Lysine biosynthesis integrates carbon availability and energy homeostasis under fluctuating CO2

Lysine metabolism connects amino acid biosynthesis with mitochondrial respiration through coordinated synthesis and degradation pathways that interface with the tricarboxylic acid (TCA) cycle and the mitochondrial electron transport chain (mETC). The critical role of this pathway is underscored by the embryonic lethality of the Arabidopsis L,L-diaminopimelate aminotransferase mutant (dapat), which is defective in a key step of lysine biosynthesis. Hypomorphic dapat mutant plants exhibit profound metabolic reprogramming and a constitutive energy-limited phenotype under non-stress conditions, suggesting that lysine biosynthesis contributes to basal metabolic homeostasis. We therefore hypothesized that impaired lysine biosynthesis restricts metabolic flexibility, but that changes in CO₂ availability may partially compensate through carbon and nitrogen remodeling. To test this, we performed comprehensive metabolite profiling of wild-type and dapat mutant plants under low-, ambient-, and elevated-CO₂ conditions. Elevated CO₂ (eCO₂) induced broad reorganization of carbon and nitrogen metabolism in both genotypes, reducing photorespiratory and stress-associated amino acids and modulating key metabolic ratios, including glycine/serine and malate/aspartate, in a genotype- and time-dependent manner. Proteomics revealed DAPAT photosynthetic compensation under ambient CO₂, with RuBisCO over-accumulation and suppressed TOR activity, as indicated by decreased RPS6 phosphorylation, which eCO₂ restored in parallel with phenotypic rescue. These adjustments were associated with partial attenuation of the DAPAT metabolic imbalance. Our findings reveal functional connections among lysine biosynthesis, photorespiration, and CO₂-responsive metabolic flexibility, demonstrating that lysine metabolism serves as a regulatory node linking amino acid homeostasis to carbon availability and respiratory adjustment. This provides mechanistic insight into how plants maintain energy balance under fluctuating CO₂ environments.