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Wang S, Zheng L, Wei X, Qu Z, Du L, Wang S, Zhang N. Amino acid insertion in Bat MHC-I enhances complex stability and augments peptide presentation. Commun Biol 2024; 7:586. [PMID: 38755285 PMCID: PMC11099071 DOI: 10.1038/s42003-024-06292-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 05/05/2024] [Indexed: 05/18/2024] Open
Abstract
Bats serve as reservoirs for numerous zoonotic viruses, yet they typically remain asymptomatic owing to their unique immune system. Of particular significance is the MHC-I in bats, which plays crucial role in anti-viral response and exhibits polymorphic amino acid (AA) insertions. This study demonstrated that both 5AA and 3AA insertions enhance the thermal stability of the bat MHC-I complex and enrich the diversity of bound peptides in terms of quantity and length distribution, by stabilizing the 310 helix, a region prone to conformational changes during peptide loading. However, the mismatched insertion could diminish the stability of bat pMHC-I. We proposed that a suitable insertion may help bat MHC-I adapt to high body temperatures during flight while enhancing antiviral responses. Moreover, this site-specific insertions may represent a strategy of evolutionary adaptation of MHC-I molecules to fluctuations in body temperature, as similar insertions have been found in other lower vertebrates.
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Affiliation(s)
- Suqiu Wang
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, PR China
| | - Liangzhen Zheng
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, PR China
- Shanghai Zelixir Biotech Company Ltd., Shanghai, 200030, PR China
| | - Xiaohui Wei
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, PR China
| | - Zehui Qu
- The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, PR China
| | - Liubao Du
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, PR China
| | - Sheng Wang
- Shanghai Zelixir Biotech Company Ltd., Shanghai, 200030, PR China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, PR China
| | - Nianzhi Zhang
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, PR China.
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Hu J, Song L, Ning M, Niu X, Han M, Gao C, Feng X, Cai H, Li T, Li F, Li H, Gong D, Song W, Liu L, Pu J, Liu J, Smith J, Sun H, Huang Y. A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families. BMC Biol 2024; 22:31. [PMID: 38317190 PMCID: PMC10845735 DOI: 10.1186/s12915-024-01817-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A virus (IAV), harbors almost all subtypes of IAVs and resists to many IAVs which cause extreme virulence in chicken and human. However, the response of duck's adaptive immune system to IAV infection is poorly characterized due to lack of a detailed gene map of the major histocompatibility complex (MHC). RESULTS We herein reported a chromosome-scale Beijing duck assembly by integrating Nanopore, Bionano, and Hi-C data. This new reference genome SKLA1.0 covers 40 chromosomes, improves the contig N50 of the previous duck assembly with highest contiguity (ZJU1.0) of more than a 5.79-fold, surpasses the chicken and zebra finch references in sequence contiguity and contains a complete genomic map of the MHC. Our 3D MHC genomic map demonstrated that gene family arrangement in this region was primordial; however, families such as AnplMHCI, AnplMHCIIβ, AnplDMB, NKRL (NK cell receptor-like genes) and BTN underwent gene expansion events making this area complex. These gene families are distributed in two TADs and genes sharing the same TAD may work in a co-regulated model. CONCLUSIONS These observations supported the hypothesis that duck's adaptive immunity had been optimized with expanded and diversified key immune genes which might help duck to combat influenza virus. This work provided a high-quality Beijing duck genome for biological research and shed light on new strategies for AIV control.
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Affiliation(s)
- Jiaxiang Hu
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Linfei Song
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Mengfei Ning
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Xinyu Niu
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Mengying Han
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Chuze Gao
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Xingwei Feng
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Han Cai
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Te Li
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Fangtao Li
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Huifang Li
- Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Daoqing Gong
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Weitao Song
- Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Long Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Juan Pu
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Jinhua Liu
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Honglei Sun
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China.
| | - Yinhua Huang
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China.
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Minias P, Edwards SV, Babik W. Ancient duplication, coevolution, and selection at the MHC class IIA and IIB genes of birds. Front Immunol 2023; 14:1250824. [PMID: 37965325 PMCID: PMC10641522 DOI: 10.3389/fimmu.2023.1250824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/18/2023] [Indexed: 11/16/2023] Open
Abstract
Introduction The Major Histocompatibility Complex (MHC) of vertebrates is a dynamically evolving multigene family primarily responsible for recognizing non-self peptide antigens and triggering a pathogen-specific adaptive immune response. In birds, the MHC was previously thought to evolve via concerted evolution with high degree of gene homogenization and the rapid loss of orthology. However, the discovery of two ancient avian MHC-IIB gene lineages (DAB1 and DAB2) originating before the radiation of extant birds indicated that despite the action of concerted evolution, orthology may be detectable for long evolutionary periods. Methods Here, we take advantage of rapidly accumulating digital genomic resources to search for the signal of an ancient duplication at the avian MHC-IIA genes, as well as to compare phylogenetic distribution and selection between MHC-IIA and IIB gene lineages. Results The analysis of MHC sequences from over 230 species representing ca. 70 bird families revealed the presence of two ancient MHC-IIA gene lineages (DAA1 and DAA2) and showed that their phylogenetic distribution matches exactly the distribution of DAB1 and DAB2 lineages, suggesting tight coevolution. The early post-duplication divergence of DAA1 and DAA2 was driven by positive selection fixing radical amino acid differences within the membrane-proximal domain and, most probably, being functionally related to the interactions between α2 and β2 chains of the MHC-II heterodimer. We detected no evidence for an overall (gene-wide) relaxation or intensification of selection at either DAA1/DAB1 or DAA2/DAB2, but codon-specific differences in selection signature were found at the peptide-binding sites between the two gene lineages, perhaps implying specialization to different pathogen regimes. Discussion Our results suggest that specific pairing of MHC-II α and β chains may have an adaptive significance, a conclusion that advances knowledge on the macroevolution of the avian MHC-II and opens exciting novel directions for future research.
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Affiliation(s)
- Piotr Minias
- University of Lodz, Faculty of Biology and Environmental Protection, Department of Biodiversity Studies and Bioeducation, Lodz, Poland
| | - Scott V. Edwards
- Harvard University, Museum of Comparative Zoology, Cambridge, MA, United States
- Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, MA, United States
| | - Wiesław Babik
- Jagiellonian University, Institute of Environmental Sciences, Faculty of Biology, Kraków, Poland
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Wong-Benito V, de Rijke J, Dixon B. Antigen presentation in vertebrates: Structural and functional aspects. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 144:104702. [PMID: 37116963 DOI: 10.1016/j.dci.2023.104702] [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: 02/11/2023] [Revised: 03/20/2023] [Accepted: 03/29/2023] [Indexed: 06/05/2023]
Abstract
Antigen presentation is a key process of the immune system and is responsible for the activation of T cells. The main characters are the major histocompatibility complex class I (MHC-I) and class II (MHC-II) molecules, and accessory proteins that act as chaperones for these glycoproteins. Current knowledge of this process and also the elucidation of the structural features of these proteins, has been extensively reviewed in humans. Unfortunately, this is not the case for non-human species, wherein the function and structural characteristic of the antigen presentation proteins is far from being understood. The majority of previous studies in non-human species, especially in teleost fish and lower vertebrates, are limited to the transcriptomic level, which leads to gaps in the knowledge about the functional process of antigen presentation in these species. This review summarizes what is known so far about antigen presentation pathways in vertebrates from a structural and functional perspective. The focus is not only on the MHC receptors, but also, on the forgotten characters of these pathways such as the proteins of the peptide loading complex, and the MHC-II chaperone invariant chain.
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Affiliation(s)
| | - Jill de Rijke
- Department of Biology, University of Waterloo, Canada
| | - Brian Dixon
- Department of Biology, University of Waterloo, Canada.
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Winternitz J, Chakarov N, Rinaud T, Ottensmann M, Krüger O. High functional allelic diversity and copy number in both MHC classes in the common buzzard. BMC Ecol Evol 2023; 23:24. [PMID: 37355591 PMCID: PMC10290333 DOI: 10.1186/s12862-023-02135-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 06/12/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC), which encodes molecules that recognize various pathogens and parasites and initiates the adaptive immune response in vertebrates, is renowned for its exceptional polymorphism and is a model of adaptive gene evolution. In birds, the number of MHC genes and sequence diversity varies greatly among taxa, believed due to evolutionary history and differential selection pressures. Earlier characterization studies and recent comparative studies suggest that non-passerine species have relatively few MHC gene copies compared to passerines. Additionally, comparative studies that have looked at partial MHC sequences have speculated that non-passerines have opposite patterns of selection on MHC class I (MHC-I) and class II (MHC-II) loci than passerines: namely, greater sequence diversity and signals of selection on MHC-II than MHC-I. However, new sequencing technology is revealing much greater MHC variation than previously expected while also facilitating full sequence variant detection directly from genomic data. Our study aims to take advantage of high-throughput sequencing methods to fully characterize both classes and domains of MHC of a non-passerine bird of prey, the common buzzard (Buteo buteo), to test predictions of MHC variation and differential selection on MHC classes. RESULTS Using genetic, genomic, and transcriptomic high-throughput sequencing data, we established common buzzards have at least three loci that produce functional alleles at both MHC classes. In total, we characterize 91 alleles from 113 common buzzard chicks for MHC-I exon 3 and 41 alleles from 125 chicks for MHC-IIB exon 2. Among these alleles, we found greater sequence polymorphism and stronger diversifying selection at MHC-IIB exon 2 than MHC-I exon 3, suggesting differential selection pressures on MHC classes. However, upon further investigation of the entire peptide-binding groove by including genomic data from MHC-I exon 2 and MHC-IIA exon 2, this turned out to be false. MHC-I exon 2 was as polymorphic as MHC-IIB exon 2 and MHC-IIA exon 2 was essentially invariant. Thus, comparisons between MHC-I and MHC-II that included both domains of the peptide-binding groove showed no differences in polymorphism nor diversifying selection between the classes. Nevertheless, selection analysis indicates balancing selection has been acting on common buzzard MHC and phylogenetic inference revealed that trans-species polymorphism is present between common buzzards and species separated for over 33 million years for class I and class II. CONCLUSIONS We characterize and confirm the functionality of unexpectedly high copy number and allelic diversity in both MHC classes of a bird of prey. While balancing selection is acting on both classes, there is no evidence of differential selection pressure on MHC classes in common buzzards and this result may hold more generally once more data for understudied MHC exons becomes available.
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Affiliation(s)
- Jamie Winternitz
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Nayden Chakarov
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Tony Rinaud
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Meinolf Ottensmann
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Oliver Krüger
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
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Halabi S, Kaufman J. New vistas unfold: Chicken MHC molecules reveal unexpected ways to present peptides to the immune system. Front Immunol 2022; 13:886672. [PMID: 35967451 PMCID: PMC9372762 DOI: 10.3389/fimmu.2022.886672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/07/2022] [Indexed: 11/27/2022] Open
Abstract
The functions of a wide variety of molecules with structures similar to the classical class I and class II molecules encoded by the major histocompatibility complex (MHC) have been studied by biochemical and structural studies over decades, with many aspects for humans and mice now enshrined in textbooks as dogma. However, there is much variation of the MHC and MHC molecules among the other jawed vertebrates, understood in the most detail for the domestic chicken. Among the many unexpected features in chickens is the co-evolution between polymorphic TAP and tapasin genes with a dominantly-expressed class I gene based on a different genomic arrangement compared to typical mammals. Another important discovery was the hierarchy of class I alleles for a suite of properties including size of peptide repertoire, stability and cell surface expression level, which is also found in humans although not as extreme, and which led to the concept of generalists and specialists in response to infectious pathogens. Structural studies of chicken class I molecules have provided molecular explanations for the differences in peptide binding compared to typical mammals. These unexpected phenomena include the stringent binding with three anchor residues and acidic residues at the peptide C-terminus for fastidious alleles, and the remodelling binding sites, relaxed binding of anchor residues in broad hydrophobic pockets and extension at the peptide C-terminus for promiscuous alleles. The first few studies for chicken class II molecules have already uncovered unanticipated structural features, including an allele that binds peptides by a decamer core. It seems likely that the understanding of how MHC molecules bind and present peptides to lymphocytes will broaden considerably with further unexpected discoveries through biochemical and structural studies for chickens and other non-mammalian vertebrates.
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Affiliation(s)
- Samer Halabi
- Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Jim Kaufman
- Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Jim Kaufman,
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Mancilla-Morales MD, Velarde E, Contreras-Rodríguez A, Gómez-Lunar Z, Rosas-Rodríguez JA, Heras J, Soñanez-Organis JG, Ruiz EA. Characterization, Selection, and Trans-Species Polymorphism in the MHC Class II of Heermann’s Gull (Charadriiformes). Genes (Basel) 2022; 13:genes13050917. [PMID: 35627302 PMCID: PMC9140796 DOI: 10.3390/genes13050917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 11/16/2022] Open
Abstract
The major histocompatibility complex (MHC) enables vertebrates to cope with pathogens and maintain healthy populations, thus making it a unique set of loci for addressing ecology and evolutionary biology questions. The aim of our study was to examine the variability of Heermann’s Gull MHC class II (MHCIIB) and compare these loci with other Charadriiformes. Fifty-nine MHCIIB haplotypes were recovered from sixty-eight Heermann’s Gulls by cloning, of them, twelve were identified as putative true alleles, forty-five as unique alleles, and two as pseudogenes. Intra and interspecific relationships indicated at least two loci in Heermann’s Gull MHCIIB and trans-species polymorphism among Charadriiformes (coinciding with the documented evidence of two ancient avian MHCIIB lineages, except in the Charadriidae family). Additionally, sites under diversifying selection revealed a better match with peptide-binding sites inferred in birds than those described in humans. Despite the negative anthropogenic activity reported on Isla Rasa, Heermann’s Gull showed MHCIIB variability consistent with population expansion, possibly due to a sudden growth following conservation efforts. Duplication must play an essential role in shaping Charadriiformes MHCIIB variability, buffering selective pressures through balancing selection. These findings suggest that MHC copy number and protected islands can contribute to seabird conservation.
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Affiliation(s)
- Misael Daniel Mancilla-Morales
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de Mexico CP 11340, Mexico
- Correspondence: (M.D.M.-M.); (J.G.S.-O.); (E.A.R.)
| | - Enriqueta Velarde
- Instituto de Ciencias Marinas y Pesquerías, Universidad Veracruzana, Hidalgo 617, Colonia Río Jamapa, Boca del Rio, Veracruz CP 94290, Mexico;
| | - Araceli Contreras-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de Mexico CP 11340, Mexico; (A.C.-R.); (Z.G.-L.)
| | - Zulema Gómez-Lunar
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de Mexico CP 11340, Mexico; (A.C.-R.); (Z.G.-L.)
| | - Jesús A. Rosas-Rodríguez
- Departamento de Ciencias Químico-Biológicas y Agropecuarias, Universidad de Sonora, Lázaro Cárdenas del Río No. 100, Francisco Villa, Navojoa CP 85880, Mexico;
| | - Joseph Heras
- Departament of Biology, California State University, San Bernardino, 5500 University Parkway, San Bernardino, CA 92407, USA;
| | - José G. Soñanez-Organis
- Departamento de Ciencias Químico-Biológicas y Agropecuarias, Universidad de Sonora, Lázaro Cárdenas del Río No. 100, Francisco Villa, Navojoa CP 85880, Mexico;
- Correspondence: (M.D.M.-M.); (J.G.S.-O.); (E.A.R.)
| | - Enrico A. Ruiz
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de Mexico CP 11340, Mexico
- Correspondence: (M.D.M.-M.); (J.G.S.-O.); (E.A.R.)
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Duan Y, Wang Y, Li Z, Ma L, Wei X, Yang J, Xiao R, Xia C. The unique structure of the zebrafish TNF-α homotrimer. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 122:104129. [PMID: 33989682 DOI: 10.1016/j.dci.2021.104129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
In the current study, zebrafish TNF-α1 (zTNF-α1) was crystallized, and the structure was analyzed. The zTNF-α1 trimer is composed of three monomers whose height and width are 50 Å and 60 Å, respectively. Compared with human TNF-α, zTNF-α1 shows only ~30% amino acid identity, the EF loop of each monomer lacks three amino acids, the CD loop is increased by four amino acids, and the AA'' loop is increased by one amino acid. In addition, an A″-β-chain is added to the zTNF-α1 monomer, forming two β-sheet layers with 6:5 β-chains. The top of the trimer is missing three amino acids and the inner coil because the EF loop seals the central hole at the top, forming a unique structure. In conclusion, the results elucidated the structure of the zTNF-α1 trimer, providing immunological knowledge for studying TNF-α function in the zebrafish animal model and structural information for exploring TNF-α family evolution.
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Affiliation(s)
- Yulu Duan
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Yawen Wang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Zibin Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Lizhen Ma
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Xiaohui Wei
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Junqi Yang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Ruiqi Xiao
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
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Identification of Novel T-Cell Epitopes on Infectious Bronchitis Virus N Protein and Development of a Multi-epitope Vaccine. J Virol 2021; 95:e0066721. [PMID: 34105997 DOI: 10.1128/jvi.00667-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cellular immune responses play a key role in the control of viral infection. The nucleocapsid (N) protein of infectious bronchitis virus (IBV) is a major immunogenic protein that can induce protective immunity. To screen for potential T-cell epitopes on IBV N protein, 40 overlapping peptides covering the entirety of the N protein were designed and synthesized. Four T-cell epitope peptides were identified by gamma interferon (IFN-γ) enzyme-linked immunosorbent spot (ELISpot), intracellular cytokine staining, and carboxyfluorescein succinimidyl ester (CFSE) lymphocyte proliferation assays; among them, three peptides (N211-230, N271-290, and N381-400) were cytotoxic T lymphocyte (CTL) epitopes, and one peptide (N261-280) was a dual-specific T-cell epitope, which can be recognized by both CD8+ and CD4+ T cells. Multi-epitope gene transcription cassettes comprising four neutralizing epitope domains and four T-cell epitope peptides were synthesized and inserted into the genome of Newcastle disease virus strain La Sota between the P and M genes. Recombinant IBV multi-epitope vaccine candidate rLa Sota/SBNT was generated via reverse genetics, and its immune protection efficacy was evaluated in specific-pathogen-free chickens. Our results show that rLa Sota/SBNT induced IBV-specific neutralizing antibody and T-cell responses and provided significant protection against homologous and heterologous IBV challenge. Thus, the T-cell epitope peptides identified in this study could be good candidates for IBV vaccine development, and recombinant Newcastle disease virus-expressing IBV multi-epitope genes represent a safe and effective vaccine candidate for controlling infectious bronchitis. IMPORTANCE T-cell-mediated immune responses are critical for the elimination of IBV-infected cells. To screen conserved T-cell epitopes in the IBV N protein, 40 overlapping peptides covering the entirety of the N protein were designed and synthesized. By combining IFN-γ ELISpot, intracellular cytokine staining, and CFSE lymphocyte proliferation assays, we identified three CTL epitopes and one dual-specific T-cell epitope. The value of T-cell epitope peptides identified in the N protein was further verified by the design of an IBV multi-epitope vaccine. Results show that IBV multi-epitope vaccine candidate rLa Sota/SBNT provided cross protection against challenges with a QX-like or a TW-like IBV strain. So, T-cell-mediated immune responses play an important role in the control of viral infection, and conserved T-cell epitopes serve as promising candidates for use in multi-epitope vaccine construction. Our results provide a new perspective for the development of a safer and more effective IBV vaccine.
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Wu Y, Zhang N, Hashimoto K, Xia C, Dijkstra JM. Structural Comparison Between MHC Classes I and II; in Evolution, a Class-II-Like Molecule Probably Came First. Front Immunol 2021; 12:621153. [PMID: 34194421 PMCID: PMC8236899 DOI: 10.3389/fimmu.2021.621153] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 05/04/2021] [Indexed: 01/03/2023] Open
Abstract
Structures of peptide-loaded major histocompatibility complex class I (pMHC-I) and class II (pMHC-II) complexes are similar. However, whereas pMHC-II complexes include similar-sized IIα and IIβ chains, pMHC-I complexes include a heavy chain (HC) and a single domain molecule β2-microglobulin (β2-m). Recently, we elucidated several pMHC-I and pMHC-II structures of primitive vertebrate species. In the present study, a comprehensive comparison of pMHC-I and pMHC-II structures helps to understand pMHC structural evolution and supports the earlier proposed—though debated—direction of MHC evolution from class II-type to class I. Extant pMHC-II structures share major functional characteristics with a deduced MHC-II-type homodimer ancestor. Evolutionary establishment of pMHC-I presumably involved important new functions such as (i) increased peptide selectivity by binding the peptides in a closed groove (ii), structural amplification of peptide ligand sequence differences by binding in a non-relaxed fashion, and (iii) increased peptide selectivity by syngeneic heterotrimer complex formation between peptide, HC, and β2-m. These new functions were associated with structures that since their establishment in early pMHC-I have been very well conserved, including a shifted and reorganized P1 pocket (aka A pocket), and insertion of a β2-m hydrophobic knob into the peptide binding domain β-sheet floor. A comparison between divergent species indicates better sequence conservation of peptide binding domains among MHC-I than among MHC-II, agreeing with more demanding interactions within pMHC-I complexes. In lungfishes, genes encoding fusions of all MHC-IIα and MHC-IIβ extracellular domains were identified, and although these lungfish genes presumably derived from classical MHC-II, they provide an alternative mechanistic hypothesis for how evolution from class II-type to class I may have occurred.
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Affiliation(s)
- Yanan Wu
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Nianzhi Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Keiichiro Hashimoto
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Johannes M Dijkstra
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
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11
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Halabi S, Ghosh M, Stevanović S, Rammensee HG, Bertzbach LD, Kaufer BB, Moncrieffe MC, Kaspers B, Härtle S, Kaufman J. The dominantly expressed class II molecule from a resistant MHC haplotype presents only a few Marek's disease virus peptides by using an unprecedented binding motif. PLoS Biol 2021; 19:e3001057. [PMID: 33901176 PMCID: PMC8101999 DOI: 10.1371/journal.pbio.3001057] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 05/06/2021] [Accepted: 03/31/2021] [Indexed: 12/14/2022] Open
Abstract
Viral diseases pose major threats to humans and other animals, including the billions of chickens that are an important food source as well as a public health concern due to zoonotic pathogens. Unlike humans and other typical mammals, the major histocompatibility complex (MHC) of chickens can confer decisive resistance or susceptibility to many viral diseases. An iconic example is Marek's disease, caused by an oncogenic herpesvirus with over 100 genes. Classical MHC class I and class II molecules present antigenic peptides to T lymphocytes, and it has been hard to understand how such MHC molecules could be involved in susceptibility to Marek's disease, given the potential number of peptides from over 100 genes. We used a new in vitro infection system and immunopeptidomics to determine peptide motifs for the 2 class II molecules expressed by the MHC haplotype B2, which is known to confer resistance to Marek's disease. Surprisingly, we found that the vast majority of viral peptide epitopes presented by chicken class II molecules arise from only 4 viral genes, nearly all having the peptide motif for BL2*02, the dominantly expressed class II molecule in chickens. We expressed BL2*02 linked to several Marek's disease virus (MDV) peptides and determined one X-ray crystal structure, showing how a single small amino acid in the binding site causes a crinkle in the peptide, leading to a core binding peptide of 10 amino acids, compared to the 9 amino acids in all other reported class II molecules. The limited number of potential T cell epitopes from such a complex virus can explain the differential MHC-determined resistance to MDV, but raises questions of mechanism and opportunities for vaccine targets in this important food species, as well as providing a basis for understanding class II molecules in other species including humans.
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Affiliation(s)
- Samer Halabi
- University of Cambridge, Department of Pathology, Cambridge, United Kingdom
- University of Edinburgh, Institute for Immunology and Infection Research, Edinburgh, United Kingdom
| | - Michael Ghosh
- University of Tübingen, Department of Immunology, Institute of Cell Biology, Tübingen, Germany
| | - Stefan Stevanović
- University of Tübingen, Department of Immunology, Institute of Cell Biology, Tübingen, Germany
| | - Hans-Georg Rammensee
- University of Tübingen, Department of Immunology, Institute of Cell Biology, Tübingen, Germany
| | | | | | | | - Bernd Kaspers
- Ludwig Maximillians University, Veterinary Faculty, Planegg, Germany
| | - Sonja Härtle
- Ludwig Maximillians University, Veterinary Faculty, Planegg, Germany
| | - Jim Kaufman
- University of Cambridge, Department of Pathology, Cambridge, United Kingdom
- University of Edinburgh, Institute for Immunology and Infection Research, Edinburgh, United Kingdom
- University of Cambridge, Department of Veterinary Medicine, Cambridge, United Kingdom
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12
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Wang Y, Qu Z, Ma L, Wei X, Zhang N, Zhang B, Xia C. The Crystal Structure of the MHC Class I (MHC-I) Molecule in the Green Anole Lizard Demonstrates the Unique MHC-I System in Reptiles. THE JOURNAL OF IMMUNOLOGY 2021; 206:1653-1667. [PMID: 33637616 DOI: 10.4049/jimmunol.2000992] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/16/2021] [Indexed: 12/13/2022]
Abstract
The reptile MHC class I (MCH-I) and MHC class II proteins are the key molecules in the immune system; however, their structure has not been investigated. The crystal structure of green anole lizard peptide-MHC-I-β2m (pMHC-I or pAnca-UA*0101) was determined in the current study. Subsequently, the features of pAnca-UA*0101 were analyzed and compared with the characteristics of pMHC-I of four classes of vertebrates. The amino acid sequence identities between Anca-UA*0101 and MHC-I from other species are <50%; however, the differences between the species were reflected in the topological structure. Significant characteristics of pAnca-UA*0101 include a specific flip of ∼88° and an upward shift adjacent to the C terminus of the α1- and α2-helical regions, respectively. Additionally, the lizard MHC-I molecule has an insertion of 2 aa (VE) at positions 55 and 56. The pushing force from 55-56VE triggers the flip of the α1 helix. Mutagenesis experiments confirmed that the 55-56VE insertion in the α1 helix enhances the stability of pAnca-UA*0101. The peptide presentation profile and motif of pAnca-UA*0101 were confirmed. Based on these results, the proteins of three reptile lizard viruses were used for the screening and confirmation of the candidate epitopes. These data enhance our understanding of the systematic differences between five classes of vertebrates at the gene and protein levels, the formation of the pMHC-I complex, and the evolution of the MHC-I system.
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Affiliation(s)
- Yawen Wang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zehui Qu
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Lizhen Ma
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xiaohui Wei
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Nianzhi Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Bing Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
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13
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Zhang L, Liu Y, Meng G, Liang R, Zhang B, Xia C. Structural and Biophysical Insights into the TCRαβ Complex in Chickens. iScience 2020; 23:101828. [PMID: 33305184 PMCID: PMC7711287 DOI: 10.1016/j.isci.2020.101828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/16/2020] [Accepted: 11/16/2020] [Indexed: 10/25/2022] Open
Abstract
In this work, chicken HPAIV H5N1 epitope-specific TCRαβ (ch-TCRαβ) was isolated and its structure was determined. The Cα domain of ch-TCRαβ does not exhibit the typical structure of human TCRαβ, and the DE loop extends outward, resulting in close proximity between the Cα domain of ch-TCRαβ and CD3εδ/γ. The FG loop of the Cβ domain of ch-TCRαβ is shorter. The changes in the C domains of ch-TCRαβ and the difference in chicken CD3εδ/γ confirm that the complexes formed by TCRαβ and CD3εδ/γ differ from those in humans. In the chicken complex, a positively charged cleft is formed between the two CDR3 loops that might accommodate the acidic side chains of the chicken pMHC-I-bound HPAIV epitope intermediate portion oriented toward ch-TCRαβ. This is the first reported structure of chicken TCRαβ, and it provides a structural model of the ancestral TCR system in the immune synapses between T cells and antigen-presenting cells in lower vertebrates.
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Affiliation(s)
- Lijie Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China.,Joint National Laboratory for Antibody Drug Engineering, Key Laboratory of Cell and Molecular Immunology, School of Medical Sciences, Henan University, Kaifeng 475004, China
| | - Yanjie Liu
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China
| | - Geng Meng
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China
| | - Ruiying Liang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China
| | - Bing Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China
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14
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Almeida T, Gaigher A, Muñoz-Mérida A, Neves F, Castro LFC, Flajnik MF, Ohta Y, Esteves PJ, Veríssimo A. Cartilaginous fish class II genes reveal unprecedented old allelic lineages and confirm the late evolutionary emergence of DM. Mol Immunol 2020; 128:125-138. [PMID: 33126081 PMCID: PMC8010645 DOI: 10.1016/j.molimm.2020.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/22/2020] [Accepted: 10/03/2020] [Indexed: 12/16/2022]
Abstract
Cartilaginous fish (chimaeras, rays and sharks) are the most basal extant jawed vertebrates with an adaptive immune system based on the Major Histocompatibility Complex (MHC). Despite being a key taxon in the evolution of vertebrate adaptive immunity, no comprehensive characterization of MHC class II genes has been undertaken for the group. We performed extensive bioinformatic searches on a taxonomically diverse dataset of transcriptomes and genomes of cartilaginous fish targeting MHC class II sequences. Class IIα and IIβ sequences were retrieved from all taxa analyzed and showed typical features of classical class II genes. Phylogenetic trees of the immunoglobulin superfamily domain showed two divergent and remarkably ancient lineages of class II genes in Selachians (sharks), originating >350 million years ago. Close linkage of lineage-specific pairs of IIα and IIβ genes was found, confirming previous results, with genes from distinct lineages segregating as alleles. Nonclassical class II DM sequences were not retrieved from these data and classical class II sequences lacked the conserved residues shown to interact with DM molecules, supporting claims that the DM system arose only in the lobe-finned fish lineage leading to tetrapods. Based on our search methods, other divergent class II genes are unlikely in cartilaginous fish.
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Affiliation(s)
- Tereza Almeida
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Department of Biology, Faculty of Sciences - University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal; Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201, USA
| | - Arnaud Gaigher
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Antonio Muñoz-Mérida
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Fabiana Neves
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - L Filipe C Castro
- Department of Biology, Faculty of Sciences - University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal; CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201, USA
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201, USA
| | - Pedro J Esteves
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Department of Biology, Faculty of Sciences - University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Ana Veríssimo
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
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