Integration of proteomic, metabolomic, and ubiquitinomic analyses reveals potential mechanisms underlying low-phosphorus stress adaptation in soybean roots

• Low-phosphorus (P) stress is a critical factor limiting soybean growth and yield. Ubiquitination, a post-translational protein modification, is increasingly recognised as a regulator of plant adaptive responses to nutrient limitation, including P deficiency. However, the mechanisms by which ubiquitination mediates soybean tolerance to low P remain underexplored. The present study aimed to elucidate the molecular basis of P efficiency in soybean, focusing on the role of ubiquitination.• A P-efficient soybean genotype, Qiandou 11, was hydroponically cultivated under low or normal P levels to investigate P uptake mechanisms. Proteomic, metabolomic, and ubiquitinomic analyses were performed to identify the metabolic pathways and proteins regulating the soybean root system in response to P deficiency.• The results indicated that QD11 rapidly adapted to P deficiency by increasing the levels of small-molecule-size organic acids and enhancing specific root length. A total of 377 differentially accumulated metabolites and 1,059 differentially expressed proteins (DEPs) were identified. The sample with the largest number of DEPs was selected for ubiquitination analysis, revealing 929 differential ubiquitination sites (585 upregulated and 344 downregulated) in 585 proteins. Notably, these proteins were significantly enriched in glycolysis, phenylpropane biosynthesis, and isoflavone biosynthesis pathways. Integrated multi-omics analysis revealed that phosphoenolpyruvate carboxylase and phenylalanine ammonia-lyase are hub proteins involved in carbon allocation during the soybean root response to low-P stress, and their regulation may be mediated by ubiquitination.• These findings elucidate ubiquitin-mediated regulatory mechanisms and key physiological traits associated with low-P tolerance in soybean. This study provides valuable insights for breeding P-efficient soybean varieties.