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Benedetto A, Robotti E, Belay MH, Ghignone A, Fabbris A, Goggi E, Cerruti S, Manfredi M, Barberis E, Peletto S, Arillo A, Giaccio N, Masini MA, Brandi J, Cecconi D, Marengo E, Brizio P. Multi-Omics Approaches for Freshness Estimation and Detection of Illicit Conservation Treatments in Sea Bass ( Dicentrarchus Labrax): Data Fusion Applications. Int J Mol Sci 2024; 25:1509. [PMID: 38338789 PMCID: PMC10855268 DOI: 10.3390/ijms25031509] [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: 12/30/2023] [Revised: 01/18/2024] [Accepted: 01/20/2024] [Indexed: 02/12/2024] Open
Abstract
Fish freshness consists of complex endogenous and exogenous processes; therefore, the use of a few parameters to unravel illicit practices could be insufficient. Moreover, the development of strategies for the identification of such practices based on additives known to prevent and/or delay fish spoilage is still limited. The paper deals with the identification of the effect played by a Cafodos solution on the conservation state of sea bass at both short-term (3 h) and long-term (24 h). Controls and treated samples were characterized by a multi-omic approach involving proteomics, lipidomics, metabolomics, and metagenomics. Different parts of the fish samples were studied (muscle, skin, eye, and gills) and sampled through a non-invasive procedure based on EVA strips functionalized by ionic exchange resins. Data fusion methods were then applied to build models able to discriminate between controls and treated samples and identify the possible markers of the applied treatment. The approach was effective in the identification of the effect played by Cafodos that proved to be different in the short- and long-term and complex, involving proteins, lipids, and small molecules to a different extent.
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Affiliation(s)
- Alessandro Benedetto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (S.P.); (A.A.); (N.G.); (P.B.)
| | - Elisa Robotti
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Michel 11, 15121 Alessandria, Italy; (M.H.B.); (A.G.); (A.F.); (E.G.); (S.C.); (E.B.); (M.A.M.); (E.M.)
| | - Masho Hilawie Belay
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Michel 11, 15121 Alessandria, Italy; (M.H.B.); (A.G.); (A.F.); (E.G.); (S.C.); (E.B.); (M.A.M.); (E.M.)
- Department of Chemistry, Mekelle University, Mekelle P.O. Box 231, Ethiopia
| | - Arianna Ghignone
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Michel 11, 15121 Alessandria, Italy; (M.H.B.); (A.G.); (A.F.); (E.G.); (S.C.); (E.B.); (M.A.M.); (E.M.)
| | - Alessia Fabbris
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Michel 11, 15121 Alessandria, Italy; (M.H.B.); (A.G.); (A.F.); (E.G.); (S.C.); (E.B.); (M.A.M.); (E.M.)
| | - Eleonora Goggi
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Michel 11, 15121 Alessandria, Italy; (M.H.B.); (A.G.); (A.F.); (E.G.); (S.C.); (E.B.); (M.A.M.); (E.M.)
| | - Simone Cerruti
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Michel 11, 15121 Alessandria, Italy; (M.H.B.); (A.G.); (A.F.); (E.G.); (S.C.); (E.B.); (M.A.M.); (E.M.)
| | - Marcello Manfredi
- Department of Translational Medicine, University of Piemonte Orientale, Via Solaroli 17, 28100 Novara, Italy;
| | - Elettra Barberis
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Michel 11, 15121 Alessandria, Italy; (M.H.B.); (A.G.); (A.F.); (E.G.); (S.C.); (E.B.); (M.A.M.); (E.M.)
| | - Simone Peletto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (S.P.); (A.A.); (N.G.); (P.B.)
| | - Alessandra Arillo
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (S.P.); (A.A.); (N.G.); (P.B.)
| | - Nunzia Giaccio
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (S.P.); (A.A.); (N.G.); (P.B.)
| | - Maria Angela Masini
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Michel 11, 15121 Alessandria, Italy; (M.H.B.); (A.G.); (A.F.); (E.G.); (S.C.); (E.B.); (M.A.M.); (E.M.)
| | - Jessica Brandi
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; (J.B.); (D.C.)
| | - Daniela Cecconi
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; (J.B.); (D.C.)
| | - Emilio Marengo
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Michel 11, 15121 Alessandria, Italy; (M.H.B.); (A.G.); (A.F.); (E.G.); (S.C.); (E.B.); (M.A.M.); (E.M.)
| | - Paola Brizio
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (S.P.); (A.A.); (N.G.); (P.B.)
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Xiong LM, Zhang L, Long Z, Zhao X, Ying YR, Xiao TY, Xiong ST. TBK1 upregulates the interferon response against virus by the TBK1-IRF3/7 axis in yellow catfish (Pelteobagrus fulvidraco). FISH & SHELLFISH IMMUNOLOGY 2024; 144:109272. [PMID: 38061442 DOI: 10.1016/j.fsi.2023.109272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 12/31/2023]
Abstract
Yellow catfish (Pelteobagrus fulvidraco) is an important economic species of freshwater fish, widely distributed in China. Recently, viral diseases of yellow catfish have been identified in Chian (Hubei province), arising more attention to the viral immunity in P. fulvidraco. Tumor necrosis factor (TNF) receptor-associated factor NF-κB activator (TANK)-binding kinase 1 (TBK1) plays an essential role in IFN production and innate antiviral immunity. In the present study, we characterized the P. fulvidraco TBK1 (PfTBK1) and reported its function in interferon response. The full-length open reading frame (ORF) is 2184 bp encoding a protein with 727 amino acids, which is composed of four conserved domains, including KD, ULD, CCD1, and CCD2, similar to TBK1 in other species. Pftbk1 was widely expressed in all detected tissues by qPCR and was not inducible by the spring viremia of carp virus (SVCV), a single-strand RNA virus. In addition, the cellular distribution indicated that PfTBK1 was only located in the cytoplasm. Moreover, PfTBK1 induced strong IFN promoter activities through the Jak-stat pathway, and PfTBK1 interacted with and significantly phosphorylated IFN regulatory factor 3/7 (IRF3/7) in P. fulvidraco, promoting the nuclear translocation of pfIRF3 and PfIRF7, and PfTBK1 upregulated IFN response by PfTBK1-PfIRF3/7 axis. Above all, PfTBK1 triggered IFN response and strongly inhibited the replication of SVCV in EPC cells through induction of IFN downstream IFN-stimulated genes (ISGs). Summarily, this work reveals that PfTBK1 plays a positive regulatory role in IFN induction through the TBK1-IRF3/7 axis, laying a foundation for further exploring the molecular mechanism of the antiviral process in P. fulvidraco.
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Affiliation(s)
- Li-Ming Xiong
- Fisheries College, Hunan Agricultural University, Changsha, 410128, China; Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Lei Zhang
- Fisheries College, Hunan Agricultural University, Changsha, 410128, China; Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Zhe Long
- Fisheries College, Hunan Agricultural University, Changsha, 410128, China; Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Xiang Zhao
- Fisheries College, Hunan Agricultural University, Changsha, 410128, China; Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, 410128, China; Yuelushan Lab, Changsha, 410128, China
| | - Yan-Rong Ying
- Fisheries College, Hunan Agricultural University, Changsha, 410128, China; Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, 410128, China
| | - Tiao-Yi Xiao
- Fisheries College, Hunan Agricultural University, Changsha, 410128, China; Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, 410128, China; Yuelushan Lab, Changsha, 410128, China
| | - Shu-Ting Xiong
- Fisheries College, Hunan Agricultural University, Changsha, 410128, China; Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, 410128, China; Yuelushan Lab, Changsha, 410128, China.
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Tong JF, Gan RH, Yu L, Bu SY, Sun JL, Wen X, Song FB, Zhou L, Gui JF, Luo J. Molecular and functional characterization of golden pompano (Trachinotus blochii) TBK1 on IFN regulation. FISH & SHELLFISH IMMUNOLOGY 2023; 143:109163. [PMID: 37838211 DOI: 10.1016/j.fsi.2023.109163] [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: 06/20/2023] [Revised: 09/14/2023] [Accepted: 10/11/2023] [Indexed: 10/16/2023]
Abstract
The golden pompano (Trachinotus blochii), a pivotal commercial marine species in China, has gained significant popularity worldwide. However, accompanied with rapid growth and high density aquaculture, golden pompano has been seriously threatened by Nervous necrosis virus (NNV), while its molecular biology research regarding the innate immune system remains unexplored, which is crucial for understanding the activation of interferon (IFN) production and antiviral responses. In this study, we aimed to identify the characterization and function of golden pompano TANK-binding kinase 1 (gpTBK1), thereby providing evidence of the conservation of this classical factor in the RLR pathway among marine fish. Initially, we found the expression of gpTBK1 upregulation in diseased golden pompano with NNV infection and we successfully cloned the full-length open reading frame (ORF) of gpTBK1, consisting of 2172 nucleotides encoding 723 amino acids, from the head kidney. Subsequent analysis of the amino acid sequence revealed homology between gpTBK1 and other fish TBK1 proteins, with conserved N-terminal Serine/Threonine protein kinases catalytic domain (S_TKc) and C-terminal coiled coil domain (CCD). Moreover, the expression pattern showed that gpTBK1 exhibited ubiquitous expression across all evaluated tissues. Furthermore, functional identification experiments indicated that gpTBK1 activated interferon promoters' activity in golden pompano and induced the expression of downstream IFN-stimulated genes (ISGs). Notably, gpTBK1 was found to co-localize and interact with gpIRF3 in the cytoplasm. Collectively, these data provide a comprehensive analysis of the characterization and functional role of gpTBK1 in promoting interferon production. This research may facilitate the further study of the innate antiviral response, particularly the anti-NNV mechanisms, in golden pompano.
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Affiliation(s)
- Jin-Feng Tong
- College of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, 570228, China
| | - Rui-Hai Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Lang Yu
- College of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, 570228, China
| | - Shao-Yang Bu
- College of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, 570228, China
| | - Jun-Long Sun
- College of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, 570228, China
| | - Xin Wen
- College of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, 570228, China
| | - Fei-Biao Song
- College of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, 570228, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jian Luo
- College of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, 570228, China.
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Zheng Q, Gao F, Liu Z, Sun C, Dong J, Zhang H, Ke X, Lu M. Nile tilapia TBK1 interacts with STING and TRAF3 and is involved in the IFN-β pathway in the immune response. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109125. [PMID: 37805113 DOI: 10.1016/j.fsi.2023.109125] [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: 07/27/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/09/2023]
Abstract
Nile tilapia (Oreochromis niloticus) occupies an important position in the culture of economic fish in China. However, the high mortality caused by streptococcal disease has had a significant impact on the tilapia farming industry. Therefore, it is necessary to clarify the immune mechanism of tilapia in response to Streptococcus agalactiae. As a hub in the natural immune signaling pathway, the junction molecule can help the organism defend against and clear pathogens and is crucial in the signaling pathway. In this study, the cDNA sequence of Nile tilapia TBK1 was cloned, and the expression profile was examined in normal fish and challenged fish. The cDNA sequence of the TBK1 gene was 3378 bp, and its open reading frame (ORF) was 2172 bp, encoding 723 amino acids. The deduced TBK1 protein contained an S_TKc domain, a coiled coil domain and a ubiquitin-like domain (ULD). TBK1 had the highest homology with zebra mbuna (Maylandia zebra) and Lake Malawi cichlid fish (Astatotilapia calliptera), both at 97.59%. In the phylogenetic tree, TBK1 forms a large branch with other scleractinian fish. TBK1 expression was highest in the brain and lowest in the liver. LPS, Poly I:C, and S. agalactiae challenge resulted in significant changes in TBK1 expression in the tissues examined. The subcellular localization showed that TBK1-GFP was distributed in the cytoplasm and could significantly increase IFN-β activation. Pull-down results showed that there was an interaction between TBK1 and TRAF3 and an interaction between STING protein and TBK1 protein. The above results provide a basis for further investigation into the mechanism of TBK1 involvement in the signaling pathway.
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Affiliation(s)
- Qiuyue Zheng
- Pearl River Fisheries Research Institute/Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Chinese Academy of Fishery Science, Guangzhou, 510380, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Fengying Gao
- Pearl River Fisheries Research Institute/Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Chinese Academy of Fishery Science, Guangzhou, 510380, China.
| | - Zhigang Liu
- Pearl River Fisheries Research Institute/Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Chinese Academy of Fishery Science, Guangzhou, 510380, China
| | - Chengfei Sun
- Pearl River Fisheries Research Institute/Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Chinese Academy of Fishery Science, Guangzhou, 510380, China
| | - Junjian Dong
- Pearl River Fisheries Research Institute/Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Chinese Academy of Fishery Science, Guangzhou, 510380, China
| | - Hetong Zhang
- Pearl River Fisheries Research Institute/Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Chinese Academy of Fishery Science, Guangzhou, 510380, China
| | - Xiaoli Ke
- Pearl River Fisheries Research Institute/Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Chinese Academy of Fishery Science, Guangzhou, 510380, China
| | - Maixin Lu
- Pearl River Fisheries Research Institute/Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Chinese Academy of Fishery Science, Guangzhou, 510380, China
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Yu H, Jia X, Pang Y, Niu H, Du B, Xu X, Li J. Identification of multifunctionality of grass carp (Ctenopharyngodon idella) TBK1 during bacterial infection. FISH & SHELLFISH IMMUNOLOGY 2023; 136:108630. [PMID: 36906050 DOI: 10.1016/j.fsi.2023.108630] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
TBK1 is an atypical IκB kinase family member with a set of functions. It is involved in congenital immunization and autophagy in mammals. In this study, we reported that grass carp TBK1 gene expression could be upregulated by bacterial infection. Overexpression of TBK1 could decrease the number of adhesive bacteria in CIK cells. TBK1 could promote cellular migration, proliferation, vitality, and anti-apoptosis ability. Furthermore, the expression of TBK1 could activate the NF-κB signaling pathway by inducing inflammatory cytokines. In addition, we found that the grass carp TBK1 could cause the autophagy level of CIK cells within the decreasing level of p62 protein. Our finding indicated that TBK1 participated in grass carp innate immune progress and autophagy. This study provides evidence of the positive regulation of TBK1 in teleost innate immunity with its multiple functions. It thus may provide important information about the defense and immune mechanisms used by teleost against pathogens.
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Affiliation(s)
- Hongyan Yu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Xuewen Jia
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yifan Pang
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Huiqin Niu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Biao Du
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.
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6
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Zhou Y, Fu HC, Wang YY, Huang HZ, Fu XZ, Li NQ. The dynamic immune responses of Mandarin fish (Siniperca chuatsi) to ISKNV in early infection based on full-length transcriptome analysis and weighted gene co-expression network analysis. FISH & SHELLFISH IMMUNOLOGY 2022; 122:191-205. [PMID: 35158068 DOI: 10.1016/j.fsi.2022.02.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 05/26/2023]
Abstract
Mandarin fish (Siniperca chuatsi) been seriously harmed by infectious spleen and kidney necrosis virus (ISKNV) in recent years, but the early immune response mechanism of infection is still unknown. Here, we performed RNA sequencing on the spleens of mandarin fish infected with ISKNV at 0, 12, 24, 48, and 72 h post-infection (hpi) using short-read Illumina RNA sequencing and long-read Pacific Biosciences isoform sequencing to generate a full-length transcriptome. The immune responses of mandarin fish infected with ISKNV at the molecular level were characterized by RNA-seq analysis and weighted gene co-expression network analysis (WGCNA). A total of 26,528 full-length transcript sequences were obtained. There were 2,729 (1,680 up-regulated and 1,112 down-regulated), 1,874 (1,136 up-regulated and 738 down-regulated), 2,032 (1,158 up-regulated and 847 down-regulated), and 4,176 (2,233 up-regulated and 1,943 down-regulated) differentially expressed genes (DEGs) in mandarin fish at 12, 24, 48, and 72 hpi, compared with uninfected fish, respectively. A total of four modules of co-expressed DEGs identified by WGCNA were significantly positively correlated to the four time points after infection, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the immune-related DEGs in all these modules were mainly enriched in Phagosome, Endocytosis, Herpes simplex infection, and Cytokine-cytokine receptor interaction pathways. Further analysis showed that oher signaling pathways, including CAMs, NOD-like receptor and ER protein processing, Intestinal immune network for IgA production, TLR pathway, and Apoptosis significantly enriched in four modules corresponding to 12, 24, 48, and 72 hpi respectively, had specifically participated in the immune response. Hub genes identified based on the high-degree nodes in the WGCN, including CAM3, IL-8, CCL21, STING, SNX1, PFR and TBK1, and some DEGs such as MHCI, MHCII, TfR, STING, TNF α, TBK1, IRF1, and NF-kB, BCR, IgA and Bcl-XL had involved in dynamic molecular response of mandarin fish to ISKNV infection. In sum, this study provides a set of full-length transcriptome of the spleen tissue of mandarin fish for the first time and revealed a group of immune genes and pathways involved in different temporal responses to ISKNV infection, which has implications for resource conservation and aiding the development of strategies to prevent virus early infection for mandarin fish.
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Affiliation(s)
- Yu Zhou
- School of Basic Medicine and Biological Sciences, Fisheries Research Institute, Soochow University, Suzhou, 215123, China
| | - Huang-Cui Fu
- School of Basic Medicine and Biological Sciences, Fisheries Research Institute, Soochow University, Suzhou, 215123, China
| | - Ying-Ying Wang
- School of Basic Medicine and Biological Sciences, Fisheries Research Institute, Soochow University, Suzhou, 215123, China
| | - He-Zhong Huang
- School of Basic Medicine and Biological Sciences, Fisheries Research Institute, Soochow University, Suzhou, 215123, China.
| | - Xiao-Zhe Fu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquatic Animal Immune Technology, Guangdong Provinces, Guangzhou, 510380, China
| | - Ning-Qiu Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquatic Animal Immune Technology, Guangdong Provinces, Guangzhou, 510380, China
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7
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Tong JF, Zhou L, Li S, Lu LF, Li ZC, Li Z, Gan RH, Mou CY, Zhang QY, Wang ZW, Zhang XJ, Wang Y, Gui JF. Two Duplicated Ptpn6 Homeologs Cooperatively and Negatively Regulate RLR-Mediated IFN Response in Hexaploid Gibel Carp. Front Immunol 2021; 12:780667. [PMID: 34899743 PMCID: PMC8662705 DOI: 10.3389/fimmu.2021.780667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/11/2021] [Indexed: 01/28/2023] Open
Abstract
Src homology region 2 domain-containing phosphatase 1 (SHP1), encoded by the protein tyrosine phosphatase nonreceptor type 6 (ptpn6) gene, belongs to the family of protein tyrosine phosphatases (PTPs) and participates in multiple signaling pathways of immune cells. However, the mechanism of SHP1 in regulating fish immunity is largely unknown. In this study, we first identified two gibel carp (Carassius gibelio) ptpn6 homeologs (Cgptpn6-A and Cgptpn6-B), each of which had three alleles with high identities. Then, relative to Cgptpn6-B, dominant expression in adult tissues and higher upregulated expression of Cgptpn6-A induced by polyinosinic-polycytidylic acid (poly I:C), poly deoxyadenylic-deoxythymidylic (dA:dT) acid and spring viremia of carp virus (SVCV) were uncovered. Finally, we demonstrated that CgSHP1-A (encoded by the Cgptpn6-A gene) and CgSHP1-B (encoded by the Cgptpn6-B gene) act as negative regulators of the RIG-I-like receptor (RLR)-mediated interferon (IFN) response via two mechanisms: the inhibition of CaTBK1-induced phosphorylation of CaMITA shared by CgSHP1-A and CgSHP1-B, and the autophagic degradation of CaMITA exclusively by CgSHP1-A. Meanwhile, the data support that CgSHP1-A and CgSHP1-B have sub-functionalized and that CgSHP1-A overwhelmingly dominates CgSHP1-B in the process of RLR-mediated IFN response. The current study not only sheds light on the regulative mechanism of SHP1 in fish immunity, but also provides a typical case of duplicated gene evolutionary fates.
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Affiliation(s)
- Jin-Feng Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
| | - Shun Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Long-Feng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhuo-Cong Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
| | - Rui-Hai Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
| | - Cheng-Yan Mou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Qi-Ya Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
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