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Chang J, Zhang J, Chu L, Liu A, Hou X, Zhu X, Huang X, Xing Q, Hu J, Bao Z. Ampk-mediated regulation of cardiac energy metabolism: Implications for thermotolerance in Argopecten irradians irradians. Gene 2024; 933:148922. [PMID: 39244169 DOI: 10.1016/j.gene.2024.148922] [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: 03/20/2024] [Revised: 08/24/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
AMPK is a key regulator of metabolism in eukaryotes across various pathways related to energy regulation. Although extensive investigations of AMPK have been conducted in mammals and some model organisms, research on AMPK in scallops is comparatively limited. In this study, three AMPK family genes (AiAMPKα, AiAMPKβ and AiAMPKγ) in scallop Argopecten irradians irradians were identified through genome scanning. Structure prediction and phylogenetic analyses of AiAMPKs were performed to determine their structural features and evolutionary relationships. Spatiotemporal expression patterns of AiAMPKs at different developmental stages and in healthy adult tissues were analyzed to elucidate the function of AiAMPKs in bay scallops' growth and development. The spatiotemporally specific expression of AiAMPKs implied their important roles in growth and development of bay scallops. Heat stress experiment was performed to determine the regulations of AiAMPKs in four kinds of thermosensitive tissues. Expression profiles revealed distinct molecular mechanisms of AiAMPKs in different tissues in response to heat stress: significant down-regulations in mobile hemocytes, but dominant up-regulations occurring in stationary gills, mantles and hearts. Functional verification including knock-down of AiAMPKα and inhibition of AiAMPK was separately conducted in the thermotolerant tissue heart at the post-transcription and translation levels. The thermotolerant index Arrhenius break temperature (ABT) showed a significant decrease and the rate-amplitude product (RAP) peaked earlier in the individuals after RNAi targeting AiAMPKα, displaying an earlier transition to anaerobic metabolism under heat stress, indicating an impairing ability of aerobic metabolism. After AiAMPK inhibition, widespread down-regulations of genes in key energy metabolism pathways, RNA polymerase II-mediated transcription, and aminoacyl-tRNA synthesis pathways were obviously observed, revealing the post-translational inhibition of AiAMPK hindered cardiac energy metabolism, basal transcription and translation. Overall, our findings provide evidences for exploring the molecular mechanisms of energy regulation in thermotolerant traits in bay scallops under ongoing global warming.
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Affiliation(s)
- Jiaxi Chang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Junhao Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Longfei Chu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Ancheng Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Xiujiang Hou
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Xinghai Zhu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution of the Ocean University of China (SOI-OUC), Sanya 572000, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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Yang H, Zhou L, Zheng Y, Yu T, Wu B, Liu Z, Sun X. Myocyte enhancer factor 2 upregulates expression of myostatin promoter in Yesso scallop, Patinopecten yessoensis. Comp Biochem Physiol B Biochem Mol Biol 2024; 275:111024. [PMID: 39173872 DOI: 10.1016/j.cbpb.2024.111024] [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: 06/06/2024] [Revised: 08/18/2024] [Accepted: 08/19/2024] [Indexed: 08/24/2024]
Abstract
Myostatin (MSTN) plays an important role in muscle development in animals, especially for mammals and fishes. However, little information has been reported on the regulation of MSTN in marine invertebrates, such as bivalves. In the present study, we cloned the MSTN promoter sequence of Yesso scallop Patinopecten yessoensis, identifying 4 transcription start sites, eleven TATA boxes and one E-box. Additionally, transcription factor binding sites, including myocyte enhancer factor 2 (MEF2) and POU homeodomain protein, were identified. The interaction between the MSTN promoter and MEF2 was analyzed to reveal the transcriptional activity of different fragment sizes of promoters through the dual-luciferase reporter assays. The highest transcriptional activity was found in recombinant plasmids with the most MEF2 binding sites, indicating that this transcription factor upregulates MSTN in Yesso scallop. This study provides new insight into the regulation of muscle growth and development in this species.
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Affiliation(s)
- Hongsu Yang
- Fisheries College, Zhejiang Ocean University, Zhoushan 316022, China; State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Liqing Zhou
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Yanxin Zheng
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Changdao 265800, China
| | - Tao Yu
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Changdao 265800, China
| | - Biao Wu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Zhihong Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Xiujun Sun
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China.
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Sun X, Zhang T, Li L, Tu K, Yu T, Wu B, Zhou L, Tian J, Liu Z. MicroRNA expression signature in the striated and smooth adductor muscles of Yesso scallop Patinopecten yessoensis. Genomics 2022; 114:110409. [PMID: 35714827 DOI: 10.1016/j.ygeno.2022.110409] [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: 12/21/2021] [Revised: 04/25/2022] [Accepted: 06/10/2022] [Indexed: 11/18/2022]
Abstract
Increasing evidences point to the potential role of microRNAs (miRNAs) in muscle growth and development in animals. However, knowledge on the identity of miRNAs and their targets in molluscs remains largely unknown. Scallops have one large adductor muscle, composed of fast (striated) and slow (smooth) muscle types, which display great differences in muscle fibers, meat quality, cell types and molecular components. In the present study, we performed a comprehensive investigation of miRNA transcriptomes in fast and slow adductor muscles of Yesso scallop Patinopecten yessoensis. As a result, 47 differentially expressed miRNAs representing ten miRNA families were identified between the striated and smooth adductor muscles. The KEGG enrichment analysis of their target genes were mainly associated with amino acid metabolism, energy metabolism and glycan biosynthesis. The target genes of miR-133 and miR-71 were validated by the dual-luciferase reporter assays and miRNA antagomir treatment in vivo. The identification and functional validation of these different miRNAs in scallops will greatly help our understanding of miRNA regulatory mechanism that achieves the unique muscle phenotypes in scallops. The present findings provide the direct evidences for muscle-specific miRNAs involved in muscle growth and differentiation in molluscs.
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Affiliation(s)
- Xiujun Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Tianshi Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Li Li
- National Oceanographic Center, Qingdao 266104, China
| | - Kang Tu
- Putian Institute of Aquaculture Science of Fujian Province, Putian 351100, China
| | - Tao Yu
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Changdao, China
| | - Biao Wu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Liqing Zhou
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Jiteng Tian
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Zhihong Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China.
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Transcriptomics Coupled to Proteomics Reveals Novel Targets for the Protective Role of Spermine in Diabetic Cardiomyopathy. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:5909378. [PMID: 35437457 PMCID: PMC9013312 DOI: 10.1155/2022/5909378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/04/2022] [Accepted: 03/29/2022] [Indexed: 11/17/2022]
Abstract
Background Diabetic cardiomyopathy (DbCM) is the main complication and the cause of high mortality of diabetes. Exploring the transcriptomics and proteomics of DbCM is of great significance for understanding the biology of the disease and for guiding new therapeutic targets for the potential therapeutic effect of spermine (SPM). Methods and Results By using a mouse DbCM model, we analyzed the overall transcriptome and proteome of the myocardium, before/after treatment with SPM. The general state and cardiac structure and function changes of each group were also compared. Diabetes induced an increased blood glucose and serum triglyceride content, a decreased body weight, serum insulin level, and cardiac function-related indexes, accompanied by disrupted myocardial tissue morphology and ultrastructure damage. Using RNA sequencing (RNA-seq), we identified thousands of differentially expressed genes (DEGs) in DbCM with or without SPM treatment. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that the DEGs were significantly enriched in lipid metabolism and amino acid metabolism pathways. Specifically, quantitative real-time PCR (qRT-PCR) confirmed that SPM protected DbCM by reversing the expressions of lipid metabolism and amino acid metabolism-related genes, including Alox15, Gm13033, pla2g12a, Ptges, Pnpla2, and Acot1. To further reveal the pathogenesis of DbCM, we used proteome-based data-independent acquisition (DIA) and identified 139 differentially expressed proteins (DEPs) with 67 being upregulated and 72 being downregulated in DbCM. Venn intersection analysis showed 37 coexpressed genes and proteins in DbCM, including 29 upregulation and 8 downregulation in DbCM. In the protein-protein interaction (PPI) network constructed by the STRING database, the metabolism-related coexpressed genes and proteins, such as Acot2, Ephx2, Cyp1a1, Comt, Acox1, Hadhb, Hmgcs2, Acot1, Inmt, and Cat, can interact with the identified DEGs and DEPs. Conclusion The biomarkers and canonical pathways identified in this study may hold the key to understand the mechanisms of DbCM pathobiology and provide new targets for the therapeutic effect of SPM against DbCM by targeting lipid and amino acid metabolism pathways.
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Molecular Characterization and Expression Pattern of Paramyosin in Larvae and Adults of Yesso Scallop. BIOLOGY 2022; 11:biology11030453. [PMID: 35336826 PMCID: PMC8945602 DOI: 10.3390/biology11030453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 11/22/2022]
Abstract
Simple Summary Paramyosin is an important myofibrillar protein in smooth muscle in molluscs that is not present in vertebrate muscles. This study characterized its sequence feature and expression patterns in Yesso scallop Patinopecten yessoensis and revealed the unique phosphorylation sites in scallops. The mRNA and protein expression of paramyosin was mainly found in foot and smooth adductor muscle. At late larval stages, strong paramyosin mRNA signals were detected in the symmetric positions of anterior and posterior adductor muscles. The present findings support that paramyosin may serve as the most important component of smooth muscle assembly during muscle development and catch regulation in scallops. Abstract Paramyosin is an important myofibrillar protein in molluscan smooth muscle. The full-length cDNA encoding paramyosin has been identified from Yesso scallop Patinopecten yessoensis. The length of paramyosin molecule has been found to be 3715 bp, which contains an open reading frame (ORF) of 2805 bp for 934 amino acid residues. Characterization of P. yessoensis paramyosin reveals the typical structural feature of coiled-coil protein, including six α-helix (α1-α6) and one coil (η) structures. Multiple phosphorylation sites have been predicted at the N-terminus of paramyosin, representing the unique phosphorylation sites in scallops. The highest levels of mRNA and protein expression of paramyosin have been found in foot and the smooth adductor muscle. According to whole-mount in situ hybridization (WISH), strong paramyosin mRNA signals were detected in the symmetric positions of anterior and posterior adductor muscles at late larval stages. These findings support that paramyosin may serve as the most important components for myogenesis and catch regulation in scallops. The present findings will not only help uncover the potential function of myofibrillar proteins in molluscs but also provide molecular evidence to infer evolutionary relationships among invertebrates.
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Identification and characterization of phosphoproteins in the striated and smooth adductor muscles of Yesso scallop Patinopecten yessoensis. Food Chem 2022; 372:131242. [PMID: 34818726 DOI: 10.1016/j.foodchem.2021.131242] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/17/2022]
Abstract
Many proteins are known to be phosphorylated, affecting important regulatory factors of muscle quality in the aquatic animals. The striated and smooth adductor muscles of Yesso scallop Patinopecten yessoensis were used to investigate muscle texture and identify phosphoproteins by histological methods and phosphoproteomic analysis. Our present study reveals that muscle fiber density is in relation to meat texture of the striated and smooth adductor muscles. The phosphoproteomic analysis has identified 764 down-regulated and 569 up-regulated phosphosites on 743 phosphoproteins in the smooth muscle compared to the striated part. The identification of unique phosphorylation sites in glycolytic enzymes may increase the activity of glycolytic enzymes and the rate of glycolysis in the striated adductor muscle. The present findings will provide new evidences on the role of muscle structure and protein phosphorylation in scallop muscle quality and thus help to develop strategies for improving meat quality of scallop products.
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Zhou X, Yan Q, Liu L, Chen G, Tang S, He Z, Tan Z. Maternal undernutrition alters the skeletal muscle development and methylation of myogenic factors in goat offspring. Anim Biosci 2022; 35:847-857. [PMID: 34991223 PMCID: PMC9066034 DOI: 10.5713/ab.21.0285] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/08/2021] [Indexed: 11/27/2022] Open
Abstract
Objective The effects of maternal undernutrition during midgestation on muscle fiber histology, myosin heavy chain (MyHC) expression, methylation modification of myogenic factors, and the mammalian target of rapamycin (mTOR) signaling pathway in the skeletal muscles of prenatal and postnatal goats were examined. Methods Twenty-four pregnant goats were assigned to a control (100% of the nutrients requirement, n = 12) or a restricted group (60% of the nutrients requirement, n = 12) between 45 and 100 days of gestation. Descendants were harvested at day 100 of gestation and at day 90 after birth to collect the femoris muscle tissue. Results Maternal undernutrition increased (p<0.05) the fiber area of the vastus muscle in the fetuses and enhanced (p<0.01) the proportions of MyHCI and MyHCIIA fibers in offspring, while the proportion of MyHCIIX fibers was decreased (p<0.01). DNA methylation at the +530 cytosine-guanine dinucleotide (CpG) site of the myogenic factor 5 (MYF5) promoter in restricted fetuses was increased (p<0.05), but the methylation of the MYF5 gene at the +274,280 CpG site and of the myogenic differentiation (MYOD) gene at the +252 CpG site in restricted kids was reduced (p<0.05). mTOR protein signals were downregulated (p<0.05) in the restricted offspring. Conclusion Maternal undernutrition altered the muscle fiber type in offspring, but its relationship with methylation in the promoter regions of myogenic genes needs to be elucidated.
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Affiliation(s)
- Xiaoling Zhou
- College of Animal Science, Tarim University, Alaer 843300, China.,Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China
| | - Qiongxian Yan
- Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China.,Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Changsha 410128, China
| | - Liling Liu
- College of Animal Science, Tarim University, Alaer 843300, China
| | - Genyuan Chen
- College of Animal Science, Tarim University, Alaer 843300, China
| | - Shaoxun Tang
- Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China.,University of Chinese Academy of Science, Beijing 100049, China
| | - Zhixiong He
- Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China.,Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Changsha 410128, China
| | - Zhiliang Tan
- Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China.,Hunan Co-Innovation Center of Animal Production Safety, CICAPS, Changsha 410128, China
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Wu L, Li L, Zhou L, Zhang T, Liu Z, Chen L, Wu B, Jing H, Sun X. Phalloidin fluorescence and confocal microscopy reveal the musculature development of clam Ruditapes philippinarum. Comp Biochem Physiol B Biochem Mol Biol 2021; 258:110693. [PMID: 34752895 DOI: 10.1016/j.cbpb.2021.110693] [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: 04/11/2021] [Revised: 10/27/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022]
Abstract
Knowledge of early development in bivalves is of great importance to understand the function of animal organ systems and the evolution of phenotypic diversity. Manila clam (Ruditapes philippinarum) is an economically important bivalve living in marine intertidal zones. To determine the pattern of muscle development in the clams, we investigate the characteristics of musculature development utilizing phalloidin staining and confocal microscopy. Myofilaments first appear at the early trochophore stage, and gradually become orderly arranged during the transition from trochophore to veliger. For veliger, larval muscle system is mainly composed of dorsal velum retractors, medio-dorsal velum retractors, ventral velum retractors, ventral larval retractors and anterior and posterior adductor muscles. After metamorphosis, the muscle system of late veliger has been reconstructed, showing the irreversible shrink of velum retractor muscles, the rapid growth of wedge-shaped foot and mantle margins. One of the most striking changes in settled spats is the development of sophisticated architecture of foot musculature, which consists of transverse pedal muscles, anterior foot retractor and posterior foot retractor. These findings will not only provide the basis to understand the dynamic pattern of myogenesis in the burrowing bivalves, but also provide valuable information for comparative analysis of muscle development among bivalves.
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Affiliation(s)
- Lei Wu
- Jiangsu Ocean University, Lianyungang 222005, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Li Li
- Marine Science Institute of Shandong Province, Qingdao 266104, China
| | - Liqing Zhou
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Tianshi Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Zhihong Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Limei Chen
- Tianjin Agriculture University, Tianjin 300384, China
| | - Biao Wu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Hao Jing
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Xiujun Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China.
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Sun X, Li L, Wu B, Ge J, Zheng Y, Yu T, Zhou L, Zhang T, Yang A, Liu Z. Cell type diversity in scallop adductor muscles revealed by single-cell RNA-Seq. Genomics 2021; 113:3582-3598. [PMID: 34425225 DOI: 10.1016/j.ygeno.2021.08.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 07/26/2021] [Accepted: 08/18/2021] [Indexed: 11/28/2022]
Abstract
Studies on cell atlas in marine invertebrates provide a better understanding of cell types, stem cell maintenance, and lineages of cell differentiation. To investigate the molecular features of various cell types in molluscan muscles, we performed single-cell RNA sequencing (scRNA-seq) to map cell types in scallop adductor muscles. We uncovered the cell type-specific features of 20 cell clusters defined by the expression of multiple specific molecular markers. These cell clusters are mainly classified into four broad classes, including mesenchymal stem cells, muscle cells, neurons, and haemolymph cells. In particular, we identified a diverse repertoire of neurons in the striated adductor muscle, but not in the smooth muscle. We further reconstructed the cell differentiation events using all the cell clusters by single-cell pseudotemporal trajectories. By integrating dual BrdU-PCNA immunodetection, neuron-specific staining and electron microscopy observation, we showed the spatial distribution of mesenchymal stem cells and neurons in striated adductor muscle of scallops. The present findings will not only be useful to address the cell type-specific gene expression profiles in scallop muscles, but also provide valuable resources for cross-species comparison of marine organisms.
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Affiliation(s)
- Xiujun Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Li Li
- Marine Biology Institute of Shandong Province, Qingdao 266104, China
| | - Biao Wu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Jianlong Ge
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Yanxin Zheng
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Yantai 265800, China
| | - Tao Yu
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Yantai 265800, China
| | - Liqing Zhou
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Tianshi Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Aiguo Yang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Zhihong Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China.
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Sun X, Tu K, Li L, Wu B, Wu L, Liu Z, Zhou L, Tian J, Yang A. Integrated transcriptome and metabolome analysis reveals molecular responses of the clams to acute hypoxia. MARINE ENVIRONMENTAL RESEARCH 2021; 168:105317. [PMID: 33819872 DOI: 10.1016/j.marenvres.2021.105317] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 03/13/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
Mudflat shellfish have evolved well-adapted strategies for coping with dynamic environmental fluxes and stressful conditions, including oxygen availability. The Manila clams Ruditapes philippinarum are worldwide cultured shellfish in marine intertidal zone, which usually encounter great risk of acute hypoxia exposure in coastal habitats. To reveal the effects of acute hypoxia on metabolic changes of the clams, we performed the integrated analysis of transcriptomics and metabolomics to investigate the global changes of genes and metabolites during acute hypoxia stress at the whole-organism level. The comparative transcriptome analysis reveals that the clams show the remarkable depression in a variety of biological performance, such as metabolic rates, neuronal activity, biomineralization activity, and cell proliferation and differentiation at the hypoxic condition. The metabolomic analysis reveals that amino acid metabolism plays a critical role in the metabolic changes of the clams in response to acute hypoxia. A variety of free amino acids may not only be served as the potential osmolytes for osmotic regulation, but also may contribute to energy production during the acute hypoxia exposure. The metabolite analysis also reveals several important biomarkers for metabolic changes, and provides new insights into how clams deal with acute hypoxia. These findings suggest that clams may get through acute hypoxia stress by the adaptive metabolic strategy to survive short-period of acute hypoxia which is likely to occur in their typical habitat. The present findings will not only shed lights on the molecular and metabolic mechanisms of adaptive strategies under stressful conditions, but also provide the signaling metabolites to assess the physiological states of clams in aquaculture.
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Affiliation(s)
- Xiujun Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Kang Tu
- Putian Institute of Aquaculture Science of Fujian Province, Putian, 351100, China
| | - Li Li
- Marine Biology Institute of Shandong Province, Qingdao, 266104, China
| | - Biao Wu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Lei Wu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Jiangsu Ocean University, Lianyungang, 222005, China
| | - Zhihong Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Liqing Zhou
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Jiteng Tian
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Aiguo Yang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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11
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Wei C, Sun M, Liang X, Che B, Wang N, Shi L, Fan Y. Spermine Regulates Immune and Signal Transduction Dysfunction in Diabetic Cardiomyopathy. Front Endocrinol (Lausanne) 2021; 12:740493. [PMID: 35173678 PMCID: PMC8842652 DOI: 10.3389/fendo.2021.740493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/30/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Diabetic cardiomyopathy (DCM) is a specific form of cardiomyopathy that is independent of coronary artery disease and hypertension. Exploring the transcriptomics of DCM is of great significance for understanding the biology of the disease and for guiding new therapeutic targets for the potential therapeutic effect of spermine (SPM). METHODS AND RESULTS By using a mouse DCM model, we analyzed the transcriptome of the myocardium, before/after treatment with SPM. Using RNA sequencing (RNA-seq), we identified 1,318 differentially expressed genes (DEGs), with 636 being upregulated and 682 being downregulated in DCM compared to control check (CK). We then identified 1,393 DEGs, with 887 being upregulated and 506 being downregulated in SPM compared to DCM. Kyoto Encyclopedia of Genes And Genomes (KEGG) analysis demonstrated that the DEGs were significantly enriched in the immune system and signal transduction-related pathways. UpSet Venn analysis showed that 174 DEGs in DCM could be reversed by SPM, with 45 candidates related to immune system and related signal transduction pathways. Trend analysis demonstrated the dynamic changes in gene levels in DCM and SPM treatment, shown as 49 immune and signal transduction-related candidates were significantly enriched in some classical pathways, such as complement and coagulation cascades and phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K)-protein kinase B (Akt) signaling pathway. To further reveal the protective mechanism of SPM to DCM, we predicted 14 overlapped transcription factors (TFs) and their co-factors involved in gene transcription regulation and showed gene interaction with Cytoscape. CONCLUSION The biomarkers and canonical pathways identified in this study may hold the key to understanding the mechanisms of DCM pathobiology and providing new targets for the therapeutic effect of SPM against DCM by targeting abnormal immune response and signal transduction.
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Affiliation(s)
- Can Wei
- Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Mengting Sun
- Department of Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiao Liang
- Department of Cardiovascular, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bingbing Che
- Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Ningning Wang
- Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Lili Shi
- Department of Cadre Ward, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Lili Shi, ; Ying Fan,
| | - Ying Fan
- Department of Cardiovascular, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Lili Shi, ; Ying Fan,
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12
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Algieri C, Nesci S, Trombetti F, Fabbri M, Ventrella V, Pagliarani A. Mitochondrial F 1F O-ATPase and permeability transition pore response to sulfide in the midgut gland of Mytilus galloprovincialis. Biochimie 2020; 180:222-228. [PMID: 33212166 DOI: 10.1016/j.biochi.2020.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 12/16/2022]
Abstract
The molecular mechanisms which rule the formation and opening of the mitochondrial permeability transition pore (mPTP), the lethal mechanism which permeabilizes mitochondria to water and solutes and drives the cell to death, are still unclear and particularly little investigated in invertebrates. Since Ca2+ increase in mitochondria is accompanied by mPTP opening and the participation of the mitochondrial F1FO-ATPase in the mPTP is increasingly sustained, the substitution of the natural cofactor Mg2+ by Ca2+ in the F1FO-ATPase activation has been involved in the mPTP mechanism. In mussel midgut gland mitochondria the similar kinetic properties of the Mg2+- or Ca2+-dependent F1FO-ATPase activities, namely the same affinity for ATP and bi-site activation kinetics by the ATP substrate, in spite of the higher enzyme activity and coupling efficiency of the Mg2+-dependent F1FO-ATPase, suggest that both enzyme activities are involved in the bioenergetic machinery. Other than being a mitochondrial poison and environmental contaminant, sulfide at low concentrations acts as gaseous mediator and can induce post-translational modifications of proteins. The sulfide donor NaHS, at micromolar concentrations, does not alter the two F1FO-ATPase activities, but desensitizes the mPTP to Ca2+ input. Unexpectedly, NaHS, under the conditions tested, points out a chemical refractoriness of both F1FO-ATPase activities and a failed relationship between the Ca2+-dependent F1FO-ATPase and the mPTP in mussels. The findings suggest that mPTP role and regulation may be different in different taxa and that the F1FO-ATPase insensitivity to NaHS may allow mussels to cope with environmental sulfide.
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Affiliation(s)
- Cristina Algieri
- Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, via Tolara di Sopra, 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Salvatore Nesci
- Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, via Tolara di Sopra, 50, 40064, Ozzano Emilia, Bologna, Italy.
| | - Fabiana Trombetti
- Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, via Tolara di Sopra, 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Micaela Fabbri
- Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, via Tolara di Sopra, 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Vittoria Ventrella
- Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, via Tolara di Sopra, 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Alessandra Pagliarani
- Department of Veterinary Medical Sciences (DIMEVET), University of Bologna, via Tolara di Sopra, 50, 40064, Ozzano Emilia, Bologna, Italy
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13
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Miserazzi A, Perrigault M, Sow M, Gelber C, Ciret P, Lomenech AM, Dalens JM, Weber C, Le Floch S, Lacroix C, Blanc P, Massabuau JC. Proteome changes in muscles, ganglia, and gills in Corbicula fluminea clams exposed to crude oil: Relationship with behavioural disturbances. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 223:105482. [PMID: 32371337 DOI: 10.1016/j.aquatox.2020.105482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
The use of online remote control for 24/7 behavioural monitoring can play a key role in estimating the environmental status of aquatic ecosystems. Recording the valve activity of bivalve molluscs is a relevant approach in this context. However, a clear understanding of the underlying disturbances associated with behaviour is a key step. In this work, we studied freshwater Asian clams after exposure to crude oil (measured concentration, 167 ± 28 μg·L-1) for three days in a semi-natural environment using outdoor artificial streams. Three complementary approaches to assess and explore disturbances were used: behaviour by high frequency non-invasive (HFNI) valvometry, tissue contamination with polycyclic aromatic hydrocarbons (PAH), and proteomic analysis. Two tissues were targeted: the pool adductor muscles - retractor pedal muscle - cerebral and visceral ganglia, which is the effector of any valve movement and the gills, which are on the frontline during contamination. The behavioural response was marked by an increase in valve closure-duration, a decrease in valve opening-amplitude and an increase in valve agitation index during opening periods. There was no significant PAH accumulation in the muscle plus nervous ganglia pool, contrary to the situation in the gills, although the latter remained in the low range of data available in literature. Major proteomic changes included (i) a slowdown in metabolic and/or cellular processes in muscles plus ganglia pool associated with minor toxicological effect and (ii) an increase of metabolic and/or cellular processes in gills associated with a greater toxicological effect. The nature of the proteomic changes is discussed in terms of unequal PAH distribution and allows to propose a set of explanatory mechanisms to associate behaviour to underlying physiological changes following oil exposure. First, the first tissues facing contaminated water are the inhalant siphon, the mantle edge and the gills. The routine nervous activity in the visceral ganglia should be modified by nervous information originating from these tissues. Second, the nervous activity in the visceral ganglia could be modified by its own specific contamination. Third, a decrease in nervous activity of the cerebral ganglia close to the mouth, including some kind of narcosis, could contribute to a decrease in visceral ganglia activity via a decrease or blockage of the downward neuromodulation by the cerebro-visceral connective. This whole set of events can explain the decrease of metabolic activity in the adductor muscles, contribute to initiate the catch mechanism and then deeply modify the valve behaviour.
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Affiliation(s)
- A Miserazzi
- University of Bordeaux, EPOC, UMR 5805, Arcachon, France; CNRS, EPOC, UMR 5805, Talence, France
| | - M Perrigault
- University of Bordeaux, EPOC, UMR 5805, Arcachon, France; CNRS, EPOC, UMR 5805, Talence, France
| | - M Sow
- University of Bordeaux, EPOC, UMR 5805, Arcachon, France; CNRS, EPOC, UMR 5805, Talence, France
| | - C Gelber
- Pôles d'études et de Recherche de Lacq, TOTAL, Lacq, France
| | - P Ciret
- University of Bordeaux, EPOC, UMR 5805, Arcachon, France; CNRS, EPOC, UMR 5805, Talence, France
| | - A M Lomenech
- Center of Functional Genomics, Bordeaux University, Bordeaux, France
| | - J M Dalens
- Pôles d'études et de Recherche de Lacq, TOTAL, Lacq, France
| | - C Weber
- Pôles d'études et de Recherche de Lacq, TOTAL, Lacq, France
| | | | | | - P Blanc
- CSTJF, TOTAL SA, Pau, France
| | - J C Massabuau
- University of Bordeaux, EPOC, UMR 5805, Arcachon, France; CNRS, EPOC, UMR 5805, Talence, France.
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14
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Zhou L, Liu Z, Dong Y, Sun X, Wu B, Yu T, Zheng Y, Yang A, Zhao Q, Zhao D. Transcriptomics analysis revealing candidate genes and networks for sex differentiation of yesso scallop (Patinopecten yessoensis). BMC Genomics 2019; 20:671. [PMID: 31443640 PMCID: PMC6708199 DOI: 10.1186/s12864-019-6021-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/09/2019] [Indexed: 02/06/2023] Open
Abstract
Background The Yesso scallop, Patinopecten (Mizuhopecten) yessoensis, is a commercially important bivalve in the coastal countries of Northeast Asia. It has complex modes of sex differentiation, but knowledge of the mechanisms underlying this sex determination and differentiation is limited. Results In this study, the gonad tissues from females and males at three developmental stages were used to investigate candidate genes and networks for sex differentiation via RNA-Req. A total of 901,980,606 high quality clean reads were obtained from 18 libraries, of which 417 expressed male-specific genes and 754 expressed female-specific genes. Totally, 10,074 genes differentially expressed in females and males were identified. Weighted gene co-expression network analysis (WGCNA) revealed that turquoise and green gene modules were significantly positively correlated with male gonads, while coral1 and black modules were significantly associated with female gonads. The most important gene for sex determination and differentiation was Pydmrt 1, which was the only gene discovered that determined the male sex phenotype during early gonadal differentiation. Enrichment analyses of GO terms and KEGG pathways revealed that genes involved in metabolism, genetic and environmental information processes or pathways are sex-biased. Forty-nine genes in the five modules involved in sex differentiation or determination were identified and selected to construct a gene co-expression network and a hypothesized sex differentiation pathway. Conclusions The current study focused on screening genes of sex differentiation in Yesso scallop, highlighting the potential regulatory mechanisms of gonadal development in P. yessoensis. Our data suggested that WCGNA can facilitate identification of key genes for sex differentiation and determination. Using this method, a hypothesized P. yessoensis sex determination and differentiation pathway was constructed. In this pathway, Pydmrt 1 may have a leading function. Electronic supplementary material The online version of this article (10.1186/s12864-019-6021-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Liqing Zhou
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China.,Labortory for Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhihong Liu
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China.,Labortory for Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | | | - Xiujun Sun
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China.,Labortory for Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Biao Wu
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China.,Labortory for Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Tao Yu
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Science, Changdao, China
| | - Yanxin Zheng
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Science, Changdao, China
| | - Aiguo Yang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China. .,Labortory for Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Qing Zhao
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Dan Zhao
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
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15
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Xu M, Huang J, Shi Y, Zhang H, He M. Comparative transcriptomic and proteomic analysis of yellow shell and black shell pearl oysters, Pinctada fucata martensii. BMC Genomics 2019; 20:469. [PMID: 31176356 PMCID: PMC6555990 DOI: 10.1186/s12864-019-5807-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 05/17/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The pearl oyster Pinctada fucata martensii (Pfu.), widely cultured in the South China Sea, is a precious source of sea pearls and calcifying materials. A yellow shell variety of Pfu. was obtained after years of artificial breeding. To identify differentially expressed genes between yellow shell and normal black shell pearl oysters, we performed transcriptomic sequencing and proteomic analyses using mantle edge tissues. RESULTS A total of 56,969 unigenes were obtained from transcriptomic, of which 21,610 were annotated, including 385 annotated significant up-regulated genes and 227 significant down-regulated genes in yellow shell oysters (| log2 (fold change) | ≥2 and false discovery rate < 0.001). Tyrosine metabolism, calcium signalling pathway, phototransduction, melanogenesis pathways and rhodopsin related Gene Ontology (GO) terms were enriched with significant differentially expressed genes (DEGs) in transcriptomic. Proteomic sequencing identified 1769 proteins, of which 51 were significantly differentially expressed in yellow shell oysters. Calmodulin, N66 matrix protein, nacre protein and Kazal-type serine protease inhibitor were up-regulated in yellow shell oysters at both mRNA and protein levels, while glycine-rich protein shematrin-2, mantle gene 4, and sulphide: quinone oxidoreductase were down-regulated at two omics levels. Particularly, calmodulin, nacre protein N16.3, mantle gene 4, sulphide: quinone oxidoreductase, tyrosinase-like protein 3, cytochrome P450 3A were confirmed by quantitative real-time PCR. Yellow shell oysters possessed higher total carotenoid content (TCC) compared than black shell oyster based on spectrophotography. CONCLUSIONS The yellow phenotype of pearl oysters, characterised by higher total carotenoids content, may reflect differences in retinal and rhodopsin metabolism, melanogenesis, calcium signalling pathway and biomineralisation. These results provide insights for exploring the relationships between calcium regulation, biomineralisation and yellow shell colour pigmentation.
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Affiliation(s)
- Meng Xu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Shi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Hua Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Maoxian He
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
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