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Eide M, Goksøyr A, Yadetie F, Gilabert A, Bartosova Z, Frøysa HG, Fallahi S, Zhang X, Blaser N, Jonassen I, Bruheim P, Alendal G, Brun M, Porte C, Karlsen OA. Integrative omics-analysis of lipid metabolism regulation by peroxisome proliferator-activated receptor a and b agonists in male Atlantic cod. Front Physiol 2023; 14:1129089. [PMID: 37035678 PMCID: PMC10073473 DOI: 10.3389/fphys.2023.1129089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/07/2023] [Indexed: 04/11/2023] Open
Abstract
Lipid metabolism is essential in maintaining energy homeostasis in multicellular organisms. In vertebrates, the peroxisome proliferator-activated receptors (PPARs, NR1C) regulate the expression of many genes involved in these processes. Atlantic cod (Gadus morhua) is an important fish species in the North Atlantic ecosystem and in human nutrition, with a highly fatty liver. Here we study the involvement of Atlantic cod Ppar a and b subtypes in systemic regulation of lipid metabolism using two model agonists after in vivo exposure. WY-14,643, a specific PPARA ligand in mammals, activated cod Ppara1 and Ppara2 in vitro. In vivo, WY-14,643 caused a shift in lipid transport both at transcriptional and translational level in cod. However, WY-14,643 induced fewer genes in the fatty acid beta-oxidation pathway compared to that observed in rodents. Although GW501516 serves as a specific PPARB/D ligand in mammals, this compound activated cod Ppara1 and Ppara2 as well as Pparb in vitro. In vivo, it further induced transcription of Ppar target genes and caused changes in lipid composition of liver and plasma. The integrative approach provide a foundation for understanding how Ppars are engaged in regulating lipid metabolism in Atlantic cod physiology. We have shown that WY-14,643 and GW501516 activate Atlantic cod Ppara and Pparb, affect genes in lipid metabolism pathways, and induce changes in the lipid composition in plasma and liver microsomal membranes. Particularly, the combined transcriptomic, proteomics and lipidomics analyses revealed that effects of WY-14,643 on lipid metabolism are similar to what is known in mammalian studies, suggesting conservation of Ppara functions in mediating lipid metabolic processes in fish. The alterations in the lipid profiles observed after Ppar agonist exposure suggest that other chemicals with similar Ppar receptor affinities may cause disturbances in the lipid regulation of fish. Model organism: Atlantic cod (Gadus morhua). LSID: urn:lsid:zoobank.org:act:389BE401-2718-4CF2-BBAE-2E13A97A5E7B. COL Identifier: 6K72F.
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Affiliation(s)
- Marta Eide
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Anders Goksøyr
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- *Correspondence: Anders Goksøyr,
| | - Fekadu Yadetie
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Alejandra Gilabert
- Institute of Environmental Assessment and Water Research, Spanish National Research Council (CSIC), Barcelona, Spain
- Faculty of Science, National Distance Education University (UNED), Madrid, Spain
| | - Zdenka Bartosova
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Håvard G. Frøysa
- Department of Mathematics, University of Bergen, Bergen, Norway
- Institute of Marine Research (IMR), Bergen, Norway
| | - Shirin Fallahi
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Xiaokang Zhang
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Nello Blaser
- Department of Informatics, University of Bergen, Bergen, Norway
| | - Inge Jonassen
- Department of Informatics, University of Bergen, Bergen, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Guttorm Alendal
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Morten Brun
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Cinta Porte
- Institute of Environmental Assessment and Water Research, Spanish National Research Council (CSIC), Barcelona, Spain
| | - Odd André Karlsen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
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Galindo-Luján R, Pont L, Minic Z, Berezovski MV, Sanz-Nebot V, Benavente F. Characterization and differentiation of quinoa seed proteomes by label-free mass spectrometry-based shotgun proteomics. Food Chem 2021; 363:130250. [PMID: 34120052 DOI: 10.1016/j.foodchem.2021.130250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 11/19/2022]
Abstract
Quinoa seed proteins are of prime importance in human nutrition and in plant breeding for cultivar identification and improvement. In this study, proteins from seeds of black, red, white quinoa from Peru and white quinoa from Bolivia (also known as royal) were extracted, digested and analyzed by nano-liquid chromatography coupled to Orbitrap tandem mass spectrometry (LC-MS/MS). The raw mass spectra data were processed for identification and label-free quantification (LFQ) using MaxQuant/Andromeda against a specific quinoa database from The National Center for Biotechnology Information (NCBI). In total, 1,211 quinoa proteins (85 were uncharacterized) were identified. Inspection and visualization using Venn diagrams, heat maps and Gene Ontology (GO) graphs revealed proteome similarities and differences between the four varieties. The presented data provides the most comprehensive experimental quinoa seed proteome map existing to date in the literature, as a starting point for more specific characterization and nutritional studies of quinoa and quinoa-containing foodstuff.
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Affiliation(s)
- Rocío Galindo-Luján
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB), University of Barcelona, 08028 Barcelona, Spain
| | - Laura Pont
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB), University of Barcelona, 08028 Barcelona, Spain
| | - Zoran Minic
- John L. Holmes Mass Spectrometry Facility, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Maxim V Berezovski
- John L. Holmes Mass Spectrometry Facility, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Victoria Sanz-Nebot
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB), University of Barcelona, 08028 Barcelona, Spain
| | - Fernando Benavente
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB), University of Barcelona, 08028 Barcelona, Spain.
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Lacerda MPF, Marcelino MY, Lourencetti NMS, Neto ÁB, Gattas EA, Mendes-Giannini MJS, Fusco-Almeida AM. Methodologies and Applications of Proteomics for Study of Yeast Strains: An Update. Curr Protein Pept Sci 2019; 20:893-906. [PMID: 31322071 DOI: 10.2174/1389203720666190715145131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 11/22/2022]
Abstract
Yeasts are one of the mostly used microorganisms as models in several studies. A wide range of applications in different processes can be attributed to their intrinsic characteristics. They are eukaryotes and therefore valuable expression hosts that require elaborate post-translational modifications. Their arsenal of proteins has become a valuable biochemical tool for the catalysis of several reactions of great value to the food (beverages), pharmaceutical and energy industries. Currently, the main challenge in systemic yeast biology is the understanding of the expression, function and regulation of the protein pool encoded by such microorganisms. In this review, we will provide an overview of the proteomic methodologies used in the analysis of yeasts. This research focuses on the advantages and improvements in their most recent applications with an understanding of the functionality of the proteins of these microorganisms, as well as an update of the advances of methodologies employed in mass spectrometry.
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Affiliation(s)
- Maria Priscila F Lacerda
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Mônica Yonashiro Marcelino
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Natália M S Lourencetti
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Álvaro Baptista Neto
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Engineering of Bioprocesses and Biotechnology, Araraquara, Brazil
| | - Edwil A Gattas
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Engineering of Bioprocesses and Biotechnology, Araraquara, Brazil
| | | | - Ana Marisa Fusco-Almeida
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
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