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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] [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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Zhang Y, Zhang X. Virus-Induced Histone Lactylation Promotes Virus Infection in Crustacean. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401017. [PMID: 38874057 PMCID: PMC11321649 DOI: 10.1002/advs.202401017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 06/04/2024] [Indexed: 06/15/2024]
Abstract
As "non-cellular organisms", viruses need to infect living cells to survive themselves. The virus infection must alter host's metabolisms. However, the influence of the metabolites from the altered metabolisms of virus-infected host cells on virus-host interactions remains largely unclear. To address this issue, shrimp, a representative species of crustaceans, is challenged with white spot syndrome virus (WSSV) in this study. The in vivo results presented that the WSSV infection enhanced shrimp glycolysis, leading to the accumulation of lactate. The lactate accumulation in turn promoted the site-specific histone lactylation (H3K18la and H4K12la) in a p300/HDAC1/HDAC3-dependent manner. H3K18la and H4K12la are enriched in the promoters of 75 target genes, of which the H3K18la and H4K12la modification upregulated the expression of ribosomal protein S6 kinases 2 (S6K2) in the virus-infected hosts to promote the virus infection. Further data revealed that the virus-encoded miR-N20 targeted hypoxia inducible factor-1α (HIF-1α) to inhibit the host glycolysis, leading to the suppression of H3K18la and H4K12la. Therefore, the findings contributed novel insights into the effects and the underlying mechanism of the virus-induced histone lactylation on the virus-host interactions, providing new targets for the control of virus infection.
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Affiliation(s)
- Yu Zhang
- College of Life SciencesZhejiang UniversityHangzhou310058P. R. China
- Department of Clinical PharmacologyKey Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang ProvinceAffiliated Hangzhou First People's HospitalCancer CenterWestlake University School of MedicineHangzhou310006P. R. China
| | - Xiaobo Zhang
- College of Life SciencesZhejiang UniversityHangzhou310058P. R. China
- Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao)Qingdao266003P. R. China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Zhuhai519000P. R. China
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3
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Alam MS, Islam MN, Das M, Islam SF, Rabbane MG, Karim E, Roy A, Alam MS, Ahmed R, Kibria ASM. RNAi-Based Therapy: Combating Shrimp Viral Diseases. Viruses 2023; 15:2050. [PMID: 37896827 PMCID: PMC10612085 DOI: 10.3390/v15102050] [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: 08/11/2023] [Revised: 09/18/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Shrimp aquaculture has become a vital industry, meeting the growing global demand for seafood. Shrimp viral diseases have posed significant challenges to the aquaculture industry, causing major economic losses worldwide. Conventional treatment methods have proven to be ineffective in controlling these diseases. However, recent advances in RNA interference (RNAi) technology have opened new possibilities for combating shrimp viral diseases. This cutting-edge technology uses cellular machinery to silence specific viral genes, preventing viral replication and spread. Numerous studies have shown the effectiveness of RNAi-based therapies in various model organisms, paving the way for their use in shrimp health. By precisely targeting viral pathogens, RNAi has the potential to provide a sustainable and environmentally friendly solution to combat viral diseases in shrimp aquaculture. This review paper provides an overview of RNAi-based therapy and its potential as a game-changer for shrimp viral diseases. We discuss the principles of RNAi, its application in combating viral infections, and the current progress made in RNAi-based therapy for shrimp viral diseases. We also address the challenges and prospects of this innovative approach.
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Affiliation(s)
- Md. Shahanoor Alam
- Department of Genetics and Fish Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh;
| | - Mohammad Nazrul Islam
- Department of Biotechnology, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh;
| | - Mousumi Das
- Department of Aquaculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh;
| | - Sk. Farzana Islam
- Department of Fisheries (DoF), Government of the People’s Republic of Bangladesh, Matshya Bhaban, Ramna, Dhaka 1000, Bangladesh; (S.F.I.); (R.A.)
| | - Md. Golam Rabbane
- Department of Fisheries, Faculty of Biological Sciences, University of Dhaka, Dhaka 1000, Bangladesh;
| | - Ehsanul Karim
- Bangladesh Fisheries Research Institute, Mymensingh 2201, Bangladesh;
| | - Animesh Roy
- Department of Fisheries Biology and Aquatic Environment, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh;
| | - Mohammad Shafiqul Alam
- Department of Genetics and Fish Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh;
| | - Raju Ahmed
- Department of Fisheries (DoF), Government of the People’s Republic of Bangladesh, Matshya Bhaban, Ramna, Dhaka 1000, Bangladesh; (S.F.I.); (R.A.)
| | - Abu Syed Md. Kibria
- Department of Aquaculture, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh;
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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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Gong Y, Zhang X. RNAi-based antiviral immunity of shrimp. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 115:103907. [PMID: 33122015 DOI: 10.1016/j.dci.2020.103907] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/26/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Abstract
As a kind of important economic marine crustaceans in aquaculture, shrimp can be infected by more than 20 viruses. To fight against the virus invasion, shrimp have developed the innate immunity, including RNA interference (RNAi). RNAi, mediated by short interfering RNAs (siRNAs) or microRNAs (miRNAs), plays important roles in virus-host interactions. At present, RNAi is considered to be an efficient antiviral response of shrimp. The siRNA-based RNAi, first recognized as an antiviral response of animals to resist RNA viruses, has emerged in animals as an efficient antiviral strategy against the invasion of DNA viruses and RNA viruses. In shrimp, as well as in other animals, siRNA contains a seed region (2nd-7th nt) and a supplementary region (12th-17th nt). Based on the findings in shrimp and other animals, miRNAs are essential regulators of virus-host interactions, such as virus infection/latency, and host apoptosis, autophagy and phagocytosis. Except for the seed sequence (2nd-7th), the complementary bases (to the target mRNA sequence) of a miRNA 9th-18th non-seed sequence are essential for the miRNA targeting. So far, rapidly growing evidences have supported the existence of functional RNAi machinery in shrimp. In this review, we summarize the progress of RNAi in the antiviral immune response of shrimp. The potential applications of RNAi to control shrimp diseases were also summarized.
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Affiliation(s)
- Yi Gong
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, People's Republic of China
| | - Xiaobo Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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6
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Cui Y, Wan H, Zhang X. miRNA in food simultaneously controls animal viral disease and human tumorigenesis. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:995-1006. [PMID: 33614246 PMCID: PMC7868940 DOI: 10.1016/j.omtn.2021.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/14/2021] [Indexed: 12/11/2022]
Abstract
During virus infection in animals, the virus completes its life cycle in a host cell. A virus infection results in the metabolic deregulation of its host and leads to metabolic disorders, ultimately paving the way for cancer progression. Because metabolic disorders in virus infections occurring in animal are similar to metabolic disorders in human tumorigenesis, animal antiviral microRNAs (miRNAs), which maintain the metabolic homeostasis of animal cells, in essence, may have anti-tumor activity in humans. However, that issue has not been investigated. In this study, shrimp miR-34, a potential antiviral miRNA of shrimp against white spot syndrome virus (WSSV) infection, was identified. Overexpression of shrimp miR-34 in shrimp fed bacteria expressing miR-34 suppressed WSSV infection by targeting the viral wsv330 and wsv359 genes. Furthermore, the expression of shrimp miR-34 in mice fed miR-34-overexpressing shrimp suppressed breast cancer progression by targeting human CCND1, CDK6, CCNE2, E2F3, FOSL1, and MET genes. Therefore, our study suggests that the miRNAs in food could be an effective strategy for synchronously controlling viral diseases of economic animals and cancers in humans.
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Affiliation(s)
- Yalei Cui
- College of Life Sciences and Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Haitao Wan
- College of Life Sciences and Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Xiaobo Zhang
- College of Life Sciences and Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, Zhejiang University, Hangzhou 310058, People's Republic of China
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7
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He JH, Xia Q, Weng S, He J, Xu X. Identification of infectious spleen and kidney necrosis virus (ISKNV)-encoded microRNAs. Virus Genes 2020; 56:724-733. [PMID: 33033882 DOI: 10.1007/s11262-020-01798-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/25/2020] [Indexed: 10/23/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that post-transcriptionally regulate gene expression by complementary binding to target mRNAs. Virus-encoded miRNAs play important roles in virus life cycle and virus-host interactions. Viruses from the Megalocytivirus genus, family Iridoviridae, infect a wide range of fishes, bringing great challenges to aquaculture. Infectious spleen and kidney necrosis virus (ISKNV) is the type species of the Megalocytivirus genus. In this study, using Illumina sequencing coupled with miRNA precursor prediction and stem-loop real-time PCR, 14 putative ISKNV-encoded miRNAs were preliminarily identified from ISKNV-infected mandarin fish MFF-1 cells. To initially study their functions, inhibitors of the 14 viral miRNAs were synthesized and transfected into MFF-1 cells, which were further infected with ISKNV. The results showed that these viral miRNAs could affect the virus titers in the supernatant of ISKNV-infected cells and the expression of major capsid protein (MCP). Moreover, we observed that inhibition of several ISKNV miRNAs had different effects on MCP expression and on titer of released virus, suggesting complex roles of viral miRNAs in ISKNV infection. The current study may provide a fundamental information for further identification and functional studies on miRNAs encoded by Megalocytivirus.
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Affiliation(s)
- Jian-Hui He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Qiong Xia
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, People's Republic of China.,Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Jianguo He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China. .,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, People's Republic of China. .,Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, People's Republic of China.
| | - Xiaopeng Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China. .,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, People's Republic of China. .,Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, People's Republic of China.
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8
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Rosani U, Abbadi M, Green T, Bai CM, Turolla E, Arcangeli G, Wegner KM, Venier P. Parallel analysis of miRNAs and mRNAs suggests distinct regulatory networks in Crassostrea gigas infected by Ostreid herpesvirus 1. BMC Genomics 2020; 21:620. [PMID: 32912133 PMCID: PMC7488030 DOI: 10.1186/s12864-020-07026-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/25/2020] [Indexed: 12/17/2022] Open
Abstract
Background Since 2008, the aquaculture production of Crassostrea gigas was heavily affected by mass mortalities associated to Ostreid herpesvirus 1 (OsHV-1) microvariants worldwide. Transcriptomic studies revealed the major antiviral pathways of the oyster immune response while other findings suggested that also small non-coding RNAs (sncRNA) such as microRNAs might act as key regulators of the oyster response against OsHV-1. To explore the explicit connection between small non-coding and protein-coding transcripts, we performed paired whole transcriptome analysis of sncRNA and messenger RNA (mRNA) in six oysters selected for different intensities of OsHV-1 infection. Results The mRNA profiles of the naturally infected oysters were mostly governed by the transcriptional activity of OsHV-1, with several differentially expressed genes mapping to the interferon, toll, apoptosis, and pro-PO pathways. In contrast, miRNA profiles suggested more complex regulatory mechanisms, with 15 differentially expressed miRNAs (DE-miRNA) pointing to a possible modulation of the host response during OsHV-1 infection. We predicted 68 interactions between DE-miRNAs and oyster 3′-UTRs, but only few of them involved antiviral genes. The sncRNA reads assigned to OsHV-1 rather resembled mRNA degradation products, suggesting the absence of genuine viral miRNAs. Conclusions We provided data describing the miRNAome during OsHV-1 infection in C. gigas. This information can be used to understand the role of miRNAs in healthy and diseased oysters, to identify new targets for functional studies and, eventually to disentangle cause and effect relationships during viral infections in marine mollusks.
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Affiliation(s)
- Umberto Rosani
- Department of Biology, University of Padova, 35121, Padova, Italy. .,Coastal Ecology Section, AWI - Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Wadden Sea Station Sylt, 25992, List, Germany.
| | - Miriam Abbadi
- Istituto Zooprofilattico delle Venezie, Legnaro, Italy
| | - Timothy Green
- Centre for Shellfish Research & Department of Fisheries and Aquaculture, Vancouver Island University, Nanaimo, BC, V9R 5S5, Canada
| | - Chang-Ming Bai
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | | | | | - K Mathias Wegner
- Coastal Ecology Section, AWI - Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Wadden Sea Station Sylt, 25992, List, Germany
| | - Paola Venier
- Department of Biology, University of Padova, 35121, Padova, Italy.
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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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10
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Sun Y, Zhang X. Role of DCP1-DCP2 complex regulated by viral and host microRNAs in DNA virus infection. FISH & SHELLFISH IMMUNOLOGY 2019; 92:21-30. [PMID: 31146005 DOI: 10.1016/j.fsi.2019.05.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/23/2019] [Accepted: 05/25/2019] [Indexed: 06/09/2023]
Abstract
The DCP1-DCP2 complex can regulate the antiviral immunity of animals by the decapping of retrovirus RNAs and the suppression of RNAi during RNA virus infection. However, the influence of DCP1-DCP2 complex on DNA virus infection and the regulation of DCP1-DCP2 complex by microRNAs (miRNAs) remain unclear. In this study, the role of miRNA-regulated DCP1-DCP2 complex in DNA virus infection was characterized. Our results showed that the DCP1-DCP2 complex played a positive role in the infection of white spot syndrome virus (WSSV), a DNA virus of shrimp. In the DCP1-DCP2 complex, the N-terminal regulatory domain of DCP2 was interacted with the EVH1 domain of DCP1. Furthermore, shrimp miRNA miR-87 inhibited WSSV infection by targeting the host DCP2 gene and viral miRNA WSSV-miR-N46 took a negative effect on WSSV replication by targeting the host DCP1 gene. Therefore, our study provided novel insights into the underlying mechanism of DCP1-DCP2 complex and its regulation by miRNAs in virus-host interactions. IMPORTANCE: During RNA virus infection, the DCP1-DCP2 complex can play important roles in the animal antiviral immunity by decapping retrovirus RNAs and suppressing RNAi. In the present study, the findings indicated that the silencing of DCP1 and DCP2 inhibited the infection of WSSV, a DNA virus of shrimp, suggesting that the DCP1-DCP2 complex facilitated DNA virus infection. Due to the suppressive role of the DCP1-DCP2 complex in shrimp RNAi against WSSV infection, the DCP1-DCP2 complex could promote WSSV infection in shrimp. The results showed that WSSV-miR-N46 and shrimp miR-87 could respectively suppress the expressions of DCP1 and DCP2 to affect virus infection. Therefore, our study contributed novel aspects of the DCP1-DCP2 complex and its regulation by miRNAs in virus-host interactions.
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Affiliation(s)
- Yuechao Sun
- College of Life Sciences and Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xiaobo Zhang
- College of Life Sciences and Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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11
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Encinas-García T, Mendoza-Cano F, Porchas-Cornejo M, Peña-Rodríguez A, Enríquez-Espinoza T, Sánchez-Paz A. The white spot syndrome virus hijacks the expression of the Penaeus vannamei Toll signaling pathway to evade host immunity and facilitate its replication. FISH & SHELLFISH IMMUNOLOGY 2019; 92:905-912. [PMID: 31302285 DOI: 10.1016/j.fsi.2019.07.026] [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: 05/20/2019] [Revised: 07/03/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
The white spot syndrome virus (WSSV), the most lethal pathogen of shrimp, is a dsDNA virus with approximately a 300,000 base pairs and contains approximately 180-500 predicted open reading frames (ORFs), of which only 6% show homology to any known protein from other viruses or organisms. Although most of its ORFs encode enzymes for nucleotide metabolism, DNA replication, and protein modification, the WSSV uses some of its encoded proteins successfully to take control of the metabolism of the host and avoid immune responses. The contribution of the shrimp innate immune response to prevent viral invasions is recognized but yet not fully understood. Thus, the role of several components of Toll pathway of the shrimp Penaeus vannamei against WSSV has been previously described, and the consequential effects occurring through the cascade remain unknown. In the current study the effects of WSSV over various components of the shrimp Toll pathway were studied. The gene expression of Spätzle, Toll, Tube, Cactus and Dorsal was altered after 6-12 h post inoculation. The expression of LvToll3, LvCactus, LvDorsal, decreased ~4.4-, ~3.7- and ~7.3-fold at 48, 24 and 48 hpi, respectively. Furthermore, a remarkable reduction (~18-fold) in the expression of the gene encoding LvCactus in WSSV infected specimens was observed at 6 hpi. This may be a sophisticated strategy exploited by WSSV to evade the Toll-mediated immune action, and to promote its replication, thereby contributing to viral fitness.
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Affiliation(s)
- Trinidad Encinas-García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Laboratorio de Análisis, Referencia y Diagnóstico en Sanidad Acuícola, Calle Hermosa, 101. Col. Los Ángeles, Hermosillo, Sonora, C. P. 83106, Mexico
| | - Fernando Mendoza-Cano
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Laboratorio de Análisis, Referencia y Diagnóstico en Sanidad Acuícola, Calle Hermosa, 101. Col. Los Ángeles, Hermosillo, Sonora, C. P. 83106, Mexico
| | - Marco Porchas-Cornejo
- Centro de Investigaciones Biológicas del Noroeste, S.C. Km 2.35 Carretera a Las Tinajas, S/N Colonia Tinajas, Guaymas, Sonora, C.P. 85460, Mexico
| | - Alberto Peña-Rodríguez
- CONACyT, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), IPN 195, Col. Playa Palo de Santa Rita, La Paz, BCS, 23096, Mexico
| | - Tania Enríquez-Espinoza
- Universidad Estatal de Sonora. Unidad Académica Hermosillo, Ley Federal del Trabajo s/n, Hermosillo, Sonora, C. P. 83100, Mexico
| | - Arturo Sánchez-Paz
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Laboratorio de Análisis, Referencia y Diagnóstico en Sanidad Acuícola, Calle Hermosa, 101. Col. Los Ángeles, Hermosillo, Sonora, C. P. 83106, Mexico.
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12
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Li C, Weng S, He J. WSSV-host interaction: Host response and immune evasion. FISH & SHELLFISH IMMUNOLOGY 2019; 84:558-571. [PMID: 30352263 DOI: 10.1016/j.fsi.2018.10.043] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/15/2018] [Accepted: 10/20/2018] [Indexed: 06/08/2023]
Abstract
As invertebrates, shrimps rely on multiple innate defense reactions, including humoral immunity and cellular immunity to recognize and eliminate various invaders, such as viruses. White spot syndrome virus (WSSV) causes the most prevalent and devastating viral disease in penaeid shrimps, which are the most widely cultured species in the coastal waters worldwide. In the last couple of decades, studies about WSSV implicate a dual role of the immune system in protecting shrimps against the infection; these studies also explore on the pathogenesis of WSSV infection. Herein, we review our current knowledge of the innate immune responses of shrimps to WSSV, as well as the molecular mechanisms used by this virus to evade host immune responses or actively subvert them for its own benefit. Deciphering the interactions between WSSV and the shrimp host is paramount to understanding the mechanisms that regulate the balance between immune-mediated protection and pathogenesis during viral infection and to the development of a safe and effective WSSV defensive strategy.
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Affiliation(s)
- Chaozheng Li
- State Key Laboratory for Biocontrol / School of Marine Sciences, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, Guangzhou, PR China
| | - Shaoping Weng
- State Key Laboratory for Biocontrol / School of Marine Sciences, Sun Yat-sen University, Guangzhou, PR China; School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, Guangzhou, PR China
| | - Jianguo He
- State Key Laboratory for Biocontrol / School of Marine Sciences, Sun Yat-sen University, Guangzhou, PR China; School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, Guangzhou, PR China.
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13
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Nucleic Acid Sensing in Invertebrate Antiviral Immunity. NUCLEIC ACID SENSING AND IMMUNITY - PART B 2019; 345:287-360. [DOI: 10.1016/bs.ircmb.2018.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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14
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Gong Y, Ju C, Zhang X. Shrimp miR-1000 Functions in Antiviral Immunity by Simultaneously Triggering the Degradation of Two Viral mRNAs. Front Immunol 2018; 9:2999. [PMID: 30619352 PMCID: PMC6305465 DOI: 10.3389/fimmu.2018.02999] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 12/04/2018] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) function as crucial suppressors of gene expression via translational repression or direct mRNA degradation. However, the mechanism of multi-gene regulation by a host miRNA in antiviral immunity has not been extensively explored. In this study, the regulation of two white spot syndrome virus (WSSV) genes by its host (Marsupenaeus japonicus shrimp) miRNA (shrimp miR-1000) was characterized. The miRNA target gene prediction showed that only two virus genes (wsv191 and wsv407) might be the targets of miR-1000. The results of insect cell transfection assays revealed that shrimp miR-1000 could target multiple virus genes (wsv191 and wsv407). The mRNA degradation analysis and RNA FISH (fluorescence in situ hybridization) analysis indicated that miR-1000 triggered the mRNA degradation of target genes through 5′-3′ exonucleolytic digestion in vivo and thereby inhibited the virus infection in shrimp. The miRNA-mediated 5′-3′ exonucleolytic digestion of target mRNAs stopped near the 3′UTR (3′untranslated region) sequence complementary to the seed sequence of miR-1000. Therefore, our study provided novel insights into how a host miRNA targeted multiple viral genes and prevented host from virus infection.
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Affiliation(s)
- Yi Gong
- Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chenyu Ju
- Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaobo Zhang
- Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, College of Life Sciences, Zhejiang University, Hangzhou, China
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15
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Huang JY, Kang ST, Chen IT, Chang LK, Lin SS, Kou GH, Chu CY, Lo CF. Shrimp miR-10a Is Co-opted by White Spot Syndrome Virus to Increase Viral Gene Expression and Viral Replication. Front Immunol 2017; 8:1084. [PMID: 28932224 PMCID: PMC5592198 DOI: 10.3389/fimmu.2017.01084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 08/21/2017] [Indexed: 12/18/2022] Open
Abstract
Members of the microRNA miR-10 family are highly conserved and play many important roles in diverse biological mechanisms, including immune-related responses and cancer-related processes in certain types of cancer. In this study, we found the most highly upregulated shrimp microRNA from Penaeus vannamei during white spot syndrome virus (WSSV) infection was miR-10a. After confirming the expression level of miR-10a by northern blot and quantitative RT-PCR, an in vivo experiment showed that the viral copy number was decreased in miR-10a-inhibited shrimp. We found that miR-10a targeted the 5′ untranslated region (UTR) of at least three viral genes (vp26, vp28, and wssv102), and plasmids that were controlled by the 5′ UTR of these genes produced enhanced luciferase signals in transfected SF9 cells. These results suggest a previously unreported role for shrimp miR-10a and even a new type of host–virus interaction, whereby a co-opts the key cellular regulator miR-10a to globally enhance the translation of viral proteins.
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Affiliation(s)
- Jiun-Yan Huang
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.,Center for Shrimp Disease Control and Genetic Improvement, National Cheng Kung University, Tainan, Taiwan.,Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Shih-Ting Kang
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.,Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - I-Tung Chen
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.,Center for Shrimp Disease Control and Genetic Improvement, National Cheng Kung University, Tainan, Taiwan
| | - Li-Kwan Chang
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Guang-Hsiung Kou
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Chia-Ying Chu
- Department of Life Science, National Taiwan University, Taipei, Taiwan.,Center for Systems Biology, National Taiwan University, Taipei, Taiwan
| | - Chu-Fang Lo
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.,Center for Shrimp Disease Control and Genetic Improvement, National Cheng Kung University, Tainan, Taiwan
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16
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Yang F, Wei J, Zhang S, Zhang X. Shrimp miR-S8 Suppresses the Stemness of Human Melanoma Stem-like Cells by Targeting the Transcription Factor YB-1. Cancer Res 2017; 77:5543-5553. [PMID: 28855207 DOI: 10.1158/0008-5472.can-17-1375] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/01/2017] [Accepted: 08/22/2017] [Indexed: 11/16/2022]
Abstract
Cross-species regulation of gene expression by microRNA is a possible untapped opportunity for miRNA-based therapy. In this study, we report a novel approach to ablate melanoma stem-like cells by targeting the transcription factor YB-1, which is significantly and selectively upregulated in these cells in melanoma. Silencing YB-1 expression was sufficient to significantly inhibit the stemness of melanoma stem-like cells. In exploring YB-1 targeting, we discovered that the shrimp microRNA miR-S8 could suppress human YB-1 expression in melanoma stem-like cells. Mechanistic investigations revealed that miR-S8 recognized the 3'UTR of YB-1 mRNA and mediated its degradation. In tumor cell and xenograft experiments, miR-S8 suppressed the tumorigenic capacity of melanoma stem-like cells by targeting human YB-1. Overall, our results illuminated a novel aspect of miRNA-mediated cross-species gene expression and its use in regulating cancer stem-like cells. Cancer Res; 77(20); 5543-53. ©2017 AACR.
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Affiliation(s)
- Fan Yang
- College of Life Sciences and Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, Zhejiang University, Hangzhou, People's Republic of China
| | - Jun Wei
- College of Life Sciences and Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, Zhejiang University, Hangzhou, People's Republic of China
| | - Song Zhang
- College of Life Sciences and Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, Zhejiang University, Hangzhou, People's Republic of China
| | - Xiaobo Zhang
- College of Life Sciences and Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, Zhejiang University, Hangzhou, People's Republic of China.
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17
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Shu L, Zhang X. Shrimp miR-12 Suppresses White Spot Syndrome Virus Infection by Synchronously Triggering Antiviral Phagocytosis and Apoptosis Pathways. Front Immunol 2017; 8:855. [PMID: 28824612 PMCID: PMC5534442 DOI: 10.3389/fimmu.2017.00855] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/06/2017] [Indexed: 01/04/2023] Open
Abstract
Growing evidence has indicated that the innate immune system can be regulated by microRNAs (miRNAs). However, the mechanism underlying miRNA-mediated simultaneous activation of multiple immune pathways remains unknown. To address this issue, the role of host miR-12 in shrimp (Marsupenaeus japonicus) antiviral immune responses was characterized in the present study. The results indicated that miR-12 participated in virus infection, host phagocytosis, and apoptosis in defense against white spot syndrome virus invasion. miR-12 could simultaneously trigger phagocytosis, apoptosis, and antiviral immunity through the synchronous downregulation of the expression of shrimp genes [PTEN (phosphatase and tensin homolog) and BI-1(transmembrane BAX inhibitor motif containing 6)] and the viral gene (wsv024). Further analysis showed that miR-12 could synchronously mediate the 5′–3′ exonucleolytic degradation of its target mRNAs, and this degradation terminated in the vicinity of the 3′ untranslated region sequence complementary to the seed sequence of miR-12. Therefore, the present study showed novel aspects of the miRNA-mediated simultaneous regulation of multiple immune pathways.
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Affiliation(s)
- Le Shu
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, Zhejiang University, Hangzhou, China
| | - Xiaobo Zhang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, Zhejiang University, Hangzhou, China
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18
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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19
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Liao X, Yang L, Zhang Q, Chen J. microRNA expression changes after lipopolysaccharide treatment in gills of amphioxus Branchiostoma belcheri. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 70:39-44. [PMID: 28069432 DOI: 10.1016/j.dci.2017.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 01/05/2017] [Accepted: 01/05/2017] [Indexed: 06/06/2023]
Abstract
Recently, amphioxus has served as a model for studying the origin and evolution of vertebrate immunity. However, little is known about how microRNAs (miRNAs) are involved in the immune defense in amphioxus. In this article, we identified the amphioxus miRNAs in the acute-phase response to lipopolysaccharide (LPS). We determined the time point for the peak of immune response in amphioxus after LPS challenge by evaluating the expression of Branchiostoma belcheri toll-like receptor 1, NF-κb (c-Rel), and big defensin which react with pathogen-associated molecular patterns(PAMPs). Then we chose 12 h as the point to perform miRNA microarray analysis to select the differentially expressed miRNAs. Furthermore, we used quantitative real-time PCR to detect the expression patterns of selected amphioxus miRNAs under effective LPS challenge during the time course. The microarray data revealed that the miRNA expression file was significantly changed after LPS stimulation. The changes of the 10 most upregulated and 7 most downregualted miRNAs in gills of the amphioxus following challenge with LPS revealed a temporal induction kinetic. Our current study will provide valuable information to take an insight into molecular mechanism of innate immune and the evolution of the miRNA family.
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Affiliation(s)
- Xin Liao
- School of Life Sciences, Nanjing University, China; Beihai Marine Station of Evo-devo Institute, Nanjing University, China
| | - Liu Yang
- Department of Biomedical Research Center, The First People's Hospital of Kunming, China
| | - Qilin Zhang
- School of Life Sciences, Nanjing University, China; Beihai Marine Station of Evo-devo Institute, Nanjing University, China
| | - Junyuan Chen
- Beihai Marine Station of Evo-devo Institute, Nanjing University, China; Nanjing Institute of Geology and Paleontology, Nanjing, China.
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20
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Chen W, Yi L, Feng S, Zhao L, Li J, Zhou M, Liang R, Gu N, Wu Z, Tu J, Lin L. Characterization of microRNAs in orange-spotted grouper (Epinephelus coioides) fin cells upon red-spotted grouper nervous necrosis virus infection. FISH & SHELLFISH IMMUNOLOGY 2017; 63:228-236. [PMID: 28232192 DOI: 10.1016/j.fsi.2017.02.031] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Revised: 02/17/2017] [Accepted: 02/18/2017] [Indexed: 06/06/2023]
Abstract
Nervous necrosis virus (NNV), one of the most prevalent fish pathogens, has caused fatal disease of viral nervous necrosis (VNN) in many marine and freshwater fishes, and resulted in heavy economic losses in aquaculture industry worldwide. However, the molecular mechanisms underlying the pathogenicity of NNV remain elusive. In this study, the expression profiles of microRNA (miRNA) were investigated in grouper fin (GF-1) cells infected with red-spotted grouper nervous necrosis virus (RGNNV) via deep sequencing technique. The results showed that a total of 220 miRNAs were identified by aligning the small RNA sequences with the miRNA database of zebrafish, and 18 novel miRNAs were predicted using miRDeep2 software. Compared with the non-infected groups, 51 and 16 differentially expressed miRNAs (DE-miRNAs) were identified in the samples infected with RGNNV at 3 and 24 h, respectively. Six DE-miRNAs were randomly selected to validate their expressions using quantitative reverse transcription polymerase chain reaction (qRT-PCR), the results showed that their expression profiles were consistent with those obtained by deep sequencing. The target genes of the DE-miRNAs covered a wide range of functions, such as regulation of transcription, oxidation-reduction process, proteolysis, regulation of apoptotic process, and immune response. In addition, the effects of four DE-miRNAs including miR-1, miR-30b, miR-150, and miR-184 on RGNNV replication were evaluated, and the results showed that over-expression of each of the four miRNAs promoted the replication of RGNNV. These data provide insight into the molecular mechanism of RGNNV infection, and will benefit for the development of effective strategies to control RGNNV infection.
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Affiliation(s)
- Wenjie Chen
- College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China; Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Lizhu Yi
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Shuangshuang Feng
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Lijuan Zhao
- College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China; Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jun Li
- College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China; School of Biological Sciences, Lake Superior State University, Sault Ste. Marie, MI 49783, USA
| | - Meng Zhou
- College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Rishen Liang
- College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Na Gu
- College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Zaohe Wu
- College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Jiagang Tu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Li Lin
- College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China; Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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21
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Two White Spot Syndrome Virus MicroRNAs Target the Dorsal Gene To Promote Virus Infection in Marsupenaeus japonicus Shrimp. J Virol 2017; 91:JVI.02261-16. [PMID: 28179524 DOI: 10.1128/jvi.02261-16] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 01/27/2017] [Indexed: 01/10/2023] Open
Abstract
In eukaryotes, microRNAs (miRNAs) serve as regulators of many biological processes, including virus infection. An miRNA can generally target diverse genes during virus-host interactions. However, the regulation of gene expression by multiple miRNAs has not yet been extensively explored during virus infection. This study found that the Spaztle (Spz)-Toll-Dorsal-antilipopolysaccharide factor (ALF) signaling pathway plays a very important role in antiviral immunity against invasion of white spot syndrome virus (WSSV) in shrimp (Marsupenaeus japonicus). Dorsal, the central gene in the Toll pathway, was targeted by two viral miRNAs (WSSV-miR-N13 and WSSV-miR-N23) during WSSV infection. The regulation of Dorsal expression by viral miRNAs suppressed the Spz-Toll-Dorsal-ALF signaling pathway in shrimp in vivo, leading to virus infection. Our study contributes novel insights into the viral miRNA-mediated Toll signaling pathway during the virus-host interaction.IMPORTANCE An miRNA can target diverse genes during virus-host interactions. However, the regulation of gene expression by multiple miRNAs during virus infection has not yet been extensively explored. The results of this study indicated that the shrimp Dorsal gene, the central gene in the Toll pathway, was targeted by two viral miRNAs during infection with white spot syndrome virus. Regulation of Dorsal expression by viral miRNAs suppressed the Spz-Toll-Dorsal-ALF signaling pathway in shrimp in vivo, leading to virus infection. Our study provides new insight into the viral miRNA-mediated Toll signaling pathway in virus-host interactions.
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22
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Zhao MR, Meng C, Xie XL, Li CH, Liu HP. Characterization of microRNAs by deep sequencing in red claw crayfish Cherax quadricarinatus haematopoietic tissue cells after white spot syndrome virus infection. FISH & SHELLFISH IMMUNOLOGY 2016; 59:469-483. [PMID: 27825947 DOI: 10.1016/j.fsi.2016.11.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 06/06/2023]
Abstract
White spot syndrome virus (WSSV) is one of the most prevalent and widespread viruses in both shrimp and crayfish aquaculture. MicroRNAs (miRNAs) are crucial post-transcriptional regulators and play critical roles in cell differentiation and proliferation, apoptosis, signal transduction and immunity. In this study, miRNA expression profiles were identified via deep sequencing in red claw crayfish Cherax quadricarinatus haematopoietic tissue (Hpt) cell cultures infected with WSSV at both early (i.e., 1 hpi) and late (i.e., 12 hpi) infection stages. The results showed that 2 known miRNAs, namely, miR-7 and miR-184 play key roles in immunity. Meanwhile, 106 novel miRNA candidates were predicted by software in these combined miRNA transcriptomes. Compared with two control groups, 36 miRNAs showed significantly different expression levels after WSSV challenge. Furthermore, 10 differentially expressed miRNAs in WSSV-exposed Hpt cells were randomly selected for expression analysis by quantitative real-time RT-PCR. Consistent with the expression profiles identified by deep sequencing, RT-PCR showed a significant increase or decrease in miRNA expression in Hpt cells after WSSV infection. Prediction of targets of miRNAs such as miR-7, cqu-miR-52, cqu-miR-126 and cqu-miR-141 revealed that their target genes have diverse biological roles, including not only immunity but also transcriptional regulation, energy metabolism, cell communication, cell differentiation, cell death, autophagy, endocytosis and apoptosis. These results provide insight into the molecular mechanism of WSSV infection and highlight the function of miRNAs in the regulation of the immune response against WSSV infection in crustaceans.
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Affiliation(s)
- Meng-Ru Zhao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, PR China; School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, PR China
| | - Chuang Meng
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Xiao-Lu Xie
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Cheng-Hua Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, PR China.
| | - Hai-Peng Liu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, PR China; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen 361102, Fujian, PR China.
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23
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Shu L, Li C, Zhang X. The role of shrimp miR-965 in virus infection. FISH & SHELLFISH IMMUNOLOGY 2016; 54:427-434. [PMID: 27134077 DOI: 10.1016/j.fsi.2016.04.129] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 04/25/2016] [Accepted: 04/27/2016] [Indexed: 06/05/2023]
Abstract
RNAi, mediated by microRNAs (miRNAs), has attracted increasing attention for its important role in cross-talk between host and virus. However, the role of host miRNA in the virus infection in vivo has not been intensively investigated. In this study, the effects of a shrimp miRNA (miR-965) on the white spot syndrome virus (WSSV) infection were characterized. The results indicated that the expression of miR-965 was significantly upregulated in shrimp in response to the WSSV challenge, suggesting its involvement in the virus infection. The miR-965 silencing led to significant increases of WSSV copies and virus-infected shrimp mortality, while the miR-965 overexpression resulted in the decreased WSSV copies and virus-infected shrimp mortality, indicating that miR-965 played a negative role in the WSSV infection. The further data revealed that miR-965 inhibited the virus infection by targeting the viral wsv240 gene, an important gene required for the WSSV infection in shrimp. The results demonstrated that miR-965 could promote the shrimp phagocytosis against virus infection by targeting the shrimp ATG5 (autophagy related 5) gene. Therefore, our findings presented novel evidence to better understand the anfractuous host-virus interactions in vivo.
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Affiliation(s)
- Le Shu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Changrun Li
- Institute of Health Sciences, Anhui University, People's Republic of China.
| | - Xiaobo Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China.
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24
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Kaewkascholkul N, Somboonviwat K, Asakawa S, Hirono I, Tassanakajon A, Somboonwiwat K. Shrimp miRNAs regulate innate immune response against white spot syndrome virus infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 60:191-201. [PMID: 26945623 DOI: 10.1016/j.dci.2016.03.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/01/2016] [Accepted: 03/01/2016] [Indexed: 06/05/2023]
Abstract
MicroRNAs are short noncoding RNAs of RNA interference pathways that regulate gene expression through partial complementary base-pairing to target mRNAs. In this study, miRNAs that are expressed in white spot syndrome virus (WSSV)-infected Penaeus monodon, were identified using next generation sequencing. Forty-six miRNA homologs were identified from WSSV-infected shrimp hemocyte. Stem-loop real-time RT-PCR analysis showed that 11 out of 16 selected miRNAs were differentially expressed upon WSSV infection. Of those, pmo-miR-315 and pmo-miR-750 were highly responsive miRNAs. miRNA target prediction revealed that the miRNAs were targeted at 5'UTR, ORF, and 3'UTR of several immune-related genes such as genes encoding antimicrobial peptides, signaling transduction proteins, heat shock proteins, oxidative stress proteins, proteinases or proteinase inhibitors, proteins in blood clotting system, apoptosis-related proteins, proteins in prophenoloxidase system, pattern recognition proteins and other immune molecules. The highly conserved miRNA homolog, pmo-bantam, was characterized for its function in shrimp. The pmo-bantam was predicted to target the 3'UTR of Kunitz-type serine protease inhibitor (KuSPI). Binding of pmo-bantam to the target sequence of KuSPI gene was analyzed by luciferase reporter assay. Correlation of pmo-bantam and KuSPI expression was observed in lymphoid organ of WSSV-infected shrimp. These results implied that miRNAs might play roles as immune gene regulators in shrimp antiviral response.
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Affiliation(s)
- Napol Kaewkascholkul
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Kulwadee Somboonviwat
- Software Engineering Program, International College, King Mongkut's Institute of Technology Ladkrabang, Chalongkrung Road, Ladkrabang, Bangkok 10520, Thailand
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Minato-ku, Tokyo, Japan
| | - Anchalee Tassanakajon
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand; Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Kunlaya Somboonwiwat
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand; Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand.
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25
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Virus-derived small RNAs in the penaeid shrimp Fenneropenaeus chinensis during acute infection of the DNA virus WSSV. Sci Rep 2016; 6:28678. [PMID: 27349643 PMCID: PMC4923869 DOI: 10.1038/srep28678] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 06/06/2016] [Indexed: 01/16/2023] Open
Abstract
Small interfering RNAs (siRNAs) and microRNAs (miRNAs) are two classes of small RNAs (sRNAs) that are critical for virus-host interplay via the RNA interference (RNAi) pathway. One virus-derived siRNA and numerous miRNAs has been reported for the double-stranded DNA virus white spot syndrome virus (WSSV), however, the expression profiles of these different types of sRNAs have not been assessed. Here, by sequencing the sRNAs and mRNAs of WSSV-infected Chinese shrimp (Fenneropenaeus chinensis), we found that the viral transcripts were universally targeted by WSSV-derived siRNAs, supporting a pivotal role for RNAi in the anti-viral immunity of shrimp. The genesis of WSSV-derived siRNAs was associated with long RNA structures. Moreover, by separating miRNAs from siRNAs, 12 WSSV miRNAs were identified. Investigation of conserved viral miRNA targets in different host species indicated the involvement of viral miRNAs in host immune responses. Collectively, our data provide new insights into the role of the RNAi pathway in the interplay between DNA viruses and crustaceans.
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26
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Zeng Y. The cDNA Sequence of Two Hemocyanin Subunits from Red Swamp Crayfish Procambarus clarkii and their Responses to White Spot Syndrome Virus Infection. JOURNAL OF AQUATIC ANIMAL HEALTH 2016; 28:39-45. [PMID: 26949985 DOI: 10.1080/08997659.2015.1125966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Hemocyanin, the respiratory protein of crustaceans, participates in the innate immune defense in these organisms. We cloned two hemocyanin subunit genes (PcHc1 and PcHc2), by using a degenerate primer PCR and rapid amplification of cDNA ends (RACE) approach, from the hepatopancreas of red swamp crayfish Procambarus clarkii. The transcripts of these two subunits were only detected in the hepatopancreas by reverse transcriptase quantitative PCR (RT-qPCR) analysis. The neighbor-joining and maximum parsimony phylogenetic analyses indicated that PcHc2 associated with a clade belong to the α-type hemocyanins and PcHc1 associated with another clade belonging to the β-type hemocyanins. The data obtained from the RT-qPCR indicated that the mRNA expression levels of these subunit genes followed almost the same regulation pattern in the crayfish challenged with white spot syndrome virus (WSSV). The fluctuation of mRNA expression levels of these two subunits after the WSSV challenge indicated that both of them may participate in the antiviral immune response of crayfish. Received April 12, 2015; accepted November 22, 2015.
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Affiliation(s)
- Yong Zeng
- a College of Life Science , Yantai University , Shandong 264005 , China
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27
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Verbruggen B, Bickley LK, van Aerle R, Bateman KS, Stentiford GD, Santos EM, Tyler CR. Molecular Mechanisms of White Spot Syndrome Virus Infection and Perspectives on Treatments. Viruses 2016; 8:E23. [PMID: 26797629 PMCID: PMC4728583 DOI: 10.3390/v8010023] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 12/18/2015] [Accepted: 01/06/2016] [Indexed: 02/07/2023] Open
Abstract
Since its emergence in the 1990s, White Spot Disease (WSD) has had major economic and societal impact in the crustacean aquaculture sector. Over the years shrimp farming alone has experienced billion dollar losses through WSD. The disease is caused by the White Spot Syndrome Virus (WSSV), a large dsDNA virus and the only member of the Nimaviridae family. Susceptibility to WSSV in a wide range of crustacean hosts makes it a major risk factor in the translocation of live animals and in commodity products. Currently there are no effective treatments for this disease. Understanding the molecular basis of disease processes has contributed significantly to the treatment of many human and animal pathogens, and with a similar aim considerable efforts have been directed towards understanding host-pathogen molecular interactions for WSD. Work on the molecular mechanisms of pathogenesis in aquatic crustaceans has been restricted by a lack of sequenced and annotated genomes for host species. Nevertheless, some of the key host-pathogen interactions have been established: between viral envelope proteins and host cell receptors at initiation of infection, involvement of various immune system pathways in response to WSSV, and the roles of various host and virus miRNAs in mitigation or progression of disease. Despite these advances, many fundamental knowledge gaps remain; for example, the roles of the majority of WSSV proteins are still unknown. In this review we assess current knowledge of how WSSV infects and replicates in its host, and critique strategies for WSD treatment.
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Affiliation(s)
- Bas Verbruggen
- Biosciences, College of Life & Environmental Sciences, Geoffrey Pope Building, University of Exeter, Exeter, Devon EX4, UK.
| | - Lisa K Bickley
- Biosciences, College of Life & Environmental Sciences, Geoffrey Pope Building, University of Exeter, Exeter, Devon EX4, UK.
| | - Ronny van Aerle
- European Union Reference Laboratory for Crustacean Diseases, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK.
| | - Kelly S Bateman
- European Union Reference Laboratory for Crustacean Diseases, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK.
| | - Grant D Stentiford
- European Union Reference Laboratory for Crustacean Diseases, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK.
| | - Eduarda M Santos
- Biosciences, College of Life & Environmental Sciences, Geoffrey Pope Building, University of Exeter, Exeter, Devon EX4, UK.
| | - Charles R Tyler
- Biosciences, College of Life & Environmental Sciences, Geoffrey Pope Building, University of Exeter, Exeter, Devon EX4, UK.
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28
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Ren Q, Huang Y, He Y, Wang W, Zhang X. A white spot syndrome virus microRNA promotes the virus infection by targeting the host STAT. Sci Rep 2015; 5:18384. [PMID: 26671453 PMCID: PMC4680916 DOI: 10.1038/srep18384] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/17/2015] [Indexed: 12/29/2022] Open
Abstract
JAK/STAT pathway plays an important role in invertebrates during virus infection. However the microRNA (miRNA)-mediated regulation of JAK/STAT is not intensively investigated. Viral miRNAs, encoded by virus genome, have emerged as important regulators in the virus-host interactions. In this study, a WSSV (white spot syndrome virus)-encoded miRNA (WSSV-miR-22) was characterized in shrimp during virus infection. The results showed that the viral miRNA could promote WSSV infection in shrimp by targeting the host STAT gene. When the expression of JAK or STAT was knocked down by sequence-specific siRNA, the WSSV copies in shrimp were significantly increased, indicating that the JAK/STAT played positive roles in the antiviral immunity of shrimp. The further findings revealed that TEP1 and TEP2 were the effectors of JAK-STAT signaling pathway. The silencing of TEP1 or TEP2 led to an increase of WSSV copies in shrimp, showing TEP1 and TEP2 were involved in the shrimp immune response against virus infection. Therefore our study presented a novel viral miRNA-mediated JAK/STAT-TEP1/TEP2 signaling pathway in virus infection.
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Affiliation(s)
- Qian Ren
- Key Laboratory of Animal Virology of Ministry of Agriculture and College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China.,Jiangsu Key Laboratory for Biodiversity &Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Ying Huang
- Jiangsu Key Laboratory for Biodiversity &Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Yaodong He
- Key Laboratory of Animal Virology of Ministry of Agriculture and College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Wen Wang
- Jiangsu Key Laboratory for Biodiversity &Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Xiaobo Zhang
- Key Laboratory of Animal Virology of Ministry of Agriculture and College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
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29
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Cui Y, Huang T, Zhang X. RNA editing of microRNA prevents RNA-induced silencing complex recognition of target mRNA. Open Biol 2015; 5:150126. [PMID: 26674414 PMCID: PMC4703055 DOI: 10.1098/rsob.150126] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/17/2015] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) integrate with Argonaut (Ago) to create the RNA-induced silencing complex, and regulate gene expression by silencing target mRNAs. RNA editing of miRNA may affect miRNA processing, assembly of the Ago complex and target mRNA binding. However, the function of edited miRNA, assembled within the Ago complex, has not been extensively investigated. In this study, sequence analysis of the Ago complex of Marsupenaeus japonicus shrimp infected with white spot syndrome virus (WSSV) revealed that host ADAR (adenosine deaminase acting on RNA) catalysed A-to-I RNA editing of a viral miRNA (WSSV-miR-N12) at the +16 site. This editing of the non-seed sequence did not affect association of the edited miRNA with the Ago protein, but inhibited interaction between the miRNA and its target gene (wsv399). The WSSV early gene wsv399 inhibited WSSV infection. As a result, the RNA editing of miRNA caused virus latency. Our results highlight a novel example of miRNA editing in the miRNA-induced silencing complex.
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Affiliation(s)
- Yalei Cui
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Tianzhi Huang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Xiaobo Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
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30
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Abstract
Small RNAs, 21-24 nucleotides in length, are non-coding RNAs found in most multicellular organisms, as well as in some viruses. There are three main types of small RNAs including microRNA (miRNA), small-interfering RNA (siRNA), and piwi-interacting RNA (piRNA). Small RNAs play key roles in the genetic regulation of eukaryotes; at least 50% of all eukaryote genes are the targets of small RNAs. In recent years, studies have shown that some unique small RNAs are involved in the immune response of crustaceans, leading to lower or higher immune responses to infections and diseases. SiRNAs could be used as therapy for virus infection. In this review, we provide an overview of the diverse roles of small RNAs in the immune defense mechanisms of crustaceans.
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Affiliation(s)
- Yaodong He
- Ocean College, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Chenyu Ju
- Collaborative Innovation Center of Deep-sea Biology and College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Xiaobo Zhang
- Collaborative Innovation Center of Deep-sea Biology and College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China.
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31
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Yang L, Yang G, Zhang X. The miR-100-mediated pathway regulates apoptosis against virus infection in shrimp. FISH & SHELLFISH IMMUNOLOGY 2014; 40:146-153. [PMID: 24972342 DOI: 10.1016/j.fsi.2014.06.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Revised: 05/12/2014] [Accepted: 06/17/2014] [Indexed: 06/03/2023]
Abstract
The process of programmed cell death process or apoptosis can be regulated by microRNAs, 21-25 nt short non-coding RNAs. However, a comprehensive view of apoptosis-associated miRNAs has not been intensively characterized. In this study, the shrimp miRNA microarray data showed that 199 miRNAs were involved in the regulation of apoptosis, among which 8 miRNAs were evolutionarily conserved in animals. The loss-of-function experiments in vivo in shrimp revealed that miR-100 was served as an anti-apoptosis miRNA through targeting the mRNA of trypsin gene. The results indicated that the silencing of miR-100 expression resulted in the increase of apoptotic activity of shrimp hemocytes and further led to the decreases of virus genome copies in shrimp and virus-infected shrimp mortality compared with the controls. The findings showed that miR-100-trypsin signaling pathway played an important role in the antiviral immunity by regulating apoptosis. Therefore, our study presented a novel miR-100-mediated pathway in the regulation of apoptosis.
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Affiliation(s)
- Lu Yang
- Key Laboratory of Animal Virology of Ministry of Agriculture and College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Geng Yang
- Key Laboratory of Animal Virology of Ministry of Agriculture and College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Xiaobo Zhang
- Key Laboratory of Animal Virology of Ministry of Agriculture and College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China.
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32
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Abstract
Viruses, in particular DNA viruses, generate microRNAs (miRNAs) to control the expression of host and viral genes. Due to their essential roles in virus-host interactions, viral miRNAs have attracted extensive investigations in recent years. To date, however, most studies on viral miRNAs have been conducted in cell lines. In this study, the viral miRNAs from white spot syndrome virus (WSSV) were characterized in shrimp in vivo. On the basis of our previous study and small RNA sequencing in this study, a total of 89 putative WSSV miRNAs were identified. As revealed by miRNA microarray analysis and Northern blotting, the expression of viral miRNAs was tissue specific in vivo. The results indicated that the viral miRNA WSSV-miR-N24 could target the shrimp caspase 8 gene, and this miRNA further repressed the apoptosis of shrimp hemocytes in vivo. As a result, the number of WSSV copies in shrimp in vivo was significantly increased compared with the control level (WSSV only). Therefore, our study presents the first report on the in vivo molecular events of viral miRNA in antiviral apoptosis.
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33
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Abstract
Viral microRNAs (miRNAs), most of which are characterized in cell lines, have been found to play important roles in the virus life cycle to avoid attack by the host immune system or to keep virus in the latency state. Viral miRNAs targeting virus genes can inhibit virus infection. In this study, in vivo findings in Marsupenaeus japonicus shrimp revealed that the viral miRNAs could target virus genes and further promote the virus infection. The results showed that white spot syndrome virus (WSSV)-encoded miRNAs WSSV-miR-66 and WSSV-miR-68 were transcribed at the early stage of WSSV infection. When the expression of WSSV-miR-66 and WSSV-miR-68 was silenced with sequence-specific anti-miRNA oligonucleotides (AMOs), the number of copies of WSSV and the WSSV-infected shrimp mortality were significantly decreased, indicating that the two viral miRNAs had a great effect on virus infection. It was revealed that the WSSV wsv094 and wsv177 genes were the targets of WSSV-miR-66 and that the wsv248 and wsv309 genes were the targets of WSSV-miR-68. The data demonstrate that the four target genes play negative roles in the WSSV infection. The targeting of the four virus genes by WSSV-miR-66 and WSSV-miR-68 led to the promotion of virus infection. Therefore, our in vivo findings show a novel aspect of viral miRNAs in virus-host interactions.
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34
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Tan TT, Chen M, Harikrishna JA, Khairuddin N, Mohd Shamsudin MI, Zhang G, Bhassu S. Deep parallel sequencing reveals conserved and novel miRNAs in gill and hepatopancreas of giant freshwater prawn. FISH & SHELLFISH IMMUNOLOGY 2013; 35:1061-1069. [PMID: 23816854 DOI: 10.1016/j.fsi.2013.06.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 06/12/2013] [Accepted: 06/12/2013] [Indexed: 06/02/2023]
Abstract
MicroRNAs (miRNAs) are ~20-22 nucleotides, non protein-coding RNA regulatory genes that post-transcriptionally regulate many protein-coding genes, influencing critical biological and metabolic processes. While the number of known microRNA is increasing, there is currently no published data for miRNA from giant freshwater prawns, Macrobrachium rosenbergii (M. rosenbergii), a commercially cultured and economically important food species. In this study, we identified novel miRNAs in the gill and hepatopancreas of M. rosenbergii. Through a deep parallel sequencing analysis and an in silico data analysis approach, 327 miRNA families were identified from small RNA libraries with reference to both the de novo transcriptome of M. rosenbergii obtained from RNA-Seq and to miRBase (Release 18.0, November 2012). Based on the identified mature miRNA and recovered precursor sequences that form appropriate hairpin structures, three conserved miRNA (miR125, miR750, miR993) and 27 novel miRNA candidates encoding messenger-like non-coding RNA were identified. miR-125, miR-750, G-m0002/H-m0009, G-m0005, G-m0008/H-m0016, G-m0011/H-m0027 and G-m0015 were selected for experimental validation with stem-loop quantitative RT-PCR and were found to be coherent with the expression profile of deep sequencing data as evaluated with Pearson's correlation coefficient (r = 0.835178 for miRNA in gill, r = 0.724131 for miRNA in hepatopancreas). Using a combinatorial approach of pathway enrichment analysis and inverse expression relationship of miRNA and mRNA, four co-expressed novel miRNA candidates (G-m0005, G-m0008/H-m0016, G-m0011/H-m0027, and G-m0015) were found to be associated with energy metabolism. In addition, the expression of the three novel miRNA candidates (G-m0005, G-m0008/H-m0016, and G-m0011/H-m0027) were also found to be significantly reduced at 9 and 24 h post infection in M. rosenbergii challenged with infectious hypodermal and hematopoietic necrosis virus, suggesting a functional role of these miRNAs in crustacean immune defense.
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Affiliation(s)
- Tian Tian Tan
- Genomic Research and Breeding Laboratory, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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35
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Vijayendran D, Airs PM, Dolezal K, Bonning BC. Arthropod viruses and small RNAs. J Invertebr Pathol 2013; 114:186-95. [PMID: 23932976 DOI: 10.1016/j.jip.2013.07.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 07/25/2013] [Accepted: 07/28/2013] [Indexed: 01/09/2023]
Abstract
The recently characterized small RNAs provide a new paradigm for physiological studies. These molecules have been shown to be integral players in processes as diverse as development and innate immunity against bacteria and viruses in eukaryotes. Several of the well-characterized small RNAs including small interfering RNAs, microRNAs and PIWI-interacting RNAs are emerging as important players in mediating arthropod host-virus interactions. Understanding the role of small RNAs in arthropod host-virus molecular interactions will facilitate manipulation of these pathways for both management of arthropod pests of agricultural and medical importance, and for protection of beneficial arthropods such as honey bees and shrimp. This review highlights recent research on the role of small RNAs in arthropod host-virus interactions with reference to other host-pathogen systems.
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36
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Host defense against DNA virus infection in shrimp is mediated by the siRNA pathway. Eur J Immunol 2012; 43:137-46. [DOI: 10.1002/eji.201242806] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Revised: 09/06/2012] [Accepted: 10/08/2012] [Indexed: 12/14/2022]
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