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Cocuron JC, Alonso AP. 13C-labeling reveals non-conventional pathways providing carbon for hydroxy fatty acid synthesis in Physaria fendleri. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1754-1766. [PMID: 37668184 PMCID: PMC11275461 DOI: 10.1093/jxb/erad343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023]
Abstract
Physaria fendleri is a member of the Brassicaceae that produces in its embryos hydroxy fatty acids, constituents of oils that are very valuable and widely used by industry for cosmetics, lubricants, biofuels, etc. Free of toxins and rich in hydroxy fatty acids, Physaria provides a promising alternative to imported castor oil and is on the verge of being commercialized. This study aims to identify important biochemical step(s) for oil synthesis in Physaria, which may serve as target(s) for future crop improvement. To advance towards this goal, the endosperm composition was analysed by LC-MS/MS to develop and validate culture conditions that mimic the development of the embryos in planta. Using developing Physaria embryos in culture and 13C-labeling, our studies revealed that: (i) Physaria embryos metabolize carbon into biomass with an efficiency significantly lower than other photosynthetic embryos; (ii) the plastidic malic enzyme provides 42% of the pyruvate used for de novo fatty acid synthesis, which is the highest measured so far in developing 'green' oilseed embryos; and (iii) Physaria uses non-conventional pathways to channel carbon into oil, namely the Rubisco shunt, which fixes CO2 released in the plastid, and the reversibility of isocitrate dehydrogenase, which provides additional carbon for fatty acid elongation.
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Affiliation(s)
| | - Ana Paula Alonso
- BioAnalytical Facility, University of North Texas, Denton, TX 76203, USA
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
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Sagun JV, Yadav UP, Alonso AP. Progress in understanding and improving oil content and quality in seeds. FRONTIERS IN PLANT SCIENCE 2023; 14:1116894. [PMID: 36778708 PMCID: PMC9909563 DOI: 10.3389/fpls.2023.1116894] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
The world's population is projected to increase by two billion by 2050, resulting in food and energy insecurity. Oilseed crops have been identified as key to address these challenges: they produce and store lipids in the seeds as triacylglycerols that can serve as a source of food/feed, renewable fuels, and other industrially-relevant chemicals. Therefore, improving seed oil content and composition has generated immense interest. Research efforts aiming to unravel the regulatory pathways involved in fatty acid synthesis and to identify targets for metabolic engineering have made tremendous progress. This review provides a summary of the current knowledge of oil metabolism and discusses how photochemical activity and unconventional pathways can contribute to high carbon conversion efficiency in seeds. It also highlights the importance of 13C-metabolic flux analysis as a tool to gain insights on the pathways that regulate oil biosynthesis in seeds. Finally, a list of key genes and regulators that have been recently targeted to enhance seed oil production are reviewed and additional possible targets in the metabolic pathways are proposed to achieve desirable oil content and quality.
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Affiliation(s)
| | | | - Ana Paula Alonso
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
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Koley S, Chu KL, Mukherjee T, Morley SA, Klebanovych A, Czymmek KJ, Allen DK. Metabolic synergy in Camelina reproductive tissues for seed development. SCIENCE ADVANCES 2022; 8:eabo7683. [PMID: 36306367 PMCID: PMC9616503 DOI: 10.1126/sciadv.abo7683] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/14/2022] [Indexed: 06/15/2023]
Abstract
Photosynthesis in fruits is well documented, but its contribution to seed development and yield remains largely unquantified. In oilseeds, the pods are green and elevated with direct access to sunlight. With 13C labeling in planta and through an intact pod labeling system, a unique multi-tissue comprehensive flux model mechanistically described how pods assimilate up to one-half (33 to 45%) of seed carbon by proximal photosynthesis in Camelina sativa. By capturing integrated tissue metabolism, the studies reveal the contribution of plant architecture beyond leaves, to enable seed filling and maximize the number of viable seeds. The latent capacity of the pod wall in the absence of leaves contributes approximately 79% of seed biomass, supporting greater seed sink capacity and higher theoretical yields that suggest an opportunity for crop productivity gains.
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Affiliation(s)
- Somnath Koley
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Kevin L. Chu
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- United States Department of Agriculture-Agricultural Research Service, Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Stewart A. Morley
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- United States Department of Agriculture-Agricultural Research Service, Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | | | - Doug K. Allen
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- United States Department of Agriculture-Agricultural Research Service, Donald Danforth Plant Science Center, St. Louis, MO, USA
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Cloutier M, Xiang D, Gao P, Kochian LV, Zou J, Datla R, Wang E. Integrative Modeling of Gene Expression and Metabolic Networks of Arabidopsis Embryos for Identification of Seed Oil Causal Genes. FRONTIERS IN PLANT SCIENCE 2021; 12:642938. [PMID: 33889166 PMCID: PMC8056077 DOI: 10.3389/fpls.2021.642938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Fatty acids in crop seeds are a major source for both vegetable oils and industrial applications. Genetic improvement of fatty acid composition and oil content is critical to meet the current and future demands of plant-based renewable seed oils. Addressing this challenge can be approached by network modeling to capture key contributors of seed metabolism and to identify underpinning genetic targets for engineering the traits associated with seed oil composition and content. Here, we present a dynamic model, using an Ordinary Differential Equations model and integrated time-course gene expression data, to describe metabolic networks during Arabidopsis thaliana seed development. Through in silico perturbation of genes, targets were predicted in seed oil traits. Validation and supporting evidence were obtained for several of these predictions using published reports in the scientific literature. Furthermore, we investigated two predicted targets using omics datasets for both gene expression and metabolites from the seed embryo, and demonstrated the applicability of this network-based model. This work highlights that integration of dynamic gene expression atlases generates informative models which can be explored to dissect metabolic pathways and lead to the identification of causal genes associated with seed oil traits.
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Affiliation(s)
- Mathieu Cloutier
- Laboratory of Bioinformatics and Systems Biology, National Research Council Canada, Montreal, QC, Canada
| | - Daoquan Xiang
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Peng Gao
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Leon V. Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jitao Zou
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Raju Datla
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Edwin Wang
- Laboratory of Bioinformatics and Systems Biology, National Research Council Canada, Montreal, QC, Canada
- Centre for Health Genomics and Informatics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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Romsdahl TB, Kambhampati S, Koley S, Yadav UP, Alonso AP, Allen DK, Chapman KD. Analyzing Mass Spectrometry Imaging Data of 13C-Labeled Phospholipids in Camelina sativa and Thlaspi arvense (Pennycress) Embryos. Metabolites 2021; 11:metabo11030148. [PMID: 33806402 PMCID: PMC7999836 DOI: 10.3390/metabo11030148] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 12/20/2022] Open
Abstract
The combination of 13C-isotopic labeling and mass spectrometry imaging (MSI) offers an approach to analyze metabolic flux in situ. However, combining isotopic labeling and MSI presents technical challenges ranging from sample preparation, label incorporation, data collection, and analysis. Isotopic labeling and MSI individually create large, complex data sets, and this is compounded when both methods are combined. Therefore, analyzing isotopically labeled MSI data requires streamlined procedures to support biologically meaningful interpretations. Using currently available software and techniques, here we describe a workflow to analyze 13C-labeled isotopologues of the membrane lipid and storage oil lipid intermediate―phosphatidylcholine (PC). Our results with embryos of the oilseed crops, Camelina sativa and Thlaspi arvense (pennycress), demonstrated greater 13C-isotopic labeling in the cotyledons of developing embryos compared with the embryonic axis. Greater isotopic enrichment in PC molecular species with more saturated and longer chain fatty acids suggest different flux patterns related to fatty acid desaturation and elongation pathways. The ability to evaluate MSI data of isotopically labeled plant embryos will facilitate the potential to investigate spatial aspects of metabolic flux in situ.
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Affiliation(s)
- Trevor B. Romsdahl
- Department of Biological Sciences & BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA; (T.B.R.); (U.P.Y.); (A.P.A.)
| | | | - Somnath Koley
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (S.K.); (S.K.)
| | - Umesh P. Yadav
- Department of Biological Sciences & BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA; (T.B.R.); (U.P.Y.); (A.P.A.)
| | - Ana Paula Alonso
- Department of Biological Sciences & BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA; (T.B.R.); (U.P.Y.); (A.P.A.)
| | - Doug K. Allen
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (S.K.); (S.K.)
- United States Department of Agriculture, Agriculture Research Service, St. Louis, MO 63132, USA
- Correspondence: (D.K.A.); or (K.D.C.); Tel.: +1-940-565-2969 (K.D.C.)
| | - Kent D. Chapman
- Department of Biological Sciences & BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA; (T.B.R.); (U.P.Y.); (A.P.A.)
- Correspondence: (D.K.A.); or (K.D.C.); Tel.: +1-940-565-2969 (K.D.C.)
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