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Anjos C, Duarte D, Fatsini E, Matias D, Cabrita E. Comparative transcriptome analysis reveals molecular damage associated with cryopreservation in Crassostrea angulata D-larvae rather than to cryoprotectant exposure. BMC Genomics 2024; 25:591. [PMID: 38867206 PMCID: PMC11167747 DOI: 10.1186/s12864-024-10473-1] [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: 10/25/2023] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND The Portuguese oyster Crassostrea angulata, a bivalve of significant economic and ecological importance, has faced a decline in both production and natural populations due to pathologies, climate change, and anthropogenic factors. To safeguard its genetic diversity and improve reproductive management, cryopreservation emerges as a valuable strategy. However, the cryopreservation methodologies lead to some damage in structures and functions of the cells and tissues that can affect post-thaw quality. Transcriptomics may help to understand the molecular consequences related to cryopreservation steps and therefore to identify different freezability biomarkers. This study investigates the molecular damage induced by cryopreservation in C. angulata D-larvae, focusing on two critical steps: exposure to cryoprotectant solution and the freezing/thawing process. RESULTS Expression analysis revealed 3 differentially expressed genes between larvae exposed to cryoprotectant solution and fresh larvae and 611 differentially expressed genes in cryopreserved larvae against fresh larvae. The most significantly enriched gene ontology terms were "carbohydrate metabolic process", "integral component of membrane" and "chitin binding" for biological processes, cellular components and molecular functions, respectively. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified the "neuroactive ligand receptor interaction", "endocytosis" and "spliceosome" as the most enriched pathways. RNA sequencing results were validate by quantitative RT-PCR, once both techniques presented the same gene expression tendency and a group of 11 genes were considered important molecular biomarkers to be used in further studies for the evaluation of cryodamage. CONCLUSIONS The current work provided valuable insights into the molecular repercussions of cryopreservation on D-larvae of Crassostrea angulata, revealing that the freezing process had a more pronounced impact on larval quality compared to any potential cryoprotectant-induced toxicity. Additionally, was identify 11 genes serving as biomarkers of freezability for D-larvae quality assessment. This research contributes to the development of more effective cryopreservation protocols and detection methods for cryodamage in this species.
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Affiliation(s)
- Catarina Anjos
- Centre of Marine Sciences-CCMAR/CIMAR.LA, University of Algarve, Faro, 8005-139, Portugal
- Portuguese Institute for Sea and Atmosphere-IPMA, Av. 5 de Outubro, Olhão, 8700-305, Portugal
| | - Daniel Duarte
- Centre of Marine Sciences-CCMAR/CIMAR.LA, University of Algarve, Faro, 8005-139, Portugal
| | - Elvira Fatsini
- Centre of Marine Sciences-CCMAR/CIMAR.LA, University of Algarve, Faro, 8005-139, Portugal
| | - Domitília Matias
- Portuguese Institute for Sea and Atmosphere-IPMA, Av. 5 de Outubro, Olhão, 8700-305, Portugal
| | - Elsa Cabrita
- Centre of Marine Sciences-CCMAR/CIMAR.LA, University of Algarve, Faro, 8005-139, Portugal.
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Lu H, Chen W, Peng K, Huang M, Zhao J, Chen X, Sun Y, Ruan Z, Li C, Liu D, Liu Z, Li H, Zhang Y, Huang W. Rapid adaptive and acute stimulatory responses to low salinity stress in Pacific white shrimp (Litopenaeus vannamei): Insights from integrative transcriptomic and proteomic analysis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 48:101149. [PMID: 37883838 DOI: 10.1016/j.cbd.2023.101149] [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: 09/04/2023] [Revised: 09/28/2023] [Accepted: 10/15/2023] [Indexed: 10/28/2023]
Abstract
The Pacific white shrimp (Litopenaeus vannamei) is a euryhaline crustacean capable of tolerating a wide range of ambient salinity, but the strategies of hepatopancreas to rapid adaptive or acute stimulatory responses to extremely low salinity fluctuations remains unclear. In this study, we integrated transcriptomic and proteomic analyses on the hepatopancreas derived from rapid adaptative (RA) and acute stimulatory (AS) responses to extremely low salinity stress (0.3 ppt) to unveil specific regulatory mechanisms. The RA group displayed normal epithelial cells and tubule structures, while the AS group showed histological changes and lesions. A total of 754 and 649 differentially expressed genes (DEGs) were identified in RA and AS treatments, respectively. For proteome, a total of 206 and 66 differentially expressed proteins (DEPs) were obtained in the RA/CT and AS/CT comparison groups, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were conducted among the DEGs and DEPs, revealing that metabolic related pathways were significantly enriched pathways in both comparison groups. In addition, correlation analysis of transcriptomic and proteomic results showed that 20 and 3 pairs of DEGs/DEPs were identified in RA vs. CT and AS vs. CT comparison groups, respectively. This study is the first report on the rapid adaptive and acute stimulatory transcriptomic and proteomic responses of L. vannamei to extremely low salinity, shedding light on the mechanisms underlying osmoregulation in euryhaline crustaceans.
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Affiliation(s)
- Huijie Lu
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Wenchun Chen
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Kai Peng
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Minwei Huang
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jichen Zhao
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xiaoying Chen
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yuping Sun
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Zhuohao Ruan
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chaozheng Li
- Maoming Branch Center of Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Maoming 525099, China; State Key Laboratory of Biocontrol and School of Life Sciences, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ding Liu
- Guangdong Provincial Engineering Research Center of Prawn Culture, Guangdong Havwii Agricultural Group Co., Ltd., Zhanjiang 524000, China
| | - Zhenxing Liu
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Huo Li
- Guangdong Provincial Engineering and Technology Research Center, Guangdong Jinyang Biotechnology Co., Ltd., Maoming 525027, China
| | - Yong Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wen Huang
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; Maoming Branch Center of Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Maoming 525099, China; Guangdong Provincial Engineering Research Center of Prawn Culture, Guangdong Havwii Agricultural Group Co., Ltd., Zhanjiang 524000, China; Guangdong Provincial Engineering and Technology Research Center, Guangdong Jinyang Biotechnology Co., Ltd., Maoming 525027, China.
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Su M, Liu N, Zhang Z, Zhang J. Osmoregulatory strategies of estuarine fish Scatophagus argus in response to environmental salinity changes. BMC Genomics 2022; 23:545. [PMID: 35907798 PMCID: PMC9339187 DOI: 10.1186/s12864-022-08784-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 07/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Scatophagus argus, an estuarine inhabitant, can rapidly adapt to different salinity environments. However, the knowledge of the molecular mechanisms underlying its strong salinity tolerance remains unclear. The gill, as the main osmoregulatory organ, plays a vital role in the salinity adaptation of the fish, and thus relative studies are constructive to reveal unique osmoregulatory mechanisms in S. argus. RESULTS In the present study, iTRAQ coupled with nanoLC-MS/MS techniques were employed to explore branchial osmoregulatory mechanisms in S. argus acclimated to different salinities. Among 1,604 identified proteins, 796 differentially expressed proteins (DEPs) were detected. To further assess osmoregulatory strategies in the gills under different salinities, DEPs related to osmoregulatory (22), non-directional (18), hypo- (52), and hypersaline (40) stress responses were selected. Functional annotation analysis of these selected DEPs indicated that the cellular ion regulation (e.g. Na+-K+-ATPase [NKA] and Na+-K+-2Cl- cotransporter 1 [NKCC1]) and ATP synthesis were deeply involved in the osmoregulatory process. As an osmoregulatory protein, NKCC1 expression was inhibited under hyposaline stress but showed the opposite trend in hypersaline conditions. The expression levels of NKA α1 and β1 were only increased under hypersaline challenge. However, hyposaline treatments could enhance branchial NKA activity, which was inhibited under hypersaline environments, and correspondingly, reduced ATP content was observed in gill tissues exposed to hyposaline conditions, while its contents were increased in hypersaline groups. In vitro experiments indicated that Na+, K+, and Cl- ions were pumped out of branchial cells under hypoosmotic stress, whereas they were absorbed into cells under hyperosmotic conditions. Based on our results, we speculated that NKCC1-mediated Na+ influx was inhibited, and proper Na+ efflux was maintained by improving NKA activity under hyposaline stress, promoting the rapid adaptation of branchial cells to the hyposaline condition. Meanwhile, branchial cells prevented excessive loss of ions by increasing NKA internalization and reducing ATP synthesis. In contrast, excess ions in cells exposed to the hyperosmotic medium were excreted with sufficient energy supply, and reduced NKA activity and enhanced NKCC1-mediated Na+ influx were considered a compensatory regulation. CONCLUSIONS S. argus exhibited divergent osmoregulatory strategies in the gills when encountering hypoosmotic and hyperosmotic stresses, facilitating effective adaptabilities to a wide range of environmental salinity fluctuation.
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Affiliation(s)
- Maoliang Su
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Nanxi Liu
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Zhengqi Zhang
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Junbin Zhang
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
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Integrated Omics Approaches Revealed the Osmotic Stress-Responsive Genes and Microbiota in Gill of Marine Medaka. mSystems 2022; 7:e0004722. [PMID: 35285678 PMCID: PMC9040874 DOI: 10.1128/msystems.00047-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This is the first study using the transcriptome and 16S rRNA gene sequencing to report the hypotonic responsive genes in gill cells and the compositions of gill microbiota in marine medaka. The overlapped glycosaminoglycan- and chitin-related pathways suggest host-bacterium interaction in fish gill during osmotic stress.
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Xiang Y, Sun C, Zhao Y, Li L, Yang X, Wu Y, Chen S, Wei Y, Li C, Wang Y. Label-free proteomic analysis reveals freshness-related proteins in sea bass (Lateolabrax japonicus) fillets stored on ice. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112885] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Zhang Y, Liu J, Yu J, Zhang H, Yang Z. Relationship between the Phenylpropanoid Pathway and Dwarfism of Paspalum seashore Based on RNA-Seq and iTRAQ. Int J Mol Sci 2021; 22:ijms22179568. [PMID: 34502485 PMCID: PMC8431245 DOI: 10.3390/ijms22179568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 11/24/2022] Open
Abstract
Seashore paspalum is a major warm-season turfgrass requiring frequent mowing. The use of dwarf cultivars with slow growth is a promising method to decrease mowing frequency. The present study was conducted to provide an in-depth understanding of the molecular mechanism of T51 dwarfing in the phenylpropane pathway and to screen the key genes related to dwarfing. For this purpose, we obtained transcriptomic information based on RNA-Seq and proteomic information based on iTRAQ for the dwarf mutant T51 of seashore paspalum. The combined results of transcriptomic and proteomic analysis were used to identify the differential expression pattern of genes at the translational and transcriptional levels. A total of 8311 DEGs were detected at the transcription level, of which 2540 were upregulated and 5771 were downregulated. Based on the transcripts, 2910 proteins were identified using iTRAQ, of which 392 (155 upregulated and 237 downregulated) were DEPs. The phenylpropane pathway was found to be significantly enriched at both the transcriptional and translational levels. Combined with the decrease in lignin content and the increase in flavonoid content in T51, we found that the dwarf phenotype of T51 is closely related to the abnormal synthesis of lignin and flavonoids in the phenylpropane pathway. CCR and HCT may be the key genes for T51 dwarf. This study provides the basis for further study on the dwarfing mechanism of seashore paspalum. The screening of key genes lays a foundation for further studies on the molecular mechanism of seashore paspalum dwarfing.
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Lai KP, Gong Z, Tse WKF. Zebrafish as the toxicant screening model: Transgenic and omics approaches. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 234:105813. [PMID: 33812311 DOI: 10.1016/j.aquatox.2021.105813] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/04/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
The production of large amounts of synthetic industrial and biomedical compounds, together with environmental pollutants, poses a risk to our ecosystem and induces negative effects on the health of wildlife and human beings. With the emergence of the global problem of chemical contamination, the adverse biological effects of these chemicals are gaining attention among the scientific communities, industry, governments, and the public. Among these chemicals, endocrine disrupting chemicals (EDCs) are regarded as one of the major global issues that potentially affecting our health. There is an urgent need of understanding the potential hazards of such chemicals. Zebrafish have been widely used in the aquatic toxicology. In this review, we first discuss the strategy of transgenic lines that used in the toxicological studies, followed by summarizing the current omics approaches (transcriptomics, proteomics, metabolomics, and epigenomics) on toxicities of EDCs in this model. We will also discuss the possible transgenerational effects in zebrafish and future prospective of the integrated omics approaches with customized transgenic organism. To conclude, we summarize the current findings in the field, and provide our opinions on future environmental toxicity research in the zebrafish model.
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Affiliation(s)
- Keng Po Lai
- Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin 541004, PR China; Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin 541004, PR China; Department of Chemistry, City University of Hong Kong, Hong Kong SAR, PR China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, PR China.
| | - Zhiyuan Gong
- Department of Biological Sciences, National University of Singapore, 117543, Singapore.
| | - William Ka Fai Tse
- Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan.
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Wang W, Du J, Chen L, Zeng Y, Tan X, Shi Q, Pan X, Wu Z, Zeng Y. Transcriptomic, proteomic, and physiological comparative analyses of flooding mitigation of the damage induced by low-temperature stress in direct seeded early indica rice at the seedling stage. BMC Genomics 2021; 22:176. [PMID: 33706696 PMCID: PMC7952222 DOI: 10.1186/s12864-021-07458-9] [Citation(s) in RCA: 10] [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] [Received: 07/25/2020] [Accepted: 02/19/2021] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Low temperature (LT) often occurs at the seedling stage in the early rice-growing season, especially for direct seeded early-season indica rice, and using flooding irrigation can mitigate LT damage in rice seedlings. The molecular mechanism by which flooding mitigates the damage induced by LT stress has not been fully elucidated. Thus, LT stress at 8 °C, LT accompanied by flooding (LTF) and CK (control) treatments were established for 3 days to determine the transcriptomic, proteomic and physiological response in direct seeded rice seedlings at the seedling stage. RESULTS LT damaged chloroplasts, and thylakoid lamellae, and increased osmiophilic bodies and starch grains compared to CK, but LTF alleviated the damage to chloroplast structure caused by LT. The physiological characteristics of treated plants showed that compared with LT, LTF significantly increased the contents of rubisco, chlorophyll, PEPCK, ATP and GA3 but significantly decreased soluble protein, MDA and ABA contents. 4D-label-free quantitative proteomic profiling showed that photosynthesis-responsive proteins, such as phytochrome, as well as chlorophyll and the tricarboxylic acid cycle were significantly downregulated in LT/CK and LTF/CK comparison groups. However, compared with LT, phytochrome, chlorophyllide oxygenase activity and the glucan branching enzyme in LTF were significantly upregulated in rice leaves. Transcriptomic and proteomic studies identified 72,818 transcripts and 5639 proteins, and 4983 genes that were identified at both the transcriptome and proteome levels. Differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were significantly enriched in glycine, serine and threonine metabolism, biosynthesis of secondary metabolites, glycolysis/gluconeogenesis and metabolic pathways. CONCLUSION Through transcriptomic, proteomic and physiological analyses, we determined that a variety of metabolic pathway changes were induced by LT and LTF. GO and KEGG enrichment analyses demonstrated that DEGs and DEPs were associated with photosynthesis pathways, antioxidant enzymes and energy metabolism pathway-related proteins. Our study provided new insights for efforts to reduce the damage to direct seeded rice caused by low-temperature stress and provided a breeding target for low temperature flooding-resistant cultivars. Further analysis of translational regulation and metabolites may help to elucidate the molecular mechanisms by which flooding mitigates low-temperature stress in direct seeded early indica rice at the seedling stage.
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Affiliation(s)
- Wenxia Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education / Collaborative Innovation Center for the Modernization Production of Double Cropping Rice / College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jie Du
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education / Collaborative Innovation Center for the Modernization Production of Double Cropping Rice / College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Liming Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education / Collaborative Innovation Center for the Modernization Production of Double Cropping Rice / College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yongjun Zeng
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education / Collaborative Innovation Center for the Modernization Production of Double Cropping Rice / College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xueming Tan
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education / Collaborative Innovation Center for the Modernization Production of Double Cropping Rice / College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qinghua Shi
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education / Collaborative Innovation Center for the Modernization Production of Double Cropping Rice / College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaohua Pan
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education / Collaborative Innovation Center for the Modernization Production of Double Cropping Rice / College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ziming Wu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education / Collaborative Innovation Center for the Modernization Production of Double Cropping Rice / College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Yanhua Zeng
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education / Collaborative Innovation Center for the Modernization Production of Double Cropping Rice / College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China.
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Mikalsen SO, Tausen M, Í Kongsstovu S. Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies. BMC Genomics 2020; 21:223. [PMID: 32160866 PMCID: PMC7066803 DOI: 10.1186/s12864-020-6620-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/25/2020] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Based on an initial collecting of database sequences from the gap junction protein gene family (also called connexin genes) in a few teleosts, the naming of these sequences appeared variable. The reasons could be (i) that the structure in this family is variable across teleosts, or (ii) unfortunate naming. Rather clear rules for the naming of genes in fish and mammals have been outlined by nomenclature committees, including the naming of orthologous and ohnologous genes. We therefore analyzed the connexin gene family in teleosts in more detail. We covered the range of divergence times in teleosts (eel, Atlantic herring, zebrafish, Atlantic cod, three-spined stickleback, Japanese pufferfish and spotted pufferfish; listed from early divergence to late divergence). RESULTS The gene family pattern of connexin genes is similar across the analyzed teleosts. However, (i) several nomenclature systems are used, (ii) specific orthologous groups contain genes that are named differently in different species, (iii) several distinct genes have the same name in a species, and (iv) some genes have incorrect names. The latter includes a human connexin pseudogene, claimed as GJA4P, but which in reality is Cx39.2P (a delta subfamily gene often called GJD2like). We point out the ohnologous pairs of genes in teleosts, and we suggest a more consistent nomenclature following the outlined rules from the nomenclature committees. We further show that connexin sequences can indicate some errors in two high-quality chromosome assemblies that became available very recently. CONCLUSIONS Minimal consistency exists in the present practice of naming teleost connexin genes. A consistent and unified nomenclature would be an advantage for future automatic annotations and would make various types of subsequent genetic analyses easier. Additionally, roughly 5% of the connexin sequences point out misassemblies in the new high-quality chromosome assemblies from herring and cod.
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Affiliation(s)
- Svein-Ole Mikalsen
- Faculty of Science and Technology, University of the Faroe Islands, Vestara Bryggja 15, FO-100, Tórshavn, Faroe Islands.
| | - Marni Tausen
- Faculty of Science and Technology, University of the Faroe Islands, Vestara Bryggja 15, FO-100, Tórshavn, Faroe Islands
- Present affiliation: Bioinformatics Research Centre, Aarhus University, C. F. Møllers Allé 8, 8000, Aarhus C, Denmark
| | - Sunnvør Í Kongsstovu
- Faculty of Science and Technology, University of the Faroe Islands, Vestara Bryggja 15, FO-100, Tórshavn, Faroe Islands
- Amplexa Genetics A/S, Hoyvíksvegur 51, FO-100, Tórshavn, Faroe Islands
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Xu Q, Li X, Ma L, Loor JJ, Coleman DN, Jia H, Liu G, Xu C, Wang Y, Li X. Adipose tissue proteomic analysis in ketotic or healthy Holstein cows in early lactation1. J Anim Sci 2019; 97:2837-2849. [PMID: 31267132 DOI: 10.1093/jas/skz132] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/12/2019] [Indexed: 12/20/2022] Open
Abstract
Ketosis is a major metabolic disorder of high-yielding dairy cows during the transition period. Although metabolic adaptations of the adipose tissue are critical for a successful transition, beyond lipolysis, alterations within adipose tissue during ketosis are not well known. The objective of this study was to investigate the adipose tissue proteome of healthy or ketotic postpartum cows to gain insights into biological adaptations that may contribute to disease outcomes. Adipose tissue biopsy was collected on 5 healthy and 5 ketotic cows at 17 (±4) d postpartum and ketosis was defined according to the clinical symptoms and serum β-hydroxybutyrate concentration. Morphology micrographs stained by hematoxylin-eosin showed that adipocytes were smaller in ketotic cows than in healthy cows. The isobaric tag for relative and absolute quantification was applied to quantitatively identify differentially expressed proteins (DEP) in the adipose tissue. We identified a total of 924 proteins, 81 of which were differentially expressed between ketotic and healthy cows (P < 0.05 and fold changes >1.5 or <0.67). These DEP included enzymes and proteins associated with various carbohydrate, lipid, and amino acid metabolism processes. The top pathways differing between ketosis and control cows were glycolysis/gluconeogenesis, glucagon signaling pathway, cysteine and methionine metabolism, biosynthesis of amino acids, and the cGMP-PKG signaling pathway. The identified DEP were further validated by western blot and co-immunoprecipitation assay. Key enzymes associated with carbohydrate metabolism such as pyruvate kinase 2, pyruvate dehydrogenase E1 component subunit α), lactate dehydrogenase A , phosphoglucomutase 1, and 6-phosphofructokinase 1 were upregulated in ketotic cows. The expression and phosphorylation state of critical regulators of lipolysis such as perilipin-1 and hormone-sensitive lipase were also upregulated in ketotic cows. Furthermore, key proteins involved in maintaining innate immune response such as lipopolysaccharide binding protein and regakine-1 were downregulated in ketotic cows. Overall, data indicate that ketotic cows during the transition period have altered carbohydrate, lipid metabolism, and impaired immune function in the adipose tissue. This proteomics analysis in adipose tissue of ketotic cows identified several pathways and proteins that are components of the adaptation to ketosis.
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Affiliation(s)
- Qiushi Xu
- Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, Jilin, China
| | - Xiaobing Li
- Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, Jilin, China
| | - Li Ma
- Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, Jilin, China
| | - Juan J Loor
- Department of Animal Sciences and Division of Nutritional Sciences, Mammalian NutriPhysioGenomics, University of Illinois, Urbana, IL
| | - Danielle N Coleman
- Department of Animal Sciences and Division of Nutritional Sciences, Mammalian NutriPhysioGenomics, University of Illinois, Urbana, IL
| | - Hongdou Jia
- Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, Jilin, China
| | - Guowen Liu
- Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, Jilin, China
| | - Chuang Xu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yazhe Wang
- Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, Jilin, China
| | - Xinwei Li
- Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, 5333 Xi'an Road, Changchun, Jilin, China
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Fu S, Ding M, Liang Q, Yang Y, Chen M, Wei X, Wang A, Liao S, Ye J. The key differentially expressed genes and proteins related to immune response in the spleen of pufferfish (Takifugu obscurus) infected by Aeromonas hydrophila. FISH & SHELLFISH IMMUNOLOGY 2019; 91:1-11. [PMID: 31085326 DOI: 10.1016/j.fsi.2019.05.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 06/09/2023]
Abstract
The immune mechanism elicited in pufferfish (Takifugu obscurus) against the invasion of Aeromonas hydrophila is still poorly understood. We examined the spleen of pufferfish at the transcriptome and proteome levels by using Illumina-seq and TMT coupled mass spectrometry after 12 h infection by A. hydrophila, respectively. A total of 2,339 genes (1,512 up-regulated and 827 down-regulated) and 537 (237 up-regulated and 300 down-regulated) proteins were identified. GO and KEGG analyses revealed that the responses to stimulus were the main biological processes, intestinal immune network for IgT production and calcium signaling pathway. Fourteen genes (8 up-regulated and 6 down-regulated) and proteins (5 up-regulated and 9 down-regulated) involved immune responses or signal transduction were validated by qRT-PCR and parallel reaction monitoring to confirm the reliability of the transcriptomic and proteomic analyses, respectively. Moreover, qRT-PCR and flow cytometry were used to detect dynamics of the genes in calcium signaling pathway and changes of concentration of cytoplasm Ca2+ in spleen cells within a 72 h challenge. This study provides the findings regarding immune response, especially intestinal immune network for IgT production pathway and calcium signaling pathway at the molecular, protein and cellular in pufferfish after infection by A. hydrophila. These results would provide a new insight and molecular targets into the response to pathogenic infection in pufferfish.
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Affiliation(s)
- Shengli Fu
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Mingmei Ding
- School of Medicine, Sun Yat-Sen University, Guangzhou, 510006, PR China
| | - Qingjian Liang
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Yanjian Yang
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Meng Chen
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Xiufang Wei
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Anli Wang
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Shaoan Liao
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China.
| | - Jianmin Ye
- School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China.
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12
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Analyses of the molecular mechanisms associated with salinity adaption of Trachidermus fasciatus through combined iTRAQ-based proteomics and RNA sequencing-based transcriptomics. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 136:40-53. [DOI: 10.1016/j.pbiomolbio.2018.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/30/2018] [Accepted: 02/06/2018] [Indexed: 01/16/2023]
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13
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Ye H, Lin Q, Luo H. Applications of transcriptomics and proteomics in understanding fish immunity. FISH & SHELLFISH IMMUNOLOGY 2018; 77:319-327. [PMID: 29631024 DOI: 10.1016/j.fsi.2018.03.046] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 03/22/2018] [Accepted: 03/27/2018] [Indexed: 06/08/2023]
Abstract
With the development of intensive aquaculture, economic losses increasingly result from fish mortality due to pathogen infection. In recent years, a growing number of researchers have used transcriptomic and proteomic analyses to study fish immune responses to exogenous pathogen infection. Integrating transcriptomic and proteomic analyses provides a better understanding of the fish immune system including gene expression, regulation, and the intricate biological processes underlying immune responses against infection. This review focuses on the recent advances in the fields of transcriptomics and proteomics, which have contributed to our understanding of fish immunity to exogenous pathogens.
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Affiliation(s)
- Hua Ye
- College of Animal Science, Southwest University, Chongqing 402460, China; Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Hui Luo
- College of Animal Science, Southwest University, Chongqing 402460, China.
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14
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Xu Y, Shi J, Hao W, Xiang T, Zhou H, Wang W, Meng Q, Ding Z. iTRAQ-based quantitative proteomic analysis of Procambarus clakii hemocytes during Spiroplasma eriocheiris infection. FISH & SHELLFISH IMMUNOLOGY 2018; 77:438-444. [PMID: 29625245 DOI: 10.1016/j.fsi.2018.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/13/2018] [Accepted: 04/02/2018] [Indexed: 06/08/2023]
Abstract
As a new-found aquaculture pathogen, Spiroplasma eriocheiris, has resulted in inconceivable economic losses in aquaculture. In the infection of S. eriocheiris, the Procambarus clakii hemocytes have indicated to be major target cells. What was designed to examine in our study is the hemocytes' immune response at the protein levels. Before the pathogen was injected and after 192 h of post-injection, the differential proteomes of the crayfish hemocytes were analyzed immediately by isobaric tags for relative and absolute quantization (iTRAQ) labeling, followed by liquid chromatogramphytandem mass spectrometry (LC-MS/MS). This research had identified a total of 285 differentially expressed proteins. Eighty-three and 202 proteins were up-regulated and down-regulated, respectively, caused by the S. eriocheiris infection. Up-regulated proteins included alpha-2-macroglobulin (α2M), vitellogenin, ferritin, etc. Down-regulated proteins, involved with serine protease, peroxiredoxin 6, 14-3-3-like protein, C-type lectin, cdc42 homolog precursor, etc. The prophenoloxidase-activating system, antimicrobial action involved in the immune responses of P. clarkii is considered to be damaged due to S. eriocheiris infection. The present work could lay the foundation for future research on the proteins related to the susceptibility/resistance of P. clarkii to S. eriocheiris. In addition, it is helpful for our understanding molecular mechanism of disease processes in crayfishes.
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Affiliation(s)
- Yinbin Xu
- Jiangsu Key Laboratory for Biodiversity & Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Jinyan Shi
- Jiangsu Key Laboratory for Biofunctional Molecules & Aquatic Institute of Jiangsu Second Normal University, College of Life Science and Chemistry, Jiangsu Second Normal University, 77 West Beijing Road, Nanjing, 210013, China
| | - Wenjing Hao
- Jiangsu Key Laboratory for Biodiversity & Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Tao Xiang
- Jiangsu Key Laboratory for Biodiversity & Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Haifeng Zhou
- Jiangsu Key Laboratory for Biodiversity & Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Wen Wang
- Jiangsu Key Laboratory for Biodiversity & Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Qingguo Meng
- Jiangsu Key Laboratory for Biodiversity & Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China.
| | - Zhengfeng Ding
- Jiangsu Key Laboratory for Biofunctional Molecules & Aquatic Institute of Jiangsu Second Normal University, College of Life Science and Chemistry, Jiangsu Second Normal University, 77 West Beijing Road, Nanjing, 210013, China.
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15
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Cao Q, Gu J, Wang D, Liang F, Zhang H, Li X, Yin S. Physiological mechanism of osmoregulatory adaptation in anguillid eels. FISH PHYSIOLOGY AND BIOCHEMISTRY 2018; 44:423-433. [PMID: 29344774 PMCID: PMC5862950 DOI: 10.1007/s10695-018-0464-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 01/03/2018] [Indexed: 06/07/2023]
Abstract
In recent years, the production of eel larvae has dramatic declines due to reductions in spawning stocks, overfishing, growth habitat destruction and access reductions, and pollution. Therefore, it is particularly important and urgent for artificial production of glass eels. However, the technique of artificial hatching and rearing larvae is still immature, which has long been regarded as an extremely difficult task. One of the huge gaps is artificial condition which is far from the natural condition to develop their capability of osmoregulation. Thus, understanding their osmoregulatory mechanisms will help to improve the breed and adapt to the changes in the environment. In this paper, we give a general review for a study progress of osmoregulatory mechanisms in eels from five aspects including tissues and organs, ion transporters, hormones, proteins, and high throughput sequencing methods.
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Affiliation(s)
- Quanquan Cao
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu Province, 210023, China
| | - Jie Gu
- Institute of Life Science, Jiangsu University, Zhenjiang, Jiangsu, 212000, China
| | - Dan Wang
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu Province, 210023, China
| | - Fenfei Liang
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu Province, 210023, China
| | - Hongye Zhang
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu Province, 210023, China
| | - Xinru Li
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu Province, 210023, China
| | - Shaowu Yin
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu Province, 210023, China.
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16
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Gu J, Dai S, Liu H, Cao Q, Yin S, Lai KP, Tse WKF, Wong CKC, Shi H. Identification of immune-related genes in gill cells of Japanese eels (Anguilla japonica) in adaptation to water salinity changes. FISH & SHELLFISH IMMUNOLOGY 2018; 73:288-296. [PMID: 29269288 DOI: 10.1016/j.fsi.2017.12.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/06/2017] [Accepted: 12/17/2017] [Indexed: 06/07/2023]
Abstract
The changes in ambient salinity influence ion and water homeostasis, hormones secretion, and immune response in fish gills. The physiological functions of hormones and ion transporters in the regulation of gill-osmoregulation have been widely studied, however the modulation of immune response under salinity changes is not determined. Using transcriptome sequencing, we obtained a comprehensive profile of osmo-responsive genes in gill cells of Japanese eel (Anguilla japonica). Herein, we applied bioinformatics analysis to identify the immune-related genes that were significantly higher expressed in gill pavement cells (PVCs) and mitochondrial-rich cells (MRCs) in freshwater (FW) than seawater (SW) adapted fish. We validated the data using the real-time qPCR, which showed a high correlation between the RNA-seq and real-time qPCR data. In addition, the immunohistochemistry results confirmed the changes of the expression of selected immune-related genes, including C-reactive protein (CRP) in PVCs, toll-like receptor 2 (TLR2) in MRCs and interleukin-1 receptor type 2 (IL-1R2) in both PVCs and MRCs. Collectively our results demonstrated that those immune-related genes respond to salinity changes, and might trigger related special signaling pathways and network. This study provides new insights into the impacts of ambient salinity changes on adaptive immune response in fish gill cells.
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Affiliation(s)
- Jie Gu
- Institute of Life Science, Jiangsu University, Zhenjiang, Jiangsu, 212000, China
| | - Shuya Dai
- Institute of Life Science, Jiangsu University, Zhenjiang, Jiangsu, 212000, China
| | - Haitao Liu
- Institute of Life Science, Jiangsu University, Zhenjiang, Jiangsu, 212000, China
| | - Quanquan Cao
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Shaowu Yin
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Keng Po Lai
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong
| | | | | | - Haifeng Shi
- Institute of Life Science, Jiangsu University, Zhenjiang, Jiangsu, 212000, China.
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17
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Mu H, Sun J, Heras H, Chu KH, Qiu JW. Dataset for the proteomic and transcriptomic analyses of perivitelline fluid proteins in Pomacea snail eggs. Data Brief 2017; 15:203-207. [PMID: 29021998 PMCID: PMC5633349 DOI: 10.1016/j.dib.2017.09.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 08/03/2017] [Accepted: 09/12/2017] [Indexed: 11/30/2022] Open
Abstract
This article describes how the proteomic and transcriptomic data were produced during a study of the reproductive proteins of Pomacea maculata, an aquatic apple snail laying colorful aerial eggs, and provides public access to the data. The data are related to a research article titled ‘An integrated proteomic and transcriptomic analysis of perivitelline fluid proteins in a freshwater gastropod laying aerial eggs’ (Mu et al., 2017) [1]. RNA was extracted from the albumen gland and other tissues and sequenced on an Illumina Hiseq. 2000. The assembled transcriptome was translated into protein sequences and then used for protein identification. Proteins from the perivitelline fluid of P. maculata were separated in SDS-PAGE and analyzed by LTQ-Orbitrap Elite coupled to an Easy-nLC. The translated transcriptome data are provided in this article. Proteomic data (.raw file format) are available via ProteomeXchange with the identifier PXD006718.
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Affiliation(s)
- Huawei Mu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Jin Sun
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Horacio Heras
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), Universidad Nacional de La Plata (UNLP)-CONICET CCT-La Plata, La Plata, Argentina.,Cátedra de Química Biológica, Facultad de Ciencias Naturales y Museo, UNLP, Argentina
| | - Ka Hou Chu
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
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18
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Wang L, Shao C, Xu W, Zhou Q, Wang N, Chen S. Proteome profiling reveals immune responses in Japanese flounder (Paralichthys olivaceus) infected with Edwardsiella tarda by iTRAQ analysis. FISH & SHELLFISH IMMUNOLOGY 2017; 66:325-333. [PMID: 28511951 DOI: 10.1016/j.fsi.2017.05.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 05/04/2017] [Accepted: 05/06/2017] [Indexed: 06/07/2023]
Abstract
The liver is an important organ for bacterial pathogen attack in fish. The differential proteomic response of the Japanese flounder liver to Edwardsiella tarda infection was examined using isobaric tags for relative and absolute quantitation (iTRAQ) labeling followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 3290 proteins were identified and classified into categories related to biological process (51.4%), molecular function (63.6%), and cellular component (57.7%). KEGG enrichment analysis indicated the complement and coagulation cascade pathways and the mineral absorption pathway were significantly enriched. Among the differentially expressed proteins, those involved in mediating complement cascade (e.g. complement component C7, C8, C9, complement factor H, complement factor Bf/C2) and mineral absorption (e.g. ferritin, STEAP-4) were most significantly upregulated during infection. Subsequently, five significantly upregulated (C4, C8beta, ferritin middle subunit, PRDX4-like and KRT18) and one significantly downregulated (transferrin) candidate immune proteins were validated by multiple reaction monitoring (MRM) assays. Furthermore, changes in expression of 15 proteins in the complement cascade and mineral absorption pathways were validated at the transcriptional level using quantitative real-time PCR (qPCR). The transcriptional levels of four transcription factors (p21Ras, Rab-31-like, NF-κB, STAT3) were also investigated by qPCR following infection with E. tarda. This study contributes to understanding the defense mechanisms of the liver in fish.
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Affiliation(s)
- Lei Wang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Changwei Shao
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Wenteng Xu
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Qian Zhou
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Na Wang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Songlin Chen
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, 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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Dick JM. Chemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress. PeerJ 2017; 5:e3421. [PMID: 28603672 PMCID: PMC5463988 DOI: 10.7717/peerj.3421] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/16/2017] [Indexed: 12/19/2022] Open
Abstract
The changes of protein expression that are monitored in proteomic experiments are a type of biological transformation that also involves changes in chemical composition. Accompanying the myriad molecular-level interactions that underlie any proteomic transformation, there is an overall thermodynamic potential that is sensitive to microenvironmental conditions, including local oxidation and hydration potential. Here, up- and down-expressed proteins identified in 71 comparative proteomics studies were analyzed using the average oxidation state of carbon (ZC) and water demand per residue (\documentclass[12pt]{minimal}
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}{}${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$\end{document}n¯H2O), calculated using elemental abundances and stoichiometric reactions to form proteins from basis species. Experimental lowering of oxygen availability (hypoxia) or water activity (hyperosmotic stress) generally results in decreased ZC or \documentclass[12pt]{minimal}
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}{}${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$\end{document}n¯H2O of up-expressed compared to down-expressed proteins. This correspondence of chemical composition with experimental conditions provides evidence for attraction of the proteomes to a low-energy state. An opposite compositional change, toward higher average oxidation or hydration state, is found for proteomic transformations in colorectal and pancreatic cancer, and in two experiments for adipose-derived stem cells. Calculations of chemical affinity were used to estimate the thermodynamic potentials for proteomic transformations as a function of fugacity of O2 and activity of H2O, which serve as scales of oxidation and hydration potential. Diagrams summarizing the relative potential for formation of up- and down-expressed proteins have predicted equipotential lines that cluster around particular values of oxygen fugacity and water activity for similar datasets. The changes in chemical composition of proteomes are likely linked with reactions among other cellular molecules. A redox balance calculation indicates that an increase in the lipid to protein ratio in cancer cells by 20% over hypoxic cells would generate a large enough electron sink for oxidation of the cancer proteomes. The datasets and computer code used here are made available in a new R package, canprot.
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Wang T, Long X, Chen X, Liu Y, Liu Z, Han S, Yan S. Integrated transcriptome, proteome and physiology analysis of Epinephelus coioides after exposure to copper nanoparticles or copper sulfate. Nanotoxicology 2017; 11:236-246. [DOI: 10.1080/17435390.2017.1290291] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tao Wang
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, PR China
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, PR China
| | - Xiaohua Long
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, PR China
| | - Xiaoyan Chen
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, PR China
| | - Yuanrui Liu
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, PR China
| | - Zhaopu Liu
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, PR China
| | - Shiqun Han
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, PR China
| | - Shaohua Yan
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, PR China
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, PR China
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21
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Mu H, Sun J, Heras H, Chu KH, Qiu JW. An integrated proteomic and transcriptomic analysis of perivitelline fluid proteins in a freshwater gastropod laying aerial eggs. J Proteomics 2017; 155:22-30. [PMID: 28095328 DOI: 10.1016/j.jprot.2017.01.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 01/04/2017] [Accepted: 01/08/2017] [Indexed: 11/27/2022]
Abstract
Proteins of the egg perivitelline fluid (PVF) that surrounds the embryo are critical for embryonic development in many animals, but little is known about their identities. Using an integrated proteomic and transcriptomic approach, we identified 64 proteins from the PVF of Pomacea maculata, a freshwater snail adopting aerial oviposition. Proteins were classified into eight functional groups: major multifunctional perivitellin subunits, immune response, energy metabolism, protein degradation, oxidation-reduction, signaling and binding, transcription and translation, and others. Comparison of gene expression levels between tissues showed that 22 PVF genes were exclusively expressed in albumen gland, the female organ that secretes PVF. Base substitution analysis of PVF and housekeeping genes between P. maculata and its closely related species Pomacea canaliculata showed that the reproductive proteins had a higher mean evolutionary rate. Predicted 3D structures of selected PVF proteins showed that some nonsynonymous substitutions are located at or near the binding regions that may affect protein function. The proteome and sequence divergence analysis revealed a substantial amount of maternal investment in embryonic nutrition and defense, and higher adaptive selective pressure on PVF protein-coding genes when compared with housekeeping genes, providing insight into the adaptations associated with the unusual reproductive strategy in these mollusks. SIGNIFICANCE There has been great interest in studying reproduction-related proteins as such studies may not only answer fundamental questions about speciation and evolution, but also solve practical problems of animal infertility and pest outbreak. Our study has demonstrated the effectiveness of an integrated proteomic and transcriptomic approach in understanding the heavy maternal investment of proteins in the eggs of a non-model snail, and how the reproductive proteins may have evolved during the transition from laying underwater eggs to aerial eggs.
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Affiliation(s)
- Huawei Mu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Jin Sun
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Horacio Heras
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), Universidad Nacional de La Plata (UNLP)-CONICET CCT-La Plata, La Plata, Argentina; Cátedra de Química Biológica, Facultad de Ciencias Naturales y Museo, UNLP, Argentina
| | - Ka Hou Chu
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.
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22
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Proteomic response of mouse pituitary gland under heat stress revealed active regulation of stress responsive proteins. J Therm Biol 2016; 61:82-90. [DOI: 10.1016/j.jtherbio.2016.08.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 08/27/2016] [Accepted: 08/29/2016] [Indexed: 11/22/2022]
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23
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Zhao X, Yu H, Kong L, Li Q. Gene Co-Expression Network Analysis Reveals the Correlation Patterns Among Genes in Euryhaline Adaptation of Crassostrea gigas. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:535-544. [PMID: 27704223 DOI: 10.1007/s10126-016-9715-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 07/06/2016] [Indexed: 06/06/2023]
Abstract
The Pacific oyster Crassostrea gigas is a dominant aquaculture species in many intertidal zones throughout the Pacific and Atlantic Oceans and can tolerate a wide range of salinity. Studying the gene expression profiles of oyster gills had found differentially expressed genes (DEGs) involved in salinity tolerance. A systematic study of cellular response to salinity stress may provide insights into the mechanism of acquired salinity tolerance. Here, weighted gene co-expression network analysis (WGCNA) was carried out using RNA-seq data from gill transcriptome in response to different salinity. A total of 25,463 genes were parsed into 22 gene modules, of which 5 gene modules were identified as salinity-related modules. Brown module was the only one significantly correlated with salinity and free amino acids (FAAs) contents, which was associated with cellular metabolism, biosynthesis of amino acids, oxidation reduction, electron transport, nitrogen compound metabolism, and others. The enriched pathways in brown module were mainly about FAAs metabolism. The other four modules were significantly correlated with certain FAAs, and were over-represented in certain salinity. These results indicated that C. gigas triggered different FAAs in different salinity stress. This study represents the first RNA-seq gene network analysis in oysters responding to different salinity stresses. These results provide a systems-level framework to help understand the complexity of cellular process in response to osmotic stress and show the function and regulated genes of different FAAs at the molecular level.
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Affiliation(s)
- Xuelin Zhao
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
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24
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Wang BG, Wu Y, Qiu L, Shah NP, Xu F, Wei H. Integration of genomic and proteomic data to identify candidate genes in HT-29 cells after incubation with Bifidobacterium bifidum ATCC 29521. J Dairy Sci 2016; 99:6874-6888. [PMID: 27372578 DOI: 10.3168/jds.2015-10577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/31/2016] [Indexed: 11/19/2022]
Abstract
As the predominant group inhabiting the human gastrointestinal tract, bifidobacteria play a vital role in human nutrition, therapeutics, and health by shaping and maintaining the gut ecosystem, reducing blood cholesterol, and promoting the supply of nutrients. The interaction between bacterial cells and human intestinal epithelial cell lines has been studied for decades in an attempt to understand the mechanisms of action. These studies, however, have been limited by lack of genomic and proteomic database to aid in achieving comprehensive understanding of these mechanisms at molecular levels. Microarray data (GSE: 74119) coupled with isobaric tags for relative and absolute quantitation (iTRAQ) were performed to detect differentially expressed genes and proteins in HT-29 cells after incubation with Bifidobacterium bifidum. Real-time quantitative PCR, gene ontology, and Kyoto Encyclopedia of Genes and Genomes analyses were further conducted for mRNA validation, functional annotation, and pathway identification, respectively. According to the results of microarray, 1,717 differentially expressed genes, including 1,693 upregulated and 24 downregulated genes, were selected and classified by the gene ontology database. The iTRAQ analysis identified 43 differentially expressed proteins, where 29 proteins were upregulated and 14 proteins were downregulated. Eighty-two candidate genes showing consistent differences with microarray and iTRAQ were further validated in HT-29 and Caco-2 cells by real-time quantitative PCR. Nine of the top genes showing interesting results with high confidence were further investigated in vivo in mice intestine samples. Integration of genomic and proteomic data provides an approach to identify candidate genes that are more likely to function in ubiquitin-mediated proteolysis, positive regulation of apoptosis, membrane proteins, and transferase catalysis. These findings might contribute to our understanding of molecular mechanisms regulating the interaction between probiotics and intestinal epithelial cell lines.
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Affiliation(s)
- Bao-Gui Wang
- State Key Laboratory of Food Science and Engineering, Nanchang University, Nanchang, Jiangxi 330047, P. R. China
| | - Yaoping Wu
- State Key Laboratory of Food Science and Engineering, Nanchang University, Nanchang, Jiangxi 330047, P. R. China
| | - Liang Qiu
- State Key Laboratory of Food Science and Engineering, Nanchang University, Nanchang, Jiangxi 330047, P. R. China; Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, P.R. China
| | - Nagendra P Shah
- Food and Nutritional Science, School of Biological Sciences, The University of Hong Kong, Hong Kong
| | - Feng Xu
- State Key Laboratory of Food Science and Engineering, Nanchang University, Nanchang, Jiangxi 330047, P. R. China
| | - Hua Wei
- State Key Laboratory of Food Science and Engineering, Nanchang University, Nanchang, Jiangxi 330047, P. R. China.
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Jia Y, Yin S, Li L, Li P, Liang F, Wang X, Wang X, Wang L, Su X. iTRAQ proteomic analysis of salinity acclimation proteins in the gill of tropical marbled eel (Anguilla marmorata). FISH PHYSIOLOGY AND BIOCHEMISTRY 2016; 42:935-946. [PMID: 26721661 DOI: 10.1007/s10695-015-0186-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 12/21/2015] [Indexed: 06/05/2023]
Abstract
Osmoregulation plays an important role in the migration process of catadromous fish. The osmoregulatory mechanisms of tropical marbled eel (Anguilla marmorata), a typical catadromous fish, did not gain sufficient attention, especially at the molecular level. In order to enrich the protein database of A. marmorata, a proteomic analysis has been carried out by iTRAQ technique. Among 1937 identified proteins in gill of marbled eel, the expression of 1560 proteins (80 %) was quantified. Compared with the protein expression level in the gill of marbled eel in freshwater (salinity of 0 ‰), 336 proteins were up-regulated and 67 proteins were down-regulated in seawater (salinity of 25 ‰); 33 proteins were up-regulated and 32 proteins were down-regulated in brackish water (salinity of 10 ‰). These up-regulated proteins including Na(+)/K(+)-ATPase, V-type proton ATPase, sodium-potassium-chloride co-transporter and heat shock protein 90 were enriched in many KEGG-annotated pathways, which are related to different functions of the gill. The up-regulated oxidative phosphorylation and seleno-compound metabolism pathways involve the synthesis and consumption of ATP, which represents extra energy consumption. Another identified pathway is the ribosome pathway in which a large number of up-regulated proteins are involved. It is also more notable that tight junction and cardiac muscle contraction pathways may have correlation with ion transport in gill cells. This is the first report describing the proteome of A. marmorata for acclimating to the change of salinity. These results provide a functional database for migratory fish and point out some possible new interactions on osmoregulation in A. marmorata.
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Affiliation(s)
- Yihe Jia
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China
| | - Shaowu Yin
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China.
| | - Li Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China
| | - Fenfei Liang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China
| | - Xiaolu Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China
| | - Xiaojun Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China
| | - Li Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China
| | - Xinhua Su
- Department of Life Sciences, Glasgow Caledonian University, Cowcaddens Road, Glasgow, UK
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Wang Y, Xiao X, Wang X, Zeng J, Kang H, Fan X, Sha L, Zhang H, Zhou Y. RNA-Seq and iTRAQ Reveal the Dwarfing Mechanism of Dwarf Polish Wheat (Triticum polonicum L.). Int J Biol Sci 2016; 12:653-66. [PMID: 27194943 PMCID: PMC4870709 DOI: 10.7150/ijbs.14577] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/15/2016] [Indexed: 11/05/2022] Open
Abstract
The dwarfing mechanism of Rht-dp in dwarf Polish wheat (DPW) is unknown. Each internode of DPW was significantly shorter than it in high Polish wheat (HPW), and the dwarfism was insensitive to photoperiod, abscisic acid (ABA), gibberellin (GA), cytokinin (CK), auxin and brassinolide (BR). To understand the mechanism, three sets of transcripts, DPW, HPW, and a chimeric set (a combination of DPW and HPW), were constructed using RNA sequencing (RNA-Seq). Based on the chimeric transcripts, 2,446 proteins were identified using isobaric tags for relative and absolute quantification (iTRAQ). A total of 108 unigenes and 12 proteins were considered as dwarfism-related differentially expressed genes (DEGs) and differentially expressed proteins (DEPs), respectively. Among of these DEGs and DEPs, 6 DEGs and 6 DEPs were found to be involved in flavonoid and S-adenosyl-methionine (SAM) metabolisms; 5 DEGs and 3 DEPs were involved in cellulose metabolism, cell wall plasticity and cell expansion; 2 DEGs were auxin transporters; 2 DEPs were histones; 1 DEP was a peroxidase. These DEGs and DEPs reduced lignin and cellulose contents, increased flavonoid content, possibly decreased S-adenosyl-methionine (SAM) and polyamine contents and increased S-adenosyl-L-homocysteine hydrolase (SAHH) content in DPW stems, which could limit auxin transport and reduce extensibility of the cell wall, finally limited cell expansion (the cell size of DPW was significantly smaller than HPW cells) and caused dwarfism in DPW.
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Affiliation(s)
- Yi Wang
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Xue Xiao
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Xiaolu Wang
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Jian Zeng
- 2. College of Resources, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Houyang Kang
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Xing Fan
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Lina Sha
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Haiqin Zhang
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Yonghong Zhou
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
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27
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Lau MCC, Kwong EML, Lai KP, Li JW, Ho JCH, Chan TF, Wong CKC, Jiang YJ, Tse WKF. Pathogenesis of POLR1C-dependent Type 3 Treacher Collins Syndrome revealed by a zebrafish model. Biochim Biophys Acta Mol Basis Dis 2016; 1862:1147-58. [PMID: 26972049 DOI: 10.1016/j.bbadis.2016.03.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 02/05/2016] [Accepted: 03/09/2016] [Indexed: 10/22/2022]
Abstract
Treacher Collins Syndrome (TCS) is a rare congenital birth disorder (1 in 50,000 live births) characterized by severe craniofacial defects, including the downward slanting palpebral fissures, hypoplasia of the facial bones, and cleft palate (CP). Over 90% of patients with TCS have a mutation in the TCOF1 gene. However, some patients exhibit mutations in two new causative genes, POLR1C and POLR1D, which encode subunits of RNA polymerases I and III, that affect ribosome biogenesis. In this study, we examine the role of POLR1C in TCS using zebrafish as a model system. Our data confirmed that polr1c is highly expressed in the facial region, and dysfunction of this gene by knockdown or knock-out resulted in mis-expression of neural crest cells during early development that leads to TCS phenotype. Next generation sequencing and bioinformatics analysis of the polr1c mutants further demonstrated the up-regulated p53 pathway and predicted skeletal disorders. Lastly, we partially rescued the TCS facial phenotype in the background of p53 mutants, which supported the hypothesis that POLR1C-dependent type 3 TCS is associated with the p53 pathway.
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Affiliation(s)
| | | | - Keng Po Lai
- School of Biological Sciences, The University of Hong Kong, Hong Kong
| | - Jing-Woei Li
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | | | - Ting-Fung Chan
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | | | - Yun-Jin Jiang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Taiwan
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28
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Liu YC, Hsu SD, Chou CH, Huang WY, Chen YH, Liu CY, Lyu GJ, Huang SZ, Aganezov S, Alekseyev MA, Hsiao CD, Huang HD. Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome. BMC Genomics 2016; 17 Suppl 1:13. [PMID: 26818233 PMCID: PMC4895481 DOI: 10.1186/s12864-015-2306-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Background Anguilla japonica (Japanese eel) is currently one of the most important research subjects in eastern Asia aquaculture. Enigmatic life cycle of the organism makes study of artificial reproduction extremely limited. Henceforth genomic and transcriptomic resources of eels are urgently needed to help solving the problems surrounding this organism across multiple fields. We hereby provide a reconstructed transcriptome from deep sequencing of juvenile (glass eels) whole body samples. The provided expressed sequence tags were used to annotate the currently available draft genome sequence. Homologous information derived from the annotation result was applied to improve the group of scaffolds into available linkage groups. Results With the transcriptome sequence data combined with publicly available expressed sequence tags evidences, 18,121 genes were structurally and functionally annotated on the draft genome. Among them, 3,921 genes were located in the 19 linkage groups. 137 scaffolds covering 13 million bases were grouped into the linkage groups in additional to the original partial linkage groups, increasing the linkage group coverage from 13 to 14 %. Conclusions This annotation provide information of the coding regions of the genes supported by transcriptome based evidence. The derived homologous evidences pave the way for phylogenetic analysis of important genetic traits and the improvement of the genome assembly. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2306-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu-Chen Liu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC
| | - Sheng-Da Hsu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC
| | - Chih-Hung Chou
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC
| | - Wei-Yun Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC
| | - Yu-Hung Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC
| | - Chia-Yu Liu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC
| | - Guan-Jay Lyu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC
| | - Shao-Zhen Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC
| | - Sergey Aganezov
- Computational Biology Institute & Department of Mathematics, George Washington University, Washington, DC, USA.,Department of Higher Mathematics, ITMO University, St. Petersburg, Russia
| | - Max A Alekseyev
- Computational Biology Institute & Department of Mathematics, George Washington University, Washington, DC, USA
| | - Chung-Der Hsiao
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, ROC.
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC. .,Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, 300, Taiwan, ROC. .,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan.
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29
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Hou L, Xiu Y, Wang J, Liu X, Liu Y, Gu W, Wang W, Meng Q. iTRAQ-based quantitative proteomic analysis of Macrobrachium rosenbergii hemocytes during Spiroplasma eriocheiris infection. J Proteomics 2015; 136:112-22. [PMID: 26746008 DOI: 10.1016/j.jprot.2015.12.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/15/2015] [Accepted: 12/25/2015] [Indexed: 12/01/2022]
Abstract
UNLABELLED Spiroplasma eriocheiris, as a novel aquaculture pathogen, has led into catastrophic economic losses in aquaculture. The Macrobrachium rosenbergii hemocytes were major target cells in S. eriocheiris infection. Our study was designed to examine the hemocytes' immune response at the protein levels. The differential proteomes of the prawn hemocytes were analyzed immediately prior to injection with the pathogen, and at 192h post-injection by isobaric tags for relative and absolute quantization (iTRAQ) labeling, followed by liquid chromatogramphytandem mass spectrometry (LC-MS/MS). A total of 69 differentially expressed proteins were identified. Forty-nine proteins were up-regulated and 20 proteins were down-regulated resulting from a S. eriocheiris infection. Up-regulated proteins included vertebrate gliacolin-like protein, vitellogenin, Gram-negative binding protein 1, alpha2 macroglobulin isoform 2 (a2M), etc. Down-regulated proteins, involved with beta-1,3-glucan-binding protein (BGBP), immunoglobulin like, Rab7, lipopolysaccharide and β-1,3-glucan (LGBP), actin-related protein, etc. Selected bioactive factors (tachylectin, α2M and vitellogenin, BGBP, C-type lectin, LGBP and Rab7) were verified by their immune roles in the S. eriocheiris infection using real-time PCR. The present work could serve as a basis for future studies on the proteins implicated in the susceptibility/resistance of M. rosenbergii to S. eriocheiris, as well as contribute to our understanding of disease processes in prawns. BIOLOGICAL SIGNIFICANCE This is the first time using an iTRAQ approach to analyze proteomes of M. rosenbergii mobilized against S. eriocheiris infection and substantiated the hemocytes' proteomic changes in M. rosenbergii using an infection model. The results reported here can provide a significant step forward toward a more complete elucidation of the immune relationship between M. rosenbergii and the pathogen S. eriocheiris.
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Affiliation(s)
- Libo Hou
- Jiangsu Key Laboratory for Biodiversity & Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China; Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Yunji Xiu
- Jiangsu Key Laboratory for Biodiversity & Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China; Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China; Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Jian Wang
- Jiangsu Key Laboratory for Biodiversity & Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China; Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Xiaoqian Liu
- Jiangsu Province Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Yuhan Liu
- Jiangsu Key Laboratory for Biodiversity & Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China; Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Wei Gu
- Jiangsu Key Laboratory for Biodiversity & Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China; Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Wen Wang
- Jiangsu Key Laboratory for Biodiversity & Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China; Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Qingguo Meng
- Jiangsu Key Laboratory for Biodiversity & Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China; Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China.
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30
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Lai KP, Li JW, Gu J, Chan TF, Tse WKF, Wong CKC. Transcriptomic analysis reveals specific osmoregulatory adaptive responses in gill mitochondria-rich cells and pavement cells of the Japanese eel. BMC Genomics 2015; 16:1072. [PMID: 26678671 PMCID: PMC4683740 DOI: 10.1186/s12864-015-2271-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/03/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Homeostasis of ions and water is important for the maintenance of cellular functions. The regulation of the homeostasis is particularly important in euryhaline fish that migrate between freshwater (FW) and seawater (SW) environments. The fish gill, the major tissue that forms an interface separating the extracellular fluids and external water environment, has an effective transport system to maintain and regulate a constant body osmolality. In fish gills, the two major epithelial cells, pavement cells (PVCs) and mitochondria-rich cells (MRCs), are known to play key and complementary roles in ion transport at the interface. Discovering the robust mechanisms underlying the two cell types' response to osmotic stress would benefit our understanding of the fundamental mechanism allowing PVCs and MRCs to handle osmotic stress. Owing to the limited genomic data available on estuarine species, existing knowledge in this area is slim. In this study, transcriptome analyses were conducted using PVCs and MRCs isolated from Japanese eels adapted to FW or SW environments to provide a genome-wide molecular study to unravel the fundamental processes at work. RESULTS The study identified more than 12,000 transcripts in the gill cells. Interestingly, remarkable differential expressed genes (DEGs) were identified in PVCs (970 transcripts) instead of MRCs (400 transcripts) in gills of fish adapted to FW or SW. Since PVCs cover more than 90 % of the gill epithelial surface, the greater change in gene expression patterns in PVCs in response to external osmolality is anticipated. In the integrity pathway analysis, 19 common biological functions were identified in PVCs and MRCs. In the enriched signaling pathways analysis, most pathways differed between PVCs and MRCs; 14 enriched pathways were identified in PVCs and 12 in MRCs. The results suggest that the osmoregulatory responses in PVCs and MRCs are cell-type specific, which supports the complementary functions of the cells in osmoregulation. CONCLUSIONS This is the first study to provide transcriptomic analysis of PVCs and MRCs in gills of eels adapted to FW or SW environments. It describes the cell-type specific transcriptomic network in different tonicity. The findings consolidate the known osmoregulatory pathways and provide molecular insight in osmoregulation. The presented data will be useful for researchers to select their targets for further studies.
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Affiliation(s)
- Keng Po Lai
- School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Pok Fu Lam, Hong Kong
| | - Jing-Woei Li
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.,Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Je Gu
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Ting-Fung Chan
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - William Ka Fai Tse
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong.
| | - Chris Kong Chu Wong
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong. .,Croucher Institute for Environmental Sciences, Hong Kong Baptist University, Pok Fu Lam, Hong Kong.
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31
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Leguen I, Le Cam A, Montfort J, Peron S, Fautrel A. Transcriptomic Analysis of Trout Gill Ionocytes in Fresh Water and Sea Water Using Laser Capture Microdissection Combined with Microarray Analysis. PLoS One 2015; 10:e0139938. [PMID: 26439495 PMCID: PMC4595143 DOI: 10.1371/journal.pone.0139938] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/18/2015] [Indexed: 12/22/2022] Open
Abstract
Fish gills represent a complex organ composed of several cell types that perform multiple physiological functions. Among these cells, ionocytes are implicated in the maintenance of ion homeostasis. However, because the ionocyte represents only a small percent of whole gill tissue, its specific transcriptome can be overlooked among the numerous cell types included in the gill. The objective of this study is to better understand ionocyte functions by comparing the RNA expression of this cell type in freshwater and seawater acclimated rainbow trout. To realize this objective, ionocytes were captured from gill cryosections using laser capture microdissection after immunohistochemistry. Then, transcriptome analyses were performed on an Agilent trout oligonucleotide microarray. Gene expression analysis identified 108 unique annotated genes differentially expressed between freshwater and seawater ionocytes, with a fold change higher than 3. Most of these genes were up-regulated in freshwater cells. Interestingly, several genes implicated in ion transport, extracellular matrix and structural cellular proteins appeared up-regulated in freshwater ionocytes. Among them, several ion transporters, such as CIC2, SLC26A6, and NBC, were validated by qPCR and/or in situ hybridization. The latter technique allowed us to localize the transcripts of these ion transporters in only ionocytes and more particularly in the freshwater cells. Genes involved in metabolism and also several genes implicated in transcriptional regulation, cell signaling and the cell cycle were also enhanced in freshwater ionocytes. In conclusion, laser capture microdissection combined with microarray analysis allowed for the determination of the transcriptional signature of scarce cells in fish gills, such as ionocytes, and aided characterization of the transcriptome of these cells in freshwater and seawater acclimated trout.
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Affiliation(s)
- Isabelle Leguen
- INRA, UR1037 Fish Physiology and Genomics, Rennes, France
- * E-mail:
| | - Aurélie Le Cam
- INRA, UR1037 Fish Physiology and Genomics, Rennes, France
| | | | - Sandrine Peron
- INRA, UR1037 Fish Physiology and Genomics, Rennes, France
| | - Alain Fautrel
- INSERM UMR991, Rennes, France
- Université de Rennes 1 Plateforme H2P2, Biosit, Rennes, France
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Hsu HY, Chen SH, Cha YR, Tsukamoto K, Lin CY, Han YS. De Novo Assembly of the Whole Transcriptome of the Wild Embryo, Preleptocephalus, Leptocephalus, and Glass Eel of Anguilla japonica and Deciphering the Digestive and Absorptive Capacities during Early Development. PLoS One 2015; 10:e0139105. [PMID: 26406914 PMCID: PMC4583181 DOI: 10.1371/journal.pone.0139105] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 09/09/2015] [Indexed: 11/19/2022] Open
Abstract
Natural stocks of Japanese eel (Anguilla japonica) have decreased drastically because of overfishing, habitat destruction, and changes in the ocean environment over the past few decades. However, to date, artificial mass production of glass eels is far from reality because of the lack of appropriate feed for the eel larvae. In this study, wild glass eel, leptocephali, preleptocephali, and embryos were collected to conduct RNA-seq. Approximately 279 million reads were generated and assembled into 224,043 transcripts. The transcript levels of genes coding for digestive enzymes and nutrient transporters were investigated to estimate the capacities for nutrient digestion and absorption during early development. The results showed that the transcript levels of protein digestion enzymes were higher than those of carbohydrate and lipid digestion enzymes in the preleptocephali and leptocephali, and the transcript levels of amino acid transporters were also higher than those of glucose and fructose transporters and the cholesterol transporter. In addition, the transcript levels of glucose and fructose transporters were significantly raising in the leptocephali. Moreover, the transcript levels of protein, carbohydrate, and lipid digestion enzymes were balanced in the glass eel, but the transcript levels of amino acid transporters were higher than those of glucose and cholesterol transporters. These findings implied that preleptocephali and leptocephali prefer high-protein food, and the nutritional requirements of monosaccharides and lipids for the eel larvae vary with growth. An online database (http://molas.iis.sinica.edu.tw/jpeel/) that will provide the sequences and the annotated results of assembled transcripts was established for the eel research community.
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Affiliation(s)
- Hsiang-Yi Hsu
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Shu-Hwa Chen
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Yuh-Ru Cha
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Katsumi Tsukamoto
- Department of Marine Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Japan
| | - Chung-Yen Lin
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
- * E-mail: (YSH); (CYL)
| | - Yu-San Han
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, Taiwan
- * E-mail: (YSH); (CYL)
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Zeng J, He X, Quan X, Cai S, Han Y, Nadira UA, Zhang G. Identification of the proteins associated with low potassium tolerance in cultivated and Tibetan wild barley. J Proteomics 2015; 126:1-11. [DOI: 10.1016/j.jprot.2015.05.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/11/2015] [Accepted: 05/20/2015] [Indexed: 02/02/2023]
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Tse WKF, Sun J, Zhang H, Lai KP, Gu J, Sheung Law AY, Yee Yeung BH, Ching Chow S, Qiu JW, Wong CKC. Data for transcriptomic and iTRAQ proteomic analysis of Anguilla japonica gills in response to osmotic stress. Data Brief 2015. [PMID: 26217731 PMCID: PMC4510098 DOI: 10.1016/j.dib.2015.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
This article contains data related to the two research articles titled Transcriptomic and iTRAQ proteomic approaches reveal novel short-term hyperosmotic stress responsive proteins in the gill of the Japanese eel (Anguilla japonica) (Tse et al. [1]) and iTRAQ-based quantitative proteomic analysis reveals acute hypo-osmotic responsive proteins in the gills of the Japanese eel (Anguilla japonica) (Tse et al. [2]). The two research articles show the usefulness of combining transcriptomic and proteomic approaches to provide molecular insights of osmoregulation mechanism in a non-model organism, the Japanese eel. The information presented here combines the raw data from the two studies and provides an overview on the physiological functions of fish gills.
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Affiliation(s)
- William Ka Fai Tse
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Jin Sun
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Huoming Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Keng Po Lai
- School of Biological Science, the University of Hong Kong, Hong Kong SAR, China
| | - Jie Gu
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | | | | | - Sheung Ching Chow
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Chris Kong Chu Wong
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China ; Croucher Institute for Environmental Sciences, Hong Kong Baptist University, Hong Kong SAR, China
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Transcriptomic and proteomic analyses of splenic immune mechanisms of rainbow trout (Oncorhynchus mykiss) infected by Aeromonas salmonicida subsp. salmonicida. J Proteomics 2015; 122:41-54. [DOI: 10.1016/j.jprot.2015.03.031] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/28/2015] [Accepted: 03/30/2015] [Indexed: 01/17/2023]
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Chen L, Sun J, Zhang H, Au DWT, Lam PKS, Zhang W, Bajic VB, Qiu JW, Qian PY. Hepatic proteomic responses in marine medaka (Oryzias melastigma) chronically exposed to antifouling compound butenolide [5-octylfuran-2(5H)-one] or 4,5-dichloro-2-N-octyl-4-isothiazolin-3-one (DCOIT). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:1851-1859. [PMID: 25555223 DOI: 10.1021/es5046748] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The pollution of antifoulant SeaNine 211, with 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one (DCOIT) as active ingredient, in coastal environment raises concerns on its adverse effects, including endocrine disruption and impairment of reproductive function in marine organisms. In the present study, we investigated the hepatic protein expression profiles of both male and female marine medaka (Oryzias melastigma) exposed to low concentrations of DCOIT at 2.55 μg/L (0.009 μM) or butenolide, a promising antifouling agent, at 2.31 μg/L (0.012 μM) for 28 days. The results showed that proteins involved in phase I (CYP450 enzyme) metabolism, phase II (UDPGT and GST) conjugation as well as mobilization of retinoid storage, an effective nonenzymatic antioxidant, were consistently up-regulated, possibly facilitating the accelerated detoxification of butenolide. Increased synthesis of bile acid would promote the immediate excretion of butenolide metabolites. Activation of fatty acid β-oxidation and ATP synthesis were consistent with elevated energy consumption for butenolide degradation and excretion. However, DCOIT did not significantly affect the detoxification system of male medaka, but induced a marked increase of vitellogenin (VTG) by 2.3-fold in the liver of male medaka, suggesting that there is estrogenic activity of DCOIT in endocrine disruption. Overall, this study identified the molecular mechanisms and provided sensitive biomarkers characteristic of butenolide and DCOIT in the liver of marine medaka. The low concentrations of butenolide and DCOIT used in the exposure regimes highlight the needs for systematic evaluation of their environmental risk. In addition, the potent estrogenic activity of DCOIT should be considered in the continued applications of SeaNine 211.
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Affiliation(s)
- Lianguo Chen
- Division of Life Science and Environmental Science Programs, Hong Kong University of Science and Technology , Hong Kong, China
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Wong MKS, Ozaki H, Suzuki Y, Iwasaki W, Takei Y. Discovery of osmotic sensitive transcription factors in fish intestine via a transcriptomic approach. BMC Genomics 2014; 15:1134. [PMID: 25520040 PMCID: PMC4377849 DOI: 10.1186/1471-2164-15-1134] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 12/09/2014] [Indexed: 11/10/2022] Open
Abstract
Background Teleost intestine is crucial for seawater acclimation by sensing osmolality of imbibed seawater and regulating drinking and water/ion absorption. Regulatory genes for transforming intestinal function have not been identified. A transcriptomic approach was used to search for such genes in the intestine of euryhaline medaka. Results Quantitative RNA-seq by Illumina Hi-Seq Sequencing method was performed to analyze intestinal gene expression 0 h, 1 h, 3 h, 1 d, and 7 d after seawater transfer. Gene ontology (GO) enrichment results showed that cell adhesion, signal transduction, and protein phosphorylation gene categories were augmented soon after transfer, indicating a rapid reorganization of cellular components and functions. Among >50 transiently up-regulated transcription factors selected via co-expression correlation and GO selection, five transcription factors, including CEBPB and CEBPD, were confirmed by quantitative PCR to be specific to hyperosmotic stress, while others were also up-regulated after freshwater control transfer, including some well-known osmotic-stress transcription factors such as SGK1 and TSC22D3/Ostf1. Protein interaction networks suggest a high degree of overlapping among the signaling of transcription factors that respond to osmotic and general stresses, which sheds light on the interpretation of their roles during hyperosmotic stress and emergency. Conclusions Since cortisol is an important hormone for seawater acclimation as well as for general stress in teleosts, emergency and osmotic challenges could have been evolved in parallel and resulted in the overlapped signaling networks. Our results revealed important interactions among transcription factors and offer a multifactorial perspective of genes involved in seawater acclimation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1134) contains supplementary material, which is available to authorized users.
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Lam SH, Lui EY, Li Z, Cai S, Sung WK, Mathavan S, Lam TJ, Ip YK. Differential transcriptomic analyses revealed genes and signaling pathways involved in iono-osmoregulation and cellular remodeling in the gills of euryhaline Mozambique tilapia, Oreochromis mossambicus. BMC Genomics 2014; 15:921. [PMID: 25342237 PMCID: PMC4213501 DOI: 10.1186/1471-2164-15-921] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 10/13/2014] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The Mozambique tilapia Oreochromis mossambicus has the ability to adapt to a broad range of environmental salinities and has long been used for investigating iono-osmoregulation. However, to date most studies have focused mainly on several key molecules or parameters hence yielding a limited perspective of the versatile iono-osmoregulation in the euryhaline fish. This study aimed to capture transcriptome-wide differences between the freshwater- and seawater-acclimated gills of the Mozambique tilapia. RESULTS We have identified over 5000 annotated gene transcripts with high homology (E-value <1.0E-50) to human genes that were differentially expressed in freshwater- and seawater-acclimated gills of the Mozambique tilapia. These putative human homologs were found to be significantly associated with over 50 canonical signaling pathways that are operating in at least 23 biological processes in relation to branchial iono-osmoregulation and cellular remodeling. The analysis revealed multiple signaling pathways in freshwater-acclimated gills acting in concert to maintain cellular homeostasis under hypo-osmotic environment while seawater-acclimated gills abounded with molecular signals to cope with the higher cellular turn-over rate, energetics and iono-regulatory demands under hyper-osmostic stress. Additionally, over 100 transcripts encoding putative inorganic ion transporters/channels were identified, of which several are well established in gill iono-regulation while the remainder are lesser known. We have also validated the expression profiles of 47 representative genes in freshwater- and seawater-acclimated gills, as well as in hypersaline-acclimated (two-fold salinity of seawater) gills. The findings confirmed that many of these responsive genes retained their expression profiles in hypersaline-acclimated gills as in seawater-acclimated gills, although several genes had changed significantly in their expression level/direction in hypersaline-acclimated gills. CONCLUSIONS This is the first study that has provided an unprecedented transcriptomic-wide perspective of gill iono-osmoregulation since such studies were initiated more than 80 years ago. It has expanded our molecular perspective from a relatively few well-studied molecules to a plethora of gene transcripts and a myriad of canonical signaling pathways driving various biological processes that are operating in gills under hypo-osmotic and hyper-osmotic stresses. These findings would provide insights and resources to fuel future studies on gill iono-osmoregulation and cellular remodeling in response to salinity challenge and acclimation.
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Affiliation(s)
- Siew Hong Lam
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive, 117411 Singapore, Singapore.
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Zhang F, Wang Z, Dong W, Sun C, Wang H, Song A, He L, Fang W, Chen F, Teng N. Transcriptomic and proteomic analysis reveals mechanisms of embryo abortion during chrysanthemum cross breeding. Sci Rep 2014; 4:6536. [PMID: 25288482 PMCID: PMC4187010 DOI: 10.1038/srep06536] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/26/2014] [Indexed: 12/25/2022] Open
Abstract
Embryo abortion is the main cause of failure in chrysanthemum cross breeding, and the genes and proteins associated with embryo abortion are poorly understood. Here, we applied RNA sequencing and isobaric tags for relative and absolute quantitation (iTRAQ) to analyse transcriptomic and proteomic profiles of normal and abortive embryos. More than 68,000 annotated unigenes and 700 proteins were obtained from normal and abortive embryos. Functional analysis showed that 140 differentially expressed genes (DEGs) and 41 differentially expressed proteins (DEPs) were involved in embryo abortion. Most DEGs and DEPs associated with cell death, protein degradation, reactive oxygen species scavenging, and stress-response transcriptional factors were significantly up-regulated in abortive embryos relative to normal embryos. In contrast, most genes and proteins related to cell division and expansion, the cytoskeleton, protein synthesis and energy metabolism were significantly down-regulated in abortive embryos. Furthermore, abortive embryos had the highest activity of three executioner caspase-like enzymes. These results indicate that embryo abortion may be related to programmed cell death and the senescence- or death-associated genes or proteins contribute to embryo abortion. This adds to our understanding of embryo abortion and will aid in the cross breeding of chrysanthemum and other crops in the future.
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Affiliation(s)
- Fengjiao Zhang
- 1] College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China [2] Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology &Equipment, Nanjing 210095, China
| | - Zhiquan Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wen Dong
- China Rural Technology Development Center, Beijing 100045, China
| | - Chunqing Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Haibin Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Lizhong He
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Fadi Chen
- 1] College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China [2] Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology &Equipment, Nanjing 210095, China
| | - Nianjun Teng
- 1] College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China [2] Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology &Equipment, Nanjing 210095, China
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Tse WKF, Sun J, Zhang H, Lai KP, Gu J, Qiu JW, Wong CKC. iTRAQ-based quantitative proteomic analysis reveals acute hypo-osmotic responsive proteins in the gills of the Japanese eel (Anguilla japonica). J Proteomics 2014; 105:133-43. [PMID: 24503184 DOI: 10.1016/j.jprot.2014.01.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/09/2014] [Accepted: 01/23/2014] [Indexed: 10/25/2022]
Abstract
UNLABELLED Osmoregulation in fish has been a classical research topic for several decades. Salmon and eels are the widely used model animals because of their wide distribution in different geographical locations and spawning migration between fresh- and salt-water habitats. Numerous fish osmoregulatory hormones and ion transporters were identified for their essential roles in acclimation and adaptation to waters of different salinities. Because of the lack of a genomic database, the scope of most studies, however, is very limited. Recently, our group reported the first high-throughput transcriptomic and proteomic studies to identify hyperosmotic-responsive genes/proteins in gills of Japanese eels. In this study, we aimed to decipher changes in hypo-osmotic-responsive proteins in fish acclimating from seawater (SW) to freshwater (FW) conditions. We collected gill samples from SW-adapted and SW-to-FW-acclimating fish. The respective gill proteins were extracted and labeled using isobaric tags for relative and absolute quantitation (iTRAQ) and analyzed using a high-resolution mass spectrometer. In the short-term transfer from SW to FW, 51 hypo-responsive proteins were detected, and 24 unique hypo-osmotic-responsive proteins were identified (15 up-regulated and nine down-regulated proteins). Our data support the use of an omics approach to facilitate the application of functional genomics in non-model organisms. BIOLOGICAL SIGNIFICANCE By combining transcriptomic and proteomic approaches, the study has provided the most comprehensive, targeted investigation of eel gill hypo-osmotic responsive proteins that provides molecular insights of osmoregulation mechanisms in a non-model organism, eel. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Affiliation(s)
| | - Jin Sun
- Department of Biology, Hong Kong Baptist University, Hong Kong
| | - Huoming Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong
| | - Keng Po Lai
- School of Biological Science, The University of Hong Kong, Hong Kong
| | - Jie Gu
- Department of Biology, Hong Kong Baptist University, Hong Kong
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong
| | - Chris Kong Chu Wong
- Department of Biology, Hong Kong Baptist University, Hong Kong; Croucher Institute for Environmental Sciences, Hong Kong Baptist University, Hong Kong.
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