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Wiśniewska MM, Kyslík J, Alama-Bermejo G, Lövy A, Kolísko M, Holzer AS, Kosakyan A. Comparative transcriptomics reveal stage-dependent parasitic adaptations in the myxozoan Sphaerospora molnari. BMC Genomics 2025; 26:103. [PMID: 39901063 PMCID: PMC11792419 DOI: 10.1186/s12864-025-11265-x] [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: 02/28/2024] [Accepted: 01/20/2025] [Indexed: 02/05/2025] Open
Abstract
BACKGROUND Parasitism as a life strategy has independently evolved multiple times within the eukaryotic tree of life. Each lineage has developed mechanisms to invade hosts, exploit resources, and ensure replication, but our knowledge of survival mechanisms in many parasitic taxa remain extremely limited. One such group is the Myxozoa, which are obligate, dixenous cnidarians. Evidence suggests that myxozoans evolved from free-living ancestors to endoparasites around 600 million years ago and are likely one of the first metazoan parasites on Earth. Some myxozoans pose significant threats to farmed and wild fish populations, negatively impacting aquaculture and fish stocks; one such example is Sphaerospora molnari, which forms spores in the gills of common carp (Cyprinus carpio), disrupting gill epithelia and causing somatic and respiratory failure. Sphaerospora molnari undergoes sequential development in different organs of its host, with large numbers of morphologically distinct stages occurring in the blood, liver, and gills of carp. We hypothesize that these parasite life-stages differ in regards to their host exploitation, pathogenicity, and host immune evasion strategies and mechanisms. We performed stage-specific transcriptomic profiling to identify differentially expressed key functional gene groups that relate to these functions and provide a fundamental understanding of the mechanisms S. molnari uses to optimize its parasitic lifestyle. We aimed to identify genes that are likely related to parasite pathogenicity and host cell exploitation mechanisms, and we hypothesize that genes unique to S. molnari might be indicative of evolutionary innovations and specific adaptations to host environments. RESULTS We used parasite isolation protocols and comparative transcriptomics to study early proliferative and spore-forming stages of S. molnari, unveiling variation in gene expression between each stage. We discovered several apparent innovations in the S. molnari transcriptome, including proteins that are likely to function in the uptake of previously unknown key nutrients, immune evasion factors that may contribute to long-term survival in hosts, and proteins that likely improve adhesion to host cells that may have arisen from horizontal gene transfer. Notably, we identified genes that are similar to known virulence factors in other parasitic organisms, particularly blood and intestinal parasites like Plasmodium, Trypanosoma, and Giardia. Many of these genes are absent in published cnidarian and myxozoan datasets and appear to be specific to S. molnari; they may therefore represent potential innovations enabling Sphaerospora to exploit the host's blood system. CONCLUSIONS In order to address the threat posed by myxozoans to both cultured fish species and wild stocks, it is imperative to deepen our understanding of their genetics. Sphaerospora molnari offers an appealing model for stage-specific transcriptomic profiling and for identifying differentially expressed key functional gene groups related to parasite development. We identified genes that are thus far unique to S. molnari, which reveal their evolutionary novelty and likely role as adaptations to specific host niches. In addition, we describe the pathogenicity-associated genetic toolbox of S. molnari and discuss the implications of our discoveries for disease control by shedding light on specific targets for potential intervention strategies.
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Affiliation(s)
- Monika M Wiśniewska
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
| | - Jiří Kyslík
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Gema Alama-Bermejo
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Fish Health Division, University of Veterinary Medicine, Vienna, Austria
| | - Alena Lövy
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Astrid S Holzer
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Fish Health Division, University of Veterinary Medicine, Vienna, Austria
| | - Anush Kosakyan
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.
- National Biodiversity Future Center (NBFC), Palermo, Italy.
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Eltijani A, Embregts CWE, Magadan S, Wang J, Brugman S, Boudinot P, Wiegertjes GF, Forlenza M. Distinct distribution and responses of IgM +, IgT1 + and IgT2 + B cells in common carp. Front Immunol 2024; 15:1490776. [PMID: 39588374 PMCID: PMC11586371 DOI: 10.3389/fimmu.2024.1490776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Accepted: 10/24/2024] [Indexed: 11/27/2024] Open
Abstract
In teleosts, the immunoglobulin classes produced by B cells are IgM, IgD, and IgT/IgZ. IgT was initially described as an immunoglobulin specialized in mucosal responses; accumulating evidence, however, shows that it is also involved in systemic immune responses. Two types of IgT/IgZ (IgT1 and IgT2) were previously described in common carp, but their further characterization was hampered by the lack of specific tool. In the current study, we developed and validated polyclonal antibodies against carp IgT1 and IgT2 and used them in combination with well validated monoclonal antibody against carp IgM (WCI12), to study the distribution of IgM+, IgT1+ and IgT2+ B cells or their secreted immunoglobulins in various mucosal and systemic organs of carp. Finally, we also preliminary assessed the B cell response to infection with the blood-borne parasite Trypanoplasma borreli. Using these tools, we report on the distinct expression of soluble immunoglobulins in systemic and mucosal compartments. IgT1 and IgM were expressed in mucosal as well as systemic organs and responded to systemic parasitic infection, whereas IgT2 was preferentially expressed at mucosal sites and did not respond to systemic infections. By studying the distribution of B cells in different organs, compartmentalization of the three B cell subtypes was observed in gills and gut, whereas splenic B cells appeared as organized clusters around ellipsoids. Our results provide insights into the distribution and to some extent the function of B cells in carp, indicating that our newly developed tools are valuable for future studies aiming at the further characterization of immune responses of carp to infections and vaccination.
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Affiliation(s)
- Awatif Eltijani
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Carmen W. E. Embregts
- Cell Biology and Immunology Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Susana Magadan
- Immunology Laboratory, Research Centre for Nanomaterials and Biomedicine (CINBIO), Universidade de Vigo, Vigo, Spain
| | - Jingjing Wang
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, Netherlands
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Sylvia Brugman
- Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Pierre Boudinot
- French National Institute for Agriculture, Food and Environment (INRAE), Department of Virology and Molecular Immunology, Jouy-en-Josas, France
| | - Geert F. Wiegertjes
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Maria Forlenza
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, Netherlands
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Rasal KD, Kumar PV, Risha S, Asgolkar P, Harshavarthini M, Acharya A, Shinde S, Dhere S, Rasal A, Sonwane A, Brahmane M, Sundaray JK, Nagpure N. Genetic improvement and genomic resources of important cyprinid species: status and future perspectives for sustainable production. Front Genet 2024; 15:1398084. [PMID: 39364006 PMCID: PMC11446788 DOI: 10.3389/fgene.2024.1398084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 09/02/2024] [Indexed: 10/05/2024] Open
Abstract
Cyprinid species are the most cultured aquatic species around the world in terms of quantity and total value. They account for 25% of global aquaculture production and significantly contribute to fulfilling the demand for fish food. The aquaculture of these species is facing severe concerns in terms of seed quality, rising feed costs, disease outbreaks, introgression of exotic species, environmental impacts, and anthropogenic activities. Numerous researchers have explored biological issues and potential methods to enhance cyprinid aquaculture. Selective breeding is extensively employed in cyprinid species to enhance specific traits like growth and disease resistance. In this context, we have discussed the efforts made to improve important cyprinid aquaculture practices through genetic and genomic approaches. The recent advances in DNA sequencing technologies and genomic tools have revolutionized the understanding of biological research. The generation of a complete genome and other genomic resources in cyprinid species has significantly strengthened molecular-level investigations into disease resistance, growth, reproduction, and adaptation to changing environments. We conducted a comprehensive review of genomic research in important cyprinid species, encompassing genome, transcriptome, proteome, metagenome, epigenome, etc. This review reveals that considerable data has been generated for cyprinid species. However, the seamless integration of this valuable data into genetic selection programs has yet to be achieved. In the upcoming years, genomic techniques, gene transfer, genome editing tools are expected to bring a paradigm shift in sustainable cyprinid aquaculture production. The comprehensive information presented here will offer insights for the cyprinid aquaculture research community.
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Affiliation(s)
- Kiran D Rasal
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | | | - Shasti Risha
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | - Prachi Asgolkar
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | - M Harshavarthini
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | - Arpit Acharya
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | - Siba Shinde
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | - Siyag Dhere
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | - Avinash Rasal
- ICAR - Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - Arvind Sonwane
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | - Manoj Brahmane
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | - Jitendra K Sundaray
- ICAR - Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - Naresh Nagpure
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, India
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Zhang Y, Zhang J, Fan H, Lu R, Nie G. Database construction and comparative genomics analysis of genes involved in nutritional metabolic diseases in fish. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101241. [PMID: 38733902 DOI: 10.1016/j.cbd.2024.101241] [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: 03/17/2024] [Revised: 04/24/2024] [Accepted: 05/04/2024] [Indexed: 05/13/2024]
Abstract
Nutritional metabolic diseases in fish frequently arise in the setting of intensive aquaculture. The etiology and pathogenesis of these conditions involve energy metabolic disorders influenced by both internal genetic factors and external environmental conditions. The exploration of genes associated with nutritional and metabolic disorder has sparked considerable interest within both the aquaculture scientific community and the industry. High-throughput sequencing technology offers researchers extensive genetic information. Effectively mining, analyzing, and securely storing this data is crucial, especially for advancing disease prevention and treatment strategies. Presently, the exploration and application of gene databases concerning nutritional and metabolic disorders in fish are at a nascent stag. Therefore, this study focused on the model organism zebrafish and five primary economic fish species as the subjects of investigation. Using information from KEGG, OMIM, and existing literature, a novel gene database associated with nutritional metabolic diseases in fish was meticulously constructed. This database encompassed 4583 genes for Danio rerio, 6287 for Cyprinus carpio, 3289 for Takifugu rubripes, 3548 for Larimichthys crocea, 3816 for Oreochromis niloticus, and 5708 for Oncorhynchus mykiss. Through a comparative systems biology approach, we discerned a relatively high conservation of genes linked to nutritional metabolic diseases across these fish species, with over 54.9 % of genes being conserved throughout all six species. Additionally, the analysis pinpointed the existence of 13 species-specific genes within the genomes of large yellow croaker, tilapia, and rainbow trout. These genes exhibit the potential to serve as novel candidate targets for addressing nutritional metabolic diseases.
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Affiliation(s)
- Yuru Zhang
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China; College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang 453007, PR China
| | - Junmei Zhang
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China; College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang 453007, PR China
| | - Haiying Fan
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China; College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang 453007, PR China
| | - Ronghua Lu
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China; College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang 453007, PR China
| | - Guoxing Nie
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China; College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang 453007, PR China.
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Okano M, Miyamae J, Sakurai K, Yamaguchi T, Uehara R, Katakura F, Moritomo T. Subgenomic T cell receptor alpha and delta (TRA/TRD) loci in common carp. FISH & SHELLFISH IMMUNOLOGY 2024; 146:109421. [PMID: 38325591 DOI: 10.1016/j.fsi.2024.109421] [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: 11/29/2023] [Revised: 01/10/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
In jawed vertebrates, the T cell receptor alpha (TRA) and delta (TRD) genes, which encode the TRα and TRδ chains, respectively, are located as a nested structure on a single chromosome. To date, no animal has been reported to harbor multiple TRA/TRD loci on different chromosomes. Therefore, herein, we describe the first full annotation of the TRA/TRD genomic regions of common carp, an allo-tetraploid fish species that experiences cyprinid-specific whole-genome duplication (WGD) in evolution. Fine genomic maps of TRA/TRD genomic regions 1 and 2, on LG30 and LG22, respectively, were constructed using the annotations of complete sets of TRA and TRD genes, including TRA/TRD variable (V), TRA junction (J), and constant (C), TRD diversity (D), and the J and C genes. The structure and synteny of the TRA/TRD genomic regions were highly conserved in zebrafish, indicating that these regions are on individual chromosomes. Furthermore, analysis of the variable regions of the TRA and TRD genes in a monoclonal T cell line revealed that both subgenomic regions 1 and 2 were indeed rearranged. Although carp TRAV and TRDV genes were phylogenetically divided into different lineages, they were mixed and organized into the TRA/TRD V gene clusters on the genome, similar to that in other vertebrates. Notably, 285 potential TRA/TRD V genes were detected in the TRA/TRD genomic regions, which is the most abundant number of genes in vertebrates and approximately two-fold that in zebrafish. The recombination signal sequences (RSSs) at the end of each V gene differed between TRAV and TRDV, suggesting that RSS variations might separate each V gene into a TRα or TRδ chain. This study is the first to describe subgenomic TRA/TRD loci in animals. Our findings provide fundamental insights to elucidate the impact of WGD on the evolution of immune repertoire.
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Affiliation(s)
- Masaharu Okano
- Department of Legal Medicine, Nihon University School of Dentistry, Kanda-Surugadai 1-8-13, Chiyoda-Ku, Tokyo, 101-8310, Japan
| | - Jiro Miyamae
- Faculty of Veterinary Medicine, Okayama University of Science, Ikoino-oka 1-3, Imabari, Ehime, 794-8555, Japan
| | - Kohei Sakurai
- Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Kameino 1866, Fujisawa, Kanagawa 252-0880, Japan
| | - Takuya Yamaguchi
- Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Kameino 1866, Fujisawa, Kanagawa 252-0880, Japan
| | - Ren Uehara
- Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Kameino 1866, Fujisawa, Kanagawa 252-0880, Japan
| | - Fumihiko Katakura
- Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Kameino 1866, Fujisawa, Kanagawa 252-0880, Japan.
| | - Tadaaki Moritomo
- Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Kameino 1866, Fujisawa, Kanagawa 252-0880, Japan
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6
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Kapitunova AI, Dominova IN, Zhukov VV. γM Crystallin Genes in the Eye Lens of a Juvenile Common Carp Cyprinus carpio: Transcription Levels and Phylogenetic Aspect. J EVOL BIOCHEM PHYS+ 2022. [DOI: 10.1134/s0022093022040081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Petit J, Wiegertjes GF. Conservation of members of the free fatty acid receptor gene family in common carp. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 126:104240. [PMID: 34461159 DOI: 10.1016/j.dci.2021.104240] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
Accumulating evidence supports the crucial role intestinal microbiota and their metabolites play in the homeostasis of organisms. An important class of metabolites that have been shown to affect the immune system are short chain fatty acids (SCFAs). These SCFAs can affect the host cells via passive diffusion or via ligation to receptors, among others G-protein coupled receptor (GPR) 41 and 43. GPR41 and GPR43 are both part of a family of GPR40-related receptors. Mammalian studies have shown an important role for GPR41 and GPR43 in the modulation of immune responses by SCFAs. However, up till date, no validated coding sequences for orthologues of these SCFA receptors have been published for teleost fish. We used genomic resources and cDNA cloning, to identify and validate ten coding sequences for gpr40L genes in common carp. Phylogenetic analysis showed a division into three subclasses, putatively named class a, b and c, and showed the common carp genes had a closer phylogenetic relationship to mammalian GPR43 than to mammalian GPR41. Synteny analysis revealed a clear conservation of syntenic relationships between gpr40L in the genomes of spotted gar and common carp with the relevant region in the human genome. This conservation of synteny validates the genes identified, as gpr40L. Finally, presence of gpr40L genes was investigated in silico for genomes of 25 different, mostly teleost, fish species largely confirming the observations for gpr40L of common carp with regards to both, subdivision in three subclasses a-c and conservation of synteny. Our data provide an important first step towards an understanding of the role and function of receptors for SCFAs and immunomodulation in fish.
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Affiliation(s)
- Jules Petit
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University and Research, PO Box 338, 6700, AH, Wageningen, the Netherlands
| | - Geert F Wiegertjes
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University and Research, PO Box 338, 6700, AH, Wageningen, the Netherlands.
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Nissa MU, Pinto N, Mukherjee A, Reddy PJ, Ghosh B, Sun Z, Ghantasala S, Chetanya C, Shenoy SV, Moritz RL, Goswami M, Srivastava S. Organ-Based Proteome and Post-Translational Modification Profiling of a Widely Cultivated Tropical Water Fish, Labeo rohita. J Proteome Res 2021; 21:420-437. [PMID: 34962809 DOI: 10.1021/acs.jproteome.1c00759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteomics has enormous applications in human and animal research. However, proteomic studies in fisheries science are quite scanty particularly for economically important species. Few proteomic studies have been carried out in model fish species, but comprehensive proteomics of aquaculture species are still scarce. This study aimed to perform a comprehensive organ-based protein profiling of important tissue samples for one of the most important aquaculture species,Labeo rohita.Deep proteomic profiling of 17 histologically normal tissues, blood plasma, and embryo provided mass-spectrometric evidence for 8498 proteins at 1% false discovery rate that make up about 26% of the total annotated protein-coding sequences in Rohu. Tissue-wise expression analysis was performed, and the presence of several biologically important proteins was also verified using a targeted proteomic approach. We identified the global post-translational modifications (PTMs) in terms of acetylation (N-terminus and lysine), methylation (N-terminus, lysine, and arginine), and phosphorylation (serine, threonine, and tyrosine) to present a comprehensive proteome resource. An interactive web-based portal has been developed for an overall landscape of protein expression across the studied tissues of Labeo rohita (www.fishprot.org). This draft proteome map of Labeo rohita would advance basic and applied research in aquaculture to meet the most critical challenge of providing food and nutritional security to an increasing world population.
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Affiliation(s)
- Mehar Un Nissa
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Nevil Pinto
- Central Institute of Fisheries Education, Indian Council of Agricultural Research, Versova, Mumbai, Maharashtra 400061, India
| | - Arijit Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | | | - Biplab Ghosh
- Regional Centre for Biotechnology, Faridabad 121001, India
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Saicharan Ghantasala
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Chetanya Chetanya
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sanjyot Vinayak Shenoy
- Department of Mathematics, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Mukunda Goswami
- Central Institute of Fisheries Education, Indian Council of Agricultural Research, Versova, Mumbai, Maharashtra 400061, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Lu Z, Tang M, Zhang M, Li Y, Shi F, Zhan F, Zhao L, Li J, Lin L, Qin Z. Expression and functional analysis of the BCL2-Associated agonist of cell death (BAD) gene in grass carp (Ctenopharyngodon idella) during bacterial infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 123:104160. [PMID: 34087289 DOI: 10.1016/j.dci.2021.104160] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/27/2021] [Accepted: 05/29/2021] [Indexed: 06/12/2023]
Abstract
The BCL2-associated agonist of cell death protein is a key participant in apoptosis dependent on mitochondria and in disease progression that involves the regulation of cell death, such as tumorigenesis, diabetes, sepsis shock, and epilepsy. Nevertheless, the mechanisms underlying the immune responses to teleost BAD bacterial infection and mitochondrial-dependent apoptosis remains unclear. In order to elucidate the mechanisms involved, in this study, a Ctenopharyngodon idella (grass carp) BAD gene named GcBAD1 was firstly cloned and characterized. The results indicated that the ORF (open reading frame) of GcBAD1 was 438 bp in length, encoding a 145-amino acid putative protein of 16.66 kDa. This deduced amino acid sequence has a better identity than another teleost species according to a phylogenetic analysis, and contains a Bcl2-BAD-1 domain. In healthy grass carp fish, the mRNA transcripts of GcBAD1 were widely present in the studied tissues, which could be ranked as follows; spleen > brain > middle-kidney > head-kidney > liver > gills > intestines > heart and muscle. In addition, during infection by Aeromonas hydrophila and Staphylococcus aureus, the mRNA transcription and protein levels expression of GcBAD1 in the head-kidney, spleen, and liver tissues of the fish were significantly up-regulated. Moreover, when the C. idellus kidney cell line (CIK) cells were incubated with Lipopolysaccharide (LPS) and lipoteichoic acid (LTA), the GcBAD1 expression transcripts were also significantly up-regulated. Additionally, overexpression of GcBAD1 in CIK cells was able to activate apoptosis-related genes, including those encoding p53, Cytochrome C (CytoC), caspase-3, and caspase-9. Besides, in the TUNEL assays, when pEGFP-BAD1 was over-expressed, the number of red signals associated with apoptosis were significantly increased in the CIK cells infected with LPS or LTA at 12 h. This study demonstrates that GcBAD1 has a significant role in the mitochondrial apoptosis pathway of grass carp's innate immunity. Our findings provide new insight into the potential mechanisms of teleost antibacterial immunity.
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Affiliation(s)
- Zhijie Lu
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering, Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai, University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China
| | - Meizhen Tang
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering, Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai, University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China
| | - Menglan Zhang
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering, Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai, University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China
| | - Yanan Li
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering, Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai, University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China
| | - Fei Shi
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering, Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai, University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China
| | - Fanbin Zhan
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering, Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai, University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China
| | - Lijuan Zhao
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering, Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai, University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China
| | - Jun Li
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering, Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai, University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China; School of Biological Sciences, Lake Superior State University, Sault Ste. Marie, MI, 49783, USA
| | - Li Lin
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering, Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai, University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China.
| | - Zhendong Qin
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering, Technology Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai, University of Agriculture and Engineering, Guangzhou, Guangdong Province, 510222, China.
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10
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Li JT, Wang Q, Huang Yang MD, Li QS, Cui MS, Dong ZJ, Wang HW, Yu JH, Zhao YJ, Yang CR, Wang YX, Sun XQ, Zhang Y, Zhao R, Jia ZY, Wang XY. Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish. Nat Genet 2021; 53:1493-1503. [PMID: 34594040 PMCID: PMC8492472 DOI: 10.1038/s41588-021-00933-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 08/05/2021] [Indexed: 02/08/2023]
Abstract
How two subgenomes in allo-tetraploids adapt to coexistence and coordinate through structure and expression evolution requires extensive studies. In the present study, we report an improved genome assembly of allo-tetraploid common carp, an updated genome annotation of allo-tetraploid goldfish and the chromosome-scale assemblies of a progenitor-like diploid Puntius tetrazona and an outgroup diploid Paracanthobrama guichenoti. Parallel subgenome structure evolution in the allo-tetraploids was featured with equivalent chromosome components, higher protein identities, similar transposon divergence and contents, homoeologous exchanges, better synteny level, strong sequence compensation and symmetric purifying selection. Furthermore, we observed subgenome expression divergence processes in the allo-tetraploids, including inter-/intrasubgenome trans-splicing events, expression dominance, decreased expression levels, dosage compensation, stronger expression correlation, dynamic functionalization and balancing of differential expression. The potential disorders introduced by different progenitors in the allo-tetraploids were hypothesized to be alleviated by increasing structural homogeneity and performing versatile expression processes. Resequencing three common carp strains revealed two major ecotypes and uncovered candidate genes relevant to growth and survival rate.
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Affiliation(s)
- Jiong-Tang Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China.
| | - Qi Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Mei-Di Huang Yang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Qing-Song Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Ming-Shu Cui
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
- Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zai-Jie Dong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Wuxi, China
| | - Hong-Wei Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Ju-Hua Yu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Wuxi, China
| | - Yu-Jie Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Chen-Ru Yang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Ya-Xin Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Xiao-Qing Sun
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Yan Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Ran Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Zhi-Ying Jia
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Xi-Yin Wang
- North China University of Science and Technology, Tangshan, China
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11
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Szczygieł J, Kamińska-Gibas T, Petit J, Jurecka P, Wiegertjes G, Irnazarow I. Re-evaluation of common carp (Cyprinus carpio L.) housekeeping genes for gene expression studies - considering duplicated genes. FISH & SHELLFISH IMMUNOLOGY 2021; 115:58-69. [PMID: 34033909 DOI: 10.1016/j.fsi.2021.05.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 05/10/2021] [Accepted: 05/17/2021] [Indexed: 06/12/2023]
Abstract
Quantitative real-time PCR is one of the most widely used techniques for measuring changes in the expression of target transcripts due to its sensitivity, specificity, and cost-effectiveness. However, the essential step that determines appropriate and correct data interpretation is the selection of proper endogenous control genes. Identifying useful reference genes with stable expression is critical for accurate normalization and precise results. Functional divergence of duplicated genes in tetraploid species, like common carp, can complicate the choice for a proper reference gene. In the present study, we determined the expression stability of duplicated genes of 40s, b2m, ef1α, gapdh, g6pd, and odc1 in different tissues of common carp (Cyprinus carpio L.). Gene expression analysis comprised healthy control fish, fish under bacterial and parasitic infections, and across the early stage of common carp development. Obtained data were compared with the actb gene, which is used widely as a reference in RT-qPCR analysis. The application of the three different algorithms - geNorm, NormFinder, BestKeeper, allowed comparative evaluation of the expression stability of the tested genes. Subsequently, the RefFinder, a web-based tool, was used to rank the examined housekeeping genes comprehensively. We demonstrate variable transcription stability levels in the examined mRNAs as well as differences in expression between paralog gene copies. The 40s, b2m, ef1α and actb genes showed the most stable expression across all physiological conditions and tissues. The gapdh, odc1, and g6pd gene variants demonstrated lower stability. Differences in expression patterns between duplicated genes underline the possibility of functional divergence between them. This aspect should be considered in polyploid species before selecting the reference gene(s). Our study also points on the importance of choice for a reference gene (paralog) when expressing newly identified genes and the spatial expression profile is performed. SUBJECTS: Aquaculture, Molecular Biology, Fish Science.
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Affiliation(s)
- Joanna Szczygieł
- Polish Academy of Sciences, Institute of Ichthyobiology and Aquaculture in Golysz, Kalinowa 2, Zaborze, 43-520 Chybie, Poland
| | - Teresa Kamińska-Gibas
- Polish Academy of Sciences, Institute of Ichthyobiology and Aquaculture in Golysz, Kalinowa 2, Zaborze, 43-520 Chybie, Poland
| | - Jules Petit
- Aquaculture and Fisheries Group, Wageningen Institute of Animal Sciences, Wageningen University and Research, PO Box 338, 6700 AH, Wageningen, The Netherlands
| | - Patrycja Jurecka
- Polish Academy of Sciences, Institute of Ichthyobiology and Aquaculture in Golysz, Kalinowa 2, Zaborze, 43-520 Chybie, Poland
| | - Geert Wiegertjes
- Aquaculture and Fisheries Group, Wageningen Institute of Animal Sciences, Wageningen University and Research, PO Box 338, 6700 AH, Wageningen, The Netherlands
| | - Ilgiz Irnazarow
- Polish Academy of Sciences, Institute of Ichthyobiology and Aquaculture in Golysz, Kalinowa 2, Zaborze, 43-520 Chybie, Poland.
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12
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Yan X, Wang J, Li H, Gao L, Geng J, Ma Z, Liu J, Zhang J, Xie P, Chen L. Combined transcriptome and proteome analyses reveal differences in the longissimus dorsi muscle between Kazakh cattle and Xinjiang brown cattle. Anim Biosci 2021; 34:1439-1450. [PMID: 33677919 PMCID: PMC8495333 DOI: 10.5713/ab.20.0751] [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: 10/31/2020] [Accepted: 01/29/2021] [Indexed: 01/09/2023] Open
Abstract
Objective With the rapid development of proteomics sequencing and RNA sequencing technology, multi-omics analysis has become a current research hotspot. Our previous study indicated that Xinjiang brown cattle have better meat quality than Kazakh cattle. In this study, Xinjiang brown cattle and Kazakh cattle were used as the research objects. Methods Proteome sequencing and RNA sequencing technology were used to analyze the proteome and transcriptome of the longissimus dorsi muscle of the two breeds of adult steers (n = 3). Results In this project, 22,677 transcripts and 1,874 proteins were identified through quantitative analysis of the transcriptome and proteome. By comparing the identified transcriptome and proteome, we found that 1,737 genes were identified at both the transcriptome and proteome levels. The results of the study revealed 12 differentially expressed genes and proteins: troponin I1, crystallin alpha B, cysteine, and glycine rich protein 3, phosphotriesterase-related, myosin-binding protein H, glutathione s-transferase mu 3, myosin light chain 3, nidogen 2, dihydropyrimidinase like 2, glutamate-oxaloacetic transaminase 1, receptor accessory protein 5, and aspartoacylase. We performed functional enrichment of these differentially expressed genes and proteins. The Kyoto encyclopedia of genes and genomes results showed that these differentially expressed genes and proteins are enriched in the fatty acid degradation and histidine metabolism signaling pathways. We performed parallel reaction monitoring (PRM) verification of the differentially expressed proteins, and the PRM results were consistent with the sequencing results. Conclusion Our study provided and identified the differentially expressed genes and proteins. In addition, identifying functional genes and proteins with important breeding value will provide genetic resources and technical support for the breeding and industrialization of new genetically modified beef cattle breeds.
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Affiliation(s)
- XiangMin Yan
- Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Urumqi 830057, China
| | - Jia Wang
- College of Geographic Science, Shanxi Normal University, Linfen 041000, China
| | - Hongbo Li
- Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Urumqi 830057, China
| | - Liang Gao
- Yili Vocational and Technical College, Yili, 835000, China
| | - Juan Geng
- Xinjiang Animal Husbandry General Station, Urumqi 830057, China
| | - Zhen Ma
- Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Urumqi 830057, China
| | - Jianming Liu
- Yili Animal Husbandry General Station, Yili 835000, China
| | - Jinshan Zhang
- Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Urumqi 830057, China
| | - Penggui Xie
- Yili Vocational and Technical College, Yili, 835000, China
| | - Lei Chen
- College of Animal Science and Technology, Shihezi University, Shihezi 832000, China
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13
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Wentzel AS, Petit J, van Veen WG, Fink IR, Scheer MH, Piazzon MC, Forlenza M, Spaink HP, Wiegertjes GF. Transcriptome sequencing supports a conservation of macrophage polarization in fish. Sci Rep 2020; 10:13470. [PMID: 32778701 PMCID: PMC7418020 DOI: 10.1038/s41598-020-70248-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022] Open
Abstract
Mammalian macrophages can adopt polarization states that, depending on the exact stimuli present in their extracellular environment, can lead to very different functions. Although these different polarization states have been shown primarily for macrophages of humans and mice, it is likely that polarized macrophages with corresponding phenotypes exist across mammals. Evidence of functional conservation in macrophages from teleost fish suggests that the same, or at least comparable polarization states should also be present in teleosts. However, corresponding transcriptional profiles of marker genes have not been reported thus far. In this study we confirm that macrophages from common carp can polarize into M1- and M2 phenotypes with conserved functions and corresponding transcriptional profiles compared to mammalian macrophages. Carp M1 macrophages show increased production of nitric oxide and a transcriptional profile with increased pro-inflammatory cytokines and mediators, including il6, il12 and saa. Carp M2 macrophages show increased arginase activity and a transcriptional profile with increased anti-inflammatory mediators, including cyr61, timp2b and tgm2b. Our RNA sequencing approach allowed us to list, in an unbiased manner, markers discriminating between M1 and M2 macrophages of teleost fish. We discuss the importance of our findings for the evaluation of immunostimulants for aquaculture and for the identification of gene targets to generate transgenic zebrafish for detailed studies on M1 and M2 macrophages. Above all, we discuss the striking degree of evolutionary conservation of macrophage polarization in a lower vertebrate.
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Affiliation(s)
- Annelieke S Wentzel
- Cell Biology and Immunology Group, Aquaculture and Fisheries Group, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Jules Petit
- Aquaculture and Fisheries Group, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Wouter G van Veen
- Experimental Zoology Group, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Inge Rosenbek Fink
- Cell Biology and Immunology Group, Aquaculture and Fisheries Group, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Marleen H Scheer
- Cell Biology and Immunology Group, Aquaculture and Fisheries Group, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - M Carla Piazzon
- Fish Pathology Group, Institute of Aquaculture Torre de La Sal (IATS-CSIC), 12595, Ribera de Cabanes, Castellón, Spain
| | - Maria Forlenza
- Cell Biology and Immunology Group, Aquaculture and Fisheries Group, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Herman P Spaink
- Institute of Biology, Leiden University, Einsteinweg 55, 2332 CC, Leiden, The Netherlands
| | - Geert F Wiegertjes
- Aquaculture and Fisheries Group, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands.
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14
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Wentzel AS, Janssen JJE, de Boer VCJ, van Veen WG, Forlenza M, Wiegertjes GF. Fish Macrophages Show Distinct Metabolic Signatures Upon Polarization. Front Immunol 2020; 11:152. [PMID: 32158446 PMCID: PMC7052297 DOI: 10.3389/fimmu.2020.00152] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 01/21/2020] [Indexed: 01/09/2023] Open
Abstract
Macrophages play important roles in conditions ranging from host immune defense to tissue regeneration and polarize their functional phenotype accordingly. Next to differences in the use of L-arginine and the production of different cytokines, inflammatory M1 macrophages and anti-inflammatory M2 macrophages are also metabolically distinct. In mammals, M1 macrophages show metabolic reprogramming toward glycolysis, while M2 macrophages rely on oxidative phosphorylation to generate energy. The presence of polarized functional immune phenotypes conserved from mammals to fish led us to hypothesize that a similar metabolic reprogramming in polarized macrophages exists in carp. We studied mitochondrial function of M1 and M2 carp macrophages under basal and stressed conditions to determine oxidative capacity by real-time measurements of oxygen consumption and glycolytic capacity by measuring lactate-based acidification. In M1 macrophages, we found increased nitric oxide production and irg1 expression in addition to altered oxidative phosphorylation and glycolysis. In M2 macrophages, we found increased arginase activity, and both oxidative phosphorylation and glycolysis were similar to control macrophages. These results indicate that M1 and M2 carp macrophages show distinct metabolic signatures and indicate that metabolic reprogramming may occur in carp M1 macrophages. This immunometabolic reprogramming likely supports the inflammatory phenotype of polarized macrophages in teleost fish such as carp, similar to what has been shown in mammals.
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Affiliation(s)
- Annelieke S Wentzel
- Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, Netherlands
| | - Joëlle J E Janssen
- Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, Netherlands.,Human and Animal Physiology Group, Wageningen University & Research, Wageningen, Netherlands
| | - Vincent C J de Boer
- Human and Animal Physiology Group, Wageningen University & Research, Wageningen, Netherlands
| | - Wouter G van Veen
- Experimental Zoology Group, Wageningen University & Research, Wageningen, Netherlands
| | - Maria Forlenza
- Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, Netherlands
| | - Geert F Wiegertjes
- Aquaculture and Fisheries Group, Wageningen University & Research, Wageningen, Netherlands
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15
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Tadmor-Levi R, Doron-Faigenboim A, Marcos-Hadad E, Petit J, Hulata G, Forlenza M, Wiegertjes GF, David L. Different transcriptional response between susceptible and resistant common carp (Cyprinus carpio) fish hints on the mechanism of CyHV-3 disease resistance. BMC Genomics 2019; 20:1019. [PMID: 31878870 PMCID: PMC6933926 DOI: 10.1186/s12864-019-6391-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/12/2019] [Indexed: 02/08/2023] Open
Abstract
Background Infectious disease outbreaks form major setbacks to aquaculture production and to further development of this important sector. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus widely hampering production of common carp (Cyprinus carpio), one of the most farmed fish species worldwide. Genetically disease resistant strains are highly sought after as a sustainable solution to this problem. To study the genetic basis and cellular pathways underlying disease resistance, RNA-Seq was used to characterize transcriptional responses of susceptible and resistant fish at day 4 after CyHV-3 infection. Results In susceptible fish, over four times more differentially expressed genes were up-regulated between day 0 and 4 compared to resistant fish. Susceptible and resistant fish responded distinctively to infection as only 55 (9%) of the up-regulated genes were shared by these two fish types. Susceptible fish elicited a typical anti-viral response, involving interferon and interferon responsive genes, earlier than resistant fish did. Furthermore, chemokine profiles indicated that the two fish types elicited different cellular immunity responses. A comparative phylogenetic approach assisted in chemokine copies annotation pointing to different orthologous copies common to bony-fishes and even carp-specific paralogs that were differentially regulated and contributed to the different response of these two fish types. Susceptible fish up-regulated more ccl19 chemokines, which attract T-cells and macrophages, the anti-viral role of which is established, whereas resistant fish up-regulated more cxcl8/il8 chemokines, which attract neutrophils, the antiviral role of which is unfamiliar. Conclusions Taken together, by pointing out transcriptional differences between susceptible and resistant fish in response to CyHV-3 infection, this study unraveled possible genes and pathways that take part in disease resistance mechanisms in fish and thus, enhances our understanding of fish immunogenetics and supports the development of sustainable and safe aquaculture.
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Affiliation(s)
- Roni Tadmor-Levi
- Department of Animal Sciences, RH Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.,National Natural History Collections and Department of Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Evgeniya Marcos-Hadad
- Department of Animal Sciences, RH Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jules Petit
- Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, Netherlands.,Aquaculture and Fisheries Group, Wageningen University & Research, Wageningen, Netherlands
| | - Gideon Hulata
- Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Maria Forlenza
- Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, Netherlands
| | - Geert F Wiegertjes
- Aquaculture and Fisheries Group, Wageningen University & Research, Wageningen, Netherlands
| | - Lior David
- Department of Animal Sciences, RH Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
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16
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Swaleh SB, Banday UZ, Usmani N. Comparative study of biochemical, histological and molecular biomarkers of heavy metal contamination in Cyprinus carpio collected from warm-monomictic lake and government culture pond. CHEMOSPHERE 2019; 236:124182. [PMID: 31307788 DOI: 10.1016/j.chemosphere.2019.06.152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 06/10/2023]
Abstract
The study investigated the metallothionein (MT) and glutathione peroxidase (GPX) genes expression in freshwater fish Cyprinus carpio dwelling in Warm-monomictic Lake (Dal) and Government culture pond. Oxidative stress induced by heavy metals in the fish body manipulates stress genes expression resulting in the production of scavenger protein (for free metal ions) metallothionein. It interacts with Cu, Cr, Ni and Cd via metal-thiolate bond relieving the metal load from fish body. Maximum fold change was observed in liver, muscle and midgut tissue. Similar rise seen in GPX indicates defence against lipid peroxidation. MT and GPX genes data were compared with beta-actin gene used as an internal control. Limnological studies of both the sites (temperature, dissolved oxygen, pH, total dissolved solids, conductivity), were essential to ensure the quality of water in which the dominant species (C. carpio) was thriving, as these fishes are transported for human consumption. Heavy metal concentration (water, tissues, gut content), bioindices, biochemical parameters and histological alterations were studied to observe the impact of elements selected.
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Affiliation(s)
- Sadiya Binte Swaleh
- Aquatic Toxicology Laboratory, Department of Zoology, Aligarh Muslim University, Aligarh, 202002, India.
| | - Umarah Zahoor Banday
- Aquatic Toxicology Laboratory, Department of Zoology, Aligarh Muslim University, Aligarh, 202002, India.
| | - Nazura Usmani
- Aquatic Toxicology Laboratory, Department of Zoology, Aligarh Muslim University, Aligarh, 202002, India.
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17
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Tan G, Polychronopoulos D, Lenhard B. CNEr: A toolkit for exploring extreme noncoding conservation. PLoS Comput Biol 2019; 15:e1006940. [PMID: 31449516 PMCID: PMC6730951 DOI: 10.1371/journal.pcbi.1006940] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 09/06/2019] [Accepted: 06/25/2019] [Indexed: 12/18/2022] Open
Abstract
Conserved Noncoding Elements (CNEs) are elements exhibiting extreme noncoding conservation in Metazoan genomes. They cluster around developmental genes and act as long-range enhancers, yet nothing that we know about their function explains the observed conservation levels. Clusters of CNEs coincide with topologically associating domains (TADs), indicating ancient origins and stability of TAD locations. This has suggested further hypotheses about the still elusive origin of CNEs, and has provided a comparative genomics-based method of estimating the position of TADs around developmentally regulated genes in genomes where chromatin conformation capture data is missing. To enable researchers in gene regulation and chromatin biology to start deciphering this phenomenon, we developed CNEr, a R/Bioconductor toolkit for large-scale identification of CNEs and for studying their genomic properties. We apply CNEr to two novel genome comparisons—fruit fly vs tsetse fly, and two sea urchin genomes—and report novel insights gained from their analysis. We also show how to reveal interesting characteristics of CNEs by coupling CNEr with existing Bioconductor packages. CNEr is available at Bioconductor (https://bioconductor.org/packages/CNEr/) and maintained at github (https://github.com/ge11232002/CNEr).
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Affiliation(s)
- Ge Tan
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Dimitris Polychronopoulos
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Boris Lenhard
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, London, United Kingdom
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
- * E-mail:
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18
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Multiple interacting QTLs affect disease challenge survival in common carp (Cyprinus carpio). Heredity (Edinb) 2019; 123:565-578. [PMID: 31036952 DOI: 10.1038/s41437-019-0224-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 03/20/2019] [Accepted: 04/12/2019] [Indexed: 11/08/2022] Open
Abstract
With the steady growth of the human population, food security becomes a prime challenge. Aquaculture is the fastest growing sector providing proteins from an animal source, but outbreaks of infectious diseases repeatedly hamper the production and further development of this sector. Breeding of disease-resistant strains is a desired sustainable solution to this problem. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus damaging production of common carp, an important food and ornamental fish. Previously, we have demonstrated successful introgression of CyHV-3 resistance from a feral strain to commercial strains. Here, we used genotyping by sequencing to identify two novel quantitative trait loci (QTLs) for disease survival that map to different linkage groups than two other QTLs that we previously identified. Effects of these four QTLs were validated and further studied in 14 families with various levels of disease resistance. CyHV-3 survival was found to be a quantitative trait conditioned by mild additive QTL effects and by intricate dominant allelic and epistatic QTL-QTL interactions. Both rare feral alleles and alleles common to feral and cultured strains contributed to survival. This and other advantages of feral alleles introgression were demonstrated. These QTLs, which affected survival of individuals within families, had no significant effect on variation in cumulative family % survival, suggesting that more between family variation remains to be explored. Unraveling the underlying genetics of survival is important for enhancing the breeding of resistant strains and our knowledge of disease resistance mechanisms.
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19
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Petit J, Bailey EC, Wheeler RT, de Oliveira CAF, Forlenza M, Wiegertjes GF. Studies Into β-Glucan Recognition in Fish Suggests a Key Role for the C-Type Lectin Pathway. Front Immunol 2019; 10:280. [PMID: 30863400 PMCID: PMC6400144 DOI: 10.3389/fimmu.2019.00280] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 02/01/2019] [Indexed: 11/17/2022] Open
Abstract
Immune-modulatory effects of β-glucans are generally considered beneficial to fish health. Despite the frequent application of β-glucans in aquaculture practice, the exact receptors and downstream signalling remains to be described for fish. In mammals, Dectin-1 is a member of the C-type lectin receptor (CLR) family and the best-described receptor for β-glucans. In fish genomes, no clear homologue of Dectin-1 could be identified so far. Yet, in previous studies we could activate carp macrophages with curdlan, considered a Dectin-1-specific β-(1,3)-glucan ligand in mammals. It was therefore proposed that immune-modulatory effects of β-glucan in carp macrophages could be triggered by a member of the CLR family activating the classical CLR signalling pathway, different from Dectin-1. In the current study, we used primary macrophages of common carp to examine immune modulation by β-glucans using transcriptome analysis of RNA isolated 6 h after stimulation with two different β-glucan preparations. Pathway analysis of differentially expressed genes (DEGs) showed that both β-glucans regulate a comparable signalling pathway typical of CLR activation. Carp genome analysis identified 239 genes encoding for proteins with at least one C-type Lectin Domains (CTLD). Narrowing the search for candidate β-glucan receptors, based on the presence of a conserved glucan-binding motif, identified 13 genes encoding a WxH sugar-binding motif in their CTLD. These genes, however, were not expressed in macrophages. Instead, among the β-glucan-stimulated DEGs, a total of six CTLD-encoding genes were significantly regulated, all of which were down-regulated in carp macrophages. Several candidates had a protein architecture similar to Dectin-1, therefore potential conservation of synteny of the mammalian Dectin-1 region was investigated by mining the zebrafish genome. Partial conservation of synteny with a region on the zebrafish chromosome 16 highlighted two genes as candidate β-glucan receptor. Altogether, the regulation of a gene expression profile typical of a signalling pathway associated with CLR activation and, the identification of several candidate β-glucan receptors, suggest that immune-modulatory effects of β-glucan in carp macrophages could be a result of signalling mediated by a member of the CLR family.
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Affiliation(s)
- Jules Petit
- Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, Netherlands
| | - Erin C. Bailey
- Department of Molecular & Biomedical Sciences, University of Maine, Orono, ME, United States
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, United States
| | - Robert T. Wheeler
- Department of Molecular & Biomedical Sciences, University of Maine, Orono, ME, United States
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, United States
| | | | - Maria Forlenza
- Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, Netherlands
| | - Geert F. Wiegertjes
- Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, Netherlands
- Aquaculture and Fisheries Group, Wageningen University & Research, Wageningen, Netherlands
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20
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Katakura F, Nishiya K, Wentzel AS, Hino E, Miyamae J, Okano M, Wiegertjes GF, Moritomo T. Paralogs of Common Carp Granulocyte Colony-Stimulating Factor (G-CSF) Have Different Functions Regarding Development, Trafficking and Activation of Neutrophils. Front Immunol 2019; 10:255. [PMID: 30837998 PMCID: PMC6389648 DOI: 10.3389/fimmu.2019.00255] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/29/2019] [Indexed: 01/08/2023] Open
Abstract
Mammalian granulocyte colony-stimulating factor (G-CSF; CSF3) is a primary cytokine that promotes the development, mobilization, and activation of neutrophils and their precursors. Teleosts have been reported to possess two paralogs as a likely result of the teleost-wide whole genome duplication (WGD) event, but functional divergence of G-CSF paralogs remains poorly understood. Common carp are an allotetraploid species owing to an additional WGD event in the carp lineage and here, we report on genomic synteny, sequence similarity, and phylogeny of four common carp G-CSF paralogs (g-csfa1 and g-csfa2; g-csfb1 and g-csfb2). G-csfa1 and g-csfa2 show differential and relatively high gene expression levels, while g-csfb1 and g-csfb2 show low basal gene expression levels in most tissues. All paralogs are expressed higher in macrophages than in other leukocyte sub-types and are highly up-regulated by treatment of macrophages with mitogens. Recombinant G-CSFa1 and G-CSFb1 both promoted the proliferation of kidney hematopoietic cells, while only G-CSFb1 induced the differentiation of kidney cells along the neutrophil-lineage. Colony-forming unit assays revealed that G-CSFb1 alone stimulates the formation of CFU-G colonies from head- and trunk-kidney whereas the combination of G-CSFa1 and G-CSFb1 stimulates the formation of both CFU-G and CFU-GM colonies. Recombinant G-CSFa1 and G-CSFb1 also exhibit chemotactic activity against kidney neutrophils and up-regulation of cxcr1 mRNA expression was highest in neutrophils after G-CSFb1 stimulation. Furthermore, G-CSFb1 more than G-CSFa1 induced priming of kidney neutrophils through up-regulation of a NADPH-oxidase component p47 phox . In vivo administration of G-CSF paralogs increased the number of circulating blood neutrophils of carp. Our findings demonstrate that gene duplications in teleosts can lead to functional divergence between paralogs and shed light on the sub-functionalization of G-CSF paralogs in cyprinid fish.
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Affiliation(s)
- Fumihiko Katakura
- Laboratory of Comparative Immunology, Department of Veterinary Medicine, Nihon University, Fujisawa, Japan
| | - Kohei Nishiya
- Laboratory of Comparative Immunology, Department of Veterinary Medicine, Nihon University, Fujisawa, Japan
| | - Annelieke S. Wentzel
- Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, Netherlands
| | - Erika Hino
- Laboratory of Comparative Immunology, Department of Veterinary Medicine, Nihon University, Fujisawa, Japan
| | - Jiro Miyamae
- Laboratory of Comparative Immunology, Department of Veterinary Medicine, Nihon University, Fujisawa, Japan
| | - Masaharu Okano
- Laboratory of Comparative Immunology, Department of Veterinary Medicine, Nihon University, Fujisawa, Japan
| | - Geert F. Wiegertjes
- Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, Netherlands
- Aquaculture and Fisheries Group, Wageningen Institute of Animal Science, Wageningen University & Research, Wageningen, Netherlands
| | - Tadaaki Moritomo
- Laboratory of Comparative Immunology, Department of Veterinary Medicine, Nihon University, Fujisawa, Japan
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21
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Maekawa S, Wang PC, Chen SC. Comparative Study of Immune Reaction Against Bacterial Infection From Transcriptome Analysis. Front Immunol 2019; 10:153. [PMID: 30804945 PMCID: PMC6370674 DOI: 10.3389/fimmu.2019.00153] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/17/2019] [Indexed: 12/28/2022] Open
Abstract
Transcriptome analysis is a powerful tool that enables a deep understanding of complicated physiological pathways, including immune responses. RNA sequencing (RNA-Seq)-based transcriptome analysis and various bioinformatics tools have also been used to study non-model animals, including aquaculture species for which reference genomes are not available. Rapid developments in these techniques have not only accelerated investigations into the process of pathogenic infection and defense strategies in fish, but also used to identify immunity-related genes in fish. These findings will contribute to fish immunotherapy for the prevention and treatment of bacterial infections through the design of more specific and effective immune stimulants, adjuvants, and vaccines. Until now, there has been little information regarding the universality and diversity of immune reactions against pathogenic infection in fish. Therefore, one of the aims of this paper is to introduce the RNA-Seq technique for examination of immune responses in pathogen-infected fish. This review also aims to highlight comparative studies of immune responses against bacteria, based on our previous findings in largemouth bass (Micropterus salmoides) against Nocardia seriolae, gray mullet (Mugil cephalus) against Lactococcus garvieae, orange-spotted grouper (Epinephelus coioides) against Vibrio harveyi, and koi carp (Cyprinus carpio) against Aeromonas sobria, using RNA-seq techniques. We demonstrated that only 39 differentially expressed genes (DEGs) were present in all species. However, the number of specific DEGs in each species was relatively higher than that of common DEGs; 493 DEGs in largemouth bass against N. seriolae, 819 DEGs in mullets against L. garvieae, 909 in groupers against V. harveyi, and 1471 in carps against A. sobria. The DEGs in different fish species were also representative of specific immune-related pathways. The results of this study will enhance our understanding of the immune responses of fish, and will aid in the development of effective vaccines, therapies, and disease-resistant strains.
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Affiliation(s)
- Shun Maekawa
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Pei-Chi Wang
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan.,Southern Taiwan Fish Disease Centre, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Shih-Chu Chen
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan.,Southern Taiwan Fish Disease Centre, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan.,International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung, Taiwan.,Research Center for Animal Biologics, National Pingtung University of Science and Technology, Pingtung, Taiwan
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22
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Saleh M, Kumar G, Abdel-Baki AAS, Dkhil MA, El-Matbouli M, Al-Quraishy S. Quantitative proteomic profiling of immune responses to Ichthyophthirius multifiliis in common carp skin mucus. FISH & SHELLFISH IMMUNOLOGY 2019; 84:834-842. [PMID: 30385245 DOI: 10.1016/j.fsi.2018.10.078] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/23/2018] [Accepted: 10/28/2018] [Indexed: 06/08/2023]
Abstract
Ichthyophthirius multifiliis, a ciliated protozoan parasite, causes ichthyophthiriasis and leads to considerable economic losses to the aquaculture industry. Understanding the fish immune response and host-parasite interactions could support developing novel strategies for better disease management and control. Fish skin mucus is the first line of defence against infections through the epidermis. Yet, the common carp, Cyprinus carpio, protein-based defence strategies against infection with I. multifiliis at this barrier remain elusive. The skin mucus proteome of common carp was investigated at 1 day and 9 days post-exposure with I. multifiliis. Using nano-LC ESI MS/MS and statistical analysis, the abundance of 19 immune related and signal transduction proteins was found to be differentially regulated in skin mucus of common carp in response to I. multifiliis. The analysis revealed increased abundance values of epithelial chloride channel protein, galactose-specific lectin nattection, high choriolytic enzyme 1 (nephrosin), lysozyme C, granulin and protein-glutamine gamma-glutamyltransferase 2 in I. multifiliis-exposed carp skin mucus. Multiple lectins and a diverse array of distinct serpins with protease inhibitor activity were identified likely implicated in lectin pathway activation and regulation of proteolysis, indicating that these proteins contribute to the carp innate immune system and the protective properties of skin mucus. The results obtained from this proteomic analysis enables a better understanding of fish host response to parasitic infection and gives insights into the key role skin mucus plays in protecting fish against deleterious effects of I. multifiliis.
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Affiliation(s)
- Mona Saleh
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria.
| | - Gokhlesh Kumar
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Abdel-Azeem S Abdel-Baki
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia; Zoology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Mohamed A Dkhil
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia; Department of Zoology and Entomology, Faculty of Science, Helwan University, Cairo, Egypt
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Saleh Al-Quraishy
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
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23
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Shevchenko A, Schuhmann A, Thomas H, Wetzel G. Fine Endmesolithic fish caviar meal discovered by proteomics in foodcrusts from archaeological site Friesack 4 (Brandenburg, Germany). PLoS One 2018; 13:e0206483. [PMID: 30485287 PMCID: PMC6261446 DOI: 10.1371/journal.pone.0206483] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/12/2018] [Indexed: 01/19/2023] Open
Abstract
The role of aquatic resources in ancient economies and paleodiet is important for understanding the evolution of prehistorical societies. Charred food remains from ancient pottery are valuable molecular evidence of dietary habits in antiquity. However, conventional archaeometric approaches applied in their analysis lack organismal specificity, are affected by abundant environmental contaminants, do not elucidate food processing recipes and are limited in the inland regions where diverse dietary resources are available. We performed proteomics analysis of charred organic deposits adhered on early ceramics from Mesolithic-Neolithic inland site Friesack 4 (Brandenburg, Germany). One of pots—a small coarse bowl radiocarbon dated to the end of the 5th millennium BC—was attributed to Endmesolithic pottery. Proteomics of foodcrust from this vessel identified fine carp roe meal and revealed details of a prehistorical culinary recipe. Ancient proteins were unequivocally distinguished from contemporary contaminants by computing deamidation ratios of glutamine residues. These data paint a broader picture of the site-specific exploitation of aquatic resources and contribute to better understanding of the dietary context of Neolithic transition in European inland.
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Affiliation(s)
- Anna Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Andrea Schuhmann
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Henrik Thomas
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Günter Wetzel
- Brandenburgisches Landesamt für Denkmalpflege und Archaeologisches Landesmuseum (BLDAM), Aussenstelle Cottbus, Germany
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24
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Zhang C, Su S, Li X, Li B, Yang B, Zhu J, Wang W. Comparative transcriptomics identifies genes differentially expressed in the intestine of a new fast-growing strain of common carp with higher unsaturated fatty acid content in muscle. PLoS One 2018; 13:e0206615. [PMID: 30395585 PMCID: PMC6218049 DOI: 10.1371/journal.pone.0206615] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 10/16/2018] [Indexed: 01/01/2023] Open
Abstract
We have created a new, fast-growing strain of common carp with higher unsaturated fatty acid content in muscle. To better understand the impacts of gene regulation in intestinal tissue on growth and unsaturated fatty acid content, we conducted a comparative RNA-Seq transcriptome analysis between intestine samples of Selected and Control groups (and corroborated selected results by PCR). After eight weeks of cage culture, weight gain of the Selected group was 20.84% higher. In muscles of the control group, monounsaturated fatty acids (FAs) were more abundant, whereas polyunsaturated FAs were more abundant in muscles of the Selected group. In total, we found 106 differentially expressed genes (DEGs) between the two groups. Only the endocytosis pathway was significantly enriched in DEGs, with two upregulated genes: il2rb and ehd1. The latter is involved in the growth hormone/insulin-like growth factor (Gh/Igf) axis, which plays a key role in the regulation of growth in animals. tll2, which is known to be associated with intestinal regeneration, was extremely highly upregulated in both transcriptomic (infinite) and qPCR (610.70) analyses. Two of the upregulated genes are associated with the fatty acid metabolism, several genes are likely to be indicators of heightened transcription levels, several are associated with metabolic and developmental roles, several with neuronal functions (including two with vision), several with the immune system, and two downregulated genes with the development of vasculature. The higher growth rate of the Selected group is likely to be at least partially attributed to increased endocytosis efficiency and genetically-driven behavioural differences (higher aggression levels). There are some indications that this new strain might have slightly impaired immune responses, and a higher propensity for inherited diseases leading to sight impairment, as well for neurodegenerative diseases in general, but these indications still need to be confirmed.
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Affiliation(s)
- Chengfeng Zhang
- College of Fisheries, Huazhong Agricultural University, Wuhan, PR China
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, PR China
| | - Shengyan Su
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, PR China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, PR China
| | - Xinyuan Li
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, PR China
| | - Bing Li
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, PR China
| | - Baojuan Yang
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, PR China
| | - Jian Zhu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, PR China
- * E-mail: (JZ); (WW)
| | - Weimin Wang
- College of Fisheries, Huazhong Agricultural University, Wuhan, PR China
- * E-mail: (JZ); (WW)
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25
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Chen L, Peng W, Kong S, Pu F, Chen B, Zhou Z, Feng J, Li X, Xu P. Genetic Mapping of Head Size Related Traits in Common Carp ( Cyprinus carpio). Front Genet 2018; 9:448. [PMID: 30356829 PMCID: PMC6190898 DOI: 10.3389/fgene.2018.00448] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 09/18/2018] [Indexed: 12/23/2022] Open
Abstract
Head size is important economic trait for many aquaculture fish which is directly linked to their carcass yield. The genetic basis of head size trait remains unclear in many widely cultured fish species. Common carp (Cyprinus carpio) is one of the most widely studied fish due to its importance on both economic and environmental aspects. In this study, we performed genome-wide association study using 433 Yellow River carp individuals from multiple families to identify loci and genes potentially associated with head size related traits including head length (HL), head length/body length ratio (HBR), eye diameter (ED), and eye cross (EC). QTL mapping was utilized to filter the effects of population stratification and improve power for the candidates identification in the largest surveyed family with a published genetic linkage map. Twelve SNPs showed significant for head size traits in GWAS and 18 QTLs were identified in QTL mapping. Our study combining both GWAS and QTL mapping could compensate the deficiency from each other and advance our understanding of head size traits in common carp. To acquire a better understanding of the correlation between head size and body growth, we also performed comparisons between QTLs of head size traits and growth-related traits. Candidate genes underlying head size traits were identified surrounding the significant SNPs, including parvalbumin, srpk2, fsrp5, igf1, igf3, grb10, igf1r, notch2, sfrp2. Many of these genes have been identified with potential functions on bone formation and growth. Igf1 was a putative gene associated with both head size and body growth in Yellow River carp. The teleost-specific igf3 was a candidate head size related gene, related to both HL and HBR. Our study also indicated the importance of Igf signaling pathway for both growth and head size determination in common carp, which could be potentially used in future selective breeding in common carp as well as other species.
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Affiliation(s)
- Lin Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,College of Fisheries, Henan Normal University, Xinxiang, China
| | - Wenzhu Peng
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Shengnan Kong
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,College of Fisheries, Henan Normal University, Xinxiang, China
| | - Fei Pu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Baohua Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Zhixiong Zhou
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Jianxin Feng
- Henan Academy of Fishery Sciences, Zhengzhou, China
| | - Xuejun Li
- College of Fisheries, Henan Normal University, Xinxiang, China
| | - Peng Xu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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26
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Travin D, Popov I, Guler AT, Medvedev D, van der Plas-Duivesteijn S, Varela M, Kolder ICRM, Meijer AH, Spaink HP, Palmblad M. COMICS: Cartoon Visualization of Omics Data in Spatial Context Using Anatomical Ontologies. J Proteome Res 2018; 17:739-744. [PMID: 29083911 PMCID: PMC5772887 DOI: 10.1021/acs.jproteome.7b00615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
COMICS
is an interactive and open-access web platform for integration
and visualization of molecular expression data in anatomograms of
zebrafish, carp, and mouse model systems. Anatomical ontologies are
used to map omics data across experiments and between an experiment
and a particular visualization in a data-dependent manner. COMICS
is built on top of several existing resources. Zebrafish and mouse
anatomical ontologies with their controlled vocabulary (CV) and defined
hierarchy are used with the ontoCAT R package to aggregate data for
comparison and visualization. Libraries from the QGIS geographical
information system are used with the R packages “maps”
and “maptools” to visualize and interact with molecular
expression data in anatomical drawings of the model systems. COMICS
allows users to upload their own data from omics experiments, using
any gene or protein nomenclature they wish, as long as CV terms are
used to define anatomical regions or developmental stages. Common
nomenclatures such as the ZFIN gene names and UniProt accessions are
provided additional support. COMICS can be used to generate publication-quality
visualizations of gene and protein expression across experiments.
Unlike previous tools that have used anatomical ontologies to interpret
imaging data in several animal models, including zebrafish, COMICS
is designed to take spatially resolved data generated by dissection
or fractionation and display this data in visually clear anatomical
representations rather than large data tables. COMICS is optimized
for ease-of-use, with a minimalistic web interface and automatic selection
of the appropriate visual representation depending on the input data.
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Affiliation(s)
- Dmitrii Travin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , 119234 Moscow, Russian Federation
| | - Iaroslav Popov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , 119234 Moscow, Russian Federation
| | - Arzu Tugce Guler
- Center for Proteomics and Metabolomics, Leiden University Medical Center , PO Box 9600, 2300 RC, Leiden The Netherlands
| | - Dmitry Medvedev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , 119234 Moscow, Russian Federation
| | | | - Monica Varela
- Institute of Biology, Leiden University , PO Box 9502, 2300 RA, Leiden The Netherlands
| | - Iris C R M Kolder
- Institute of Biology, Leiden University , PO Box 9502, 2300 RA, Leiden The Netherlands
| | - Annemarie H Meijer
- Institute of Biology, Leiden University , PO Box 9502, 2300 RA, Leiden The Netherlands
| | - Herman P Spaink
- Institute of Biology, Leiden University , PO Box 9502, 2300 RA, Leiden The Netherlands
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center , PO Box 9600, 2300 RC, Leiden The Netherlands
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27
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Petit J, David L, Dirks R, Wiegertjes GF. Genomic and transcriptomic approaches to study immunology in cyprinids: What is next? DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:48-62. [PMID: 28257855 DOI: 10.1016/j.dci.2017.02.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 02/24/2017] [Accepted: 02/26/2017] [Indexed: 06/06/2023]
Abstract
Accelerated by the introduction of Next-Generation Sequencing (NGS), a number of genomes of cyprinid fish species have been drafted, leading to a highly valuable collective resource of comparative genome information on cyprinids (Cyprinidae). In addition, NGS-based transcriptome analyses of different developmental stages, organs, or cell types, increasingly contribute to the understanding of complex physiological processes, including immune responses. Cyprinids are a highly interesting family because they comprise one of the most-diversified families of teleosts and because of their variation in ploidy level, with diploid, triploid, tetraploid, hexaploid and sometimes even octoploid species. The wealth of data obtained from NGS technologies provides both challenges and opportunities for immunological research, which will be discussed here. Correct interpretation of ploidy effects on immune responses requires knowledge of the degree of functional divergence between duplicated genes, which can differ even between closely-related cyprinid fish species. We summarize NGS-based progress in analysing immune responses and discuss the importance of respecting the presence of (multiple) duplicated gene sequences when performing transcriptome analyses for detailed understanding of complex physiological processes. Progressively, advances in NGS technology are providing workable methods to further elucidate the implications of gene duplication events and functional divergence of duplicates genes and proteins involved in immune responses in cyprinids. We conclude with discussing how future applications of NGS technologies and analysis methods could enhance immunological research and understanding.
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Affiliation(s)
- Jules Petit
- Cell Biology and Immunology Group, Wageningen Institute of Animal Sciences, Wageningen University, PO Box 338, 6700 AH, Wageningen, The Netherlands
| | - Lior David
- Department of Animal Sciences, R. H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Ron Dirks
- ZF-screens B.V., J.H, Oortweg 19, 2333 CH, Leiden, The Netherlands
| | - Geert F Wiegertjes
- Cell Biology and Immunology Group, Wageningen Institute of Animal Sciences, Wageningen University, PO Box 338, 6700 AH, Wageningen, The Netherlands.
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28
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Oomen RA, Hutchings JA. Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing. Facets (Ott) 2017. [DOI: 10.1139/facets-2017-0015] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The need to better understand how plasticity and evolution affect organismal responses to environmental variability is paramount in the face of global climate change. The potential for using RNA sequencing (RNA-seq) to study complex responses by non-model organisms to the environment is evident in a rapidly growing body of literature. This is particularly true of fishes for which research has been motivated by their ecological importance, socioeconomic value, and increased use as model species for medical and genetic research. Here, we review studies that have used RNA-seq to study transcriptomic responses to continuous abiotic variables to which fishes have likely evolved a response and that are predicted to be affected by climate change (e.g., salinity, temperature, dissolved oxygen concentration, and pH). Field and laboratory experiments demonstrate the potential for individuals to respond plastically to short- and long-term environmental stress and reveal molecular mechanisms underlying developmental and transgenerational plasticity, as well as adaptation to different environmental regimes. We discuss experimental, analytical, and conceptual issues that have arisen from this work and suggest avenues for future study.
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Affiliation(s)
- Rebekah A. Oomen
- Department of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway
- Institute of Marine Research, Flødevigen Research Station, 4817 His, Norway
| | - Jeffrey A. Hutchings
- Department of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway
- Institute of Marine Research, Flødevigen Research Station, 4817 His, Norway
- Department of Natural Sciences, University of Agder, 4604 Kristiansand, Norway
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A Comparative Study on Antioxidant System in Fish Hepatopancreas and Intestine Affected by Choline Deficiency: Different Change Patterns of Varied Antioxidant Enzyme Genes and Nrf2 Signaling Factors. PLoS One 2017; 12:e0169888. [PMID: 28099509 PMCID: PMC5242466 DOI: 10.1371/journal.pone.0169888] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/22/2016] [Indexed: 01/24/2023] Open
Abstract
The liver and intestine are susceptible to the oxidative damage which could result in several diseases. Choline deficiency induced oxidative damage in rat liver cells. Thus, this study aimed to investigate the potential molecular mechanisms responsible for choline deficiency-induced oxidative damage. Juvenile Jian carp were fed diets differing in choline content [165 (deficient group), 310, 607, 896, 1167 and 1820 mg/kg diet] respectively for 65 days. Oxidative damage, antioxidant enzyme activities and related gene expressions in the hepatopancreas and intestine were measured. Choline deficiency decreased choline and phosphatidylcholine contents, and induced oxidative damage in both organs, as evidenced by increased levels of oxidative-stress markers (malondialdehyde, protein carbonyl and 8-hydroxydeoxyguanosine), coupled with decreased activities of antioxidant enzymes [Copper-zinc superoxide dismutase (CuZnSOD), manganese superoxide dismutase (MnSOD), glutathione peroxidase (GPx) and glutathione-S-transferase (GST)]. However, choline deficiency increased glutathione contents in the hepatopancreas and intestine. Furthermore, dietary choline deficiency downregulated mRNA levels of MnSOD, GPx1b, GST-rho, mGST3 and Kelch-like ECH associating protein 1 (Keap1b) in the hepatopancreas, MnSOD, GPx1b, GPx4a, GPx4b, GST-rho, GST-theta, GST-mu, GST-alpha, GST-pi and GST-kappa in the intestine, as well as intestinal Nrf2 protein levels. In contrast, choline deficiency upregulated the mRNA levels of GPx4a, GPx4b, mGST1, mGST2, GST-theta, GST-mu, Keap1a and PKC in the hepatopancreas, mGST3, nuclear factor erythoid 2-related factor 2 (Nrf2) and Keap1a in the intestine, as well as hepatopancreatic Nrf2 protein levels. This study provides new evidence that choline deficiency-induced oxidative damage is associated with changes in the transcription of antioxidant enzyme and Nrf2/Keap1 signaling molecules in the hepatopancreas and intestine. Additionally, this study firstly indicated that choline deficiency induced varied change patterns of different GPx and GST isoforms. Meanwhile, the changes of some GPx and GST isoforms caused by choline deficiency in the intestine were contrary to those in the hepatopancreas.
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