1
|
Zheng Q, Liu Z, Sun C, Dong J, Zhang H, Ke X, Gao F, Lu M. Molecular characterization, expression and functional analysis of TAK1, TAB1 and TAB2 in Nile tilapia (Oreochromis niloticus). FISH & SHELLFISH IMMUNOLOGY 2024; 145:109359. [PMID: 38184182 DOI: 10.1016/j.fsi.2024.109359] [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: 11/01/2023] [Revised: 12/27/2023] [Accepted: 01/04/2024] [Indexed: 01/08/2024]
Abstract
The MAPK pathway is the common intersection of signal transduction pathways such as inflammation, differentiation and proliferation and plays an important role in the process of antiviral immunity. Streptococcus agalactiae will have a great impact on tilapia aquaculture, so it is necessary to study the immune response mechanism of tilapia to S. agalactiae. In this study, we isolated the cDNA sequences of TAK1, TAB1 and TAB2 from Nile tilapia (Oreochromis niloticus). The TAK1 gene was 3492 bp in length, contained an open reading frame (ORF) of 1809 bp and encoded a polypeptide of 602 amino acids. The cDNA sequence of the TAB1 gene was 4001 bp, and its ORF was 1491 bp, which encoded 497 amino acids. The cDNA sequence of the TAB2 gene was 4792 bp, and its ORF was 2217 bp, encoding 738 amino acids. TAK1 has an S_TKc domain and a coiled coil structure; the TAB1 protein structure contains a PP2C_SIG domain and a conserved PYVDXA/TXF sequence model; and TAB2 contains a CUE domain, a coiled coil domain and a Znf_RBZ domain. Homology analysis showed that TAK1 and TAB1 had the highest homology with Neolamprologus brichardi, and TAB2 had the highest homology with Simochromis diagramma (98.28 %). In the phylogenetic tree, TAK1, TAB1 and TAB2 formed a large branch with other scleractinian fishes. The tissue expression analysis showed that the expression of TAK1, TAB1 and TAB2 was highest in the muscle. The expression of TAK1, TAB1 and TAB2 was significantly induced in most of the tested tissues after stimulation with LPS, Poly I:C and S. agalactiae. The subcellular localization results showed that TAK1 was located in the cytoplasm, and TAB1 and TAB2 had certain distributions in the cytoplasm and nucleus. Coimmunoprecipitation (Co-IP) results showed that TRAF6 did not interact with the TAK1 protein but interacted with TAB2, while TAB1 did not interact with P38γ but interacted with TAK1. There was also an interaction between TAK1 and TAB2.
Collapse
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
| | - 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.
| | - 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.
| | - 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
| |
Collapse
|
2
|
Yang X, Ai Y, Chen L, Wang C, Liu J, Zhang J, Li J, Wu H, Xiao J, Chang M, Feng H. PRKX down-regulates TAK1/IRF7 signaling in the antiviral innate immunity of black carp Mylopharyngodon piceus. Front Immunol 2023; 13:999219. [PMID: 36713382 PMCID: PMC9875139 DOI: 10.3389/fimmu.2022.999219] [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: 07/20/2022] [Accepted: 12/21/2022] [Indexed: 01/13/2023] Open
Abstract
TGF-β-activated kinase-1 (TAK1), tightly related to innate immunity, is phosphorylated and activated by X-linked protein kinase (PRKX) in humans and mammals, which belongs to the c-AMP-dependent protein kinase family. However, the relationship between PRKX and TAK1 remains unknown in teleost. It has been reported in vertebrates for the first time that TAK1 of black carp (bcTAK1) interacts with bcIRF7 and is capable to up-regulate bcIRF7-mediated IFN signaling in our previous study. In this study, the role of PRKX homologue of black carp (Mylopharyngodon piceus) (bcPRKX) in bcTAK1/IFN signaling has been explored. Overexpression of bcPRKX suppressed the transcription of interferon promoters but enhanced the transcription of NF-κB promoter. Mylopharyngodon piceus kidney (MPK) cells transfected with shRNA targeting bcPRKX gene presented enhanced antiviral activity against spring viremia of carp virus (SVCV), in which the mRNA levels of the antiviral proteins were increased, including MX1, Viperin and PKR. Overexpressed bcPRKX dampened bcTAK1/bcIRF7/IFN signaling in the luciferase reporter assay and plaque assay. The interaction between bcTAK1 and bcPRKX has been identified by the immunofluorescence (IF) staining and co-immunoprecipitation (co-IP) assay. In addition, we found that bcPRKX can trigger the degradation of bcTAK1. However, the lysosome inhibitor chloroquine, but not the proteasome inhibitor MG-132, prevented the bcTAK1 degradation mediated by bcPRKX. Thus, we conclude that bcPRKX inhibits bcTAK1/bcIRF7/IFN signaling during the innate immune activation by targeting bcTAK1 and triggers lysosome-dependent degradation of bcTAK1.
Collapse
Affiliation(s)
- Xiao Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Yue Ai
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Liang Chen
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Chanyuan Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Ji Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jie Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jun Li
- Key Laboratory of Hunan Province for Study and Utilization of Ethnic Medicinal Plant Resources, College of Biological and Food Engineering, Huaihua University, Huaihua, China
| | - Hui Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jun Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Mingxian Chang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Hao Feng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China,*Correspondence: Hao Feng,
| |
Collapse
|
3
|
Chen X, Li W, Chen T, Ren X, Zhu J, Hu F, Luo J, Xing L, Zhou H, Sun J, Jiang Q, Zhang Y, Xi Q. miR-146a-5p promotes epithelium regeneration against LPS-induced inflammatory injury via targeting TAB1/TAK1/NF-κB signaling pathway. Int J Biol Macromol 2022; 221:1031-1040. [PMID: 36096257 DOI: 10.1016/j.ijbiomac.2022.09.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/13/2022] [Accepted: 09/05/2022] [Indexed: 11/30/2022]
Abstract
Intestinal inflammation often restricts the health and production of animals. MiR-146a has been proved to be an anti-inflammatory molecule in inflammatory disorders, but its role in the intestinal injury and regeneration remains unclear. The study aimed to explore the inflammatory response of intestinal epithelial cells (IECs) in intestinal tissue-specific miR-146a-5p knockout mouse models. We identified the role of miR-146a-5p in inhibiting inflammatory response and promoting proliferation under lipopolysaccharide (LPS) stimulation in vitro and vivo. LPS stimulation significantly increased the expression of TNF-α, IL6 and inhibited IPEC-J2 cell proliferation. Overexpression of miR-146a-5p can reverse the effect of LPS stimulation, and promote the proliferation of intestinal epithelial cells. In the LPS challenge experiment in intestine-specific miR-146a knock-out mice (CKO) and Floxp+/+ mice (CON), CKO mice were more sensitive to LPS stimulation, with more weight loss and more severe intestinal morphological damage than CON mice. Also, miR-146a-5p regulated LPS-induced intestinal injury, inflammation by targeting TAB1. Taken together, miR-146a may function as an anti-inflammatory factor in IECs by targeting TAB1/TAK1-IKK-NF-κB signaling pathway. miR-146a-5p may represent a promising biomarker for inflammatory disorders, and may provide an effective therapeutic method to alleviate weaning stress in piglets and some experimental basis to improve the intestinal health of livestock.
Collapse
Affiliation(s)
- Xingping Chen
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, No. 483 Wushan Road, Guangzhou 510642, China; Key Laboratory of Animal Nutrition in Jiangxi Province, Jiangxi Agricultural University, Nanchang, China
| | - Weite Li
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, No. 483 Wushan Road, Guangzhou 510642, China
| | - Ting Chen
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, No. 483 Wushan Road, Guangzhou 510642, China
| | - Xiaohui Ren
- Ocean College of Hebei Agricultural University, Qinhuangdao 066003, China
| | - Jiahao Zhu
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, No. 483 Wushan Road, Guangzhou 510642, China
| | - Fangxin Hu
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, No. 483 Wushan Road, Guangzhou 510642, China
| | - Junyi Luo
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, No. 483 Wushan Road, Guangzhou 510642, China
| | - Lipeng Xing
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, No. 483 Wushan Road, Guangzhou 510642, China
| | - Hao Zhou
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, No. 483 Wushan Road, Guangzhou 510642, China
| | - Jiajie Sun
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, No. 483 Wushan Road, Guangzhou 510642, China
| | - Qingyan Jiang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, No. 483 Wushan Road, Guangzhou 510642, China
| | - Yongliang Zhang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, No. 483 Wushan Road, Guangzhou 510642, China.
| | - Qianyun Xi
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, No. 483 Wushan Road, Guangzhou 510642, China.
| |
Collapse
|
4
|
Floresta G, Zagni C, Gentile D, Patamia V, Rescifina A. Artificial Intelligence Technologies for COVID-19 De Novo Drug Design. Int J Mol Sci 2022; 23:ijms23063261. [PMID: 35328682 PMCID: PMC8949797 DOI: 10.3390/ijms23063261] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 12/16/2022] Open
Abstract
The recent covid crisis has provided important lessons for academia and industry regarding digital reorganization. Among the fascinating lessons from these times is the huge potential of data analytics and artificial intelligence. The crisis exponentially accelerated the adoption of analytics and artificial intelligence, and this momentum is predicted to continue into the 2020s and beyond. Drug development is a costly and time-consuming business, and only a minority of approved drugs generate returns exceeding the research and development costs. As a result, there is a huge drive to make drug discovery cheaper and faster. With modern algorithms and hardware, it is not too surprising that the new technologies of artificial intelligence and other computational simulation tools can help drug developers. In only two years of covid research, many novel molecules have been designed/identified using artificial intelligence methods with astonishing results in terms of time and effectiveness. This paper reviews the most significant research on artificial intelligence in de novo drug design for COVID-19 pharmaceutical research.
Collapse
|
5
|
Wang Q, Ai Y, Wang C, Liu Y, Zhong H, Yan W, He Y, Deng Z, Zou J, Feng H. PKACα negatively regulates TAK1/IRF7 signaling in black carp Mylopharyngodon piceus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 127:104306. [PMID: 34736993 DOI: 10.1016/j.dci.2021.104306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/16/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
Protein Kinase A catalytic subunit α (PKACα), plays an important role in the PKA and NF-κB signaling pathway in mammals. However, the function of PKACα in teleost fish remains largely unknown. In this study, PKACα from black carp (bcPKACα) has been cloned and its role in the innate immune antiviral signaling pathway was investigated. The open reading frame of bcPKACα gene contains 1056 nucleotides and the immunofluorescence assay verified that PKACα was mainly distributed in the cytoplasm. The reporter assay showed that bcPKACα expression and co-expression of bcPKACα and black carp TAK1 (bcTAK1) could activate the transcription of NF-κB. However, bcTAK1/bcIRF7-mediated IFN transcription was inhibited by bcPKACα. Knockdown of bcPKACα showed slightly enhanced antiviral activity against spring viremia of carp virus (SVCV) compared with control group. Accordingly, the antiviral activity against SVCV and grass carp reovirus (GCRV) of EPC cells co-expressing bcPKACα, bcTAK1 and bcIRF7 was obviously lower than that of EPC cells co-expressing bcTAK1 and bcIRF7. The similar subcellular distribution and interaction between bcPKACα and bcTAK1 were detected by immunofluorescent staining and co-immunoprecipitation assay separately. The data generated in this study demonstrates that bcPKACα associates with bcTAK1 and positively regulates NF-κB signaling, however, negatively regulates TAK1/IRF7 signaling pathway.
Collapse
Affiliation(s)
- Qun Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yue Ai
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Chanyuan Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yankai Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Huijuan Zhong
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Weiyi Yan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yunfan He
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Zhuoyi Deng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Jun Zou
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Hao Feng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| |
Collapse
|
6
|
Xu Y, Zhu B, Zhang R, Tang J, Liu Y, Wang W, Wang Z, Mao Y, Zeng G, Yan J. TAK1 of blunt snout bream promotes NF-κB activation via interaction with TAB1 in response to pathogenic bacteria. FISH & SHELLFISH IMMUNOLOGY 2022; 120:481-496. [PMID: 34923116 DOI: 10.1016/j.fsi.2021.12.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Transforming growth factor-β activated kinase-1 (TAK1) is an important upstream signaling molecules involved in the NF-κB signaling pathway. TAK1 interacts with TAB1 to form the TAK1-TAB1 complex, which elicits NF-κB activation through a series of cascade reactions in mammals. However, the function of TAK1 in blunt snout bream (Megalobrama amblycephala ( maTak1) and the effects of their interaction between TAK1 and TAB1 on the NF-κB activation still remains largely unknown. In the present study, maTak1 was cloned and characterized successfully based on transcriptome data. Its open reading frame is composed of 1626 nucleotides and the predicted maTAK1 protein contains 541 amino acids, which includes an N-terminal Serine/Threonine protein kinases (S/TKc) and a C-terminal coiled-coil region. Phylogenetic analysis showed that maTAK1 were clustered with those of other teleosts. MaTak1 displayed ubiquitous transcriptional expression in all the examined tissues of healthy blunt snout bream but with varied expression levels. And maTrak1 expression was dramatically enhanced in different tissues and MAF cells after LPS stimulation and A. hydrophila challenge. The result from subcellular localization analysis indicated that both maTAK1 and maTAB1 were cytoplasmic protein. The activity of NF-κB promoter could not be induced by overexpression of maTak1 or maTab1 alone, however, it could be enhanced by co-expression of maTak1 and maTab1. Co-immunoprecipitation and subcellular co-localization assay revealed that maTAK1 can combine with maTAB1 directly. The transcriptional expression level of pro-inflammatory cytokines (IL-1β, IL-6 and IL-8) increased distinctly after the overexpression of maTak1 and maTab1. Taken together, the data obtained in this study demonstrated that the direct interaction between maTAK1 and maTAB1 might play a pivotal role in mediating host innate immune response to pathogen invasion by the production of pro-inflammatory cytokines via NF-κB signaling pathway, which might lay a solid foundation for the establishment of novel therapeutic approach to combat bacterial infection in fish.
Collapse
Affiliation(s)
- Yandong Xu
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China
| | - Bi Zhu
- Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Ru Zhang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China
| | - Jianzhou Tang
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Yang Liu
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China
| | - Wenjun Wang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China
| | - Zuzhen Wang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China
| | - Ying Mao
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China; Yueyang Maternal and Child Health-Care Hospital, Department of Medical Genetics, Yueyang, 414000, China
| | - Guoqing Zeng
- Hunan Fisheries Science Institute, Changsha, 410153, China
| | - Jinpeng Yan
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, 410017, China.
| |
Collapse
|
7
|
Kesarwani V, Gupta R, Vetukuri RR, Kushwaha SK, Gandhi S. Identification of Unique Peptides for SARS-CoV-2 Diagnostics and Vaccine Development by an In Silico Proteomics Approach. Front Immunol 2021; 12:725240. [PMID: 34630400 PMCID: PMC8498204 DOI: 10.3389/fimmu.2021.725240] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/10/2021] [Indexed: 12/23/2022] Open
Abstract
Ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus strains is posing new COVID-19 diagnosis and treatment challenges. To help efforts to meet these challenges we examined data acquired from proteomic analyses of human SARS-CoV-2-infected cell lines and samples from COVID-19 patients. Initially, 129 unique peptides were identified, which were rigorously evaluated for repeats, disorders, polymorphisms, antigenicity, immunogenicity, toxicity, allergens, sequence similarity to human proteins, and contributions from other potential cross-reacting pathogenic species or the human saliva microbiome. We also screened SARS-CoV-2-infected NBHE and A549 cell lines for presence of antigenic peptides, and identified paratope peptides from crystal structures of SARS-CoV-2 antigen-antibody complexes. We then selected four antigen peptides for docking with known viral unbound T-cell receptor (TCR), class I and II peptide major histocompatibility complex (pMHC), and identified paratope sequences. We also tested the paratope binding affinity of SARS-CoV T- and B-cell peptides that had been previously experimentally validated. The resultant antigenic peptides have high potential for generating SARS-CoV-2-specific antibodies, and the paratope peptides can be directly used to develop a COVID-19 diagnostics assay. The presented genomics and proteomics-based in-silico approaches have apparent utility for identifying new diagnostic peptides that could be used to fight SARS-CoV-2.
Collapse
Affiliation(s)
| | - Rupal Gupta
- DBT-National Institute of Animal Biotechnology (NIAB), Hyderabad, India.,Amity Institute of Biotechnology, Amity University, Mumbai, India
| | - Ramesh Raju Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Sonu Gandhi
- DBT-National Institute of Animal Biotechnology (NIAB), Hyderabad, India
| |
Collapse
|
8
|
Liu J, Yan Y, Yan J, Wang J, Wei J, Xiao J, Zeng Y, Feng H. Multi-omics analysis revealed crucial genes and pathways associated with black carp antiviral innate immunity. FISH & SHELLFISH IMMUNOLOGY 2020; 106:724-732. [PMID: 32871249 DOI: 10.1016/j.fsi.2020.08.047] [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: 06/22/2020] [Revised: 08/22/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Multi-omics strategy contributes as an indispensable and efficient approach for the investigation of the innate immunity in vertebrates. To explore the crucial genes and pathways involved in the antiviral innate immunity of black carp (Mylopharyngodon piceus), the comparative phosphoproteomics and transcriptomics of Mylopharyngodon piceus kidney (MPK) cells with/without GCRV infection were performed in this manuscript. In phosphoproteomics analysis, 2637 phosphosites corresponding to 1532 proteins were identified and quantified, in which 1372 proteins were identified as differentially expressed proteins (DEPs) with 683 upregulated and 689 downregulated in GCRV infected cells. Functional annotation, enrichment analysis and pathway analysis highlighted that a large number of DEPs were enriched in immune related pathways including TLR pathway and NLR pathway. In transcriptomics analysis, a total of 2936 genes were identified as differentially expressed genes (DEGs), in which 2290 and 646 genes were upregulated and downregulated respectively after GCRV infection. As expected, pathway analysis based on DEGs also showed that a large proportion of DEGs were enriched in immune related pathways including TLR and RLR pathway. A combined list of DEPs and DEGs that enriched in above pathways were imported in Cytoscape for network analysis, reconstruction and visualization. The integrative study suggested that several significant DEPs and DEGs, such as MAP3K7 (TAK1), JUN, MAP2K2, CASP8, IL8 and IRF7 might be functionally crucial in host antiviral innate immunity. Thus, this study contributes as an indispensable reference map for the further investigation of the innate immune system of black carp.
Collapse
Affiliation(s)
- Ji Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yujie Yan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China; National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Jun Yan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Junting Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China; National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Jing Wei
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Jun Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China; College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yong Zeng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China; National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, China.
| | - Hao Feng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
| |
Collapse
|
9
|
Xie X, Cao Y, Dai Y, Chen Z, Wei J, Tan Y, Wu H, Feng H. Black carp RIPK1 negatively regulates MAVS-mediated antiviral signaling during the innate immune activation. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 109:103726. [PMID: 32376280 DOI: 10.1016/j.dci.2020.103726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 03/30/2020] [Accepted: 04/28/2020] [Indexed: 06/11/2023]
Abstract
Receptor-interacting serine/threonine protein kinase 1 (RIPK1) is an important regulator of necroptosis and involved in innate immune response in human and mammal; however, its function in teleost fish mains largely unknown. In this paper, the RIPK1 homologue of black carp (Mylopharyngodon piceus) has been cloned and characterized to explore its role in immunity. Black carp RIPK1 (bcRIPK1) possesses the similar structure to its mammalian counterpart, which has been identified as a cytosolic protein by immunofluorescence staining. Overexpressed bcRIPK1 in host cells led to the decreased transcription of interferon (IFN) and interferon stimulated genes, and exogenous bcRIPK1 in EPC cells led to the decreased transcription of interferon promoters in reporter assay. Our previous study has identified that black carp MAVS (bcMAVS) functions as an antiviral adaptor protein against both grass carp reovirus (GCRV) and spring viremia of carp virus (SVCV). The reporter assay showed that the IFN-inducing ability of bcMAVS was dampened by bcRIPK1 and the plaque assay demonstrated that the antiviral activity of bcMAVS was inhibited by bcRIPK1. The immunofluorescent staining and co-immunoprecipitation identified the interaction between these two molecules. Thus, the data generated in this paper support the conclusion that bcRIPK1 interacts with bcMAVS and negatively regulates bcMAVS-mediated antiviral signaling.
Collapse
Affiliation(s)
- Xinchi Xie
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yingyi Cao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yuhan Dai
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Zhaoyuan Chen
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Jing Wei
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yaqi Tan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Hui Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Hao Feng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| |
Collapse
|
10
|
Wang Y, Wang Q, Li Y, Yin J, Ren Y, Shi C, Bergmann SM, Zhu X, Zeng W. Integrated analysis of mRNA-miRNA expression in Tilapia infected with Tilapia lake virus (TiLV) and identifies primarily immuneresponse genes. FISH & SHELLFISH IMMUNOLOGY 2020; 99:208-226. [PMID: 32001353 DOI: 10.1016/j.fsi.2020.01.041] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/27/2019] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
We investigated differential gene expression in Tilapia infected with the Tilapia Lake virus (TiLV).We used high-throughput sequencing to identify mRNAs and miRNAs involved in TiLV infection progression We identified 25,359 differentially expressed genes that included 863 new genes. We identified 1770, 4142 and 4947 differently expressed genes comparing non-infected controls with 24 and 120 h infections and between the infected groups, respectively. These genes were enriched to 291 GO terms and 62 KEGG pathways and included immune system progress and virion genes. High-throughput miRNA sequencing identified 316 conserved miRNAs, 525 known miRNAs and 592 novel miRNAs. Furthermore, 138, 198 and 153 differently expressed miRNAs were found between the 3 groups listed above, respectively. Target prediction revealed numerous genes including erythropoietin isoform X2, double-stranded RNA-specific adenosine deaminase isoform X1, bone morphogenetic protein 4 and tapasin-related protein that are involved in immune responsiveness. Moreover, these target genes overlapped with differentially expressed mRNAs obtained from RNA-seq. These target genes were significantly enriched to GO terms and KEGG pathways including immune system progress, virion and Wnt signaling pathways. Expression patterns of differentially expressed mRNA and miRNAs were validated in 20 mRNA and 19 miRNAs by qRT-PCR. We also were able to construct a miRNA-mRNA target network that can further understand the molecular mechanisms on the pathogenesis of TiLV and guide future research in developing effective agents and strategies to combat TiLV infections in Tilapia.
Collapse
Affiliation(s)
- Yingying Wang
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, 510380, PR China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, PR China.
| | - Qing Wang
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, 510380, PR China.
| | - Yingying Li
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, 510380, PR China
| | - Jiyuan Yin
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, 510380, PR China
| | - Yan Ren
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, 510380, PR China
| | - Cunbin Shi
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, 510380, PR China
| | - Sven M Bergmann
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Infectology, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Xinping Zhu
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, 510380, PR China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, PR China
| | - Weiwei Zeng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528231, China.
| |
Collapse
|