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Liu L, Xie Y, Yahaya BS, Wu F. GIGANTEA Unveiled: Exploring Its Diverse Roles and Mechanisms. Genes (Basel) 2024; 15:94. [PMID: 38254983 PMCID: PMC10815842 DOI: 10.3390/genes15010094] [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: 11/19/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
GIGANTEA (GI) is a conserved nuclear protein crucial for orchestrating the clock-associated feedback loop in the circadian system by integrating light input, modulating gating mechanisms, and regulating circadian clock resetting. It serves as a core component which transmits blue light signals for circadian rhythm resetting and overseeing floral initiation. Beyond circadian functions, GI influences various aspects of plant development (chlorophyll accumulation, hypocotyl elongation, stomatal opening, and anthocyanin metabolism). GI has also been implicated to play a pivotal role in response to stresses such as freezing, thermomorphogenic stresses, salinity, drought, and osmotic stresses. Positioned at the hub of complex genetic networks, GI interacts with hormonal signaling pathways like abscisic acid (ABA), gibberellin (GA), salicylic acid (SA), and brassinosteroids (BRs) at multiple regulatory levels. This intricate interplay enables GI to balance stress responses, promoting growth and flowering, and optimize plant productivity. This review delves into the multifaceted roles of GI, supported by genetic and molecular evidence, and recent insights into the dynamic interplay between flowering and stress responses, which enhance plants' adaptability to environmental challenges.
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Affiliation(s)
- Ling Liu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin 644000, China;
| | - Yuxin Xie
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (B.S.Y.)
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China
| | - Baba Salifu Yahaya
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (B.S.Y.)
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (B.S.Y.)
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China
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Con P, Hamar J, Biran J, Kültz D, Cnaani A. Cell-based homologous expression system for in-vitro characterization of environmental effects on transmembrane peptide transport in fish. Curr Res Physiol 2024; 7:100118. [PMID: 38298473 PMCID: PMC10825657 DOI: 10.1016/j.crphys.2024.100118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 12/28/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024] Open
Abstract
All organisms encounter environmental changes that lead to physiological adjustments that could drive evolutionary adaptations. The ability to adjust performance in order to cope with environmental changes depends on the organism's physiological plasticity. These adjustments can be reflected in behavioral, physiological, and molecular changes, which interact and affect each other. Deciphering the role of molecular adjustments in physiological changes will help to understand how multiple levels of biological organization are synchronized during adaptations. Transmembrane transporters, which facilitate a cell's interaction with its surroundings, are prime targets for molecular studies of the environmental effects on an organism's physiology. Fish are subjected to environmental fluctuations and exhibit different coping mechanisms. To study the molecular adjustments of fish transporters to their external surrounding, suitable experimental systems must be established. The Mozambique tilapia (Oreochromis mossambicus) is an excellent model for environmental stress studies, due to its extreme salinity tolerance. We established a homologous cellular-based expression system and uptake assay that allowed us to study the effects of environmental conditions on transmembrane transport. We applied our expression system to investigate the effects of environmental conditions on the activity of PepT2, a transmembrane transporter critical in the absorption of dietary peptides and drugs. We created a stable, modified fish cell-line, in which we exogenously expressed the tilapia PepT2, and tested the effects of water temperature and salinity on the uptake of a fluorescent di-peptide, β-Ala-Lys-AMCA. While temperature affected only Vmax, medium salinity had a bi-directional effect, with significantly reduced Vmax in hyposaline conditions and significantly increased Km in hypersaline conditions. These assays demonstrate the importance of suitable experimental systems for fish ecophysiology studies. Furthermore, our in-vitro results show how the effect of hypersaline conditions on the transporter activity can explain expression shifts seen in the intestine of saltwater-acclimated fish, emphasizing the importance of complimentary studies in better understanding environmental physiology. This research highlights the advantages of using homologous expression systems to study environmental effects encountered by fish, in a relevant cellular context. The presented tools and methods can be adapted to study other transporters in-vitro.
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Affiliation(s)
- Pazit Con
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
- Department of Animal Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jens Hamar
- Department of Animal Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Jakob Biran
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Dietmar Kültz
- Department of Animal Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Avner Cnaani
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
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Root L, Kültz D. Effects of pejus and pessimum zone salinity stress on gill proteome networks and energy homeostasis in Oreochromis mossambicus. Proteomics 2024; 24:e2300121. [PMID: 37475512 DOI: 10.1002/pmic.202300121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/08/2023] [Accepted: 07/10/2023] [Indexed: 07/22/2023]
Abstract
Salinity tolerance in fish involves a suite of physiological changes, but a cohesive theory leading to a mechanistic understanding at the organismal level is lacking. To examine the potential of adapting energy homeostasis theory in the context of salinity stress in teleost fish, Oreochromis mossambicus were acclimated to hypersalinity at multiple rates and durations to determine salinity ranges of tolerance and resistance. Over 3000 proteins were quantified simultaneously to analyze molecular phenotypes associated with hypersalinity. A species- and tissue-specific data-independent acquisition (DIA) assay library of MSMS spectra was created. Protein networks representing complex molecular phenotypes associated with salinity acclimation were generated. O. mossambicus has a wide "zone of resistance" from 75 g/kg salinity to 120 g/kg. Crossing into the zone of resistance resulted in marked phenotypic changes including blood osmolality over 400 mOsm/kg, reduced body condition, and cessation of feeding. Protein networks impacted by hypersalinity consist of electron transport chain (ETC) proteins and specific osmoregulatory proteins. Cytoskeletal, cell adhesion, and extracellular matrix proteins are enriched in networks that are sensitive to the critical salinity threshold. These network analyses identify specific proteome changes that are associated with distinct zones described by energy homeostasis theory and distinguish them from general hypersalinity-induced proteome changes.
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Affiliation(s)
- Larken Root
- Department of Animal Sciences, University of California Davis, Davis, California, USA
| | - Dietmar Kültz
- Department of Animal Sciences, University of California Davis, Davis, California, USA
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Kim C, Cnaani A, Kültz D. Removal of evolutionarily conserved functional MYC domains in a tilapia cell line using a vector-based CRISPR/Cas9 system. Sci Rep 2023; 13:12086. [PMID: 37495710 PMCID: PMC10371998 DOI: 10.1038/s41598-023-37928-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/29/2023] [Indexed: 07/28/2023] Open
Abstract
MYC transcription factors have critical roles in facilitating a variety of cellular functions that have been highly conserved among species during evolution. However, despite circumstantial evidence for an involvement of MYC in animal osmoregulation, mechanistic links between MYC function and osmoregulation are missing. Mozambique tilapia (Oreochromis mossambicus) represents an excellent model system to study these links because it is highly euryhaline and highly tolerant to osmotic (salinity) stress at both the whole organism and cellular levels of biological organization. Here, we utilize an O. mossambicus brain cell line and an optimized vector-based CRISPR/Cas9 system to functionally disrupt MYC in the tilapia genome and to establish causal links between MYC and cell functions, including cellular osmoregulation. A cell isolation and dilution strategy yielded polyclonal myca (a gene encoding MYC) knockout (ko) cell pools with low genetic variability and high gene editing efficiencies (as high as 98.2%). Subsequent isolation and dilution of cells from these pools produced a myca ko cell line harboring a 1-bp deletion that caused a frameshift mutation. This frameshift functionally inactivated the transcriptional regulatory and DNA-binding domains predicted by bioinformatics and structural analyses. Both the polyclonal and monoclonal myca ko cell lines were viable, propagated well in standard medium, and differed from wild-type cells in morphology. As such, they represent a new tool for causally linking myca to cellular osmoregulation and other cell functions.
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Affiliation(s)
- Chanhee Kim
- Department of Animal Sciences, University of California, Davis, CA, 95616, USA
| | - Avner Cnaani
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, 7528809, Rishon LeZion, Israel
| | - Dietmar Kültz
- Department of Animal Sciences, University of California, Davis, CA, 95616, USA.
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Integrating transcriptomic and metabolomic analysis to understand muscle qualities of red swamp crayfish (Procambarus clarkii) under transport stress. Food Res Int 2023; 164:112361. [PMID: 36737949 DOI: 10.1016/j.foodres.2022.112361] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/10/2022] [Accepted: 12/24/2022] [Indexed: 01/04/2023]
Abstract
This study investigated the transport stress (crowding stress and duration) on the physicochemical properties, energy metabolism and antioxidant enzyme activities of the red swamp crayfish (Procambarus clarkii) tail muscle (CTM). Besides, transcriptomic and metabolomic were conducted to elucidate the possible mechanism of CTM alternations during transport stress. The survival rate of crayfish gradually decreased with the external crowding stress and crowding time increasing. The transport stress also led to the increased distance among muscle fibers, water mobility and energy consumption, and the decreased of water holding capacity (WHC), hardness of CTM. The hepatopancreas exhibited more sensitive to crowding stress than muscle. The multi-omics analysis revealed that transport stress could interfere the translation and protein folding functions of ribosomal proteins, fatty acid metabolism and degradation, physiological functions of mitochondria in CTM. This study could provide critical information to increase the understanding of the regulation mechanism of crayfish when subjected to transport stress.
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Liu B, Gao Q, Liu B, Song C, Sun C, Liu M, Liu X, Liu Y, Li Z, Zhou Q, Zhu H. Application of Transcriptome Analysis to Understand the Adverse Effects of Hypotonic Stress on Different Development Stages in the Giant Freshwater Prawn Macrobrachium rosenbergii Post-Larvae. Antioxidants (Basel) 2022; 11:antiox11030440. [PMID: 35326091 PMCID: PMC8944765 DOI: 10.3390/antiox11030440] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/18/2022] [Accepted: 02/20/2022] [Indexed: 01/27/2023] Open
Abstract
Salinity is one of the important environmental factors affecting survival and growth of aquatic animals. However, the impact of low-salinity stress on M. rosenbergii post-larvae at different development stages remains elusive. Therefore, the aim of this study was to explore the underlying mechanisms of hypotonic stress at different development stages of M. rosenbergii post-larvae through transcriptome analysis and antioxidant parameters detection. The salinity of the control group was 15 psu (S15) and the hypotonic stress group was 6 psu (S6). Samples were collected at 7 days-post-hatch (dph), 14 dph and 21 dph larvae. The results showed that hypotonic stress caused oxidative damage in post-larvae evidenced by decreased glutathione peroxidase (GSH-Px); superoxide dismutase (SOD); anti-superoxide anion free radical (ASAFR); and increased malondialdehyde (MDA); nitric oxide (NO); and inducible nitric oxide synthase (iNOS) levels. Transcriptome analysis showed that there were 1428, 1187, 132 DEGs including 301, 366, 4 up-regulated genes and 1127, 821, 128 down-regulated genes at 7 dph, 14 dph and 21 dph larvae under hypotonic stress, respectively. Furthermore, GO and KEGG enrichment indicated that hypotonic stress led to dysregulation of immune signals including lysosome and autophagy in the 7 dph larvae. The autophagy-related genes including beclin 1-associated autophagy-related key regulator (Barkor); ubiquitin-like modifier-activating enzyme ATG7 (ATG7); Beclin; autophagy-related protein 13 (ATG13); nuclear receptor-binding factor 2 (Nrbf2); ubiquitin-like-conjugating enzyme ATG3 (ATG3); vacuole membrane protein 1 (VMP1); and autophagy-related protein 2 (ATG2) decreased at 7 dph, and 14 dph larvae, and then increased at 21 dph larvae under hypotonic stress. In the 14 dph and 21 dph larvae, the renin-angiotensin system was activated. In conclusion, our data indicated that hypotonic stress reduced the antioxidant capacity and impaired the immune system in post-larvae, but as development progresses, the adaptability of post-larvae to hypotonic stress gradually increased, and might reach a new homeostasis through the RAS signaling pathway.
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Affiliation(s)
- Bo Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (B.L.); (M.L.); (X.L.); (Y.L.); (Q.Z.)
- Key Laboratory of Aquatic Animal Nutrition and Health, Freshwater Fisheries Research Center, Chinese Academy of Fishery Science, Wuxi 214081, China; (C.S.); (C.S.)
| | - Qiang Gao
- Zhejiang Institute of Freshwater Fishery, Huzhou 313001, China;
| | - Bo Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (B.L.); (M.L.); (X.L.); (Y.L.); (Q.Z.)
- Key Laboratory of Aquatic Animal Nutrition and Health, Freshwater Fisheries Research Center, Chinese Academy of Fishery Science, Wuxi 214081, China; (C.S.); (C.S.)
- Correspondence:
| | - Changyou Song
- Key Laboratory of Aquatic Animal Nutrition and Health, Freshwater Fisheries Research Center, Chinese Academy of Fishery Science, Wuxi 214081, China; (C.S.); (C.S.)
| | - Cunxin Sun
- Key Laboratory of Aquatic Animal Nutrition and Health, Freshwater Fisheries Research Center, Chinese Academy of Fishery Science, Wuxi 214081, China; (C.S.); (C.S.)
| | - Mingyang Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (B.L.); (M.L.); (X.L.); (Y.L.); (Q.Z.)
| | - Xin Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (B.L.); (M.L.); (X.L.); (Y.L.); (Q.Z.)
| | - Yunke Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (B.L.); (M.L.); (X.L.); (Y.L.); (Q.Z.)
| | - Zhengzhong Li
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China;
| | - Qunlan Zhou
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (B.L.); (M.L.); (X.L.); (Y.L.); (Q.Z.)
- Key Laboratory of Aquatic Animal Nutrition and Health, Freshwater Fisheries Research Center, Chinese Academy of Fishery Science, Wuxi 214081, China; (C.S.); (C.S.)
| | - Hao Zhu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Yangpu District, Shanghai 201306, China;
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Root L, Campo A, MacNiven L, Con P, Cnaani A, Kültz D. Nonlinear effects of environmental salinity on the gill transcriptome versus proteome of Oreochromis niloticus modulate epithelial cell turnover. Genomics 2021; 113:3235-3249. [PMID: 34298068 DOI: 10.1016/j.ygeno.2021.07.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/25/2021] [Accepted: 07/14/2021] [Indexed: 12/27/2022]
Abstract
A data-independent acquisition (DIA) assay library for targeted quantitation of thousands of Oreochromis niloticus gill proteins using a label- and gel-free workflow was generated and used to compare protein and mRNA abundances. This approach generated complimentary rather than redundant data for 1899 unique genes in gills of tilapia acclimated to freshwater and brackish water. Functional enrichment analyses identified mitochondrial energy metabolism, serine protease and immunity-related functions, and cytoskeleton/ extracellular matrix organization as major processes controlled by salinity in O. niloticus gills. Non-linearity in salinity-dependent transcriptome versus proteome regulation was revealed for specific functional groups of genes. The relationship was more linear for other molecular functions/ cellular processes, suggesting that the salinity-dependent regulation of O. niloticus gill function relies on post-transcriptional mechanisms for some functions/ processes more than others. This integrative systems biology approach can be adopted for other tissues and organisms to study cellular dynamics for many changing ecological contexts.
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Affiliation(s)
- Larken Root
- Department of Animal Sciences, University of California Davis, Meyer Hall, One Shields Avenue, Davis, CA 95616, USA
| | - Aurora Campo
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel
| | - Leah MacNiven
- Department of Animal Sciences, University of California Davis, Meyer Hall, One Shields Avenue, Davis, CA 95616, USA
| | - Pazit Con
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel
| | - Avner Cnaani
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, P.O. Box 15159, Rishon LeZion 7528809, Israel
| | - Dietmar Kültz
- Department of Animal Sciences, University of California Davis, Meyer Hall, One Shields Avenue, Davis, CA 95616, USA.
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Root L, Campo A, MacNiven L, Con P, Cnaani A, Kültz D. A data-independent acquisition (DIA) assay library for quantitation of environmental effects on the kidney proteome of Oreochromis niloticus. Mol Ecol Resour 2021; 21:2486-2503. [PMID: 34101993 DOI: 10.1111/1755-0998.13445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 04/30/2021] [Accepted: 06/01/2021] [Indexed: 12/31/2022]
Abstract
Interactions of organisms with their environment are complex and environmental regulation at different levels of biological organization is often nonlinear. Therefore, the genotype to phenotype continuum requires study at multiple levels of organization. While studies of transcriptome regulation are now common for many species, quantitative studies of environmental effects on proteomes are needed. Here we report the generation of a data-independent acquisition (DIA) assay library that enables simultaneous targeted proteomics of thousands of Oreochromis niloticus kidney proteins using a label- and gel-free workflow that is well suited for ecologically relevant field samples. We demonstrate the usefulness of this DIA assay library by discerning environmental effects on the kidney proteome of O. niloticus. Moreover, we demonstrate that the DIA assay library approach generates data that are complimentary rather than redundant to transcriptomic data. Transcript and protein abundance differences in kidneys of tilapia acclimated to freshwater and brackish water (25 g/kg) were correlated for 2114 unique genes. A high degree of non-linearity in salinity-dependent regulation of transcriptomes and proteomes was revealed suggesting that the regulation of O. niloticus renal function by environmental salinity relies heavily on post-transcriptional mechanisms. The application of functional enrichment analyses using STRING and KEGG to DIA assay data sets is demonstrated by identifying myo-inositol metabolism, antioxidant and xenobiotic functions, and signalling mechanisms as key elements controlled by salinity in tilapia kidneys. The DIA assay library resource presented here can be adopted for other tissues and other organisms to study proteome dynamics during changing ecological contexts.
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Affiliation(s)
- Larken Root
- Department of Animal Sciences, University of California Davis, Davis, CA, USA
| | - Aurora Campo
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Leah MacNiven
- Department of Animal Sciences, University of California Davis, Davis, CA, USA
| | - Pazit Con
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Avner Cnaani
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Dietmar Kültz
- Department of Animal Sciences, University of California Davis, Davis, CA, USA
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Dong Z, Coates D. Bioactive Molecular Discovery Using Deer Antlers as a Model of Mammalian Regeneration. J Proteome Res 2021; 20:2167-2181. [PMID: 33769828 DOI: 10.1021/acs.jproteome.1c00003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The ability to activate and regulate stem cells during wound healing and tissue regeneration is a promising field that is resulting in innovative approaches in the field of regenerative medicine. The regenerative capacity of invertebrates has been well documented; however, in mammals, stem cells that drive organ regeneration are rare. Deer antlers are the only known mammalian structure that can annually regenerate to produce a tissue containing dermis, blood vessels, nerves, cartilage, and bone. The neural crest derived stem cells that drive this process result in antlers growing at up to 2 cm/day. Deer antlers thus provide superior attributes compared to lower-order animal models, when investigating the regulation of stem cell-based regeneration. Antler stem cells can therefore be used as a model to investigate the bioactive molecules, biological processes, and pathways involved in the maintenance of a stem cell niche, and their activation and differentiation during organ formation. This review examines stem cell-based regeneration with a focus on deer antlers, a neural crest stem cell-based mammalian regenerative structure. It then discusses the omics technical platforms highlighting the proteomics approaches used for investigating the molecular mechanisms underlying stem cell regulation in antler tissues.
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Affiliation(s)
- Zhen Dong
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin 9016, New Zealand
| | - Dawn Coates
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin 9016, New Zealand
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Role of Transportome in the Gills of Chinese Mitten Crabs in Response to Salinity Change: A Meta-Analysis of RNA-Seq Datasets. BIOLOGY 2021; 10:biology10010039. [PMID: 33430106 PMCID: PMC7827906 DOI: 10.3390/biology10010039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 12/26/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022]
Abstract
Chinese mitten crab (CMC) or Eriocheir sinensis is a strong osmoregulator that can keep rigorous cellular homeostasis. CMC can flourish in freshwater, as well as seawater, habitats and represents the most important species for freshwater aquaculture. Salt stress can have direct effects on several stages (e.g., reproduction, molting, growth, etc.) of the CMC life cycle. To get a better overview of the genes involved in the gills of CMC under different salinity conditions, we conducted an RNA-Seq meta-analysis on the transcriptomes of four publicly available datasets. The meta-analysis identified 405 differentially expressed transcripts (DETs), of which 40% were classified into various transporter classes, including accessory factors and primary active transporters as the major transport classes. A network analysis of the DETs revealed that adaptation to salinity is a highly regulated mechanism in which different functional modules play essential roles. To the best of our knowledge, this study is the first to conduct a transcriptome meta-analysis of gills from crab RNA-Seq datasets under salinity. Additionally, this study is also the first to focus on the differential expression of diverse transporters and channels (transportome) in CMC. Our meta-analysis opens new avenues for a better understanding of the osmoregulation mechanism and the selection of potential transporters associated with salinity change.
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Multiple stressor responses are regulated by sirtuins in Mytilus congeners. Comp Biochem Physiol A Mol Integr Physiol 2020; 246:110719. [DOI: 10.1016/j.cbpa.2020.110719] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 02/06/2023]
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Yang Z, Zhou J, Wei B, Cheng Y, Zhang L, Zhen X. Comparative transcriptome analysis reveals osmotic-regulated genes in the gill of Chinese mitten crab (Eriocheir sinensis). PLoS One 2019; 14:e0210469. [PMID: 30629688 PMCID: PMC6328174 DOI: 10.1371/journal.pone.0210469] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 12/24/2018] [Indexed: 11/19/2022] Open
Abstract
Salinity is one of the most important abiotic factors directly affecting the reproduction, molting, growth, immune, physiological and metabolic activities of Chinese mitten crab (Eriocheir sinensis). This species has strong osmoregulatory capacity and can maintain stringent internal homeostasis. However, the mechanisms conferring tolerance to salinity fluctuations are not well understood. To reveal the genes and pathways involved in osmoregulation, adult male crabs (body weight = 110 ± 5 g) were acclimated for 144 h in freshwater (FW, 0 ppt) or seawater (SW, 25 ppt). Changes in the transcriptome of crab gills were then analysed by RNA-Seq, and 174,903 unigenes were obtained. Comparison of genes between FW- SW-acclimated groups identified 932 genes that were significantly differentially expressed in the gill, comprising 433 and 499 up- and downregulated transcripts. Gene Ontology functional enrichment analysis revealed that important biological processes related to salt stress were significantly enriched, including energy metabolism, ion transport, signal transduction and antioxidant activity. Kyoto Encyclopaedia of Genes and Genomes enrichment analysis mapped the differentially expressed genes to 241 specific metabolic pathways, and pathways related to energy metabolism, oxidative phosphorylation and the tricarboxylic acid (TCA)/citrate cycle were significantly enriched. Salinity stress altered the expression of many enzymes involved in energy metabolism, ion transport, signal transduction and antioxidant pathways, including citrate synthase (CS), Na+/K+-ATPase (NKA), Na+-K+-2Cl cotransporter-1 (NKCC1), dopamine receptor D1 (DRD1), synaptic binding protein 1 (STXBP1), Cu2+/Zn2+ superoxide dismutase (SOD1) and glutathione S-transferase (GST). Additionally, the obtained transcriptomic sequencing data provided a useful resource for identification of novel genes, and further physiological analysis of Chinese mitten crab.
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Affiliation(s)
- Zhigang Yang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Centre for Research on Environmental Ecology and Fish Nutrition (CREEFN) of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- * E-mail: (ZGY); (YXC)
| | - Junyu Zhou
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Centre for Research on Environmental Ecology and Fish Nutrition (CREEFN) of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Banghong Wei
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Centre for Research on Environmental Ecology and Fish Nutrition (CREEFN) of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Yongxu Cheng
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Centre for Research on Environmental Ecology and Fish Nutrition (CREEFN) of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- * E-mail: (ZGY); (YXC)
| | - Long Zhang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Centre for Research on Environmental Ecology and Fish Nutrition (CREEFN) of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Xiaomin Zhen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Centre for Research on Environmental Ecology and Fish Nutrition (CREEFN) of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
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13
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Liu Z, Zhou Z, Wang L, Li M, Wang W, Yi Q, Huang S, Song L. Dopamine and Serotonin Modulate Free Amino Acids Production and Na +/K + Pump Activity in Chinese Mitten Crab Eriocheir sinensis Under Acute Salinity Stress. Front Physiol 2018; 9:1080. [PMID: 30364201 PMCID: PMC6192224 DOI: 10.3389/fphys.2018.01080] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 07/19/2018] [Indexed: 01/08/2023] Open
Abstract
The Chinese mitten crab Eriocheir sinensis lives in saline or fresh water during different life stages and exhibits a complex life history, making it an ideal model to study the salinity adaptation of euryhaline animals. In this study, RNA-seq techniques, and determinations of free amino acids (FAAs), monoamine neurotransmitters, and Na+/K+ pump activity, were employed to understand the osmoregulatory mechanism in Chinese mitten crab. A total of 15,138 differentially expressed genes were obtained from 12 transcriptome libraries. GO enrichment analysis revealed that the mRNA expression profiles were completely remodeled from 12 to 24 h after salinity stress. The neuroendocrine system was activated under stimulation, and the monoamine neurotransmitters including dopamine (DA) and serotonin (5-HT) were released to modulate osmoregulation. Furthermore, the Na+/K+ pump in crab hemocytes was significantly inhibited post salinity stress, resulting in increased intracellular ion concentrations and osmotic pressure to sustain the osmotic balance. Moreover, six key FAAs, including alanine (Ala), proline (Pro), glycine (Gly), glutamate (Glu), arginine (Arg), and aspartate (Asp), were overexpressed to modulate the extracellular osmotic balance during salinity adaptation. Interestingly, the immune genes were not enriched in the GO analysis, implying that the immune system might not contribute fundamentally to the tolerance upon fluctuating ambient salinity in the Chinese mitten crab. These results collectively demonstrated that the Chinese mitten crab had evolved an efficient regulation mechanism by modulating the FAAs production and Na+/K+ pump activity to sustain the osmotic balance independent of the immune system, in which the neuroendocrine modulation, especially generated by the monoamine neurotransmitter, played an indispensable role.
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Affiliation(s)
- Zhaoqun Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China
| | - Zhi Zhou
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Meijia Li
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China
| | - Weilin Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China
| | - Qilin Yi
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China
| | - Shu Huang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China
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14
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Effects of the acclimation to high salinity on intestinal ion and peptide transporters in two tilapia species that differ in their salinity tolerance. Comp Biochem Physiol A Mol Integr Physiol 2018; 218:16-23. [PMID: 29366921 DOI: 10.1016/j.cbpa.2018.01.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/11/2018] [Accepted: 01/11/2018] [Indexed: 02/06/2023]
Abstract
Tilapiine species, widely distributed across habitats with diverse water salinities, are important to aquaculture as well as a laboratory model. The effects of water salinity on two tilapia species, that differ in their salinity tolerance, was evaluated. Oreochromis niloticus reared in brackish-water, showed a significant decrease in growth and feed efficiency, whereas O. mossambicus reared in seawater did not show any significant changes. The expression and activity of Na+/K+-ATPase (NKA), V-type H+-ATPase (VHA) and carbonic anhydrase (CA), as well as expression levels of genes encoding two HCO3- and three peptide transporters (nbc1, slc26a6, slc15a1a, slc15a1b and slc15a2) were measured in three intestinal sections of these two species, grown in freshwater and brackish/sea-water. Overall, the spatial distribution along the intestine of the genes examined in this study was similar between the two species, with the exception of tcaIV. The salinity response, on the other hand, varied greatly between these species. In O. mossambicus, there was a salinity-dependent increased expression of most of the examined genes (except slc26a6 and slc15a2), while in O. niloticus the expression of most genes did not change, or even decreased (tcaIV, nbc1 and slc15a1b). This study highlighted differences in the intestinal response to salinity acclimation between closely- related species that differ in their salinity tolerance. O. mossambicus, which has a high salinity tolerance, showed expression patterns and responses similar to marine species, and differed from the low-salinity-tolerance O. niloticus, which showed a response that differed from the accepted models, that are based on marine and diadromous fishes.
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15
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Karmous I, Trevisan R, El Ferjani E, Chaoui A, Sheehan D. Redox biology response in germinating Phaseolus vulgaris seeds exposed to copper: Evidence for differential redox buffering in seedlings and cotyledon. PLoS One 2017; 12:e0184396. [PMID: 28981522 PMCID: PMC5628808 DOI: 10.1371/journal.pone.0184396] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 08/23/2017] [Indexed: 12/27/2022] Open
Abstract
In agriculture, heavy metal contamination of soil interferes with processes associated with plant growth, development and productivity. Here, we describe oxidative and redox changes, and deleterious injury within cotyledons and seedlings caused by exposure of germinating (Phaseolus vulgaris L. var. soisson nain hâtif) seeds to copper (Cu). Cu induced a marked delay in seedling growth, and was associated with biochemical disturbances in terms of intracellular oxidative status, redox regulation and energy metabolism. In response to these alterations, modulation of activities of antioxidant proteins (thioredoxin and glutathione reductase, peroxiredoxin) occurred, thus preventing oxidative damage. In addition, oxidative modification of proteins was detected in both cotyledons and seedlings by one- and two-dimensional electrophoresis. These modified proteins may play roles in redox buffering. The changes in activities of redox proteins underline their fundamental roles in controlling redox homeostasis. However, observed differential redox responses in cotyledon and seedling tissues showed a major capacity of the seedlings' redox systems to protect the reduced status of protein thiols, thus suggesting quantitatively greater antioxidant protection of proteins in seedlings compared to cotyledon. To our knowledge, this is the first comprehensive redox biology investigation of the effect of Cu on seed germination.
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Affiliation(s)
- Inès Karmous
- Plant Toxicology and Molecular Biology of Microorganisms, Faculty of Sciences of Bizerta, Zarzouna, Tunisia
| | - Rafael Trevisan
- Nicholas School of the Environment, Duke University, Durham, North Carolina, United States of America
| | - Ezzeddine El Ferjani
- Plant Toxicology and Molecular Biology of Microorganisms, Faculty of Sciences of Bizerta, Zarzouna, Tunisia
| | - Abdelilah Chaoui
- Plant Toxicology and Molecular Biology of Microorganisms, Faculty of Sciences of Bizerta, Zarzouna, Tunisia
| | - David Sheehan
- College of Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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16
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Con P, Nitzan T, Cnaani A. Salinity-Dependent Shift in the Localization of Three Peptide Transporters along the Intestine of the Mozambique Tilapia ( Oreochromis mossambicus). Front Physiol 2017; 8:8. [PMID: 28167916 PMCID: PMC5253378 DOI: 10.3389/fphys.2017.00008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/05/2017] [Indexed: 12/15/2022] Open
Abstract
The peptide transporter (PepT) systems are well-known for their importance to protein absorption in all vertebrate species. These symporters use H+ gradient at the apical membrane of the intestinal epithelial cells to mediate the absorption of small peptides. In fish, the intestine is a multifunctional organ, involved in osmoregulation, acid-base regulation, and nutrient absorption. Therefore, we expected environmental stimuli to affect peptide absorption. We examined the effect of three environmental factors; salinity, pH and feeding, on the expression, activity and localization of three PepT transporters (PepT1a, PepT1b, PepT2) along the intestine of the Mozambique tilapia (Oreochromis mossambicus). Quantitative real time PCR (qPCR) analysis demonstrated that the two PepT1 variants are typical to the proximal intestinal section while PepT2 is typical to the distal intestinal sections. Immunofluorescence analysis with custom-made antibodies supported the qPCR results, localized both transporters on the apical membrane of enterocytes and provided the first evidence for the participation of PepT2 in nutrient absorption. This first description of segment-specific expression and localization points to a complementary role of the different peptide transporters, corresponding to the changes in nutrient availability along the intestine. Both gene expression and absorption activity assays showed that an increase in water salinity shifted the localization of the PepT genes transcription and activity down along the intestinal tract. Additionally, an unexpected pH effect was found on the absorption of small peptides, with increased activity at higher pH levels. This work emphasizes the relationships between different functions of the fish intestine and how they are affected by environmental conditions.
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Affiliation(s)
- Pazit Con
- Agricultural Research Organization, Institute of Animal ScienceRishon Letziyon, Israel; Department of Animal Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University of JerusalemRehovot, Israel
| | - Tali Nitzan
- Agricultural Research Organization, Institute of Animal Science Rishon Letziyon, Israel
| | - Avner Cnaani
- Agricultural Research Organization, Institute of Animal Science Rishon Letziyon, Israel
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17
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Kalujnaia S, Hazon N, Cramb G. Myo-inositol phosphate synthase expression in the European eel (Anguilla anguilla) and Nile tilapia (Oreochromis niloticus): effect of seawater acclimation. Am J Physiol Regul Integr Comp Physiol 2016; 311:R287-98. [PMID: 27252471 PMCID: PMC5008666 DOI: 10.1152/ajpregu.00056.2016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/25/2016] [Indexed: 11/29/2022]
Abstract
A single MIPS gene (Isyna1/Ino1) exists in eel and tilapia genomes with a single myo-d-inositol 3-phosphate synthase (MIPS) transcript identified in all eel tissues, although two MIPS spliced variants [termed MIPS(s) and MIPS(l)] are found in all tilapia tissues. The larger tilapia transcript [MIPS(l)] results from the inclusion of the 87-nucleotide intron between exons 5 and 6 in the genomic sequence. In most tilapia tissues, the MIPS(s) transcript exhibits much higher abundance (generally >10-fold) with the exception of white skeletal muscle and oocytes, in which the MIPS(l) transcript predominates. SW acclimation resulted in large (6- to 32-fold) increases in mRNA expression for both MIPS(s) and MIPS(l) in all tilapia tissues tested, whereas in the eel, changes in expression were limited to a more modest 2.5-fold increase and only in the kidney. Western blots identified a number of species- and tissue-specific immunoreactive MIPS proteins ranging from 40 to 67 kDa molecular weight. SW acclimation failed to affect the abundance of any immunoreactive protein in any tissue tested from the eel. However, a major 67-kDa immunoreactive protein (presumed to be MIPS) found in tilapia tissues exhibited 11- and 54-fold increases in expression in gill and fin samples from SW-acclimated fish. Immunohistochemical investigations revealed specific immunoreactivity in the gill, fin, skin, and intestine taken from only SW-acclimated tilapia. Immunofluorescence indicated that MIPS was expressed within gill chondrocytes and epithelial cells of the primary filaments, basal epithelial cell layers of the skin and fin, the cytosol of columnar intestinal epithelial and mucous cells, as well as unknown entero-endocrine-like cells.
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Affiliation(s)
- Svetlana Kalujnaia
- School of Medicine, University of St. Andrews, St. Andrews, United Kingdom; and
| | - Neil Hazon
- School of Biology, University of St. Andrews, St. Andrews, United Kingdom
| | - Gordon Cramb
- School of Medicine, University of St. Andrews, St. Andrews, United Kingdom; and
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18
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Muraeva OA, Maltseva AL, Mikhailova NA, Granovitch AI. Mechanisms of adaption to salinity stress in marine gastropods Littorina saxatilis: a proteomic analysis. ACTA ACUST UNITED AC 2016. [DOI: 10.1134/s1990519x16020085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Marco-Ramell A, de Almeida AM, Cristobal S, Rodrigues P, Roncada P, Bassols A. Proteomics and the search for welfare and stress biomarkers in animal production in the one-health context. MOLECULAR BIOSYSTEMS 2016; 12:2024-35. [DOI: 10.1039/c5mb00788g] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Stress and welfare are important factors in animal production in the context of growing production optimization and scrutiny by the general public.
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Affiliation(s)
- A. Marco-Ramell
- Departament de Bioquímica i Biologia Molecular
- Facultat de Veterinària
- Universitat Autònoma de Barcelona
- 08193 Cerdanyola del Vallès
- Spain
| | - A. M. de Almeida
- Instituto de Biologia Experimental e Tecnologica
- Oeiras
- Portugal
- CIISA/FMV – Centro Interdisciplinar de Investigação em Sanidade Animal
- Faculdade de Medicina Veterinária
| | - S. Cristobal
- Department of Clinical and Experimental Medicine
- Cell Biology
- Faculty of Medicine
- Linköping University
- Linköping
| | - P. Rodrigues
- CCMAR
- Center of Marine Science
- University of Algarve
- 8005-139 Faro
- Portugal
| | - P. Roncada
- Istituto Sperimentale Italiano L. Spallanzani
- Milano
- Italy
| | - A. Bassols
- Departament de Bioquímica i Biologia Molecular
- Facultat de Veterinària
- Universitat Autònoma de Barcelona
- 08193 Cerdanyola del Vallès
- Spain
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20
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Ronkin D, Seroussi E, Nitzan T, Doron-Faigenboim A, Cnaani A. Intestinal transcriptome analysis revealed differential salinity adaptation between two tilapiine species. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2015; 13:35-43. [DOI: 10.1016/j.cbd.2015.01.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/19/2015] [Accepted: 01/19/2015] [Indexed: 11/27/2022]
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21
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Maneja RH, Dineshram R, Thiyagarajan V, Skiftesvik AB, Frommel AY, Clemmesen C, Geffen AJ, Browman HI. The proteome of Atlantic herring (Clupea harengus L.) larvae is resistant to elevated pCO2. MARINE POLLUTION BULLETIN 2014; 86:154-160. [PMID: 25110053 DOI: 10.1016/j.marpolbul.2014.07.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 07/17/2014] [Accepted: 07/20/2014] [Indexed: 05/28/2023]
Abstract
Elevated anthropogenic pCO2 can delay growth and impair otolith structure and function in the larvae of some fishes. These effects may concurrently alter the larva's proteome expression pattern. To test this hypothesis, Atlantic herring larvae were exposed to ambient (370 μatm) and elevated (1800 μatm) pCO2 for one-month. The proteome structure of the larvae was examined using a 2-DE and mass spectrometry. The length of herring larvae was marginally less in the elevated pCO2 treatment compared to the control. The proteome structure was also different between the control and treatment, but only slightly: the expression of a small number of proteins was altered by a factor of less than 2-fold at elevated pCO2. This comparative proteome analysis suggests that the proteome of herring larvae is resilient to elevated pCO2. These observations suggest that herring larvae can cope with levels of CO2 projected for near future without significant proteome-wide changes.
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Affiliation(s)
- Rommel H Maneja
- Center for Environment and Water, Research Institute, King Fahd University of Petroleum and Minerals, 31261 Dhahran, Saudi Arabia; Helmholtz-Zentrum für Ozeanforschung Kiel-GEOMAR, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - R Dineshram
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Vengatesen Thiyagarajan
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region.
| | | | - Andrea Y Frommel
- Helmholtz-Zentrum für Ozeanforschung Kiel-GEOMAR, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Catriona Clemmesen
- Helmholtz-Zentrum für Ozeanforschung Kiel-GEOMAR, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Audrey J Geffen
- Department of Biology, University of Bergen, PO Box 7803, N-5020 Bergen, Norway
| | - Howard I Browman
- Institute of Marine Research, Austevoll Research Station, 5392 Storebø, Norway.
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22
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Li E, Wang S, Li C, Wang X, Chen K, Chen L. Transcriptome sequencing revealed the genes and pathways involved in salinity stress of Chinese mitten crab, Eriocheir sinensis. Physiol Genomics 2014; 46:177-90. [DOI: 10.1152/physiolgenomics.00191.2013] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A total of 276.9 million reads were obtained and assembled into 206, 371 contigs with an average length of 614 bp and N50 of 1,470 bp. Comparison of digital gene expression between treatment and control group reveals 1,151 and 941 genes were significantly differentially expressed in crab gill and muscle, respectively. In gill and muscle, protein ubiquitination, ubiquinone biosynthesis, oxidative phosphorylation, and mitochondria dysfunction pathways were the top pathways differentially expressed following the challenge. EIF 2 signaling pathway and IGF-1 signaling pathway were the top ones among the signal-related pathways. Most of the amino acid metabolism pathways were found to be involved in this process. The expression patterns of 15 differentially expressed genes were validated by quantitative real-time RT-PCR (average correlation coefficient 0.80). This is the first report of expression analysis of genes and pathways involved in osmoregulation of Eriocheir sinensis through transcriptome sequencing. The findings of this study will further promote the understanding of the underlying molecular mechanism of salinity stress adaptation for crustacean species.
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Affiliation(s)
- Erchao Li
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Shaolin Wang
- Department of Psychiatry & Neurobiology Science, University of Virginia, Charlottesville, Virginia; and
| | - Chao Li
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama
| | - Xiaodan Wang
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Ke Chen
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Liqiao Chen
- School of Life Sciences, East China Normal University, Shanghai, China
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23
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Das M, Banerjee B, Choudhury MG, Saha N. Environmental hypertonicity causes induction of gluconeogenesis in the air-breathing singhi catfish, Heteropneustes fossilis. PLoS One 2013; 8:e85535. [PMID: 24376888 PMCID: PMC3869940 DOI: 10.1371/journal.pone.0085535] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 11/27/2013] [Indexed: 02/01/2023] Open
Abstract
The air-breathing singhi catfish (Heteropneustes fossilis) is frequently being challenged by different environmental insults such as hyper-ammonia, dehydration and osmotic stresses in their natural habitats throughout the year. The present study investigated the effect of hyperosmotic stress, due to exposure to hypertonic environment (300 mM mannitol) for 14 days, on gluconeogenesis in this catfish. In situ exposure to hypertonic environment led to significant stimulation of gluconeogenic fluxes from the perfused liver after 7 days of exposure, followed by further increase after 14 days in presence of three different potential gluconeogenic substrates (lactate, pyruvate and glutamate). Environmental hypertonicity also caused a significant increase of activities of key gluconeogenic enzymes, namely phosphoenolpyruvate carboxykinase, fructose 1, 6-bisphosphatase and glucose 6-phosphatase by about 2-6 fold in liver, and 3-6 fold in kidney tissues. This was accompanied by more abundance of enzyme proteins by about 1.8–3.7 fold and mRNAs by about 2.2–5.2 fold in both the tissues with a maximum increase after 14 days of exposure. Hence, the increase in activities of key gluconeogenic enzymes under hypertonic stress appeared to be as a result of transcriptional regulation of genes. Immunocytochemical analysis further confirmed the tissue specific localized expression of these enzymes in both the tissues with the possibility of expressing more in the same localized places. The induction of gluconeogenesis during exposure to environmental hypertonicity possibly occurs as a consequence of changes in hydration status/cell volume of different cell types. Thus, these adaptational strategies related to gluconeogenesis that are observed in this catfish under hypertonic stress probably help in maintaining glucose homeostasis and also for a proper energy supply to support metabolic demands mainly for ion transport and other altered metabolic processes under various environmental hypertonic stress-related insults.
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Affiliation(s)
- Manas Das
- Biochemical Adaptation Laboratory, Department of Zoology, North-Eastern Hill University, Shillong, India
| | - Bodhisattwa Banerjee
- Biochemical Adaptation Laboratory, Department of Zoology, North-Eastern Hill University, Shillong, India
| | - Mahua G. Choudhury
- Biochemical Adaptation Laboratory, Department of Zoology, North-Eastern Hill University, Shillong, India
| | - Nirmalendu Saha
- Biochemical Adaptation Laboratory, Department of Zoology, North-Eastern Hill University, Shillong, India
- * E-mail:
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24
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Gardell AM, Yang J, Sacchi R, Fangue NA, Hammock BD, Kültz D. Tilapia (Oreochromis mossambicus) brain cells respond to hyperosmotic challenge by inducing myo-inositol biosynthesis. ACTA ACUST UNITED AC 2013; 216:4615-25. [PMID: 24072790 DOI: 10.1242/jeb.088906] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This study aimed to determine the regulation of the de novo myo-inositol biosynthetic (MIB) pathway in Mozambique tilapia (Oreochromis mossambicus) brain following acute (25 ppt) and chronic (30, 60 and 90 ppt) salinity acclimations. The MIB pathway plays an important role in accumulating the compatible osmolyte, myo-inositol, in cells in response to hyperosmotic challenge and consists of two enzymes, myo-inositol phosphate synthase and inositol monophosphatase. In tilapia brain, MIB enzyme transcriptional regulation was found to robustly increase in a time (acute acclimation) or dose (chronic acclimation) dependent manner. Blood plasma osmolality and Na(+) and Cl(-) concentrations were also measured and significantly increased in response to both acute and chronic salinity challenges. Interestingly, highly significant positive correlations were found between MIB enzyme mRNA and blood plasma osmolality in both acute and chronic salinity acclimations. Additionally, a mass spectrometry assay was established and used to quantify total myo-inositol concentration in tilapia brain, which closely mirrored the hyperosmotic MIB pathway induction. Thus, myo-inositol is a major compatible osmolyte that is accumulated in brain cells when exposed to acute and chronic hyperosmotic challenge. These data show that the MIB pathway is highly induced in response to environmental salinity challenge in tilapia brain and that this induction is likely prompted by increases in blood plasma osmolality. Because the MIB pathway uses glucose-6-phosphate as a substrate and large amounts of myo-inositol are being synthesized, our data also illustrate that the MIB pathway likely contributes to the high energetic demand posed by salinity challenge.
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Affiliation(s)
- Alison M Gardell
- Department of Animal Science, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
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25
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Abstract
Zebrafish offer a unique vertebrate model for research areas such as drug development, disease modeling and other biological exploration. There is significant conservation of genetics and other cellular networks among zebrafish and other vertebrate models, including humans. Here we discuss the recent work and efforts made in different fields of biology to explore the potential of zebrafish. Along with this, we also reviewed the concept of systems biology. A biological system is made up of a large number of components that interact in a huge variety of combinations. To understand completely the behavior of a system, it is important to know its components and interactions, and this can be achieved through a systems biology approach. At the end of the paper we present a concept of integrating zebrafish into the systems biology approach.
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Affiliation(s)
- Mian Yahya Mushtaq
- a Natural Products Laboratory, Institute of Biology, Leiden University , Leiden , The Netherlands
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26
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Tse WKF, Sun J, Zhang H, Law AYS, Yeung BHY, Chow SC, Qiu JW, Wong CKC. Transcriptomic and iTRAQ proteomic approaches reveal novel short-term hyperosmotic stress responsive proteins in the gill of the Japanese eel (Anguilla japonica). J Proteomics 2013; 89:81-94. [PMID: 23735544 DOI: 10.1016/j.jprot.2013.05.026] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/22/2013] [Accepted: 05/18/2013] [Indexed: 01/18/2023]
Abstract
UNLABELLED Osmoregulation is critical for the survival of fishes that migrate between freshwater (FW) and seawater (SW). The eel, as a catadromous fish, has been studied for decades to reveal the mechanisms of osmoregulation. These studies, however, have been limited by the lack of a genomic database to decipher the mechanism of osmoregulation at a molecular level. In this study, using high-throughput transcriptomic and proteomic technologies, we have provided the first genome-wide study to identify hyperosmotic responsive proteins in the gills of the Japanese eel. Deep sequencing using the 454 platform produced over 660,000 reads with a mean length of 385 bp. For the proteomic study, we collected gill samples from three different treatment groups of fish that had fully adapted to FW/SW or were transferred from FW to SW for 6h. The respective group of gill proteins were extracted and labeled using an isobaric tag for relative and absolute quantitation (iTRAQ) using LTQ-Orbitrap, a high resolution mass spectrometer. Among the 1519 proteins identified from the gill samples, 96 proteins were differentially expressed between FW and SW adapted fish. Nineteen hyperosmotic responsive proteins were detected (10 up-regulated and 9 down-regulated proteins) after 6h post FW to SW transfer. BIOLOGICAL SIGNIFICANCE The study has provided the most comprehensive, targeted investigation of eel gill proteins to date, and shown the powerfulness of combining transcriptomic and proteomic approaches to provide molecular insights of osmoregulation mechanisms in a non-model organism, eel.
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Functional Proteomic Profiling of Phosphodiesterases Using SeraFILE Separations Platform. INTERNATIONAL JOURNAL OF PROTEOMICS 2012; 2012:515372. [PMID: 23227336 PMCID: PMC3512300 DOI: 10.1155/2012/515372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 06/29/2012] [Accepted: 07/02/2012] [Indexed: 11/25/2022]
Abstract
Functional proteomic profiling can help identify targets for disease diagnosis and therapy. Available methods are limited by the inability to profile many functional properties measured by enzymes kinetics. The functional proteomic profiling approach proposed here seeks to overcome such limitations. It begins with surface-based proteome separations of tissue/cell-line extracts, using SeraFILE, a proprietary protein separations platform. Enzyme kinetic properties of resulting subproteomes are then characterized, and the data integrated into proteomic profiles. As a model, SeraFILE-derived subproteomes of cyclic nucleotide-hydrolyzing phosphodiesterases (PDEs) from bovine brain homogenate (BBH) and rat brain homogenate (RBH) were characterized for cAMP hydrolysis activity in the presence (challenge condition) and absence of cGMP. Functional profiles of RBH and BBH were compiled from the enzyme activity response to the challenge condition in each of the respective subproteomes. Intersample analysis showed that comparable profiles differed in only a few data points, and that distinctive subproteomes can be generated from comparable tissue samples from different animals. These results demonstrate that the proposed methods provide a means to simplify intersample differences, and to localize proteins attributable to sample-specific responses. It can be potentially applied for disease and nondisease sample comparison in biomarker discovery and drug discovery profiling.
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Slattery M, Ankisetty S, Corrales J, Marsh-Hunkin KE, Gochfeld DJ, Willett KL, Rimoldi JM. Marine proteomics: a critical assessment of an emerging technology. JOURNAL OF NATURAL PRODUCTS 2012; 75:1833-1877. [PMID: 23009278 DOI: 10.1021/np300366a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The application of proteomics to marine sciences has increased in recent years because the proteome represents the interface between genotypic and phenotypic variability and, thus, corresponds to the broadest possible biomarker for eco-physiological responses and adaptations. Likewise, proteomics can provide important functional information regarding biosynthetic pathways, as well as insights into mechanism of action, of novel marine natural products. The goal of this review is to (1) explore the application of proteomics methodologies to marine systems, (2) assess the technical approaches that have been used, and (3) evaluate the pros and cons of this proteomic research, with the intent of providing a critical analysis of its future roles in marine sciences. To date, proteomics techniques have been utilized to investigate marine microbe, plant, invertebrate, and vertebrate physiology, developmental biology, seafood safety, susceptibility to disease, and responses to environmental change. However, marine proteomics studies often suffer from poor experimental design, sample processing/optimization difficulties, and data analysis/interpretation issues. Moreover, a major limitation is the lack of available annotated genomes and proteomes for most marine organisms, including several "model species". Even with these challenges in mind, there is no doubt that marine proteomics is a rapidly expanding and powerful integrative molecular research tool from which our knowledge of the marine environment, and the natural products from this resource, will be significantly expanded.
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Affiliation(s)
- Marc Slattery
- Department of Pharmacognosy, School of Pharmacy, The University of Mississippi, University, Mississippi 38677, USA.
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Pedriali A, Riva C, Parolini M, Cristoni S, Sheehan D, Binelli A. A redox proteomic investigation of oxidative stress caused by benzoylecgonine in the freshwater bivalveDreissena polymorpha. Drug Test Anal 2012; 5:646-56. [DOI: 10.1002/dta.1409] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 08/04/2012] [Accepted: 08/13/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Alessandra Pedriali
- University of Milan; Department of Life Sciences; via Celoria 26; 20133; Milan; Italy
| | - Consuelo Riva
- University of Milan; Department of Life Sciences; via Celoria 26; 20133; Milan; Italy
| | - Marco Parolini
- University of Milan; Department of Life Sciences; via Celoria 26; 20133; Milan; Italy
| | - Simone Cristoni
- ISB Ion Source & Biotechnologies S.r.l.; via Lepetit 34; 21040; Gerenzano (VA); Italy
| | - David Sheehan
- Proteomics Research Group; Department of Biochemistry and Environmental Research Institute University College Cork; Lee Maltings, Prospect Row, Mardyke; Cork; Ireland
| | - Andrea Binelli
- University of Milan; Department of Life Sciences; via Celoria 26; 20133; Milan; Italy
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Dowd WW. Challenges for Biological Interpretation of Environmental Proteomics Data in Non-model Organisms. Integr Comp Biol 2012; 52:705-20. [DOI: 10.1093/icb/ics093] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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Corrado G, Alagna F, Rocco M, Renzone G, Varricchio P, Coppola V, Coppola M, Garonna A, Baldoni L, Scaloni A, Rao R. Molecular interactions between the olive and the fruit fly Bactrocera oleae. BMC PLANT BIOLOGY 2012; 12:86. [PMID: 22694925 PMCID: PMC3733423 DOI: 10.1186/1471-2229-12-86] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 05/22/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND The fruit fly Bactrocera oleae is the primary biotic stressor of cultivated olives, causing direct and indirect damages that significantly reduce both the yield and the quality of olive oil. To study the olive-B. oleae interaction, we conducted transcriptomic and proteomic investigations of the molecular response of the drupe. The identifications of genes and proteins involved in the fruit response were performed using a Suppression Subtractive Hybridisation technique and a combined bi-dimensional electrophoresis/nanoLC-ESI-LIT-MS/MS approach, respectively. RESULTS We identified 196 ESTs and 26 protein spots as differentially expressed in olives with larval feeding tunnels. A bioinformatic analysis of the identified non-redundant EST and protein collection indicated that different molecular processes were affected, such as stress response, phytohormone signalling, transcriptional control and primary metabolism, and that a considerable proportion of the ESTs could not be classified. The altered expression of 20 transcripts was also analysed by real-time PCR, and the most striking differences were further confirmed in the fruit of a different olive variety. We also cloned the full-length coding sequences of two genes, Oe-chitinase I and Oe-PR27, and showed that these are wound-inducible genes and activated by B. oleae punctures. CONCLUSIONS This study represents the first report that reveals the molecular players and signalling pathways involved in the interaction between the olive fruit and its most damaging biotic stressor. Drupe response is complex, involving genes and proteins involved in photosynthesis as well as in the production of ROS, the activation of different stress response pathways and the production of compounds involved in direct defence against phytophagous larvae. Among the latter, trypsin inhibitors should play a major role in drupe resistance reaction.
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Affiliation(s)
- Giandomenico Corrado
- Dipartimento di Scienze del Suolo, Pianta, Ambiente e Produzioni Animali, Universita’ degli Studi di Napoli Federico II, Via Università 100, Portici, Napoli, 80055, Italy
| | - Fiammetta Alagna
- Istituto di Genetica Vegetale, Consiglio Nazionale delle Ricerche, Via della Madonna Alta 130, Perugia, 06128, Italy
| | - Mariapina Rocco
- Dipartimento di Scienze per la Biologia, la Geologia e l’Ambiente, Universita’ del Sannio, Via dei Mulini 59/A, Benevento, 82100, Italy
| | - Giovanni Renzone
- Istituto per il Sistema Produzione Animale in Ambiente Mediterraneo, Consiglio Nazionale delle Ricerche, Via Argine 1085, Napoli, 80147, Italy
| | - Paola Varricchio
- Dipartimento di Scienze del Suolo, Pianta, Ambiente e Produzioni Animali, Universita’ degli Studi di Napoli Federico II, Via Università 100, Portici, Napoli, 80055, Italy
| | - Valentina Coppola
- Dipartimento di Scienze del Suolo, Pianta, Ambiente e Produzioni Animali, Universita’ degli Studi di Napoli Federico II, Via Università 100, Portici, Napoli, 80055, Italy
| | - Mariangela Coppola
- Dipartimento di Scienze del Suolo, Pianta, Ambiente e Produzioni Animali, Universita’ degli Studi di Napoli Federico II, Via Università 100, Portici, Napoli, 80055, Italy
| | - Antonio Garonna
- Dipartimento di Entomologia e Zoologia Agraria “F. Silvestri”, Universita’ degli Studi di Napoli Federico II, Via Università 100, Portici, 80055, Italy
| | - Luciana Baldoni
- Istituto di Genetica Vegetale, Consiglio Nazionale delle Ricerche, Via della Madonna Alta 130, Perugia, 06128, Italy
| | - Andrea Scaloni
- Istituto per il Sistema Produzione Animale in Ambiente Mediterraneo, Consiglio Nazionale delle Ricerche, Via Argine 1085, Napoli, 80147, Italy
| | - Rosa Rao
- Dipartimento di Scienze del Suolo, Pianta, Ambiente e Produzioni Animali, Universita’ degli Studi di Napoli Federico II, Via Università 100, Portici, Napoli, 80055, Italy
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Muralidharan S, Thompson E, Raftos D, Birch G, Haynes PA. Quantitative proteomics of heavy metal stress responses in Sydney rock oysters. Proteomics 2012; 12:906-21. [DOI: 10.1002/pmic.201100417] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sridevi Muralidharan
- Department of Chemistry and Biomolecular Sciences; Macquarie University; North Ryde NSW Australia
| | - Emma Thompson
- Department of Biological Sciences; Macquarie University; North Ryde NSW Australia
| | - David Raftos
- Department of Biological Sciences; Macquarie University; North Ryde NSW Australia
| | - Gavin Birch
- School of Geosciences; University of Sydney; NSW Australia
| | - Paul A. Haynes
- Department of Chemistry and Biomolecular Sciences; Macquarie University; North Ryde NSW Australia
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Barman HK, Patra SK, Das V, Mohapatra SD, Jayasankar P, Mohapatra C, Mohanta R, Panda RP, Rath SN. Identification and characterization of differentially expressed transcripts in the gills of freshwater prawn (Macrobrachium rosenbergii) under salt stress. ScientificWorldJournal 2012; 2012:149361. [PMID: 22619594 PMCID: PMC3349099 DOI: 10.1100/2012/149361] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 11/15/2011] [Indexed: 11/17/2022] Open
Abstract
The giant freshwater prawn, Macrobrachium rosenbergii, is an economically important species. It is a euryhaline shrimp, surviving in wide-range salinity conditions. A change in gene expression has been suggested as an important component for stress management. To better understand the osmoregulatory mechanisms mediated by the gill, a subtractive and suppressive hybridization (SSH) tool was used to identify expressed transcripts linked to adaptations in saline water. A total of 117 transcripts represented potentially expressed under salinity conditions. BLAST analysis identified 22% as known genes, 9% as uncharacterized showing homologous to unannotated ESTs, and 69% as unknown sequences. All the identified known genes representing broad spectrum of biological pathways were particularly linked to stress tolerance including salinity tolerance. Expression analysis of 10 known genes and 7 unknown/uncharacterized genes suggested their upregulation in the gills of prawn exposed to saline water as compared to control indicating that these are likely to be associated with salinity acclimation. Rapid amplification of cDNA ends (RACE) was used for obtaining full-length cDNA of MRSW-40 clone that was highly upregulated during salt exposure. The sequenced ESTs presented here will have potential implications for future understanding about salinity acclimation and/or tolerance of the prawn.
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Affiliation(s)
- Hirak Kumar Barman
- Fish Genetics and Biotechnology Division, Central Institute of Freshwater Aquaculture, Indian Council of Agricultural Research, Kausalyaganga, Bhubaneswar, Odisha 751002, India.
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Rodrigues PM, Silva TS, Dias J, Jessen F. PROTEOMICS in aquaculture: applications and trends. J Proteomics 2012; 75:4325-45. [PMID: 22498885 DOI: 10.1016/j.jprot.2012.03.042] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 03/18/2012] [Accepted: 03/24/2012] [Indexed: 01/15/2023]
Abstract
Over the last forty years global aquaculture presented a growth rate of 6.9% per annum with an amazing production of 52.5 million tonnes in 2008, and a contribution of 43% of aquatic animal food for human consumption. In order to meet the world's health requirements of fish protein, a continuous growth in production is still expected for decades to come. Aquaculture is, though, a very competitive market, and a global awareness regarding the use of scientific knowledge and emerging technologies to obtain a better farmed organism through a sustainable production has enhanced the importance of proteomics in seafood biology research. Proteomics, as a powerful comparative tool, has therefore been increasingly used over the last decade to address different questions in aquaculture, regarding welfare, nutrition, health, quality, and safety. In this paper we will give an overview of these biological questions and the role of proteomics in their investigation, outlining the advantages, disadvantages and future challenges. A brief description of the proteomics technical approaches will be presented. Special focus will be on the latest trends related to the aquaculture production of fish with defined nutritional, health or quality properties for functional foods and the integration of proteomics techniques in addressing this challenging issue.
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Affiliation(s)
- Pedro M Rodrigues
- Centro de Ciências do Mar do Algarve (CCMar), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
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An SSH library responsive to azadirachtin A constructed in Spodoptera litura Fabricius cell lines. J Biotechnol 2012; 159:115-20. [PMID: 22425906 DOI: 10.1016/j.jbiotec.2012.02.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 12/24/2011] [Accepted: 02/26/2012] [Indexed: 11/23/2022]
Abstract
The present study revealed differentially expressed genes responsive to azadirachtin A (Aza) in Spodoptera litura cell line through suppression subtractive hybridization. In the Aza-responsive SSH library, approximately 270 sequences represent 53 different identified genes encoding proteins with various predicted functions, and the percentages of the gene clusters were 26.09% (genetic information processing), 11.41% (cell growth and death), 7.07% (metabolism), 6.52% (signal transduction/transport) and 2.72% (immunity), respectively. Eleven clones homologous to identified genes were selected to be confirmed through quantitative real time polymerase chain reaction. Among the eleven clones validated, all but one transcript of lipase showed an increase in SL cell line collected from ETA, whereas the transcripts of other genes were lower in the SL cell line collected from ETA compared with that of UETA. These genes were considered to be related to the response of SL cell line to Aza. These will provide a new clue to uncover the molecular mechanisms of Aza acting on SL cell line.
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Prunet P, Øverli Ø, Douxfils J, Bernardini G, Kestemont P, Baron D. Fish welfare and genomics. FISH PHYSIOLOGY AND BIOCHEMISTRY 2012; 38:43-60. [PMID: 21671026 DOI: 10.1007/s10695-011-9522-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 05/31/2011] [Indexed: 05/30/2023]
Abstract
There is a considerable public and scientific debate concerning welfare of fish in aquaculture. In this review, we will consider fish welfare as an integration of physiological, behavioral, and cognitive/emotional responses, all of which are essentially adaptative responses to stressful situations. An overview of fish welfare in this context suggests that understanding will rely on knowledge of all components of allostatic responses to stress and environmental perturbations. The development of genomic technologies provides new approaches to this task, exemplified by how genome-wide analysis of genetic structures and corresponding expression patterns can lead to the discovery of new aspects of adaptative responses. We will illustrate how the genomic approach may give rise to new biomarkers for fish welfare and also increase our understanding of the interaction between physiological, behavioral, and emotional responses. In a first part, we present data on expression of candidate genes selected a priori. This is a common avenue to develop molecular biomarkers capable of diagnosing a stress condition at its earliest onset, in order to allow quick corrective intervention in an aquaculture setting. However, most of these studies address isolated physiological functions and stress responses that may not be truly indicative of animal welfare, and there is only rudimentary understanding of genes related to possible cognitive and emotional responses in fish. We also present an overview on transcriptomic analysis related to the effect of aquaculture stressors, environmental changes (temperature, salinity, hypoxia), or concerning specific behavioral patterns. These studies illustrate the potential of genomic approaches to characterize the complexity of the molecular mechanisms which underlies not only physiological but also behavioral responses in relation to fish welfare. Thirdly, we address proteomic studies on biological responses to stressors such as salinity change and hypoxia. We will also consider proteomic studies developed in mammals in relation to anxiety and depressive status which may lead to new potential candidates in fish. Finally, in the conclusion, we will suggest new developments to facilitate an integrated view of fish welfare. This includes use of laser microdissection in the transcriptomic/proteomic studies, development of meta-analysis methods for extracting information from genomic data sets, and implementation of technological advances for high-throughput proteomic studies. Development of these new approaches should be as productive for our understanding of the biological processes underlying fish welfare as it has been for the progress of pathophysiological research.
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Affiliation(s)
- P Prunet
- UR1037 SCRIBE, IFR140, INRA, Campus de Beaulieu, Rennes, France.
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Blank M, Mikkat S, Verleih M, Bastrop R. Proteomic Comparison of Two Invasive Polychaete Species and Their Naturally Occurring F1-hybrids. J Proteome Res 2012; 11:897-905. [DOI: 10.1021/pr200710z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Miriam Blank
- Biozentrum Grindel und Zoologisches Museum, Universität Hamburg , Martin-Luther-King-Platz 3, 20146 Hamburg, Germany.
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Wong KKW, Lane AC, Leung PTY, Thiyagarajan V. Response of larval barnacle proteome to CO(2)-driven seawater acidification. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2011; 6:310-21. [PMID: 21831737 DOI: 10.1016/j.cbd.2011.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 07/05/2011] [Accepted: 07/12/2011] [Indexed: 12/30/2022]
Abstract
The majority of benthic marine invertebrates have a complex life cycle, during which the pelagic larvae select a suitable substrate, attach to it, and then metamorphose into benthic adults. Anthropogenic ocean acidification (OA) is postulated to affect larval metamorphic success through an altered protein expression pattern (proteome structure) and post-translational modifications. To test this hypothesis, larvae of an economically and ecologically important barnacle species Balanus amphitrite, were cultured from nauplius to the cyprid stage in the present (control) and in the projected elevated concentrations of CO(2) for the year 2100 (the OA treatment). Cyprid response to OA was analyzed at the total proteome level as well as two protein post-translational modification (phosphorylation and glycosylation) levels using a 2-DE based proteomic approach. The cyprid proteome showed OA-driven changes. Proteins that were differentially up or down regulated by OA come from three major groups, namely those related to energy-metabolism, respiration, and molecular chaperones, illustrating a potential strategy that the barnacle larvae may employ to tolerate OA stress. The differentially expressed proteins were tentatively identified as OA-responsive, effectively creating unique protein expression signatures for OA scenario of 2100. This study showed the promise of using a sentinel and non-model species to examine the impact of OA at the proteome level.
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Affiliation(s)
- Kelvin K W Wong
- Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong
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Tomanek L. Environmental proteomics: changes in the proteome of marine organisms in response to environmental stress, pollutants, infection, symbiosis, and development. ANNUAL REVIEW OF MARINE SCIENCE 2011; 3:373-99. [PMID: 21329210 DOI: 10.1146/annurev-marine-120709-142729] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Environmental proteomics, the study of changes in the abundance of proteins and their post-translational modifications, has become a powerful tool for generating hypotheses regarding how the environment affects the biology of marine organisms. Proteomics discovers hitherto unknown cellular effects of environmental stressors such as changes in thermal, osmotic, and anaerobic conditions. Proteomic analyses have advanced the characterization of the biological effects of pollutants and identified comprehensive and pollutant-specific sets of biomarkers, especially those highlighting post-translational modifications. Proteomic analyses of infected organisms have highlighted the broader changes occurring during immune responses and how the same pathways are attenuated during the maintenance of symbiotic relationships. Finally, proteomic changes occurring during the early life stages of marine organisms emphasize the importance of signaling events during development in a rapidly changing environment. Changes in proteins functioning in energy metabolism, cytoskeleton, protein stabilization and turnover, oxidative stress, and signaling are common responses to environmental change.
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Affiliation(s)
- Lars Tomanek
- California Polytechnic State University, Department of Biological Sciences, Center for Coastal Marine Sciences, Environmental Proteomics Laboratory, San Luis Obispo, California 93407-0401, USA.
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Tedesco S, Doyle H, Blasco J, Redmond G, Sheehan D. Oxidative stress and toxicity of gold nanoparticles in Mytilus edulis. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2010; 100:178-86. [PMID: 20382436 DOI: 10.1016/j.aquatox.2010.03.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2009] [Revised: 02/26/2010] [Accepted: 03/02/2010] [Indexed: 05/09/2023]
Abstract
Gold nanoparticles (AuNP) have potential applications in drug delivery, cancer diagnosis and therapy, food industry and environment remediation. However, little is known about their potential toxicity or fate in the environment. Mytilus edulis was exposed in tanks to 750 ppb AuNP (average diameter 5.3 ± 1 nm) for 24h to study in vivo biological effects of nanoparticles. Traditional biomarkers and an affinity procedure selective for thiol-containing proteins followed by two-dimensional electrophoresis (2DE) separations were used to study toxicity and oxidative stress responses. Results were compared to those obtained for treatment with cadmium chloride, a well known pro-oxidant. M. edulis mainly accumulated AuNP in digestive gland which also showed higher lipid peroxidation. One-dimensional SDS/PAGE (1DE) and 2DE analysis of digestive gland samples revealed decreased thiol-containing proteins for AuNP. Lysosomal membrane stability measured in haemolymph gave lower values for neutral red retention time (NRRT) in both treatments but was greater in AuNP. Oxidative stress occurred within 24h of AuNP exposure in M. edulis. Previously we showed that larger diameter AuNP caused modest effects, indicating that nanoparticle size is a key factor in biological responses to nanoparticles. This study suggests that M. edulis is a suitable model animal for environmental toxicology studies of nanoparticles.
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Affiliation(s)
- Sara Tedesco
- Environmental Research Institute of University College Cork, Cork, Ireland
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Guerzoni ME. Human food chain and microorganisms: a case of co-evolution. Front Microbiol 2010; 1:106. [PMID: 21607079 PMCID: PMC3095396 DOI: 10.3389/fmicb.2010.00106] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 08/06/2010] [Indexed: 11/13/2022] Open
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Pinto PI, Matsumura H, Thorne MA, Power DM, Terauchi R, Reinhardt R, Canário AV. Gill transcriptome response to changes in environmental calcium in the green spotted puffer fish. BMC Genomics 2010; 11:476. [PMID: 20716350 PMCID: PMC3091672 DOI: 10.1186/1471-2164-11-476] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 08/17/2010] [Indexed: 12/13/2022] Open
Abstract
Background Calcium ion is tightly regulated in body fluids and for euryhaline fish, which are exposed to rapid changes in environmental [Ca2+], homeostasis is especially challenging. The gill is the main organ of active calcium uptake and therefore plays a crucial role in the maintenance of calcium ion homeostasis. To study the molecular basis of the short-term responses to changing calcium availability, the whole gill transcriptome obtained by Super Serial Analysis of Gene Expression (SuperSAGE) of the euryhaline teleost green spotted puffer fish, Tetraodon nigroviridis, exposed to water with altered [Ca2+] was analysed. Results Transfer of T. nigroviridis from 10 ppt water salinity containing 2.9 mM Ca2+ to high (10 mM Ca2+ ) and low (0.01 mM Ca2+) calcium water of similar salinity for 2-12 h resulted in 1,339 differentially expressed SuperSAGE tags (26-bp transcript identifiers) in gills. Of these 869 tags (65%) were mapped to T. nigroviridis cDNAs or genomic DNA and 497 (57%) were assigned to known proteins. Thirteen percent of the genes matched multiple tags indicating alternative RNA transcripts. The main enriched gene ontology groups belong to Ca2+ signaling/homeostasis but also muscle contraction, cytoskeleton, energy production/homeostasis and tissue remodeling. K-means clustering identified co-expressed transcripts with distinct patterns in response to water [Ca2+] and exposure time. Conclusions The generated transcript expression patterns provide a framework of novel water calcium-responsive genes in the gill during the initial response after transfer to different [Ca2+]. This molecular response entails initial perception of alterations, activation of signaling networks and effectors and suggests active remodeling of cytoskeletal proteins during the initial acclimation process. Genes related to energy production and energy homeostasis are also up-regulated, probably reflecting the increased energetic needs of the acclimation response. This study is the first genome-wide transcriptome analysis of fish gills and is an important resource for future research on the short-term mechanisms involved in the gill acclimation responses to environmental Ca2+ changes and osmoregulation.
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Affiliation(s)
- Patrícia Is Pinto
- Centro de Ciências do Mar, CIMAR-Laboratório Associado, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
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Williams GA, De Pirro M, Cartwright S, Khangura K, Ng W, Leung PT, Morritt D. Come rain or shine: the combined effects of physical stresses on physiological and protein‐level responses of an intertidal limpet in the monsoonal tropics. Funct Ecol 2010. [DOI: 10.1111/j.1365-2435.2010.01760.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gray A. Williams
- The Swire Institute of Marine Science and Division of Ecology & Biodiversity, The School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China
| | - Maurizio De Pirro
- Academy Sea Environment, Lungomare dei navigatori 44, 58019 Monte Argentario, Italy
| | - Stephen Cartwright
- The Swire Institute of Marine Science and Division of Ecology & Biodiversity, The School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China
| | - Kiki Khangura
- The Swire Institute of Marine Science and Division of Ecology & Biodiversity, The School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China
| | - Wai‐Chuen Ng
- The Swire Institute of Marine Science and Division of Ecology & Biodiversity, The School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China
| | - Priscilla T.Y. Leung
- The Swire Institute of Marine Science and Division of Ecology & Biodiversity, The School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China
| | - David Morritt
- School of Biological Sciences, Royal Holloway, University of London, Egham, TW20 0EX, UK
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44
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Piñeiro C, Cañas B, Carrera M. The role of proteomics in the study of the influence of climate change on seafood products. Food Res Int 2010. [DOI: 10.1016/j.foodres.2009.11.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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45
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Evans TG. Co-ordination of osmotic stress responses through osmosensing and signal transduction events in fishes. JOURNAL OF FISH BIOLOGY 2010; 76:1903-1925. [PMID: 20557646 DOI: 10.1111/j.1095-8649.2010.02590.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
This review centres upon the molecular regulation of osmotic stress responses in fishes, focusing on how osmosensing and signal transduction events co-ordinate changes in the activity and abundance of effector proteins during osmotic stress and how these events integrate into osmotic stress responses of varying magnitude. The concluding sections discuss the relevance of osmosensory signal transduction to the evolution of euryhalinity and present experimental approaches that may best stimulate future research. Iterating the importance of osmosensing and signal transduction during fish osmoregulation may be pertinent amidst the increased use of genomic technologies that typically focus solely on changes in the abundances of gene products, and may limit insight into critical upstream events that occur mainly through post-translational mechanisms.
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Affiliation(s)
- T G Evans
- Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA.
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46
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Mykles DL, Ghalambor CK, Stillman JH, Tomanek L. Grand Challenges in Comparative Physiology: Integration Across Disciplines and Across Levels of Biological Organization. Integr Comp Biol 2010; 50:6-16. [DOI: 10.1093/icb/icq015] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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47
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Thorne MAS, Burns G, Fraser KPP, Hillyard G, Clark MS. Transcription profiling of acute temperature stress in the Antarctic plunderfish Harpagifer antarcticus. Mar Genomics 2010; 3:35-44. [PMID: 21798195 DOI: 10.1016/j.margen.2010.02.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 02/03/2010] [Accepted: 02/11/2010] [Indexed: 11/15/2022]
Abstract
Harpagifer antarcticus (the Antarctic plunderfish), a shallow-water benthic fish distributed around the Antarctic Peninsula, is a member of the notothenioid family, one of whose adaptations to the cold waters of Antarctica has been the loss of the classic heat shock response. In order to gain a more comprehensive understanding of the effects of temperature stress on H. antarcticus, we constructed a liver cDNA library and a 10,371 feature microarray. This was hybridized with material from a time course series of animals held at 6°C for 48h. The resulting expression profiles show that this fish displays the classical vertebrate acute inflammatory response. There was also a pronounced signal for increased energy requirements via up-regulation of genes involved in the β oxidation of fatty acids and also a strong signature of response to oxidative stress. Genes in the latter category did not include the "classic" antioxidants such as glutathione S-transferase, but genes involved in the production of reducing potential in the form of NADPH, peroxisome proliferation via peroxisomal acyl co-enzyme A oxidase 1 and genes known to be up-regulated by hypoxia-inducible factor 1 (HIF1). These identifications provide clear support for oxygen being the whole animal limiting factor at least in acute short-term temperature challenges. The classical heat shock proteins were not up-regulated during this trial, although numerous clones for each were present on the gene chip, confirming the lack of this response in this species. These data significantly increase our knowledge of the cellular stress response from animals in this unique environment.
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Affiliation(s)
- M A S Thorne
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, UK
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48
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Hori TS, Gamperl AK, Afonso LOB, Johnson SC, Hubert S, Kimball J, Bowman S, Rise ML. Heat-shock responsive genes identified and validated in Atlantic cod (Gadus morhua) liver, head kidney and skeletal muscle using genomic techniques. BMC Genomics 2010; 11:72. [PMID: 20109224 PMCID: PMC2830189 DOI: 10.1186/1471-2164-11-72] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Accepted: 01/28/2010] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Daily and seasonal changes in temperature are challenges that fish within aquaculture settings cannot completely avoid, and are known to elicit complex organismal and cellular stress responses. We conducted a large-scale gene discovery and transcript expression study in order to better understand the genes that are potentially involved in the physiological and cellular aspects of stress caused by heat-shock. We used suppression subtractive hybridization (SSH) cDNA library construction and characterization to identify transcripts that were dysregulated by heat-shock in liver, skeletal muscle and head kidney of Atlantic cod. These tissues were selected due to their roles in metabolic regulation, locomotion and growth, and immune function, respectively. Fish were exposed for 3 hours to an 8 degrees C elevation in temperature, and then allowed to recover for 24 hours at the original temperature (i.e. 10 degrees C). Tissue samples obtained before heat-shock (BHS), at the cessation of heat-shock (CS), and 3, 12, and 24 hours after the cessation of heat-shock (ACS), were used for reciprocal SSH library construction and quantitative reverse transcription - polymerase chain reaction (QPCR) analysis of gene expression using samples from a group that was transferred but not heat-shocked (CT) as controls. RESULTS We sequenced and characterized 4394 ESTs (1524 from liver, 1451 from head kidney and 1419 from skeletal muscle) from three "forward subtracted" libraries (enriched for genes up-regulated by heat-shock) and 1586 from the liver "reverse subtracted" library (enriched for genes down-regulated by heat-shock), for a total of 5980 ESTs. Several cDNAs encoding putative chaperones belonging to the heat-shock protein (HSP) family were found in these libraries, and "protein folding" was among the gene ontology (GO) terms with the highest proportion in the libraries. QPCR analysis of HSP90alpha and HSP70-1 (synonym: HSPA1A) mRNA expression showed significant up-regulation in all three tissues studied. These transcripts were more than 100-fold up-regulated in liver following heat-shock. We also identified HSP47, GRP78 and GRP94-like transcripts, which were significantly up-regulated in all 3 tissues studied. Toll-like receptor 22 (TLR22) transcript, found in the liver reverse SSH library, was shown by QPCR to be significantly down-regulated in the head kidney after heat-shock. CONCLUSION Chaperones are an important part of the cellular response to stress, and genes identified in this work may play important roles in resistance to thermal-stress. Moreover, the transcript for one key immune response gene (TLR22) was down-regulated by heat-shock, and this down-regulation may be a component of heat-induced immunosuppression.
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Affiliation(s)
- Tiago S Hori
- Ocean Sciences Centre, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - A Kurt Gamperl
- Ocean Sciences Centre, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Luis OB Afonso
- British Columbia Centre for Aquatic Health Sciences, Campbell River, BC, V9W 2C2, Canada
| | - Stewart C Johnson
- Pacific Biological Station, Department for Fisheries and Oceans, Nanaimo, BC, V9T 6N7, Canada
| | - Sophie Hubert
- The Atlantic Genome Centre, Halifax, NS, B3H 3Z1, Canada
| | - Jennifer Kimball
- Institute for Marine Biosciences, National Research Council of Canada, Halifax, NS, B3H 3Z1, Canada
| | - Sharen Bowman
- The Atlantic Genome Centre, Halifax, NS, B3H 3Z1, Canada
| | - Matthew L Rise
- Ocean Sciences Centre, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
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49
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Dowd WW, Harris BN, Cech JJ, Kültz D. Proteomic and physiological responses of leopard sharks (Triakis semifasciata) to salinity change. J Exp Biol 2010; 213:210-24. [DOI: 10.1242/jeb.031781] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
SUMMARY
Partially euryhaline elasmobranchs may tolerate physiologically challenging, variable salinity conditions in estuaries as a trade-off to reduce predation risk or to gain access to abundant food resources. To further understand these trade-offs and to evaluate the underlying mechanisms, we examined the responses of juvenile leopard sharks to salinity changes using a suite of measurements at multiple organizational levels: gill and rectal gland proteomes (using 2-D gel electrophoresis and tandem mass spectrometry), tissue biochemistry (Na+/K+-ATPase, caspase 3/7 and chymotrypsin-like proteasome activities), organismal physiology (hematology, plasma composition, muscle moisture) and individual behavior. Our proteomics results reveal coordinated molecular responses to low salinity – several of which are common to both rectal gland and gill – including changes in amino acid and inositol (i.e. osmolyte) metabolism, energy metabolism and proteins related to transcription, translation and protein degradation. Overall, leopard sharks employ a strategy of maintaining plasma urea, ion concentrations and Na+/K+-ATPase activities in the short-term, possibly because they rarely spend extended periods in low salinity conditions in the wild, but the sharks osmoconform to the surrounding conditions by 3 weeks. We found no evidence of apoptosis at the time points tested, while both tissues exhibited proteomic changes related to the cytoskeleton, suggesting that leopard sharks remodel existing osmoregulatory epithelial cells and activate physiological acclimatory responses to solve the problems posed by low salinity exposure. The behavioral measurements reveal increased activity in the lowest salinity in the short-term, while activity decreased in the lowest salinity in the long-term. Our data suggest that physiological/behavioral trade-offs are involved in using estuarine habitats, and pathway modeling implicates tumor necrosis factor α (TNFα) as a key node of the elasmobranch hyposmotic response network.
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Affiliation(s)
- W. W. Dowd
- Physiological Genomics Group, Department of Animal Science, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - B. N. Harris
- Department of Biology, 3386 Spieth Hall, University of California, Riverside, CA 92521, USA
| | - J. J. Cech
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - D. Kültz
- Physiological Genomics Group, Department of Animal Science, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
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50
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Sáez AG, Lozano E, Zaldívar-Riverón A. Evolutionary history of Na,K-ATPases and their osmoregulatory role. Genetica 2009; 136:479-90. [PMID: 19214758 DOI: 10.1007/s10709-009-9356-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Accepted: 01/26/2009] [Indexed: 01/07/2023]
Abstract
The Na/K pump, or Na,K-ATPase, is a key enzyme to the homeostasis of osmotic pressure, cell volume, and the maintenance of electrochemical gradients. Its alpha subunit, which holds most of its functions, belongs to a large family of ATPases known as P-type, and to the subfamily IIC, which also includes H,K-ATPases. In this study, we attempt to describe the evolutionary history of IIC ATPases by doing phylogenetic analysis with most of the currently available protein sequences (over 200), and pay special attention to the relationship between their diversity and their osmoregulatory role. We include proteins derived from many completed or ongoing genome projects, many of whose IIC ATPases have not been phylogenetically analyzed previously. We show that the most likely origin of IIC proteins is prokaryotic, and that many of them are present in non-metazoans, such as algae, protozoans or fungi. We also suggest that the pre-metazoan ancestor, represented by the choanoflagellate Monosiga brevicollis, whose genome has been sequenced, presented at least two IIC-type proteins. One of these proteins would have given rise to most current animal IIC ATPases, whereas the other apparently evolved into a lineage that, so far, has only been found in nematodes. We also propose that early deuterostomes presented a single IIC gene, from which all the extant diversity of vertebrate IIC proteins originated by gene and genome duplications.
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Affiliation(s)
- Alberto G Sáez
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain.
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