Impaired lysine biosynthesis drives constitutive energy stress priming and darkness stress responses

Plant survival under prolonged darkness relies on dynamic metabolic reprogramming that redirects limited carbon resources toward mitochondrial respiration and nutrient remobilization. Although amino acids function as alternative respiratory substrates during carbon starvation, how their biosynthesis integrates into this metabolic adjustment remains poorly understood. Here, we investigated the role of lysine biosynthesis using the dapat mutant, which exhibits photoperiod-dependent hypersensitivity to extended darkness. Under short-day conditions, dapat plants exhibited accelerated senescence. reduced photosystem II maximum quantum efficiency, pronounced protein degradation, and accumulation of amino acid, ultimately failing to recover after nine days of darkness. By contrast, survival was largely restored under neutral-day conditions, indicating that restricted carbohydrate reserves during short-day growth exacerbate the mutant phenotype. Remarkably, transcript profiling further revealed that reduced DAPAT activity constitutively activates a catabolic program, including genes associated with amino acid degradation, alternative respiratory pathways, senescence, and autophagy, even under non-stress conditions. Together, these findings identify DAPAT-mediated lysine biosynthesis as a central metabolic hub linking carbon availability to energy and stress signaling. Disruption of this pathway compromises metabolic flexibility and limits the capacity to withstand prolonged carbon starvation. Our results provide new insights into how primary metabolism coordinates stress responses to extended darkness and highlight amino acid biosynthesis as an important component of plant resilience under energy-deprived darkness conditions.