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Olmedo P, Vidal J, Ponce E, Defilippi BG, Pérez-Donoso AG, Meneses C, Carpentier S, Pedreschi R, Campos-Vargas R. Proteomic and Low-Polar Metabolite Profiling Reveal Unique Dynamics in Fatty Acid Metabolism during Flower and Berry Development of Table Grapes. Int J Mol Sci 2023; 24:15360. [PMID: 37895040 PMCID: PMC10607693 DOI: 10.3390/ijms242015360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
Grapevine development and ripening are complex processes that involve several biochemical pathways, including fatty acid and lipid metabolism. Fatty acids are essential components of lipids, which play crucial roles in fruit maturation and flavor development. However, the dynamics of fatty acid metabolism in grape flowers and berries are poorly understood. In this study, we present those dynamics and investigate the mechanisms of fatty acid homeostasis on 'Thompson Seedless' berries using metabolomic and proteomic analyses. Low-polar metabolite profiling indicated a higher abundance of fatty acids at the pre-flowering and pre-veraison stages. Proteomic analyses revealed that grape flowers and berries display unique profiles of proteins involved in fatty acid biosynthesis, triacylglycerol assembly, fatty acid β-oxidation, and lipid signaling. These findings show, for the first time, that fatty acid metabolism also plays an important role in the development of non-oil-rich tissues, opening new perspectives about lipid function and its relation to berry quality.
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Affiliation(s)
- Patricio Olmedo
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Quillota 2260000, Chile; (P.O.); (J.V.); (E.P.)
| | - Juan Vidal
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Quillota 2260000, Chile; (P.O.); (J.V.); (E.P.)
| | - Excequel Ponce
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Quillota 2260000, Chile; (P.O.); (J.V.); (E.P.)
| | - Bruno G. Defilippi
- Unidad de Postcosecha, Instituto de Investigaciones Agropecuarias (INIA) La Platina, Santiago 8831314, Chile;
| | - Alonso G. Pérez-Donoso
- Departamento de Fruticultura y Enología, Facultad de Agronomía y Sistemas Naturales, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (A.G.P.-D.); (C.M.)
| | - Claudio Meneses
- Departamento de Fruticultura y Enología, Facultad de Agronomía y Sistemas Naturales, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (A.G.P.-D.); (C.M.)
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago 8370186, Chile
- Millennium Institute Center for Genome Regulation (CRG), Santiago 7800003, Chile
| | - Sebastien Carpentier
- Facility for Systems Biology Based Mass Spectrometry SYBIOMA, KU Leuven, B-3000 Leuven, Belgium;
- Bioversity International, Biodiversity for Food & Agriculture, B-3001 Leuven, Belgium
| | - Romina Pedreschi
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Quillota 2260000, Chile; (P.O.); (J.V.); (E.P.)
- Millennium Institute Center for Genome Regulation (CRG), Santiago 7800003, Chile
| | - Reinaldo Campos-Vargas
- Centro de Estudios Postcosecha, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8831314, Chile;
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Savoi S, Santiago A, Orduña L, Matus JT. Transcriptomic and metabolomic integration as a resource in grapevine to study fruit metabolite quality traits. FRONTIERS IN PLANT SCIENCE 2022; 13:937927. [PMID: 36340350 PMCID: PMC9630917 DOI: 10.3389/fpls.2022.937927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Transcriptomics and metabolomics are methodologies being increasingly chosen to perform molecular studies in grapevine (Vitis vinifera L.), focusing either on plant and fruit development or on interaction with abiotic or biotic factors. Currently, the integration of these approaches has become of utmost relevance when studying key plant physiological and metabolic processes. The results from these analyses can undoubtedly be incorporated in breeding programs whereby genes associated with better fruit quality (e.g., those enhancing the accumulation of health-promoting compounds) or with stress resistance (e.g., those regulating beneficial responses to environmental transition) can be used as selection markers in crop improvement programs. Despite the vast amount of data being generated, integrative transcriptome/metabolome meta-analyses (i.e., the joint analysis of several studies) have not yet been fully accomplished in this species, mainly due to particular specificities of metabolomic studies, such as differences in data acquisition (i.e., different compounds being investigated), unappropriated and unstandardized metadata, or simply no deposition of data in public repositories. These meta-analyses require a high computational capacity for data mining a priori, but they also need appropriate tools to explore and visualize the integrated results. This perspective article explores the universe of omics studies conducted in V. vinifera, focusing on fruit-transcriptome and metabolome analyses as leading approaches to understand berry physiology, secondary metabolism, and quality. Moreover, we show how omics data can be integrated in a simple format and offered to the research community as a web resource, giving the chance to inspect potential gene-to-gene and gene-to-metabolite relationships that can later be tested in hypothesis-driven research. In the frame of the activities promoted by the COST Action CA17111 INTEGRAPE, we present the first grapevine transcriptomic and metabolomic integrated database (TransMetaDb) developed within the Vitis Visualization (VitViz) platform (https://tomsbiolab.com/vitviz). This tool also enables the user to conduct and explore meta-analyses utilizing different experiments, therefore hopefully motivating the community to generate Findable, Accessible, Interoperable and Reusable (F.A.I.R.) data to be included in the future.
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Affiliation(s)
- Stefania Savoi
- Department of Agricultural, Forest and Food Sciences, University of Turin, Grugliasco, Italy
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Spain
| | - Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Spain
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Liu S, Kerr ED, Pegg CL, Schulz BL. Proteomics and glycoproteomics of beer and wine. Proteomics 2022; 22:e2100329. [PMID: 35716130 DOI: 10.1002/pmic.202100329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/29/2022] [Accepted: 06/14/2022] [Indexed: 12/14/2022]
Abstract
Beer and wine are fermented beverages that contain abundant proteins released from barley or grapes, and secreted from yeast. These proteins are associated with many quality attributes including turbidity, foamability, effervescence, flavour and colour. Many grape proteins and secreted yeast proteins are glycosylated, and barley proteins can be glycated under the high temperatures in the beer making process. The emergence of high-resolution mass spectrometry has allowed proteomic and glycoproteomic analyses of these complex mixtures of proteins towards understanding their role in determining beer and wine attributes. In this review, we summarise recent studies of proteomic and glycoproteomic analyses of beer and wine including their strategies for mass spectrometry (MS)-based identification, quantification and characterisation of the glyco/proteomes of fermented beverages to control product quality.
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Affiliation(s)
- Shulei Liu
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Edward D Kerr
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
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Kim S, Cheong K, Park J, Kim M, Kim J, Seo M, Chae GY, Jang MJ, Mang H, Kwon S, Kim Y, Koo N, Min CW, Kim K, Oh N, Kim K, Jeon J, Kim H, Lee Y, Sohn KH, McCann HC, Ye S, Kim ST, Park K, Lee Y, Choi D. TGFam-Finder: a novel solution for target-gene family annotation in plants. THE NEW PHYTOLOGIST 2020; 227:1568-1581. [PMID: 32392385 PMCID: PMC7496378 DOI: 10.1111/nph.16645] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/21/2020] [Indexed: 05/26/2023]
Abstract
Whole-genome annotation error that omits essential protein-coding genes hinders further research. We developed Target Gene Family Finder (TGFam-Finder), an alternative tool for the structural annotation of protein-coding genes containing target domain(s) of interest in plant genomes. TGFam-Finder took considerably reduced annotation run-time and improved accuracy compared to conventional annotation tools. Large-scale re-annotation of 50 plant genomes identified an average of 150, 166 and 86 additional far-red-impaired response 1, nucleotide-binding and leucine-rich-repeat, and cytochrome P450 genes, respectively, that were missed in previous annotations. We detected significantly higher number of translated genes in the new annotations using mass spectrometry data from seven plant species compared to previous annotations. TGFam-Finder along with the new gene models can provide an optimized platform for comprehensive functional, comparative, and evolutionary studies in plants.
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Affiliation(s)
- Seungill Kim
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
- Department of Environmental HorticultureUniversity of SeoulSeoul02504Korea
| | - Kyeongchae Cheong
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826Korea
| | - Jieun Park
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
| | - Myung‐Shin Kim
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826Korea
| | - Jihyun Kim
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
| | - Min‐Ki Seo
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
| | - Geun Young Chae
- Department of Environmental HorticultureUniversity of SeoulSeoul02504Korea
| | - Min Jeong Jang
- Department of Environmental HorticultureUniversity of SeoulSeoul02504Korea
| | - Hyunggon Mang
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
| | - Sun‐Ho Kwon
- Department of PharmacologySeoul National University College of MedicineSeoul03080Korea
| | - Yong‐Min Kim
- Korean Bioinformation CenterKorea Research Institute of Bioscience and BiotechnologyDaejeon34141Korea
| | - Namjin Koo
- Korean Bioinformation CenterKorea Research Institute of Bioscience and BiotechnologyDaejeon34141Korea
| | - Cheol Woo Min
- Department of Plant BioscienceLife and Energy Convergence Research InstitutePusan National UniversityMiryang627‐706Korea
| | - Kwang‐Soo Kim
- Department of Biomedical ScienceCollege of Life ScienceCHA UniversitySeongnam13488Korea
| | - Nuri Oh
- Department of Biomedical ScienceCollege of Life ScienceCHA UniversitySeongnam13488Korea
| | - Ki‐Tae Kim
- Department of Agricultural BiotechnologySeoul National UniversitySeoul08826Korea
| | - Jongbum Jeon
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826Korea
| | - Hyunbin Kim
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826Korea
| | - Yoon‐Young Lee
- Department of Life SciencesPohang University of Science and TechnologyPohangGyeongbuk37673Korea
| | - Kee Hoon Sohn
- Department of Life SciencesPohang University of Science and TechnologyPohangGyeongbuk37673Korea
- School of Interdisciplinary Bioscience and BioengineeringPohang University of Science and TechnologyPohangGyeongbuk37673Korea
| | - Honour C. McCann
- New Zealand Institute for Advanced StudyMassey University AucklandAuckland0632New Zealand
| | - Sang‐Kyu Ye
- Department of PharmacologySeoul National University College of MedicineSeoul03080Korea
| | - Sun Tae Kim
- Department of Plant BioscienceLife and Energy Convergence Research InstitutePusan National UniversityMiryang627‐706Korea
| | - Kyung‐Soon Park
- Department of Biomedical ScienceCollege of Life ScienceCHA UniversitySeongnam13488Korea
| | - Yong‐Hwan Lee
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826Korea
- Department of Agricultural BiotechnologySeoul National UniversitySeoul08826Korea
| | - Doil Choi
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826Korea
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