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Li Y, Xu Q, Liu H, Dai X. Differential expression of microRNAs in giant freshwater prawn (Macrobrachium rosenbergii) during the infection of Vibrio parahaemolyticus. FISH & SHELLFISH IMMUNOLOGY 2024; 153:109827. [PMID: 39134232 DOI: 10.1016/j.fsi.2024.109827] [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: 04/10/2024] [Revised: 07/26/2024] [Accepted: 08/09/2024] [Indexed: 08/22/2024]
Abstract
MicroRNAs (miRNAs) are a category of small non-coding RNAs regarded as vital regulatory factors in various biological processes, especially immune regulation. The differently expressed miRNAs in Macrobrachium rosenbergii after the challenge of Vibrio parahaemolyticus were identified using high-throughput sequencing. A total of 18 known as well as 12 novel miRNAs were markedly differently expressed during the bacterial infection. The results of the target gene prediction and enrichment analysis indicated that a total of 230 target genes involved in a large variety of signaling pathways and biological processes were mediated by the miRNAs identified in the current research. Additionally, the effects of novel-miR-56, a representative differentially expressed miRNA identified in the previous infection experiment, on the immune-related gene expression in M. rosenbergii were explored. The expression of the immune-related genes including Spätzle1(Spz1), Spz4, Toll-like receptor 1 (TLR1), TLR2, TLR3, immune deficiency (IMD), myeloid differentiation factor 88 (MyD88), anti-lipopolysaccharide factor 1 (ALF1), crustin1, as well as prophenoloxidase (proPO) was significantly repressed in the novel-miR-56-overexpressed prawns. The expression of these genes tested in the novel-miR-56-overexpressed M. rosenbergii was still signally lower than the control in the subsequent V. parahaemolyticus challenge, despite the gene expression in each treatment increased significantly after the infection. Additionally, the cumulative mortality of the agomiR-56-treated prawns was significantly higher than the other treatments post the bacterial challenge. These results suggested that novel-miR-56 might function as a negative regulator of the immune-related gene expression of M. rosenbergii in the innate immune defense against V. parahaemolyticus.
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Affiliation(s)
- Yun Li
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China
| | - Qi Xu
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China
| | - Hong Liu
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China
| | - Xilin Dai
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation Center for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China.
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Hou Y, Liao T, Zhang F, Zhang T, Wang L, Lv W, Li Z. MicroRNA transcriptome analysis reveals the immune regulatory mechanism of Crassostrea hongkongesis against Vibrio harveyi infection. FISH & SHELLFISH IMMUNOLOGY 2024; 145:109354. [PMID: 38171431 DOI: 10.1016/j.fsi.2023.109354] [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: 10/22/2023] [Revised: 12/21/2023] [Accepted: 12/29/2023] [Indexed: 01/05/2024]
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that modulate target-genes expression and play crucial roles in post-transcriptional regulation and immune system regulation. The Hong Kong oyster (Crassostrea hongkongesis), as the main marine aquaculture shellfish in the South China Sea, not only has high economic and ecological value, but also is an ideal model for conducting research on pathogen host interaction. Vibrio harveyi, a Gram negative luminescent marine bacterium, is widely distributed in coastal water environments and can cause large-scale death of C. hongkongesis. However, little in formation is available on the immune regulatory mechanisms of C. hongkongesis infected with V. harveyi. Therefore, we performed microRNA transcriptome analysis for elucidating the immunoregulation mechanism of C. hongkongesis infected with V. harveyi. The results show that a total of 308468208 clean reads and 288371159 clean tags were obtained. 222 differentially expressed miRNAs were identified. A total of 388 target genes that were differentially expressed and negatively correlated with miRNA expression were predicted by 222 DEmiRs. GO enrichment analysis of 388 DETGs showed that they were mainly enriched in the immune-related term of membrane-bounded vesicle, endocytic vesicle lumen, antigen processing and presentation of exogenous peptide antigen via MHC class I, antigen processing and presentation of peptide antigen via MHC class I, and other immune-related term. KEGG enrichment analysis showed that DETGs were mainly enriched in the Complement and coagulation cascades, Herpes simplex virus 1 infection, Bacterial invasion of epithelial cells, Antigen processing and presentation and NOD-like receptor signaling pathway. The 16 key DEmiRs and their target genes form a regulatory network for seven immune-related pathways. These results suggest that V. harveyi infection induces a complex miRNA response with wide-ranging effects on immune gene expression in the C. hongkongesis. This study explored the immune response of C. hongkongesis to V. harveyi infection at the level of miRNAs, which provides new ideas for the healthy culture and selective breeding of C. hongkongesis.
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Affiliation(s)
- Yongkang Hou
- College of Fishery, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Taoliang Liao
- College of Fishery, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Fangqi Zhang
- College of Fishery, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Teng Zhang
- College of Fishery, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Lijun Wang
- College of Fishery, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Wengang Lv
- College of Fishery, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Zhimin Li
- College of Fishery, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China.
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Peng X, Zhong Z, Zhong H, Gong J, Du T, Ding L, Lan X, Tu H, Tang Q, Xia Z, Yang G, Yi S. Histopathological observation and comparative transcriptome analysis reveal immune response mechanisms to Aeromonas dhakensis infection in Macrobrachium rosenbergii. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109151. [PMID: 37838210 DOI: 10.1016/j.fsi.2023.109151] [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: 09/15/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 10/16/2023]
Abstract
The Macrobrachium rosenbergii industry is threatened by various Aeromonas, resulting in high mortality of adult prawns. However, there are few studies on the immune response of M. rosenbergii infected with Aeromonas dhakensis. In this study, we observed the hepatopancreas and gills histopathologically, performed a comparative transcriptome analysis of the hepatopancreas, and analyzed the candidate gene expression of immune-related genes in the hemolymph, hepatopancreas, and gills of M. rosenbergii that had been infected with A. dhakensis. Histopathology revealed the hepatopancreas was successively inflamed, followed by cellular vacuolation, lumen deformation, and finally tissue erosion; partial and severe inflammation of the gills occurred successively, and eventually the gill tissue atrophy and the gill filaments detached from the gill arch. Transcriptome analysis showed that a total of 77,742 unigenes and 8664 differentially expressed genes (DEGs), and the immune-related DEGs were mainly enriched in lysosome and phagosome pathways. In addition, 4 immune-related candidate genes (RhoA, CASP9, PKC, and DSCIGN) based on KEGG and PPI analysis were monitored at 6, 12, and 24h post injection (hpi) in hepatopancreas, hemolymph and gills. Their spatio-temporal expression results indicated that A. dhakensis have activated the immune system of M. rosenbergii. The present study may provide new information on the complex immune mechanism of M. rosenbergii.
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Affiliation(s)
- Xin Peng
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou, 313000, China
| | - Zhenxiao Zhong
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou, 313000, China
| | - Hua Zhong
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou, 313000, China
| | - Jinlin Gong
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou, 313000, China
| | - Tingting Du
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou, 313000, China
| | - Li Ding
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou, 313000, China
| | - Xuan Lan
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou, 313000, China
| | - Haihui Tu
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou, 313000, China
| | - Qiongying Tang
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou, 313000, China.
| | - Zhenglong Xia
- Jiangsu Shufeng Prawn Breeding Co. LTD, Gaoyou, 225654, China
| | - Guoliang Yang
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou, 313000, China; Jiangsu Shufeng Prawn Breeding Co. LTD, Gaoyou, 225654, China
| | - Shaokui Yi
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou, 313000, China.
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Zhang L, Xu S, Zhang Z, Zhang X, Liu X. Transcriptomic profiling and characterization of microRNAs in Macrobrachium rosenbergii potentially involved in immune response to Enterobacter cloacae infection. Microb Pathog 2023; 183:106291. [PMID: 37557932 DOI: 10.1016/j.micpath.2023.106291] [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: 06/11/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/11/2023]
Abstract
Enterobacter cloacae is a member of the Enterobacter family, which could prevent Macrobrachium rosenbergii from growing and cause mass mortality. However, no research has focused on microRNA immunity in M. rosenbergii infected with E. cloacae. To clarify the immune response mechanisms, transcriptomic analysis was performed on the miRNAs of M. rosenbergii infected with E. cloacae YZ3 strain. Following quality screening, 10,616,712 clean reads were obtained from the control group and 12,726,421 from the infected group. Among 899 known miRNAs, 446 differentially expressed miRNAs (DEMs) were identified. Meanwhile, 59 novel miRNAs were predicted, along with 39 DEMs. Target genes of DEMs have been predicted in order to gain a deeper understanding of the immune-related functions. GO and KEGG pathway analysis revealed the biological functions and signaling pathways of target genes. The results indicated that E. cloacae significantly affected the NOD-like receptor, RIG-I-like receptor and Toll-like receptor pathways. Ten DEMs were randomly selected, and their expression level was verified by Quantitative Real-time PCR technology. Overall, this study highlights the influential role of miRNAs in the innate immune system of M. rosenbergii, which has important implications for developing new strategies to prevent and treat related diseases in the future.
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Affiliation(s)
- Liwen Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Sunan Xu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zheling Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiaojun Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.
| | - Xiaodan Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China; International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, China.
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Wang F, Zhao F, Tan A, Deng Y, Wang L, Gong H, Lai Y, Huang Z, Li F. Integrated analysis of a miRNA-mRNA network related to immunity and autophagy in Macrobrachium rosenbergii infected with Aeromonas hydrophila. FISH & SHELLFISH IMMUNOLOGY 2023; 141:109052. [PMID: 37678481 DOI: 10.1016/j.fsi.2023.109052] [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: 08/09/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/09/2023]
Abstract
MicroRNAs (miRNAs) are a group of RNAs that regulate gene expression in the post-transcriptionally. miRNAs can regulate numerous processes, such as the immune response, due to their dynamic expression patterns. The giant freshwater prawn Macrobrachium rosenbergii is a major freshwater aquaculture prawn that is attacked by various bacteria, including Aeromonas hydrophila. For this study, we performed an analysis of the miRNA and mRNA transcriptome analysis of M. rosenbergii which was infected with A. hydrophila. We identified 56 differentially expressed miRNAs (DEMs) and 1542 differentially expressed mRNAs. Furthermore, an integrated analysis of miRNA-mRNA expression led to the identification of 729 differentially predicted target genes (DETGs) of the DEMs. Multiple functional categories related to immunity, apoptosis, and autophagy were found to be enriched in the DETGs. During the infection of M. rosenbergii by A. hydrophila, an elaborate regulatory network involving Toll and immune deficiency (IMD) signaling, mitogen-activated protein kinase (MAPK) signaling, lysosome, and cell apoptosis was formed by a complex interplay of 40 crucial DEMs and 22 DETGs, all associated with the immune and autophagy pathway. The findings suggest that infection with A. hydrophila triggers intricate responses in both miRNA and mRNA, significantly impacting immune and autophagy processes in M. rosenbergii.
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Affiliation(s)
- Feifei Wang
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China; Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Fei Zhao
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
| | - Aiping Tan
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Yuting Deng
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Ling Wang
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, 526238, China
| | - Hua Gong
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Yingliao Lai
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Zhibin Huang
- Key Laboratory of Fishery Drug Development of Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Fuhua Li
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
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SiouNing AS, Seong TS, Kondo H, Bhassu S. MicroRNA Regulation in Infectious Diseases and Its Potential as a Biosensor in Future Aquaculture Industry: A Review. Molecules 2023; 28:molecules28114357. [PMID: 37298833 DOI: 10.3390/molecules28114357] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/26/2023] [Accepted: 05/03/2023] [Indexed: 06/12/2023] Open
Abstract
An infectious disease is the most apprehensive problem in aquaculture as it can lead to high mortality in aquatic organisms and massive economic loss. Even though significant progress has been accomplished in therapeutic, prevention, and diagnostic using several potential technologies, more robust inventions and breakthroughs should be achieved to control the spread of infectious diseases. MicroRNA (miRNA) is an endogenous small non-coding RNA that post-transcriptionally regulates the protein-coding genes. It involves various biological regulatory mechanisms in organisms such as cell differentiation, proliferation, immune responses, development, apoptosis, and others. Furthermore, an miRNA also acts as a mediator to either regulate host responses or enhance the replication of diseases during infection. Therefore, the emergence of miRNAs could be potential candidates for the establishment of diagnostic tools for numerous infectious diseases. Interestingly, studies have revealed that miRNAs can be used as biomarkers and biosensors to detect diseases, and can also be used to design vaccines to attenuate pathogens. This review provides an overview of miRNA biogenesis and specifically focuses on its regulation during infection in aquatic organisms, especially on the host immune responses and how miRNAs enhance the replication of pathogens in the organism. In addition to that, we explored the potential applications, including diagnostic methods and treatments, that can be employed in the aquaculture industry.
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Affiliation(s)
- Aileen See SiouNing
- Animal Genomic and Genetics Evolutionary Laboratory, Department of Genetics and Microbiology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
- Terra Aqua Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), Research Management and Innovation Complex, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Tang Swee Seong
- Terra Aqua Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), Research Management and Innovation Complex, University of Malaya, Kuala Lumpur 50603, Malaysia
- Microbial Biochemistry Laboratory, Division of Microbiology and Molecular Genetic, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Subha Bhassu
- Animal Genomic and Genetics Evolutionary Laboratory, Department of Genetics and Microbiology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
- Terra Aqua Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), Research Management and Innovation Complex, University of Malaya, Kuala Lumpur 50603, Malaysia
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