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Zhang W, Zhang L, Feng Y, Lin D, Yang Z, Zhang Z, Ma Y. Genome-wide profiling of DNA methylome and transcriptome reveals epigenetic regulation of Urechis unicinctus response to sulfide stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172238. [PMID: 38582121 DOI: 10.1016/j.scitotenv.2024.172238] [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: 01/29/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
Sulfide is a well-known environmental pollutant that can have detrimental effects on most organisms. However, few metazoans living in sulfide-rich environments have developed mechanisms to tolerate and adapt to sulfide stress. Epigenetic mechanisms, including DNA methylation, have been shown to play a vital role in environmental stress adaptation. Nevertheless, the precise function of DNA methylation in biological sulfide adaptation remains unclear. Urechis unicinctus, a benthic organism inhabiting sulfide-rich intertidal environments, is an ideal model organism for studying adaptation to sulfide environments. In this study, we conducted a comprehensive analysis of the DNA methylome and transcriptome of U. unicinctus after exposure to 50 μM sulfide. The results revealed dynamic changes in the DNA methylation (5-methylcytosine) landscape in response to sulfide stress, with U. unicinctus exhibiting elevated DNA methylation levels following stress exposure. Integrating differentially expressed genes (DEGs) and differentially methylated regions (DMRs), we identified a crucial role of gene body methylation in predicting gene expression. Furthermore, using a DNA methyltransferase inhibitor, we validated the involvement of DNA methylation in the sulfide stress response and the gene regulatory network influenced by DNA methylation. The results indicated that by modulating DNA methylation levels during sulfide stress, the expression of glutathione S-transferase, glutamyl aminopeptidase, and cytochrome c oxidase could be up-regulated, thereby facilitating the metabolism and detoxification of exogenous sulfides. Moreover, DNA methylation was found to regulate and enhance the oxidative phosphorylation pathway, including NADH dehydrogenase, isocitrate dehydrogenase, and ATP synthase. Additionally, DNA methylation influenced the regulation of Cytochrome P450 and macrophage migration inhibitory factor, both of which are closely associated with oxidative stress and stress resistance. Our findings not only emphasize the role of DNA methylation in sulfide adaptation but also provide novel insights into the potential mechanisms through which marine organisms adapt to environmental changes.
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Affiliation(s)
- Wenqing Zhang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Long Zhang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Yuxin Feng
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Dawei Lin
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Zhi Yang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Zhifeng Zhang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China; Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Yubin Ma
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
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Wang Y, Wang Q, Chen L, Li B. The lysosome-phagosome pathway mediates immune regulatory mechanisms in Mesocentrotus nudus against Vibrio coralliilyticus infection. FISH & SHELLFISH IMMUNOLOGY 2023; 139:108864. [PMID: 37277051 DOI: 10.1016/j.fsi.2023.108864] [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: 02/11/2023] [Revised: 05/20/2023] [Accepted: 05/29/2023] [Indexed: 06/07/2023]
Abstract
Sea urchins are a popular model species for studying invertebrate diseases. The immune regulatory mechanisms of the sea urchin Mesocentrotus nudus during pathogenic infection are currently unknown. This study aimed to reveal the potential molecular mechanisms of M. nudus during resistance to Vibrio coralliilyticus infection by integrative transcriptomic and proteomic analyses. Here, we identified a total of 135,868 unigenes and 4,351 proteins in the four infection periods of 0 h, 20 h, 60 h and 100 h in M. nudus. In the I20, I60 and I100 infection comparison groups, 10,861, 15,201 and 8,809 differentially expressed genes (DEGs) and 2,188, 2,386 and 2,516 differentially expressed proteins (DEPs) were identified, respectively. We performed an integrated comparative analysis of the transcriptome and proteome throughout the infection phase and found very a low correlation between transcriptome and proteome changes. KEGG pathway analysis revealed that most upregulated DEGs and DEPs were involved in immune strategies. Notably, "lysosome" and "phagosome" activated throughout the infection process, could be considered the two most important enrichment pathways at the mRNA and protein levels. The significant increase in phagocytosis of infected M. nudus coelomocytes further demonstrated that the lysosome-phagosome pathway played an important immunological role in M. nudus resistance to pathogenic infection. Key gene expression profiles and protein‒protein interaction analysis revealed that cathepsin family and V-ATPase family genes might be key bridges in the lysosome-phagosome pathway. In addition, the expression patterns of key immune genes were verified using qRT‒PCR, and the different expression trends of candidate genes reflected, to some extent, the regulatory mechanism of immune homeostasis mediated by the lysosome-phagosome pathway in M. nudus against pathogenic infection. This work will provide new insights into the immune regulatory mechanisms of sea urchins under pathogenic stress and help identify key potential genes/proteins for sea urchin immune responses.
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Affiliation(s)
- Yanxia Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; University of Chinese Academy of Science, Beijing, 10049, China
| | - Quanchao Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Linlin Chen
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Baoquan Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
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Mou CY, Li Q, Huang ZP, Ke HY, Zhao H, Zhao ZM, Duan YL, Li HD, Xiao Y, Qian ZM, Du J, Zhou J, Zhang L. PacBio single-molecule long-read sequencing provides new insights into the complexity of full-length transcripts in oriental river prawn, macrobrachium nipponense. BMC Genomics 2023; 24:340. [PMID: 37340366 DOI: 10.1186/s12864-023-09442-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 06/11/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND Oriental river prawn (Macrobrachium nipponense) is one of the most dominant species in shrimp farming in China, which is a rich source of protein and contributes to a significant impact on the quality of human life. Thus, more complete and accurate annotation of gene models are important for the breeding research of oriental river prawn. RESULTS A full-length transcriptome of oriental river prawn muscle was obtained using the PacBio Sequel platform. Then, 37.99 Gb of subreads were sequenced, including 584,498 circular consensus sequences, among which 512,216 were full length non-chimeric sequences. After Illumina-based correction of long PacBio reads, 6,599 error-corrected isoforms were identified. Transcriptome structural analysis revealed 2,263 and 2,555 alternative splicing (AS) events and alternative polyadenylation (APA) sites, respectively. In total, 620 novel genes (NGs), 197 putative transcription factors (TFs), and 291 novel long non-coding RNAs (lncRNAs) were identified. CONCLUSIONS In summary, this study offers novel insights into the transcriptome complexity and diversity of this prawn species, and provides valuable information for understanding the genomic structure and improving the draft genome annotation of oriental river prawn.
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Affiliation(s)
- Cheng-Yan Mou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Qiang Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Zhi-Peng Huang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Hong-Yu Ke
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Han Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Zhong-Meng Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Yuan-Liang Duan
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Hua-Dong Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Yu Xiao
- Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 610066, China
| | - Zhou-Ming Qian
- Chengdu Eaters Agricultural Group Co., Ltd, Chengdu, Sichuan, 610000, China
| | - Jun Du
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Jian Zhou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China.
| | - Lu Zhang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China.
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Yuan T, Hashimoto K, Tazaki A, Hasegawa M, Kurniasari F, Ohta C, Aoki M, Ohgami N, Kato M. Potential application of a hydrotalcite-like compound for reduction of toxicity to aquatic organisms via rapid and efficient removal of hydrogen sulfide. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 321:115861. [PMID: 36050136 DOI: 10.1016/j.jenvman.2022.115861] [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: 03/24/2022] [Revised: 07/20/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
Hydrogen sulfide (H2S) is known to have wide ranging toxicities not only as a gas but also as dissolved forms in aquatic environments. The diversity of aquatic organisms can be severely affected by hydrogen sulfide at very low concentrations, indicating the urgent necessity to develop an efficient method for removal of hydrogen sulfide in water. In this study, the removal capacity for hydrogen sulfide of our originally developed hydrotalcite-like compound composed of magnesium and iron (MF-HT) was investigated and its potential application for reduction of toxicity to aquatic organisms was evaluated. The MF-HT experimentally showed a high adsorption capacity of 146.5 mg/g with a fast adsorption equilibrium time of 45 min, both of which are top-class compared with those of other adsorbents previously reported. In fact, removal of hydrogen sulfide (1.2-152.5 mg/L) at an average rate of >97.6% was achieved in groundwater samples (n = 16) by the MF-HT within 60 min. The toxicities of groundwater, indicated by inhibition rate for microalgae (primary producers) and immobilization rate for crustaceans (secondary consumers), were reduced by 96.1% and 82.5% in 2-fold and 4-fold diluted groundwater, respectively, after treatment with the MF-HT for 60 min. These results indicate that MF-HT has an excellent safety record for aquatic organisms. After clarifying the adsorption mechanism, excellent reusability of MF-HT was also confirmed after regeneration using 1 M Na2CO3 solution. Considering the efficacy, speed, safety and cost of MF-HT, it could be a novel promising material for solving the problem of hydrogen sulfide pollution in the hydrosphere.
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Affiliation(s)
- Tian Yuan
- Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan; Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Kazunori Hashimoto
- Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan; Department of Molecular Biology, Faculty of Pharmacy, Meijo University, Nagoya, Aichi, Japan; Voluntary Body for International Healthcare in Universities, Nagoya, Aichi, Japan
| | - Akira Tazaki
- Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan; Voluntary Body for International Healthcare in Universities, Nagoya, Aichi, Japan
| | - Masahiro Hasegawa
- Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Fitri Kurniasari
- Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan; Voluntary Body for International Healthcare in Universities, Nagoya, Aichi, Japan
| | - Chihiro Ohta
- Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Masayo Aoki
- Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan; Voluntary Body for International Healthcare in Universities, Nagoya, Aichi, Japan
| | - Nobutaka Ohgami
- Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan; Voluntary Body for International Healthcare in Universities, Nagoya, Aichi, Japan
| | - Masashi Kato
- Department of Occupational and Environmental Health, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan; Voluntary Body for International Healthcare in Universities, Nagoya, Aichi, Japan.
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Jiang S, Zhang W, Xiong Y, Cheng D, Wang J, Jin S, Gong Y, Wu Y, Qiao H, Fu H. Hepatopancreas transcriptome analyses provide new insights into the molecular regulatory mechanism of fast ovary maturation in Macrobrachium nipponense. BMC Genomics 2022; 23:625. [PMID: 36045344 PMCID: PMC9429573 DOI: 10.1186/s12864-022-08851-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/16/2022] [Indexed: 12/02/2022] Open
Abstract
Background Macrobrachium nipponense is an economically and ecologically important freshwater prawn that is widely farmed in China. In contrast to other species of marine shrimp, M. nipponense has a short sexual maturity period, resulting in not only high stocking densities, but also a reduced survival rate and increased risk of hypoxia. Therefore, there is an urgent need to study the molecular mechanisms underlying fast ovary maturation in this species. Results Comparative transcriptome analysis was performed using hepatopancreatic tissue from female M. nipponense across five ovarian maturation stages to explore differentially expressed genes and pathways involved in ovarian maturation. In total, 118.01 Gb of data were generated from 15 transcriptomes. Approximately 90.46% of clean reads were mapped from the M. nipponense reference genome. A comprehensive comparative analysis between successive ovarian maturation stages generated 230–5814 differentially expressed genes. Gene Ontology (GO) enrichment was highly concentrated in the “biological process” category in all four comparison groups, and mainly focused on energy synthesis and accumulation, energy decomposition and transport. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results showed that, among 20 significantly enriched KEGG pathways, nine were involved in the synthesis, degradation, and metabolism of carbohydrates, lipids, and other nutrient intermediates, suggesting that the hepatopancreas has an important role in energy supply during ovarian maturation. Furthermore, the “Insect hormone biosynthesis” pathway was found to have a dominant role in the development of the ovary from immaturity to maturity, supporting the hypothesis that ecdysteroid- and juvenile hormone-signaling pathways have an important role in hepatopancreas regulation of ovarian maturation. Conclusion Taken together, this study sheds light on the role of the hepatopancreas in the molecular regulation of ovary maturation in M. nipponense. The present study provided new insights for understanding the mechanisms of reproductive regulation in crustaceans.
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