Untargeted Metabolomics Unravel the Effect of SlPBB2 on Tomato Fruit Quality and Associated Plant Metabolism

<b>Background</b>: Proteasomes are protein complexes that mediate proteolysis to degrade unneeded or damaged proteins, and they play an indispensable role in plant growth and development. However, their regulatory effects on tomato fruit quality and the underlying metabolic mechanisms remain largely elusive. This study aimed to elucidate the metabolic regulatory mechanisms of proteasomes in tomato fruits through untargeted metabolome analysis. <b>Methods</b>: An untargeted metabolomics approach was employed to profile the metabolic changes in tomato fruits. Metabolites were detected and identified under both positive and negative ion modes. Metabolic profiles were compared between wild-type (WT) tomato fruits and <i>SlPBB2</i> RNA interference (<i>SlPBB2</i>-RNAi) lines. Specifically, the <i>SlPBB2</i>-RNAi line refers to a transgenic tomato line constructed via Agrobacterium-mediated transformation, where the expression of the proteasome component gene <i>SlPBB2</i> was stably downregulated by RNA interference technology to clarify its regulatory role in fruit metabolism. KEGG enrichment analysis was performed to annotate the functions of differential metabolites. <b>Results</b>: A total of 568 and 333 metabolites were identified in positive and negative ion modes, respectively. Comparative analysis revealed 43 differentially abundant metabolites between WT and <i>SlPBB2</i>-RNAi fruits, including D-glucose, pyruvic acid, leucine, and naringenin. KEGG enrichment analysis further identified key metabolites involved in the carbon fixation pathway of photosynthetic organisms, with L-malic acid being a prominent representative. Reduced accumulation of D-glucose and pyruvic acid in <i>SlPBB2</i>-RNAi fruits suggested the inhibition of the citrate cycle, a core pathway in cellular energy metabolism. This metabolic perturbation was associated with decreased chlorophyll content in <i>SlPBB2</i>-RNAi plants, implying impaired photosynthetic carbon fixation and energy metabolism. <b>Conclusions</b>: This study uncovers the metabolic regulatory role of SlPBB2-mediated proteasome function in tomato fruits, providing novel insights into the link between proteasomal activity and fruit metabolic homeostasis from a metabolomic perspective. These findings offer new theoretical foundations for developing strategies to improve tomato nutritional quality.