Integrated Transcriptomic and Metabolomic Analysis Reveals the Adaptive Mechanism of Penicillium digitatum under Modified Atmosphere Packaging Based on Amino Acid Metabolism

This study employed integrated multi-omics approaches to elucidate, from the perspective of amino acid metabolism, the adaptive mechanism of Penicillium digitatum under modified atmosphere packaging (MAP) conditions. Comparative analysis of natural air (Air), controlled atmosphere (CA), and MAP treatments revealed that MAP upregulated the expression of the hercynylcysteine S-oxide synthase (HCSOS), aldehyde dehydrogenase (ALDH), and monoamine oxidase (MAO) genes, thereby enhancing histidine-derived ergothioneine and methionine levels, and subsequently boosting glutathione-mediated redox homeostasis. Meanwhile, MAP induced the expression of the dihydroxyacid dehydratase (DHAD), saccharopine dehydrogenase (SDH), and arginosuccinate lyase (ASL) genes, redirecting valine, lysine, and arginine into the tricarboxylic acid (TCA) cycle to fuel ATP production. MAP also enhanced ASL-mediated arginine degradation and urea cycle activity, reducing arginine accumulation when compared to CA treatment. In contrast, while MAP induced upregulated expression of the pyrroline-5-carboxylate dehydrogenase (P5CDH) and D-amino acid oxidase (DAAO) genes, CA treatment promoted proline accumulation, reflecting stress-specific metabolic flexibility. Collectively, these findings demonstrate that MAP triggers transcriptional reprogramming of amino acid metabolism to coordinate oxidative defense, energy generation, and osmotic balance. By modulating these metabolic pathways and regulatory genes under MAP conditions, fungal adaptability can be disrupted. Hence, this study provides a promising strategy for suppressing green mold development, extending the postharvest shelf life, and improving the quality of fruits and vegetables.