Lactylome Profiling Reveals the Potential Role of Lysine Lactylation in Regulating Soybean Seed Quality

Lysine lactylation (Kla), a recently discovered post-translational modification (PTM) that influences gene expression, metabolic pathways, and cellular signaling. While the importance of Kla is well-documented in mammals, its presence and impact in plant systems, particularly in soybeans, remain largely unknown. This study initiates the first proteomic analysis of lactylation in both wild-type (ZYD) and cultivated-type (SN14) soybeans. We established the first global lysine lactylation proteome profile in soybean seeds, identifying 783 Kla sites across 327 proteins. Our analysis revealed that the wild variety showed higher levels of protein content, lactate content, and lactylation levels. Moreover, we observed distinct Kla patterns between wild and cultivated soybeans, primarily affecting the lipid, carbohydrate, amino acid, and energy metabolism. Intriguingly, our results showed that metabolites associated with oil biosynthesis were downregulated in wild soybeans, while proteins linked to storage protein pathways were significantly upregulated, suggesting that Kla may play a role in negatively regulating the oil content while enhancing the protein content in soybean seeds. Taken together, this research provides the first comprehensive evidence of lactylation in soybeans and suggests its role in regulating oil and protein content in seeds. The findings open new avenues for improving soybean seed quality through targeted metabolic engineering and breeding strategies.