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Hao T, Song Z, Zhang M, Zhang L, Yang J, Li J, Sun J. Reconstruction of Metabolic-Protein Interaction Integrated Network of Eriocheir sinensis and Analysis of Ecdysone Synthesis. Genes (Basel) 2024; 15:410. [PMID: 38674345 PMCID: PMC11049885 DOI: 10.3390/genes15040410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Integrated networks have become a new interest in genome-scale network research due to their ability to comprehensively reflect and analyze the molecular processes in cells. Currently, none of the integrated networks have been reported for higher organisms. Eriocheir sinensis is a typical aquatic animal that grows through ecdysis. Ecdysone has been identified to be a crucial regulator of ecdysis, but the influence factors and regulatory mechanisms of ecdysone synthesis in E. sinensis are still unclear. In this work, the genome-scale metabolic network and protein-protein interaction network of E. sinensis were integrated to reconstruct a metabolic-protein interaction integrated network (MPIN). The MPIN was used to analyze the influence factors of ecdysone synthesis through flux variation analysis. In total, 236 integrated reactions (IRs) were found to influence the ecdysone synthesis of which 16 IRs had a significant impact. These IRs constitute three ecdysone synthesis routes. It is found that there might be alternative pathways to obtain cholesterol for ecdysone synthesis in E. sinensis instead of absorbing it directly from the feeds. The MPIN reconstructed in this work is the first integrated network for higher organisms. The analysis based on the MPIN supplies important information for the mechanism analysis of ecdysone synthesis in E. sinensis.
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Affiliation(s)
- Tong Hao
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China; (T.H.); (Z.S.); (M.Z.); (L.Z.); (J.Y.)
| | - Zhentao Song
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China; (T.H.); (Z.S.); (M.Z.); (L.Z.); (J.Y.)
| | - Mingzhi Zhang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China; (T.H.); (Z.S.); (M.Z.); (L.Z.); (J.Y.)
| | - Lingrui Zhang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China; (T.H.); (Z.S.); (M.Z.); (L.Z.); (J.Y.)
| | - Jiarui Yang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China; (T.H.); (Z.S.); (M.Z.); (L.Z.); (J.Y.)
| | - Jingjing Li
- Tianjin Fisheries Research Institute, Tianjin 300211, China;
| | - Jinsheng Sun
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China; (T.H.); (Z.S.); (M.Z.); (L.Z.); (J.Y.)
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Wang L, Gao J, Cao X, Du J, Cao L, Nie Z, Xu G, Dong Z. Integrated Analysis of Transcriptomics and Metabolomics Unveil the Novel Insight of One-Year-Old Precocious Mechanism in the Chinese Mitten Crab, Eriocheir sinensis. Int J Mol Sci 2023; 24:11171. [PMID: 37446357 DOI: 10.3390/ijms241311171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Eriocheir sinensis is traditionally a native high-value crab that is widely distributed in eastern Asia, and the precocity is considered the bottleneck problem affecting the development of the industry. The precocious E. sinensis is defined as a crab that reaches complete sexual maturation during the first year of its lifespan rather than as normally in the second year. However, the exact regulatory mechanisms underlying the precocity are still unclear to date. This study is the first to explore the mechanism of precocity with transcriptome-metabolome association analysis between the precocious and normal sexually mature E. sinensis. Our results indicated that the phenylalanine metabolism (map00360) and neuroactive ligand-receptor interaction (map04080) pathways play an important role in the precocity in the ovary of E. sinensis. In map00360, the predicted aromatic-L-amino-acid decarboxylase and 4-hydroxyphenylpyruvate dioxygenase isoform X1 genes and the phenethylamine, phenylethyl alcohol, trans-2-hydroxycinnamate, and L-tyrosine metabolites were all down-regulated in the ovary of the precocious E. sinensis. The map04080 was the common KEGG pathway in the ovary and hepatopancreas between the precocious and normal crab. In the ovary, the predicted growth hormone secretagogue receptor type 1 gene was up-regulated, and the L-glutamate metabolite was down-regulated in the precocious E. sinensis. In the hepatopancreas, the predicted forkhead box protein I2 gene and taurine metabolite were up-regulated and the the L-glutamate metabolite was down-regulated in the precocious crab. There was no common pathway in the testis. Numerous common pathways in the hepatopancreas between male precocious and normal crab were identified. The specific amino acids, fatty acids and flavorful nucleotide (inosine monophosphate (MP), cytidine MP, adenosine MP, uridine MP, and guanosine MP) contents in the hepatopancreas and gonads further confirmed the above omics results. Our results suggest that the phenylalanine metabolism may affect the ovarian development by changing the contents of the neurotransmitter and tyrosine. The neuroactive ligand-receptor interaction pathway may affect the growth by changing the expressions of related genes and affect the umami taste of the gonads and hepatopancreas through the differences of L-glutamate metabolite in the precocious E. sinensis. The results provided valuable and novel insights on the precocious mechanism and may have a significant impact on the development of the E. sinensis aquaculture industry.
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Affiliation(s)
- Lanmei Wang
- Key Laboratory of Freshwater, Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Wuxi 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Jiancao Gao
- Key Laboratory of Freshwater, Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Wuxi 214081, China
| | - Xi Cao
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Jinliang Du
- Key Laboratory of Freshwater, Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Wuxi 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Liping Cao
- Key Laboratory of Freshwater, Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Wuxi 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Zhijuan Nie
- Key Laboratory of Freshwater, Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Wuxi 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Gangchun Xu
- Key Laboratory of Freshwater, Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Wuxi 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Zaijie Dong
- Key Laboratory of Freshwater, Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Wuxi 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
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Effects of Protein Level on the Production and Growth Performance of Juvenile Chinese Mitten Crab (Eriocheir sinensis) and Environmental Parameters in Paddy Fields. WATER 2022. [DOI: 10.3390/w14121941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Rice–crab co-culture systems represent integrated agriculture–aquaculture systems developed in China over the last 30 years. The rice–crab co-culture area comprised approximately 1.386 × 105 hm2 in 2019. However, there is no specific feed designed for Chinese mitten crab (Eriocheir sinensis) cultured in this system until now. In this study, we investigated feed formulae for the nutritional requirements of Chinese mitten crab in this mode. The control group was not fed with any artificial feed (Co), and the experimental groups were fed with three different feeds of 15% (T15), 30% (T30), or 45% (T45) protein content, respectively. Growth performance variations in E. sinensis were investigated along with water quality, phytoplankton, zooplankton, aquatic vascular plants, and benthic animals in the paddy fields to determine the effect of crabs and their diet on the paddy ecosystem. Dietary protein levels had no significant effect on water quality. The biomass and species of phytoplankton, zooplankton, aquatic vascular plants, and zoobenthos in the paddy field were affected by crabs and their diet. Morphological parameters of crabs were significantly more pronounced in the high-protein group than in the other groups. However, the T45 diet negatively affected production by increasing feed costs, causing precocious puberty and inducing water eutrophication. In conclusion, adding a 15% protein compound feed can meet the nutritional needs of crabs, reduce culture costs, and improve water quality. The discharged water had low ammonia nitrogen and nitrite content and no eutrophication occurred, so the water could be recycled. These findings provide a scientific reference for supporting rice and fish co-cultivation.
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Xue J, Liu H, Jiang T, Chen X, Yang J. Shape variation in the carapace of Chinese mitten crabs ( Eriocheir sinensis H. Milne Edwards, 1853) in Yangcheng Lake during the year-long culture period. THE EUROPEAN ZOOLOGICAL JOURNAL 2022. [DOI: 10.1080/24750263.2022.2038290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- J. Xue
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - H. Liu
- Key Laboratory of Fishery Ecological Environment Assessment and Resource Conservation in Middle and Lower Reaches of the Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - T. Jiang
- Key Laboratory of Fishery Ecological Environment Assessment and Resource Conservation in Middle and Lower Reaches of the Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - X. Chen
- Key Laboratory of Fishery Ecological Environment Assessment and Resource Conservation in Middle and Lower Reaches of the Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - J. Yang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- Key Laboratory of Fishery Ecological Environment Assessment and Resource Conservation in Middle and Lower Reaches of the Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
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Koutsouveli V, Cárdenas P, Santodomingo N, Marina A, Morato E, Rapp HT, Riesgo A. The Molecular Machinery of Gametogenesis in Geodia Demosponges (Porifera): Evolutionary Origins of a Conserved Toolkit across Animals. Mol Biol Evol 2020; 37:3485-3506. [PMID: 32929503 PMCID: PMC7743902 DOI: 10.1093/molbev/msaa183] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
All animals are capable of undergoing gametogenesis. The ability of forming haploid cells from diploid cells through meiosis and recombination appeared early in eukaryotes, whereas further gamete differentiation is mostly a metazoan signature. Morphologically, the gametogenic process presents many similarities across animal taxa, but little is known about its conservation at the molecular level. Porifera are the earliest divergent animals and therefore are an ideal phylum to understand evolution of the gametogenic toolkits. Although sponge gametogenesis is well known at the histological level, the molecular toolkits for gamete production are largely unknown. Our goal was to identify the genes and their expression levels which regulate oogenesis and spermatogenesis in five gonochoristic and oviparous species of the genus Geodia, using both RNAseq and proteomic analyses. In the early stages of both female and male gametogenesis, genes involved in germ cell fate and cell-renewal were upregulated. Then, molecular signals involved in retinoic acid pathway could trigger the meiotic processes. During later stages of oogenesis, female sponges expressed genes involved in cell growth, vitellogenesis, and extracellular matrix reassembly, which are conserved elements of oocyte maturation in Metazoa. Likewise, in spermatogenesis, genes regulating the whole meiotic cycle, chromatin compaction, and flagellum axoneme formation, that are common across Metazoa were overexpressed in the sponges. Finally, molecular signals possibly related to sperm capacitation were identified during late stages of spermatogenesis for the first time in Porifera. In conclusion, the activated molecular toolkit during gametogenesis in sponges was remarkably similar to that deployed during gametogenesis in vertebrates.
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Affiliation(s)
- Vasiliki Koutsouveli
- Department of Life Sciences, The Natural History Museum of London, London, United Kingdom
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, BMC, Uppsala, Sweden
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, BMC, Uppsala, Sweden
| | - Nadiezhda Santodomingo
- Department of Life Sciences, The Natural History Museum of London, London, United Kingdom
| | - Anabel Marina
- Servicio de Proteómica, Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid (UAM) and Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Esperanza Morato
- Servicio de Proteómica, Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid (UAM) and Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Hans Tore Rapp
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ana Riesgo
- Department of Life Sciences, The Natural History Museum of London, London, United Kingdom
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Environmental Pollutants Impair Transcriptional Regulation of the Vitellogenin Gene in the Burrowing Mud Crab (Macrophthalmus Japonicus). APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9071401] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Vitellogenesis is a pivotal reproductive process of the yolk formation in crustaceans. Vitellogenin (VTG) is the precursor of main yolk proteins and synthesized by endogenous estrogens. The intertidal mud crab (Macrophthalmus japonicus) inhabits sediment and is a good indicator for assessing polluted benthic environments. The purpose of this study was to identify potential responses of M. japonicus VTG under environmental stresses caused by chemical pollutants, such as 1, 10, and 30 µg L−1 concentrations in di(2-ethylhexyl) phthalate (DEHP), bisphenol A (BPA) and irgarol. We characterized the M. japonicus VTG gene and analyzed the transcriptional expression of VTG mRNA in M. japonicus exposed to various chemicals and exposure periods. A phylogenetic analysis revealed that the M. japonicus VTG clustered closely with Eriocheir sinensis (Chinese mitten crab) VTG, in contrast with another clade that included the VTG ortholog of other crabs. The basal level of VTG expression was the highest in the hepatopancreas and ovaries, and tissues. VTG expression significantly increased in the ovaries and hepatopancreas after 24 h exposure to DEHP. Increased responses of VTG transcripts were found in M. japonicus exposed to DEHP and BPA for 96 h; however, VTG expression decreased in both tissues after irgarol exposure. After an exposure of 7 d, VTG expression significantly increased in the ovaries and hepatopancreas for all concentrations of all chemicals. These results suggest that the crustacean embryogenesis and endocrine processes are impaired by the environmental chemical pollutants DEHP, BPA, and irgarol.
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