1
|
Wan G, Wang Z, Zhang X, Tian Y, Zhou X, Ge L, Xiong G, Wang X, Hu Y. Genomic and transcriptome insight into the structure and immunity role of TRIM proteins in Chinese soft-shelled turtles (Pelodiscus sinensis) after Aeromonas hydrophila infection. Mol Biol Rep 2024; 51:263. [PMID: 38302771 DOI: 10.1007/s11033-023-09139-0] [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: 10/09/2023] [Accepted: 12/11/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND TRIM proteins, recognized as a class of E3 ubiquitin ligases, are increasingly acknowledged for their antipathogen immune functions in mammals and fish. In the Chinese soft-shelled turtle (Pelodiscus sinensis), a secondary aquatic reptile that occupies a unique evolutionary position, the TRIM gene has rarely been reported. METHODS AND RESULTS In the present study, 48 PsTRIM proteins were identified from the genome of Pelodiscus sinensis via Hidden Markov Model (HMM) searches and Signal Transduction ATPases with Numerous Domains (SMART) analysis. These PsTRIMs were found across 43 distinct scaffolds, and phylogenetic analyses classified them into three principal clades. The PsTRIMs feature a conserved assembly of either RING-B-box-coiled-coil (RBCC) or B-box-coiled-coil (BBC) domains at the N-terminus, in addition to eight unique domains at the C-terminus, including the B30.2 domain, 19 of which were identified. Expression profiling revealed ubiquitous expression of the 48 PsTRIMs across various P. sinensis tissues. Notably, seven PsTRIMs exhibited significant differential expression in liver transcriptomes following infection with Aeromonas hydrophila. Weighted gene coexpression network analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis implicated PsTRIM14 and PsTRIM28 as key players in host defense against bacterial invasion. Real-time quantitative PCR results indicated that PsTRIM1, PsTRIM2, PsTRIM14, and PsTRIM28 experienced marked upregulation in P. sinensis livers at 12 h post-infection with A. hydrophila. CONCLUSIONS Our study is the first to comprehensively identify and analyze the functions of TRIM genes in P. sinensis, unveiling their considerable diversity and potential roles in modulating immune responses.
Collapse
Affiliation(s)
- Gang Wan
- College of Fisheries, Hunan Agricultural University, Changsha, 410128, China
| | - Ziao Wang
- Hunan Biological and Electromechanical Polytechnic, Changsha, 410127, China
| | - Xingyue Zhang
- College of Fisheries, Hunan Agricultural University, Changsha, 410128, China
| | - Yu Tian
- College of Fisheries, Hunan Agricultural University, Changsha, 410128, China
| | - Xianwen Zhou
- Affair Center of Animal Husbandry and Aquaculture in Xiang Xi Autonomous Prefecture, Jishou, 416000, Hunan, China
| | - Lingrui Ge
- Hunan Biological and Electromechanical Polytechnic, Changsha, 410127, China
| | - Gang Xiong
- Hunan Biological and Electromechanical Polytechnic, Changsha, 410127, China
| | - Xiaoqing Wang
- College of Fisheries, Hunan Agricultural University, Changsha, 410128, China.
| | - Yazhou Hu
- College of Fisheries, Hunan Agricultural University, Changsha, 410128, China.
| |
Collapse
|
2
|
Gao FY, Zhou X, Lu MX, Wang M, Liu ZG, Cao JM, Ke XL, Yi MM. Nile tilapia TRIM39 recruits I3K413 and I3KL45 as adaptors and is involved in the NF-κB pathway. JOURNAL OF FISH BIOLOGY 2022; 101:144-153. [PMID: 35514248 DOI: 10.1111/jfb.15079] [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: 03/31/2022] [Accepted: 04/29/2022] [Indexed: 06/14/2023]
Abstract
Tripartite motif (TRIM) proteins play a regulatory function in cancer, cell apoptosis and innate immunity. To understand the role of TRIM39 in Nile tilapia (Oreochromis niloticus), TRIM39 cDNA was isolated. The total length of TRIM39 cDNA was 5025 bp. The deduced OnTRIM39 protein contains 549 amino acids and has conserved domains of the TRIM family, which are the RING, B-box, coiled-coil and PRY-SPRY domains. OnTRIM39 mRNA was widely expressed in various tissues. After challenge with Streptococcus agalactiae and stimulation with polyinosinic polycytidylic acid [poly (I:C)] and lipopolysaccharides (LPS), the amount of OnTRIM39 transcript was changed in various tested tissues. OnTRIM39 overexpression increased NF-κB activity. OnTRIM39 was present in the cytoplasm. Mass spectrometry of proteins pulled down with recombinant OnTRIM39 showed that 250 proteins potentially interact with OnTRIM39. The authors selected I3K4I3 from the 250 candidate proteins to verify its interaction with TRIM39. They also selected I3KL45, a member of the same 14-3-3 protein family, to verify its interaction with TRIM39. The results of pull-down assays showed that OnTRIM39 interacted with both I3K413 and I3KL45. These results contribute to further study of the innate immune mechanism of tilapia.
Collapse
Affiliation(s)
- Feng-Ying Gao
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture/Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
| | - Xin Zhou
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Mai-Xin Lu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture/Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
| | - Miao Wang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture/Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
| | - Zhi-Gang Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture/Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
| | - Jiang-Meng Cao
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture/Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
| | - Xiao-Li Ke
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture/Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
| | - Meng-Meng Yi
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture/Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
| |
Collapse
|
3
|
Qin B, Xiao T, Ding C, Deng Y, Lv Z, Su J. Genome-Wide Identification and Expression Analysis of Potential Antiviral Tripartite Motif Proteins (TRIMs) in Grass Carp ( Ctenopharyngodon idella). BIOLOGY 2021; 10:biology10121252. [PMID: 34943167 PMCID: PMC8698530 DOI: 10.3390/biology10121252] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/22/2021] [Accepted: 11/30/2021] [Indexed: 02/08/2023]
Abstract
Tripartite motif proteins (TRIMs), especially B30.2 domain-containing TRIMs (TRIMs-B30.2), are increasingly well known for their antiviral immune functions in mammals, while antiviral TRIMs are far from being identified in teleosts. In the present study, we identified a total of 42 CiTRIMs from the genome of grass carp, Ctenopharyngodon idella, an important cultured teleost in China, based on hmmsearch and SMART analysis. Among these CiTRIMs, the gene loci of 37 CiTRIMs were located on different chromosomes and shared gene collinearities with homologous counterparts from human and zebrafish genomes. They possessed intact conserved RBCC or RB domain assemblies at their N-termini and eight different domains, including the B30.2 domain, at their C-termini. A total of 19 TRIMs-B30.2 were identified, and most of them were clustered into a large branch of CiTRIMs in the dendrogram. Tissue expression analysis showed that 42 CiTRIMs were universally expressed in various grass carp tissues. A total of 11 significantly differentially expressed CiTRIMs were found in two sets of grass carp transcriptomes during grass carp reovirus (GCRV) infection. Three of them, including Cibtr40, CiTRIM103 and CiTRIM109, which all belonged to TRIMs-B30.2, were associated with the type I interferon response during GCRV infection by weighted network co-expression and gene expression trend analyses, suggesting their involvement in antiviral immunity. These findings may offer useful information for understanding the structure, evolution, and function of TRIMs in teleosts and provide potential antiviral immune molecule markers for grass carp.
Collapse
Affiliation(s)
| | | | | | | | - Zhao Lv
- Correspondence: (Z.L.); (J.S.)
| | | |
Collapse
|
4
|
Yu HZ, Li NY, Zeng XD, Song JC, Yu XD, Su HN, Chen CX, Yi L, Lu ZJ. Transcriptome Analyses of Diaphorina citri Midgut Responses to Candidatus Liberibacter Asiaticus Infection. INSECTS 2020; 11:insects11030171. [PMID: 32156093 PMCID: PMC7143376 DOI: 10.3390/insects11030171] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/29/2020] [Accepted: 03/05/2020] [Indexed: 11/13/2022]
Abstract
The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama (Hemiptera: Liviidae), is an important transmission vector of the citrus greening disease Candidatus Liberibacter asiaticus (CLas). The D. citri midgut exhibits an important tissue barrier against CLas infection. However, the molecular mechanism of the midgut response to CLas infection has not been comprehensively elucidated. In this study, we identified 778 differentially expressed genes (DEGs) in the midgut upon CLas infection, by comparative transcriptome analyses, including 499 upregulated DEGs and 279 downregulated DEGs. Functional annotation analysis showed that these DEGs were associated with ubiquitination, the immune response, the ribosome, endocytosis, the cytoskeleton and insecticide resistance. KEGG enrichment analysis revealed that most of the DEGs were primarily involved in endocytosis and the ribosome. A total of fourteen DEG functions were further validated by reverse transcription quantitative PCR (RT-qPCR). This study will contribute to our understanding of the molecular interaction between CLas and D. citri.
Collapse
Affiliation(s)
- Hai-Zhong Yu
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (H.-Z.Y.); (N.-Y.L.); (X.-D.Z.); (J.-C.S.); (X.-D.Y.); (H.-N.S.); (L.Y.)
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou 341000, China
| | - Ning-Yan Li
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (H.-Z.Y.); (N.-Y.L.); (X.-D.Z.); (J.-C.S.); (X.-D.Y.); (H.-N.S.); (L.Y.)
| | - Xiang-Dong Zeng
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (H.-Z.Y.); (N.-Y.L.); (X.-D.Z.); (J.-C.S.); (X.-D.Y.); (H.-N.S.); (L.Y.)
| | - Jian-Chun Song
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (H.-Z.Y.); (N.-Y.L.); (X.-D.Z.); (J.-C.S.); (X.-D.Y.); (H.-N.S.); (L.Y.)
| | - Xiu-Dao Yu
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (H.-Z.Y.); (N.-Y.L.); (X.-D.Z.); (J.-C.S.); (X.-D.Y.); (H.-N.S.); (L.Y.)
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou 341000, China
| | - Hua-Nan Su
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (H.-Z.Y.); (N.-Y.L.); (X.-D.Z.); (J.-C.S.); (X.-D.Y.); (H.-N.S.); (L.Y.)
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou 341000, China
| | | | - Long Yi
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (H.-Z.Y.); (N.-Y.L.); (X.-D.Z.); (J.-C.S.); (X.-D.Y.); (H.-N.S.); (L.Y.)
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou 341000, China
| | - Zhan-Jun Lu
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (H.-Z.Y.); (N.-Y.L.); (X.-D.Z.); (J.-C.S.); (X.-D.Y.); (H.-N.S.); (L.Y.)
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou 341000, China
- Correspondence:
| |
Collapse
|
5
|
Shi Y, Hu S, Duan W, Ding T, Zhao Z. The distinct evolutionary properties of the tripartite motif-containing protein 39 in the Chinese softshell turtle based on its structural and functional characterization. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 99:103407. [PMID: 31158386 DOI: 10.1016/j.dci.2019.103407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 06/09/2023]
Abstract
The tripartite motif (TRIM)-containing proteins are a diverse family of proteins that are involved in the regulation of innate immune responses. TRIM39 is a member of the TRIM family and contains E3 ubiquitin ligase activity. In this study, a TRIM39 homolog from the Chinese softshell turtle (Pelodiscus sinensis), PsTRIM39, was identified, and its functional characterization was investigated. PsTRIM39 is a protein of 470 amino acids containing a conserved RING-finger domain, B-BOX domain, PRY domain and SPRY domain in the TRIM family. Sequence structure and phylogenetic analysis indicated PsTRIM39 has the closest relationship with that of birds. Transcriptional profiling analysis revealed that PsTRIM39 mRNA was upregulated after challenge with Aeromonas hydrophila or the soft-shelled turtle virus, iridovirus. The subcellular localization of PsTRIM39 was in the cytoplasm, which is similar to that of fish. Furthermore, PsTRIM39 colocalized with lysosomes in Fathead minnow (FHM) cells, indicating that it may play a role in immune-related function. An NFκB functional assay showed that overexpression of PsTRIM39 enhanced NFκB activity in FHM cells, which is different from that of mammalian TRIM39. Taken together, these results provide, for the first time, the structural and functional characterization of a TRIM family member in the innate immune responses of reptiles and suggest that PsTRIM39 has distinct evolutionary properties representing the transitional stage from lower vertebrates to higher vertebrates in evolution.
Collapse
Affiliation(s)
- Yan Shi
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Sufei Hu
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Wen Duan
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Tie Ding
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Zhe Zhao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China.
| |
Collapse
|
6
|
Martínez R, Navarro-Martín L, Luccarelli C, Codina AE, Raldúa D, Barata C, Tauler R, Piña B. Unravelling the mechanisms of PFOS toxicity by combining morphological and transcriptomic analyses in zebrafish embryos. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 674:462-471. [PMID: 31022537 DOI: 10.1016/j.scitotenv.2019.04.200] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
Exposure to PFOS (perfluorooctanesulfonate) has been related to toxic effects on lipid metabolism, immunological response, and different endocrine systems. We present here a transcriptomic analysis of zebrafish embryos exposed to different concentrations of PFOS (0.03-1.0 mg/L) from 48 to 120 hpf. No major survival or morphological alterations (swimming bladder inflation, kyphosis, eye separation and size…) were observed below the 1.0 mg/L mark. Conversely, we observed significant increase in transcripts related to lipid transport and metabolism even at the lowest used concentration. In addition, we observed a general decrease on transcripts related to natural immunity and defense again infections, which adds to the recent concerns about PFOS as immunotoxicant, particularly in humans. Derived PoD (Point of Departure) values for transcriptional changes (0.011 mg/L) were about 200-fold lower than the corresponding PoD values for morphometric effects (2.53 mg/L), and close to levels observed in human blood serum or bird eggs. Our data suggest that currently applicable tolerable levels of PFOS in commercial goods should be re-evaluated, taking into account its potential effects on lipid metabolism and the immune system.
Collapse
Affiliation(s)
- Rubén Martínez
- IDAEA-CSIC, Jordi Girona, 18, 08034 Barcelona, Spain; Universitat de Barcelona (UB), Barcelona 08007, Spain.
| | | | | | - Anna E Codina
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain.
| | | | - Carlos Barata
- IDAEA-CSIC, Jordi Girona, 18, 08034 Barcelona, Spain.
| | - Romà Tauler
- IDAEA-CSIC, Jordi Girona, 18, 08034 Barcelona, Spain.
| | - Benjamin Piña
- IDAEA-CSIC, Jordi Girona, 18, 08034 Barcelona, Spain.
| |
Collapse
|
7
|
Magnadóttir B, Hayes P, Hristova M, Bragason BT, Nicholas AP, Dodds AW, Guðmundsdóttir S, Lange S. Post-translational protein deimination in cod (Gadus morhua L.) ontogeny novel roles in tissue remodelling and mucosal immune defences? DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 87:157-170. [PMID: 29908202 DOI: 10.1016/j.dci.2018.06.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 06/08/2023]
Abstract
Peptidylarginine deiminases (PADs) are calcium dependent enzymes with physiological and pathophysiological roles conserved throughout phylogeny. PADs promote post-translational deimination of protein arginine to citrulline, altering the structure and function of target proteins. Deiminated proteins were detected in the early developmental stages of cod from 11 days post fertilisation to 70 days post hatching. Deiminated proteins were present in mucosal surfaces and in liver, pancreas, spleen, gut, muscle, brain and eye during early cod larval development. Deiminated protein targets identified in skin mucosa included nuclear histones; cytoskeletal proteins such as tubulin and beta-actin; metabolic and immune related proteins such as galectin, mannan-binding lectin, toll-like receptor, kininogen, Beta2-microglobulin, aldehyde dehydrogenase, bloodthirsty and preproapolipoprotein A-I. Deiminated histone H3, a marker for anti-pathogenic neutrophil extracellular traps, was particularly elevated in mucosal tissues in immunostimulated cod larvae. PAD-mediated protein deimination may facilitate protein moonlighting, allowing the same protein to exhibit a range of biological functions, in tissue remodelling and mucosal immune defences in teleost ontogeny.
Collapse
Affiliation(s)
- Bergljót Magnadóttir
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Polly Hayes
- Department of Biomedical Sciences, University of Westminster, London, W1W 6UW, UK.
| | - Mariya Hristova
- Perinatal Brain Protection and Repair Group, EGA Institute for Women's Health, University College London, WC1E 6HX, London, UK.
| | - Birkir Thor Bragason
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Anthony P Nicholas
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Alister W Dodds
- MRC Immunochemistry Unit, Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Sigríður Guðmundsdóttir
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, Department of Biomedical Sciences, University of Westminster, London, W1W 6UW, UK.
| |
Collapse
|
8
|
Shi H, Zhou T, Wang X, Yang Y, Wu C, Liu S, Bao L, Li N, Yuan Z, Jin Y, Tan S, Wang W, Zhong X, Qin G, Geng X, Gao D, Dunham R, Liu Z. Genome-wide association analysis of intra-specific QTL associated with the resistance for enteric septicemia of catfish. Mol Genet Genomics 2018; 293:1365-1378. [PMID: 29967962 DOI: 10.1007/s00438-018-1463-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 06/19/2018] [Indexed: 02/07/2023]
Abstract
Disease resistance is one of the most important traits for aquaculture industry. For catfish industry, enteric septicemia of catfish (ESC), caused by the bacterial pathogen Edwardsiella ictaluri, is the most severe disease, causing enormous economic losses every year. In this study, we used three channel catfish families with 900 individuals (300 fish per family) and the 690K catfish SNP array, and conducted a genome-wide association study to detect the quantitative trait loci (QTL) associated with ESC resistance. Three significant QTL, with two of located on LG1 and one on LG26, and three suggestive QTL located on LG1, LG3, and LG21, respectively, were identified to be associated with ESC resistance. With a well-assembled- and -annotated reference genome sequence, genes around the involved QTL regions were identified. Among these genes, 37 genes had known functions in immunity, which may be involved in ESC resistance. Notably, nlrc3 and nlrp12 identified here were also found in QTL regions of ESC resistance in the channel catfish × blue catfish interspecific hybrid system, suggesting this QTL was operating within both intra-specific channel catfish populations and interspecific hybrid backcross populations. Many of the genes of the Class I MHC pathway, for mediated antigen processing and presentation, were found in the QTL regions. The positional correlation found in this study and the expressional correlation found in previous studies indicated that Class I MHC pathway was significantly associated with ESC resistance. This study validated one QTL previously identified using the second and fourth generation of the interspecific hybrid backcross progenies, and identified five additional QTL among channel catfish families. Taken together, it appears that there are only a few major QTL for ESC disease resistance, making marker-assisted selection an effective approach for genetic improvements of ESC resistance.
Collapse
Affiliation(s)
- Huitong Shi
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Xiaozhu Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yujia Yang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Chenglong Wu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Lisui Bao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ning Li
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zihao Yuan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yulin Jin
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Suxu Tan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Wenwen Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Xiaoxiao Zhong
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Guyu Qin
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Xin Geng
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Dongya Gao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Rex Dunham
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zhanjiang Liu
- Department of Biology, College of Art and Sciences, Syracuse University, Syracuse, NY, 13244, USA.
| |
Collapse
|
9
|
Luo K, Li Y, Xia L, Hu W, Gao W, Guo L, Tian G, Qi Z, Yuan H, Xu Q. Analysis of the expression patterns of the novel large multigene TRIM gene family (finTRIM) in zebrafish. FISH & SHELLFISH IMMUNOLOGY 2017; 66:224-230. [PMID: 28461211 DOI: 10.1016/j.fsi.2017.04.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/24/2017] [Accepted: 04/27/2017] [Indexed: 06/07/2023]
Abstract
Tripartite motif (TRIM) proteins are receiving increased research interest because of their roles in a wide range of cellular biological processes in innate immunity. In zebrafish (Danio rerio), the functions of the finTRIM (ftr) family are unclear. In the present study, we investigated the expression pattern of ftr12, ftr51, ftr67, ftr82, ftr83, and ftr84 in zebrafish for the first time. The results showed that ftr12, ftr67, and ftr84 are maternally expressed in the oocyte and highly expressed at the early stage (0-4 hpf) of embryo (P < 0.05), suggesting their involvement in the embryonic innate defense system. The ftr82 gene was highly expressed at 8 hpf (P < 0.05), which implied that the embryos could synthesize their own immunity-related mRNAs. However, ftr51 and ftr83 were highest at 8 hpf (2.33 and 51.53 relative to β-actin respectively) and might mediate embryonic development. The expression levels of ftr12, ftr51, and ftr67 were highest in the gill, intestines, and liver, respectively. Ftr82, ftr83, and ftr84 were predominantly expressed in the kidney, suggesting that these finTRIMs might play roles in both immunity and non-immunity-related tissue compartments. Zebrafish embryonic fibroblast (ZF4) cells were infected with Grass carp reovirus (GCRV) and Spring viremia of carp virus (SVCV). During GCRV infection, the expression of ftr12 was significantly upregulated from 12 h to 24 h; and ftr51 and ftr67 increased from 3 h to 12 h. The expressions of ftr82, ftr83, and ftr84 were only upregulated at 12 h, 12 h, and 24 h, respectively. All of these genes were significantly downregulated at 48 h (P < 0.05). Challenge with SVCV upregulated the expressions of ftr12 and ftr51 at 12 h and 48 h (P < 0.05), respectively, and ftr67 reached its highest expression level at 3 h. ftr82 showed only a slight upregulation at 6 h and 48 h, and ftr83 and ftr84 were consecutively increased, reaching their highest levels at 12 h (P < 0.05). Meanwhile, ftr67 and ftr83 were significantly downregulated at 48 h (P < 0.05). Our research demonstrated that ftr12, ftr51, ftr67, ftr82, ftr83, and ftr84 probably have important roles in innate immune responses and in non-immunity-related tissues.
Collapse
Affiliation(s)
- Kai Luo
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434020, China
| | - Youshen Li
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434020, China
| | - Lihai Xia
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434020, China
| | - Wei Hu
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434020, China; School of Animal Science, Yangtze University, Jingzhou 434020, China
| | - Weihua Gao
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434020, China; School of Animal Science, Yangtze University, Jingzhou 434020, China
| | - Liwei Guo
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434020, China
| | - Guangming Tian
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434020, China
| | - Zhitao Qi
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434020, China
| | - Hanwen Yuan
- College of Marine and Biotechnology, Guangxi University for Nationalities, Nanning, Guangxi 530006, China; Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Nanning, Guangxi 530006, China.
| | - Qiaoqing Xu
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434020, China; School of Animal Science, Yangtze University, Jingzhou 434020, China.
| |
Collapse
|
10
|
Yu Y, Huang X, Liu J, Zhang J, Hu Y, Yang Y, Huang Y, Qin Q. Fish TRIM32 functions as a critical antiviral molecule against iridovirus and nodavirus. FISH & SHELLFISH IMMUNOLOGY 2017; 60:33-43. [PMID: 27847343 DOI: 10.1016/j.fsi.2016.11.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/07/2016] [Accepted: 11/12/2016] [Indexed: 06/06/2023]
Abstract
Tripartite motif-containing 32 (TRIM32) has been demonstrated to pay vital roles in cancer, genetic disorders and antiviral immunity. However, the molecular functions of fish TRIM32 still remained largely unknown. Here, a novel TRIM32 gene from orange spotted grouper (EcTRIM32) was cloned and characterized. EcTRIM32 encoded a 685-aa protein which showed 93%, and 60% identity to large yellow croaker (Larimichthys crocea) and human (Homo sapiens), respectively. Amino acid alignment showed that EcTRIM32 contained a conserved RING-finger domain, a BBOX domain and NHL domain. In healthy grouper, the transcript of EcTRIM32 was predominantly detected in brain, liver, intestine, spleen and skin. After injection with Singapore grouper iridovirus (SGIV) and polyI:C, the relative expression of EcTRIM32 in grouper spleen was differently regulated, suggested that EcTRIM32 was involved in antiviral immune response. In transfected grouper spleen (GS) cells, EcTRIM32 displayed bright fluorescence aggregates or spots in the cytoplasm. Notably, the deletion RING domain altered its precise localization and distributed throughout the cytoplasm in GS cells. In EcTRIM32 overexpressing cells, the replication of SGIV or red-spotted grouper nervous necrosis virus (RGNNV) was significantly inhibited compared to the vector control cells. Moreover, the overexpression of EcTRIM32 positively regulated the interferon immune response, evidenced by the significant increase of the expression level of interferon related signaling molecules, including interferon regulatory factor 3 (IRF3), IRF7, interferon-stimulated gene 15 (ISG15), interferon-induced 35-kDa protein (IFP35), MXI, TIR-domain-containing adaptor-inducing interferon-β (TRIF) and melanoma differentiation-associated protein 5 (MDA5). Further studies showed that overexpression of EcTRIM32 significantly enhanced the MDA5-mediated interferon immune response, but decreased stimulator of interferon genes (STING)-mediated interferon immune response. Meanwhile, the expression levels of pro-inflammation cytokines, including TNFα, IL-6 and IL-8 were up-regulated by the ectopic expression of EcTRIM32. We speculated that the regulation of IRF7, and pro-inflammation cytokines by EcTRIM32 overexpression might contribute critical roles in SGIV infection. In addition, the deletion of RING domain not only significantly weakened the antiviral roles of EcTRIM32, but also obviously affected the regulatory effects of EcTRIM32 on interferon immune and inflammation response. Together, our results firstly demonstrated that fish TRIM32 acted as an antiviral factor against both DNA and RNA virus infection.
Collapse
Affiliation(s)
- Yepin Yu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Xiaohong Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Jiaxin Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Jingcheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Yin Hu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Ying Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Youhua Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China.
| | - Qiwei Qin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China; College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China.
| |
Collapse
|
11
|
Poynter SJ, DeWitte-Orr SJ. Fish interferon-stimulated genes: The antiviral effectors. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 65:218-225. [PMID: 27451256 DOI: 10.1016/j.dci.2016.07.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 07/18/2016] [Accepted: 07/18/2016] [Indexed: 06/06/2023]
Abstract
Type I interferons (IFN) are the cornerstone cytokine of innate antiviral immunity. In response to a viral infection, IFN signaling results in the expression of a diverse group of genes known as interferon-stimulated genes (ISGs). These ISGs are responsible for interfering with viral replication and infectivity, helping to limit viral infection within a cell. In mammals, many antiviral effector ISGs have been identified and the antiviral mechanisms are at least partially elucidated. In fish fewer ISGs have been identified and while there is evidence they limit viral infection, almost nothing is known of their respective antiviral mechanisms. This review discusses seven ISGs common to mammals and fish and three ISGs that are unique to fish. The lack of understanding regarding fish ISG's antiviral effector functions is highlighted and draws attention to the need for research in this aspect of aquatic innate immunity.
Collapse
Affiliation(s)
- Sarah J Poynter
- Department of Biology, 200 University Ave W, Waterloo, ON N2L 3G1, Canada.
| | - Stephanie J DeWitte-Orr
- Department of Health Sciences and Biology, 75 University Ave W, Waterloo, ON N2L 3G1, Canada.
| |
Collapse
|
12
|
Wang W, Huang Y, Yu Y, Yang Y, Xu M, Chen X, Ni S, Qin Q, Huang X. Fish TRIM39 regulates cell cycle progression and exerts its antiviral function against iridovirus and nodavirus. FISH & SHELLFISH IMMUNOLOGY 2016; 50:1-10. [PMID: 26784918 DOI: 10.1016/j.fsi.2016.01.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 06/05/2023]
Abstract
The tripartite motif (TRIM)-containing proteins exert important immune regulatory roles through regulating different signaling pathways in response to different stimuli. TRIM39, a member of the TRIM family, is a RING domain-containing E3 ubiquitin ligase which could regulate cell cycle progression and apoptosis. However, the antiviral activity of TRIM39 is not explored. Here, a TRIM39 homolog from grouper, Epinephelus coioides (EcTRIM39) was cloned, and its effects on cell cycle progression and fish virus replication were investigated. The full-length EcTRIM39 cDNA was composed of 2535 bp and encoded a polypeptide of 543 amino acids with 70% identity with TRIM39 homologs from bicolor damselfish. Amino acid alignment analysis indicated that EcTRIM39 contained a RING finger, B-box and SPRY domain. Expression profile analysis revealed that EcTRIM39 was abundant in intestine, spleen and skin. Upon different stimuli in vivo, the EcTRIM39 transcript was obviously up-regulated after challenging with Singapore grouper iridovirus (SGIV), and polyinosinic-polycytidylic acid (poly I:C). Using fluorescence microscopy, we found that EcTRIM39 localized in the cytoplasm and formed aggregates in grouper spleen (GS) cells. The ectopic expression of EcTRIM39 in vitro affected the cell cycle progression via mediating G1/S transition. Moreover, the RING domain was essential for its accurate localization and effect on cell cycle. In addition, overexpression of EcTRIM39 significantly inhibited viral gene transcription of SGIV and red-spotted grouper nervous necrosis virus (RGNNV) in vitro, and the mutant of RING exerted the opposite effect. Together, our results demonstrated that fish TRIM39 not only regulated the cell cycle progression, but also acted as an important regulator of fish innate immune response against viruses.
Collapse
Affiliation(s)
- Wei Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, China
| | - Youhua Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Yepin Yu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ying Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, China
| | - Meng Xu
- State Key Laboratory Breeding Base for Sustainable Exploitation of Tropical Biotic Resources, College of Marine Science, Hainan University, Haikou, 570228, China
| | - Xiuli Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, China
| | - Songwei Ni
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qiwei Qin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.
| | - Xiaohong Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.
| |
Collapse
|