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Zhang X, Ge L, Jin G, Liu Y, Yu Q, Chen W, Chen L, Dong T, Miyagishima KJ, Shen J, Yang J, Lv G, Xu Y, Yang Q, Ye L, Yi S, Li H, Zhang Q, Chen G, Liu W, Yang Y, Li W, Ou J. Cold-induced FOXO1 nuclear transport aids cold survival and tissue storage. Nat Commun 2024; 15:2859. [PMID: 38570500 PMCID: PMC10991392 DOI: 10.1038/s41467-024-47095-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/19/2024] [Indexed: 04/05/2024] Open
Abstract
Cold-induced injuries severely limit opportunities and outcomes of hypothermic therapies and organ preservation, calling for better understanding of cold adaptation. Here, by surveying cold-altered chromatin accessibility and integrated CUT&Tag/RNA-seq analyses in human stem cells, we reveal forkhead box O1 (FOXO1) as a key transcription factor for autonomous cold adaptation. Accordingly, we find a nonconventional, temperature-sensitive FOXO1 transport mechanism involving the nuclear pore complex protein RANBP2, SUMO-modification of transporter proteins Importin-7 and Exportin-1, and a SUMO-interacting motif on FOXO1. Our conclusions are supported by cold survival experiments with human cell models and zebrafish larvae. Promoting FOXO1 nuclear entry by the Exportin-1 inhibitor KPT-330 enhances cold tolerance in pre-diabetic obese mice, and greatly prolongs the shelf-life of human and mouse pancreatic tissues and islets. Transplantation of mouse islets cold-stored for 14 days reestablishes normoglycemia in diabetic mice. Our findings uncover a regulatory network and potential therapeutic targets to boost spontaneous cold adaptation.
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Affiliation(s)
- Xiaomei Zhang
- Department of Hepatic Surgery and Liver transplantation Center of the Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Department of Cancer Biology, Dana-Farber Cancer Institute; Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Lihao Ge
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China
| | - Guanghui Jin
- Department of Hepatic Surgery and Liver transplantation Center of the Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yasong Liu
- Department of Hepatic Surgery and Liver transplantation Center of the Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China
| | - Qingfen Yu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Weizhao Chen
- Department of Hepatic Surgery and Liver transplantation Center of the Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Liang Chen
- Department of Hepatic Surgery and Liver transplantation Center of the Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Tao Dong
- Department of Hepatic Surgery and Liver transplantation Center of the Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Kiyoharu J Miyagishima
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Juan Shen
- Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Guangdong province engineering laboratory for transplantation medicine, Guangzhou, China
| | - Jinghong Yang
- Department of Hepatic Surgery and Liver transplantation Center of the Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Guo Lv
- Guangdong province engineering laboratory for transplantation medicine, Guangzhou, China
| | - Yan Xu
- Cell-gene Therapy Translational Medicine Research Center, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qing Yang
- Department of Hepatic Surgery and Liver transplantation Center of the Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China
| | - Linsen Ye
- Department of Hepatic Surgery and Liver transplantation Center of the Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shuhong Yi
- Department of Hepatic Surgery and Liver transplantation Center of the Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China
| | - Hua Li
- Department of Hepatic Surgery and Liver transplantation Center of the Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China
| | - Qi Zhang
- Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Guangdong province engineering laboratory for transplantation medicine, Guangzhou, China
- Cell-gene Therapy Translational Medicine Research Center, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Guihua Chen
- Department of Hepatic Surgery and Liver transplantation Center of the Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Guangdong province engineering laboratory for transplantation medicine, Guangzhou, China
| | - Wei Liu
- Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
- Guangdong province engineering laboratory for transplantation medicine, Guangzhou, China.
| | - Yang Yang
- Department of Hepatic Surgery and Liver transplantation Center of the Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China.
- Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
- Guangdong province engineering laboratory for transplantation medicine, Guangzhou, China.
| | - Wei Li
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Jingxing Ou
- Department of Hepatic Surgery and Liver transplantation Center of the Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University, Guangzhou, China.
- Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
- Guangdong province engineering laboratory for transplantation medicine, Guangzhou, China.
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Zhao Z, Zhao H, Wang X, Zhang L, Mou C, Huang Z, Ke H, Duan Y, Zhou J, Li Q. Effects of different temperatures on Leiocassis longirostris gill structure and intestinal microbial composition. Sci Rep 2024; 14:7150. [PMID: 38532085 DOI: 10.1038/s41598-024-57731-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/21/2024] [Indexed: 03/28/2024] Open
Abstract
Fish are poikilothermic vertebrates and their physiological activities are affected by water temperature. In recent years, extreme weather has occurred frequently, and temperature changes have adversely affected the growth of farmed fish. To explore the changes in gill tissue structure caused by changing the water temperature and the relationship between the intestinal microbiota and the Leiocassis longirostris host adaptation mechanism, gill tissue sections and intestinal microbial 16S rRNA amplicon sequencing were conducted under different temperature stress (low temperature 4 °C, normal temperature 26 °C and high temperature 32 °C). The results showed that heat stress and cold stress caused injury and swelling, terminal congestion, cell vacuolation, and necrosis of the gill tissue of L. longirostris. For intestinal microbiota, the abundances of Pseudomonadota and Bacillota increased at the cold stress, while the abundances of Fusobacteriota and Bacteroidota increased at the heat stress. The number of opportunistic bacteria, mainly Aeromonas and Acinetobacter, was the highest under cold stress. In addition, the richness of the intestinal microbiota decreased significantly at heat and cold stresses, while evenness increased. Prediction of intestinal microbiota function showed that most common functions, such as metabolism of cofactors and vitamins, energy metabolism and replication and repair, were decreased significantly at heat stress and cold stress, and phylogenetic relationship analysis revealed significant differences among the groups. In conclusion, the change of temperature altered the gill tissue structure, and affected the structure and homeostasis of the intestinal microbiota, thus affecting the survival time of L. longirostris, and cold stress had a greater effect than heat stress.
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Affiliation(s)
- Zhongmeng Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Han Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Xiongyan Wang
- Sichuan Water Conservancy Vocational College, Chongzhou, Sichuan, China
| | - Lu Zhang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Chengyan Mou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Zhipeng Huang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Hongyu Ke
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Yuanliang Duan
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Jian Zhou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Qiang Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China.
- , 1611 Xiyuan Avenue, Chengdu, China.
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Zhu Z, Yang Q, Tian X, Man D, Wang J, Zhang J, Han B. MSTRG3207 promotes apoptosis in zebrafish ZF4 cells via sponging dre-miR-736/bbc3/LOC101885512 axis during cold acclimation. Gene 2024; 894:148010. [PMID: 37981079 DOI: 10.1016/j.gene.2023.148010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/04/2023] [Accepted: 11/15/2023] [Indexed: 11/21/2023]
Abstract
Long non-coding RNAs (lncRNAs) play essential roles in a variety of biological processes. It has been recently reported that lncRNAs can regulate mRNA expression by binding to microRNAs (miRNAs) as competing endogenous RNAs (ceRNAs). However, the involvement of this regulatory mechanism during cold acclimation in fish remains unclear. In this study, we constructed a ceRNA network mediated by lncRNAs in cold-acclimated zebrafish ZF4 cells through bioinformatic analysis of the mRNA, miRNA, and lncRNA profiles obtained from ZF4 cells cultured at 18 °C for 30 days. A previously uncharacterized lncRNA, MSTRG3207, was selected for further analysis. MSTRG3207 was upregulated and dre-miR-736 was downregulated during cold acclimation. MSTRG3207 was cloned by rapid amplification of cDNA ends (RACE) and functionally characterized. The binding of MSTRG3207 to dre-miR-736 was validated by dual-luciferase reporter assay. Under cold acclimation, MSTRG3207 promoted apoptosis by sponging dre-miR-736 and upregulating bbc3 and LOC101885512, two apoptotic genes targeted by dre-miR-736. Taken together, our findings indicate that MSTRG3207 upregulation promotes apoptosis by sponging dre-miR-736 during cold acclimation in fish.
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Affiliation(s)
- Zhongqiu Zhu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Qianting Yang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaoying Tian
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Da Man
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Jian Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Junfang Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, China; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai 201306, China; Marine Biomedical Science and Technology Innovation Platform of Lin-gang Special Area, Shanghai, China.
| | - Bingshe Han
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Marine Biomedical Science and Technology Innovation Platform of Lin-gang Special Area, Shanghai, China.
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Liu J, Liu T, Liu Y, Wang Y, Liu L, Gong L, Liu B, Lü Z. Comparative Transcriptome Analyses Provide New Insights into the Evolution of Divergent Thermal Resistance in Two Eel Gobies. Curr Issues Mol Biol 2023; 46:153-170. [PMID: 38248314 PMCID: PMC10813846 DOI: 10.3390/cimb46010012] [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: 11/16/2023] [Revised: 12/16/2023] [Accepted: 12/21/2023] [Indexed: 01/23/2024] Open
Abstract
Adaptation to thermal conditions in tidal mudflats always involves tolerating frequent fluctuations and often extreme environmental temperatures. Regulation of gene expression plays a fundamental role in the evolution of these thermal adaptations. To identify the key gene regulatory networks associated with the thermal adaptation, we investigated the capability of cold tolerance, as well as the transcriptomic changes under cold stress in two mudflat inhabitants (Odontamblyopus lacepedii and O. rebecca) with contrasting latitude affinity. Our results revealed a remarkable divergent capacity of cold tolerance (CTmin: 0.61 °C vs. 9.57 °C) between the two gobies. Analysis of transcriptomic changes under cold stress unveiled 193 differentially expressed genes exhibiting similar expression profiles across all tissues and species, including several classic metabolic and circadian rhythm molecules such as ACOD and CIART that may represent the core cold response machinery in eel gobies. Meanwhile, some genes show a unique expression spectrum in the more cold-tolerant O. lacepedii suggesting their roles in the enhanced cold tolerance and hence the extreme thermal adaptations. In addition, a weighted gene co-expression network analysis (WGCNA) revealed a subset of metabolic hub genes including MYH11 and LIPT2 showing distinct down-regulation in O. lacepedii when exposed to cold stress which highlights the role of reduced energy consumption in the enhanced cold tolerance of eel gobies. These findings not only provide new insights into how mudflat teleosts could cope with cold stress and their potential evolutionary strategies for adapting to their thermal environment, but also have important implications for sound management and conservation of their fishery resources in a scenario of global climate warming in the marine realm.
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Affiliation(s)
- Jing Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
| | - Tianwei Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
| | - Yantao Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
| | - Yuzhen Wang
- National Engineering Research Center for Facilitated Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
| | - Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
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Hu J, Zhang M, Yan K, Zhang Y, Li Y, Zhu J, Wang G, Wang X, Li Y, Huang X, Tang J, Zheng R, Xu S, Wang D, Wang Y, Yan X. Cold Stress Induces Apoptosis in Silver Pomfret via DUSP-JNK Pathway. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:846-857. [PMID: 37658990 DOI: 10.1007/s10126-023-10245-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/14/2023] [Indexed: 09/05/2023]
Abstract
We cultured silver pomfret for 20 days, decreasing water temperature from 18 to 8 ℃, and sampled muscle every 5 days. Muscle fiber degeneration and apoptosis began to increase at 13 ℃ detected by HE and TUNEL staining. Further analysis of transcriptome revealed that several apoptosis-related pathways were highly enriched by differentially expressed genes (DEGs). We analyzed 10 DEGs from these pathways by RT-qPCR during the temperature-decreasing process. JNK1, PIDD, CytC, Casp 3, and GADD45 were up-regulated after 15 and 20 days, while DUSP3, JNK2, and PARP genes were down-regulated after 15 and 20 days. DUSP5 was up-regulated from 10 to 20 days, and C-JUN was up-regulated after 20 days. We analyzed apoptosis in PaM cells under different temperatures (26 ℃, 23 ℃, 20 ℃, 17 ℃, and 14 ℃). The cell viability significantly declined from 14 to 20 ℃; the TUNEL and IHC results showed that the apoptosis signal increased with the temperature dropping, especially in 17 ℃ and 14 ℃; DUSP5, JNK1, CytC, C-JUN, Casp 3, and GADD45 were up-regulated at 17 ℃ and 14 ℃, and PIDD was up-regulated at 20 ℃, 17 ℃, and 14 ℃. DUSP3 was up-regulated at 20 ℃ but down-regulated at 17 ℃ and 14 ℃, and PARP was down-regulated at 17 ℃ and 14 ℃. JNK2 was up-regulated at 20 ℃ but down-regulated at 17 ℃ and 14 ℃. Our results suggest that DUSP could help inhibit apoptosis in the initial stage of cold stress, but low temperature could down-regulate it and up-regulate JNK-C-JUN, inducing apoptosis in a later stage. These data provide a basis for the study of the response mechanism of fish to cold.
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Affiliation(s)
- Jiabao Hu
- College of Marine Sciences, Ningbo University, Ningbo, China
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Man Zhang
- College of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Kaiheng Yan
- College of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Youyi Zhang
- College of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Yaya Li
- College of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Jiajie Zhu
- College of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Guanlin Wang
- College of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Xiangbing Wang
- College of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Yuanbo Li
- College of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Xiang Huang
- College of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Jie Tang
- College of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Rongyue Zheng
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China
| | - Shanliang Xu
- College of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
- Ningbo Institute of Oceanography, Ningbo, China
| | - Danli Wang
- College of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Yajun Wang
- College of Marine Sciences, Ningbo University, Ningbo, China.
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China.
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China.
| | - Xiaojun Yan
- College of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
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de Oliveira EF, Araújo BC, Marques VH, de Mello PH, Moreira RG, Honji RM. Influence of Docosahexaenoic and Eicosapentaenoic Acid Ratio and Temperature on the Growth Performance, Fatty Acid Profile, and Liver Morphology of Dusky Grouper ( Epinephelus marginatus) (Teleostei: Serranidae) Juveniles. Animals (Basel) 2023; 13:3212. [PMID: 37893939 PMCID: PMC10603700 DOI: 10.3390/ani13203212] [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: 08/03/2023] [Revised: 10/01/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
An 8-week trial was performed to evaluate the influence of docosahexaenoic (DHA) and eicosapentaenoic acid (EPA) ratios and temperature on the fatty acid (FA) metabolism and liver morphology of Epinephelus marginatus. A basal diet was manufactured, and DHA (D1:0.5%; D2:0.75%; D3:1%; and D4:1.5%) and EPA (D1:1.0%; D2:0.75%; D3:0.5%; and D4:0%) levels were added. E. marginatus were kept in twelve tanks with a lower temperature (LT, 23.17 ± 0.12 °C) and twelve with a higher temperature (HT, 28.63 ± 0.06 °C). The DHA/EPA ratio did not affect performance, regardless of the temperature, but the animals fed with the D4 diet showed better growth at HT. A higher lipid deposition and a large lipid vacuole area in the hepatocytes at HT were observed, regardless of the diet. Triacylglycerol (TG) in reflected the diet FA profile mainly in the muscle and liver, whereas the phospholipid (PL) was less influenced by the diet. The same DHA content in the TG fraction of muscle (D3 and D4) were observed at LT; however, only the DHA/EPA ratio of D4 could be differentially stored in the TG fraction of muscle (HT). Monounsaturated and polyunsaturated FA increased in the PL of the eyes at HT, whereas saturated FA was reduced in the TG and PL fractions at LT. These results evidence the importance of temperature and a balanced DHA/EPA ratio in the diet of marine fish.
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Affiliation(s)
- Ethiene Fernandes de Oliveira
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo (IB/USP), Rua do Matão, trav. 14, nº 321, São Paulo 05508-090, SP, Brazil; (E.F.d.O.); (R.G.M.)
| | - Bruno Cavalheiro Araújo
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Mogi das Cruzes 08701-970, SP, Brazil;
| | - Victor Hugo Marques
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo (IB/USP), Rua do Matão, trav. 14, nº 321, São Paulo 05508-090, SP, Brazil; (E.F.d.O.); (R.G.M.)
| | - Paulo Henrique de Mello
- Beacon Development, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia;
| | - Renata Guimarães Moreira
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo (IB/USP), Rua do Matão, trav. 14, nº 321, São Paulo 05508-090, SP, Brazil; (E.F.d.O.); (R.G.M.)
| | - Renato Massaaki Honji
- Centro de Biologia Marinha, Universidade de São Paulo (CEBIMar/USP), Rodovia Manoel Hipólito do Rego, km 131,5, São Sebastião 11612-109, SP, Brazil
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Yang C, Fan H, Ge L, Ma Q, Jiang M, Wen H. Comparative analysis of quantitative phosphoproteomics between two tilapias ( Oreochromis niloticus and Oreochromis aureus) under low-temperature stress. PeerJ 2023; 11:e15599. [PMID: 37456864 PMCID: PMC10340112 DOI: 10.7717/peerj.15599] [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: 02/02/2023] [Accepted: 05/30/2023] [Indexed: 07/18/2023] Open
Abstract
As an important farmed fish, tilapia has poor tolerance to low-temperatures. At the same time, different tilapia strains have apparent differences in low-temperature tolerance. In this study, using the iTRAQ method, the phosphorylated proteomics of two tilapia strains (Oreochromis niloticus and Oreochromis aureus) with different tolerances to low-temperature stress were quantitatively and comparatively analyzed, to clarify the physiological mechanism of tilapia's response to low-temperature stress. Through the GO and IPR analyses of differentially phosphorylated proteins, a number of similarities in physiological activities and regulatory effects were found between the two tilapias in response to low-temperature stress. Many differentially phosphorylated proteins are mainly involved in lipid metabolism, cell proliferation and apoptosis. However, the difference in endurance of low temperature of these two tilapias might be related to the differences in categories, expression and modification level of genetic products which were involved in the aforementioned physiological processes. And meanwhile, the enrichment results of KEGG showed the changes of multiple immune-related and growth-related phosphorylated proteins in the cytokine-cytokine receptor interaction pathway in O. aureus are more prominent. Furthermore, the significantly enriched pathway of carbohydrate digestion and absorption in O. niloticus may indicate that low-temperature stress exerts a more severe impact on energy metabolism. The relative results would help elucidating the molecular mechanism by which tilapia responds to low-temperature stress, and developing culture of tilapia species.
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Affiliation(s)
- Changgeng Yang
- Life Science & Technology School, Lingnan Normal University, Zhanjiang, China
| | - Hua Fan
- Life Science & Technology School, Lingnan Normal University, Zhanjiang, China
| | - Liya Ge
- Life Science & Technology School, Lingnan Normal University, Zhanjiang, China
| | - Qian Ma
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Ming Jiang
- Fish Nutrition and Feed Division, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Hua Wen
- Fish Nutrition and Feed Division, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
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8
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Wang Y, Wang HM, Zhou Y, Hu LH, Wan JM, Yang JH, Niu HB, Hong XP, Hu P, Chen LB, Hu P, Chen LB. Dusp1 regulates thermal tolerance limits in zebrafish by maintaining mitochondrial integrity. Zool Res 2023; 44:126-141. [PMID: 36419379 PMCID: PMC9841188 DOI: 10.24272/j.issn.2095-8137.2022.397] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Temperature tolerance restricts the distribution of a species. However, the molecular and cellular mechanisms that set the thermal tolerance limits of an organism are poorly understood. Here, we report on the function of dual-specificity phosphatase 1 (DUSP1) in thermal tolerance regulation. Notably, we found that dusp1 -/- zebrafish grew normally but survived within a narrowed temperature range. The higher susceptibility of these mutant fish to both cold and heat challenges was attributed to accelerated cell death caused by aggravated mitochondrial dysfunction and over-production of reactive oxygen species in the gills. The DUSP1-MAPK-DRP1 axis was identified as a key pathway regulating these processes in both fish and human cells. These observations suggest that DUSP1 may play a role in maintaining mitochondrial integrity and redox homeostasis. We therefore propose that maintenance of cellular redox homeostasis may be a key mechanism for coping with cellular thermal stress and that the interplay between signaling pathways regulating redox homeostasis in the most thermosensitive tissue (i.e., gills) may play an important role in setting the thermal tolerance limit of zebrafish.
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Affiliation(s)
- Ying Wang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China
| | - Hua-Min Wang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China
| | - Yan Zhou
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China
| | - Ling-Hong Hu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China
| | - Jing-Ming Wan
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China
| | - Ji-Hui Yang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China
| | - Hong-Bo Niu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China
| | - Xiu-Ping Hong
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China
| | - Peng Hu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China
| | - Liang-Biao Chen
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 200120, China,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 200120, China,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 200120, China,E-mail:
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Wu N, Wen H, Xu P, Chen J, Xue M, Li J, Wang M, Song C, Li H. PPAR Signaling Maintains Metabolic Homeostasis under Hypothermia in Freshwater Drum ( Aplodinotus grunniens). Metabolites 2023; 13:102. [PMID: 36677027 PMCID: PMC9865675 DOI: 10.3390/metabo13010102] [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: 12/05/2022] [Revised: 01/02/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Aplodinotus grunniens, known as freshwater drum, is a kind of eurythermal freshwater fish that is widely distributed in North America. In 2019, our research group reached a milestone on its artificial breeding and cultivation and have investigated its physiological adaption to the environment, providing a breakthrough and prospects for aquaculture. However, its adaptability and metabolic homeostasis to hypothermia is not fully understood. In this experiment, cold stress was conducted at 18 °C (LT18) and 10 °C (LT10) with 25 °C as control (Con) for 8 days to explore the effects of short-term hypothermia on the physiology and metabolism of freshwater drum. From the results, the level of free essential amino acids in LT18 and LT10 decreased significantly after 2 days cold stress compared with Con. Furthermore, plasma total triglyceride (TG) content and lipase (LPS) activity were decreased at LT10 for 2d. With RNA-seq in the liver, metabolic-related signaling, especially amino acid synthesis and lipid metabolism, was inhibited by hypothermia. Specifically, the PPAR signaling pathway is correlated with the inhibition of lipid and amino acid metabolism induced by hypothermia. These data confirmed that PPAR signaling maintains lipid and amino acid metabolic homeostasis during cold stress. These results give a theoretical foundation for hypothermia resistance in the area of metabolic homeostasis for freshwater drum.
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Affiliation(s)
- Ningyuan Wu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, No. 9 Shanshui East Road, Wuxi 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Haibo Wen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, No. 9 Shanshui East Road, Wuxi 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Pao Xu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, No. 9 Shanshui East Road, Wuxi 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Jianxiang Chen
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Miaomiao Xue
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Jianlin Li
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, No. 9 Shanshui East Road, Wuxi 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Meiyao Wang
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, No. 9 Shanshui East Road, Wuxi 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Changyou Song
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, No. 9 Shanshui East Road, Wuxi 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Hongxia Li
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, No. 9 Shanshui East Road, Wuxi 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
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10
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Duan Y, Li Q, Zhou J, Zhao H, Zhao Z, Wang L, Luo M, Du J, Dong Z. Studies on the molecular level changes and potential resistance mechanism of Coreius guichenoti under temperature stimulation. Front Genet 2022; 13:1015505. [PMID: 36263436 PMCID: PMC9574000 DOI: 10.3389/fgene.2022.1015505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/15/2022] [Indexed: 12/02/2022] Open
Abstract
In this study, we used transcriptome and proteome technology to analyze molecular level changes in tissues of Coreius guichenoti cultured at high temperature (HT) and low temperature (LT). We also screened for specific anti-stress genes and proteins and evaluated the relationships between them. We identified 201,803 unigenes and 10,623 proteins. Compared with the normal temperature (NT), 408 genes and 1,204 proteins were up- or down-regulated in brain tissues, respectively, at HT, and the numbers were 8 and 149 at LT. In gill tissues, the numbers were 101 and 1,745 at HT and 27 and 511 at LT. In gill tissues at both temperatures, the degree of down-regulation (average, HT 204.67-fold, LT 443.13-fold) was much greater than that of up-regulation (average, HT 28.69-fold, LT 17.68-fold). The protein expression in brain (average, up 52.67-fold, down 13.54-fold) and gill (average, up 73.02-fold, down 12.92-fold) tissues increased more at HT than at LT. The protein expression in brain (up 3.77-fold, down 4.79-fold) tissues decreased more at LT than at HT, whereas the protein expression in gill (up 8.64-fold, down 4.35-fold) tissues was up-regulated more at LT than at HT. At HT, brain tissues were mainly enriched in pathways related to metabolism and DNA repair; at LT, they were mainly enriched in cancer-related pathways. At both temperatures, gill tissues were mainly enriched in pathways related to cell proliferation, apoptosis, immunity, and inflammation. Additionally, Kyoto Encyclopedia of Genes and Genomes pathway analysis showed more differentially expressed proteins in gill tissues than in brain tissues at HT and LT, and temperature stimulation led to the strengthening of metabolic pathways in both tissues. Of the 96 genes we identified as potentially being highly related to temperature stress (59 from transcriptome and 38 from proteome data), we detected heat shock protein 70 in both the transcriptome and proteome. Our results improved our understanding of the differential relationship between gene expression and protein expression in C. guichenoti. Identifying important temperature stress genes will help lay a foundation for cultivating C. guichenoti, and even other fish species, that are resistant to HT or LT.
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Affiliation(s)
- Yuanliang Duan
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi, China
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Qiang Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Jian Zhou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Han Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Zhongmeng Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Lanmei Wang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi, China
| | - Mingkun Luo
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi, China
| | - Jun Du
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Zaijie Dong
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi, China
- *Correspondence: Zaijie Dong,
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11
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Liu R, Long Y, Liu R, Song G, Li Q, Yan H, Cui Z. Understanding the Function and Mechanism of Zebrafish Tmem39b in Regulating Cold Resistance. Int J Mol Sci 2022; 23:ijms231911442. [PMID: 36232766 PMCID: PMC9569763 DOI: 10.3390/ijms231911442] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/17/2022] [Accepted: 09/18/2022] [Indexed: 11/22/2022] Open
Abstract
Autophagy and endoplasmic reticulum (ER) stress response are among the key pathways regulating cold resistance of fish through eliminating damaged cellular components and facilitating the restoration of cell homeostasis upon exposure to acute cold stress. The transmembrane protein 39A (TMEM39A) was reported to regulate both autophagy and ER stress response, but its vertebrate-specific paralog, the transmembrane protein 39B (TMEM39B), has not been characterized. In the current study, we generate tmem39b-knockout zebrafish lines and characterize their survival ability under acute cold stress. We observed that the dysfunction of Tmem39b remarkably decreased the cold resilience of both the larval and adult zebrafish. Gene transcription in the larvae exposed to cold stress and rewarming were characterized by RNA sequencing (RNA-seq) to explore the mechanisms underlying functions of Tmem39b in regulating cold resistance. The results indicate that the deficiency of Tmem39b attenuates the up-regulation of both cold- and rewarming-induced genes. The cold-induced transcription factor genes bif1.2, fosab, and egr1, and the rewarming-activated immune genes c3a.3, il11a, and sting1 are the representatives influenced by Tmem39b dysfunction. However, the loss of tmem39b has little effect on the transcription of the ER stress response- and autophagy-related genes. The measurements of the phosphorylated H2A histone family member X (at Ser 139, abbreviated as γH2AX) demonstrate that zebrafish Tmem39b protects the cells against DNA damage caused by exposure to the cold-warming stress and facilitates tissue damage repair during the recovery phase. The gene modules underlying the functions of Tmem39b in zebrafish are highly enriched in biological processes associated with immune response. The dysfunction of Tmem39b also attenuates the up-regulation of tissue C-reactive protein (CRP) content upon rewarming. Together, our data shed new light on the function and mechanism of Tmem39b in regulating the cold resistance of fish.
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Affiliation(s)
- Renyan Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Long
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (Y.L.); (Z.C.); Tel.: +86-27-68780100 (Y.L.); +86-27-68780090 (Z.C.)
| | - Ran Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Guili Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Qing Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Huawei Yan
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Zongbin Cui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (Y.L.); (Z.C.); Tel.: +86-27-68780100 (Y.L.); +86-27-68780090 (Z.C.)
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12
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Liu M, Zou X, Fu M, Bai X, Zhao Y, Chen X, Wang X, Wang P, Huang S. Mild cold stress specifically disturbs clustering movement of DFCs and sequential organ left-right patterning in zebrafish. Front Cell Dev Biol 2022; 10:952844. [PMID: 36211472 PMCID: PMC9539758 DOI: 10.3389/fcell.2022.952844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/02/2022] [Indexed: 11/13/2022] Open
Abstract
In poikilothermic animals, the distinct acclimatization ability of different organs has been previously addressed, while the tissue-specific role of cold stress in early development is largely unknown. In this study, we discovered that despite its role in delaying embryonic development, mild cold stress (22°C) does not disturb multiple-organ progenitor specification, but does give rise to organ left-right (LR) patterning defects. Regarding the mechanism, the data showed that mild cold stress downregulated the expression of cell-adhesion genes cdh1 and cdh2 during gastrulation, especially in dorsal forerunner cells (DFCs), which partially disturbed the clustering movement of DFCs, Kupffer’s vesicle (KV) morphogenesis, and ciliogenesis. As a result, the defects of KV/cilia disrupted asymmetric nodal signaling and subsequent heart and liver LR patterning. In conclusion, our data novelly identified that, in early development, DFCs are more sensitive to mild cold stress, and mild cold stress repressed the expression of cell adhesion-related gene cdh1 and cdh2. This role partially disturbed the clustering movement of DFCs, which resulted in defective KV/cilia development and sequential organ LR patterning defects.
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Affiliation(s)
- Min Liu
- Development and Regeneration Key Laboratory of Sichuan Province, Department of Anatomy and Histology and Embryology, School of Basic Medical Sciences, Chengdu Medical College, Chengdu, China
- Department of Cardiology, the First Affiliated Hospital, Chengdu Medical College, Chengdu, China
| | - Xinyu Zou
- School of Pharmacy, Chengdu Medical College, Chengdu, China
| | - Mao Fu
- School of Pharmacy, Chengdu Medical College, Chengdu, China
| | - Xinping Bai
- School of Clinical Medicine, Chengdu Medical College, Chengdu, China
| | - Yongyan Zhao
- School of Clinical Medicine, Chengdu Medical College, Chengdu, China
| | - Xin Chen
- School of Public Health, Chengdu Medical College, Chengdu, China
| | - Xiaoyu Wang
- School of Biomedical Sciences, Chengdu Medical College, Chengdu, China
| | - Peijian Wang
- Department of Cardiology, the First Affiliated Hospital, Chengdu Medical College, Chengdu, China
- *Correspondence: Peijian Wang, ; Sizhou Huang,
| | - Sizhou Huang
- Development and Regeneration Key Laboratory of Sichuan Province, Department of Anatomy and Histology and Embryology, School of Basic Medical Sciences, Chengdu Medical College, Chengdu, China
- *Correspondence: Peijian Wang, ; Sizhou Huang,
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Liu R, Liu R, Song G, Li Q, Cui Z, Long Y. Mitochondria Dysfunction and Cell Apoptosis Limit Resistance of Nile Tilapia (Oreochromis niloticus) to Lethal Cold Stress. Animals (Basel) 2022; 12:ani12182382. [PMID: 36139242 PMCID: PMC9495169 DOI: 10.3390/ani12182382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Sensitivity of Nile tilapia (Oreochromis niloticus) to cold stress represents a major concern for both aquaculture and theoretical study; however, the cellular and molecular mechanisms determining cold susceptibility of it remain largely unknown. In this study, we first estimated the median survival time of juvenile Nile tilapia under exposure to lethal cold stress (12 °C). The fish were classified as cold-sensitive or cold-tolerant based on their behavioral manifestation after exposed to 12 °C for 3 days. Subsequently, histological, biochemical and gene expression analyses were performed for the fish with different cold resistance to explore the cellular and molecular events underlying cold susceptibility of Nile tilapia. We found that exposure of Nile tilapia to lethal cold stress caused systemic tissue structure changes, mitochondrial swelling and dysfunction, induction of apoptosis and endoplasmic reticulum (ER) stress-related genes and cell apoptosis. The extent of these adverse cellular and molecular events determines an individual’s ability to survive cold stress. Our data indicate that mitochondria dysfunction and mitochondria-mediated cell apoptosis are the main factors limiting Nile tilapia’s cold resistance. Abstract Inability of Nile tilapia (Oreochromis niloticus) to withstand cold stress represents a major economic concern, which restricts the culture area, limits the growing period and even results in mass mortality in cold seasons. However, the cellular and molecular mechanisms determining cold susceptibility of Nile tilapia remain largely unknown. In this study, we characterized the ability of juvenile Nile tilapia to survive lethal cold stress (12 °C) and the median survival time (LT50) of the experimental fish under exposure to 12 °C cold stress was estimated as 3.14 d. After being exposed to 12 °C for 3 d, the survivors that lost equilibrium (LE) and those that swam normally (NO) were regarded as cold-sensitive and cold-tolerant, respectively. The untreated (Ctrl), NO and LE fish were subjected to histological, biochemical and gene expression analyses to explore the cellular and molecular events underlying cold susceptibility of Nile tilapia. Exposure of Nile tilapia to lethal cold stress caused systemic tissue structure changes, mitochondrial swelling and dysfunction, induction of apoptosis and endoplasmic reticulum (ER) stress-related genes and cell apoptosis. The extent of these adverse cellular and molecular events determines an individual’s ability to survive cold stress. Our data indicate that mitochondria dysfunction and mitochondria-mediated cell apoptosis are the main factors limiting Nile tilapia’s cold resistance.
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Affiliation(s)
- Ran Liu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Renyan Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guili Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Qing Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zongbin Cui
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yong Long
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- Correspondence: ; Tel.: +86-27-68780100
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14
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Yan Q, Li W, Gong X, Hu R, Chen L. Transcriptomic and Phenotypic Analysis of CRISPR/Cas9-Mediated gluk2 Knockout in Zebrafish. Genes (Basel) 2022; 13:genes13081441. [PMID: 36011351 PMCID: PMC9408333 DOI: 10.3390/genes13081441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
As a subtype of kainite receptors (KARs), GluK2 plays a role in the perception of cold in the periphery sensory neuron. However, the molecular mechanism for gluk2 on the cold stress in fish has not been reported. In this article, real-time PCR assays showed that gluk2 was highly expressed in the brain and eyes of adult zebrafish. To study the functions of gluk2, gene knockout was carried out using the CRISPR/Cas9 system. According to RNA-seq analysis, we selected the differentially expressed genes (DEGs) that had significant differences in at least three tissues of the liver, gill, intestine, skin, brain, and eyes. Gene Ontology (GO) enrichment analysis revealed that cry1ba, cry2, per1b, per2, hsp70.1, hsp70.2, hsp70l, hsp90aa1.1, hsp90aa1.2, hspb1, trpv1, slc27a1b, park2, ucp3, and METRNL were significantly enriched in the ‘Response to temperature stimulus’ pathway. Through behavioral phenotyping assay, the gluk2−/− larval mutant displayed obvious deficiency in cold stress. Furthermore, TUNEL (TdT-mediated dUTP Nick-End Labeling) staining proved that the gill apoptosis of gluk2−/− mutant was increased approximately 60 times compared with the wild-type after gradient cooling to 8 °C for 15 h. Overall, our data suggested that gluk2 was necessary for cold tolerance in zebrafish.
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15
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Nie M, Ni W, Wang L, Gao Q, Liu D, Tian F, Wang Z, Zhang C, Qi D. Insights Into miRNA-mRNA Regulatory Mechanisms of Cold Adaptation in Gymnocypris eckloni: Ubiquitin-Mediated Proteolysis Is Pivotal for Adaptive Energy Metabolism. Front Genet 2022; 13:903995. [PMID: 35937996 PMCID: PMC9354851 DOI: 10.3389/fgene.2022.903995] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/03/2022] [Indexed: 12/02/2022] Open
Abstract
This study aimed to understand cold stress adaptations mechanism in fish. Thus, the transcriptional response to cold conditions in Gymnocypris eckloni was evaluated using RNA-seq and microRNA (miRNA)-seq analyses. Low-temperature (LT) group G. eckloni was cultivated outdoors in waters cooled to 2–4°C for 3 weeks, while individuals in the control temperature (CT) group were exposed to 14–16°C. Significantly different responses were observed in both mRNA and miRNA expression profiles, with more mRNAs (1,833 and 1,869 mRNAs were up- and downregulated, respectively) and fewer miRNAs (15 and 6 were up- and downregulated, respectively) observed in the LT group individuals relative to the CT group individuals. A miRNA-mRNA network involved in the regulation of G. eckloni responses to cold stress was constructed; this network included ubiquitin-mediated proteolysis, protein processing, and oxidative phosphorylation. These results provided new insights into mechanisms of cold tolerance by fish, including decreased metabolic activity in addition to proteolysis.
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Affiliation(s)
- Miaomiao Nie
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Weilin Ni
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Lihan Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Qiang Gao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Dan Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Fei Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Zhenji Wang
- Fishery Environmental Monitoring Station of Qinghai Province, Xining, China
| | - Cunfang Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- *Correspondence: Delin Qi,
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16
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Kim C, Wang X, Kültz D. Prediction and Experimental Validation of a New Salinity-Responsive Cis-Regulatory Element (CRE) in a Tilapia Cell Line. Life (Basel) 2022; 12:life12060787. [PMID: 35743818 PMCID: PMC9225295 DOI: 10.3390/life12060787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/12/2022] [Accepted: 05/16/2022] [Indexed: 11/16/2022] Open
Abstract
Transcriptional regulation is a major mechanism by which organisms integrate gene x environment interactions. It can be achieved by coordinated interplay between cis-regulatory elements (CREs) and transcription factors (TFs). Euryhaline tilapia (Oreochromis mossambicus) tolerate a wide range of salinity and thus are an appropriate model to examine transcriptional regulatory mechanisms during salinity stress in fish. Quantitative proteomics in combination with the transcription inhibitor actinomycin D revealed 19 proteins that are transcriptionally upregulated by hyperosmolality in tilapia brain (OmB) cells. We searched the extended proximal promoter up to intron1 of each corresponding gene for common motifs using motif discovery tools. The top-ranked motif identified (STREME1) represents a binding site for the Forkhead box TF L1 (FoxL1). STREME1 function during hyperosmolality was experimentally validated by choosing two of the 19 genes, chloride intracellular channel 2 (clic2) and uridine phosphorylase 1 (upp1), that are enriched in STREME1 in their extended promoters. Transcriptional induction of these genes during hyperosmolality requires STREME1, as evidenced by motif mutagenesis. We conclude that STREME1 represents a new functional CRE that contributes to gene x environment interactions during salinity stress in tilapia. Moreover, our results indicate that FoxL1 family TFs are contribute to hyperosmotic induction of genes in euryhaline fish.
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Affiliation(s)
- Chanhee Kim
- Stress-Induced Evolution Laboratory, Department of Animal Sciences, University of California, Davis, CA 95616, USA;
| | - Xiaodan Wang
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai 200241, China;
| | - Dietmar Kültz
- Stress-Induced Evolution Laboratory, Department of Animal Sciences, University of California, Davis, CA 95616, USA;
- Correspondence: ; Tel.: +1-530-752-2991
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17
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Wang H, Wang Y, Niu M, Hu L, Chen L. Cold Acclimation for Enhancing the Cold Tolerance of Zebrafish Cells. Front Physiol 2022; 12:813451. [PMID: 35153820 PMCID: PMC8832062 DOI: 10.3389/fphys.2021.813451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/23/2021] [Indexed: 11/13/2022] Open
Abstract
Cold stress is an important threat in the life history of fish. However, current research on the tolerance mechanisms of fish to cold stress is incomplete. To explore the relevant molecular mechanisms enabling cold stress tolerance in fish, here we studied ZF4 cells subjected to short-term (4 days) low temperature stress and long-term (3 months) low temperature acclimation. The results showed that cell viability decreased and the cytoskeleton shrank under short-term (4 days) low temperature stress, while the cell viability and the cytoskeleton became normal after cold acclimation at 18°C for 3 months. Further, when the cells were transferred to the lower temperature (13°C), the survival rate was higher in the acclimated than non-acclimated group. By investigating the oxidative stress pathway, we found that the ROS (reactive oxygen species) content increased under short-term (4 days) cold stress, coupled with changes in glutathione (GSH), catalase (CAT), superoxide dismutase (SOD) enzyme activity levels. In addition, overproduction of ROS disrupted physiological cellular homeostasis that generated apoptosis via the activation of the mitochondrial pathway. However, when compared with the non-domesticated group, both ROS levels and apoptosis were lowered in the long-term (3 months) domesticated cells. Taken together, these findings suggest that cold acclimation can improve the low temperature tolerance of the cells. This exploration of the mechanism by which zebrafish cells tolerate cold stress, thus contributes to laying the foundation for future study of the molecular mechanism of cold adaptation in fish.
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Affiliation(s)
- Huamin Wang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, China
| | - Ying Wang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, China
| | - Minghui Niu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, China
| | - Linghong Hu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, China
| | - Liangbiao Chen
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, China
- *Correspondence: Liangbiao Chen,
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Fan X, Guo Q, Zhang J, Du H, Qin X. Response mechanism of ♀ Epinephelus fuscoguttatus × ♂ Epinephelus lanceolatus under low-temperature and waterless stresses using TMT proteomic analysis. PROTOPLASMA 2022; 259:217-231. [PMID: 33950303 PMCID: PMC8752522 DOI: 10.1007/s00709-021-01654-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
♀Epinephelus fuscoguttatus × ♂Epinephelus lanceolatus, a hybrid grouper created from artificial breeding, has been widely developed over the past decades. However, the study focusing on lukewarm high-protein-content fish species using advanced techniques has rarely been reported. In this work, the TMT (tandem mass tag)-assisted technique was employed to explore its differentially expressed proteins and response mechanisms under low-temperature dormant and waterless stresses. Our findings suggest that 162 and 258 differentially expressed proteins were identified under low-temperature dormant and waterless stresses, respectively. The waterless preservation treatment further identifies 93 differentially expressed proteins. The identified proteins are categorized and found to participate in lipid metabolism, glycometabolism, oxidative stress, immune response, protein and amino acid metabolism, signal transduction, and other functions. Accordingly, the factors that affect the response mechanisms are highlighted to provide new evidences at protein level.
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Affiliation(s)
- Xiuping Fan
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Products of Guangdong Higher Education Institution, Zhanjiang, 524088, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, 524088, China
| | - Qiaoyu Guo
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Products of Guangdong Higher Education Institution, Zhanjiang, 524088, China
| | - Jiasheng Zhang
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Products of Guangdong Higher Education Institution, Zhanjiang, 524088, China
| | - Huan Du
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Products of Guangdong Higher Education Institution, Zhanjiang, 524088, China
| | - Xiaoming Qin
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Products of Guangdong Higher Education Institution, Zhanjiang, 524088, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, 524088, China.
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19
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Chu PY, Li JX, Hsu TH, Gong HY, Lin CY, Wang JH, Huang CW. Identification of Genes Related to Cold Tolerance and Novel Genetic Markers for Molecular Breeding in Taiwan Tilapia ( Oreochromis spp.) via Transcriptome Analysis. Animals (Basel) 2021; 11:ani11123538. [PMID: 34944312 PMCID: PMC8697892 DOI: 10.3390/ani11123538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022] Open
Abstract
Taiwan tilapia is one of the primary species used in aquaculture practices in Taiwan. However, as a tropical fish, it is sensitive to cold temperatures that can lead to high mortality rates during winter months. Genetic and broodstock management strategies using marker-assisted selection and breeding are the best tools currently available to improve seed varieties for tilapia species. The purpose of this study was to develop molecular markers for cold stress-related genes using digital gene expression analysis of next-generation transcriptome sequencing in Taiwan tilapia (Oreochromis spp.). We constructed and sequenced cDNA libraries from the brain, gill, liver, and muscle tissues of cold-tolerance (CT) and cold-sensitivity (CS) strains. Approximately 35,214,833,100 nucleotides of raw sequencing reads were generated, and these were assembled into 128,147 unigenes possessing a total length of 185,382,926 bp and an average length of 1446 bp. A total of 25,844 unigenes were annotated using five protein databases and Venny analysis, and 38,377 simple sequence repeats (SSRs) and 65,527 single nucleotide polymorphisms (SNPs) were identified. Furthermore, from the 38-cold tolerance-related genes that were identified using differential gene expression analysis in the four tissues, 13 microsatellites and 37 single nucleotide polymorphism markers were identified. The results of the genotype analysis revealed that the selected markers could be used for population genetics. In addition to the diversity assessment, one of the SNP markers was determined to be significantly related to cold-tolerance traits and could be used as a molecular marker to assist in the selection and verification of cold-tolerant populations. The specific genetic markers explored in this study can be used for the identification of genetic polymorphisms and cold tolerance traits in Taiwan tilapia, and they can also be used to further explore the physiological and biochemical molecular regulation pathways of fish that are involved in their tolerance to environmental temperature stress.
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Affiliation(s)
- Pei-Yun Chu
- Department of Aquaculture, National Taiwan Ocean University, Keelung City 20224, Taiwan; (P.-Y.C.); (J.-X.L.); (T.-H.H.); (H.-Y.G.)
| | - Jia-Xian Li
- Department of Aquaculture, National Taiwan Ocean University, Keelung City 20224, Taiwan; (P.-Y.C.); (J.-X.L.); (T.-H.H.); (H.-Y.G.)
| | - Te-Hua Hsu
- Department of Aquaculture, National Taiwan Ocean University, Keelung City 20224, Taiwan; (P.-Y.C.); (J.-X.L.); (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung City 20224, Taiwan
| | - Hong-Yi Gong
- Department of Aquaculture, National Taiwan Ocean University, Keelung City 20224, Taiwan; (P.-Y.C.); (J.-X.L.); (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung City 20224, Taiwan
| | - Chung-Yen Lin
- Institute of Information Science, Academia Sinica, Taipei 11529, Taiwan;
| | - Jung-Hua Wang
- Department of Electrical Engineering, National Taiwan Ocean University, Keelung City 20224, Taiwan;
- AI Research Center, National Taiwan Ocean University, Keelung City 20224, Taiwan
| | - Chang-Wen Huang
- Department of Aquaculture, National Taiwan Ocean University, Keelung City 20224, Taiwan; (P.-Y.C.); (J.-X.L.); (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung City 20224, Taiwan
- Correspondence: ; Tel.: +886-2-2462-2192 (ext. 5238)
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20
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Cascarano MC, Stavrakidis-Zachou O, Mladineo I, Thompson KD, Papandroulakis N, Katharios P. Mediterranean Aquaculture in a Changing Climate: Temperature Effects on Pathogens and Diseases of Three Farmed Fish Species. Pathogens 2021; 10:1205. [PMID: 34578236 PMCID: PMC8466566 DOI: 10.3390/pathogens10091205] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/03/2021] [Accepted: 09/13/2021] [Indexed: 02/07/2023] Open
Abstract
Climate change is expected to have a drastic effect on aquaculture worldwide. As we move forward with the agenda to increase and diversify aquaculture production, rising temperatures will have a progressively relevant impact on fish farming, linked to a multitude of issues associated with fish welfare. Temperature affects the physiology of both fish and pathogens, and has the potential to lead to significant increases in disease outbreaks within aquaculture systems, resulting in severe financial impacts. Significant shifts in future temperature regimes are projected for the Mediterranean Sea. We therefore aim to review and discuss the existing knowledge relating to disease outbreaks in the context of climate change in Mediterranean finfish aquaculture. The objective is to describe the effects of temperature on the physiology of both fish and pathogens, and moreover to list and discuss the principal diseases of the three main fish species farmed in the Mediterranean, namely gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax), and meagre (Argyrosomus regius). We will attempt to link the pathology of each disease to a specific temperature range, while discussing potential future disease threats associated with the available climate change trends for the Mediterranean Sea.
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Affiliation(s)
- Maria Chiara Cascarano
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, 71500 Heraklion, Greece; (M.C.C.); (O.S.-Z.); (N.P.)
- Department of Biology, University of Crete, 71003 Heraklion, Greece
| | - Orestis Stavrakidis-Zachou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, 71500 Heraklion, Greece; (M.C.C.); (O.S.-Z.); (N.P.)
- Department of Biology, University of Crete, 71003 Heraklion, Greece
| | - Ivona Mladineo
- Biology Center of Czech Academy of Sciences, Laboratory of Functional Helminthology, Institute of Parasitology, 370 05 Ceske Budejovice, Czech Republic;
| | - Kim D. Thompson
- Vaccines and Diagnostics, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian EH26 0PZ, UK;
| | - Nikos Papandroulakis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, 71500 Heraklion, Greece; (M.C.C.); (O.S.-Z.); (N.P.)
| | - Pantelis Katharios
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, 71500 Heraklion, Greece; (M.C.C.); (O.S.-Z.); (N.P.)
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21
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Miao BB, Niu SF, Wu RX, Liang ZB, Tang BG, Zhai Y, Xu XQ. Gene Expression Profile and Co-Expression Network of Pearl Gentian Grouper under Cold Stress by Integrating Illumina and PacBio Sequences. Animals (Basel) 2021; 11:ani11061745. [PMID: 34208015 PMCID: PMC8230743 DOI: 10.3390/ani11061745] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary In this study, we investigated the liver transcriptomic responses of pearl gentian grouper towards cold stress. Some cold-related key genes and biological pathways were screened, of which energy-related metabolic pathways and genes had higher expression levels under cold stress. This suggested that energy homeostasis plays a crucial role in the physiological adjustments of pearl gentian grouper when exposed to the cold stress environment. Our results will expedite the understanding of different fishes adaptive mechanisms to profound environmental temperature changes and provide insights into the molecular breeding of cold-tolerant pearl gentian grouper varieties. Abstract Pearl gentian grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) is a fish of high commercial value in the aquaculture industry in Asia. However, this hybrid fish is not cold-tolerant, and its molecular regulation mechanism underlying cold stress remains largely elusive. This study thus investigated the liver transcriptomic responses of pearl gentian grouper by comparing the gene expression of cold stress groups (20, 15, 12, and 12 °C for 6 h) with that of control group (25 °C) using PacBio SMRT-Seq and Illumina RNA-Seq technologies. In SMRT-Seq analysis, a total of 11,033 full-length transcripts were generated and used as reference sequences for further RNA-Seq analysis. In RNA-Seq analysis, 3271 differentially expressed genes (DEGs), two low-temperature specific modules (tan and blue modules), and two significantly expressed gene sets (profiles 0 and 19) were screened by differential expression analysis, weighted gene co-expression networks analysis (WGCNA), and short time-series expression miner (STEM), respectively. The intersection of the above analyses further revealed some key genes, such as PCK, ALDOB, FBP, G6pC, CPT1A, PPARα, SOCS3, PPP1CC, CYP2J, HMGCR, CDKN1B, and GADD45Bc. These genes were significantly enriched in carbohydrate metabolism, lipid metabolism, signal transduction, and endocrine system pathways. All these pathways were linked to biological functions relevant to cold adaptation, such as energy metabolism, stress-induced cell membrane changes, and transduction of stress signals. Taken together, our study explores an overall and complex regulation network of the functional genes in the liver of pearl gentian grouper, which could benefit the species in preventing damage caused by cold stress.
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Affiliation(s)
- Ben-Ben Miao
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (B.-B.M.); (S.-F.N.); (Z.-B.L.); (B.-G.T.); (Y.Z.); (X.-Q.X.)
| | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (B.-B.M.); (S.-F.N.); (Z.-B.L.); (B.-G.T.); (Y.Z.); (X.-Q.X.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China
| | - Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (B.-B.M.); (S.-F.N.); (Z.-B.L.); (B.-G.T.); (Y.Z.); (X.-Q.X.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China
- Correspondence:
| | - Zhen-Bang Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (B.-B.M.); (S.-F.N.); (Z.-B.L.); (B.-G.T.); (Y.Z.); (X.-Q.X.)
| | - Bao-Gui Tang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (B.-B.M.); (S.-F.N.); (Z.-B.L.); (B.-G.T.); (Y.Z.); (X.-Q.X.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China
| | - Yun Zhai
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (B.-B.M.); (S.-F.N.); (Z.-B.L.); (B.-G.T.); (Y.Z.); (X.-Q.X.)
| | - Xue-Qi Xu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (B.-B.M.); (S.-F.N.); (Z.-B.L.); (B.-G.T.); (Y.Z.); (X.-Q.X.)
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22
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Long Y, Liu R, Song G, Li Q, Cui Z. Establishment and characterization of a cold-sensitive neural cell line from the brain of tilapia (Oreochromis niloticus). JOURNAL OF FISH BIOLOGY 2021; 98:842-854. [PMID: 33258111 DOI: 10.1111/jfb.14637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/19/2020] [Accepted: 11/27/2020] [Indexed: 06/12/2023]
Abstract
The aquaculture of tilapia (Oreochromis sp.) is adversely affected by the sensitivity to cold stress. A large number of genes in tilapia were found to be regulated by cold stress, but their functions and mechanisms in cold tolerance remain largely unknown, partially due to the lack of a suitable in vitro model. An immortal neural cell line designated as tilapia brain neural (TBN) was established from brain tissue of the genetically improved farmed tilapia strain of Nile tilapia (Oreochromis niloticus). The TBN cells show a neuron-like morphology at low density and form a fibroblast-like monolayer at high density. Transcriptome profiling through RNA-sequencing revealed that a total of 15,011 genes were expressed in the TBN cells. The TBN cells express a wide array of marker genes for neural cells. A comparative analysis of the featured genes among the 17 cell clusters isolated from the subventricular zone of mouse brain revealed the highest transcriptome similarity between the TBN cells and the transient amplifying progenitors (TAPs). The TBN cells tolerate relatively high culture temperatures, and the highest growth rate was observed for the cells cultured at 32°C compared with those at 30°C, 28°C and 26°C. Nonetheless, this cell line is cold sensitive. Exposure of the cells to 16°C or lower temperatures significantly decreased cell confluences and induced apoptosis. The TBN cells were more sensitive to cold stress than the ZF4 cells (embryonic zebrafish fibroblasts). Moreover, the TBN cells can be efficiently transfected through electroporation. This study provides an invaluable research tool to understand the nature of cold sensitivity of tilapia and to dissect the function and mechanism of genes in regulating cold tolerance of fish.
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Affiliation(s)
- Yong Long
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Ran Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Guili Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Qing Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zongbin Cui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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23
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Deng W, Sun J, Chang ZG, Gou NN, Wu WY, Luo XL, Zhou JS, Yu HB, Ji H. Energy response and fatty acid metabolism in Onychostoma macrolepis exposed to low-temperature stress. J Therm Biol 2020; 94:102725. [PMID: 33292981 DOI: 10.1016/j.jtherbio.2020.102725] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 08/11/2020] [Accepted: 09/01/2020] [Indexed: 10/23/2022]
Abstract
Temperature is a key environmental factor, and understanding how its fluctuations affect physiological and metabolic processes is critical for fish. The present study characterizes the energy response and fatty acid metabolism in Onychostoma macrolepis exposed to low temperature (10 °C). The results demonstrated that cold stress remarkably disrupted the energy homeostasis of O. macrolepis, then the AMP-activated protein kinase (AMPK) could strategically mobilize carbohydrates and lipids. In particular, when the O. macrolepis were faced with cold stress, the lipolysis was stimulated along with the enhanced fatty acid β-oxidation for energy, while the fatty acid synthesis was supressed in the early stage. Additionally, the fatty acid composition analysis suggested that saturated fatty acid (SFA) might accumulate while monounsaturated fatty acid (MUFA) and polyunsaturated fatty acid (PUFA) in storage lipids (mainly containing non-polar lipid, NPL) could be utilized to supply energy during cold acclimation. Altogether, this study may provide some meritorious for understanding the cold-tolerant mechanism of fish in the viewpoint of energy balance combined with fatty acid metabolism, and thus to contribute to this species rearing in fish farms in the future.
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Affiliation(s)
- Wei Deng
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, 712100, China
| | - Jian Sun
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, 712100, China
| | - Zhi-Guang Chang
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, 712100, China
| | - Ni-Na Gou
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, 712100, China
| | - Wen-Yi Wu
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, 712100, China
| | - Xiao-Long Luo
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, 712100, China
| | - Ji-Shu Zhou
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, 712100, China
| | - Hai-Bo Yu
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, 712100, China.
| | - Hong Ji
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, 712100, China.
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Liu L, Zhang R, Wang X, Zhu H, Tian Z. Transcriptome analysis reveals molecular mechanisms responsive to acute cold stress in the tropical stenothermal fish tiger barb (Puntius tetrazona). BMC Genomics 2020; 21:737. [PMID: 33096997 PMCID: PMC7584086 DOI: 10.1186/s12864-020-07139-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 10/11/2020] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Tropical stenothermal fish exhibit special tolerance and response to cold stress. However current knowledge of the molecular mechanisms response to cold stress in aquatic ectotherms is largely drawn from eurythermal or extreme stenothermal species. The tiger barb Puntius tetrazona is a tropical stenothermal fish, with great popularity in aquarium trade and research. RESULTS To investigate the response mechanism of P. tetrazona to low temperature, fish were exposed to increasing levels of acute cold stress. Histopathological analysis showed that the brain, gill, liver and muscle tissues appeared serious damage after cold stress (13 °C). Brain, gill, liver and muscle tissues from control (CTRL) groups (27 °C) and COLD stress groups (13 °C) of eight-month fish (gender-neutral) were sampled and assessed for transcriptomic profiling by high-throughput sequencing. 83.0 Gb of raw data were generated, filtered and assembled for de novo transcriptome assembly. According to the transcriptome reference, we obtained 392,878 transcripts and 238,878 unigenes, of which 89.29% of the latter were annotated. There were 23,743 differently expressed genes (DEGs) been filtered from four pairs of tissues (brain, gill, liver and muscle) between these cold stress and control groups. These DEGs were mainly involved in circadian entrainment, circadian rhythm, biosynthesis of steroid and fatty acid. There were 64 shared DEGs between the four pairs of groups, and five were related to ubiquitylation/deubiquitylation. Our results suggested that ubiquitin-mediated protein degradation might be necessary for tropical stenothermal fish coping with acute cold stress. Also, the significant cold-induced expression of heat shock 70 kDa protein (HSP70) and cold-induced RNA-binding protein (CIRBP) was verified. These results suggested that the expression of the molecular chaperones HSP70 and CIRBP in P. tetrazona might play a critical role in coping with acute cold stress. CONCLUSIONS This is the first transcriptome analysis of P. tetrazona using RNA-Seq technology. Novel findings about tropical stenothermal fish under cold stress (such as HSP70 and CIRBP genes) are presented here. This study contributes new insights into the molecular mechanisms of tropical stenothermal species response to acute cold stress.
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Affiliation(s)
- Lili Liu
- Beijing Key Laboratory of Fishery Biotechnology, Beijing Fisheries Research Institute, Beijing, 100068 China
| | - Rong Zhang
- Beijing Key Laboratory of Fishery Biotechnology, Beijing Fisheries Research Institute, Beijing, 100068 China
| | - Xiaowen Wang
- Beijing Key Laboratory of Fishery Biotechnology, Beijing Fisheries Research Institute, Beijing, 100068 China
| | - Hua Zhu
- Beijing Key Laboratory of Fishery Biotechnology, Beijing Fisheries Research Institute, Beijing, 100068 China
| | - Zhaohui Tian
- Beijing Key Laboratory of Fishery Biotechnology, Beijing Fisheries Research Institute, Beijing, 100068 China
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25
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Guan WZ, Qiu GF. Transcriptome analysis of the growth performance of hybrid mandarin fish after food conversion. PLoS One 2020; 15:e0240308. [PMID: 33035258 PMCID: PMC7546499 DOI: 10.1371/journal.pone.0240308] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/24/2020] [Indexed: 11/18/2022] Open
Abstract
During recent years, China has become a hotspot for the domestication of mandarin fish, and this is of great commercial value. Although the food preference of domesticated mandarin fish has been studied, little is known about genes regulating their growth. We raised hybrid mandarin fish on artificial feed for 3 months, the results showed that the survival rate of hybrid mandarin fish was 60.00%. Their total length and body weight were 18.34 ±0.43 cm and 100.44 ±4.87 g. The absolute length and weight gain rates were 0.14 cm/d and 1.08 g/d, respectively. Finally, RNA sequencing (RNA-Seq) was performed to identify potential genes and pathways activated in response to growth performance. The transcriptome analysis generated 68, 197 transcripts and 45,871 unigenes. Among them, 1025 genes were up-regulated and 593 genes were down-regulated between the fast- and slow-growth fish. Finally, we obtained 32 differentially expressed genes, which were mainly related to fatty acid biosynthesis (e.g. FASN and ACACB), collecting duct acid secretion (e.g. ATP6E and KCC4), cell cycle (e.g. CDC20 and CCNB), and the insulin-like growth factor (IGF) system (IGFBP1). These pathways might be related to the growth of hybrid mandarin fish. In addition, more potential single nucleotide polymorphisms (SNPs) were detected in the fast-growth fish than in the slow-growth fish. The results suggest that the interaction of metabolism and abundant alleles might determine the growth of hybrid mandarin fish after food conversion.
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Affiliation(s)
- Wen-Zhi Guan
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- Shanghai Fisheries Research Institute, Shanghai Fisheries Technical Extension Station, Shanghai, China
| | - Gao-Feng Qiu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- * E-mail: (GFQ); (FL)
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26
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Logan ML, Cox CL. Genetic Constraints, Transcriptome Plasticity, and the Evolutionary Response to Climate Change. Front Genet 2020; 11:538226. [PMID: 33193610 PMCID: PMC7531272 DOI: 10.3389/fgene.2020.538226] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 08/20/2020] [Indexed: 12/23/2022] Open
Abstract
In situ adaptation to climate change will be critical for the persistence of many ectotherm species due to their relative lack of dispersal capacity. Climate change is causing increases in both the mean and the variance of environmental temperature, each of which may act as agents of selection on different traits. Importantly, these traits may not be heritable or have the capacity to evolve independently from one another. When genetic constraints prevent the "baseline" values of thermal performance traits from evolving rapidly, phenotypic plasticity driven by gene expression might become critical. We review the literature for evidence that thermal performance traits in ectotherms are heritable and have genetic architectures that permit their unconstrained evolution. Next, we examine the relationship between gene expression and both the magnitude and duration of thermal stress. Finally, we identify genes that are likely to be important for adaptation to a changing climate and determine whether they show patterns consistent with thermal adaptation. Although few studies have measured narrow-sense heritabilities of thermal performance traits, current evidence suggests that the end points of thermal reaction norms (tolerance limits) are moderately heritable and have the potential to evolve rapidly. By contrast, performance at intermediate temperatures has substantially lower evolutionary potential. Moreover, evolution in many species appears to be constrained by genetic correlations such that populations can adapt to either increases in mean temperature or temperature variability, but not both. Finally, many species have the capacity for plastic expression of the transcriptome in response to temperature shifts, with the number of differentially expressed genes increasing with the magnitude, but not the duration, of thermal stress. We use these observations to develop a conceptual model that describes the likely trajectory of genome evolution in response to changes in environmental temperature. Our results indicate that extreme weather events, rather than gradual increases in mean temperature, are more likely to drive genetic and phenotypic change in wild ectotherms.
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Affiliation(s)
- Michael L Logan
- Department of Biology, University of Nevada, Reno, Reno, NV, United States.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - Christian L Cox
- Department of Biological Sciences and Institute of Environment, Florida International University, Miami, FL, United States
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27
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Bowen L, von Biela VR, McCormick SD, Regish AM, Waters SC, Durbin-Johnson B, Britton M, Settles ML, Donnelly DS, Laske SM, Carey MP, Brown RJ, Zimmerman CE. Transcriptomic response to elevated water temperatures in adult migrating Yukon River Chinook salmon ( Oncorhynchus tshawytscha). CONSERVATION PHYSIOLOGY 2020; 8:coaa084. [PMID: 34512988 PMCID: PMC7486460 DOI: 10.1093/conphys/coaa084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/01/2020] [Accepted: 08/25/2020] [Indexed: 06/01/2023]
Abstract
Chinook salmon (Oncorhynchus tshawytscha) declines are widespread and may be attributed, at least in part, to warming river temperatures. Water temperatures in the Yukon River and tributaries often exceed 18°C, a threshold commonly associated with heat stress and elevated mortality in Pacific salmon. Untangling the complex web of direct and indirect physiological effects of heat stress on salmon is difficult in a natural setting with innumerable system challenges but is necessary to increase our understanding of both lethal and sublethal impacts of heat stress on populations. The goal of this study was to characterize the cellular stress response in multiple Chinook salmon tissues after acute elevated temperature challenges. We conducted a controlled 4-hour temperature exposure (control, 18°C and 21°C) experiment on the bank of the Yukon River followed by gene expression (GE) profiling using a 3'-Tag-RNA-Seq protocol. The full transcriptome was analysed for 22 Chinook salmon in muscle, gill and liver tissue. Both the 21°C and 18°C treatments induced greater activity in genes associated with protein folding (e.g. HSP70, HSP90 mRNA) processes in all tissues. Global GE patterns indicate that transcriptomic responses to heat stress were highly tissue-specific, underscoring the importance of analyzing multiple tissues for determination of physiological effect. Primary superclusters (i.e. groupings of loosely related terms) of altered biological processes were identified in each tissue type, including regulation of DNA damage response (gill), regulation by host of viral transcription (liver) and regulation of the force of heart contraction (muscle) in the 21°C treatment. This study provides insight into mechanisms potentially affecting adult Chinook salmon as they encounter warm water during their spawning migration in the Yukon River and suggests that both basic and more specialized cellular functions may be disrupted.
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Affiliation(s)
- Lizabeth Bowen
- U.S. Geological Survey, Western Ecological Research Center, One Shields Avenue, Davis, CA, 95616, USA
| | - Vanessa R von Biela
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA
| | - Stephen D McCormick
- U.S. Geological Survey, Leetown Science Center, Conte Anadromous Fish Research Laboratory, 1 Migratory Way, Turner Falls, Massachusetts, 01376, USA
- Department of Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Amy M Regish
- U.S. Geological Survey, Leetown Science Center, Conte Anadromous Fish Research Laboratory, 1 Migratory Way, Turner Falls, Massachusetts, 01376, USA
| | - Shannon C Waters
- U.S. Geological Survey, Western Ecological Research Center, One Shields Avenue, Davis, CA, 95616, USA
| | - Blythe Durbin-Johnson
- University of California, Genome Center and Bioinformatics Core Facility, One Shields Avenue, Davis, CA, 95616, USA
| | - Monica Britton
- University of California, Genome Center and Bioinformatics Core Facility, One Shields Avenue, Davis, CA, 95616, USA
| | - Matthew L Settles
- University of California, Genome Center and Bioinformatics Core Facility, One Shields Avenue, Davis, CA, 95616, USA
| | - Daniel S Donnelly
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA
| | - Sarah M Laske
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA
| | - Michael P Carey
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA
| | - Randy J Brown
- U.S. Fish and Wildlife Service, 101 12 Avenue, Room 110, Fairbanks, AK, 99701, USA
| | - Christian E Zimmerman
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA
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Nie M, Lu Y, Zou C, Wang L, Zhang P, You F. Insight into AMPK regulation mechanism in vivo and in vitro: Responses to low temperatures in the olive flounder Paralichthys olivaceus. J Therm Biol 2020; 91:102640. [PMID: 32716881 DOI: 10.1016/j.jtherbio.2020.102640] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 05/04/2020] [Accepted: 06/11/2020] [Indexed: 01/07/2023]
Abstract
The olive flounder, Paralichthys olivaceus, is a commercially important maricultured fish in China, Japan, and Korea. Low winter temperatures influence its survival and growth and affect the output of the aquaculture industry. Energy metabolism is essential for fish survival, and the central energy-regulating factor - 5'-AMP-activated protein kinase (AMPK) - plays an important role in responses to cold stress. However, the mechanism of AMPK pathway regulation in fish coping with cold stress remains poorly understood. In the present study, the expression of AMPK and its upstream (LKB1 and CaMKKβ) and downstream genes (SITR1, FOXO1A, and TFAM) in the brain, muscle, and heart was analyzed while the flounder was under cold stress (0.2 ± 0.2 °C). The results showed that low temperatures activated LKB1, CaMKKβ, and AMPK genes in the brain, and the activated AMPK induced expression of SITR1, FOXO1A, and TFAM. In the muscle tissue, the expression patterns of these genes presented a trend of initially decreasing and then increasing, and there was a delay in the response to low temperatures. At the cellular level, comparative analysis of the effects of the activator 5-aminoimidazole-4-carboxamide1-β-D-ribofuranoside (AICAR) and inhibitor compound C of the AMPK pathway demonstrated that cold stress was similar to AICAR, which activated the AMPK pathway with hysteresis. Thus, the regulation mechanism of AMPK under cold stress was preliminarily analyzed. In general, AMPK was involved not only in responses to low temperatures but also in energy regulation under cold stress.
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Affiliation(s)
- Miaomiao Nie
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao. China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yunliang Lu
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, China
| | - Congcong Zou
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao. China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Lijuan Wang
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao. China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Peijun Zhang
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao. China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Feng You
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao. China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.
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Li BJ, Zhu ZX, Qin H, Meng ZN, Lin HR, Xia JH. Genome-Wide Characterization of Alternative Splicing Events and Their Responses to Cold Stress in Tilapia. Front Genet 2020; 11:244. [PMID: 32256528 PMCID: PMC7093569 DOI: 10.3389/fgene.2020.00244] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/28/2020] [Indexed: 12/15/2022] Open
Abstract
Alternative splicing (AS) is an important post-transcriptional regulatory mechanism for cells to generate transcript variability and proteome diversity. No systematic investigation of AS events among different tissues in response to stressors is available for tilapia currently. In this study, AS among different tissues was identified and the cold stress-related AS events were explored in a Nile tilapia (Oreochromis niloticus) line based on 42 RNA-seq datasets using a bioinformatics pipeline. 14,796 (82.76%; SD = 2,840) of the expression genes showed AS events. The two most abundant AS types were alternative transcription start site (TSS) and terminal site (TTS) in tilapia. Testis, brain and kidney possess the most abundant AS gene number, while the blood, muscle and liver possess the least number in each tissue. Furthermore, 208 differentially alternative splicing (DAS) genes in heart and 483 DAS in brain in response to cold stress. The number of AS types for alternative exon end, exon skipping and retention of single intron increased significantly under cold stress. GO enrichment and pathway overrepresentation analysis indicated that many DAS genes, e.g., genes in circadian clock pathway, may influence expression of downstream genes under cold stress. Our study revealed that AS exists extensively in tilapia and plays an important role in cold adaption.
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Affiliation(s)
| | | | | | | | | | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
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Wen X, Hu Y, Zhang X, Wei X, Wang T, Yin S. Integrated application of multi-omics provides insights into cold stress responses in pufferfish Takifugu fasciatus. BMC Genomics 2019; 20:563. [PMID: 31286856 PMCID: PMC6615287 DOI: 10.1186/s12864-019-5915-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 06/18/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND T. fasciatus (Takifugu fasciatus) faces the same problem as most warm water fish: the water temperature falls far below the optimal growth temperature in winter, causing a massive death of T. fasciatus and large economic losses. Understanding of the cold-tolerance mechanisms of this species is still limited. Integrated application of multi-omics research can provide a wealth of information to help us improve our understanding of low-temperature tolerance in fish. RESULTS To gain a comprehensive and unbiased molecular understanding of cold-tolerance in T. fasciatus, we characterized mRNA-seq and metabolomics of T. fasciatus livers using Illumina HiSeq 2500 and UHPLC-Q-TOF MS. We identified 2544 up-regulated and 2622 down-regulated genes in the liver of T. fasciatus. A total of 40 differential metabolites were identified, including 9 down-regulated and 31 up-regulated metabolites. In combination with previous studies on proteomics, we have established an mRNA-protein-metabolite interaction network. There are 17 DEMs (differentially-expressed metabolites) and 14 DEGs-DEPs (differentially co-expressed genes and proteins) in the interaction network that are mainly involved in fatty acids metabolism, membrane transport, signal transduction, and DNA damage and defense. We then validated a number of genes in the interaction network by qRT-PCR. Additionally, a number of SNPs (single nucleotide polymorphisms) were revealed through the transcriptome data. These results provide key information for further understanding of the molecular mechanisms of T. fasciatus under cold stress. CONCLUSION The data generated by integrated application of multi-omics can facilitate our understanding of the molecular mechanisms of fish response to low temperature stress. We have not only identified potential genes and SNPs involved in cold tolerance, but also show that some nutrient metabolites may be added to the diet to help the overwintering of T. fasciatus.
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Affiliation(s)
- Xin Wen
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023 China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005 Jiangsu China
| | - Yadong Hu
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023 China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005 Jiangsu China
| | - Xinyu Zhang
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023 China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005 Jiangsu China
| | - Xiaozhen Wei
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023 China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005 Jiangsu China
| | - Tao Wang
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023 China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005 Jiangsu China
| | - Shaowu Yin
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023 China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005 Jiangsu China
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Wen X, Zhang X, Hu Y, Xu J, Wang T, Yin S. iTRAQ-based quantitative proteomic analysis of Takifugu fasciatus liver in response to low-temperature stress. J Proteomics 2019; 201:27-36. [PMID: 30954612 DOI: 10.1016/j.jprot.2019.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/25/2019] [Accepted: 04/03/2019] [Indexed: 10/27/2022]
Abstract
Low temperatures profoundly influence the physiological and behavioural processes of ectotherms, especially teleosts, which have made them the subjects of strong interest over time. However, the characteristics of fish cold-tolerance at the protein level remain unclear. Therefore, to shed further light on the molecular mechanisms of low temperature adaptation in fish, we conducted quantitative proteomics on the T. fasciatus liver using iTRAQ. Comparing the proteomic profiles of the T. fasciatus liver at 12 °C and 26 °C, a total of 3741 proteins were identified, and 160 were differentially abundant proteins (DAPs). Among the DAPs, the most significant changes were noted in proteins involved in oxidative stress (nine proteins), mitochondrial enzymes (eleven proteins) and signal transduction (thirteen proteins). The KEGG enrichment analysis indicated significant enhancement of D-arginine and D-ornithine metabolism, MAPK signalling, Wnt signalling and Gap junction pathway. Subsequently, three significantly up-regulated proteins (CIRB, HSP90 and GST) and two significantly down-regulated proteins (FLNB and A2ML1) were validated with parallel reaction monitoring (PRM) assays. Furthermore, the changes in abundance of proteins that are involved in oxidative stress, mitochondrial enzymes and signal transduction were validated at the transcriptional level with qPCR. These verification results show that the experimental data of iTRAQ are reliable. Our results not only deepen the understanding of the mechanisms underlying low-temperature tolerance in fish, but they also may contribute to the enhancement of cold tolerance during its breeding process. SIGNIFICANCE OF THE STUDY: The study focused on a comparative quantitative proteomics analysis of the T. fasciatus liver in response to low temperatures using iTRAQ, which has not yet been reported in the literatures. The results showed that the effect of low temperature on T. fasciatus is significant, including a detoxification of metabolic by-products and oxidative stress, an activation of the mitochondrial enzyme to strengthen energy metabolism, and a negative effect on signal transduction, which result in dysfunction or suboptimal performance. These low-temperature-related changes in the liver proteome of T. fasciatus can facilitate the understanding of the low temperature-related response that takes place in similar conditions in the liver and may contribute to the breeding of cold-resistant strains.
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Affiliation(s)
- Xin Wen
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Xinyu Zhang
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Yadong Hu
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Jiejie Xu
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Tao Wang
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China.
| | - Shaowu Yin
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China.
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Nie M, Tan X, Lu Y, Wu Z, Li J, Xu D, Zhang P, You F. Network of microRNA-transcriptional factor-mRNA in cold response of turbot Scophthalmus maximus. FISH PHYSIOLOGY AND BIOCHEMISTRY 2019; 45:583-597. [PMID: 30790148 DOI: 10.1007/s10695-019-00611-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 01/21/2019] [Indexed: 05/19/2023]
Abstract
The aim of this study is to understand fish cold-tolerant mechanism. We analyzed the transcriptional reactions to the cold condition in turbot Scophthalmus maximus by using RNA-seq and microRNA (miRNA)-seq. Meio-gynogenetic diploid turbots were treated at 0 °C to distinguish the cold-tolerant (CT) and cold-sensitive (CS) groups. The results showed that there were quite different responses at both mRNA and miRNA levels, with more up-regulated mRNAs (1069 vs. 194) and less down-regulated miRNAs (4 vs. 1) in CT versus CS relative to the control group. The network of miRNA-transcription factor-mRNA, regulating turbot different response to cold stress, was constructed, which involved in cell cycle, component of cell membrane, signal transduction, and circadian rhythm pathways. The above information demonstrates mechanisms by which cold tolerance is increased in fish.
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Affiliation(s)
- Miaomiao Nie
- CAS Key Laboratory of Experimental Marine Biology, National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 10049, People's Republic of China
| | - Xungang Tan
- CAS Key Laboratory of Experimental Marine Biology, National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China
| | - Yunliang Lu
- CAS Key Laboratory of Experimental Marine Biology, National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China
| | - Zhihao Wu
- CAS Key Laboratory of Experimental Marine Biology, National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China
| | - Jun Li
- CAS Key Laboratory of Experimental Marine Biology, National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China
| | - Dongdong Xu
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhoushan, 316100, Zhejiang Province, People's Republic of China
| | - Peijun Zhang
- CAS Key Laboratory of Experimental Marine Biology, National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China
| | - Feng You
- CAS Key Laboratory of Experimental Marine Biology, National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, People's Republic of China.
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Nitzan T, Kokou F, Doron-Faigenboim A, Slosman T, Biran J, Mizrahi I, Zak T, Benet A, Cnaani A. Transcriptome Analysis Reveals Common and Differential Response to Low Temperature Exposure Between Tolerant and Sensitive Blue Tilapia ( Oreochromis aureus). Front Genet 2019; 10:100. [PMID: 30863423 PMCID: PMC6399464 DOI: 10.3389/fgene.2019.00100] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/29/2019] [Indexed: 12/14/2022] Open
Abstract
Tilapias are very important to the world's aquaculture. As befitting fish of their tropical origin, their distribution, and culture practices are highly affected by low temperatures. In this study, we used genetic and genomic methodologies to reveal pathways involved in the response and tolerance of blue tilapia (Oreochromis aureus) to low temperature stress. Cold tolerance was characterized in 66 families of blue tilapia. Fish from cold-tolerant and cold-sensitive families were sampled at 24 and 12°C, and the transcriptional responses to low-temperature exposure were measured in the gills and liver by high-throughput mRNA sequencing. Four hundred and ninety four genes displayed a similar temperature-dependent expression in both tolerant and sensitive fish and in the two tissues, representing the core molecular response to low temperature exposure. KEGG pathway analysis of these genes revealed down-regulation of focal-adhesion and other cell-extracellular matrix (ECM) interactions, and up-regulation of proteasome and various intra-cellular proteolytic activities. Differential responses between cold-tolerant and cold-sensitive fish were found with genes and pathways that were up-regulated in one group and down-regulated in the other. This reverse response was characterized by genes involved in metabolic pathways such as glycolysis/gluconeogenesis in the gills and biosynthesis of amino-acids in the liver, with low temperature down-regulation in tolerant fish and up-regulation in sensitive fish.
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Affiliation(s)
- Tali Nitzan
- Institute of Animal Science, Agricultural Research Organization, Rishon LeZion, Israel
| | - Fotini Kokou
- Institute of Animal Science, Agricultural Research Organization, Rishon LeZion, Israel.,Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Adi Doron-Faigenboim
- Institute of Animal Science, Agricultural Research Organization, Rishon LeZion, Israel
| | - Tatiana Slosman
- Institute of Animal Science, Agricultural Research Organization, Rishon LeZion, Israel
| | - Jakob Biran
- Institute of Animal Science, Agricultural Research Organization, Rishon LeZion, Israel
| | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tatyana Zak
- The Aquaculture Research Station, Ministry of Agriculture and Rural Development, Dor, Israel
| | - Ayana Benet
- The Aquaculture Research Station, Ministry of Agriculture and Rural Development, Dor, Israel
| | - Avner Cnaani
- Institute of Animal Science, Agricultural Research Organization, Rishon LeZion, Israel
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Zhou T, Gui L, Liu M, Li W, Hu P, Duarte DFC, Niu H, Chen L. Transcriptomic responses to low temperature stress in the Nile tilapia, Oreochromis niloticus. FISH & SHELLFISH IMMUNOLOGY 2019; 84:1145-1156. [PMID: 30408600 DOI: 10.1016/j.fsi.2018.10.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/03/2018] [Accepted: 10/07/2018] [Indexed: 06/08/2023]
Abstract
The Nile tilapia, Oreochromis niloticus, is a species of high economic value and extensively cultured. The limited stress tolerance of this species to a low temperature usually leads to mass mortality and great loss. Nevertheless, there is limited information on the molecular mechanisms underlying the susceptibility to low temperature in the tilapia. In this study, tilapia was treated at 28 °C to a lethal temperature of 8 °C by a gradual decrement. Transcriptomic response of the immune organ, kidney, in tilapia was characterized using RNA-seq. In total, 2191 genes were annotated for significant expression, which were mainly associated with metabolism and immunity. Pathway analysis showed that immune-related pathways of phagosome and cell adhesion molecules (CAMs) pathway were significantly down-regulated under low temperature. Moreover, ferroptosis, a significantly changed pathway involved in tissue damage and acute renal failure, is reported here for the first time. The levels of serum parameters associated with kidney damage such as urea and uric acid (UA) increased significantly under low temperature. The immunofluorescence staining of the kidney showed that cell apoptosis occurred at low temperature. The results of the present study indicate that exposure to low temperature can cause kidney disfunction and down-regulate the immune-related pathway in the kidney of tilapia. This study provides new insight into the mechanism of kidney damage in fish under low temperature.
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Affiliation(s)
- Tao Zhou
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Lang Gui
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Mingli Liu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Wenhao Li
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Peng Hu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Daniel F C Duarte
- Faculty of Sciences and Technology, University of Algarve, Faro, Portugal
| | - Hongbo Niu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Liangbiao Chen
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.
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Li BJ, Jiang DL, Meng ZN, Zhang Y, Zhu ZX, Lin HR, Xia JH. Genome-wide identification and differentially expression analysis of lncRNAs in tilapia. BMC Genomics 2018; 19:729. [PMID: 30286721 PMCID: PMC6172845 DOI: 10.1186/s12864-018-5115-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 09/25/2018] [Indexed: 12/28/2022] Open
Abstract
Background Long noncoding RNAs (LncRNAs) play important roles in fundamental biological processes. However, knowledge about the genome-wide distribution and stress-related expression of lncRNAs in tilapia is still limited. Results Genome-wide identification of lncRNAs in the tilapia genome was carried out in this study using bioinformatics tools. 103 RNAseq datasets that generated in our laboratory or collected from NCBI database were analyzed. In total, 72,276 high-confidence lncRNAs were identified. The averaged positive correlation coefficient (r_mean = 0.286) between overlapped lncRNA and mRNA pairs showed significant differences with the values for all lncRNA-mRNA pairs (r_mean = 0.176, z statistics = − 2.45, p value = 0.00071) and mRNA-mRNA pairs (r_mean = 0.186, z statistics = − 2.23, p value = 0.0129). Weighted correlation network analysis of the lncRNA and mRNA datasets from 12 tissues identified 21 modules and many interesting mRNA genes that clustered with lncRNAs. Overrepresentation test indicated that these mRNAs enriched in many biological processes, such as meiosis (p = 0.00164), DNA replication (p = 0.00246), metabolic process (p = 0.000838) and in molecular function, e.g., helicase activity (p = 0.000102) and catalytic activity (p = 0.0000612). Differential expression (DE) analysis identified 99 stress-related lncRNA genes and 1955 tissue-specific DE lncRNA genes. MiRNA-lncRNA interaction analysis detected 72,267 lncRNAs containing motifs with sequence complementary to 458 miRNAs. Conclusions This study provides an invaluable resource for further studies on molecular bases of lncRNAs in tilapia genomes. Further function analysis of the lncRNAs will help to elucidate their roles in regulating stress-related adaptation in tilapia. Electronic supplementary material The online version of this article (10.1186/s12864-018-5115-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bi Jun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Dan Li Jiang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zi Ning Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zong Xian Zhu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Hao Ran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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Wang W, Lin Y, Teng F, Ji D, Xu Y, Chen C, Xie C. Comparative transcriptome analysis between heat-tolerant and sensitive Pyropia haitanensis strains in response to high temperature stress. ALGAL RES 2018. [DOI: 10.1016/j.algal.2017.11.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Ma D, Xue Y, Zhang Y, Sun Y, Meng A, Liu F. The rising zebrafish research in China: Meeting report of the 3rd Chinese Zebrafish Principal Investigator Meeting & the Inaugural Meeting of China Zebrafish Society. J Genet Genomics 2016; 43:617-620. [PMID: 27769691 DOI: 10.1016/j.jgg.2016.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 10/20/2022]
Affiliation(s)
- Dongyuan Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanyuan Xue
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yifan Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yonghua Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, China Zebrafish Resource Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Anming Meng
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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