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Wang Z, Wang Y, Guan Y, Chen Z, Zhai Y, Wu Y, Zhou Y, Hu J, Chen L. Transcriptome analysis of Chinese mitten crabs ( Eriocheir sinensis) gills in response to ammonia stress. PeerJ 2024; 12:e16786. [PMID: 38250716 PMCID: PMC10798153 DOI: 10.7717/peerj.16786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024] Open
Abstract
The Chinese mitten crab (Eriocheir sinensis) is an important commercial species in China. E. sinensis is typically farmed in rice-crab symbiosis, as an important ecological farming model. However, E. sinensis is often exposed to a high ammonia environment due to the application of nitrogen fertilizers essential for rice growth. We investigated the molecular mechanisms in the gills of E. sinensis exposed to high ammonia at transcriptional and histological levels. We randomly assigned E. sinensis to two groups (control group, CG; ammonia stress group, AG), and gill samples were excised from the CG and AG groups for histopathological and transcriptome analyses. The histopathological evaluation revealed that ammonia stress damaged the gills of E. sinensis. The transcriptome analysis showed that some essential genes, including Xanthine dehydrogenase (XDH), Ubiquitin C-terminal hydrolase-L3 (UCHL3), O-linked N-acetylglucosamine transferase (OGT), Cathepsin B (CTSB), and Ubiquitin-conjugating enzyme E2 W (UBE2W) changed significantly during ammonia exposure. These genes are related to ammonia detoxification, the immune response, and apoptosis. This study demonstrated the molecular response mechanism of E. sinensis gills to ammonia stress at the transcriptional and histological levels. This study provides insight for further study on the molecular mechanism of ammonia stress in crustaceans and supplies technical support for rice crab symbiosis.
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Affiliation(s)
- Zhengfei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers Universtiy, Yancheng, Jiangsu Province, China
| | - Yue Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers Universtiy, Yancheng, Jiangsu Province, China
| | - Yayun Guan
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers Universtiy, Yancheng, Jiangsu Province, China
| | - Zhuofan Chen
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers Universtiy, Yancheng, Jiangsu Province, China
| | - Yaotong Zhai
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers Universtiy, Yancheng, Jiangsu Province, China
| | - Ya Wu
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Ying Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers Universtiy, Yancheng, Jiangsu Province, China
| | - Jinghao Hu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers Universtiy, Yancheng, Jiangsu Province, China
| | - Lulu Chen
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers Universtiy, Yancheng, Jiangsu Province, China
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Yuan H, Xie M, Hu N, Zheng Y, Hou C, Tan B, Shi L, Zhang S. Growth, immunity and transcriptome response to different stocking densities in Litopenaeus vannamei. FISH & SHELLFISH IMMUNOLOGY 2023; 139:108924. [PMID: 37406891 DOI: 10.1016/j.fsi.2023.108924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/11/2023] [Accepted: 07/02/2023] [Indexed: 07/07/2023]
Abstract
The effects of different stocking densities on Litopenaeus vannamei were investigated from the aspects of growth performance, immune response and transcriptome in this experiment. L. vannamei (initial body weight: 0.30 ± 0.02 g) were reared for 8 weeks at three stocking densities of 100 (LSD), 200 (MSD) and 300 (HSD) shrimp/m³, respectively. The results showed that the survival rate (SR), final body weight (FBW), weight gain rate (WGR), specific growth ratio (SGR) and protein efficiency ratio (PER) of L. vannamei significantly decreased, while the feed factor (FCR) significantly increased with the increase of stocking density. After Vibrio parahemolyticus infection, the SR of L. vannamei in the HSD group was significantly lower than that in the LSD and MSD groups. Increasing stocking density significantly increased the activities of aspartate aminotransferase (AST), alanine aminotransferase (ALT) and lysozyme (LYS) while significantly decreased the activities of catalase (CAT) and phenol oxidase (PO) in the serum of L. vannamei. Similar changes of the gene expression as the activities of immune enzymes were found in the hemocytes. Pairwise comparison between the LSD, MSD and HSD group in the transcriptome analysis identified that there were 304, 1376 and 2083 differentially expressed genes (DEGs) in LSD vs MSD, MSD vs HSD and LSD vs HSD, respectively. Among them, most of the immune-related DEGs were down-regulated and metabolism-related DEGs were up-regulated with the increasing stocking density. In addition, KEGG enrichment pathway analysis revealed that several immune and metabolic related pathways including PI3K-Akt signaling pathway and AMPK signaling pathway were significantly enriched. Of these, the PI3K-Akt signaling pathway had the most DEGs and was also the most significantly enriched pathway. Furthermore, 16 DEGs (such as FOXO, PCK2 and CTSC, etc.) and partial immune enzyme activity (such as AST, CAT and PO, etc.) changes were closely correlated with the increase of stocking density when partial immune-related DEGs and immune-related enzymes were analyzed jointly. All these results indicated that changes in stocking density had a significant effect on the growth performance, immunity and transcriptome of L. vannamei.
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Affiliation(s)
- Hang Yuan
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Minghua Xie
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Naijie Hu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Yudong Zheng
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Cuihong Hou
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Beiping Tan
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, China; GuangDong Engineering Technology Research Center of Aquatic Animals Precision Nutrition and High Efficiency Feed, Zhanjiang, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, 524088, China
| | - Lili Shi
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Shuang Zhang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China; Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, China; GuangDong Engineering Technology Research Center of Aquatic Animals Precision Nutrition and High Efficiency Feed, Zhanjiang, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, 524088, China.
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Gul I, Abbas MN, Kausar S, Luo J, Gao X, Mu Y, Fan W, Cui H. Insight into crustacean cathepsins: Structure-evolutionary relationships and functional roles in physiological processes. FISH & SHELLFISH IMMUNOLOGY 2023:108852. [PMID: 37295735 DOI: 10.1016/j.fsi.2023.108852] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023]
Abstract
Cathepsins belong to a group of proteins that are present in both prokaryotic and eukaryotic organisms and have an extremely high degree of evolutionary conservation. These proteins are functionally active in extracellular environments as soluble enzymatic proteins or attached to plasma membrane receptors. In addition, they occur in cellular secretory vesicles, mitochondria, the cytosol, and within the nuclei of eukaryotic cells. Cathepsins are classified into various groups based on their sequence variations, leading to their structural and functional diversification. The molecular understanding of the physiology of crustaceans has shown that proteases, including cathepsins, are expressed ubiquitously. They also contain one of the central regulatory systems for crustacean reproduction, growth, and immune responses. This review focuses on various aspects of the crustaceans cathepsins and emphasizes their biological roles in different physiological processes such as reproduction, growth, development, and immune responses. We also describe the bioactivity of crustaceans cathepsins. Because of the vital biological roles that cathepsins play as cellular proteases in physiological processes, they have been proposed as potential novel targets for the development of management strategies for the aquaculture industries.
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Affiliation(s)
- Isma Gul
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716, China; State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Muhammad Nadeem Abbas
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716, China; State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Saima Kausar
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716, China; State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Jili Luo
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716, China; State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Xinyue Gao
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716, China; State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Yuhang Mu
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716, China; State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Wenhui Fan
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716, China; Department of Neurology, Chongqing Ninth People's Hospital, Chongqing, 400700, China.
| | - Honghuan Cui
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716, China; State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China.
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Chen YH, He JG. Effects of environmental stress on shrimp innate immunity and white spot syndrome virus infection. FISH & SHELLFISH IMMUNOLOGY 2019; 84:744-755. [PMID: 30393174 DOI: 10.1016/j.fsi.2018.10.069] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/12/2018] [Accepted: 10/26/2018] [Indexed: 06/08/2023]
Abstract
The shrimp aquaculture industry is plagued by disease. Due to the lack of deep understanding of the relationship between innate immune mechanism and environmental adaptation mechanism, it is difficult to prevent and control the diseases of shrimp. The shrimp innate immune system has received much recent attention, and the functions of the humoral immune response and the cellular immune response have been preliminarily characterized. The role of environmental stress in shrimp disease has also been investigated recently, attempting to clarify the interactions among the innate immune response, the environmental stress response, and disease. Both the innate immune response and the environmental stress response have a complex relationship with shrimp diseases. Although these systems are important safeguards, allowing shrimp to adapt to adverse environments and resist infection, some pathogens, such as white spot syndrome virus, hijack these host systems. As shrimp lack an adaptive immune system, immunization therapy cannot be used to prevent and control shrimp disease. However, shrimp diseases can be controlled using ecological techniques. These techniques, which are based on the innate immune response and the environmental stress response, significantly reduce the impact of shrimp diseases. The object of this review is to summarize the recent research on shrimp environmental adaptation mechanisms, innate immune response mechanisms, and the relationship between these systems. We also suggest some directions for future research.
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Affiliation(s)
- Yi-Hong Chen
- Key Laboratory of Marine Resources and Coastal Engineering in Guangdong Province/School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275, PR China; Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, College of Life Science, South China Normal University, Guangzhou 510631, PR China
| | - Jian-Guo He
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275, PR China; Key Laboratory of Marine Resources and Coastal Engineering in Guangdong Province/School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275, PR China.
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Onming S, Thongda W, Li C, Sawatdichaikul O, McMillan N, Klinbunga S, Peatman E, Poompuang S. Bioinformatics characterization of a cathepsin B transcript from the giant river prawn, Macrobrachium rosenbergii: Homology modeling and expression analysis after Aeromonas hydrophila infection. Comp Biochem Physiol B Biochem Mol Biol 2018; 221-222:18-28. [PMID: 29649577 DOI: 10.1016/j.cbpb.2018.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Cathepsin B is a lysosomal proteolytic enzyme that has been suggested to play a role in pathological processes of immune system. In this study, the full-length cDNA sequence of cathepsin B transcript in the giant river prawn Macrobrachium rosenbergii (MrCTSB) was obtained from 454 pyrosequencing of cDNAs from hepatopancreas and muscle. It was 1158 bp in length, containing an open reading frame (ORF) of 987 bp corresponding to 328 amino acids. The predicted molecular mass and pI of MrCTSB protein was 36.04 kDa and 4.73. The major characteristics of MrCTSB protein consisted of a propeptide of C1 peptidase family at the N-terminus and a cysteine protease (Pept_C1) domain at the C-terminus. The 3-dimentional structure of MrCTSB was constructed by computer-assisted homology modeling. The folding of MrCTSB was highly conserved to human CTSB structure and the modeled MrCTSB displayed characteristics of cysteine proteinases superfamily. The docking study was performed to investigate binding interactions between known inhibitors against MrCTSB. Known inhibitors were oriented in the groove of catalytic site cleft. They bound to subsites from S2, S1, S1', and S2', respectively, with key residues in each subsite. Challenge of juvenile prawns with Aeromonas hydrophila revealed that the MrCTSB transcript in hepatopancreas significantly increased at 60-96 h post injection (hpi). This suggested that MrCTSB may play roles in innate immunity of M. rosenbergii. Our results provide useful information for a more comprehensive study in immune-related functions of MrCTSB.
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Affiliation(s)
- Saowalak Onming
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan Road, Bangkok 10900, Thailand
| | - Wilawan Thongda
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Chao Li
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao 266109, China
| | - Orathai Sawatdichaikul
- Department of Nutrition and Health, Institute of Food Research and Product Development, Kasetsart University, Bangkok 10900, Thailand
| | - Nichanun McMillan
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan Road, Bangkok 10900, Thailand
| | - Sirawut Klinbunga
- Aquatic Molecular Genetics and Biotechnology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Paholyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; Center of Excellence for Marine Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Eric Peatman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Supawadee Poompuang
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan Road, Bangkok 10900, Thailand.
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The response of glutathione peroxidase 1 and glutathione peroxidase 7 under different oxidative stresses in black tiger shrimp, Penaeus monodon. Comp Biochem Physiol B Biochem Mol Biol 2018; 217:1-13. [DOI: 10.1016/j.cbpb.2017.12.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/16/2017] [Accepted: 12/07/2017] [Indexed: 12/27/2022]
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Guo H, Xian JA, Li B, Ye CX, Wang AL, Miao YT, Liao SA. Gene expression of apoptosis-related genes, stress protein and antioxidant enzymes in hemocytes of white shrimp Litopenaeus vannamei under nitrite stress. Comp Biochem Physiol C Toxicol Pharmacol 2013; 157:366-71. [PMID: 23474501 DOI: 10.1016/j.cbpc.2013.03.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Revised: 02/26/2013] [Accepted: 03/03/2013] [Indexed: 02/07/2023]
Abstract
Apoptotic cell ratio and mRNA expression of caspase-3, cathepsin B (CTSB), heat shock protein 70 (HSP70), manganese superoxide dismutase (MnSOD), catalase (CAT), glutathione peroxidase (GPx) and thioredoxin (TRx) in hemocytes of white shrimp Litopenaeus vannamei exposed to nitrite-N (20 mg/L) was investigated at different stress time (0, 4, 8, 12, 24, 48 and 72 h). The apoptotic cell ratio and mRNA expression level of CTSB were significantly increased in shrimp exposed to nitrite-N for 48 and 72 h. Caspase-3 mRNA expression level significantly increased by 766.50% and 1811.16% for 24 and 48 h exposure, respectively. HSP70 expression level significantly increased at 8 and 72 h exposure. MnSOD mRNA expression in hemocytes up-regulated at 8 and 48 h, while CAT mRNA expression level increased at 24 and 48 h. GPx expression showed a trend that increased first and then decreased. Significant increases of GPx expression were observed at 8 and 12 h exposure. Expression level of TRx reached its highest level after 48 h exposure. These results suggest that nitrite exposure induces expression of apoptosis-related genes in hemocytes, and subsequently caused hemocyte apoptosis. Meanwhile, expression levels of HSP70 and antioxidant enzymes up-regulated to protect the hemocyte against nitrite stress.
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Affiliation(s)
- Hui Guo
- Key Laboratory of Ecology and Environmental Science of Guangdong Higher Education Institutes, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou 510631, People's Republic of China
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Timmins-Schiffman E, Nunn BL, Goodlett DR, Roberts SB. Shotgun proteomics as a viable approach for biological discovery in the Pacific oyster. CONSERVATION PHYSIOLOGY 2013; 1:cot009. [PMID: 27293593 PMCID: PMC4732435 DOI: 10.1093/conphys/cot009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 04/10/2013] [Accepted: 04/11/2013] [Indexed: 05/03/2023]
Abstract
Shotgun proteomics offers an efficient means to characterize proteins in a complex mixture, particularly when sufficient genomic resources are available. In order to assess the practical application of shotgun proteomics in the Pacific oyster (Crassostrea gigas), liquid chromatography coupled with tandem mass spectrometry was used to characterize the gill proteome. Using information from the recently published Pacific oyster genome, 1043 proteins were identified. Biological samples (n = 4) and corresponding technical replicates (three) were similar in both specific proteins identified and expression, as determined by normalized spectral abundance factor. A majority of the proteins identified (703) were present in all biological samples. Functional analysis of the protein repertoire illustrates that these proteins represent a wide range of biological processes, supporting the dynamic function of the gill. These insights are important for understanding environmental influences on the oyster, because the gill tissue acts as the interface between the oyster and its environment. In silico analysis indicated that this sequencing effort identified a large proportion of the complete gill proteome. Together, these data demonstrate that shotgun sequencing is a viable approach for biological discovery and will play an important role in future studies of oyster physiology.
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Affiliation(s)
- Emma Timmins-Schiffman
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195, USA
| | - Brook L. Nunn
- Genomic Sciences, University of Washington, Box 355065, Seattle, WA 98195, USA
| | - David R. Goodlett
- Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195, USA
| | - Steven B. Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195, USA
- Corresponding author: School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195, USA. Tel: +1 206 685 3742.
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Timmins‐Schiffman EB, Friedman CS, Metzger DC, White SJ, Roberts SB. Genomic resource development for shellfish of conservation concern. Mol Ecol Resour 2012; 13:295-305. [DOI: 10.1111/1755-0998.12052] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 11/16/2012] [Accepted: 11/20/2012] [Indexed: 01/23/2023]
Affiliation(s)
| | - Carolyn S. Friedman
- University of Washington School of Aquatic and Fishery Sciences Box 355020 Seattle WA 98195 USA
| | - Dave C. Metzger
- University of Washington School of Aquatic and Fishery Sciences Box 355020 Seattle WA 98195 USA
| | - Samuel J. White
- University of Washington School of Aquatic and Fishery Sciences Box 355020 Seattle WA 98195 USA
| | - Steven B. Roberts
- University of Washington School of Aquatic and Fishery Sciences Box 355020 Seattle WA 98195 USA
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Cathepsin B from the white shrimp Litopenaeus vannamei: cDNA sequence analysis, tissues-specific expression and biological activity. Comp Biochem Physiol B Biochem Mol Biol 2012; 161:32-40. [DOI: 10.1016/j.cbpb.2011.09.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 09/05/2011] [Accepted: 09/09/2011] [Indexed: 11/21/2022]
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de Boer ME, Berg S, Timmermans MJTN, den Dunnen JT, van Straalen NM, Ellers J, Roelofs D. High throughput nano-liter RT-qPCR to classify soil contamination using a soil arthropod. BMC Mol Biol 2011; 12:11. [PMID: 21362169 PMCID: PMC3060125 DOI: 10.1186/1471-2199-12-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 03/01/2011] [Indexed: 11/29/2022] Open
Abstract
Background To incorporate genomics data into environmental assessments a mechanistic perspective of interactions between chemicals and induced biological processes needs to be developed. Since chemical compounds with structural similarity often induce comparable biological responses in exposed animals, gene expression signatures can serve as a starting point for the assessment of chemicals and their toxicity, but only when relevant and stable gene panels are available. To design such a panel, we isolated differentially expressed gene fragments from the soil arthropod Folsomia candida, a species often used for ecotoxicological testing. Animals were exposed to two chemically distinct compounds, being a metal (cadmium) and a polycyclic aromatic hydrocarbon (phenanthrene). We investigated the affected molecular responses resulting from either treatment and developed and validated 44 qPCR assays for their responses using a high throughput nano-liter RT-qPCR platform for the analysis of the samples. Results Suppressive subtractive hybridization (SSH) was used to retrieve stress-related gene fragments. SSH libraries revealed pathways involved in mitochondrial dysfunction and protein degradation for cadmium and biotransformation for phenanthrene to be overrepresented. Amongst a small cluster of SSH-derived cadmium responsive markers were an inflammatory response protein and an endo-glucanase. Conversely, cytochrome P450 family 6 or 9 was specifically induced by phenanthrene. Differential expressions of these candidate biomarkers were also highly significant in the independently generated test sample set. Toxicity levels in different training samples were not reflected by any of the markers' intensity of expressions. Though, a model based on partial least squares differential analysis (PLS-DA) (with RMSEPs between 9 and 22% and R2s between 0.82 and 0.97) using gene expressions of 25 important qPCR assays correctly predicted the nature of exposures of test samples. Conclusions For the application of molecular bio-indication in environmental assessments, multivariate analyses obviously have an added value over univariate methods. Our results suggest that compound discrimination can be achieved by PLS-DA, based on a hard classification of the within-class rankings of samples from a test set. This study clearly shows that the use of high throughput RT-qPCR could be a valuable tool in ecotoxicology combining high throughput with analytical sensitivity.
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Affiliation(s)
- Muriel E de Boer
- VU University Amsterdam, Department of Ecological Science, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
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Krøvel AV, Søfteland L, Torstensen BE, Olsvik PA. Endosulfan in vitro toxicity in Atlantic salmon hepatocytes obtained from fish fed either fish oil or vegetable oil. Comp Biochem Physiol C Toxicol Pharmacol 2010; 151:175-86. [PMID: 19874912 DOI: 10.1016/j.cbpc.2009.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 10/08/2009] [Accepted: 10/14/2009] [Indexed: 11/29/2022]
Abstract
The composition of the feed may alter the cellular composition of an organism and thus has the potential to influence a xenobiotic response. The main aim of this study was to see if the fatty acid composition of primary hepatocytes isolated from Atlantic salmon (Salmo salar L.) obtained from fish fed either a fish oil or a vegetable oil based diet, influenced the response to endosulfan exposure in vitro. The primary cultures were exposed to six different concentrations of endosulfan (0.001, 0.01, 0.1, 1, 10 and 100 microM) for 48 h. Cell morphology as well as a molecular toolbox of 16 genes encoding stress responsive and biotransformation proteins was examined. Endosulfan exposure caused moderate cytotoxicity and steatosis in a dose-dependent manner in the hepatocytes. In general, endosulfan hepatoxicity seems to be unaffected by the fatty acid composition of the hepatocytes. Exceptions were general stress (HSP70) and markers for estrogen exposure (ZP and VTG), which appeared to be slightly less responsive in hepatocytes isolated from the vegetable oil fed fish.
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Affiliation(s)
- Anne Vatland Krøvel
- National Institute of Nutrition and Seafood Research, N-5817 Bergen, Norway.
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Gene expression profile of grass shrimp Palaemonetes pugio exposed to chronic hypoxia. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2009; 4:196-208. [DOI: 10.1016/j.cbd.2009.03.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Revised: 03/25/2009] [Accepted: 03/27/2009] [Indexed: 12/17/2022]
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Fuma S, Nakamori T, Ishii N, Kubota Y, Yoshida S, Fujimori A. Genome-wide gene expression profiling in gamma-irradiated green alga, Pseudokirchneriella subcapitata, by HiCEP. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2009; 83:301-306. [PMID: 19462152 DOI: 10.1007/s00128-009-9780-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Accepted: 05/07/2009] [Indexed: 05/27/2023]
Abstract
Transcriptome was analyzed in gamma-irradiated green alga Pseudokirchneriella subcapitata by high coverage gene expression profiling (HiCEP). Approximately 7,800 expressed genes were detected. Expression levels of 623-707 genes were affected at 100-300 Gy. Nucleotide sequences of 41 up-regulated genes were determined. The quantitative reverse transcription polymerase chain reaction validated the up-regulation. Two genes had homology to genes related to ionizing radiation. These results indicate usefulness of HiCEP for screening of stress-responsive genes in species that are ecotoxicologically important but for which genomic sequence information is lacking.
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Affiliation(s)
- Shoichi Fuma
- Environmental Radiation Effects Research Group, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555, Japan.
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Li T, Brouwer M. Bioinformatic analysis of expressed sequence tags from grass shrimp Palaemonetes pugio exposed to environmental stressors. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2009; 4:187-95. [DOI: 10.1016/j.cbd.2009.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Revised: 03/01/2009] [Accepted: 03/02/2009] [Indexed: 11/26/2022]
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Colli-Dulá R, Zúñiga-Aguilar JJ, Albores-Medina A, Zapata-Perez O. Identification of genes expressed as a result of lindane exposure in Oreochromis niloticus using differential display. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2009; 72:1406-1412. [PMID: 19403169 DOI: 10.1016/j.ecoenv.2009.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Revised: 03/23/2009] [Accepted: 03/25/2009] [Indexed: 05/27/2023]
Abstract
In order to assess the effect of lindane exposure on gene expression in tilapia (Oreochromis niloticus), twenty male fish were individually weighted and injected intraperitoneally with a single dose of lindane (19.09 mg/kg bw) using corn oil as a carrier vehicle, while a second group of twenty male fish (controls) was only injected with the carrier vehicle. Groups of four fish each were then sacrificed at 3, 6, 12, 18 and 24h after treatment application and total RNA was extracted from liver tissue. The differential display (DD) technique was then used to identify differentially expressed cDNA fragments between treatment and control fish. A total of fifty cDNA fragments were isolated and sequenced, from which only four showed homology with genes previously described in other fish species, namely the immunoglobulin heavy chain (IgH), coagulation factor V (FV), casein kinase 2 alpha (CK2a), and the receptor protein-tyrosine-like phosphatase (RPT-LP). The expression of such genes was confirmed using quantitative real time-polymerase chain reaction (QRT-PCR). Results showed that lindane exposure triggered the differential expression of these genes during the first 6, 18 and 24h subsequent to treatment application, suggesting that lindane exposure can trigger a rapid immune system response in tilapias.
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Affiliation(s)
- Reyna Colli-Dulá
- Departamento de Recursos del Mar, Cinvestav Unidad Merida, Merida, Yucatan, Mexico
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17
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Robalino J, Carnegie RB, O'Leary N, Ouvry-Patat SA, de la Vega E, Prior S, Gross PS, Browdy CL, Chapman RW, Schey KL, Warr G. Contributions of functional genomics and proteomics to the study of immune responses in the Pacific white leg shrimp Litopenaeus vannamei. Vet Immunol Immunopathol 2008; 128:110-8. [PMID: 19070907 DOI: 10.1016/j.vetimm.2008.10.329] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The need for better control of infectious diseases in shrimp aquaculture and the ecological importance of crustacea in marine ecosystems have prompted interest in the study of crustacean immune systems, particularly those of shrimp. As shrimp and other crustacea are poorly understood from the immunological point of view, functional genomic and proteomic approaches have been applied as a means of quickly obtaining molecular information regarding immune responses in these organisms. In this article, a series of results derived from transcriptomic and proteomic studies in shrimp (Litopenaeus vannamei) are discussed. Expressed Sequence Tag analysis, differential expression cloning through Suppression Subtractive Hybridization, expression profiling using microarrays, and proteomic studies using mass spectrometry, have provided a wealth of useful data and opportunities for new avenues of research. Examples of new research directions arising from these studies in shrimp include the molecular diversity of antimicrobial effectors, the role of double stranded RNA as an inducer of antiviral immunity, and the possible overlap between antibacterial and antiviral responses in the shrimp.
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Affiliation(s)
- Javier Robalino
- Marine Biomedicine and Environmental Sciences Center, Medical University of South Carolina, Hollings Marine Laboratory, United States
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Timofeyev MA, Shatilina ZM, Bedulina DS, Protopopova MV, Pavlichenko VV, Grabelnych OI, Kolesnichenko AV. Evaluation of biochemical responses in Palearctic and Lake Baikal endemic amphipod species exposed to CdCl2. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2008; 70:99-105. [PMID: 17920682 DOI: 10.1016/j.ecoenv.2007.06.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2006] [Revised: 06/10/2007] [Accepted: 06/18/2007] [Indexed: 05/25/2023]
Abstract
This study evaluated small heat shock proteins (sHSP) (related to alpha-crystallin) and antioxidant enzymes (POD, peroxidase and CAT, catalase) as possible biomarkers for use in toxicological studies. Biochemical responses to cadmium chloride in two Lake Baikal endemic amphipods (Eulimnogammarus verrucosus, Eulimnogammarus cyaneus) and Palearctic species (Gammarus lacustris) were compared. Our findings showed that cadmium chloride toxicity directly influenced POD activity and sHSP synthesis in all amphipod species. The Baikalean endemic and the Palearctic amphipod species responded by decreasing activity of POD and they exhibited a dose-dependent activation of sHSP synthesis. All measured parameters differed among species and depended on the species' ability to resist cadmium chloride toxicity. CAT activity in the Palearctic species responded significantly to cadmium chloride exposure; however, responses were negligible for both Baikalean species. We suggest that synthesis of sHSP, together with changes in POD activity, could be used as biomarkers for further studies of amphipod species including endemics from Lake Baikal.
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Affiliation(s)
- M A Timofeyev
- Irkutsk State University, Karl-Marx 1, 664003 Irkutsk, Russia; Baikalean Research Center, Karl-Marx 5-10, 664003 Irkutsk, Russia.
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Kuzmick DM, Mitchelmore CL, Hopkins WA, Rowe CL. Effects of coal combustion residues on survival, antioxidant potential, and genotoxicity resulting from full-lifecycle exposure of grass shrimp (Palaemonetes pugio Holthius). THE SCIENCE OF THE TOTAL ENVIRONMENT 2007; 373:420-30. [PMID: 17182083 DOI: 10.1016/j.scitotenv.2006.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Revised: 11/06/2006] [Accepted: 11/08/2006] [Indexed: 05/13/2023]
Abstract
Coal combustion residues (CCRs), largely derived from coal-fired electrical generation, are rich in numerous trace elements that have the potential to induce sublethal effects including oxidative stress, alterations in antioxidant status and DNA single strand breaks (SSB). CCRs are frequently discharged into natural and man-made aquatic systems. As the effects of CCRs have received relatively little attention in estuarine systems, the estuarine grass shrimp, Palaemonetes pugio, was chosen for this study. Grass shrimp were exposed in the laboratory to CCR-enriched sediments and food over a full life cycle. Survival to metamorphosis was significantly reduced in CCR-exposed larvae (17+/-4 versus 70+/-13% in the controls) but not in the juveniles or adults. The COMET assay, a general but sensitive assay for genotoxicity, was used to quantify DNA SSB in the adults. Total antioxidant potential was examined to assess the overall antioxidant scavenging capacity of CCR-exposed and non-exposed adult grass shrimp. Grass shrimp exposed to CCR significantly accumulated selenium and cadmium compared to unexposed shrimp, although an inverse relationship was seen for mercury accumulation. Chronic CCR exposure caused DNA SSB in hepatopancreas cells, as evidenced by the significantly increased percent tail DNA, tail moment, and tail length as compared to reference shrimp. However, no significant difference was observed in total antioxidant potential. Our findings suggest that genotoxicity may be an important mode of toxicity of CCR, and that DNA SSB may serve as a useful biomarker of exposure and effect of this very common, complex waste stream.
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Affiliation(s)
- Danika M Kuzmick
- University of Maryland Center for Environmental Science, Chesapeake Biological Laboratory, 1, Williams Street, PO Box 38, Solomons, MD 20688, USA
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