Environmental stress reveals new insights regarding proteome rebalancing in Arabidopsis thaliana seeds.

Seeds are resilient to genetic and envirxonmental perturbation. For example, they can compensate for the loss of highly abundant seed storage proteins (SSPs) while maintaining amino acid levels and composition, a process known as proteome rebalancing. This buffering involves large-scale adjustments in translational capacity and metabolic networks, yet it remains unclear whether such plasticity persists under environmental stress or eventually reaches a physiological limit. To address this, we examined Arabidopsis Col-0 (wild type, WT) and cruabc (a triple SSP-deficient mutant) dry seeds produced under no nitrogen supplementation, weekly nitrogen supplementation, or drought (water-deficit) treatment imposed during the seed-filling stage. Analyses of physiological traits, metabolic profiles, and proteomes revealed substantial treatment-dependent changes; however, cruabc seeds consistently remained comparable to Col-0 within each environment, indicating that rebalancing represents a robust, hard-coded plasticity operating downstream of primary stress responses. Nevertheless, the molecular routes used to achieve metabolic and proteomic homeostasis differ across environments in rebalanced seeds. Under drought during seed filling, both genotypes upregulated photosynthetic and pentose phosphate pathway components to mitigate carbon limitation and energy stress, yet cruabc maintained a more oxidative redox state. Under low nitrogen, the cruabc dry seed proteome exhibited minimal reprogramming, whereas under high nitrogen, it underwent extensive remodeling, including enhanced translation-related activity compared to WT. These findings suggest that proteome rebalancing represents a stable homeostatic endpoint that can be reset by environmental cues. However, the metabolic pathways and energetic costs required to achieve this state differ markedly between genotypes, revealing how SSP loss reshapes stress adaptation during seed maturation and desiccation. Collectively, our results refine the mechanistic framework underlying proteome rebalancing and establish a foundation for leveraging this process to enhance amino acid biofortification.