Key metabolic and proteolytic pathways contributing to cadmium tolerance in soybean

Cadmium (Cd) stress is a major problem for crop productivity and food safety. This study assessed Cd tolerance in soybean by comparing tolerant and susceptible cultivars grown hydroponically under 20 µM Cd exposure. The susceptible cultivar showed an 18 % reduction in fresh biomass and a 15 % decline in chlorophyll content under stress compared to the tolerant cultivar (P < 0.05). Elevated levels of hydrogen peroxide (H₂O₂) and malondialdehyde (MDA) were observed in the susceptible cultivar, while the tolerant cultivar exhibited significantly higher activities of different antioxidant enzymes. Transcriptomic and metabolomics analyses showed that the susceptible cultivar enhanced the amino acid biosynthesis under control conditions but declined under Cd stress. In contrast, the tolerant cultivar consistently upregulated proteasome and autophagy pathways genes and maintained higher baseline expression, while the susceptible cultivar showed larger stress-induced fold-changes. Metabolite profiling further indicated that the susceptible cultivar accumulated more dipeptides, tripeptides, and conjugated amino acids than the tolerant cultivar, a pattern directly associated with its high chlorophyll content and photosynthetic rate under control conditions. However, these peptides accumulated without efficient turnover. The tolerant cultivar maintained protein and amino acid homeostasis through enhanced autophagy and ubiquitin-proteasome system (UPS) activity, as validated by enzyme-specific ELISA, quantitative PCR (qPCR), and transmission electron microscopy. Overall, our results highlight fundamentally different strategies for coping with Cd stress: the susceptible cultivar accumulated amino acids without efficient recycling, whereas the tolerant cultivar sustains proteostasis through efficient autophagy and UPS activity. These insights identify potential molecular targets for enhancing cadmium tolerance and protein use efficiency in soybean breeding programs.