Systems-Level and Flux Analyses Reveal Metabolic Antagonism as a Primary Barrier to Oilseed Design

Plant oils are energy-dense, have wide-ranging applications, and command a market in the tens of billions of dollars, with demand forecasted to greatly outpace future supply. Oilseeds that could accumulate unusual fatty acids would be an indispensable source of sustainable chemical feedstocks as alternatives to petroleum; however, engineering crops to produce them has resulted in modest success, suggesting that the underlying metabolic constraints remain poorly understood. We show that engineering medium-chain fatty acid (MCFA) accumulation in seeds results in coordinated metabolic and regulatory responses that thwart biotechnology efforts. Generalized linear modeling (GLM) of transcriptomic, proteomic, lipidomic, and metabolomic analyses across seed development indicated intrinsic metabolic surveillance and antagonistic responses that engage fatty acid oxidation and chain elongation, actively supporting the removal of unusual fatty acids from storage lipids. Follow-up with 18O isotope-labeling of acyl-CoA pools validated peroxisomal β-oxidation, with MCFAs undergoing degradation and carbon recycling. We estimate that these processes reduce the MCFA content by an astounding 49% (223 nmol/seed) of total seed oil content (990 nmol/seed) at maturity. “Push, Pull, Package, and Protect” paradigms that are the benchmark for high lipid accumulation should include a fifth principle, “Prevent”, that addresses antagonistic metabolic responses and a real engineering opportunity.