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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.
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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.
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Liu X, Bao X, Li Z, Zhang Q. Investigation of Gene Networks in Three Components of Immune System Provides Novel Insights into Immune Response Mechanisms against Edwardsiella tarda Infection in Paralichthys olivaceus. Animals (Basel) 2023; 13:2542. [PMID: 37570350 PMCID: PMC10417057 DOI: 10.3390/ani13152542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
As a quintessential marine teleost, Paralichthys olivaceus demonstrates vulnerability to a range of pathogens. Long-term infection with Edwardsiella tarda significantly inhibits fish growth and even induces death. Gills, blood, and kidneys, pivotal components of the immune system in teleosts, elicit vital regulatory roles in immune response processes including immune cell differentiation, diseased cell clearance, and other immunity-related mechanisms. This study entailed infecting P. olivaceus with E. tarda for 48 h and examining transcriptome data from the three components at 0, 8, and 48 h post-infection employing weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) network analysis. Network analyses revealed a series of immune response processes after infection and identified multiple key modules and key, core, and hub genes including xpo1, src, tlr13, stat1, and mefv. By innovatively amalgamating WGCNA and PPI network methodologies, our investigation facilitated an in-depth examination of immune response mechanisms within three significant P. olivaceus components post-E. tarda infection. Our results provided valuable genetic resources for understanding immunity in P. olivaceus immune-related components and assisted us in further exploring the molecular mechanisms of E. tarda infection in teleosts.
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Affiliation(s)
- Xiumei Liu
- College of Life Sciences, Yantai University, Yantai 264005, China
| | - Xiaokai Bao
- School of Agriculture, Ludong University, Yantai 264025, China
| | - Zan Li
- School of Agriculture, Ludong University, Yantai 264025, China
| | - Quanqi Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
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Wang L, Wang B, Hu C, Wang C, Gao C, Jiang H, Yan Y. Influences of chronic copper exposure on intestinal histology, antioxidative and immune status, and transcriptomic response in freshwater grouper (Acrossocheilus fasciatus). FISH & SHELLFISH IMMUNOLOGY 2023; 139:108861. [PMID: 37257568 DOI: 10.1016/j.fsi.2023.108861] [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: 04/14/2023] [Revised: 05/15/2023] [Accepted: 05/29/2023] [Indexed: 06/02/2023]
Abstract
Copper (Cu) contamination is commonly found in both natural water environments and fish farms, and it can cause severe damage to different fish organs, but Cu-induced intestinal damage has been rarely studied. This study subjected three groups of freshwater grouper (Acrossocheilus fasciatus) (initial weight: 1.56 ± 0.10 g) to 0 mg/L, 0.01 mg/L, and 0.04 mg/L Cu2+ for 30 days, named Con, Cu0.01, and Cu0.04 groups, respectively. The histological observation indicated that the Cu0.04 group caused a significant decrease in villus length, lamina propria width, and muscular thickness compared to the Con group (P < 0.05). Additionally, the Cu0.04 group significantly increased intestinal superoxide dismutase (SOD), glutathione peroxidase (GPx), lysozyme (LZM) activities, as well as malondialdehyde (MDA) content than the Con group (P < 0.05). Meanwhile, the Cu0.01 and Cu0.04 groups showed significantly increased immunoglobulin M (IgM), complement 3 (C3), and glutathione (GSH) contents than the Con group (P < 0.05). Transcriptomic analysis revealed a total of 101 differentially expressed genes (DEGs), including 47 up-regulated and 54 down-regulated DEGs, were identified between the Cu0.04 and Con groups. Notably, the DEGs were mainly related to intestinal structure construction, immune functions, apoptosis, and resistance to DNA damage and pathogen infection. The findings suggest that chronic Cu exposure caused intestinal histological alterations, activated the antioxidative and immune systems, and induced systematic adaptation to cope with the physical barrier injury, DNA damage, and potential pathogen growth.
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Affiliation(s)
- Lei Wang
- School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China; Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, 241002, China; Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, 241002, China.
| | - Bin Wang
- School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China
| | - Cong Hu
- School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China
| | - Chenyang Wang
- School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China
| | - Chang Gao
- School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China
| | - He Jiang
- Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China.
| | - Yunzhi Yan
- School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China; Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, 241002, China; Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, 241002, China.
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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.
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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
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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.
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Affiliation(s)
| | | | | | | | - Zhao Lv
- Correspondence: (Z.L.); (J.S.)
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