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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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Garrity C, Garcia-Rovetta C, Rivas I, Delatorre U, Wong A, Kültz D, Peyton J, Arzi B, Vapniarsky N. Tilapia Fish Skin Treatment of Third-Degree Skin Burns in Murine Model. J Funct Biomater 2023; 14:512. [PMID: 37888177 PMCID: PMC10607444 DOI: 10.3390/jfb14100512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/25/2023] [Accepted: 10/08/2023] [Indexed: 10/28/2023] Open
Abstract
This study explored the feasibility of using fish skin bandages as a therapeutic option for third-degree skin burns. Following the California wildfires, clinical observations of animals with third-degree skin burns demonstrated increased comfort levels and reduced pain when treated with tilapia fish skin. Despite the promises of this therapy, there are few studies explaining the healing mechanisms behind the application of tilapia fish skin. In this study, mice with third-degree burns were treated with either a hydrocolloid adhesive bandage (control) (n = 16) or fish skin (n = 16) 7 days post-burn. Mice were subjected to histologic, hematologic, molecular, and gross evaluation at days 7, 16, and 28 post-burn. The fish skin offered no benefit to overall wound closure compared to hydrocolloids. Additionally, we detected no difference between fish skin and control treatments in regard to hypermetabolism or hematologic values. However, the fish skin groups exhibited 2 times more vascularization and 2 times higher expression of antimicrobial defensin peptide in comparison to controls. Proteomic analysis of the fish skin revealed the presence of antimicrobial peptides. Collectively, these data suggest that fish skin can serve as an innovative and cost-effective therapeutic alternative for burn victims to facilitate vascularization and reduce bacterial infection.
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Affiliation(s)
- Carissa Garrity
- Department of Pathology, Microbiology, and Immunology, University of California, Davis, CA 95616, USA; (C.G.); (I.R.)
| | - Christina Garcia-Rovetta
- Department of Pathology, Microbiology, and Immunology, University of California, Davis, CA 95616, USA; (C.G.); (I.R.)
| | - Iris Rivas
- Department of Pathology, Microbiology, and Immunology, University of California, Davis, CA 95616, USA; (C.G.); (I.R.)
| | - Ubaldo Delatorre
- Department of Pathology, Microbiology, and Immunology, University of California, Davis, CA 95616, USA; (C.G.); (I.R.)
| | - Alice Wong
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Dietmar Kültz
- Department of Animal Sciences and Coastal & Marine Sciences Institute, Davis, CA 95616, USA;
| | - Jamie Peyton
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
| | - Boaz Arzi
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
| | - Natalia Vapniarsky
- Department of Pathology, Microbiology, and Immunology, University of California, Davis, CA 95616, USA; (C.G.); (I.R.)
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Wu X, Lai J, Chen Y, Liu Y, Song M, Li F, Li P, Li Q, Gong Q. Combination of metabolome and proteome analyses provides insights into the mechanism underlying growth differences in Acipenser dabryanus. iScience 2023; 26:107413. [PMID: 37559901 PMCID: PMC10407750 DOI: 10.1016/j.isci.2023.107413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/26/2023] [Accepted: 07/14/2023] [Indexed: 08/11/2023] Open
Abstract
To analyze the differences between different-sized Acipenser dabryanus, we randomly selected 600 3-month-old A. dabryanus juveniles. Four months later, the blood and white muscle of these fish were analyzed. The results showed no significant difference in the length-weight relationship (LWR) b value between the large and small A. dabryanus. The levels of serum growth hormone (gh) and insulin-like growth factor 1 (igf1) in the large A. dabryanus were significantly lower than those in the small, whereas the activity levels of Total superoxide dismutase (T-sod) and catalase (cat) were opposite to the results of gh and igf1. A total of 212 and 245 metabolites showed significant changes in the positive and negative polarity mode, respectively. Among 3,308 proteins identified, 69 proteins showed upregulated expression, and 185 proteins showed downregulated expression. These results indicated that the growth advantage of A. dabryanus was closely related to glycolysis, protein synthesis, and antioxidant function.
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Affiliation(s)
- Xiaoyun Wu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Jiansheng Lai
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Yeyu Chen
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Ya Liu
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Mingjiang Song
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Feiyang Li
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Pengcheng Li
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Qingzhi Li
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
| | - Quan Gong
- The Fishery Institute of the Sichuan Academy of Agricultural Sciences, Chengdu 611730, China
- Fish Resources and Environment in the Upper Reaches of the Yangtze River Observation and Research Station of Sichuan Province, Chengdu 611730, China
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Wei F, Liang J, Tian W, Yu L, Feng Z, Hua Q. Transcriptomic and proteomic analyses provide insights into the adaptive responses to the combined impact of salinity and alkalinity in Gymnocypris przewalskii. BIORESOUR BIOPROCESS 2022; 9:104. [PMID: 38647776 PMCID: PMC10992934 DOI: 10.1186/s40643-022-00589-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/01/2022] [Indexed: 11/10/2022] Open
Abstract
Gymnocypris przewalskii is the only high-land endemic teleost living in Qinghai Lake, the largest saline-alkaline lake in China. Its osmoregulatory physiology remains elusive due to a lack of precise identification of the response proteins. In the present study, DIA/SWATH was used to identify differentially expressed proteins (DEPs) under alkaline (pH = 10.1, carbonate buffer), saline (12‰, sodium chloride), and saline-alkaline [carbonate buffer (pH = 10.1) plus 11‰ sodium chloride] stresses. A total of 66,056 unique peptides representing 7,150 proteins and 230 DEPs [the false discovery rate (FDR) ≤ 0.05, fold change (FC) ≥ 1.5] were identified under different stresses. Comparative analyses of the proteome and transcriptome indicated that over 86% of DEPs did not show consistent trends with mRNA. In addition to consistent enrichment results under different stresses, the specific DEPs involved in saline-alkaline adaptation were primarily enriched in functions of homeostasis, hormone synthesis and reactions of defense response, complement activation and reproductive development. Meanwhile, a protein-protein interaction (PPI) network analysis of these specific DEPs indicated that the hub genes were ITGAX, MMP9, C3, F2, CD74, BTK, ANXA1, NCKAP1L, and CASP8. This study accurately isolated the genes that respond to stress, and the results could be helpful for understanding the physiological regulation mechanisms regarding salinity, alkalinity, and salinity-alkalinity interactions.
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Affiliation(s)
- Fulei Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, 251 Ningda Road, Xining, 810016, People's Republic of China
| | - Jian Liang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, 251 Ningda Road, Xining, 810016, People's Republic of China.
| | - Wengen Tian
- The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, 83 Ningzhang Road, Xining, 810016, People's Republic of China
| | - Luxian Yu
- The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, 83 Ningzhang Road, Xining, 810016, People's Republic of China
| | - Zhaohui Feng
- The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, 83 Ningzhang Road, Xining, 810016, People's Republic of China
| | - Qiang Hua
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
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Kim C, Wang X, Kültz D. Prediction and Experimental Validation of a New Salinity-Responsive Cis-Regulatory Element (CRE) in a Tilapia Cell Line. Life (Basel) 2022; 12:life12060787. [PMID: 35743818 PMCID: PMC9225295 DOI: 10.3390/life12060787] [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: 04/20/2022] [Revised: 05/12/2022] [Accepted: 05/16/2022] [Indexed: 11/16/2022] Open
Abstract
Transcriptional regulation is a major mechanism by which organisms integrate gene x environment interactions. It can be achieved by coordinated interplay between cis-regulatory elements (CREs) and transcription factors (TFs). Euryhaline tilapia (Oreochromis mossambicus) tolerate a wide range of salinity and thus are an appropriate model to examine transcriptional regulatory mechanisms during salinity stress in fish. Quantitative proteomics in combination with the transcription inhibitor actinomycin D revealed 19 proteins that are transcriptionally upregulated by hyperosmolality in tilapia brain (OmB) cells. We searched the extended proximal promoter up to intron1 of each corresponding gene for common motifs using motif discovery tools. The top-ranked motif identified (STREME1) represents a binding site for the Forkhead box TF L1 (FoxL1). STREME1 function during hyperosmolality was experimentally validated by choosing two of the 19 genes, chloride intracellular channel 2 (clic2) and uridine phosphorylase 1 (upp1), that are enriched in STREME1 in their extended promoters. Transcriptional induction of these genes during hyperosmolality requires STREME1, as evidenced by motif mutagenesis. We conclude that STREME1 represents a new functional CRE that contributes to gene x environment interactions during salinity stress in tilapia. Moreover, our results indicate that FoxL1 family TFs are contribute to hyperosmotic induction of genes in euryhaline fish.
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Affiliation(s)
- Chanhee Kim
- Stress-Induced Evolution Laboratory, Department of Animal Sciences, University of California, Davis, CA 95616, USA;
| | - Xiaodan Wang
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai 200241, China;
| | - Dietmar Kültz
- Stress-Induced Evolution Laboratory, Department of Animal Sciences, University of California, Davis, CA 95616, USA;
- Correspondence: ; Tel.: +1-530-752-2991
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Li B, Yang J, Gong Y, Xiao Y, Zeng Q, Xu K, Duan Y, He J, He J, Ma H. Integrated Analysis of Liver Transcriptome, miRNA, and Proteome of Chinese Indigenous Breed Ningxiang Pig in Three Developmental Stages Uncovers Significant miRNA-mRNA-Protein Networks in Lipid Metabolism. Front Genet 2021; 12:709521. [PMID: 34603377 PMCID: PMC8481880 DOI: 10.3389/fgene.2021.709521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/19/2021] [Indexed: 11/13/2022] Open
Abstract
Liver is an important metabolic organ of mammals. During each transitional period of life, liver metabolism is programmed by a complex molecular regulatory system for multiple physiological functions, many pathways of which are regulated by hormones and cytokines, nuclear receptors, and transcription factors. To gain a comprehensive and unbiased molecular understanding of liver growth and development in Ningxiang pigs, we analyzed the mRNA, microRNA (miRNA), and proteomes of the livers of Ningxiang pigs during lactation, nursery, and fattening periods. A total of 22,411 genes (19,653 known mRNAs and 2758 novel mRNAs), 1122 miRNAs (384 known miRNAs and 738 novel miRNAs), and 1123 unique proteins with medium and high abundance were identified by high-throughput sequencing and mass spectrometry. We show that the differences in transcriptional, post-transcriptional, or protein levels were readily identified by comparing different time periods, providing evidence that functional changes that may occur during liver development are widespread. In addition, we found many overlapping differentially expressed genes (DEGs)/differentially expressed miRNAs (DEMs)/differentially expressed proteins (DEPs) related to glycolipid metabolism in any group comparison. These overlapping DEGs/DEMs/DGPs may play an important role in functional transformation during liver development. Short Time-series Expression Miner (STEM) analysis revealed multiple expression patterns of mRNA, miRNA, and protein in the liver. Furthermore, several diverse key Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including immune defense, glycolipid metabolism, protein transport and uptake, and cell proliferation and development, were identified by combined analysis of DEGs and DGPs. A number of predicted miRNA–mRNA–protein pairs were found and validated by qRT-PCR and parallel reaction monitoring (PRM) assays. The results provide new and important information about the genetic breeding of Ningxiang pigs, which represents a foundation for further understanding the molecular regulatory mechanisms of dynamic development of liver tissue, functional transformation, and lipid metabolism.
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Affiliation(s)
- Biao Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Jinzeng Yang
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Yan Gong
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Yu Xiao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Qinghua Zeng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China.,Ningxiang Pig Farm of Dalong Livestock Technology Co., Ltd., Ningxiang, China
| | - Kang Xu
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agroecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences (CAS), Changsha, China
| | - Yehui Duan
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agroecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences (CAS), Changsha, China
| | - Jianhua He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Jun He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
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8
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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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Mai Y, Peng S, Li H, Gao Y, Lai Z. NOD-like receptor signaling pathway activation: A potential mechanism underlying negative effects of benzo(α)pyrene on zebrafish. Comp Biochem Physiol C Toxicol Pharmacol 2021; 240:108935. [PMID: 33161151 DOI: 10.1016/j.cbpc.2020.108935] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/11/2020] [Accepted: 10/28/2020] [Indexed: 02/07/2023]
Abstract
Benzo(α)pyrene (BaP) is one of typical polycyclic aromatic hydrocarbons (PAHs) in aquatic environments and has been shown to cause toxic effects to aquatic animals. Although the negative effects of BaP have been investigated, the potential toxic mechanisms remain uncharacterized. To explore the potential mechanisms mediating the toxic effects of BaP, zebrafish (Danio rerio) were exposed to BaP for 15 days and the toxic effects of BaP in zebrafish liver were investigated using physiological and transcriptomic analyses. After 15-day BaP exposure, zebrafish liver exhibited abnormalities including increased cytoplasmic vacuolation, inflammatory cell infiltration, swelled nuclei and irregular pigmentation. BaP exposure also induced oxidative stress to the liver of zebrafish. Transcriptomic profiles revealed 5129 differentially expressed genes (DEGs) after 15-days of BaP exposure, and the vast majority of DEGs were up-regulated under BaP treatment. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggest that genes related to immune response were significantly dysregulated. Furthermore, the nucleotide-binding, oligomerization domain (NOD)-like receptor signaling pathway was significantly enriched and most of the genes in this pathway exhibited enhanced expression after BaP exposure. These results partially explained the mechanisms underlying the toxic effects of BaP on zebrafish liver. In conclusion, BaP has the potential to induce physiological responses in zebrafish liver through altering associated genes.
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Affiliation(s)
- Yongzhan Mai
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, People's Republic of China
| | - Songyao Peng
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, People's Republic of China
| | - Haiyan Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, People's Republic of China
| | - Yuan Gao
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, People's Republic of China
| | - Zini Lai
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, People's Republic of China; Fishery Ecological Environment Monitoring Center of Pearl River Basin, Ministry of Agriculture and Rural Affairs, Guangzhou 510380, People's Republic of China; Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, People's Republic of China.
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11
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Quan J, Kang Y, Li L, Zhao G, Sun J, Liu Z. Proteome analysis of rainbow trout (Oncorhynchus mykiss) liver responses to chronic heat stress using DIA/SWATH. J Proteomics 2020; 233:104079. [PMID: 33346158 DOI: 10.1016/j.jprot.2020.104079] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 12/22/2022]
Abstract
Aquaculture of rainbow trout (Oncorhynchus mykiss) is severely hampered by high temperatures in summer, and understanding the regulatory mechanisms controlling responses to chronic heat stress may assist the development of measures to relieve heat stress. In the present study, biochemical parameters revealed a strong stress response in rainbow trout at 24 °C, including activation of stress defence and immune systems. Liver proteome analysis under heat stress (24 °C) and control (18 °C) conditions using DIA/SWATH identified precursors (90,827), peptides (67,028), proteins (6770) and protein groups (5124), among which 460 differentially abundant proteins (DAPs; q-value < 0.05, fold change >1.5), 201 and 259 were up- and down-regulated, respectively. Many were related to heat shock proteins (HSPs), metabolism and immunity. Gene Ontology (GO) analysis showed that some DAPs induced at high temperature were involved in regulating cell homeostasis, metabolism, adaptive stress and stimulation. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified metabolic pathways, protein processing in endoplasmic reticulum, PPAR signalling, and complement and coagulation cascades. Protein-protein interaction (PPI) network analysis indicated that HSP90b1 and C3 may cooperative to affect cell membrane integrity under heat stress. Our findings assist the development of strategies to relieve heat stress in rainbow trout.
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Affiliation(s)
- Jinqiang Quan
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Yujun Kang
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Lanlan Li
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Guiyan Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Jun Sun
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Zhe Liu
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China.
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12
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Hall M, Kültz D, Almaas E. Identification of key proteins involved in stickleback environmental adaptation with system-level analysis. Physiol Genomics 2020; 52:531-548. [PMID: 32956024 DOI: 10.1152/physiolgenomics.00078.2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Using abundance measurements of 1,490 proteins from four separate populations of three-spined sticklebacks, we implemented a system-level approach to correlate proteome dynamics with environmental salinity and temperature and the fish's population and morphotype. We identified robust and accurate fingerprints that classify environmental salinity, temperature, morphotype, and the population sample origin, observing that proteins with specific functions are enriched in these fingerprints. Highly apparent functions represented in all fingerprints include ion transport, proteostasis, growth, and immunity, suggesting that these functions are most diversified in populations inhabiting different environments. Applying a differential network approach, we analyzed the network of protein interactions that differs between populations. Looking at specific population combinations of differential interaction, we identify sets of connected proteins. We find that these sets and their corresponding enriched functions reflect key processes that have diverged between the four populations. Moreover, the extent of divergence, i.e., the number of enriched functions that differ between populations, is highest when all three environmental parameters are different between two populations. Key nodes in the differential interaction network signify functions that are also inherent in the fingerprints, most prominently proteostasis-related functions. However, the differential interaction network also reveals additional functions that have diverged between populations, notably cytoskeletal organization and morphogenesis. The strength of these analyses is that the results are purely data driven. With such an unbiased approach applied on a large proteomic data set, we find the strongest signals given by the data, making it possible to develop more discriminatory and complex biomarkers for specific contexts of interest.
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Affiliation(s)
- Martina Hall
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway.,K. G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Dietmar Kültz
- Department of Animal Sciences, University of California, Davis, California
| | - Eivind Almaas
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway.,K. G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim, Norway
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Li J, Kültz D. Proteomics of Osmoregulatory Responses in Threespine Stickleback Gills. Integr Comp Biol 2020; 60:304-317. [PMID: 32458981 DOI: 10.1093/icb/icaa042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The gill proteome of threespine sticklebacks (Gasterosteus aculeatus) differs greatly in populations that inhabit diverse environments characterized by different temperature, salinity, food availability, parasites, and other parameters. To assess the contribution of a specific environmental parameter to such differences it is necessary to isolate its effects from those of other parameters. In this study the effect of environmental salinity on the gill proteome of G. aculeatus was isolated in controlled mesocosm experiments. Salinity-dependent changes in the gill proteome were analyzed by Liquid chromatography/Tandem mass spectrometry data-independent acquisition (DIA) and Skyline. Relative abundances of 1691 proteins representing the molecular phenotype of stickleback gills were quantified using previously developed MSMS spectral and assay libraries in combination with DIA quantitative proteomics. Non-directional stress responses were distinguished from osmoregulatory protein abundance changes by their consistent occurrence during both hypo- and hyper-osmotic salinity stress in six separate mesocosm experiments. If the abundance of a protein was consistently regulated in opposite directions by hyper- versus hypo-osmotic salinity stress, then it was considered an osmoregulatory protein. In contrast, if protein abundance was consistently increased irrespective of whether salinity was increased or decreased, then it was considered a non-directional response protein. KEGG pathway analysis revealed that the salivary secretion, inositol phosphate metabolism, valine, leucine, and isoleucine degradation, citrate cycle, oxidative phosphorylation, and corresponding endocrine and extracellular signaling pathways contain most of the osmoregulatory gill proteins whose abundance is directly proportional to environmental salinity. Most proteins that were inversely correlated with salinity map to KEGG pathways that represent proteostasis, immunity, and related intracellular signaling processes. Non-directional stress response proteins represent fatty and amino acid degradation, purine metabolism, focal adhesion, mRNA surveillance, phagosome, endocytosis, and associated intracellular signaling KEGG pathways. These results demonstrate that G. aculeatus responds to salinity changes by adjusting osmoregulatory mechanisms that are distinct from transient non-directional stress responses to control compatible osmolyte synthesis, transepithelial ion transport, and oxidative energy metabolism. Furthermore, this study establishes salinity as a key factor for causing the regulation of numerous proteins and KEGG pathways with established functions in proteostasis, immunity, and tissue remodeling. We conclude that the corresponding osmoregulatory gill proteins and KEGG pathways represent molecular phenotypes that promote transepithelial ion transport, cellular osmoregulation, and gill epithelial remodeling to adjust gill function to environmental salinity.
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Affiliation(s)
- Johnathon Li
- Department of Animal Sciences, University of California, Davis, Meyer Hall, One Shields Avenue, Davis, CA 95616, USA
| | - Dietmar Kültz
- Department of Animal Sciences, University of California, Davis, Meyer Hall, One Shields Avenue, Davis, CA 95616, USA
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Zhu W, Cheng X, Ren C, Chen J, Zhang Y, Chen Y, Jia X, Wang S, Sun Z, Zhang R, Zhang Z. Proteomic characterization and comparison of ram (Ovis aries) and buck (Capra hircus) spermatozoa proteome using a data independent acquisition mass spectometry (DIA-MS) approach. PLoS One 2020; 15:e0228656. [PMID: 32053710 PMCID: PMC7018057 DOI: 10.1371/journal.pone.0228656] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 01/21/2020] [Indexed: 12/14/2022] Open
Abstract
Fresh semen is most commonly used in an artificial insemination of small ruminants, because of low fertility rates of frozen sperm. Generally, when developing and applying assisted reproductive technologies, sheep and goats are classified as one species. In order to optimize sperm cryopreservation protocols in sheep and goat, differences in sperm proteomes between ram and buck are necessary to investigate, which may contribute to differences in function and fertility of spermatozoa. In the current work, a data-independent acquisition-mass spectrometry proteomic approach was used to characterize and make a comparison of ram (Ovis aries) and buck (Capra hircus) sperm proteomes. A total of 2,109 proteins were identified in ram and buck spermatozoa, with 238 differentially abundant proteins. Proteins identified in ram and buck spermatozoa are mainly involved in metabolic pathways for generation of energy and diminishing oxidative stress. Specifically, there are greater abundance of spermatozoa proteins related to the immune protective and capacity activities in ram, while protein that inhibit sperm capacitation shows greater abundance in buck. Our results not only provide novel insights into the characteristics and potential activities of spermatozoa proteins, but also expand the potential direction for sperm cryopreservation in ram and buck.
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Affiliation(s)
- Wen Zhu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P. R. China
| | - Xiao Cheng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P. R. China
| | - Chunhuan Ren
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P. R. China
| | - Jiahong Chen
- New Rural Develop Research Institute, Anhui Agricultural University, Hefei, P. R. China
| | - Yan Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P. R. China
| | - Yale Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P. R. China
| | - Xiaojiao Jia
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P. R. China
| | - Shijia Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P. R. China
| | - Zhipeng Sun
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P. R. China
| | - Renzheng Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P. R. China
| | - Zijun Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P. R. China
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Ahmed F, Kumar G, Soliman FM, Adly MA, Soliman HAM, El-Matbouli M, Saleh M. Proteomics for understanding pathogenesis, immune modulation and host pathogen interactions in aquaculture. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 32:100625. [PMID: 31639560 DOI: 10.1016/j.cbd.2019.100625] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 12/13/2022]
Abstract
Proteomic analyses techniques are considered strong tools for identifying and quantifying the protein contents in different organisms, organs and secretions. In fish biotechnology, the proteomic analyses have been used for wide range of applications such as identification of immune related proteins during infections and stresses. The proteomic approach has a significant role in understanding pathogen surviving strategies, host defence responses and subsequently, the fish pathogen interactions. Proteomic analyses were employed to highlight the virulence related proteins secreted by the pathogens to invade the fish host's defence barriers and to monitor the kinetics of protein contents of different fish organs in response to infections. The immune related proteins of fish and the virulence related proteins of pathogens are up or down regulated according to their functions in defence or pathogenesis. Therefore, the proteomic analyses are useful in understanding the virulence mechanisms of microorganisms and the fish pathogen interactions thereby supporting the development of new effective therapies. In this review, we focus and summarise the recent proteomic profiling studies exploring pathogen virulence activities and fish immune responses to stressors and infections.
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Affiliation(s)
- Fatma Ahmed
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria; Department of Zoology, Faculty of Science, Sohag University, Sohag, Egypt
| | - Gokhlesh Kumar
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Faiza M Soliman
- Department of Zoology, Faculty of Science, Sohag University, Sohag, Egypt
| | - Mohamed A Adly
- Department of Zoology, Faculty of Science, Sohag University, Sohag, Egypt
| | - Hamdy A M Soliman
- Department of Zoology, Faculty of Science, Sohag University, Sohag, Egypt
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Mona Saleh
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria.
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Zhang G, Li J, Zhang J, Liang X, Zhang X, Wang T, Yin S. Integrated Analysis of Transcriptomic, miRNA and Proteomic Changes of a Novel Hybrid Yellow Catfish Uncovers Key Roles for miRNAs in Heterosis. Mol Cell Proteomics 2019; 18:1437-1453. [PMID: 31092672 PMCID: PMC6601203 DOI: 10.1074/mcp.ra118.001297] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/09/2019] [Indexed: 01/14/2023] Open
Abstract
Heterosis is a complex biological phenomenon in which hybridization produces offspring that exhibit superior phenotypic characteristics compared with the parents. Heterosis is widely utilized in agriculture, for example in fish farming; however, its underlying molecular basis remains elusive. To gain a comprehensive and unbiased molecular understanding of fish heterosis, we analyzed the mRNA, miRNA, and proteomes of the livers of three catfish species, Pelteobagrus fulvidraco, P. vachelli, and their hybrid, the hybrid yellow catfish "Huangyou-1" (P. fulvidraco ♀ × P. vachelli ♂). Using next-generation sequencing and mass spectrometry, we show that the nonadditive, homoeolog expression bias and expression level dominance pattern were readily identified at the transcriptional, post-transcriptional, or protein levels, providing the evidence for the widespread presence of dominant models during hybridization. A number of predicted miRNA-mRNA-protein pairs were found and validated by qRT-PCR and PRM assays. Furthermore, several diverse key pathways were identified, including immune defense, metabolism, digestion and absorption, and cell proliferation and development, suggesting the vital mechanisms involved in the generation of the heterosis phenotype in progenies. We propose that the high parental expression of genes/proteins (growth, nutrition, feeding, and disease resistance) coupled with low parental miRNAs of the offspring, are inherited from the mother or father, thus indicating that the offspring were enriched with the advantages of the father or mother. We provide new and important information about the molecular mechanisms of heterosis, which represents a significant step toward a more complete elucidation of this phenomenon.
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Affiliation(s)
- Guosong Zhang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; §Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong 274015, China
| | - Jie Li
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Jiajia Zhang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Xia Liang
- §Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong 274015, China
| | - Xinyu Zhang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Tao Wang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Shaowu Yin
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China.
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