j.1365-2761.2012.01442.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 04/25/2012] [Accepted: 04/30/2012] [Indexed: 06/02/2023]
Abstract
The grass carp, Ctenopharyngodon idella (Valenciennes), is one of the most extensively aquacultured freshwater fish in China. However, because of the lack of effective control measures and the high-density culture environment, considerable economic losses are caused by infection of C. idella with the parasitic ciliate, Ichthyophthirius multifiliis. The major histocompatibility (MH) DAB gene belongs to antigen-presented genes in the class II genomic region, which is associated with parasite resistance. To understand the relationship of the DAB gene with I. multifiliis infection in grass carp, the expression profiles of MH II-DAB were studied in tissues using real-time quantitative polymerase chain reaction. The results showed that expression of the MH II-DAB gene was up-regulated in head kidney after I. multifiliis infection, and the expression peak appeared earlier in the study (case) group than in the control group. The obvious up-regulation peak of MH II-DAB gene was found at days 2 and 4 in skin; at 12 h to day 4 in spleen; at 12 h and days 1 and 6 in gill; and at day 10 in blood, whereas the MH II-DAB gene was down-regulated in liver and intestines after I. multifiliis infection. These results have implications for better understanding C. idella resistance to I. multifiliis infection.
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Affiliation(s)
- H Yu
- College of Life Science, Foshan University, Foshan, China
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15
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Bannai HP, Nonaka M. Comprehensive analysis of medaka major histocompatibility complex (MHC) class II genes: implications for evolution in teleosts. Immunogenetics 2013; 65:883-95. [PMID: 23989892 DOI: 10.1007/s00251-013-0731-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 08/19/2013] [Indexed: 12/29/2022]
Abstract
The major histocompatibility complex (MHC) class II molecules play central roles in adaptive immunity by regulating immune response via the activation of CD4 T cells. The full complement of the MHC class II genes has been elucidated only in mammalian species to date. To understand the evolution of these genes, we performed their first comprehensive analysis in nonmammalian species using a teleost, medaka (Oryzias latipes). Based on a database search, cDNA cloning, and genomic PCR, medaka was shown to possess five pairs of expressed class II genes, comprising one IIA and one IIB gene. Each pair was located on a different chromosome and was not linked to the class I genes. Only one pair showed a high degree of polymorphism and was considered to be classical class II genes, whereas the other four pairs were nonclassical. Phylogenetic analysis of all medaka class II genes and most reported teleost class II genes revealed that the IIA and IIB genes formed separate clades, each containing three well-corresponding lineages. One lineage contained three medaka genes and all known classical class II genes of Ostariophysi and Euteleostei and was presumed to be an original lineage of the teleost MHC class II genes. The other two lineages contained one nonclassical medaka gene each and some Euteleostei genes. These results indicate that multiple lineages of the teleost MHC class II genes have been conserved for hundreds of millions of years and that the tightly linked IIA and IIB genes have undergone concerted evolution.
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Affiliation(s)
- Hidemi P Bannai
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
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16
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MHC polymorphism and disease-resistance to Edwardsiella tarda in six turbot (Scophthalmus maximus) families. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s11434-012-5179-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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17
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Ren L, Yang Z, Wang T, Sun Y, Guo Y, Zhang Z, Fei J, Bao Y, Qin T, Wang J, Huang Y, Hu X, Zhao Y, Li N. Characterization of the MHC class II α-chain gene in ducks. Immunogenetics 2011; 63:667-78. [PMID: 21660591 DOI: 10.1007/s00251-011-0545-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 06/01/2011] [Indexed: 02/04/2023]
Abstract
In humans, classical MHC class II molecules include DQ, DR, and DP, which are similar in structure but consist of distinct α- and β-chains. The genes encoding these molecules are all located in the MHC class II gene region. In non-mammalian vertebrates such as chickens, only a single class II α-chain gene corresponding to the human DRA has been identified. Here, we report a characterization of the duck MHC class II α-chain (Anpl-DRA) encoding gene, which contains four exons encoding a typical signal peptide, a peptide-binding α1 domain, an immunoglobulin-like α2 domain, and Tm/Cyt, respectively. This gene is present in the duck genome as a single copy and is highly expressed in the spleen. Sequencing of cDNA and genomic DNA of the Anpl-DRA of different duck individuals/strains revealed low levels of genetic polymorphism, especially in the same strain, although most duck individuals have two different alleles. Otherwise, we found that the duck gene is located next to class II β genes, which is the same as in humans but different from the situation in chickens.
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Affiliation(s)
- Liming Ren
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China
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18
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Osborne MJ, Turner TF. Isolation and characterization of major histocompatibility class IIβ genes in an endangered North American cyprinid fish, the Rio Grande silvery minnow (Hybognathus amarus). FISH & SHELLFISH IMMUNOLOGY 2011; 30:1275-1282. [PMID: 21463692 DOI: 10.1016/j.fsi.2011.03.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 03/25/2011] [Accepted: 03/27/2011] [Indexed: 05/30/2023]
Abstract
The major histocompatibility complex (MHC) is a critical component of the adaptive immune response in vertebrates. Due to the role that MHC plays in immunity, absence of variation within these genes may cause species to be vulnerable to emerging diseases. The freshwater fish family Cyprinidae comprises the most diverse and species-rich group of freshwater fish in the world, but some are imperiled. Despite considerable species richness and the long evolutionary history of the family, there are very few reports of MHC sequences (apart from a few model species), and no sequences are reported from endemic North American cyprinids (subfamily Leuciscinae). Here we isolate and characterize the MH Class II beta genes from complementary DNA and genomic DNA of the non-model, endangered Rio Grande silvery minnow (Hybognathus amarus), a North American cyprinid. Phylogenetic reconstruction revealed two groups of divergent MH alleles that are paralogous to previously described loci found in deeply divergent cyprinid taxa including common carp, zebrafish, African large barb and bream. Both groups of alleles were under the influence of diversifying selection yet not all individuals had alleles belonging to both allelic groups. We concluded that the general organization and pattern of variation of MH class II genes in Rio Grande silvery minnow is similar to that identified in other cyprinid fishes studied to date, despite distant evolutionary relationships and evidence of a severe genetic bottleneck.
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Affiliation(s)
- Megan J Osborne
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, MSC 03-2020, 1 University of New Mexico, Albuquerque, NM 87131-0001, USA.
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19
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Abstract
The evolutionarily conserved immune system of the zebrafish (Danio rerio), in combination with its genetic tractability, position it as an excellent model system in which to elucidate the origin and function of vertebrate immune cells. We recently reported the existence of antigen-presenting mononuclear phagocytes in zebrafish, namely macrophages and dendritic cells (DCs), but have been impaired in further characterizing the biology of these cells by the lack of a specific transgenic reporter line. Using regulatory elements of a class II major histocompatibility gene, we generated a zebrafish reporter line expressing green fluorescent protein (GFP) in all APCs, macrophages, DCs, and B lymphocytes. Examination of mhc2dab:GFP; cd45:DsRed double-transgenic animals demonstrated that kidney mhc2dab:GFP(hi); cd45:DsRed(hi) cells were exclusively mature monocytes/macrophages and DCs, as revealed by morphologic and molecular analyses. Mononuclear phagocytes were found in all hematolymphoid organs, but were most abundant in the intestine and spleen, where they up-regulate the expression of inflammatory cytokines upon bacterial challenge. Finally, mhc2dab:GFP and cd45:DsRed transgenes mark mutually exclusive cell subsets in the lymphoid fraction, enabling the delineation of the major hematopoietic lineages in the adult zebrafish. These findings suggest that mhc2dab:GFP and cd45:DsRed transgenic lines will be instrumental in elucidating the immune response in the zebrafish.
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20
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Seifertová M, Šimková A. Structure, diversity and evolutionary patterns of expressed MHC class IIB genes in chub (Squalius cephalus), a cyprinid fish species from Europe. Immunogenetics 2010; 63:167-81. [DOI: 10.1007/s00251-010-0495-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 11/03/2010] [Indexed: 11/30/2022]
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21
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Diversity and evolution of MHII β genes in a non-model percid species—The Eurasian perch (Perca fluviatilis L.). Mol Immunol 2009; 46:3399-410. [DOI: 10.1016/j.molimm.2009.07.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Revised: 07/14/2009] [Accepted: 07/16/2009] [Indexed: 11/20/2022]
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22
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Xu TJ, Chen SL, Ji XS, Sha ZX. Molecular cloning, genomic structure, polymorphism and expression analysis of major histocompatibility complex class IIA and IIB genes of half-smooth tongue sole (Cynoglossus semilaevis). FISH & SHELLFISH IMMUNOLOGY 2009; 27:192-201. [PMID: 19442741 DOI: 10.1016/j.fsi.2009.04.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Revised: 04/16/2009] [Accepted: 04/21/2009] [Indexed: 05/27/2023]
Abstract
Major histocompatibility complex (MHC) genes play an important role in the immune response of vertebrates. Its function is to present foreign peptide to the T-cell. In order to study the function and molecular polymorphism of class II genes in teleost, the full lengths of MHC class IIA and IIB cDNA were cloned from half-smooth tongue sole by homology cloning and rapid amplification of cDNA ends polymerase chain reaction (RACE-PCR). Genomic organizations, molecular polymorphism, and expression profiles of class IIA and IIB were examined to study the function in fish. As in other teleost, four exons and three introns were identified in half-smooth tongue sole class IIA gene, five exons and four introns were identified in class IIB gene. The deduced amino acid sequence of class IIA had 27.3-69.8% identity with those of mammal and teleost. Nine class IIA alleles were identified from four individuals. Four different alleles observed in a single individual may infer the existence of two loci at least. The deduced amino acid sequence of class IIB had 7.9-71.9% identity with those of other species. Fifteen class IIB alleles were identified. Six different alleles observed in a single individual may suggest that there are at least three loci in class IIB genes. Real-time quantitative RT-PCR demonstrated that the MHC class IIA and IIB were ubiquitously expressed in twelve normal tissues. Challenge of half-smooth tongue sole with the pathogenic bacteria, Vibrio anguillarum, resulted in significant changes in the expression of MHC IIA and IIB mRNA in three tissues.
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Affiliation(s)
- Tian-Jun Xu
- Key Lab for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266071 Qingdao, China
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23
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Croisetière S, Tarte PD, Bernatchez L, Belhumeur P. Identification of MHC class IIβ resistance/susceptibility alleles to Aeromonas salmonicida in brook charr (Salvelinus fontinalis). Mol Immunol 2008; 45:3107-16. [PMID: 18455800 DOI: 10.1016/j.molimm.2008.03.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Revised: 03/07/2008] [Accepted: 03/10/2008] [Indexed: 10/22/2022]
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24
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Blais J, Rico C, van Oosterhout C, Cable J, Turner GF, Bernatchez L. MHC adaptive divergence between closely related and sympatric African cichlids. PLoS One 2007; 2:e734. [PMID: 17710134 PMCID: PMC1939875 DOI: 10.1371/journal.pone.0000734] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Accepted: 07/05/2007] [Indexed: 12/04/2022] Open
Abstract
Background The haplochromine cichlid species assemblages of Lake Malawi and Victoria represent some of the most important study systems in evolutionary biology. Identifying adaptive divergence between closely-related species can provide important insights into the processes that may have contributed to these spectacular radiations. Here, we studied a pair of sympatric Lake Malawi species, Pseudotropheus fainzilberi and P. emmiltos, whose reproductive isolation depends on olfactory communication. We tested the hypothesis that these species have undergone divergent selection at MHC class II genes, which are known to contribute to olfactory-based mate choice in other taxa. Methodology/Principal Findings Divergent selection on functional alleles was inferred from the higher genetic divergence at putative antigen binding sites (ABS) amino acid sequences than at putatively neutrally evolving sites at intron 1, exon 2 synonymous sequences and exon 2 amino acid residues outside the putative ABS. In addition, sympatric populations of these fish species differed significantly in communities of eukaryotic parasites. Conclusions/Significance We propose that local host-parasite coevolutionary dynamics may have driven adaptive divergence in MHC alleles, influencing odor-mediated mate choice and leading to reproductive isolation. These results provide the first evidence for a novel mechanism of adaptive speciation and the first evidence of adaptive divergence at the MHC in closely related African cichlid fishes.
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Affiliation(s)
- Jonatan Blais
- Département de Biologie, Québec-Océan, Université Laval, Quebec, Québec, Canada
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Sevilla, Spain
- Department of Biological Sciences, University of Hull, Hull, United Kingdom
| | - Ciro Rico
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Sevilla, Spain
| | | | - Joanne Cable
- School of Biological Sciences, Cardiff University, Cardiff, United Kingdom
| | - George F. Turner
- Department of Biological Sciences, University of Hull, Hull, United Kingdom
| | - Louis Bernatchez
- Département de Biologie, Québec-Océan, Université Laval, Quebec, Québec, Canada
- * To whom correspondence should be addressed. E-mail:
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25
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Zhang YX, Chen SL, Liu YG, Sha ZX, Liu ZJ. Major histocompatibility complex class IIB allele polymorphism and its association with resistance/susceptibility to Vibrio anguillarum in Japanese flounder (Paralichthys olivaceus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2006; 8:600-10. [PMID: 16874444 DOI: 10.1007/s10126-005-6185-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2005] [Accepted: 04/25/2006] [Indexed: 05/11/2023]
Abstract
The full length of major histocompatibility complex (MHC) class IIB cDNA was cloned from a Chinese population of Paralichthys olivaceus by homology cloning and rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR). The MHC IIB genomic sequence is 1,864 bp long and consists of 34-bp 5'UTR, 741-bp open reading frame, 407-bp 3'UTR, 96-bp intron1, 392-bp intron2, 85-bp intron3, and 109-bp intron4. Phylogenetic analysis showed that the putative MHC class IIB amino acid of the Chinese P. olivaceus shared 28.3% to 85.4% identity with that of the reported MHC class IIB in other species. A significant association between MHC IIB polymorphism and disease resistance/susceptibility was found in Chinese P. olivaceus. Thirteen different MHC IIB alleles were identified among 411 clones from 84 individuals. Among the 280 (268) nucleotides, 32 (11.4%) nucleotide positions were variable. Most alleles such as alleles a, b, c, d, e, f, j, k, i, m were commonly found in both resistant and susceptible stock. Via chi2 test, allele d was significantly more prevalent in individuals from susceptible stock than from resistant stock, and their percentages were 23.80% and 7.14%, respectively. In addition, allele g occurred in 9 and allele h in 4 of 42 resistant individuals that were not present in the susceptible stock; their percentages were 21.4% and 9.52%, respectively. Although allele l was found only in 8 individuals from the susceptible stock, its percentage is 19.05%.
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Affiliation(s)
- Y X Zhang
- Key Lab for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266071, Qingdao, People's Republic of China
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26
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Zhang YX, Chen SL. Molecular identification, polymorphism, and expression analysis of major histocompatibility complex class IIA and B genes of turbot (Scophthalmus maximus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2006; 8:611-23. [PMID: 16832747 DOI: 10.1007/s10126-005-6174-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2005] [Accepted: 04/29/2006] [Indexed: 05/10/2023]
Abstract
Major histocompatibility complex (MHC) class II has a central role in the adaptive immune system by presenting foreign peptides to the T-cell receptor. The full lengths of MHC class II A and B cDNA were cloned from turbot by homology cloning and rapid amplification of cDNA ends polymerase chain reaction (RACE PCR), and genomic organization, molecular polymorphism, and expression of turbot class IIB gene were examined to study the function of class IIB gene in fish. The deduced amino acid sequence of turbot class II A (GenBank accession no.DQ001730) and turbot class IIB (GenBank accession no. DQ094170) had 69.8%, 67.6%, 65.5%, 59.2%, 54.5%, 52.8%, 46.2%, 46.6%, 28.3%, 28.5%, 22.2% identity and 71.5%, 70.7%, 67.1%, 68.4%, 46.7%, 53.5%, 46.7%, 50.0%, 25.2%, 29.2%, 27.6% identity with those of Japanese flounder, striped sea bass, red sea bream, cichlid, rainbow trout, Atlantic salmon, carp, zebrafish, nurse shark, mouse and human, respectively. Eleven class IIB alleles were identified from three turbot individuals. The amino acid sequence of turbot class IIB designated as Scma-DAB*0101 had 86.9%, 88.6%, 88.6%, 89.4%, 87.8%, 86.9%, 84.1%, 86.5%, 87.3%, 77.1%, and 86.9% identity with those of turbot class IIB 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 (Scma-DAB*0201- Scma-DAB*1201), respectively. Six different class IIB alleles observed in a single individual may infer the existence of three loci at least. Semiquantitative reverse transcriptase PCR (RT-PCR) demonstrated that turbot class IIA and B were ubiquitously expressed in normal tissues. Challenge of turbot with pathogenic bacteria, Vibrio anguillarum, resulted in a significant decrease in the expression of MHC class IIB mRNA from 24 h to 48 h after infection in liver and head kidney, and a significant decrease from 24 h to 72 h after infection in spleen, followed by an increase after 96 h, respectively.
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Affiliation(s)
- Yu-Xi Zhang
- Key Lab for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
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27
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Abstract
Transplantable zebrafish tumors are a novel and very promising model in cancer research. However, further progress in this field has been contained by a lack of true inbred lines in zebrafish. To overcome this problem, we generated two lines of homozygous diploid clonal zebrafish lines (i.e., CB1 and CW1), which allowed us to carry out transplantation of any tissue, including tumors, from one fish to another within a line without rejection of the graft. The primary tumors in CB1 fish were induced by N-nitrosodiethylamine (DEN). The histologic analysis of these tumors revealed different types of hepatocellular carcinomas, hepatoblastomas, hepatoma, cholangiocarcinoma, and pancreatic carcinoma. Four spontaneous acinar cell carcinomas of pancreas were also found in 10- to 18-month-old CB1 fish. Small pieces of tissue or cell suspensions of either DEN-induced or spontaneous tumors were serially transplanted into the peritoneal cavity of syngeneic fish at different stages of development from 5-day-old larvae to adult fish. The development of grossly visible tumors occurred from 2 weeks to 3 months after tumor grafting and grew either as solitary smooth nodules or as an amorphous jelly-like mass infiltrating abdominal organs. The majority of tumors were also successfully transplanted to isogeneic (F1 generation from crossing CB1 x CW1) fish. At the present time, 19 transplantable zebrafish tumor lines have been generated and maintained for as long as 3 to 25 passages. This model provides a novel tool for studying experimental tumor biology and therapy and will become a cost effective system for high throughput screening of anticancer drugs.
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Affiliation(s)
- Igor V Mizgireuv
- Laboratory of Genetic Toxicology, N.N. Petrov Research Institute of Oncology, St. Petersburg, Russia
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28
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Ottová E, Simková A, Martin JF, de Bellocq JG, Gelnar M, Allienne JF, Morand S. Evolution and trans-species polymorphism of MHC class IIbeta genes in cyprinid fish. FISH & SHELLFISH IMMUNOLOGY 2005; 18:199-222. [PMID: 15519540 DOI: 10.1016/j.fsi.2004.07.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2004] [Revised: 06/21/2004] [Accepted: 07/14/2004] [Indexed: 05/24/2023]
Abstract
The polymorphism of DAB genes encoding MHC IIbeta was investigated in 11 cyprinid species from central Europe. The species belonged to four subfamilies: Cyprininae, Tincinae, Gobioninae and Leuciscinae. Two paralogous groups of sequences, DAB1 and DAB3, were recognised according to the similarity of their nucleotide and amino-acid sequences and from phylogenetic analyses using either partial exon 2 or partial exon 3 sequences. A high allelic variability among species was found for exon 2, indicating extensive MHC polymorphism. Time divergence estimation supports the separation of DAB1 and DAB3 groups predating the separation into fish subfamilies, and a cyprinid origin of the DAB genes. Phylogenetic trees using exon 2 support the hypothesis of trans-species polymorphism, which appears to be limited to the subfamily level, i.e. the presence of sequences from different species in the same allelic group was more often recognised within subfamilies Cyprininae and Leuciscinae than between them. Phylogenetic trees using exon 3 reflect the phylogenetic patterns previously found for Cyprinidae systematics. Specific nucleotides and amino-acids in exon 3 that separate both subfamilies, as well as the species within the Cyprininae subfamily were observed. A lack of segregation in leuciscin species was recognised and the alleles of different leuciscin species tend to share similar motifs in exon 3. This could be explained by the ancient and complicated dispersion history of Cyprininae and the radiation of Leuciscinae. The effects of selective pressures were investigated: (1) within species, (2) among lineages, and (3) among sites. From intraspecific analyses, exon 2 sequences were identified as the targets of diversifying selection, whilst the evolution of exon 3 seems to be under the influence of purifying selection. The analyses among lineages indicate positive selection in many branches when using exon 2, therefore confirming trans-species polymorphism, whilst the DAB lineages of exon 3 are potentially submitted to purifying selection to some extent. Moreover, our results suggest the secondary acquisition of function of DAB1 group after duplication. The analyses among sites reveal that exon 2 exhibits sites under positive selection mostly corresponding to the putative PBR sites involved in the alpha-helix structure of the protein.
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Affiliation(s)
- Eva Ottová
- Department of Zoology and Ecology, Faculty of Science, Masaryk University, Kotlárská 2, 61137 Brno, Czech Republic
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29
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Salomonsen J, Marston D, Avila D, Bumstead N, Johansson B, Juul-Madsen H, Olesen GD, Riegert P, Skjødt K, Vainio O, Wiles MV, Kaufman J. The properties of the single chicken MHC classical class II alpha chain ( B-LA) gene indicate an ancient origin for the DR/E-like isotype of class II molecules. Immunogenetics 2003; 55:605-14. [PMID: 14608490 DOI: 10.1007/s00251-003-0620-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2003] [Revised: 10/09/2003] [Indexed: 10/26/2022]
Abstract
In mammals, there are MHC class II molecules with distinctive sequence features, such as the classical isotypes DR, DQ and DP. These particular isotypes have not been reported in non-mammalian vertebrates. We have isolated the class II (B-L) alpha chain from outbred chickens as the basis for the cloning and sequencing of the cDNA. We found only one class II alpha chain transcript, which bears the major features of a classical class II alpha sequence, including the critical peptide-binding residues. The chicken sequence is more similar to human DR than to the DQ, DP, DO or DM isotypes, most significantly in the peptide-binding alpha(1) domain. The cDNA and genomic DNA sequences from chickens of diverse origins show few alleles, which differ in only four nucleotides and one amino acid. In contrast, significant restriction fragment length polymorphism is detected by Southern blot analysis of genomic DNA, suggesting considerable diversity around the gene. Analysis of a large back-cross family indicates that the class II alpha chain locus ( B-LA) is located roughly 5.6 cM from the MHC locus, which encodes the classical class II beta chains. Thus the chicken class II alpha chain gene is like the mammalian DR and E isotypes in three properties: the presence of the critical peptide-binding residues, the low level of polymorphism and sequence diversity, and the recombinational separation from the class II beta chain genes. These results indicate that the sequence features of this lineage are both functionally important and at least 300 million years old.
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Affiliation(s)
- Jan Salomonsen
- Department of Virology and Immunology, Royal Veterinary and Agricultural University, Stigbøjlen 7, C 1870, Frederiksberg, Denmark
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Belov K, Lam MKP, Hellman L, Colgan DJ. Evolution of the major histocompatibility complex: Isolation of class II beta cDNAs from two monotremes, the platypus and the short-beaked echidna. Immunogenetics 2003; 55:402-11. [PMID: 12942212 DOI: 10.1007/s00251-003-0598-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2003] [Revised: 07/24/2003] [Indexed: 11/29/2022]
Abstract
Extant mammals are composed of three lineages: the eutherians, the marsupials and the monotremes. The majority of the mammalian major histocompatibility complex (MHC) data is based on the eutherian mammals, which generally have three classical MHC class II beta chain gene clusters - DRB, DQB and DPB, as well as the non-classical DMB and DOB. Marsupial DMB, DAB and DBB have been characterised. Confusion still surrounds the relationship of the marsupial DAB and DBB genes with the classical eutherian class II clusters. Here we present the first monotreme MHC class II beta chain sequences. Four MHC class II beta chain sequences were isolated from a spleen cDNA library from the short-beaked echidna, and one from a spleen cDNA library from platypus using a brushtail possum DAB probe. Given the non-orthologous relationship of the monotreme sequences with marsupial and eutherian beta chain clusters, we recommend that the five new monotreme sequences be assigned the nomenclature 'DZB', signifying the description of a new mammalian beta chain cluster. Our analysis suggests that all mammalian beta chain sequences (except DMB) evolved from a common ancestor. Maximum likelihood analysis places the monotreme beta chain sequences at the base of the mammalian clade, indicating their ancestral status. However, within the mammalian clade, monophyletic clades are not robust, and elucidation of the order of gene duplication that gave rise to the present-day gene clusters is not yet possible.
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Affiliation(s)
- Katherine Belov
- Evolutionary Biology Unit, Australian Museum, 6 College St, Sydney, NSW 2010, Australia.
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31
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Abstract
The Human Genome Project transformed the quest of more than 50 years to understand the major histocompatibility complex (Mhc). The sequence of the Mhc from human and mouse, together with a large amount of sequence and mapping information from several other species, allows us to draw general conclusions about the organization and origin of this crucial part of the immune system. The Mhc is a mosaic of stretches formed by conserved and nonconserved genes. Surprisingly, of the approximately 3.6-Mb Mhc, the stretches that encode the class I and class II genes, which epitomize the Mhc, are the least conserved part, whereas the approximately 1.7-Mb stretches that encode at least 115 other genes are highly conserved. We summarize the available data to answer the questions (a) What is the Mhc? and (b) How can we define it in a general, not species-specific, way? Knowing what is essential and what is incidental helps us understand the fundamentals of the Mhc, and defining the species differences makes the model organisms more useful.
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Affiliation(s)
- Attila Kumánovics
- Center for Immunology University of Texas Southwestern Medical Center, Dallas 75390-9050, USA.
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Syed M, Vestrheim O, Mikkelsen B, Lundin M. Isolation of the promoters of Atlantic salmon MHCII genes. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2003; 5:253-260. [PMID: 14502397 DOI: 10.1007/s10126-002-0063-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2002] [Accepted: 06/13/2002] [Indexed: 05/24/2023]
Abstract
The major histocompatibility complex class II (MHCII) has a central role in the immune response of vertebrates with its function of presenting antigenic peptides to the T-cell receptors. We have isolated the promoters and intron 1 of MHCIIalpha and MHCIIbeta genes of Atlantic salmon. To isolate these promoters, we constructed an Atlantic salmon ( Salmo salar) promoter finder kit (analogous to the commercially available "human promoter finder kit"). By nucleotide sequence alignment of known MHCII promoter regions, we identified the 3 conserved regulatory X, X2, and Y boxes in the salmon promoters. The W box was not found. In contrast, a salmon-specific putative W box was identified. Both of the isolated Atlantic salmon MHCIIalpha and beta promoters (included in patent applications by Genomar A/S, Oslo, Norway) were found to be functional since they both gave positive yellow fluorescence protein signal when inserted as promoters in the pEYFP-1 reporter plasmid and transfected into the salmon head kidney cell line (SHK-1).
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Affiliation(s)
- Mohasina Syed
- Department of Morphology, Genetics and Aquatic Biology, Norwegian School of Veterinary Science, P.O. Box. 8146-Dep, N-0033 Oslo, Norway.
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33
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Noakes MA, Reimer T, Phillips RB. Genotypic characterization of an MHC class II locus in lake trout ( Salvelinus namaycush) from Lake Superior by single-stranded conformational polymorphism analysis and reference strand-mediated conformational analysis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2003; 5:270-278. [PMID: 14502399 DOI: 10.1007/s10126-002-0079-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2002] [Accepted: 07/03/2002] [Indexed: 05/24/2023]
Abstract
This study compares the genotypic information provided by reference strand-mediated conformational analysis and single-stranded confirmational polymorphism (SSCP) analysis for the major histocompatibility complex (MHC) II locus in lake trout. For this study 80 wild-caught animals from the Apostle Islands of Lake Superior were genotyped using both RSCA and SSCP analysis. Their genotypes were recorded using both methods and compared. The genotypic information provided by the 2 methods was essentially the same although some inconsistencies were observed. Both methods detected approximately 65 genotypes, and both were able to distinguish heterozygous and homozygous animals. The analyses determined that only approximately 20% of alleles were shared between 2 morphologically different populations within the sample set, and identified the dominant alleles. SSCP analysis was quicker, simple, and more robust than RSCA. SSCP analysis using fluorescence technologies could be the method of choice for future genotypic analysis of the MHC II locus in salmonids.
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Affiliation(s)
- Marc A Noakes
- Washington State University, 14204 NE Salmon Creek Avenue, Vancouver, WA 98686, USA
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Davis JM, Clay H, Lewis JL, Ghori N, Herbomel P, Ramakrishnan L. Real-time visualization of mycobacterium-macrophage interactions leading to initiation of granuloma formation in zebrafish embryos. Immunity 2002; 17:693-702. [PMID: 12479816 DOI: 10.1016/s1074-7613(02)00475-2] [Citation(s) in RCA: 383] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Infection of vertebrate hosts with pathogenic Mycobacteria, the agents of tuberculosis, produces granulomas, highly organized structures containing differentiated macrophages and lymphocytes, that sequester the pathogen. Adult zebrafish are naturally susceptible to tuberculosis caused by Mycobacterium marinum. Here, we exploit the optical transparency of zebrafish embryos to image the events of M. marinum infection in vivo. Despite the fact that the embryos do not yet have lymphocytes, infection leads to the formation of macrophage aggregates with pathological hallmarks of granulomas and activation of previously identified granuloma-specific Mycobacterium genes. Thus, Mycobacterium-macrophage interactions can initiate granuloma formation solely in the context of innate immunity. Strikingly, infection can redirect normal embryonic macrophage migration, even recruiting macrophages seemingly committed to their developmentally dictated tissue sites.
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Affiliation(s)
- J Muse Davis
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
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Cohen S. Strong positive selection and habitat-specific amino acid substitution patterns in MHC from an estuarine fish under intense pollution stress. Mol Biol Evol 2002; 19:1870-80. [PMID: 12411596 DOI: 10.1093/oxfordjournals.molbev.a004011] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Population-level studies using the major histocompatibility complex (Mhc) have linked specific alleles with specific diseases, but data requirements are high and the power to detect disease association is low. A novel use of Mhc population surveys involves mapping allelic substitutions onto the inferred structural molecular model to show functional differentiation related to local selective pressures. In the estuarine fish Fundulus heteroclitus, populations experiencing strong differences in antigenic challenges show significant differences in amino acid substitution patterns that are reflected as variation in the structural location of changes between populations. Fish from a population genetically adapted to severe chemical pollution also show novel patterns of DNA substitution at a highly variable Mhc class II B locus including strong signals of positive selection at inferred antigen-binding sites and population-specific signatures of amino acid substitution. Heavily parasitized fish from an extreme PCB-contaminated (U.S. Environmental Protection Agency Superfund) site show enhanced population-specific substitutions in the a-helix portion of the inferred antigen-binding region. In contrast, fish from an unpolluted site show a significantly different pattern focused on the first strand of the B-pleated sheet. Whether Mhc population profile differences represent the direct effects of chemical toxicants or indirect parasite-mediated selection, the result is a composite habitat-specific signature of strong selection and evolution affecting the genetic repertoire of the major histocompatibility complex.
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Affiliation(s)
- Sarah Cohen
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, 02138, USA.
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Bartl S. New major histocompatibility complex class IIB genes from nurse shark. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2002; 484:1-11. [PMID: 11418976 DOI: 10.1007/978-1-4615-1291-2_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Affiliation(s)
- S Bartl
- Moss Landing Marine Laboratories, P.O. Box 450, Moss Landing, CA 95039-0450, USA
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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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Grimholt U, Getahun A, Hermsen T, Stet RJ. The major histocompatibility class II alpha chain in salmonid fishes. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2000; 24:751-763. [PMID: 10906388 DOI: 10.1016/s0145-305x(00)00034-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In this study the characterisation of the Atlantic salmon (MhcSasa-DAA) and rainbow trout (MhcOnmy-DAA) class II alpha chain cDNA sequences is presented. The DAA sequences from these two salmonid species showed a high degree of similarity, although the Onmy-DAA(*)03 cDNA sequence differed in the cytoplasmic region. Interestingly, the Onmy-DAA(*)02 sequence has lost the second cysteine in the alpha-1 domain. However, another cysteine is present in this sequence 7 positions downstream of the cysteine which is substituted for a leucine. Despite a thorough search, only a single locus of expressed class II alpha chain sequences was identified in both salmonid species. Amplification by PCR and sequencing of the alpha-1 domain from genomic DNA of three Atlantic salmon, identified four different variants assumed to have derived from this single locus. Two of these variants originated from one individual and are likely functional alleles.
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Affiliation(s)
- U Grimholt
- Department of Morphology, Genetics and Aquatic Biology, Section of Genetics, Norwegian School of Veterinary Science, Oslo, Norway.
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Sültmann H, Murray BW, Klein J. Identification of seven genes in the major histocompatibility complex class I region of the zebrafish. Scand J Immunol 2000; 51:577-85. [PMID: 10849368 DOI: 10.1046/j.1365-3083.2000.00729.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Physical linkage of genes whose products are involved in similar physiological pathways may have functional significance. The identification of conserved gene linkage in distantly related organisms can therefore strengthen the hypothesis of selection acting towards keeping genes on a chromosome. We used the cDNA selection technique and the polymerase chain reaction (PCR) with generic primers for the identification of new genes on the genomic clones bearing the major histocompatibility complex (Mhc) class I genes of the zebrafish (Danio rerio). We found six new genes (BING1, DAXX, TAPBP, KNSL2, TAP2B and KE6) whose orthologues are known to be linked to the Mhc class II region in humans and mice. In addition, a new zebrafish Mhc class I gene, termed Dare-UFA, was detected. By contrast, a search for the human leucocyte antigen (HLA)-linked BING3, KE3 and SACM2L genes revealed that these loci are not located on the class I clones of the zebrafish. The zebrafish class I region contains repetitive elements with similarity to the DANA, SATA and LINE repeats, as well as Tc1 transposable elements. Our findings indicate a high degree of linkage conservation between the zebrafish class I and the mammalian class II regions.
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Affiliation(s)
- H Sültmann
- Max-Planck-Institut für Biologie, Abteilung Immungenetik, Tübingen, Germany
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Venkatesh B, Ning Y, Brenner S. Late changes in spliceosomal introns define clades in vertebrate evolution. Proc Natl Acad Sci U S A 1999; 96:10267-71. [PMID: 10468597 PMCID: PMC17877 DOI: 10.1073/pnas.96.18.10267] [Citation(s) in RCA: 175] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The evolutionary origin of spliceosomal introns has been the subject of much controversy. Introns are proposed to have been both lost and gained during evolution. If the gain or loss of introns are unique events in evolution, they can serve as markers for phylogenetic analysis. We have made an extensive survey of the phylogenetic distribution of seven spliceosomal introns that are present in Fugu genes, but not in their mammalian homologues; we show that these introns were acquired by actinopterygian (ray-finned) fishes at various stages of evolution. We have also investigated the intron pattern of the rhodopsin gene in fishes, and show that the four introns found in the ancestral chordate rhodopsin gene were simultaneously lost in a common ancestor of ray-finned fishes. These changes in introns serve as excellent markers for phylogenetic analysis because they reliably define clades. Our intron-based cladogram establishes the difficult-to-ascertain phylogenetic relationships of some ray-finned fishes. For example, it shows that bichirs (Polypterus) are the sister group of all other extant ray-finned fishes.
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Affiliation(s)
- B Venkatesh
- Marine Molecular Genetics Laboratory, Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609.
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Ristow SS, Grabowski LD, Thompson SM, Warr GW, Kaattari SL, de Avila JM, Thorgaard GH. Coding sequences of the MHC II beta chain of homozygous rainbow trout (Oncorhynchus mykiss). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 1999; 23:51-60. [PMID: 10220068 DOI: 10.1016/s0145-305x(98)00039-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Six lines of homozygous rainbow trout (Oncorhynchus mikiss) from different genetic and geographical backgrounds have been produced as aquatic models for biomedical research by the chromosome set manipulation techniques of androgenesis and gynogenesis. Messenger RNA from spleens was extracted. and the MHC II B cDNA sequences, amplified by RT PCR, were cloned into plasmids. Sequences of the MHC II beta2 domains were highly conserved between the different plasmids from the same and different lines of trout. Most of the variability among sequences was found in the amino terminal half of the beta1 domain, which corresponds with the peptide binding region of the MHC II molecule. This diversity suggests that the different lines of trout may exhibit differences in immune response. Rainbow trout MHC II B sequences were similar to the MHC II B sequences of the Pacific salmon (O. gorbuscha, O. tshawytscha, O. nerka, O. miasou, O. kisutch). Southern blot analysis performed on the restricted DNA of the OSU and Hot Creek trout, and the doubled haploid progeny produced by androgenesis from OSU x Hot Creek hybrids indicates that two distinct genes encode the MHC II B sequences and that these genes are unlinked.
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Affiliation(s)
- S S Ristow
- Department of Animal Sciences, Washington State University, Pullman 99164-6351, USA.
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McConnell TJ, Godwin UB, Cuthbertson BJ. Expressed major histocompatibility complex class II loci in fishes. Immunol Rev 1998; 166:294-300. [PMID: 9914920 DOI: 10.1111/j.1600-065x.1998.tb01270.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptides derived from parasites are presented to T helper cells by major histocompatibility complex (MHC) class II alpha beta heterodimeric cell-surface molecules. In mice and humans, the genes encoding these antigen-presenting molecules are known to be polymorphic and polygenic. Multiple loci for MHC class II A and B genes are proposed to allow for an increased peptide-binding repertoire. The multigenic nature of expressed MHC class II loci and the differences between these loci in fishes are the focus of this review. Particular emphasis is placed on an evolutionary comparison of class II B loci, especially two class II B loci that have undergone dramatic changes from one another suggesting an ancestral gene duplication event that took place at an early stage in the evolution of teleosts. The number of functional class II alpha beta heterodimers may have a profound impact on the organisms ability to battle constantly evolving parasitic infections.
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Affiliation(s)
- T J McConnell
- Department of Biology, East Carolina University, Greenville, North Carolina, USA.
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Abstract
Similarity in structural features would argue that sharks possess class I, class IIA and class IIB genes, coding for classical peptide-presenting molecules, as well as non-classical class I genes. Some aspects of shark major histocompatibility complex genes are similar to teleost genes and others are similar to tetrapod genes. Shark class I genes form a monophyletic group, as also seen for tetrapods, but the classical and nonclassical genes form two orthologous clades, as seen for teleosts. Teleost class I genes arose independently at least four different times with the nonclassical genes of ray-finned fishes and all the shark and lobe-finned fish class I genes forming 1 clade. The ray-finned fish classical class I genes arose separately. In phylogenetic trees of class II alpha 2 and beta 2 domains, the shark and tetrapod genes cluster more closely than the teleost genes and, unlike the teleost sequences, the class II alpha 1 domains of sharks and tetrapods lack cysteines. On the other hand, both shark and teleost genes display sequence motifs in the antigen-binding cleft that have persisted over very long time periods. The similarities may reflect common selective pressures on species in aqueous environments while differences may be due to different evolutionary rates.
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Affiliation(s)
- S Bartl
- Moss Landing Marine Laboratories, CA 95039-0450, USA.
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Kasahara M. What do the paralogous regions in the genome tell us about the origin of the adaptive immune system? Immunol Rev 1998; 166:159-75. [PMID: 9914911 DOI: 10.1111/j.1600-065x.1998.tb01261.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
During the last decade, our understanding of the immune system of ectothermic vertebrates has advanced significantly. It is now clear that all jawed vertebrates are equipped with the adaptive immune system characterized by the MHC molecules and the rearranging receptors. In contrast, there is no molecular evidence that suggests the existence of adaptive immunity in jawless vertebrates. How did the adaptive immune system emerge? Our recent work suggests that one of the driving forces that enabled the emergence of the adaptive immune system was one or more genome-wide or large-scale chromosomal duplications presumed to have taken place in a common ancestor of jawed vertebrates.
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Affiliation(s)
- M Kasahara
- Department of Biosystems Science, Graduate University for Advanced Studies, Hayama, Japan.
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Stet RJ, Kruiswijk CP, Saeij JP, Wiegertjes GF. Major histocompatibility genes in cyprinid fishes: theory and practice. Immunol Rev 1998; 166:301-16. [PMID: 9914921 DOI: 10.1111/j.1600-065x.1998.tb01271.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The first teleostean MHC sequences were described for carp. Subsequent studies in a number of cyprinid fishes showed that the class I sequences of these fishes are of particular interest. Two distinct lineages (Cyca-Z and Cyca-U) are found in the common and ginbuna crucian carp, but only the U lineage is present in zebrafish and other non-cyprinid species. The presence of the Z lineage is hypothesised to be the result of an allotetraploidisation event. Both phylogenetic analyses and amino acid sequence comparisons suggest that Cyca-Z sequences are non-classical class I sequences, probably similar to CD1. The comprehensive phylogenetic analyses of these sequences revealed different phylogenetic histories of the exons encoding the extracellular domains. The MHC genes were studied in laboratory and natural models. The natural model addressed the evolution of MHC genes in a Barbus species flock. Sequence analysis of class I and class II supported the species designation of the morphotypes present in the lake, and as a consequence the trans-species hypothesis of MHC polymorphism. The laboratory model involves the generation of gynogenetic clones, which can be divergently selected for traits such as high and low antibody response. The role of MHC molecules can be investigated further by producing a panel of isogenic lines.
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Affiliation(s)
- R J Stet
- Cell Biology and Immunology Group, Wageningen Institute of Animal Sciences, Wageningen University and Research Centre, The Netherlands.
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McConnell TJ, Godwin UB, Norton SF, Nairn RS, Kazianis S, Morizot DC. Identification and mapping of two divergent, unlinked major histocompatibility complex class II B genes in Xiphophorus fishes. Genetics 1998; 149:1921-34. [PMID: 9691047 PMCID: PMC1460285 DOI: 10.1093/genetics/149.4.1921] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have isolated two major histocompatibility complex (MHC) class II B genes from the inbred fish strain Xiphophorus maculatus Jp 163 A. We mapped one of these genes, designated here as DXB, to linkage group III, linked to a malic enzyme locus, also syntenic with human and mouse MHC. Comparison of genomic and cDNA clones shows the gene consists of six exons and five introns. The encoded beta1 domain has three amino acids deleted and a cytoplasmic tail nine amino acids longer than in other teleost class II beta chains, more similar to HLA-DRB, clawed frog Xela-F3, and nurse shark Gici-B. Key residues for disulfide bonds, glycosylation, and interaction with alpha chains are conserved. These same features are also present in a swordtail (Xiphophorus helleri) genomic DXB PCR clone. A second type of class II B clone was amplified by PCR from X. maculatus and found to be orthologous to class II genes identified in other fishes. This DAB-like gene is 63% identical to the X. maculatus DXB sequence in the conserved beta2-encoding exon and was mapped to new unassigned linkage group LG U24. The DXB gene, then, represents an unlinked duplicated locus not previously identified in teleosts.
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Affiliation(s)
- T J McConnell
- Department of Biology, East Carolina University, Greenville, North Carolina 27858-4353, USA
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Kuroda N, Wada H, Naruse K, Simada A, Shima A, Sasaki M, Nonaka M. Molecular cloning and linkage analysis of the Japanese medaka fish complement Bf/C2 gene. Immunogenetics 1996; 44:459-67. [PMID: 8824158 DOI: 10.1007/bf02602808] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Evolutionary studies of complement factor B (Bf) and C2 in lower vertebrates have revealed the presence of the Bf/C2 common ancestor-like molecule in lamprey (cyclostome) and the Bf molecule encoded by the duplicated genes closely linked to the major histocompatibility complex (MHC) in Xenopus (amphibian). To further define when Bf/C2 gene duplication occurred and when linkage between the Bf/C2 gene and the MHC was established, we amplified the Bf/C2 sequences in teleost, the Japanese medaka (Oryzias latipes), by reverse transcription - polymerase chain reaction with primers corresponding to the common amino acid sequences shared by mammalian Bf and C2. Only a single molecular species has been amplified, and the corresponding cDNA clones were isolated from the liver cDNA library. The longest insert contained 2384 nucleotides with an open reading frame of 754 residues. The deduced amino acid sequence showed 33.6% and 34.1% overall identity with the human Bf and C2 sequences, respectively, hence this clone was named medaka Bf/C2. The single-copy medaka Bf/C2 gene had exactly the same exon-intron organization as the mammalian Bf and C2 genes, and spanned about 8 kilobases. The Bf/C2 locus was mapped to the close proximity (2.9 cM) of the superoxide dismutase locus on the linkage group XX by the use of a restriction site polymorphism between two inbred strains of the medaka.
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Affiliation(s)
- N Kuroda
- Department of Biochemistry, Nagoya City University Medical School, Mizuho-Ku, Nagoya 467, Japan
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Miller KM, Withler RE. Sequence analysis of a polymorphic Mhc class II gene in Pacific salmon. Immunogenetics 1996; 43:337-51. [PMID: 8606054 DOI: 10.1007/bf02199802] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Polymorphism of the nucleotide sequences encoding 149 amino acids of linked major histocompatibility complex (Mhc) class II B1 and B2 peptides, and of the intervening intron (548-773 base pairs), was examined within and among seven Pacific salmon (Oncorhynchus) species. Levels of nucleotide diversity were higher for the B1 sequence than for B2 or the intron in comparisons both within and between species. For the codons of the peptide binding region of the B1 sequence, the level of nonsynonymous nucleotide substitution (dN) exceeded the level of synonymous substitution (dS) by a factor of ten for within-species comparisons, and by a factor of four for between-species comparisons. The excess of dN indicates that balancing selection maintains diversity at this salmonid Mhc class II locus, as is common for Mhc loci in other vertebrates. Levels of nucleotide diversity for both the exon and intron sequences were greater among than within species, and there were numerous species-specific nucleotides present in both the coding and noncoding regions. Thus, neighbor-joining analysis of both the intron and exon regions provided phylogenies in which the sequences clustered strongly by species. There was little evidence of shared ancestral (trans-species) polymorphism in the exon phylogeny, and the intron phylogeny depicted standard relationships among the Pacific salmon species. The lack of shared allelic B1 lineages in these closely related species may result from severe bottlenecks that occurred during speciation or during the ice ages that glaciated the rim of the north Pacific Ocean approximately every 100000 years in the Pleistocene.
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Affiliation(s)
- K M Miller
- Department of Fisheries and Oceans, Science Branch, Pacific Biological Station, British Columbia, Canada
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