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Yan X, Wei P, Zhang X, Guan J, Li W, Zhang L, Zheng Y, Chen Y, Zhu P, He P, Peng J. miRNA-seq provides novel insight into the response to hyper- and hypo- salinity acclimation in Crassostrea hongkongensis. Gene 2024; 924:148555. [PMID: 38772515 DOI: 10.1016/j.gene.2024.148555] [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: 12/06/2023] [Revised: 04/29/2024] [Accepted: 05/09/2024] [Indexed: 05/23/2024]
Abstract
The Hong Kong oyster, Crassostrea hongkongensis, is a significant bivalve species with economic importance. It primarily inhabits the estuarine intertidal zones in southern China, making it susceptible to salinity fluctuations. Consequently, investigating the molecular mechanisms governing salinity regulation in C. hongkongensis is essential. In this study, we conducted miRNA-seq on C. hongkongensis to compare miRNA expression differences under varying salinities (5‰, 25‰, and 35‰). The miRNA sequencing revealed 51 known miRNAs and 95 novel miRNAs across nine small RNA libraries (S5, S25, and S35). Among these miRNAs, we identified 6 down-regulated differentially expressed (DE) miRNAs in response to hypo-salinity stress (5‰), while 1 up-regulated DE miRNA and 5 down-regulated DE miRNAs were associated with hyper-salinity stress (35‰). Additionally, we predicted 931 and 768 potential target genes for hypo- and hyper-salinity stress, respectively. Functional gene annotation indicated that the target genes under hypo-salinity stress were linked to vesicle-mediated transport and metal ion binding. Conversely, those under hyper-salinity stress were primarily involved in signal transduction and metabolic processes. These findings have provided insights into the regulatory role of miRNAs, their potential target genes and associated pathways in oyster hypo- and hyper-salinity stress, which establish a foundation for future studies on the roles of miRNAs in salinity acclimation mechanisms in C. hongkongensis.
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Affiliation(s)
- Xueyu Yan
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, Guangxi 535011, China.
| | - Pinyuan Wei
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi 530021, China
| | - Xingzhi Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi 530021, China
| | - Junliang Guan
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi 530021, China
| | - Wei Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi 530021, China
| | - Li Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi 530021, China
| | - Yusi Zheng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi 530021, China
| | - Yongxian Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi 530021, China
| | - Peng Zhu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, Guangxi 535011, China
| | - Pingping He
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi 530021, China.
| | - Jinxia Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, Guangxi 530021, China.
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2
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Hsu LY, Kuo HW, Cheng W. Expression of octopamine/tyramine receptors and immune regulation in Litopenaeus vannamei under acute and chronic thermal stress. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 158:105195. [PMID: 38762098 DOI: 10.1016/j.dci.2024.105195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/06/2024] [Accepted: 05/16/2024] [Indexed: 05/20/2024]
Abstract
This study investigated the impact of hyperthermal (34 °C) and hypothermal (14 °C) stress on the expression of the octopamine/tyramine receptor (LvOA/TA-R) and immune parameters in Litopenaeus vannamei, which is a species critical to the aquaculture industry. Given the sensitivity of aquatic organisms to climate change, understanding the physiological and immune responses of L. vannamei to temperature variations is essential for developing strategies to mitigate adverse effects. This research focuses on the immune response and expression changes of LvOA/TA-R under acute (0.5, 1, and 2 h) and chronic (24, 72, and 168 h) thermal stress conditions. Our findings reveal that thermal stress induces changes in LvOA/TA-R expression and impacts immune responses. Immune parameters such as total haemocyte count, differential haemocyte count, phenoloxidase activity, respiratory bursts, lysozyme activity, clearance efficiency, and phagocytosis exhibited a general trend of significant decline under the stress conditions. LvOA/TA-R had a higher expression in haemocyte under hyperthermal stress. The study elucidated that thermal stress modifies the expression of the LvOA/TA-R and diminishes immune functionality in L. vannamei, underscoring the potential influence of climate change on industry.
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Affiliation(s)
- Li-Yang Hsu
- Department of Aquaculture, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan, ROC
| | - Hsin-Wei Kuo
- General Research Service Center, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan, ROC
| | - Winton Cheng
- Department of Aquaculture, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan, ROC.
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3
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Fu C, Fu X, Li F, Li Z, Wang A, Jiang S, Liu C, Wang H. Integrated microRNA-mRNA analysis reveals a possible molecular mechanism of enteritis susceptibility in Litopenaeus vannamei. FISH & SHELLFISH IMMUNOLOGY 2023; 136:108699. [PMID: 36935044 DOI: 10.1016/j.fsi.2023.108699] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/06/2023] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
Enteritis is one of the main diseases affecting Pacific whiteleg shrimp (Litopenaeus vannamei) in recent years, and it has resulted in huge losses to the aquaculture industry. Prior to this study, the molecular mechanism underlying enteritis in L. vannamei was unclear, and comprehensive multi-omics analysis had not been conducted. In this study, 1209 differentially expressed genes (DEGs) were identified from the hepatopancreas of L. vannamei with and without enteritis. Kyoto Encyclopedia of Genes and Genomes analysis showed that genes were significantly enriched in immune, metabolic, and endocrine regulatory pathways. Forty-eight significantly different microRNAs (miRNAs) were identified in the miRNA-Seq analysis. Further functional annotation analysis showed that the regulatory pathway of target gene enrichment of differentially expressed miRNAs was consistent with DEGs. Through miRNA-mRNA integration analysis, 47 meaningful miRNA-mRNA pairs were obtained, of which melanogenesis and pancreatic secretion were considered key pathways. Subsequent miRNA-mRNA interaction network analysis revealed that mja-miR-6493-3p, Mja-miR-6494, novel-198, novel-272, novel-261, novel-200, novel-183, novel-184, novel-237, and novel-192 may be key miRNAs involved in the regulation of these two signaling pathways. Finally, the RAS signaling pathway was found to inhibit the translation level of proteins in the hepatopancreas. These results suggest that target gene integration analysis of mRNA-miRNA can reveal the molecular mechanism underlying enteritis in L. vannamei and also provide valuable new insights for resisting enteritis.
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Affiliation(s)
- Chunpeng Fu
- Shandong Peninsula Engineering Research Center of Comprehensive Brine Utilization, Weifang University of Science and Technology, Shouguang, 262700, China.
| | - Xiaopeng Fu
- Marine and Fishery Supervision Detachment of Rizhao City, Rizhao, 276800, China
| | - Fajun Li
- Shandong Peninsula Engineering Research Center of Comprehensive Brine Utilization, Weifang University of Science and Technology, Shouguang, 262700, China
| | - Zongzhen Li
- Shandong Peninsula Engineering Research Center of Comprehensive Brine Utilization, Weifang University of Science and Technology, Shouguang, 262700, China
| | - Aili Wang
- Shandong Peninsula Engineering Research Center of Comprehensive Brine Utilization, Weifang University of Science and Technology, Shouguang, 262700, China
| | - ShanShan Jiang
- Shandong Peninsula Engineering Research Center of Comprehensive Brine Utilization, Weifang University of Science and Technology, Shouguang, 262700, China
| | - Chunqiao Liu
- Shandong Peninsula Engineering Research Center of Comprehensive Brine Utilization, Weifang University of Science and Technology, Shouguang, 262700, China
| | - Hui Wang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, China
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4
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Millard RS, Bickley LK, Bateman KS, Verbruggen B, Farbos A, Lange A, Moore KA, Stentiford GD, Tyler CR, van Aerle R, Santos EM. Resistance to white spot syndrome virus in the European shore crab is associated with suppressed virion trafficking and heightened immune responses. Front Immunol 2022; 13:1057421. [PMID: 36636327 PMCID: PMC9831657 DOI: 10.3389/fimmu.2022.1057421] [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: 09/29/2022] [Accepted: 12/01/2022] [Indexed: 12/28/2022] Open
Abstract
Introduction All decapod crustaceans are considered potentially susceptible to White Spot Syndrome Virus (WSSV) infection, but the degree of White Spot Disease (WSD) susceptibility varies widely between species. The European shore crab Carcinus maenas can be infected with the virus for long periods of time without signs of disease. Given the high mortality rate of susceptible species, the differential susceptibility of these resistant hosts offers an opportunity to investigate mechanisms of disease resistance. Methods Here, the temporal transcriptional responses (mRNA and miRNA) of C. maenas following WSSV injection were analysed and compared to a previously published dataset for the highly WSSV susceptible Penaeus vannamei to identify key genes, processes and pathways contributing to increased WSD resistance. Results We show that, in contrast to P. vannamei, the transcriptional response during the first 2 days following WSSV injection in C. maenas is limited. During the later time points (7 days onwards), two groups of crabs were identified, a recalcitrant group where no replication of the virus occurred, and a group where significant viral replication occurred, with the transcriptional profiles of the latter group resembling those of WSSV-susceptible species. We identify key differences in the molecular responses of these groups to WSSV injection. Discussion We propose that increased WSD resistance in C. maenas may result from impaired WSSV endocytosis due to the inhibition of internal vesicle budding by dynamin-1, and a delay in movement to the nucleus caused by the downregulation of cytoskeletal transcripts required for WSSV cytoskeleton docking, during early stages of the infection. This response allows resistant hosts greater time to fine-tune immune responses associated with miRNA expression, apoptosis and the melanisation cascade to defend against, and clear, invading WSSV. These findings suggest that the initial stages of infection are key to resistance to WSSV in the crab and highlight possible pathways that could be targeted in farmed crustacean to enhance resistance to WSD.
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Affiliation(s)
- Rebecca S. Millard
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Weymouth, United Kingdom,Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom,*Correspondence: Rebecca S. Millard, ; Eduarda M. Santos,
| | - Lisa K. Bickley
- Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom,Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Kelly S. Bateman
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Weymouth, United Kingdom,Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom
| | - Bas Verbruggen
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Audrey Farbos
- University of Exeter Sequencing Facility, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Anke Lange
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Karen A. Moore
- University of Exeter Sequencing Facility, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Grant D. Stentiford
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Weymouth, United Kingdom,Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom
| | - Charles R. Tyler
- Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom,Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Weymouth, United Kingdom,Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom
| | - Eduarda M. Santos
- Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom,Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom,*Correspondence: Rebecca S. Millard, ; Eduarda M. Santos,
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5
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Yoon DS, Byeon E, Kim DH, Lee MC, Shin KH, Hagiwara A, Park HG, Lee JS. Effects of temperature and combinational exposures on lipid metabolism in aquatic invertebrates. Comp Biochem Physiol C Toxicol Pharmacol 2022; 262:109449. [PMID: 36055628 DOI: 10.1016/j.cbpc.2022.109449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022]
Abstract
Studies of changes in fatty acids in response to environmental temperature changes have been conducted in many species, particularly mammals. However, few studies have considered aquatic invertebrates, even though they are particularly vulnerable to changes in environmental temperature. In this review, we summarize the process by which animals synthesize common fatty acids and point out differences between the fatty acid profiles of vertebrates and those of aquatic invertebrates. Unlike vertebrates, some aquatic invertebrates can directly synthesize polyunsaturated fatty acids (PUFAs), which can be used to respond to temperature changes. Various studies have shown that aquatic invertebrates increase the degree of saturation in their fatty acids through an increase in saturated fatty acid production or a decrease in PUFAs as the temperature increases. In addition, we summarize recent studies that have examined the complex effects of temperature and combinational stressors to determine whether the degree of saturation in aquatic invertebrates is influenced by other factors. The combined effects of carbon dioxide partial pressure, food quality, starvation, salinity, and chemical exposures have been confirmed, and fatty acid profile changes in response to high temperature were greater than those from combinational stressors.
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Affiliation(s)
- Deok-Seo Yoon
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Eunjin Byeon
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Chul Lee
- Department of Food & Nutrition, College of Bio-Nano Technology, Gachon University, Seongnam 13120, South Korea
| | - Kyung-Hoon Shin
- Department of Marine Science and Convergence Engineering, Hanyang University, Ansan 15588, South Korea
| | - Atsushi Hagiwara
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki 852-8521, Japan
| | - Heum Gi Park
- Department of Marine Ecology and Environment, College of Life Sciences, Gangneung-Wonju National University, Gangneung 25457, South Korea.
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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6
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Zhu W, Yang C, Chen X, Liu Q, Li Q, Peng M, Wang H, Chen X, Yang Q, Liao Z, Li M, Pan C, Feng P, Zeng D, Zhao Y. Single-Cell Ribonucleic Acid Sequencing Clarifies Cold Tolerance Mechanisms in the Pacific White Shrimp ( Litopenaeus Vannamei). Front Genet 2022; 12:792172. [PMID: 35096009 PMCID: PMC8790290 DOI: 10.3389/fgene.2021.792172] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/25/2021] [Indexed: 12/12/2022] Open
Abstract
To characterize the cold tolerance mechanism of the Pacific white shrimp (Litopenaeus vannamei), we performed single-cell RNA sequencing (scRNA-seq) of ∼5185 hepatopancreas cells from cold-tolerant (Lv-T) and common (Lv-C) L. vannamei at preferred and low temperatures (28°C and 10°C, respectively). The cells fell into 10 clusters and 4 cell types: embryonic, resorptive, blister-like, and fibrillar. We identified differentially expressed genes between Lv-T and Lv-C, which were mainly associated with the terms “immune system,” “cytoskeleton,” “antioxidant system,” “digestive enzyme,” and “detoxification,” as well as the pathways “metabolic pathways of oxidative phosphorylation,” “metabolism of xenobiotics by cytochrome P450,” “chemical carcinogenesis,” “drug metabolism-cytochrome P450,” and “fatty acid metabolism.” Reconstruction of fibrillar cell trajectories showed that, under low temperature stress, hepatopancreas cells had two distinct fates, cell fate 1 and cell fate 2. Cell fate 1 was mainly involved in signal transduction and sensory organ development. Cell fate 2 was mainly involved in metabolic processes. This study preliminarily clarifies the molecular mechanisms underlying cold tolerance in L. vannamei, which will be useful for the breeding of shrimp with greater cold tolerance.
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Affiliation(s)
- Weilin Zhu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Chunling Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Qingyun Liu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China.,Guangxi Shrimp and Crab Breeding Engineering Technology Research Center, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Qiangyong Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China.,Guangxi Shrimp and Crab Breeding Engineering Technology Research Center, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Min Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Huanling Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agriculture University, Wuhan, China
| | - Xiaohan Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Qiong Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Zhenping Liao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Min Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Chuanyan Pan
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Pengfei Feng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Digang Zeng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China.,Guangxi Shrimp and Crab Breeding Engineering Technology Research Center, Guangxi Academy of Fishery Sciences, Nanning, China
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7
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Significant genes in response to low temperature in Penaeus chinensis screened from multiple groups of transcriptome comparison. J Therm Biol 2022; 107:103198. [DOI: 10.1016/j.jtherbio.2022.103198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/13/2022] [Accepted: 01/21/2022] [Indexed: 01/21/2023]
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8
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Zuo H, Liu X, Luo M, Yang L, Zhu Z, Weng S, He J, Xu X. miR-10c Facilitates White Spot Syndrome Virus Infection by Targeting Toll3 in Litopenaeus vannemei. Front Immunol 2021; 12:733730. [PMID: 34950131 PMCID: PMC8688535 DOI: 10.3389/fimmu.2021.733730] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/14/2021] [Indexed: 12/03/2022] Open
Abstract
Toll-like receptors (TLRs) are canonical cell membrane receptors functioning to recognize pathogens and transduce signals to activate immune responses. It has been known that Toll3 in Pacific white shrimp Litopenaeus vannamei (LvToll3) plays a critical role in antiviral immunity by inducing the transcription of interferon regulatory factor (IRF), which mediates a signaling axis that is similar to the interferon system of vertebrates. However, the regulatory mechanism of the Toll3-IRF signaling is still unclear. In this study, a novel microRNA (miRNA) of miR-10 family, temporarily named as miR-10c, was identified from L. vannamei. miR-10c may play a nonnegligible regulatory role in shrimp immune responses since it was constitutively expressed in all detected tissues and transcriptionally induced by immune stimulation. Functional analysis validated that miR-10c could target LvToll3 to inhibit its expression, through which miR-10c blocked the nuclear translocation of IRF and facilitated white spot syndrome virus (WSSV) infection. To our knowledge, the present study revealed the first report of a Toll targeted by miRNA in crustaceans and provided a solid evidence base for supporting the role of LvToll3 in antiviral defense by activating IRF signaling in L. vannamei. Identification of the miR-10c/Toll3/IRF regulatory axis in shrimp provides new insights into the participation of miRNA in the regulation of immune responses and contributes to in-depth understanding of the mechanisms of Toll-induced immune responses in L. vannamei.
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Affiliation(s)
- Hongliang Zuo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, China
| | - Xinxin Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Mengting Luo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Linwei Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, China
| | - Zhiming Zhu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, China
| | - Jianguo He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, China
| | - Xiaopeng Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, China
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9
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Millard RS, Bickley LK, Bateman KS, Farbos A, Minardi D, Moore K, Ross SH, Stentiford GD, Tyler CR, van Aerle R, Santos EM. Global mRNA and miRNA Analysis Reveal Key Processes in the Initial Response to Infection with WSSV in the Pacific Whiteleg Shrimp. Viruses 2021; 13:v13061140. [PMID: 34199268 PMCID: PMC8231841 DOI: 10.3390/v13061140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/06/2021] [Accepted: 06/10/2021] [Indexed: 12/13/2022] Open
Abstract
White Spot Disease (WSD) presents a major barrier to penaeid shrimp production. Mechanisms underlying White Spot Syndrome Virus (WSSV) susceptibility in penaeids are poorly understood due to limited information related to early infection. We investigated mRNA and miRNA transcription in Penaeus vannamei over 36 h following infection. Over this time course, 6192 transcripts and 27 miRNAs were differentially expressed—with limited differential expression from 3–12 h post injection (hpi) and a more significant transcriptional response associated with the onset of disease symptoms (24 hpi). During early infection, regulated processes included cytoskeletal remodelling and alterations in phagocytic activity that may assist WSSV entry and translocation, novel miRNA-induced metabolic shifts, and the downregulation of ATP-dependent proton transporter subunits that may impair cellular recycling. During later infection, uncoupling of the electron transport chain may drive cellular dysfunction and lead to high mortalities in infected penaeids. We propose that post-transcriptional silencing of the immune priming gene Dscam (downregulated following infections) by a novel shrimp miRNA (Pva-pmiR-78; upregulated) as a potential mechanism preventing future recognition of WSSV that may be suppressed in surviving shrimp. Our findings improve our understanding of WSD pathogenesis in P. vannamei and provide potential avenues for future development of prophylactics and treatments.
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Affiliation(s)
- Rebecca S. Millard
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; (L.K.B.); (C.R.T.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Correspondence: (R.S.M.); (E.M.S.); Tel.: +44-(0)-1392-724607 (E.M.S.)
| | - Lisa K. Bickley
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; (L.K.B.); (C.R.T.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
| | - Kelly S. Bateman
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Audrey Farbos
- Exeter Sequencing Service, Geoffrey Pope Building, University of Exeter, Exeter EX4 4QD, UK; (A.F.); (K.M.)
| | - Diana Minardi
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Karen Moore
- Exeter Sequencing Service, Geoffrey Pope Building, University of Exeter, Exeter EX4 4QD, UK; (A.F.); (K.M.)
| | - Stuart H. Ross
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Grant D. Stentiford
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Charles R. Tyler
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; (L.K.B.); (C.R.T.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
| | - Ronny van Aerle
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Eduarda M. Santos
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; (L.K.B.); (C.R.T.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Correspondence: (R.S.M.); (E.M.S.); Tel.: +44-(0)-1392-724607 (E.M.S.)
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10
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MicroRNA transcriptome analysis of oriental river prawn Macrobrachium nipponense in responding to starvation stress. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 38:100820. [PMID: 33676153 DOI: 10.1016/j.cbd.2021.100820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/03/2021] [Accepted: 02/23/2021] [Indexed: 12/15/2022]
Abstract
Food deprivation or fasting is an important environmental factor, and a regular occurrence in both natural aquatic habitats and artificial ponds. However, the potential immunoregulatory mechanisms underlying starvation stress in crustaceans remain unclear. MicroRNAs (miRNAs) are a new class of non-coding RNAs that can regulate various biological processes, such as stress and immune responses. In the present work, miRNAs related to starvation stress responses and immune properties were identified and characterised in oriental river prawn Macrobrachium nipponense using high-throughput sequencing and bioinformatics analyses. Twelve small RNA libraries from hepatopancreas tissue were sequenced across four fasting stages lasting 0, 7, 14 or 21 days. In total, 550 miRNAs were identified including 198 putative novel miRNAs and 352 conserved miRNAs belonging to 57 families. Moreover, compared with expression levels at 0 days, 27, 27 and 43 miRNAs were differentially expressed (DE-miRNAs) at 7, 14 and 21 days, respectively. Among these, four DE-miRNAs (ame-miR-190-5p, dme-miR-307a-3p, hme-miR-2788-3p and novel_68) were co-expressed at all three timepoints. Furthermore, 661 target genes regulated by these DE-miRNAs were identified, and associated functional annotations were derived by GO enrichment and KEGG pathway analyses, which showed that most DE-miRNAs were mainly participated in metabolic processes and immune responses. Furthermore, 26 host DE-miRNAs potentially participated in interactions with white spot syndrome virus (WSSV) were identified by predicting and analysing target genes from WSSV. The further WSSV challenge under starvation stress showed that dme-miR-307a-3p played a part in the antiviral responses against WSSV. Our results demonstrate that dme-miR-307a-3p may play vital regulatory roles in responding to starvation stress and WSSV infection. The findings contribute new insight into the molecular mechanisms associated with immune responses to environmental stress in crustaceans.
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11
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Zhuo X, Qin Y, He P, Wei P, Zhang B, Chen X, Peng J. Transcriptomic analysis of Litopenaeus vannamei hepatopancreas under cold stress in cold-tolerant and cold-sensitive cultivars. Gene 2020; 764:145090. [PMID: 32861880 DOI: 10.1016/j.gene.2020.145090] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 07/22/2020] [Accepted: 08/21/2020] [Indexed: 01/19/2023]
Abstract
Litopenaeus vannamei (L. vannamei) is one of the most widely cultured shrimp species in the world. The species often suffers from cold stress. To understand the molecular mechanism of cold tolerance, we performed transcriptomic analysis on two contrasting cultivars of L. vannamei, namely, cold-tolerant Guihai 2 (GH2) and cold-sensitive Guihai1 (GH1), under a control temperature (28 °C), cold stress (16 °C), and recovery to 28 °C. A total of 84.5 Gb of sequences were generated from 12 L. vannamei hepatopancreas libraries. The de-novo assembly generated a total of 143,029 unigenes with a mean size of 1,052 bp and an N50 of 2,604 bp, of which 34.08% were annotated in the Nr database. We analyzed the differentially expressed genes (DEGs) between nine comparison groups and detected a total of 21,026 DEGs. KEGG pathways, including lysosome, sphingolipid metabolism and nitrogen metabolism, were significantly enriched by DEGs between different temperatures in GH2. Furthermore, eight of the most significantly DEGs under cold stress from the transcriptomic analysis were selected for quantitative real-time PCR (qPCR) validation. Overall, we compared gene expression changes under cold stress in cold-tolerant and cold-sensitive L. vannamei for the first time. The results may further extend our understanding of the cold stress-response mechanism in L. vannamei.
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Affiliation(s)
- Xiaofei Zhuo
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Yibin Qin
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530001, China
| | - Pingping He
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Pinyuan Wei
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Bin Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Xiaohan Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Jinxia Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China.
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12
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Wang Z, Zhou J, Li J, Lv W, Zou J, Fan L. A new insight into the intestine of Pacific white shrimp: Regulation of intestinal homeostasis and regeneration in Litopenaeus vannamei during temperature fluctuation. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 35:100687. [PMID: 32388341 DOI: 10.1016/j.cbd.2020.100687] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 01/20/2023]
Abstract
Litopenaeus vannamei (L. vannamei) is an essential aquaculture shrimp throughout the world, but its aquaculture industry is threatened by temperature fluctuation. In this study, our histological results indicated that the shrimp intestine has a self-repairing ability during temperature fluctuation; however the potential mechanisms were still unknown. Therefore, transcriptome profiles of the intestine were collected from shrimp at 28 °C (C28), 13 °C (T13) and 28 °C after their temperature rose back (R28) and were analyzed. A total of 2229 differentially expressed genes (DEGs) (986 up- and 1243 downregulated) were identified in the C28 group, and 1790 DEGs (933 up- and 857 downregulated) were identified in the R28 group when compared to their expression levels in the T13 group. According to the functional annotation using KEGG, we found that the immune system was the most enriched section of organismal systems and that the shrimp can mobilize the body's immune response to regulate organism homeostasis during temperature fluctuation, although cold stress decreased the immunity. Additionally, metabolic inhibition is a strategy to cope with cold stress, and the regulation of lipid metabolism was especially important for shrimp during temperature fluctuation. Remarkably, the Hippo signaling pathway might help the repair of intestinal structure. Our research provides the first histological analysis and transcriptome profiling for the L. vannamei intestine during the temperature fluctuation stage. These results enrich our understanding of the mechanism of intestinal self-repair and homeostasis and could provide guidance for shrimp farming.
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Affiliation(s)
- Zhenlu Wang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, PR China
| | - Jiang Zhou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, PR China
| | - Junyi Li
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, PR China
| | - Wei Lv
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, PR China
| | - Jixing Zou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, PR China.
| | - Lanfen Fan
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, PR China.
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13
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Wang Z, Feng Y, Li J, Zou J, Fan L. Integrative microRNA and mRNA analysis reveals regulation of ER stress in the Pacific white shrimp Litopenaeus vannamei under acute cold stress. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 33:100645. [DOI: 10.1016/j.cbd.2019.100645] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/21/2019] [Accepted: 11/15/2019] [Indexed: 01/12/2023]
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14
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Ji X, Jiang P, Luo J, Li M, Bai Y, Zhang J, Han B. Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells. PLoS One 2020; 15:e0226905. [PMID: 31923196 PMCID: PMC6953832 DOI: 10.1371/journal.pone.0226905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 12/07/2019] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) play vital roles in various biological processes under multiple stress conditions by leading to mRNA cleavage or translational repression. However, the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study, high-throughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control (28°C, 30 days) and cold-acclimation (18°C, 30 days) conditions. A total of 414 miRNAs, 349 known and 65 novel, were identified. Among those miRNAs, 24 (19 known and 5 novel) were up-regulated, and 23 (9 known and 14 novel) were down-regulated in cold acclimated cells. The Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analyses indicated that the target genes of known differentially expressed miRNAs (DE-miRNA) are involved in cold acclimation by regulation of phosphorylation, cell junction, intracellular signal transduction, ECM-receptor interaction and so on. Moreover, both miR-100-3p inhibitor and miR-16b mimics could protect ZF4 cells under cold stress, indicating the involvement of miRNA in cold acclimation. Further study showed that miR-100-3p and miR-16b could regulate inversely the expression of their target gene (atad5a, cyp2ae1, lamp1, rilp, atxn7, tnika, btbd9), and that overexpression of miR-100-3p disturbed the early embryonic development of zebrafish. In summary, the present data show that miRNAs are closely involved in cold acclimation in zebrafish ZF4 cells and provide information for further understanding of the roles of miRNAs in cold acclimation in fish.
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Affiliation(s)
- Xiangqin Ji
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Penglei Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Juntao Luo
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Mengjia Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Yajing Bai
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Junfang Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China
| | - Bingshe Han
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- * E-mail:
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15
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Shekhar MS, Karthic K, Kumar KV, Kumar JA, Swathi A, Hauton C, Peruzza L, Vijayan KK. Comparative analysis of shrimp (Penaeus vannamei) miRNAs expression profiles during WSSV infection under experimental conditions and in pond culture. FISH & SHELLFISH IMMUNOLOGY 2019; 93:288-295. [PMID: 31330255 DOI: 10.1016/j.fsi.2019.07.057] [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: 04/22/2019] [Revised: 06/17/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
In recent years, the importance of viral and host microRNAs (miRNAs) in mediating viral replication and control of host cellular machinery, has been realised and increasing efforts have been taken in order to understand the interactions of miRNAs from host and pathogen during infection. However, all existing studies has thus far been conducted in controlled experimental conditions and the veracity of these data for field conditions are yet to be established. In this framework, small RNA sequencing was performed to identify the miRNAs involved in shrimp (Penaeus vannamei) immune responses under two different WSSV infection conditions of natural infection and experimentally challenged conditions. The expression profiles of miRNAs of shrimp infected with WSSV under two contrasting conditions were compared and as a result, 23365 known miRNAs and 481 novel miRNAs were identified. Amongst the most abundantly expressed miRNAs, the hypoxia related miR-210 and immune pathway related miR-29b were expressed only in infected shrimps of both conditions. miR-8-5p, having a functional role in modulation of chitin biosynthesis was exclusively represented in higher numbers in the WSSV -infected shrimps under natural conditions whilst four of the miRNAs (mja-miR-6493-5p, mja-miR-6492, mmu-miR-3968, tcf-miR-9b-5p) identified from shrimps collected from pond culture targeted chitinase, an important enzyme involved in growth and moulting in shrimps, indicating an interaction between WSSV infection and moult cycle under culture conditions. Some of the miRNAs (tca-miR-87b-3p, cte-miR-277a) and miRNAs belonging to class miR-9, miR-981 that were identified only in WSSV infected shrimps under experimental conditions, are known to respond against WSSV infection in shrimps. Moreover, the miRNA target prediction revealed several immune-related gene targets such as cathepsin, c-type lectin, haemocyanin and ubiquitin protein ligase were commonly identified under both the conditions. However, the miRNAs identified from challenge experiment had wide number of gene targets as compared to the miRNAs of natural infection. The shrimp miRNA mja-miR-6489-3p, was also found to target early virus gene wsv001 of WSSV. Our study, therefore, provides the comparative analysis of miRNA expression from shrimp during WSSV infection in two different conditions.
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Affiliation(s)
- M S Shekhar
- Genetics and Biotechnology Unit, Central Institute of Brackishwater Aquaculture, 75 Santhome High Road, R.A Puram, Chennai, India.
| | - K Karthic
- Genetics and Biotechnology Unit, Central Institute of Brackishwater Aquaculture, 75 Santhome High Road, R.A Puram, Chennai, India
| | - K Vinaya Kumar
- Genetics and Biotechnology Unit, Central Institute of Brackishwater Aquaculture, 75 Santhome High Road, R.A Puram, Chennai, India
| | - J Ashok Kumar
- Genetics and Biotechnology Unit, Central Institute of Brackishwater Aquaculture, 75 Santhome High Road, R.A Puram, Chennai, India
| | - A Swathi
- Genetics and Biotechnology Unit, Central Institute of Brackishwater Aquaculture, 75 Santhome High Road, R.A Puram, Chennai, India
| | - Chris Hauton
- School of Ocean and Earth Science, University of Southampton, Hampshire, SO14 3ZH, United Kingdom
| | - L Peruzza
- School of Ocean and Earth Science, University of Southampton, Hampshire, SO14 3ZH, United Kingdom
| | - K K Vijayan
- Genetics and Biotechnology Unit, Central Institute of Brackishwater Aquaculture, 75 Santhome High Road, R.A Puram, Chennai, India
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16
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Fan L, Wang L, Wang Z. Proteomic characterization of the hepatopancreas in the Pacific white shrimp Litopenaeus vannamei under cold stress: Revealing the organism homeostasis mechanism. FISH & SHELLFISH IMMUNOLOGY 2019; 92:438-449. [PMID: 31229644 DOI: 10.1016/j.fsi.2019.06.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/25/2019] [Accepted: 06/17/2019] [Indexed: 06/09/2023]
Abstract
To understand the homeostasis mechanism of crustacean hepatopancreas to cold stress, iTRAQ proteomics based on the genome database of Litopenaeus vannamei (L. vannamei) was applied to investigate proteins changes and variety of the hepatopancreas during cold stress stage in this study. A total of 4062 distinct proteins were identified, 137 differentially expressed proteins (DEPs) including 62 differentially up-regulated proteins (DUPs) and 75 differentially down-regulated proteins (DDPs) were identified in G1 (18 °C) compared with CK (28 °C), 359 DEPs including 131 DUPs and 228 DDPs were identified in G2 (13 °C for 24 h) compared with CK. Based on bioinformatics analysis, the cold tolerance of L. vannamei might be related to energy metabolism such as amino acid, carbohydrate, lipid, and oxidative phosphorylation. Moreover, shrimp immunity was declined during cold stress stage. However, L. vannamei could cope with cold stress by enhancing the production of ATP and UFA. Notably, arginine kinase, heat shock proteins, and histones may act as positive regulators in L. vannamei under cold stress. Ten randomly selected proteins were used for validation using qRT-PCR and the expressions on the transcription level for most of the genes were similar to the results of iTRAQ. These results indicated that L. vannamei can maintain the organism homeostasis by a series of orderly regulatory process during cold stress. Furthermore, the results can provide guidance for shrimp farming.
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Affiliation(s)
- Lanfen Fan
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China; Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China.
| | - Lei Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China; Department of Pharmaceutical Engineering, College of Materials and Energy, South China Agricultural University, Guangzhou, 510642, China
| | - Zhenlu Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
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17
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Wang Z, Qu Y, Yan M, Li J, Zou J, Fan L. Physiological Responses of Pacific White Shrimp Litopenaeus vannamei to Temperature Fluctuation in Low-Salinity Water. Front Physiol 2019; 10:1025. [PMID: 31456695 PMCID: PMC6700251 DOI: 10.3389/fphys.2019.01025] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 07/24/2019] [Indexed: 12/29/2022] Open
Abstract
Temperature is a significant environmental factor in aquaculture. To investigate the physiological responses during temperature fluctuation (28~13°C), experimental shrimps (Litopenaeus vannamei) were treated with gradual cooling from acclimation temperature (AT, 28°C) to 13°C with a cooling rate of 7.5°C/day and rose back to 28°C at the same rate after 13°C for 24 h. Hepatopancreas histological changes, plasma metabolites concentrations, relative mRNA expression of unfolded protein response (UPR) pathway and apoptosis in hepatopancreas and hemocyte were investigated. The results showed that with the decline of temperature, the number and volume of the secretory cells in hepatopancreas increased significantly, the tubule lumen appeared dilatated, and the epithelial cell layer became thinner. The contents of glucose (Glu) significantly decreased to the minimum value of 13°C for 24 h. The contents of triglyceride (TG), total cholesterol (TC), and total protein (TP) increased and reached the peak of 13°C for 24 h. Alkaline phosphatase (ALP) and alanine aminotransferase (ALT) activities in plasma reached the lowest and highest value in 13°C, respectively. The expressions of all genes related to UPR and apoptosis in the hepatopancreas and hemocytes were significantly changed during the cooling process and reached the highest level of 13 and 13°C for 24 h, respectively. During re-warming stage, the histopathological symptoms got remission and each of the plasma metabolite concentrations and gene expressions returned to AT levels. These results revealed that pacific white shrimp can adapt to a certain level of temperature fluctuation by self-regulation.
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Affiliation(s)
- Zhenlu Wang
- Department of Aquaculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, South China Agricultural University, Guangzhou, China
| | - Yuexin Qu
- Department of Aquaculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, South China Agricultural University, Guangzhou, China
| | - Muting Yan
- Department of Aquaculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, South China Agricultural University, Guangzhou, China
| | - Junyi Li
- Department of Aquaculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, South China Agricultural University, Guangzhou, China
| | - Jixing Zou
- Department of Aquaculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, South China Agricultural University, Guangzhou, China
| | - Lanfen Fan
- Department of Aquaculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, South China Agricultural University, Guangzhou, China
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18
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Wang Z, Qu Y, Zhuo X, Li J, Zou J, Fan L. Investigating the physiological responses of Pacific white shrimp Litopenaeus vannamei to acute cold-stress. PeerJ 2019; 7:e7381. [PMID: 31372323 PMCID: PMC6660825 DOI: 10.7717/peerj.7381] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/29/2019] [Indexed: 11/20/2022] Open
Abstract
Background Litopenaeus vannamei is one of the most important aquaculture shrimps in the world and low temperatures present a serious challenge to its survival, growth, and distribution. Methods To investigate their physiological responses during acute cold-stress, L. vannamei were treated under acute cooling conditions from 28 to 13 °C with a cooling rate of 2.5 °C/2 h and were maintained at 13 °C for 12 h. Plasma metabolite concentrations, histological changes, and relative gene expression related to the unfolded protein response (UPR) pathway and apoptosis in the hepatopancreas and the hemocytes of L. vannamei were investigated. Results The results revealed that the concentrations of triglycerides, total cholesterol, and total protein in plasma reached their peaks at 23 °C, and then decreased to their minimum values at 13 °C for 12 h. The activity of alkaline phosphatase in the plasma decreased to its lowest level while the activity of alanine aminotransferase increased to its highest level at 13 °C for 12 h. The hepatic tubules became necrotic and the basement membranes were ruptured at 13 °C for 12 h. The gene expression related to UPR and apoptosis in the hepatopancreas and hemocytes was significantly altered by the decrease in the temperature. Discussion The results revealed that acute cold-stress caused histological damage in the hepatopancreas of L. vannamei, reducing its immunity. The three UPR pathways were involved in the process of acute cold-stress and the response of activating transcription factor 6 to UPR may be faster and more directthan the IRE1 and PERK pathways.
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Affiliation(s)
- Zhenlu Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, South China Agricultural University, Guangzhou, China
| | - Yuexin Qu
- College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, South China Agricultural University, Guangzhou, China
| | - Xiaolei Zhuo
- Qingyuan North River Fishery Science Institute, Qingyuan, China
| | - Junyi Li
- College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, South China Agricultural University, Guangzhou, China
| | - Jixing Zou
- College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, South China Agricultural University, Guangzhou, China
| | - Lanfen Fan
- College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, South China Agricultural University, Guangzhou, China
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19
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Wang Y, Wang S, Wang S, Li G, Jiang R, Li Z, Han R, Kang X, Sun G. Target gene identification and functional characterization of miR-1704 in chicken. Anim Biotechnol 2019; 31:229-236. [PMID: 31039664 DOI: 10.1080/10495398.2019.1585365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
MiRNAs are small non-coding RNAs that negatively regulate gene expression at the post-transcriptional level. SNPs in miRNA genes may lead to phenotypic variation by altering miRNA expression and their targets. In this study, miR-1704 expression profiles in nine tissues at 1 d, 6 weeks and 16 weeks old Gushi chickens were detected. MiR-1704 was widely expressed in the detection of tissues. The expression in 1 d and 6 weeks old was low abundance, while its expression at 16 weeks was very high. An rs14668705 (C > G) SNP was detected within the pre-miR-1704 in an F2 resource population of Gushi chicken crossed with Anka broiler. Bioinformatic analysis indicated that the C > G mutation could introduce a base-pair mismatch and cause the change of free energy. Experiments further revealed that the rs14668705 in precursor miR-1704 could significantly affect mature miR-1704 biogenesis and was significantly associated with body weight at the age of 0, 6, 8, 10, and 12 weeks, shank circumference at 4, 8, and 12 weeks, carcass weight, and semi-evisceration weight (p < 0.05). Insulin receptor 2 (IRS2) gene, one of the potential targets of miR-1704 was identified and further confirmed. These data suggested that miR-1704 targeted IRS2 and have an effect on body weight in chicken.
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Affiliation(s)
- Yongcai Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
| | - Shunhong Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
| | - Shanghe Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
| | - Guoxi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
| | - RuiRui Jiang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
| | - Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
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Peng JX, He PP, Wei PY, Zhang B, Zhao YZ, Li QY, Chen XL, Peng M, Zeng DG, Yang CL, Chen X. Proteomic Responses Under Cold Stress Reveal Unique Cold Tolerance Mechanisms in the Pacific White Shrimp ( Litopenaeus vannamei). Front Physiol 2018; 9:1399. [PMID: 30483139 PMCID: PMC6243039 DOI: 10.3389/fphys.2018.01399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/13/2018] [Indexed: 11/13/2022] Open
Abstract
The Pacific white shrimp (Litopenaeus vannamei), one of the most widely cultured shrimp species in the world, often suffers from cold stress. To understand the molecular mechanism of cold tolerance in Pacific white shrimp, we conducted a proteomic analysis on two contrasting shrimp cultivars, namely, cold-tolerant Guihai2 (GH2) and cold-sensitive Guihai1 (GH1), under normal temperature (28°C), under cold stress (16°C), and during recovery to 28°C. In total, 3,349 proteins were identified, among which 2,736 proteins were quantified. Based on gene ontology annotations, differentially expressed proteins largely belonged to biological processes, cellular components, and molecular functions. KEGG pathway annotations indicated that the main changes were observed in the lysosome, ribosomes, and oxidative phosphorylation. Subcellular localization analysis showed a significant increase in proteins present in cytosol, extracellular regions, and mitochondria. Combining enrichment-based clustering analysis and qRT-PCR analysis, we found that glutathione S-transferase, zinc proteinase, m7GpppX diphosphatase, AP2 transcription complex, and zinc-finger transcription factors played a major role in the cold stress response in Pacific white shrimp. Moreover, structure proteins, including different types of lectin and DAPPUDRAFT, were indispensable for cold stress tolerance of the Pacific white shrimp. Results indicate the molecular mechanisms of the Pacific white shrimp in response to cold stress and provide new insight into breeding new cultivars with increased cold tolerance.
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Affiliation(s)
- Jin-Xia Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Ping-Ping He
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Pin-Yuan Wei
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Bin Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Yong-Zhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Qiang-Yong Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Xiu-Li Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Min Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Di-Gang Zeng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Chun-Ling Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Xiaohan Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
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