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Rani NA, Robin TB, Prome AA, Ahmed N, Moin AT, Patil RB, Sikder MNA, Bappy MNI, Afrin D, Hossain FMA, Islam T, Zinnah KMA. Development of multi epitope subunit vaccines against emerging carp viruses Cyprinid herpesvirus 1 and 3 using immunoinformatics approach. Sci Rep 2024; 14:11783. [PMID: 38782944 PMCID: PMC11116410 DOI: 10.1038/s41598-024-61074-7] [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: 07/02/2023] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
Cyprinid herpesvirus is a causative agent of a destructive disease in common and koi carp (Cyprinus carpio), which leads to substantial global financial losses in aquaculture industries. Among the strains of C. herpesvirus, C. herpesvirus 1 (CyHV-1) and C. herpesvirus 3 (CyHV-3) are known as highly pathogenic to carp fishes in Europe, Asia, and Africa. To date, no effective vaccine has been developed to combat these viruses. This study aimed to develop unique multi-epitope subunit vaccines targeting the CyHV-1 and CyHV-3 using a reverse vaccinology approach. The study began with a comprehensive literature review to identify the most critical proteins, which were then subjected to in silico analyses to predict highly antigenic epitopes. These analyses involved assessing antigenicity, transmembrane topology screening, allergenecity, toxicity, and molecular docking approaches. We constructed two multi-epitope-based vaccines incorporating a suitable adjuvant and appropriate linkers. It revealed that both the vaccines are non-toxic and immunogenic. The tertiary structures of the vaccine proteins were generated, refined, and validated to ensure their suitability. The binding affinity between the vaccine constructs and TLR3 and TLR5 receptors were assessed by molecular docking studies. Molecular dynamics simulations indicated that vaccine construct V1 exhibited greater stability with both TLR3 and TLR5 based on RMSD analysis. Hydrogen bond analysis revealed a stronger binding affinity between the vaccine constructs and TLR5 compared to TLR3. Furthermore, MM-PBSA analysis suggested that both vaccine constructs exhibited a better affinity for TLR5. Considering all aspects, the results suggest that in silico development of CyHV vaccines incorporating multiple epitopes holds promise for management of diseases caused by CyHV-1 and CyHV-3. However, further in vivo trials are highly recommended to validate the efficacies of these vaccines.
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Affiliation(s)
- Nurul Amin Rani
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Tanjin Barketullah Robin
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Anindita Ash Prome
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Nadim Ahmed
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Abu Tayab Moin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, 4331, Bangladesh
| | - Rajesh B Patil
- Department of Pharmaceutical Chemistry, Sinhgad College of Pharmacy, Sinhgad Technical Education Society's, Off Sinhgad Road, Vadgaon (Bk), Pune, Maharashtra, 411041, India
| | - Mohammad Nurul Azim Sikder
- Institute of Marine Sciences, Faculty of Marine Sciences and Fisheries, University of Chittagong, Chattogram, 4331, Bangladesh
| | - Md Nazmul Islam Bappy
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
- Department of Animal and Fish Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Dilruba Afrin
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
- Department of Animal and Fish Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Ferdaus Mohd Altaf Hossain
- Faculty of Veterinary, Animal and Biomedical Science, Sylhet Agricultural University, Sylhet, Bangladesh
- Department of Dairy Science, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh.
| | - Kazi Md Ali Zinnah
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
- Department of Animal and Fish Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
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Parker J, Marten SM, Ó Corcora TC, Rajkov J, Dubin A, Roth O. The effects of primary and secondary bacterial exposure on the seahorse (Hippocampus erectus) immune response. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 153:105136. [PMID: 38185263 DOI: 10.1016/j.dci.2024.105136] [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: 10/24/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/09/2024]
Abstract
Evolutionary adaptations in the Syngnathidae teleost family (seahorses, pipefish and seadragons) culminated in an array of spectacular morphologies, key immune gene losses, and the enigmatic male pregnancy. In seahorses, genome modifications associated with immunoglobulins, complement, and major histocompatibility complex (MHC II) pathway components raise questions concerning their immunological efficiency and the evolution of compensatory measures that may act in their place. In this investigation heat-killed bacteria (Vibrio aestuarianus and Tenacibaculum maritimum) were used in a two-phased experiment to assess the immune response dynamics of Hippocampus erectus. Gill transcriptomes from double and single-exposed individuals were analysed in order to determine the differentially expressed genes contributing to immune system responses towards immune priming. Double-exposed individuals exhibited a greater adaptive immune response when compared with single-exposed individuals, while single-exposed individuals, particularly with V. aestuarianus replicates, associated more with the innate branch of the immune system. T. maritimum double-exposed replicates exhibited the strongest immune reaction, likely due to their immunological naivety towards the bacterium, while there are also potential signs of innate trained immunity. MHC II upregulated expression was identified in selected V. aestuarianus-exposed seahorses, in the absence of other pathway constituents suggesting a possible alternative or non-classical MHC II immune function in seahorses. Gene Ontology (GO) enrichment analysis highlighted prominent angiogenesis activity following secondary exposure, which could be linked to an adaptive immune process in seahorses. This investigation highlights the prominent role of T-cell mediated adaptive immune responses in seahorses when exposed to sequential foreign bacteria exposures. If classical MHC II pathway function has been lost, innate trained immunity in syngnathids could be a potential compensatory mechanism.
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Affiliation(s)
- Jamie Parker
- Marine Evolutionary Biology, Christian-Albrechts-University, D-24118, Kiel, Germany.
| | - Silke-Mareike Marten
- Marine Evolutionary Biology, Christian-Albrechts-University, D-24118, Kiel, Germany
| | - Tadhg C Ó Corcora
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, D-24105, Kiel, Germany
| | - Jelena Rajkov
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, D-24105, Kiel, Germany
| | - Arseny Dubin
- Marine Evolutionary Biology, Christian-Albrechts-University, D-24118, Kiel, Germany
| | - Olivia Roth
- Marine Evolutionary Biology, Christian-Albrechts-University, D-24118, Kiel, Germany
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Takizawa F, Hashimoto K, Miyazawa R, Ohta Y, Veríssimo A, Flajnik MF, Parra D, Tokunaga K, Suetake H, Sunyer JO, Dijkstra JM. CD4 and LAG-3 from sharks to humans: related molecules with motifs for opposing functions. Front Immunol 2023; 14:1267743. [PMID: 38187381 PMCID: PMC10768021 DOI: 10.3389/fimmu.2023.1267743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
CD4 and LAG-3 are related molecules that are receptors for MHC class II molecules. Their major functional differences are situated in their cytoplasmic tails, in which CD4 has an activation motif and LAG-3 an inhibitory motif. Here, we identify shark LAG-3 and show that a previously identified shark CD4-like gene has a genomic location, expression pattern, and motifs similar to CD4 in other vertebrates. In nurse shark (Ginglymostoma cirratum) and cloudy catshark (Scyliorhinus torazame), the highest CD4 expression was consistently found in the thymus whereas such was not the case for LAG-3. Throughout jawed vertebrates, the CD4 cytoplasmic tail possesses a Cx(C/H) motif for binding kinase LCK, and the LAG-3 cytoplasmic tail possesses (F/Y)xxL(D/E) including the previously determined FxxL inhibitory motif resembling an immunoreceptor tyrosine-based inhibition motif (ITIM). On the other hand, the acidic end of the mammalian LAG-3 cytoplasmic tail, which is believed to have an inhibitory function as well, was acquired later in evolution. The present study also identified CD4-1, CD4-2, and LAG-3 in the primitive ray-finned fishes bichirs, sturgeons, and gars, and experimentally determined these sequences for sterlet sturgeon (Acipenser ruthenus). Therefore, with CD4-1 and CD4-2 already known in teleosts (modern ray-finned fish), these two CD4 lineages have now been found within all major clades of ray-finned fish. Although different from each other, the cytoplasmic tails of ray-finned fish CD4-1 and chondrichthyan CD4 not only contain the Cx(C/H) motif but also an additional highly conserved motif which we expect to confer a function. Thus, although restricted to some species and gene copies, in evolution both CD4 and LAG-3 molecules appear to have acquired functional motifs besides their canonical Cx(C/H) and ITIM-like motifs, respectively. The presence of CD4 and LAG-3 molecules with seemingly opposing functions from the level of sharks, the oldest living vertebrates with a human-like adaptive immune system, underlines their importance for the jawed vertebrate immune system. It also emphasizes the general need of the immune system to always find a balance, leading to trade-offs, between activating and inhibiting processes.
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Affiliation(s)
- Fumio Takizawa
- Faculty of Marine Science and Technology, Fukui Prefectural University, Obama, Fukui, Japan
| | - Keiichiro Hashimoto
- Emeritus Professor, Center for Medical Science, Fujita Health University, Toyoake, Aichi, Japan
| | - Ryuichiro Miyazawa
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, United States
| | - Ana Veríssimo
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Martin F. Flajnik
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, United States
| | | | | | - Hiroaki Suetake
- Faculty of Marine Science and Technology, Fukui Prefectural University, Obama, Fukui, Japan
| | - J. Oriol Sunyer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
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Veríssimo A, Castro LFC, Muñoz-Mérida A, Almeida T, Gaigher A, Neves F, Flajnik MF, Ohta Y. An Ancestral Major Histocompatibility Complex Organization in Cartilaginous Fish: Reconstructing MHC Origin and Evolution. Mol Biol Evol 2023; 40:msad262. [PMID: 38059517 PMCID: PMC10751288 DOI: 10.1093/molbev/msad262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023] Open
Abstract
Cartilaginous fish (sharks, rays, and chimeras) comprise the oldest living jawed vertebrates with a mammalian-like adaptive immune system based on immunoglobulins (Ig), T-cell receptors (TCRs), and the major histocompatibility complex (MHC). Here, we show that the cartilaginous fish "adaptive MHC" is highly regimented and compact, containing (i) a classical MHC class Ia (MHC-Ia) region containing antigen processing (antigen peptide transporters and immunoproteasome) and presenting (MHC-Ia) genes, (ii) an MHC class II (MHC-II) region (with alpha and beta genes) with linkage to beta-2-microglobulin (β2m) and bromodomain-containing 2, (iii) nonclassical MHC class Ib (MHC-Ib) regions with 450 million-year-old lineages, and (iv) a complement C4 associated with the MHC-Ia region. No MHC-Ib genes were found outside of the elasmobranch MHC. Our data suggest that both MHC-I and MHC-II genes arose after the second round of whole-genome duplication (2R) on a human chromosome (huchr) 6 precursor. Further analysis of MHC paralogous regions across early branching taxa from all jawed vertebrate lineages revealed that Ig/TCR genes likely arose on a precursor of the huchr9/12/14 MHC paralog. The β2m gene is linked to the Ig/TCR genes in some vertebrates suggesting that it was present at 1R, perhaps as the donor of C1 domain to the primordial MHC gene. In sum, extant cartilaginous fish exhibit a conserved and prototypical MHC genomic organization with features found in various vertebrates, reflecting the ancestral arrangement for the jawed vertebrates.
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Affiliation(s)
- Ana Veríssimo
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - L Filipe C Castro
- Department of Biology, Faculty of Sciences, University of Porto, Porto 4169-007, Portugal
- CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
| | - Antonio Muñoz-Mérida
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - Tereza Almeida
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - Arnaud Gaigher
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Fabiana Neves
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
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Ravindranath MH, Ravindranath NM, Selvan SR, Hilali FE, Amato-Menker CJ, Filippone EJ. Cell Surface B2m-Free Human Leukocyte Antigen (HLA) Monomers and Dimers: Are They Neo-HLA Class and Proto-HLA? Biomolecules 2023; 13:1178. [PMID: 37627243 PMCID: PMC10452486 DOI: 10.3390/biom13081178] [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: 05/19/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 08/27/2023] Open
Abstract
Cell surface HLA-I molecules (Face-1) consist of a polypeptide heavy chain (HC) with two groove domains (G domain) and one constant domain (C-domain) as well as a light chain, B2-microglobulin (B2m). However, HCs can also independently emerge unfolded on the cell surface without peptides as B2m-free HC monomers (Face-2), B2m-free HC homodimers (Face 3), and B2m-free HC heterodimers (Face-4). The transport of these HLA variants from ER to the cell surface was confirmed by antiviral antibiotics that arrest the release of newly synthesized proteins from the ER. Face-2 occurs at low levels on the normal cell surface of the lung, bronchi, epidermis, esophagus, breast, stomach, ilium, colorectum, gall bladder, urinary bladder, seminal vesicles ovarian epithelia, endometrium, thymus, spleen, and lymphocytes. They are upregulated on immune cells upon activation by proinflammatory cytokines, anti-CD3 antibodies, antibiotics (e.g., ionomycin), phytohemagglutinin, retinoic acid, and phorbol myristate acetate. Their density on the cell surface remains high as long as the cells remain in an activated state. After activation-induced upregulation, the Face-2 molecules undergo homo- and hetero-dimerization (Face-3 and Face-4). Alterations in the redox environment promote dimerization. Heterodimerization can occur among and between the alleles of different haplotypes. The glycosylation of these variants differ from that of Face-1, and they may occur with bound exogenous peptides. Spontaneous arthritis occurs in HLA-B27+ mice lacking B2m (HLA-B27+ B2m-/-) but not in HLA-B27+ B2m+/- mice. The mice with HLA-B27 in Face-2 spontaneous configuration develop symptoms such as changes in nails and joints, hair loss, and swelling in paws, leading to ankyloses. Anti-HC-specific mAbs delay disease development. Some HLA-I polyreactive mAbs (MEM series) used for immunostaining confirm the existence of B2m-free variants in several cancer cells. The upregulation of Face-2 in human cancers occurs concomitantly with the downregulation of intact HLAs (Face-1). The HLA monomeric and dimeric variants interact with inhibitory and activating ligands (e.g., KIR), growth factors, cytokines, and neurotransmitters. Similarities in the amino acid sequences of the HLA-I variants and HLA-II β-chain suggest that Face-2 could be the progenitor of both HLA classes. These findings may support the recognition of these variants as a neo-HLA class and proto-HLA.
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Affiliation(s)
- Mepur H. Ravindranath
- Department of Hematology and Oncology, Children’s Hospital, Los Angeles, CA 90027, USA
- Terasaki Foundation Laboratory, Santa Monica, CA 90064, USA
| | - Narendranath M. Ravindranath
- Norris Dental Science Center, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90089, USA;
| | - Senthamil R. Selvan
- Division of Immunology and Hematology Devices, OHT 7: Office of In Vitro Diagnostics, Office of Product Evaluation and Quality, Center for Devices and Radiological Health, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA;
| | - Fatiha El Hilali
- Medico-Surgical, Biomedicine and Infectiology Research Laboratory, The Faculty of Medicine and Pharmacy of Laayoune & Agadir, Ibnou Zohr University, Agadir 80000, Morocco;
| | - Carly J. Amato-Menker
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV 26506, USA;
| | - Edward J. Filippone
- Division of Nephrology, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19145, USA;
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Jungi SV, Machimbirike VI, Linh NV, Sangsuriya P, Salin KR, Senapin S, Dong HT. Synthetic peptides derived from predicted B cell epitopes of nervous necrosis virus (NNV) show antigenicity and elicit immunogenic responses in Asian seabass (Lates calcarifer). FISH & SHELLFISH IMMUNOLOGY 2023:108854. [PMID: 37253409 DOI: 10.1016/j.fsi.2023.108854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 05/24/2023] [Accepted: 05/28/2023] [Indexed: 06/01/2023]
Abstract
Nervous necrosis virus (NNV) has spread throughout the world, affecting more than 120 freshwater and marine fish species. While vaccination effectively prevents disease outbreaks, the difficulty of producing sufficient viruses using cell lines continues to be a significant disadvantage for producing inactivated vaccines. This study, therefore, explored the application of synthetic peptides as potential vaccine candidates for the prevention of NNV in Asian seabass (Lates calcarifer). Using the epitope prediction tool and molecular docking, three predicted immunogenic B cell epitopes (30-32 aa) derived from NNV coat protein were selected and synthesised, corresponding to amino acid positions 5 to 34 (P1), 133 to 162 (P2) and 181 to 212 (P3). All the predicted peptides interact with Asian sea bass's MHC class II by docking. The antigenicity of these peptides was determined through ELISA and all peptides were able to react with NNV-specific antibodies. Subsequently, the immunogenicity of these synthetic peptides was investigated by immunisation of Asian seabass with individual peptides (30 μg/fish) and a peptide cocktail (P1+P2+P3, 10 μg each/fish) by intraperitoneal injection, followed by a booster dose at day 28 post-primary immunisation. There was a subset of immunised fish that were able to induce upregulation of immune genes (IL-1β, TNFα, MHCI, MHCII β, CD4, CD8, and IgM-like) in the head kidney and spleen post immunization. Importantly, antibodies derived from fish immunised with synthetic peptides reacted with whole NNV virions, and sera from P1 group could neutralise NNV in an in vitro assay. Taken together, these findings indicate that synthetic linear peptides based on predicted B cell epitopes exhibited both antigenic and immunogenic properties, suggesting that they could be potential vaccine candidates for the prevention of NNV in fish.
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Affiliation(s)
- Sumit Vinod Jungi
- Aquaculture and Aquatic Resources Management, School of Environment, Resources and Development, Asian Institute of Technology, Pathum Thanim, 12120, Thailand
| | - Vimbai Irene Machimbirike
- Marine Microbial Pathogenesis and Vaccinology Lab, Department of Ocean Sciences, Memorial University, St. John's, A1C 5S7, NL, Canada
| | - Nguyen Vu Linh
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand; Center of Excellence in Material Science and Technology, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Pakkakul Sangsuriya
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand; Aquatic Molecular Genetics and Biotechnology Research Team, BIOTEC, NSTDA, Pathum Thani, 12120, Thailand
| | - Krishna R Salin
- Aquaculture and Aquatic Resources Management, School of Environment, Resources and Development, Asian Institute of Technology, Pathum Thanim, 12120, Thailand
| | - Saengchan Senapin
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand; Fish Heath Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Ha Thanh Dong
- Aquaculture and Aquatic Resources Management, School of Environment, Resources and Development, Asian Institute of Technology, Pathum Thanim, 12120, Thailand.
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Dijkstra JM, Kondo Y. Comprehensive Sequence Analysis of Parvalbumins in Fish and Their Comparison with Parvalbumins in Tetrapod Species. BIOLOGY 2022; 11:biology11121713. [PMID: 36552222 PMCID: PMC9774829 DOI: 10.3390/biology11121713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/18/2022] [Accepted: 11/19/2022] [Indexed: 11/29/2022]
Abstract
Parvalbumins are small molecules with important functions in Ca2+ signaling, but their sequence comparisons to date, especially in fish, have been relatively poor. We here, characterize sequence motifs that distinguish parvalbumin subfamilies across vertebrate species, as well as those that distinguish individual parvalbumins (orthologues) in fish, and map them to known parvalbumin structures. As already observed by others, all classes of jawed vertebrates possess parvalbumins of both the α-parvalbumin and oncomodulin subfamilies. However, we could not find convincing phylogenetic support for the common habit of classifying all non-α-parvalbumins together as "β-parvalbumins." In teleost (modern bony) fish, we here distinguish parvalbumins 1-to-10, of which the gene copy number can differ between species. The genes for α-parvalbumins (pvalb6 and pvalb7) and oncomodulins (pvalb8 and pvalb9) are well conserved between teleost species, but considerable variation is observed in their copy numbers of the non-α/non-oncomodulin genes pvalb1-to-5 and pvalb10. Teleost parvalbumins 1-to-4 are hardly distinguishable from each other and are highly expressed in muscle, and described allergens belong to this subfamily. However, in some fish species α-parvalbumin expression is also high in muscle. Pvalb5 and pvalb10 molecules form distinct lineages, the latter even predating the origin of teleosts, but have been lost in some teleost species. The present study aspires to be a frame of reference for future studies trying to compare different parvalbumins.
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Affiliation(s)
- Johannes M. Dijkstra
- Center for Medical Science, Fujita Health University, Dengaku-gakubo 1-98, Toyoake 470-1192, Japan
| | - Yasuto Kondo
- Department of Pediatrics, Fujita Health University Bantane Hospital, Otobashi 3-6-10, Nakagawa, Nagoya 454-8509, Japan
- Correspondence:
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Islam SI, Mou MJ, Sanjida S. Application of reverse vaccinology to design a multi-epitope subunit vaccine against a new strain of Aeromonas veronii. J Genet Eng Biotechnol 2022; 20:118. [PMID: 35939149 PMCID: PMC9358925 DOI: 10.1186/s43141-022-00391-8] [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: 03/10/2022] [Accepted: 07/04/2022] [Indexed: 11/18/2022]
Abstract
Background Aeromonas veronii is one of the most common pathogens of freshwater fishes that cause sepsis and ulcers. There are increasing numbers of cases showing that it is a significant zoonotic and aquatic agent. Epidemiological studies have shown that A. veronii virulence and drug tolerance have both increased over the last few years as a result of epidemiological investigations. Cadaverine reverse transporter (CadB) and maltoporin (LamB protein) contribute to the virulence of A. veronii TH0426. TH0426 strain is currently showing severe cases on fish species, and its resistance against therapeutic has been increasing. Despite these devastating complications, there is still no effective cure or vaccine for this strain of A.veronii. Results In this regard, an immunoinformatic method was used to generate an epitope-based vaccine against this pathogen. The immunodominant epitopes were identified using the CadB and LamB protein of A. veronii. The final constructed vaccine sequence was developed to be immunogenic, non-allergenic as well as have better solubility. Molecular dynamic simulation revealed significant binding stability and structural compactness. Finally, using Escherichia coli K12 as a model, codon optimization yielded ideal GC content and a higher CAI value, which was then included in the cloning vector pET2+ (a). Conclusion Altogether, our outcomes imply that the proposed peptide vaccine might be a good option for A. veronii TH0426 prophylaxis.
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Affiliation(s)
- Sk Injamamul Islam
- Department of Fisheries and Marine Bioscience, Faculty of Biological Science, Jashore University of Science and Technology, Jashore, 7408, Bangladesh. .,Center of Excellence in Fish Infectious Diseases (CE FID), Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand. .,The International Graduate Program of Veterinary Science and Technology (VST), Department of Veterinary Microbiology, Faculty of Veterinary Science and Technology, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Moslema Jahan Mou
- Department of Genetic Engineering and Biotechnology, Faculty of Life and Earth Science, University of Rajshahi, Rajshahi, Bangladesh
| | - Saloa Sanjida
- Department of Environmental Science and Technology, Faculty of Applied Science and Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
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Some thoughts about what non-mammalian jawed vertebrates are telling us about antigen processing and peptide loading of MHC molecules. Curr Opin Immunol 2022; 77:102218. [PMID: 35687979 PMCID: PMC9586880 DOI: 10.1016/j.coi.2022.102218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/19/2022] [Accepted: 05/10/2022] [Indexed: 12/11/2022]
Abstract
The major histocompatibility complex (MHC) of mammals encodes highly polymorphic classical class I and class II molecules with crucial roles in immune responses, as well as various nonclassical molecules encoded by the MHC and elsewhere in the genome that have a variety of functions. These MHC molecules are supported by antigen processing and peptide loading pathways which are well-understood in mammals. This review considers what has been learned about the MHC, MHC molecules and the supporting pathways in non-mammalian jawed vertebrates. From the initial understanding from work with the chicken MHC, a great deal of diversity in the structure and function has been found. Are there underlying principles? The genomic organisation of the MHC varies enormously across jawed vertebrates. Total numbers of MHC genes vary among vertebrates, with only a few classical MHC genes. Some nonclassical MHC and classical pathway genes appear earlier than others. Obvious co-evolution within MHC pathways occurs in some species, but not others. The promiscuity of interactions may correlate with differences in genomic organisation.
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Use of Integrated Core Proteomics, Immuno-Informatics, and In Silico Approaches to Design a Multiepitope Vaccine against Zoonotic Pathogen Edwardsiella tarda. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2020031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Multidrug-resistant Edwardsiella tarda has been reported as the main causative agent for massive fish mortality. The pathogen is well-known for causing hemorrhagic septicemia in fish and has been linked to gastrointestinal infections in humans. Formalin-inactivated Edwardsiella vaccination has previously been found to be ineffective in aquaculture species. Therefore, based on E. tarda’s integrated core complete sequenced genomes, the study aimed to design a subunit vaccine based on T and B cell epitopes employing immunoinformatics approach. Initially, the top immunodominant and antigenic epitopes were predicted from the core complete sequenced genomes of the E. tarda genome and designed the vaccine by using linkers and adjuvant. In addition, vaccine 3D structure was predicted followed by refinement, and molecular docking was performed for the analysis of interacting residues between vaccines with TLR5, MHC-I, and MHC-II, respectively. The final vaccine constructs demonstrated strong hydrogen bond interactions. Molecular dynamic simulation of vaccine-TLR5 receptor complex showed a stable structural binding and compactness. Furthermore, E. coli used as a model organism for codon optimization proved optimal GC content and CAI value, which were subsequently cloned in vector pET2+ (a). Overall, the findings of the study imply that the designed epitope vaccine might be a good option for prophylaxis for E. tarda.
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Wong ATC, Lam DK, Poon ESK, Chan DTC, Sin SYW. Intra-specific copy number variation of MHC class II genes in the Siamese fighting fish. Immunogenetics 2022; 74:327-346. [PMID: 35229174 DOI: 10.1007/s00251-022-01255-8] [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: 09/12/2021] [Accepted: 02/04/2022] [Indexed: 11/28/2022]
Abstract
Duplicates of genes for major histocompatibility complex (MHC) molecules can be subjected to selection independently and vary markedly in their evolutionary rates, sequence polymorphism, and functional roles. Therefore, without a thorough understanding of their copy number variation (CNV) in the genome, the MHC-dependent fitness consequences within a species could be misinterpreted. Studying the intra-specific CNV of this highly polymorphic gene, however, has long been hindered by the difficulties in assigning alleles to loci and the lack of high-quality genomic data. Here, using the high-quality genome of the Siamese fighting fish (Betta splendens), a model for mate choice studies, and the whole-genome sequencing (WGS) data of 17 Betta species, we achieved locus-specific amplification of their three classical MHC class II genes - DAB1, DAB2, and DAB3. By performing quantitative PCR and depth-of-coverage analysis using the WGS data, we revealed intra-specific CNV at the DAB3 locus. We identified individuals that had two allelic copies (i.e., heterozygous or homozygous) or one allele (i.e., hemizygous) and individuals without this gene. The CNV was due to the deletion of a 20-kb-long genomic region harboring both the DAA3 and DAB3 genes. We further showed that the three DAB genes were under different modes of selection, which also applies to their corresponding DAA genes that share similar pattern of polymorphism. Our study demonstrates a combined approach to study CNV within a species, which is crucial for the understanding of multigene family evolution and the fitness consequences of CNV.
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Affiliation(s)
- Anson Tsz Chun Wong
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Derek Kong Lam
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Emily Shui Kei Poon
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - David Tsz Chung Chan
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China.
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Tian HF, Hu Q, Lu HY, Li Z. Chromosome-Scale, Haplotype-Resolved Genome Assembly of Non-Sex-Reversal Females of Swamp Eel Using High-Fidelity Long Reads and Hi-C Data. Front Genet 2022; 13:903185. [PMID: 35669182 PMCID: PMC9165713 DOI: 10.3389/fgene.2022.903185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
The Asian swamp eel (Monopterus albus) is an excellent model species for studying sex change and chromosome evolution. M. albus is also widely reared in East Asia and South-East Asia because of its great nutritional value. The low fecundity of this species (about 300 eggs per fish) greatly hinders fries production and breeding programs. Interestingly, about 3–5% of the eels could remain as females for 3 years and lay more than 3,000 eggs per fish, which are referred to as non-sex-reversal (NSR) females. Here, we presented a new chromosome-level genome assembly of such NSR females using Illumina, HiFi, and Hi-C sequencing technologies. The new assembly (Mal.V2_NSR) is 838.39 Mb in length, and the N50 of the contigs is 49.8 Mb. Compared with the previous assembly obtained using the continuous long-read sequencing technology (Mal.V1_CLR), we found a remarkable increase of continuity in the new assembly Mal.V2_NSR with a 20-times longer contig N50. Chromosomes 2 and 12 were assembled into a single contig, respectively. Meanwhile, two highly contiguous haplotype assemblies were also obtained, with contig N50 being 14.54 and 12.13 Mb, respectively. BUSCO and Merqury analyses indicate completeness and high accuracy of these three assemblies. A comparative genomic analysis revealed substantial structural variations (SVs) between Mal.V2_NSR and Mal.V1_CLR and two phased haplotype assemblies, as well as whole chromosome fusion events when compared with the zig-zag eel. Additionally, our newly obtained assembly provides a genomic view of sex-related genes and a complete landscape of the MHC genes. Therefore, these high-quality genome assemblies would provide great help for future breeding works of the swamp eel, and it is a valuable new reference for genetic and genomic studies of this species.
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Affiliation(s)
- Hai-Feng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Qiaomu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Hong-Yi Lu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Zhong Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
- *Correspondence: Zhong Li,
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Antigen Presentation and Autophagy in Teleost Adaptive Immunity. Int J Mol Sci 2022; 23:ijms23094899. [PMID: 35563287 PMCID: PMC9103719 DOI: 10.3390/ijms23094899] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 01/27/2023] Open
Abstract
Infectious diseases are a burden for aquaculture. Antigen processing and presentation (APP) to the immune effector cells that fight pathogens is key in the adaptive immune response. At the core of the adaptive immunity that appeared in lower vertebrates during evolution are the variable genes encoding the major histocompatibility complex (MHC). MHC class I molecules mainly present peptides processed in the cytosol by the proteasome and transported to the cell surface of all cells through secretory compartments. Professional antigen-presenting cells (pAPC) also express MHC class II molecules, which normally present peptides processed from exogenous antigens through lysosomal pathways. Autophagy is an intracellular self-degradation process that is conserved in all eukaryotes and is induced by starvation to contribute to cellular homeostasis. Self-digestion during autophagy mainly occurs by the fusion of autophagosomes, which engulf portions of cytosol and fuse with lysosomes (macroautophagy) or assisted by chaperones (chaperone-mediated autophagy, CMA) that deliver proteins to lysosomes. Thus, during self-degradation, antigens can be processed to be presented by the MHC to immune effector cells, thus, linking autophagy to APP. This review is focused on the essential components of the APP that are conserved in teleost fish and the increasing evidence related to the modulation of APP and autophagy during pathogen infection.
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Islam SI, Mou MJ, Sanjida S, Tariq M, Nasir S, Mahfuj S. Designing a novel mRNA vaccine against Vibrio harveyi infection in fish: an immunoinformatics approach. Genomics Inform 2022; 20:e11. [PMID: 35399010 PMCID: PMC9002004 DOI: 10.5808/gi.21065] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/07/2022] [Indexed: 11/20/2022] Open
Abstract
Vibrio harveyi belongs to the family Vibrionaceae of class Gammaproteobacteria. Around 12 Vibrio species can cause gastroenteritis (gastrointestinal illness) in humans. A large number of bacterial particles can be found in the infected cells, which may cause death. Despite these devastating complications, there is still no cure or vaccine for the bacteria. As a result, we used an immunoinformatics approach to develop a multi-epitope vaccine against the most pathogenic hemolysin gene of V. harveyi. The immunodominant T- and B-cell epitopes were identified using the hemolysin protein. We developed a vaccine employing three possible epitopes: cytotoxic T-lymphocytes, helper T-lymphocytes, and linear B-lymphocyte epitopes, after thorough testing. The vaccine was developed to be antigenic, immunogenic, and non-allergenic, as well as have a better solubility. Molecular dynamics simulation revealed significant structural stiffness and binding stability. In addition, the immunological simulation generated by computers revealed that the vaccination might elicit immune reactions Escherichia coli K12 as a model, codon optimization yielded ideal GC content and a higher codon adaptation index value, which was then included in the cloning vector pET2+ (a). Altogether, our experiment implies that the proposed peptide vaccine might be a good option for vibriosis prophylaxis.
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Affiliation(s)
- Sk Injamamul Islam
- Department of Fisheries and Marine Bioscience, Faculty of Biological Science, Jashore University of Science and Technology, Jashore 7408, Bangladesh.,Chulalongkorn University, Department of Veterinary Microbiology, Faculty of Veterinary Science and Technology, Bangkok 10330, Thailand
| | - Moslema Jahan Mou
- Department of Genetic Engineering & Biotechnology, Faculty of Earth and Life Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Saloa Sanjida
- Department of Environmental Science and Technology, Faculty of Applied Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Muhammad Tariq
- Department of Biotechnology, Faculty of Biological Sciences, University of Malakand, Chakdara 18800, Pakistan
| | - Saad Nasir
- Department of Clinical Medicine and Surgery, Faculty of Veterinary Medicine, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Sarower Mahfuj
- Department of Fisheries and Marine Bioscience, Faculty of Biological Science, Jashore University of Science and Technology, Jashore 7408, Bangladesh
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Campos-Sánchez JC, Mayor-Lafuente J, Guardiola FA, Esteban MÁ. In silico and gene expression analysis of the acute inflammatory response of gilthead seabream (Sparus aurata) after subcutaneous administration of carrageenin. FISH PHYSIOLOGY AND BIOCHEMISTRY 2021; 47:1623-1643. [PMID: 34448108 PMCID: PMC8478728 DOI: 10.1007/s10695-021-00999-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 08/08/2021] [Indexed: 05/17/2023]
Abstract
Inflammation is one of the main causes of loss of homeostasis at both the systemic and molecular levels. The aim of this study was to investigate in silico the conservation of inflammation-related proteins in the gilthead seabream (Sparus aurata L.). Open reading frames of the selected genes were used as input in the STRING database for protein-protein interaction network analysis, comparing them with other teleost protein sequences. Proteins of the large yellow croaker (Larimichthys crocea L.) presented the highest percentages of identity with the gilthead seabream protein sequence. The gene expression profile of these proteins was then studied in gilthead seabream specimens subcutaneously injected with carrageenin (1%) or phosphate-buffered saline (control) by analyzing skin samples from the injected zone 12 and 24 h after injection. Gene expression analysis indicated that the mechanisms necessary to terminate the inflammatory response to carrageenin and recover skin homeostasis were activated between 12 and 24 h after injection (at the tested dose). The gene analysis performed in this study could contribute to the identification of the main mechanisms of acute inflammatory response and validate the use of carrageenin as an inflammation model to elucidate these mechanisms in fish.
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Affiliation(s)
- Jose Carlos Campos-Sánchez
- Immunobiology for Aquaculture Group, Department of Cell Biology and Histology, Faculty of Biology, University of Murcia, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", 30100, Murcia, Spain
| | - Javier Mayor-Lafuente
- Immunobiology for Aquaculture Group, Department of Cell Biology and Histology, Faculty of Biology, University of Murcia, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", 30100, Murcia, Spain
| | - Francisco A Guardiola
- Immunobiology for Aquaculture Group, Department of Cell Biology and Histology, Faculty of Biology, University of Murcia, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", 30100, Murcia, Spain
| | - María Ángeles Esteban
- Immunobiology for Aquaculture Group, Department of Cell Biology and Histology, Faculty of Biology, University of Murcia, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", 30100, Murcia, Spain.
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Won H, Jeon HB, Kim DY, Suk HY. Differential patterns of diversity at neutral and adaptive loci in endangered Rhodeus pseudosericeus populations. Sci Rep 2021; 11:15953. [PMID: 34354168 PMCID: PMC8342555 DOI: 10.1038/s41598-021-95385-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
Given the fact that threatened species are often composed of isolated small populations, spatial continuity or demography of the populations may be major factors that have shaped the species' genetic diversity. Thus, neutral loci have been the most commonly-used markers in conservation genetics. However, the populations under the influence of different environmental factors may have evolved in response to different selective pressures, which cannot be fully reflected in neutral genetic variation. Rhodeus pseudosericeus, a bitterling species (Acheilognathidae; Cypriniformes) endemic to the Korean Peninsula, are only found in some limited areas of three rivers, Daecheon, Han and Muhan, that flow into the west coast. Here, we genotyped 24 microsatellite loci and two loci (DAB1 and DAB3) of MHC class II peptide-binding β1 domain for 222 individuals collected from seven populations. Our microsatellite analysis revealed distinctive differentiation between the populations of Daecheon and Muhan Rivers and the Han River populations, and populations were structured into two subgroups within the Han River. Apparent positive selection signatures were found in the peptide-binding residues (PBRs) of the MHC loci. The allelic distribution of MHC showed a degree of differentiation between the populations of Daecheon and Muhan Rivers and the Han River populations, partially similar to the results obtained for microsatellites, however showed rather complex patterns among populations in the Han River. Considering the apparent differences in the distribution of supertypes obtained based on the physicochemical differences induced by the polymorphisms of these PBRs, the differentiation in DAB1 between the two regional groups may result in the differences in immune function. No differentiation between these two regions was observed in the supertyping of DAB3, probably indicating that only DAB1 was associated with the response to locally specialized antigenic peptides.
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Affiliation(s)
- Hari Won
- grid.413028.c0000 0001 0674 4447Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do South Korea ,grid.410319.e0000 0004 1936 8630Department of Biology, Concordia University, 7141 Sherbrooke W., Montreal, QC H4B 1R6 Canada
| | - Hyung-Bae Jeon
- grid.410319.e0000 0004 1936 8630Department of Biology, Concordia University, 7141 Sherbrooke W., Montreal, QC H4B 1R6 Canada
| | - Dong-Young Kim
- grid.413028.c0000 0001 0674 4447Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do South Korea
| | - Ho Young Suk
- grid.413028.c0000 0001 0674 4447Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do South Korea
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Wu Y, Zhang N, Wei X, Lu S, Li S, Hashimoto K, Dijkstra JM, Xia C. The Structure of a Peptide-Loaded Shark MHC Class I Molecule Reveals Features of the Binding between β 2-Microglobulin and H Chain Conserved in Evolution. THE JOURNAL OF IMMUNOLOGY 2021; 207:308-321. [PMID: 34145057 DOI: 10.4049/jimmunol.2001165] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/23/2021] [Indexed: 12/22/2022]
Abstract
Cartilaginous fish are the most primitive extant species with MHC molecules. Using the nurse shark, the current study is, to the best of our knowledge, the first to present a peptide-loaded MHC class I (pMHC-I) structure for this class of animals. The overall structure was found to be similar between cartilaginous fish and bony animals, showing remarkable conservation of interactions between the three pMHC-I components H chain, β2-microglobulin (β2-m), and peptide ligand. In most previous studies, relatively little attention was given to the details of binding between the H chain and β2-m, and our study provides important new insights. A pronounced conserved feature involves the insertion of a large β2-m F56+W60 hydrophobic knob into a pleat of the β-sheet floor of the H chain α1α2 domain, with the knob being surrounded by conserved residues. Another conserved feature is a hydrogen bond between β2-m Y10 and a proline in the α3 domain of the H chain. By alanine substitution analysis, we found that the conserved β2-m residues Y10, D53, F56, and W60-each binding the H chain-are required for stable pMHC-I complex formation. For the β2-m residues Y10 and F56, such observations have not been reported before. The combined data indicate that for stable pMHC-I complex formation β2-m should not only bind the α1α2 domain but also the α3 domain. Knowing the conserved structural features of pMHC-I should be helpful for future elucidations of the mechanisms of pMHC-I complex formation and peptide editing.
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Affiliation(s)
- Yanan Wu
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China; and
| | - Nianzhi Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China; and
| | - Xiaohui Wei
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China; and
| | - Shuangshuang Lu
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China; and
| | - Shen Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China; and
| | - Keiichiro Hashimoto
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Johannes M Dijkstra
- 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; and
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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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Major histocompatibility complex genes and locus organization in the Komodo dragon (Varanus komodoensis). Immunogenetics 2021; 73:405-417. [PMID: 33978784 DOI: 10.1007/s00251-021-01217-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/25/2021] [Indexed: 10/21/2022]
Abstract
We performed a meta-analysis of the newly assembled Komodo dragon (Varanus komodoensis) genome to characterize the major histocompatibility complex (MHC) of the species. The MHC gene clusters of the Komodo dragon are gene dense, complex, and contain counterparts of many genes of the human MHC. Our analysis identified 20 contigs encompassing ~ 6.9 Mbp of sequence with 223 annotated genes of which many are predicted orthologs to the genes of the human MHC. These MHC contigs range in size from 13.2 kb to 21.5 Mbp, contain an average of one gene per 30 kb, and are thought to occur on at least two chromosomes. Eight contigs, each > 100 kb, could be aligned to the human MHC based on gene content, and these represent gene clusters found in each of the recognized mammalian MHC subregions. The MHC of the Komodo dragon shares organizational features of other non-mammalian taxa. Multiple class Iα and class IIβ genes are indicated, with linkage between classical class I and immunoproteasome genes and between framework class I genes and genes associated with the mammalian class III subregion. These findings are supported in both Komodo genome assemblies and provide new insight into the MHC organization of these unique squamate reptiles.
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Gong H, Wang Q, Lai Y, Zhao C, Sun C, Chen Z, Tao J, Huang Z. Study on Immune Response of Organs of Epinephelus coioides and Carassius auratus After Immersion Vaccination With Inactivated Vibrio harveyi Vaccine. Front Immunol 2021; 11:622387. [PMID: 33633740 PMCID: PMC7900426 DOI: 10.3389/fimmu.2020.622387] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/21/2020] [Indexed: 12/04/2022] Open
Abstract
Immersion vaccination relies on the response of fish mucosa-associated lymphoid tissues, the Crucian carp (Carassius auratus) and Grouper (Epinephelus coioides) were researched in this paper to examine local mucosal immune responses and associated humoral system responses following immersion vaccination. We administered 1.5 × 107 CFU/ml formalin-inactivated Vibrio harveyi cells and measured mucus and serum antibody titers as well as IgM, MHC II mRNA levels in immune organs. The mucosal antibody response preceded the serum response indicating a role for local mucosal immunity in immersion vaccination. IgM and MHC II mRNA levels were relatively greater for the spleen and head kidney indicating the importance and central position of systemic immunity. Expression levels were also high for the gills while skin levels were the lowest. IgM and MHC II mRNA levels were altered over time following vaccination and the hindgut, liver and spleen were similar indicating a close relationship, so the absolute value of r is used to analyze the correlation among different organs immunized. It can be inferred the existence of an internal immune molecular mechanism for Immune synergy hindgut-liver-spleen, from the peak time (14th day), the relative ratio of genes expression in the same tissues between the immunized grouper and the control group (26 times), and Pearson correlation coefficient (0.8<|r|<1). Injection challenges with live V. harveyi indicated that the relative protection rates for the crucian carp and Grouper was basically the same at 44.4% and 47.4%, respectively. It is believe that crucian carp may be used as a substitute for the valuable grouper in immunity experiment, just from aspect of the relative percent survival (RPS) and how it changes with time. But they were not consistent about the IgM mRNA expression between that of crucian carp and grouper after immersion the Vibrio vaccine.
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Affiliation(s)
- Hua Gong
- Key Lab of Aquatic Animal Immune Technology of Guangdong Province, Key Lab of Fishery Drug Development of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Qing Wang
- Key Lab of Aquatic Animal Immune Technology of Guangdong Province, Key Lab of Fishery Drug Development of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yingtiao Lai
- Key Lab of Aquatic Animal Immune Technology of Guangdong Province, Key Lab of Fishery Drug Development of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Changchen Zhao
- Key Lab of Aquatic Animal Immune Technology of Guangdong Province, Key Lab of Fishery Drug Development of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Chenwen Sun
- Key Lab of Aquatic Animal Immune Technology of Guangdong Province, Key Lab of Fishery Drug Development of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Zonghui Chen
- Key Lab of Aquatic Animal Immune Technology of Guangdong Province, Key Lab of Fishery Drug Development of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jiafa Tao
- Key Lab of Aquatic Animal Immune Technology of Guangdong Province, Key Lab of Fishery Drug Development of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Zhibin Huang
- Key Lab of Aquatic Animal Immune Technology of Guangdong Province, Key Lab of Fishery Drug Development of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Guangzhou, China
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Yin B, Liu H, Tan B, Dong X, Chi S, Yang Q, Zhang S. MHC II-PI 3K/Akt/mTOR Signaling Pathway Regulates Intestinal Immune Response Induced by Soy Glycinin in Hybrid Grouper: Protective Effects of Sodium Butyrate. Front Immunol 2021; 11:615980. [PMID: 33537033 PMCID: PMC7849651 DOI: 10.3389/fimmu.2020.615980] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Soy glycinin (11S) is involved in immune regulation. As an additive, sodium butyrate (SB) can relieve inflammation caused by 11S. To further delve into the mechanisms. A diet containing 50% fishmeal was the control group (FM group), and the experimental groups consisted of the FM group baseline plus 2% glycinin (GL group), 8% glycinin (GH group), and 8% glycinin + 0.13% sodium butyrate (GH-SB group). The specific growth ratio (SGR), feed utilization, and density of distal intestinal (DI) type II mucous cells were increased in the GL group. In the serum, IFN-γ was significantly upregulated in the GL group, and IgG and IL-1β were upregulated in the GH group. IgG, IL-1β, and TNF-α in the GH-SB group were significantly downregulated compared to those in the GH group. The mRNA levels of mTOR C1, mTOR C2, and Deptor were upregulated in the GL, GH, and GH-SB groups in the DI compared with those in the FM group, while the mRNA levels of mTOR C1 and Deptor in the GH group were higher than those in the GL and GH-SB groups. 4E-BP1, RICTOR, PRR5, MHC II, and CD4 were upregulated in the GH group. TSC1, mLST8, and NFY mRNA levels in the GL and GH-SB groups were upregulated compared with those in the FM and GH groups. Western blotting showed P-PI3KSer294/T-PI3K, P-AktSer473/T-Akt, and P-mTORSer2448/T-mTOR were upregulated in the GH group. Collectively, our results demonstrate that low-dose 11S could improve serum immune by secreting IFN-γ. The overexpression of IgG and IL-1β is the reason that high-dose 11S reduces serum immune function, and supplementing SB can suppress this overexpression. Low-dose 11S can block the relationship between PI3K and mTOR C2. It can also inhibit the expression of 4E-BP1 through mTOR C1. High-dose 11S upregulates 4E-BP2 through mTOR C1, aggravating intestinal inflammation. SB could relieve inflammation by blocking PI3K/mTOR C2 and inhibiting 4E-BP2. Generally speaking, the hybrid grouper obtained different serum and DI immune responses under different doses of 11S, and these responses were ultimately manifested in growth performance. SB can effectively enhance serum immunity and relieve intestinal inflammation caused by high dose 11S.
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Affiliation(s)
- Bin Yin
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Centre of Guangdong Province, Zhanjiang, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, China
| | - Hongyu Liu
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Centre of Guangdong Province, Zhanjiang, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, China
| | - Beiping Tan
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Centre of Guangdong Province, Zhanjiang, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, China
| | - Xiaohui Dong
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Centre of Guangdong Province, Zhanjiang, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, China
| | - Shuyan Chi
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Centre of Guangdong Province, Zhanjiang, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, China
| | - Qihui Yang
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Centre of Guangdong Province, Zhanjiang, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, China
| | - Shuang Zhang
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Centre of Guangdong Province, Zhanjiang, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, China
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22
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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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23
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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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24
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Abstract
Based on analysis of available genome sequences, five gene lineages of MHC class I molecules (MHC I-U, -Z, -S, -L and -P) and one gene lineage of MHC class II molecules (MHC II-D) have been identified in Osteichthyes. In the latter lineage, three MHC II molecule sublineages have been identified (MHC II-A, -B and -E). As regards MHC class I molecules in Osteichthyes, it is important to take note of the fact that the lineages U and Z in MHC I genes have been identified in almost all fish species examined so far. Phylogenetic studies into MHC II molecule genes of sublineages A and B suggest that they may be descended from the genes of the sublineage named A/B that have been identified in spotted gar (Lepisosteus oculatus). The sublineage E genes of MHC II molecules, which represent the group of non-polymorphic genes with poor expression in the tissues connected with the immune system, are present in primitive fish, i.e. in paddlefish, sturgeons and spotted gar (Lepisosteus oculatus), as well as in cyprinids (Cyprinidae), Atlantic salmon (Salmo salar), and rainbow trout (Oncorhynchus mykiss). Full elucidation of the details relating to the organisation and functioning of the particular components of the major histocompatibility complex in Osteichthyes can advance the understanding of the evolution of the MHC molecule genes and the immune mechanism.
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25
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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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26
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Almeida T, Esteves PJ, Flajnik MF, Ohta Y, Veríssimo A. An Ancient, MHC-Linked, Nonclassical Class I Lineage in Cartilaginous Fish. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 204:892-902. [PMID: 31932500 PMCID: PMC7002201 DOI: 10.4049/jimmunol.1901025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/05/2019] [Indexed: 01/08/2023]
Abstract
Cartilaginous fishes, or chondrichthyans, are the oldest jawed vertebrates that have an adaptive immune system based on the MHC and Ig superfamily-based AgR. In this basal group of jawed vertebrates, we identified a third nonclassical MHC class I lineage (UDA), which is present in all species analyzed within the two major cartilaginous subclasses, Holocephali (chimaeras) and Elasmobranchii (sharks, skates, and rays). The deduced amino acid sequences of UDA have eight out of nine typically invariant residues that bind to the N and C termini of bound peptide found in most vertebrae classical class I (UAA); additionally, the other predicted 28 peptide-binding residues are perfectly conserved in all elasmobranch UDA sequences. UDA is distinct from UAA in its differential tissue distribution and its lower expression levels and is mono- or oligomorphic unlike the highly polymorphic UAA UDA has a low copy number in elasmobranchs but is multicopy in the holocephalan spotted ratfish (Hydrolagus colliei). Using a nurse shark (Ginglymostoma cirratum) family, we found that UDA is MHC linked but separable by recombination from the tightly linked cluster of UAA, TAP, and LMP genes, the so-called class I region found in most nonmammalian vertebrates. UDA has predicted structural features that are similar to certain nonclassical class I genes in other vertebrates, and, unlike polymorpic classical class I, we anticipate that it may bind to a conserved set of specialized peptides.
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Affiliation(s)
- Tereza Almeida
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
- Department of Microbiology and Immunology, University of Maryland, Baltimore, Baltimore, MD 21201; and
| | - Pedro J Esteves
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland, Baltimore, Baltimore, MD 21201; and
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland, Baltimore, Baltimore, MD 21201; and
| | - Ana Veríssimo
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Porto, Portugal
- Virginia Institute of Marine Science, William & Mary, Gloucester Point, VA 23062
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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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28
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Smith NC, Rise ML, Christian SL. A Comparison of the Innate and Adaptive Immune Systems in Cartilaginous Fish, Ray-Finned Fish, and Lobe-Finned Fish. Front Immunol 2019; 10:2292. [PMID: 31649660 PMCID: PMC6795676 DOI: 10.3389/fimmu.2019.02292] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/10/2019] [Indexed: 12/17/2022] Open
Abstract
The immune system is composed of two subsystems-the innate immune system and the adaptive immune system. The innate immune system is the first to respond to pathogens and does not retain memory of previous responses. Innate immune responses are evolutionarily older than adaptive responses and elements of innate immunity can be found in all multicellular organisms. If a pathogen persists, the adaptive immune system will engage the pathogen with specificity and memory. Several components of the adaptive system including immunoglobulins (Igs), T cell receptors (TCR), and major histocompatibility complex (MHC), are assumed to have arisen in the first jawed vertebrates-the Gnathostomata. This review will discuss and compare components of both the innate and adaptive immune systems in Gnathostomes, particularly in Chondrichthyes (cartilaginous fish) and in Osteichthyes [bony fish: the Actinopterygii (ray-finned fish) and the Sarcopterygii (lobe-finned fish)]. While many elements of both the innate and adaptive immune systems are conserved within these species and with higher level vertebrates, some elements have marked differences. Components of the innate immune system covered here include physical barriers, such as the skin and gastrointestinal tract, cellular components, such as pattern recognition receptors and immune cells including macrophages and neutrophils, and humoral components, such as the complement system. Components of the adaptive system covered include the fundamental cells and molecules of adaptive immunity: B lymphocytes (B cells), T lymphocytes (T cells), immunoglobulins (Igs), and major histocompatibility complex (MHC). Comparative studies in fish such as those discussed here are essential for developing a comprehensive understanding of the evolution of the immune system.
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Affiliation(s)
- Nicole C Smith
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Sherri L Christian
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL, Canada
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29
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Dubin A, Jørgensen TE, Moum T, Johansen SD, Jakt LM. Complete loss of the MHC II pathway in an anglerfish, Lophius piscatorius. Biol Lett 2019; 15:20190594. [PMID: 31594494 PMCID: PMC6832177 DOI: 10.1098/rsbl.2019.0594] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Genome studies in fish provide evidence for the adaptability of the vertebrate immune system, revealing alternative immune strategies. The reported absence of the major compatibility complex (MHC) class II pathway components in certain species of pipefish (genus Syngnathus) and cod-like fishes (order Gadiformes) is of particular interest. The MHC II pathway is responsible for immunization and defence against extracellular threats through the presentation of exogenous peptides to T helper cells. Here, we demonstrate the absence of all genes encoding MHC II components (CD4, CD74 A/B, and both classical and non-classical MHC II α/β) in the genome of an anglerfish, Lophius piscatorius, indicating loss of the MHC II pathway. By contrast, it has previously been reported that another anglerfish, Antennarius striatus, retains all MHC II genes, placing the loss of MHC II in the Lophius clade to their most recent common ancestor. In the three taxa where MHC II loss has occurred, the gene loss has been restricted to four or five core MHC II components, suggesting that, in teleosts, only these genes have functions that are restricted to the MHC II pathway.
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Affiliation(s)
- Arseny Dubin
- Genomics group, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Tor Erik Jørgensen
- Genomics group, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Truls Moum
- Genomics group, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Steinar Daae Johansen
- Genomics group, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Lars Martin Jakt
- Genomics group, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
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Jeon HB, Won H, Suk HY. Polymorphism of MHC class IIB in an acheilognathid species, Rhodeus sinensis shaped by historical selection and recombination. BMC Genet 2019; 20:74. [PMID: 31519169 PMCID: PMC6743125 DOI: 10.1186/s12863-019-0775-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Rhodeus sinensis is a bitterling species occurring throughout the numerous freshwater systems on the East Asia. Here, we analyzed the diversity of the MHC class IIB (DAB) genes from this species, which may offer meaningful insights into evolutionary processes in this species as well as other bitterlings. RESULTS Using cDNA and gDNA samples from 50 individuals, we discovered classical 140 allelic sequences that could be allocated into either DAB1 (Rhsi-DAB1) or DAB3 (Rhsi-DAB3). DAB sequences completely lacking the intron, but identical or similar to Rhsi-DAB1, were also discovered from our gDNA samples, and this intron loss likely originated from the retrotransposition events of processed mDNA. The β1 domain was the most polymorphic in both Rhsi-DAB1 and -DAB3. Putative peptide biding residues (PBRs) in Rhsi-DAB1, but not in Rhsi-DAB3, exhibited a significant dN/dS, presumably indicating that different selection pressures have acted on those two DABs. Recombination between different alleles seemed to have contributed to the increase of diversity in Rhsi-DABs. Upon phylogenetic analysis, Rhsi-DAB1 and -DAB3 formed independent clusters. Several alleles from other species of Cypriniformes were embedded in the clade of Rhsi-DAB1, whereas Rhsi-DAB3 clustered with alleles from the wider range of taxa (Cyprinodontiformes), indicating that these two Rhsi-DABs have taken different historical paths. CONCLUSIONS A great deal of MHC class IIB allelic diversity was found in R. sinensis, and gene duplication, selection and recombination may have contributed to this diversity. Based on our data, it is presumed that such historical processes have commonly or differently acted on the polymorphism of Rhsi-DAB1 and -DAB3.
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Affiliation(s)
- Hyung-Bae Jeon
- Department of Life Sciences, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongsangbuk-do 38541 South Korea
- Department of Biology, Concordia University, 7141 Sherbrooke W, Montreal, Quebec H4B 1R6 Canada
| | - Hari Won
- Department of Life Sciences, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongsangbuk-do 38541 South Korea
| | - Ho Young Suk
- Department of Life Sciences, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongsangbuk-do 38541 South Korea
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31
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El-Magd MA, El-Said KS, El-Semlawy AA, Tanekhy M, Afifi M, Mohamed TM. Association of MHC IIA polymorphisms with disease resistance in Aeromonas hydrophila-challenged Nile tilapia. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 96:126-134. [PMID: 30853539 DOI: 10.1016/j.dci.2019.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/02/2019] [Accepted: 03/02/2019] [Indexed: 06/09/2023]
Abstract
The major histocompatibility complex (MHC) genes show high polymorphisms in vertebrates depending on animal immunity status. Herein, MHC class IIA gene in Aeromonas hydrophila-challenged Nile tilapia was screened for presence of polymorphisms using sequencing. Twelve nucleotides deletion polymorphism was determined with a PCR product size of 267 bp in the resistant fish and 255 bp in the control and susceptible/diseased fish. Additionally, a non-synonymous right frameshift c.712 T > G (P. 238 * > G) SNP was detected at the stop codon (*). SNP-susceptibility association analysis revealed that fish carrying GG genotype and allele G were high susceptible (risk) for A. hydrophila, and had lower immune response as indicated by significant reduction in non-specific immune parameters (total protein, globulin, IgM, phagocytic activity, phagocytic index, and lysosome activity) and mRNA level of MHC IIA, interleukin 1 beta (IL1β), tumor necrosis factor alfa (TNFα), and toll-like receptor 7 (TLR7) in the spleen and head kidney. Thus, G allele could be considered as a risk (recessive or mutant) allele for c. 712 T > G (P. 238 * > G) SNP and so selection of Nile tilapia with protective allele (T) for this SNP could improve the disease resistant of the fish.
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Affiliation(s)
- Mohammed A El-Magd
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Kafrelsheikh University, Egypt.
| | - Karim S El-Said
- Department of Chemistry (Biochemistry Branch), Faculty of Science, Tanta University, Egypt
| | - Aml A El-Semlawy
- Department of Chemistry (Biochemistry Branch), Faculty of Science, Tanta University, Egypt
| | - Mahmoud Tanekhy
- Department of Poultry and Fish Diseases, Faculty of Veterinary Medicine, Alexandria University, Egypt
| | - Mohamed Afifi
- Department of Animal Wealth Development, Biostatistics, Faculty of Veterinary Medicine, Zagazig University, Egypt
| | - Tarek M Mohamed
- Department of Chemistry (Biochemistry Branch), Faculty of Science, Tanta University, Egypt
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Transcriptome Analysis Shows That IFN-I Treatment and Concurrent SAV3 Infection Enriches MHC-I Antigen Processing and Presentation Pathways in Atlantic Salmon-Derived Macrophage/Dendritic Cells. Viruses 2019; 11:v11050464. [PMID: 31121853 PMCID: PMC6563251 DOI: 10.3390/v11050464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 01/17/2023] Open
Abstract
Type I interferons (IFNs) have been shown to play an important role in shaping adaptive immune responses in addition to their antiviral properties in immune cells. To gain insight into the impact of IFN-I-induced pathways involved in early adaptive immune responses, i.e., antigen-presenting pathways, in an Atlantic salmon-derived (Salmo salar L.) macrophage cell line (TO-cells), we used a comparative de novo transcriptome analysis where cells were treated with IFN-I or kept untreated and concurrently infected with salmonid alphavirus subtype 3 (SAV3). We found that concurrent treatment of TO-cells with IFN-I and SAV3 infection (SAV3/IFN+) significantly enriched the major histocompatibility complex class I (MHC-I) pathway unlike the non-IFN-I treated TO-cells (SAV3/IFN−) that had lower expression levels of MHC-I pathway-related genes. Genes such as the proteasomal activator (PA28) and β-2 microglobulin (β2M) were only differentially expressed in the SAV3/IFN+ cells and not in the SAV3/IFN− cells. MHC-I pathway genes like heat shock protein 90 (Hsp90), transporter of antigen associated proteins (TAPs) and tapasin had higher expression levels in the SAV3/IFN+ cells than in the SAV3/IFN− cells. There were no MHC-II pathway-related genes upregulated in SAV3/IFN+-treated cells, and cathepsin S linked to the degradation of endosomal antigens in the MHC-II pathway was downregulated in the SAV3/IFN− cells. Overall, our findings show that concurrent IFN-I treatment of TO-cells and SAV3 infection enriched gene expression linked to the MHC-I antigen presentation pathway. Data presented indicate a role of type I IFNs in strengthening antigen processing and presentation that may facilitate activation particularly of CD8+ T-cell responses following SAV3 infection, while SAV3 infection alone downplayed MHC-II pathways.
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Semple SL, Heath G, Christie D, Braunstein M, Kales SC, Dixon B. Immune stimulation of rainbow trout reveals divergent regulation of MH class II-associated invariant chain isoforms. Immunogenetics 2019; 71:407-420. [PMID: 31037384 DOI: 10.1007/s00251-019-01115-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 04/06/2019] [Indexed: 12/20/2022]
Abstract
Major histocompatibility complex (MHC) class II-associated invariant chain is a chaperone responsible for targeting the MHC class II dimer to the endocytic pathway, thus enabling the loading of exogenous antigens onto the MHC class II receptor. In the current study, in vivo and in vitro methods were used to investigate the regulation of the rainbow trout invariant chain proteins S25-7 and INVX, upon immune system activation. Whole rainbow trout and the macrophage/monocyte-like cell line RTS11 were treated with PMA at concentrations shown to induce IL-1β transcripts and homotypic aggregation of RTS11. S25-7 transcript levels remained unchanged in the gill, spleen, and liver and were found to be significantly decreased in head kidney beginning 24 h post-stimulation. Meanwhile, INVX transcript levels remained unchanged in all tissues studied. Both S25-7 and INVX proteins were produced in gill and spleen tissues but their expression was unaffected by immune system stimulation. Surprisingly, neither INVX nor S25-7 protein was detected in the secondary immune organ, the head kidney. Analysis of RTS11 cultures demonstrated that both INVX and S25-7 transcript levels significantly increased at 96 h and 120 h following PMA stimulation before returning to control levels at 168 h. Meanwhile, at the protein level in RTS11, S25-7 remained unchanged while INVX had a significant decrease at 168 h post-stimulation. These results indicate that neither INVX nor S25-7 is upregulated upon immune system activation; thus, teleosts have evolved a system of immune regulation that is different than that found in mammals.
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Affiliation(s)
- Shawna L Semple
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - George Heath
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - Darah Christie
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - Marsela Braunstein
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - Stephen C Kales
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada
| | - Brian Dixon
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo, ON, N2L 3G1, Canada.
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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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de Sá ALA, Breaux B, Burlamaqui TCT, Deiss TC, Sena L, Criscitiello MF, Schneider MPC. The Marine Mammal Class II Major Histocompatibility Complex Organization. Front Immunol 2019; 10:696. [PMID: 31019512 PMCID: PMC6459222 DOI: 10.3389/fimmu.2019.00696] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/13/2019] [Indexed: 12/17/2022] Open
Abstract
Sirenians share with cetaceans and pinnipeds several convergent traits selected for the aquatic lifestyle. Living in water poses new challenges not only for locomotion and feeding but also for combating new pathogens, which may render the immune system one of the best tools aquatic mammals have for dealing with aquatic microbial threats. So far, only cetaceans have had their class II Major Histocompatibility Complex (MHC) organization characterized, despite the importance of MHC genes for adaptive immune responses. This study aims to characterize the organization of the marine mammal class II MHC using publicly available genomes. We located class II sequences in the genomes of one sirenian, four pinnipeds and eight cetaceans using NCBI-BLAST and reannotated the sequences using local BLAST search with exon and intron libraries. Scaffolds containing class II sequences were compared using dotplot analysis and introns were used for phylogenetic analysis. The manatee class II region shares overall synteny with other mammals, however most DR loci were translocated from the canonical location, past the extended class II region. Detailed analysis of the genomes of closely related taxa revealed that this presumed translocation is shared with all other living afrotherians. Other presumptive chromosome rearrangements in Afrotheria are the deletion of DQ loci in Afrosoricida and deletion of DP in E. telfairi. Pinnipeds share the main features of dog MHC: lack of a functional pair of DPA/DPB genes and inverted DRB locus between DQ and DO subregions. All cetaceans share the Cetartiodactyla inversion separating class II genes into two subregions: class IIa, with DR and DQ genes, and class IIb, with non-classic genes and a DRB pseudogene. These results point to three distinct and unheralded class II MHC structures in marine mammals: one canonical organization but lacking DP genes in pinnipeds; one bearing an inversion separating IIa and IIb subregions lacking DP genes found in cetaceans; and one with a translocation separating the most diverse class II gene from the MHC found in afrotherians and presumptive functional DR, DQ, and DP genes. Future functional research will reveal how these aquatic mammals cope with pathogen pressures with these divergent MHC organizations.
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Affiliation(s)
- André Luiz Alves de Sá
- Laboratory of Applied Genetics, Socio-Environmental and Water Resources Institute, Federal Rural University of the Amazon, Belém, Brazil.,Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará, Belém, Brazil
| | - Breanna Breaux
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | | | - Thaddeus Charles Deiss
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Leonardo Sena
- Center of Biodiversity Advanced Studies, Biological Sciences Institute, Federal University of Pará, Belém, Brazil
| | - Michael Frederick Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Maria Paula Cruz Schneider
- Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará, Belém, Brazil
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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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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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38
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Welsh R, Song N, Sadegh-Nasseri S. What to do with HLA-DO/H-2O two decades later? Immunogenetics 2019; 71:189-196. [PMID: 30683973 PMCID: PMC6377320 DOI: 10.1007/s00251-018-01097-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/20/2018] [Indexed: 10/27/2022]
Abstract
The main objective of antigen processing is to orchestrate the selection of immunodominant epitopes for recognition by CD4 T cells. To achieve this, MHC class II molecules have evolved with a flexible peptide-binding groove in need of a bound peptide. Newly synthesized MHC-II molecules bind a class II invariant chain (Ii) upon synthesis and are shuttled to a specialized compartment, where they encounter exogenous antigens. Ii serves multiple functions, one of which is to maintain the shape of the MHC-II groove so that it can readily bind exogenous antigens upon dissociation of the Ii peptide in MHC- II compartment. MIIC contains processing enzymes, one or both accessory molecules, HLA-DM/H2-M (DM) and HLA-DO/H2-O (DO), and optimal denaturing conditions. In a process known as "editing," DM facilitates the dissociation of the invariant chain peptide, CLIP, for exchange with exogenous antigens. Despite the availability of mechanistic insights into DM functions, understanding how DO contributes to epitope selection has proven to be more challenging. The current dogma assumes that DO inhibits DM, whereas an opposing model suggests that DO fine-tunes the epitope selection process. Understanding which of these, or potentially other models of DO function is important, as DO variants have been linked to autoimmunity, cancer, and the generation of broadly neutralizing antibodies to viruses. This review therefore attempts to evaluate experimental evidence in support of these hypotheses, with an emphasis on the less discussed model, and to explore intriguing questions about the importance of DO in biology.
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Affiliation(s)
- Robin Welsh
- Graduate Program in Immunology and Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Nianbin Song
- Graduate Program in Immunology and Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Scheherazade Sadegh-Nasseri
- Graduate Program in Immunology and Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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39
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Li Y, Niu M, Zou Q. ELM-MHC: An Improved MHC Identification Method with Extreme Learning Machine Algorithm. J Proteome Res 2019; 18:1392-1401. [DOI: 10.1021/acs.jproteome.9b00012] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Yanjuan Li
- School of Information and Computer Engineering, Northeast Forestry University, Harbin 150040, China
| | - Mengting Niu
- School of Information and Computer Engineering, Northeast Forestry University, Harbin 150040, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
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40
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Ashfaq H, Soliman H, Saleh M, El-Matbouli M. CD4: a vital player in the teleost fish immune system. Vet Res 2019; 50:1. [PMID: 30616664 PMCID: PMC6323851 DOI: 10.1186/s13567-018-0620-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/21/2018] [Indexed: 12/24/2022] Open
Abstract
CD4 is a nonpolymorphic transmembrane glycoprotein molecule that is expressed on the surface of T-helper cells and plays an essential role in the immune response. It functions as a coreceptor with the T-cell receptor by binding to major histocompatibility complex class II on the surface of dendritic cells that present antigens. CD4+ T cells hold a key position in coordinating the immune system through production of several cytokines after activation and differentiation. The CD4+ T helper subtypes (T-helper 1, T-helper 2, T-helper 17, T-helper 9, and regulatory-T cells) perform different immune functions subsequent to their differentiation from the naive T cells. Different types of CD4+ T cells require different cytokines such as drivers and effectors, as well as master transcription factors for their activation. Fish cells that express CD4-related genes are activated in the presence of a pathogen and release cytokines against the pathogen. This review highlights the types of CD4+ T cells in fish and describes their direct role in cell-mediated and humoral immunity for protection against the intracellular bacterial as well as viral infections in fish.
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Affiliation(s)
- Hassan Ashfaq
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Hatem Soliman
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Mona Saleh
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria.
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41
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Ancient features of the MHC class II presentation pathway, and a model for the possible origin of MHC molecules. Immunogenetics 2018; 71:233-249. [DOI: 10.1007/s00251-018-1090-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/06/2018] [Indexed: 10/28/2022]
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42
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Abram QH, Fujiki K, Booman M, Chin-Dixon E, Wei G, Dixon B. Characterization of cDNA clones encoding major histocompatibility class II receptors from walleye (Sander vitreus). Mol Immunol 2018; 103:106-114. [PMID: 30245265 DOI: 10.1016/j.molimm.2018.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/14/2018] [Accepted: 09/14/2018] [Indexed: 01/28/2023]
Abstract
The teleost major histocompatibility (MH) class II receptor presents peptides from exogenous sources to CD4+ T cells, leading to the initiation of the adaptive immune response. The genes encoding MH class II have been identified in a number of teleost species, but not in walleye, an important recreational fish and commercial fishery in North America. In this study, we cloned and characterized the sequences encoding walleye MH class II α and β chains. These sequences contained all of the domains typical for functional MH class II α and β chain proteins, and aligned with other teleost sequences of MH class II. The walleye MH class II α amino acid sequence, along with other members of the Supraorder Percomorpharia, contains a high concentration of methionine residues in the beginning of the leader peptide. Southern blotting indicated that there is more than one gene copy for both MH class II α and β, while northern blotting analysis of both genes showed that expression of these genes is greatest in lymphoid tissues and at potential entry points for pathogens. These results help to further the understanding of MH class II receptors in teleosts, and could prove useful in the study of disease issues in walleye such as dermal sarcoma virus.
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Affiliation(s)
- Quinn H Abram
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, Ontario, N2L 3G1, Canada
| | - Kazuhiro Fujiki
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, Ontario, N2L 3G1, Canada
| | - Marije Booman
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, Ontario, N2L 3G1, Canada
| | - Emily Chin-Dixon
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, Ontario, N2L 3G1, Canada
| | - Guang Wei
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, Ontario, N2L 3G1, Canada
| | - Brian Dixon
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, Ontario, N2L 3G1, Canada.
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43
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Abstract
The adaptive immune system arose 500 million years ago in ectothermic (cold-blooded) vertebrates. Classically, the adaptive immune system has been defined by the presence of lymphocytes expressing recombination-activating gene (RAG)-dependent antigen receptors and the MHC. These features are found in all jawed vertebrates, including cartilaginous and bony fish, amphibians and reptiles and are most likely also found in the oldest class of jawed vertebrates, the extinct placoderms. However, with the discovery of an adaptive immune system in jawless fish based on an entirely different set of antigen receptors - the variable lymphocyte receptors - the divergence of T and B cells, and perhaps innate-like lymphocytes, goes back to the origin of all vertebrates. This Review explores how recent developments in comparative immunology have furthered our understanding of the origins and function of the adaptive immune system.
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Affiliation(s)
- Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD, USA.
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44
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Grayfer L, Kerimoglu B, Yaparla A, Hodgkinson JW, Xie J, Belosevic M. Mechanisms of Fish Macrophage Antimicrobial Immunity. Front Immunol 2018; 9:1105. [PMID: 29892285 PMCID: PMC5985312 DOI: 10.3389/fimmu.2018.01105] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/02/2018] [Indexed: 12/13/2022] Open
Abstract
Overcrowding conditions and temperatures shifts regularly manifest in large-scale infections of farmed fish, resulting in economic losses for the global aquaculture industries. Increased understanding of the functional mechanisms of fish antimicrobial host defenses is an important step forward in prevention of pathogen-induced morbidity and mortality in aquaculture setting. Like other vertebrates, macrophage-lineage cells are integral to fish immune responses and for this reason, much of the recent fish immunology research has focused on fish macrophage biology. These studies have revealed notable similarities as well as striking differences in the molecular strategies by which fish and higher vertebrates control their respective macrophage polarization and functionality. In this review, we address the current understanding of the biological mechanisms of teleost macrophage functional heterogeneity and immunity, focusing on the key cytokine regulators that control fish macrophage development and their antimicrobial armamentarium.
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Affiliation(s)
- Leon Grayfer
- Department of Biological Sciences, George Washington University, Washington, DC, United States
| | - Baris Kerimoglu
- Department of Biological Sciences, George Washington University, Washington, DC, United States
| | - Amulya Yaparla
- Department of Biological Sciences, George Washington University, Washington, DC, United States
| | | | - Jiasong Xie
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Miodrag Belosevic
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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45
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Li C, Jiang J, Zhang Q, Wang X. Duplicated major histocompatibility complex class II genes in the tongue sole (Cynoglossus semilaevis
). Int J Immunogenet 2018; 45:210-224. [DOI: 10.1111/iji.12368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 02/25/2018] [Accepted: 03/22/2018] [Indexed: 12/26/2022]
Affiliation(s)
- C. Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding; College of Marine Life Sciences; Ocean University of China; Qingdao China
| | - J. Jiang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding; College of Marine Life Sciences; Ocean University of China; Qingdao China
| | - Q. Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding; College of Marine Life Sciences; Ocean University of China; Qingdao China
| | - X. Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding; College of Marine Life Sciences; Ocean University of China; Qingdao China
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46
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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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47
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Dijkstra JM, Yamaguchi T, Grimholt U. Conservation of sequence motifs suggests that the nonclassical MHC class I lineages CD1/PROCR and UT were established before the emergence of tetrapod species. Immunogenetics 2017; 70:459-476. [DOI: 10.1007/s00251-017-1050-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 12/05/2017] [Indexed: 01/09/2023]
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48
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Su J, Gong Y, Cao S, Lu F, Han D, Liu H, Jin J, Yang Y, Zhu X, Xie S. Effects of dietary Tenebrio molitor meal on the growth performance, immune response and disease resistance of yellow catfish (Pelteobagrus fulvidraco). FISH & SHELLFISH IMMUNOLOGY 2017; 69:59-66. [PMID: 28807649 DOI: 10.1016/j.fsi.2017.08.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/07/2017] [Accepted: 08/10/2017] [Indexed: 06/07/2023]
Abstract
This study evaluated the influence of diets containing mealworm (Tenebrio molitor) meal in partial substitution of fishmeal on growth performance and immune responses of juvenile yellow catfish (Pelteobagrus fulvidraco). Four diets were formulated to contain 0 (the control diet), 9, 18 and 27 g mealworm meal per 100 g diet with 0%, 25%, 50% and 75% of fishmeal replacement, respectively. Yellow catfish were randomly divided into 4 groups with 3 replicates in each group. The fish in each group were fed with one of the four experimental diets for 5 weeks. Growth performance, plasma parameters (SOD, MDA, IgM, C3, lysozyme) and immune related genes (MHC II, IL-1, CypA, IgM, HE) of yellow catfish were determined at the end of the feeding trial, as well as 24 h post bacterial (Edwardsiella ictaluri) challenge. The present results showed that dietary inclusion of mealworm meal (MW) had no negative effects on the growth performance of the juvenile yellow catfish, compared to the control group. At the end of the feeding trial, plasma MDA contents of MW supplemented groups were significant lower than the control group. Plasma SOD activities increased significantly with the increasing dietary MW contents at the end of feeding trial (pre-challenge) and 24 h post challenge with E. ictaluri. Significant increase of plasma lysozyme activity was found in MW supplemented groups compared to the control group 24 h post bacterial challenge. Plasma IgM levels increased significantly with the increasing dietary MW contents at the end of feeding trial. Compared with the control group, the immune related genes of MHC II, IL-1, IgM and HE of the fish in the MW supplemented groups significantly upregulated pre-challenge or 24 h post bacterial challenge. Finally, it was observed that the survival rate of the 27% MW group was significant higher (P < 0.05) than the control group but was not significantly differed from the 18% MW group. The present results indicated that dietary inclusion level of at least 18% MW could improve the immune response and the bacterial resistance of yellow catfish without any negative growth effects.
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Affiliation(s)
- Jingzhi Su
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Yulong Gong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Shenping Cao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Fei Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Dong Han
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, PR China.
| | - Haokun Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China
| | - Junyan Jin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China
| | - Yunxia Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China
| | - Xiaoming Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China
| | - Shouqi Xie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China
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49
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Wilson AB. MHC and adaptive immunity in teleost fishes. Immunogenetics 2017; 69:521-528. [DOI: 10.1007/s00251-017-1009-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 05/29/2017] [Indexed: 12/19/2022]
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50
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Brown M, Hablützel P, Friberg IM, Thomason AG, Stewart A, Pachebat JA, Jackson JA. Seasonal immunoregulation in a naturally-occurring vertebrate. BMC Genomics 2016; 17:369. [PMID: 27189372 PMCID: PMC4870750 DOI: 10.1186/s12864-016-2701-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 05/06/2016] [Indexed: 11/10/2022] Open
Abstract
Background Fishes show seasonal patterns of immunity, but such phenomena are imperfectly understood in vertebrates generally, even in humans and mice. As these seasonal patterns may link to infectious disease risk and individual condition, the nature of their control has real practical implications. Here we characterize seasonal dynamics in the expression of conserved vertebrate immunity genes in a naturally-occurring piscine model, the three-spined stickleback. Results We made genome-wide measurements (RNAseq) of whole-fish mRNA pools (n = 36) at the end of summer and winter in contrasting habitats (riverine and lacustrine) and focussed on common trends to filter habitat-specific from overarching temporal responses. We corroborated this analysis with targeted year-round whole-fish gene expression (Q-PCR) studies in a different year (n = 478). We also considered seasonal tissue-specific expression (6 tissues) (n = 15) at a third contrasting (euryhaline) locality by Q-PCR, further validating the generality of the patterns seen in whole fish analyses. Extremes of season were the dominant predictor of immune expression (compared to sex, ontogeny or habitat). Signatures of adaptive immunity were elevated in late summer. In contrast, late winter was accompanied by signatures of innate immunity (including IL-1 signalling and non-classical complement activity) and modulated toll-like receptor signalling. Negative regulators of T-cell activity were prominent amongst winter-biased genes, suggesting that adaptive immunity is actively down-regulated during winter rather than passively tracking ambient temperature. Network analyses identified a small set of immune genes that might lie close to a regulatory axis. These genes acted as hubs linking summer-biased adaptive pathways, winter-biased innate pathways and other organismal processes, including growth, metabolic dynamics and responses to stress and temperature. Seasonal change was most pronounced in the gill, which contains a considerable concentration of T-cell activity in the stickleback. Conclusions Our results suggest major and predictable seasonal re-adjustments of immunity. Further consideration should be given to the effects of such responses in seasonally-occurring disease. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2701-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martha Brown
- IBERS, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | | | - Ida M Friberg
- School of Environment and Life sciences, University of Salford, Salford, M5 4WT, UK
| | - Anna G Thomason
- School of Environment and Life sciences, University of Salford, Salford, M5 4WT, UK
| | - Alexander Stewart
- Cardiff School of Biosciences, University of Cardiff, Cardiff, CF10 3AX, UK
| | | | - Joseph A Jackson
- School of Environment and Life sciences, University of Salford, Salford, M5 4WT, UK.
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