Metabolic flux, metabolite, and transcript analysis uncover reprogramming of metabolism toward higher seed oil

Journal Article · Tue Mar 17 00:00:00 UTC 2026 · Plant Physiology (Bethesda)

DOI: https://doi.org/10.1093/plphys/kiag148 · OSTI ID:3023990

Shi, Hai  ^[1]; McGinn, Michaela  ^[2]; Hing, Nathaphon Yu King  ^[1]; Jarvis, Brice A  ^[2]; Gautam, Barsanti  ^[2]; Kuczynski, Cathleen  ^[1]; Hilo, Alexander  ^[3]; Rolletschek, Hardy  ^[3]; Sedbrook, John C  ^[2]; Schwender, Jorg  ^[1]

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1. Brookhaven National Laboratory (BNL), Upton, NY (United States)
2. Illinois State University (ISU), Normal, IL (United States)
3. Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben (Germany)

Overexpression of WRINKLED1 (WRI1), a master regulator of glycolysis and fatty acid biosynthesis, together with DIACYLGLYCEROL ACYLTRANSFERASE1 (DGAT1), which catalyzes the final step of triacylglycerol assembly, is a promising strategy for enhancing seed oil content. However, how these regulators coordinate system-wide metabolic reprogramming at the levels of gene expression, metabolite pools, and fluxes remains poorly understood. To address this, we performed ¹³C-metabolic flux analysis, metabolomics, and transcriptomics on in vitro cultured pennycress (Thlaspi arvense L.) embryos overexpressing the native WRI1 and DGAT1 homologs. Here, in cultured embryos, WRI1/DGAT1 overexpression increased triacylglycerol accumulation by 28% while reducing protein content by 34%, relative to the wild type. Embryos showed ∼20-fold and 50-fold upregulation of WRI1 and DGAT1 along with induction of WRI1 target genes in glycolysis and fatty acid biosynthesis. Genes associated with photosynthesis and Calvin cycle functions were also upregulated, whereas genes encoding ribosomal proteins and seed storage proteins were strongly repressed, consistent with the observed lipid–protein tradeoff. Flux analysis revealed that enhanced triacylglycerol biosynthesis is supported by increased flux through the Rubisco shunt and cytosolic pyruvate kinase, while the oxidative pentose phosphate pathway and malic enzyme contributed little to NADPH or pyruvate supply. Metabolomic profiling revealed extensive perturbations in glycolytic intermediates, tricarboxylic acid cycle metabolites, and amino acids. In plant grown seeds, WRI1/DGAT1 lines also showed a modest but significant increase in total lipid content. Collectively, these findings reveal how WRI1 and DGAT1 reprogram central metabolism to enhance oil accumulation, with relevance to mature seeds.

• Research Organization: Brookhaven National Laboratory (BNL), Upton, NY (United States)
• Sponsoring Organization: USDA; USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division (CSGB); USDOE Office of Science (SC), Biological and Environmental Research (BER)
• Grant/Contract Number: SC0012704; SC0021286
• OSTI ID: 3023990
• Report Number(s): BNL-229515-2026-JAAM
• Journal Information: Plant Physiology (Bethesda), Journal Name: Plant Physiology (Bethesda) Journal Issue: 1 Vol. 201; ISSN 0032-0889; ISSN 1532-2548
• Publisher: American Society of Plant BiologistsCopyright Statement
• Country of Publication: United States
• Language: English