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Koiwai K, Kondo H, Hirono I. scRNA-seq Analysis of Hemocytes of Penaeid Shrimp Under Virus Infection. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023:10.1007/s10126-023-10221-8. [PMID: 37326798 DOI: 10.1007/s10126-023-10221-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023]
Abstract
The classification of cells in non-model organisms has lagged behind the classification of cells in model organisms that have established cluster of differentiation marker sets. To reduce fish diseases, research is needed to better understand immune-related cells, or hemocytes, in non-model organisms like shrimp and other marine invertebrates. In this study, we used Drop-seq to examine how virus infection affected the populations of hemocytes in kuruma shrimp, Penaeus japonicus, which had been artificially infected with a virus. The findings demonstrated that virus infection reduced particular cell populations in circulating hemolymph and inhibited the expression of antimicrobial peptides. We also identified the gene sets that are likely to be responsible for this reduction. Additionally, we identified functionally unknown genes as novel antimicrobial peptides, and we supported this assumption by the fact that these genes were expressed in the population of hemocytes that expressed other antimicrobial peptides. In addition, we aimed to improve the operability of the experiment by conducting Drop-seq with fixed cells as a source and discussed the impact of methanol fixation on Drop-seq data in comparison to previous results obtained without fixation. These results not only deepen our understanding of the immune system of crustaceans but also demonstrate that single-cell analysis can accelerate research on non-model organisms.
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Affiliation(s)
- Keiichiro Koiwai
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan.
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
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Jaree P, Boonchuen P, Thawonsuwan J, Kondo H, Hirono I, Somboonwiwat K. Transcriptome profiling reveals the novel immunometabolism-related genes against WSSV infection from Fenneropenaeus merguiensis. FISH & SHELLFISH IMMUNOLOGY 2022; 120:31-44. [PMID: 34758397 DOI: 10.1016/j.fsi.2021.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
The white spot syndrome virus (WSSV) has been considered a serious threat to shrimp aquaculture. Besides, the activation of cell metabolism as an immune reaction to the virus is now recognized as a piece of the pivotal puzzle of the antiviral responses. Hence, this study explores the relationship between metabolic gene expression and antiviral responses in shrimp using transcriptome analysis. The RNA-seq libraries of Fenneropenaeus merguensis hemocytes after WSSV challenge at early (6 hpi) and late (24 hpi) stages of infection were analyzed to identify differentially expressed genes (DEGs) that the WSSV subverted the expression. One-hundred-thirty-three DEGs that were expressed in response to WSSV infection at both stages were identified. Based on the GO annotation, they were related to innate immunity and metabolic pathway. The expression correlation between "full term" (NGS) and qRT-PCR of 16 representative DEGs is shown. Noticeably, the expression profiles of all the selected metabolic genes involved in glucose metabolism, lipid metabolism, amino acid metabolism, and nucleotide metabolism showed a specific correlation between NGS and qRT-PCR upon WSSV infection. Of these, we further characterized the function related to the WSSV response of glutamine: fructose-6-phosphate aminotransferase (FmGFAT), the rate-limiting enzyme of the hexosamine biosynthesis pathway, which was found to be up-regulated at the late stage of WSSV infection. Suppression of FmGFAT by RNA interference resulted in postponing the death of WSSV-infected shrimp and reduction of viral copy number. These results suggested that the FmGFAT is linked between metabolic change and WSSV responses in shrimp, where the virus-induced metabolic rewiring hijack biological compounds and/or energy sources to benefit the viral replication process.
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Affiliation(s)
- Phattarunda Jaree
- Center of Applied Shrimp Research and Innovation, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Pakpoom Boonchuen
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Jumroensri Thawonsuwan
- Songkhla Aquatic Animal Health Research Center, Department of Fisheries, Songkhla, Thailand
| | - Hidehiro Kondo
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Minato-ku, Tokyo, Japan
| | - Ikuo Hirono
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Minato-ku, Tokyo, Japan
| | - Kunlaya Somboonwiwat
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
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Koiwai K, Koyama T, Tsuda S, Toyoda A, Kikuchi K, Suzuki H, Kawano R. Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process. eLife 2021; 10:e66954. [PMID: 34132195 PMCID: PMC8266392 DOI: 10.7554/elife.66954] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/15/2021] [Indexed: 01/03/2023] Open
Abstract
Crustacean aquaculture is expected to be a major source of fishery commodities in the near future. Hemocytes are key players of the immune system in shrimps; however, their classification, maturation, and differentiation are still under debate. To date, only discrete and inconsistent information on the classification of shrimp hemocytes has been reported, showing that the morphological characteristics are not sufficient to resolve their actual roles. Our present study using single-cell RNA sequencing revealed six types of hemocytes of Marsupenaeus japonicus based on their transcriptional profiles. We identified markers of each subpopulation and predicted the differentiation pathways involved in their maturation. We also predicted cell growth factors that might play crucial roles in hemocyte differentiation. Different immune roles among these subpopulations were suggested from the analysis of differentially expressed immune-related genes. These results provide a unified classification of shrimp hemocytes, which improves the understanding of its immune system.
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Affiliation(s)
- Keiichiro Koiwai
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and TechnologyKoganeiJapan
- Laboratory of Genome Science, Tokyo University of Marine Science and TechnologyMinatoJapan
| | - Takashi Koyama
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of TokyoHamamatsuJapan
- Graduate School of Fisheries and Environmental Sciences, Nagasaki UniversityNagasakiJapan
| | | | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of GeneticsMishimaJapan
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of TokyoHamamatsuJapan
| | - Hiroaki Suzuki
- Department of Precision Mechanics, Faculty of Science and Engineering, Chuo UniversityBunkyoJapan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and TechnologyKoganeiJapan
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Zhang H, Cheng W, Zheng L, Wang P, Liu Q, Li Z, Li T, Wei Y, Mao Y, Yu X. Identification of a group D anti-lipopolysaccharide factor (ALF) from kuruma prawn (Marsupenaeus japonicus) with antibacterial activity against Vibrio parahaemolyticus. FISH & SHELLFISH IMMUNOLOGY 2020; 102:368-380. [PMID: 32360914 DOI: 10.1016/j.fsi.2020.04.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 04/16/2020] [Accepted: 04/18/2020] [Indexed: 06/11/2023]
Abstract
Anti-lipopolysaccharide factor (ALF), which belongs to the antimicrobial peptide (AMP) family, has become a relatively new weapon to combat severe infections and has been demonstrated to be active against bacteria, fungi and some viruses. In the present study, a new ALF of group D (MjALF-D; GenBank accession No. MN416688) from Marsupenaeus japonicus was detected. MjALF-D encodes a polypeptide with 124 aa, and the peptide contains a 26-residue signal peptide and a lipopolysaccharide-binding domain (LBD). The structure of MjALF-D was found to consist of three α-helices, four β-sheets and random coils. qRT-PCR analysis revealed that MjALF-D expression was primarily observed in the stomach and was universally upregulated in both the gill and stomach after challenge by lipopolysaccharide (LPS) and Vibrio parahaemolyticus. Moreover, rMjALF-D can inhibit the growth of V. parahaemolyticus. rMjALF-D could destroy the bacterial membrane and lead to cytoplasmic leakage investigated by scanning electron microscopy (SEM) and transmission electron microscopy (TEM), which may be the mechanism by which rMjALF-D inhibits V. parahaemolyticus. Additionally, rMjALF-D showed distinct binding or antibacterial ability after direct incubation with V. parahaemolyticus or bacterial genomic DNA and a certain effect on the protein expression of it. Together, these results indicated that rMjALF-D possessed the antibacterial activity against V. parahaemolyticus and the potential involvement in the innate immune response of M. japonicus.
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Affiliation(s)
- Heqian Zhang
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wenzhi Cheng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China; Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, China
| | - Libing Zheng
- National and Provincial Joint Laboratory of Exploration and Utilization of Marine Aquatic Genetic Resources, School of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Panpan Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China; Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, China
| | - Qinghui Liu
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zhen Li
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Tianjiao Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China; Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, China
| | - Yiming Wei
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China; Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, China
| | - Yong Mao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China; Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, China.
| | - Xiangyong Yu
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
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Jaree P, Kawai T, Lo CF, Tassanakajon A, Somboonwiwat K. Genome organization and definition of the Penaeus monodon viral responsive protein 15 (PmVRP15) promoter. FISH & SHELLFISH IMMUNOLOGY 2019; 93:997-1006. [PMID: 31412281 DOI: 10.1016/j.fsi.2019.08.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/06/2019] [Accepted: 08/10/2019] [Indexed: 06/10/2023]
Abstract
The viral responsive protein 15 from the black tiger shrimp Penaeus monodon (PmVRP15) is a highly responsive gene upon white spot syndrome virus (WSSV) challenge. It is identified from hemocyte and important for WSSV trafficking and assembly. However, the knowledge of PmVRP15 gene regulation is limited. In the present study, the genome organization and 5'upstream promoter sequences of PmVRP15 gene were investigated. The PmVRP15 gene was found to contain 4 exons interrupted by 3 introns and the start codon was located in the exon 2. The transcription start site and TATA box were also determined from the 5' upstream sequence. By using the narrow down experiment, the 5' upstream promoter active region was determined to be at the nucleotide positions -525 to +612. Mutagenesis of the putative transcription factor (TF) binding sites revealed that the binding site of interferon regulatory factor (IRF) (-495/-479) was a repressor-binding site whereas those of the octamer transcription factor 1 (Oct-1) (-275/-268) and the nuclear factor of activated T-cells transcription factor (NFAT) (-228/-223) were activator-binding sites. This is the first report on the transcription factors that might play essential roles in modulating the PmVRP15 gene expression. Nevertheless, the underlying regulation mechanism of PmVRP15 gene expression needs further investigation.
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Affiliation(s)
- Phattarunda Jaree
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Phayathai Rd., Bangkok, Thailand
| | - Taro Kawai
- Laboratory of Molecular Immunobiology, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Nara, Japan
| | - Chu-Fang Lo
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Anchalee Tassanakajon
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Phayathai Rd., Bangkok, Thailand
| | - Kunlaya Somboonwiwat
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Phayathai Rd., Bangkok, Thailand.
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Zhang K, Koiwai K, Kondo H, Hirono I. White spot syndrome virus (WSSV) suppresses penaeidin expression in Marsupenaeus japonicus hemocytes. FISH & SHELLFISH IMMUNOLOGY 2018; 78:233-237. [PMID: 29684609 DOI: 10.1016/j.fsi.2018.04.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/16/2018] [Accepted: 04/19/2018] [Indexed: 06/08/2023]
Abstract
Penaeidins are a unique family of antimicrobial peptides specific to penaeid shrimp and have been reported mainly function as anti-bacterial and anti-fungal. In order to investigate whether penaeidins could also respond to virus or not, we examined the effect of WSSV on MjPen-II (penaeidin in kuruma shrimp, Marsupenaeus japonicus) expression. In the control group, MjPen-II transcript level can be detected in almost all test tissues but was expressed most strongly in hemocytes. After WSSV infection, MjPen-II transcript level was significantly downregulated in hemocytes. Moreover, the proportion of MjPen-II+ hemocytes was not significantly different between non-infected and WSSV-infected shrimp, but the number of MjPen-II+ highly expressing hemocytes decreased after infection. In addition, MjPen-II was observed in the cytoplasm of granule-containing hemocytes. These results suggest that WSSV suppresses MjPen-II expression in hemocytes.
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Affiliation(s)
- Kehong Zhang
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo 108-8477, Japan; Key Laboratory of Exploproportionn and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Keiichiro Koiwai
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo 108-8477, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo 108-8477, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo 108-8477, Japan.
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Zhang K, Koiwai K, Kondo H, Hirono I. A novel white spot syndrome virus-induced gene (MjVIG1) from Marsupenaeus japonicus hemocytes. FISH & SHELLFISH IMMUNOLOGY 2018; 77:46-52. [PMID: 29567134 DOI: 10.1016/j.fsi.2018.03.026] [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: 12/28/2017] [Revised: 03/08/2018] [Accepted: 03/17/2018] [Indexed: 06/08/2023]
Abstract
cDNA of a newly recognized white spot syndrome virus (WSSV)-induced gene (MjVIG1) was characterized from Marsupenaeus japonicus hemocytes; this gene encodes a protein that lack similarity to any known characterized protein. To identify this novel gene, we mainly conducted transcript level analysis, immunostaining and flow cytometry after WSSV infection. MjV1G1 transcript levels were also measured after Yellow head virus (YHV) and Vibrio parahaemolyticus infection tests. In non-infected and WSSV-infected shrimp, MjVIG1 was observed in granule-containing hemocytes. In addition, the MjVIG1 transcript level and ratio of MjVIG1-positive hemocytes both significantly increased, and number of MjVIG1-positive hemocytes slightly increased after WSSV infection. In contrast, MjVIG1 transcript level did not change after YHV and V. parahaemolyticus infection. These results indicated that MjVIG1 might be a WSSV-specific induced gene in M. japonicus hemocytes.
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Affiliation(s)
- Kehong Zhang
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Keiichiro Koiwai
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan.
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