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Abstract
Compared to the major histocompatibility complex (MHC) of typical mammals, the chicken BF/BL region is small and simple, with most of the genes playing central roles in the adaptive immune response. However, some genes of the chicken MHC are almost certainly involved in innate immunity, such as the complement component C4 and the lectin-like receptor/ligand gene pair BNK and Blec. The poorly expressed classical class I molecule BF1 is known to be recognised by natural killer (NK) cells and, analogous to mammalian immune responses, the classical class I molecules BF1 and BF2, the CD1 homologs and the butyrophilin homologs called BG may be recognised by adaptive immune lymphocytes with semi-invariant receptors in a so-called adaptate manner. Moreover, the TRIM and BG regions next to the chicken MHC, along with the genetically unlinked Y and olfactory/scavenger receptor regions on the same chromosome, have multigene families almost certainly involved in innate and adaptate responses. On this chicken microchromosome, the simplicity of the adaptive immune gene systems contrasts with the complexity of the gene systems potentially involved in innate immunity.
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2
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Tregaskes CA, Kaufman J. Chickens as a simple system for scientific discovery: The example of the MHC. Mol Immunol 2021; 135:12-20. [PMID: 33845329 PMCID: PMC7611830 DOI: 10.1016/j.molimm.2021.03.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/08/2021] [Accepted: 03/17/2021] [Indexed: 01/07/2023]
Abstract
Chickens have played many roles in human societies over thousands of years, most recently as an important model species for scientific discovery, particularly for embryology, virology and immunology. In the last few decades, biomedical models like mice have become the most important model organism for understanding the mechanisms of disease, but for the study of outbred populations, they have many limitations. Research on humans directly addresses many questions about disease, but frank experiments into mechanisms are limited by practicality and ethics. For research into all levels of disease simultaneously, chickens combine many of the advantages of humans and of mice, and could provide an independent, integrated and overarching system to validate and/or challenge the dogmas that have arisen from current biomedical research. Moreover, some important systems are simpler in chickens than in typical mammals. An example is the major histocompatibility complex (MHC) that encodes the classical MHC molecules, which play crucial roles in the innate and adaptive immune systems. Compared to the large and complex MHCs of typical mammals, the chicken MHC is compact and simple, with single dominantly-expressed MHC molecules that can determine the response to infectious pathogens. As a result, some fundamental principles have been easier to discover in chickens, with the importance of generalist and specialist MHC alleles being the latest example.
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Affiliation(s)
- Clive A Tregaskes
- University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom
| | - Jim Kaufman
- University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom; University of Edinburgh, Institute for Immunology and Infection Research, Ashworth Laboratories, Kings Buildings, Edinburgh, EH9 3FL, United Kingdom.
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3
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Mwangi W, Maccari G, Hope JC, Entrican G, Hammond JA. The UK Veterinary Immunological Toolbox Website: promoting vaccine research by facilitating communication and removing reagent barriers. Immunology 2020; 161:25-27. [PMID: 32548865 PMCID: PMC7450168 DOI: 10.1111/imm.13227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/29/2020] [Accepted: 06/07/2020] [Indexed: 01/01/2023] Open
Abstract
Using the best animal models to study immune responses against specific pathogens or vaccines can dramatically accelerate our understanding. Veterinary species are well studied, particularly livestock, to reduce their disease burden. They have also proven to be powerful models, especially for zoonotic pathogens and novel vaccination strategies. A prerequisite for any model selection is having the right quality and range of species‐specific immunological reagents. To help promote the widest possible use of veterinary species, an open access website (https://www.immunologicaltoolbox.co.uk) has been created as a central community annotated hub for veterinary immunological reagents. The website is also the portal into services offered by the UK Immunological Toolbox project that includes antibody generation, sequencing and recombinant expression. The funding for this effort is linked into sustainable sources, but ultimate success relies on community engagement to continually increase the quality and quantity of information. It is hoped that as more users and reagent owners engage, it will become an essential resource for researchers, veterinarians and clinicians alike by removing barriers that prevent the use of the most informative animal models.
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Affiliation(s)
| | - Giuseppe Maccari
- The Pirbright Institute, Woking, UK.,Royal Free Hospital, Anthony Nolan Research Institute, London, UK
| | - Jayne C Hope
- The Roslin Institute, The University of Edinburgh, Midlothian, UK
| | - Gary Entrican
- The Roslin Institute, The University of Edinburgh, Midlothian, UK
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Hofmann T, Schmucker SS, Bessei W, Grashorn M, Stefanski V. Impact of Housing Environment on the Immune System in Chickens: A Review. Animals (Basel) 2020; 10:E1138. [PMID: 32635616 PMCID: PMC7401558 DOI: 10.3390/ani10071138] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/29/2020] [Accepted: 07/01/2020] [Indexed: 12/11/2022] Open
Abstract
During their lifespan, chickens are confronted with a wide range of acute and chronic stressors in their housing environment that may threaten their welfare and health by modulating the immune system. Especially chronic stressful conditions can exceed the individual's allostatic load, with negative consequences for immunity. A fully functional immune system is mandatory for health and welfare and, consequently, also for high productivity and safe animal products. This review provides a comprehensive overview of the impact of housing form, light regime as well as aerial ammonia and hydrogen sulfide concentrations on the immune system in chickens. Certain housing conditions are clearly associated with immunological alterations which potentially impair the success of vaccinations or affect disease susceptibility. Such poor conditions counteract sustainable poultry production. This review also outlines current knowledge gaps and provides recommendations for future research.
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Affiliation(s)
- Tanja Hofmann
- Department of Behavioral Physiology of Livestock, Institute of Animal Science, University of Hohenheim, Garbenstr, 17, 70599 Stuttgart, Germany;
| | - Sonja S. Schmucker
- Department of Behavioral Physiology of Livestock, Institute of Animal Science, University of Hohenheim, Garbenstr, 17, 70599 Stuttgart, Germany;
| | - Werner Bessei
- Department of Livestock Population Genomics, Institute of Animal Science, University of Hohenheim, Garbenstr, 17, 70599 Stuttgart, Germany; (W.B.); (M.G.)
| | - Michael Grashorn
- Department of Livestock Population Genomics, Institute of Animal Science, University of Hohenheim, Garbenstr, 17, 70599 Stuttgart, Germany; (W.B.); (M.G.)
| | - Volker Stefanski
- Department of Behavioral Physiology of Livestock, Institute of Animal Science, University of Hohenheim, Garbenstr, 17, 70599 Stuttgart, Germany;
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5
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Spottiswoode CN, Busch R. Vive la difference! Self/non-self recognition and the evolution of signatures of identity in arms races with parasites. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180206. [PMID: 30967089 PMCID: PMC6388040 DOI: 10.1098/rstb.2018.0206] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2018] [Indexed: 12/24/2022] Open
Abstract
In arms races with parasites, hosts can evolve defences exhibiting extensive variability within populations, which signals individual identity ('signatures'). However, few such systems have evolved, suggesting that the conditions for their evolution are uncommon. We review (a) polymorphic egg markings that allow hosts of brood-parasitic birds to recognize and reject parasitic eggs, and (b) polymorphic tissue antigens encoded in the major histocompatibility complex (MHC), which present self- and pathogen-derived peptides to T cells of the immune system. Despite the profound differences between these systems, they share analogous features: (i) self/non-self discrimination by a highly specific recognition system (bird eyes and T-cell antigen receptor, respectively), which antagonists may escape by evolving evasion or mimicry; (ii) a self substrate upon which diversifying selection can act (eggs, and MHC molecules); (iii) acquired knowledge of self (resulting in acceptance of own eggs, and immune tolerance); and (iv) fitness costs associated with attack on self or lack of parasite detection. We suggest that these features comprise a set of requirements for parasites to drive the evolution of identity signatures in hosts, which diminish the likelihood of recognition errors. This may help to explain the variety of trajectories arising from arms races in different antagonistic contexts. This article is part of the theme issue 'The coevolutionary biology of brood parasitism: from mechanism to pattern'.
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Affiliation(s)
- Claire N. Spottiswoode
- FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch 7701, South Africa
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Robert Busch
- Department of Life Sciences, Whitelands College, University of Roehampton, Holybourne Avenue, London SW15 4JD, UK
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6
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Kasahara M, Flajnik MF. Origin and evolution of the specialized forms of proteasomes involved in antigen presentation. Immunogenetics 2019; 71:251-261. [PMID: 30675634 DOI: 10.1007/s00251-019-01105-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 01/09/2019] [Indexed: 01/10/2023]
Abstract
Proteasomes are a multi-subunit protease complex that produces peptides bound by major histocompatibility complex (MHC) class I molecules. Phylogenetic studies indicate that two specialized forms of proteasomes, immunoproteasomes and thymoproteasomes, and the proteasome activator PA28αβ emerged in a common ancestor of jawed vertebrates which acquired adaptive immunity based on the MHC, T cell receptors, and B cell receptors ~ 500 million years ago. Comparative genomics studies now provide strong evidence that the genes coding for the immunoproteasome subunits emerged by genome-wide duplication. On the other hand, the gene encoding the thymoproteasome subunit β5t emerged by tandem duplication from the gene coding for the β5 subunit. Strikingly, birds lack immunoproteasomes, thymoproteasomes, and the proteasome activator PA28αβ, raising an interesting question of whether they have evolved any compensatory mechanisms.
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Affiliation(s)
- Masanori Kasahara
- Department of Pathology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, 060-8638, Japan.
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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7
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Hacking J, Bradford T, Pierce K, Gardner M. De novo genotyping of the major histocompatibility complex in an Australian dragon lizard, Ctenophorus decresii. T ROY SOC SOUTH AUST 2018. [DOI: 10.1080/03721426.2018.1542259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Jessica Hacking
- College of Science and Engineering, Flinders University, Bedford Park, Australia
| | - Tessa Bradford
- College of Science and Engineering, Flinders University, Bedford Park, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Kelly Pierce
- College of Science and Engineering, Flinders University, Bedford Park, Australia
| | - Michael Gardner
- College of Science and Engineering, Flinders University, Bedford Park, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, Australia
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8
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Xiao J, Xiang W, Zhang Y, Peng W, Zhao M, Niu L, Chai Y, Qi J, Wang F, Qi P, Pan C, Han L, Wang M, Kaufman J, Gao GF, Liu WJ. An Invariant Arginine in Common with MHC Class II Allows Extension at the C-Terminal End of Peptides Bound to Chicken MHC Class I. THE JOURNAL OF IMMUNOLOGY 2018; 201:3084-3095. [PMID: 30341185 DOI: 10.4049/jimmunol.1800611] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/11/2018] [Indexed: 12/30/2022]
Abstract
MHC molecules are found in all jawed vertebrates and are known to present peptides to T lymphocytes. In mammals, peptides can hang out either end of the peptide-binding groove of classical class II molecules, whereas the N and C termini of peptides are typically tightly bound to specific pockets in classical class I molecules. The chicken MHC, like many nonmammalian vertebrates, has a single dominantly expressed classical class I molecule encoded by the BF2 locus. We determined the structures of BF2*1201 bound to two peptides and found that the C terminus of one peptide hangs outside of the groove with a conformation much like the peptides bound to class II molecules. We found that BF2*1201 binds many peptides that hang out of the groove at the C terminus, and the sequences and structures of this MHC class I allele were determined to investigate the basis for this phenomenon. The classical class I molecules of mammals have a nearly invariant Tyr (Tyr84 in humans) that coordinates the peptide C terminus, but all classical class I molecules outside of mammals have an Arg in that position in common with mammalian class II molecules. We find that this invariant Arg residue switches conformation to allow peptides to hang out of the groove of BF2*1201, suggesting that this phenomenon is common in chickens and other nonmammalian vertebrates, perhaps allowing the single dominantly expressed class I molecule to bind a larger repertoire of peptides.
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Affiliation(s)
- Jin Xiao
- Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Engineering and Technology Research Center for Beijing Veterinary Peptide Vaccine Design and Preparation, Zhongmu Institutes of China Animal Husbandry Industry Co. Ltd., Beijing 100095, China.,College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Wangzhen Xiang
- Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Engineering and Technology Research Center for Beijing Veterinary Peptide Vaccine Design and Preparation, Zhongmu Institutes of China Animal Husbandry Industry Co. Ltd., Beijing 100095, China.,College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yongli Zhang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Weiyu Peng
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Min Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ling Niu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Chai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fei Wang
- Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Engineering and Technology Research Center for Beijing Veterinary Peptide Vaccine Design and Preparation, Zhongmu Institutes of China Animal Husbandry Industry Co. Ltd., Beijing 100095, China
| | - Peng Qi
- Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Engineering and Technology Research Center for Beijing Veterinary Peptide Vaccine Design and Preparation, Zhongmu Institutes of China Animal Husbandry Industry Co. Ltd., Beijing 100095, China
| | - Chungang Pan
- Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Engineering and Technology Research Center for Beijing Veterinary Peptide Vaccine Design and Preparation, Zhongmu Institutes of China Animal Husbandry Industry Co. Ltd., Beijing 100095, China
| | - Lingxia Han
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Ming Wang
- Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Engineering and Technology Research Center for Beijing Veterinary Peptide Vaccine Design and Preparation, Zhongmu Institutes of China Animal Husbandry Industry Co. Ltd., Beijing 100095, China.,College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jim Kaufman
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom; .,Department of Veterinary Medicine, University of Cambridge, Cambridge CB2 1QP, United Kingdom; and
| | - George F Gao
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China; .,NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,China Research Network of Immunity and Health, Beijing Institutes of Life Science Chinese Academy of Sciences, Beijing 100101, China
| | - William J Liu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China; .,NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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9
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The immunoproteasome and thymoproteasome: functions, evolution and human disease. Nat Immunol 2018; 19:923-931. [PMID: 30104634 DOI: 10.1038/s41590-018-0186-z] [Citation(s) in RCA: 196] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/12/2018] [Accepted: 07/19/2018] [Indexed: 01/12/2023]
Abstract
The basic principle of adaptive immunity is to strictly discriminate between self and non-self, and a central challenge to overcome is the enormous variety of pathogens that might be encountered. In cell-mediated immunity, immunological discernment takes place at a molecular or cellular level. Central to both mechanisms of discernment is the generation of antigenic peptides associated with MHC class I molecules, which is achieved by a proteolytic complex called the proteasome. To adequately accomplish the discrimination between self and non-self that is essential for adaptive immunity and self-tolerance, two proteasome subtypes have evolved via gene duplication: the immunoproteasome and the thymoproteasome. In this Review, we describe various aspects of these immunity-dedicated proteasomes, from their discovery to recent findings.
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10
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Kaufman J. Unfinished Business: Evolution of the MHC and the Adaptive Immune System of Jawed Vertebrates. Annu Rev Immunol 2018; 36:383-409. [DOI: 10.1146/annurev-immunol-051116-052450] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jim Kaufman
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB2 0ES, United Kingdom
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11
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Kaufman J. Generalists and Specialists: A New View of How MHC Class I Molecules Fight Infectious Pathogens. Trends Immunol 2018; 39:367-379. [PMID: 29396014 PMCID: PMC5929564 DOI: 10.1016/j.it.2018.01.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/22/2017] [Accepted: 01/03/2018] [Indexed: 12/24/2022]
Abstract
In comparison with the major histocompatibility complexes (MHCs) of typical mammals, the chicken MHC is simple and compact with a single dominantly expressed class I molecule that can determine the immune response. In addition to providing useful information for the poultry industry and allowing insights into the evolution of the adaptive immune system, the simplicity of the chicken MHC has allowed the discovery of phenomena that are more difficult to discern in the more complicated mammalian systems. This review discusses the new concept that poorly expressed promiscuous class I alleles act as generalists to protect against a wide variety of infectious pathogens, while highly expressed fastidious class I alleles can act as specialists to protect against new and dangerous pathogens. A broad overview of classical MHC I expression and bound peptides reveals an inverse correlation between repertoire breadth and cell-surface expression in some chicken and human alleles. Several chicken class I alleles with wide peptide-binding repertoires (promiscuity) are associated with resistance to a variety of common diseases. Conversely, a narrow peptide-binding repertoire (fastidiousness) in some human HLA-B alleles is associated with resistance to HIV progression. Cell-surface expression of some classical class I alleles depends on the regulation of translocation to the cell surface rather than of transcription or translation. MHC translocation is influenced by peptide translocation in chickens and by tapasin interaction in humans.
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Affiliation(s)
- Jim Kaufman
- University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge CB2 1QP, UK; University of Cambridge, Department of Veterinary Medicine, Madingley Road, Cambridge CB2 0ES, UK.
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12
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Parker A, Kaufman J. What chickens might tell us about the MHC class II system. Curr Opin Immunol 2017; 46:23-29. [PMID: 28433952 DOI: 10.1016/j.coi.2017.03.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/24/2017] [Indexed: 11/15/2022]
Abstract
Almost all knowledge about the structure and function of MHC class II molecules outside of mammals comes from work with chickens. Most of the genes implicated in the class II system are present in chickens, so it is likely that the machinery of antigen processing and peptide-loading is similar to mammals. However, there is only one isotype (lineage) of classical class II genes, with one monomorphic DR-like BLA gene and two polymorphic BLB genes, located near one DMA and two DMB genes. The DMB2 and BLB2 genes are widely expressed at high levels, whereas the DMB1 and BLB1 genes are only expressed at highest levels in spleen and intestine, suggesting the possibility of two class II systems in chickens.
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Affiliation(s)
- Aimée Parker
- Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, United Kingdom
| | - Jim Kaufman
- University of Cambridge, Department of Pathology, Cambridge CB2 1QP, United Kingdom; University of Cambridge, Department of Veterinary Medicine, Cambridge CB3 0ES, United Kingdom.
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13
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Lillie M, Sheng Z, Honaker CF, Dorshorst BJ, Ashwell CM, Siegel PB, Carlborg Ö. Genome-wide standing variation facilitates long-term response to bidirectional selection for antibody response in chickens. BMC Genomics 2017; 18:99. [PMID: 28100171 PMCID: PMC5244587 DOI: 10.1186/s12864-016-3414-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/12/2016] [Indexed: 12/13/2022] Open
Abstract
Background Long-term selection experiments provide a powerful approach to gain empirical insights into adaptation, allowing researchers to uncover the targets of selection and infer their contributions to the mode and tempo of adaptation. Here we implement a pooled genome re-sequencing approach to investigate the consequences of 39 generations of bidirectional selection in White Leghorn chickens on a humoral immune trait: antibody response to sheep red blood cells. Results We observed wide genome involvement in response to this selection regime. Many genomic regions were highly differentiated resulting from this experimental selection regime, an involvement of up to 20% of the chicken genome (208.8 Mb). While genetic drift has certainly contributed to this, we implement gene ontology, association analysis and population simulations to increase our confidence in candidate selective sweeps. Three strong candidate genes, MHC, SEMA5A and TGFBR2, are also presented. Conclusions The extensive genomic changes highlight the polygenic genetic architecture of antibody response in these chicken populations, which are derived from a common founder population, demonstrating the extent of standing immunogenetic variation available at the onset of selection. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3414-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mette Lillie
- Department of Medical Biochemistry and Microbiology, Genomics, Uppsala University, Uppsala, 75123, Sweden.
| | - Zheya Sheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Christa F Honaker
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Ben J Dorshorst
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Christopher M Ashwell
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Paul B Siegel
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Örjan Carlborg
- Department of Medical Biochemistry and Microbiology, Genomics, Uppsala University, Uppsala, 75123, Sweden
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14
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Markowska M, Majewski PM, Skwarło-Sońta K. Avian biological clock - Immune system relationship. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 66:130-138. [PMID: 27235884 DOI: 10.1016/j.dci.2016.05.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 05/23/2016] [Accepted: 05/23/2016] [Indexed: 06/05/2023]
Abstract
Biological rhythms in birds are driven by the master clock, which includes the suprachiasmatic nucleus, the pineal gland and the retina. Light/dark cycles are the cues that synchronize the rhythmic changes in physiological processes, including immunity. This review summarizes our investigations on the bidirectional relationships between the chicken pineal gland and the immune system. We demonstrated that, in the chicken, the main pineal hormone, melatonin, regulates innate immunity, maintains the rhythmicity of immune reactions and is involved in the seasonal changes in immunity. Using thioglycollate-induced peritonitis as a model, we showed that the activated immune system regulates the pineal gland by inhibition of melatonin production at the level of the key enzyme in its biosynthetic pathway, arylalkylamine-N-acetyltransferase (AANAT). Interleukin 6 and interleukin 18 seem to be the immune mediators influencing the pineal gland, directly inhibiting Aanat gene transcription and modulating expression of the clock genes Bmal1 and Per3, which in turn regulate Aanat.
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Affiliation(s)
- Magdalena Markowska
- University of Warsaw, Faculty of Biology, Institute of Zoology, Department of Animal Physiology, Miecznikowa 1 Str., 02-096, Warsaw, Poland.
| | - Paweł M Majewski
- University of Warsaw, Faculty of Biology, Institute of Zoology, Department of Animal Physiology, Miecznikowa 1 Str., 02-096, Warsaw, Poland
| | - Krystyna Skwarło-Sońta
- University of Warsaw, Faculty of Biology, Institute of Zoology, Department of Animal Physiology, Miecznikowa 1 Str., 02-096, Warsaw, Poland
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15
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Alternative haplotypes of antigen processing genes in zebrafish diverged early in vertebrate evolution. Proc Natl Acad Sci U S A 2016; 113:E5014-23. [PMID: 27493218 DOI: 10.1073/pnas.1607602113] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antigen processing and presentation genes found within the MHC are among the most highly polymorphic genes of vertebrate genomes, providing populations with diverse immune responses to a wide array of pathogens. Here, we describe transcriptome, exome, and whole-genome sequencing of clonal zebrafish, uncovering the most extensive diversity within the antigen processing and presentation genes of any species yet examined. Our CG2 clonal zebrafish assembly provides genomic context within a remarkably divergent haplotype of the core MHC region on chromosome 19 for six expressed genes not found in the zebrafish reference genome: mhc1uga, proteasome-β 9b (psmb9b), psmb8f, and previously unknown genes psmb13b, tap2d, and tap2e We identify ancient lineages for Psmb13 within a proteasome branch previously thought to be monomorphic and provide evidence of substantial lineage diversity within each of three major trifurcations of catalytic-type proteasome subunits in vertebrates: Psmb5/Psmb8/Psmb11, Psmb6/Psmb9/Psmb12, and Psmb7/Psmb10/Psmb13. Strikingly, nearby tap2 and MHC class I genes also retain ancient sequence lineages, indicating that alternative lineages may have been preserved throughout the entire MHC pathway since early diversification of the adaptive immune system ∼500 Mya. Furthermore, polymorphisms within the three MHC pathway steps (antigen cleavage, transport, and presentation) are each predicted to alter peptide specificity. Lastly, comparative analysis shows that antigen processing gene diversity is far more extensive than previously realized (with ancient coelacanth psmb8 lineages, shark psmb13, and tap2t and psmb10 outside the teleost MHC), implying distinct immune functions and conserved roles in shaping MHC pathway evolution throughout vertebrates.
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Chan WF, Parks-Dely JA, Magor BG, Magor KE. The Minor MHC Class I Gene UDA of Ducks Is Regulated by Let-7 MicroRNA. THE JOURNAL OF IMMUNOLOGY 2016; 197:1212-20. [DOI: 10.4049/jimmunol.1600332] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/08/2016] [Indexed: 01/10/2023]
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Abstract
The concept of co-evolution (or co-adaptation) has a long history, but application at molecular levels (e.g., 'supergenes' in genetics) is more recent, with a consensus definition still developing. One interesting example is the chicken major histocompatibility complex (MHC). In contrast to typical mammals that have many class I and class I-like genes, only two classical class I genes, two CD1 genes and some non-classical Rfp-Y genes are known in chicken, and all are found on the microchromosome that bears the MHC. Rarity of recombination between the closely linked and polymorphic genes encoding classical class I and TAPs allows co-evolution, leading to a single dominantly expressed class I molecule in each MHC haplotype, with strong functional consequences in terms of resistance to infectious pathogens. Chicken tapasin is highly polymorphic, but co-evolution with TAP and class I genes remains unclear. T-cell receptors, natural killer (NK) cell receptors, and CD8 co-receptor genes are found on non-MHC chromosomes, with some evidence for co-evolution of surface residues and number of genes along the avian and mammalian lineages. Over even longer periods, co-evolution has been invoked to explain how the adaptive immune system of jawed vertebrates arose from closely linked receptor, ligand, and antigen-processing genes in the primordial MHC.
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Affiliation(s)
- Jim Kaufman
- Department of Pathology, University of Cambridge, Cambridge, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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Ohta Y, Flajnik MF. Coevolution of MHC genes (LMP/TAP/class Ia, NKT-class Ib, NKp30-B7H6): lessons from cold-blooded vertebrates. Immunol Rev 2016; 267:6-15. [PMID: 26284468 DOI: 10.1111/imr.12324] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Comparative immunology provides the long view of what is conserved across all vertebrate taxa versus what is specific to particular organisms or group of organisms. Regarding the major histocompatibility complex (MHC) and coevolution, three striking cases have been revealed in cold-blooded vertebrates: lineages of class Ia antigen-processing and -presenting genes, evolutionary conservation of NKT-class Ib recognition, and the ancient emergence of the natural cytotoxicity receptor NKp30 and its ligand B7H6. While coevolution of transporter associated with antigen processing (TAP) and class Ia has been documented in endothermic birds and two mammals, lineages of LMP7 are restricted to ectotherms. The unambiguous discovery of natural killer T (NKT) cells in Xenopus demonstrated that NKT cells are not restricted to mammals and are likely to have emerged at the same time in evolution as classical α/β and γ/δ T cells. NK cell receptors evolve at a rapid rate, and orthologues are nearly impossible to identify in different vertebrate classes. By contrast, we have detected NKp30 in all gnathostomes, except in species where it was lost. The recently discovered ligand of NKp30, B7H6, shows strong signs of coevolution with NKp30 throughout evolution, i.e. coincident loss or expansion of both genes in some species. NKp30 also offers an attractive IgSF candidate for the invasion of the RAG transposon, which is believed to have initiated T-cell receptor/immunoglobulin adaptive immunity. Besides reviewing these intriguing features of MHC evolution and coevolution, we offer suggestions for future studies and propose a model for the primordial or proto MHC.
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Affiliation(s)
- Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland Baltimore School of Medicine, Baltimore, MD, USA
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland Baltimore School of Medicine, Baltimore, MD, USA
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O'Connor EA, Strandh M, Hasselquist D, Nilsson JÅ, Westerdahl H. The evolution of highly variable immunity genes across a passerine bird radiation. Mol Ecol 2016; 25:977-89. [DOI: 10.1111/mec.13530] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 11/24/2015] [Accepted: 12/09/2015] [Indexed: 11/29/2022]
Affiliation(s)
- E. A. O'Connor
- Molecular Ecology and Evolution Lab; Lund University; Ecology building 223 62 Lund Sweden
| | - M. Strandh
- Molecular Ecology and Evolution Lab; Lund University; Ecology building 223 62 Lund Sweden
| | - D. Hasselquist
- Molecular Ecology and Evolution Lab; Lund University; Ecology building 223 62 Lund Sweden
| | - J.-Å. Nilsson
- Molecular Ecology and Evolution Lab; Lund University; Ecology building 223 62 Lund Sweden
| | - H. Westerdahl
- Molecular Ecology and Evolution Lab; Lund University; Ecology building 223 62 Lund Sweden
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Raghavan M, Geng J. HLA-B polymorphisms and intracellular assembly modes. Mol Immunol 2015; 68:89-93. [PMID: 26239417 DOI: 10.1016/j.molimm.2015.07.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/29/2015] [Accepted: 07/07/2015] [Indexed: 02/08/2023]
Abstract
Human leukocyte antigen (HLA) class I molecules are ligands for antigen receptors of cytotoxic T cells (CTL) and inhibitory receptors of natural killer (NK) cells. The high degree of HLA class I polymorphism allows for the selection of distinct and diverse sets of antigenic peptide ligands for presentation to CTL. The extensive polymorphisms of the HLA class I genes also result in large variations in their intracellular folding and assembly characteristics. Recent findings indicate that North American HLA-B variants differ significantly in the stabilities of their peptide-deficient forms and in the requirements for the endoplasmic reticulum (ER)-resident factor tapasin for proper assembly. In HIV-infected individuals, the presence of tapasin-independent HLA-B allotypes links to more rapid progression to death. Further studies are important to better understand how the intrinsic structural characteristics of HLA class I folding intermediates affect immune responses mediated by CTL and NK cells.
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Affiliation(s)
- Malini Raghavan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Jie Geng
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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