Integrated multi-omics reveal the multidimensional mechanisms of Penicillium sp. in selenite biodegradation

. High-throughput RNA-Seq and TMT-based proteomics revealed 6175 differentially expressed genes and 695 differentially expressed proteins enriched in carbohydrate and amino acid metabolism, the tricarboxylic acid cycle, glutathione metabolism, redox processes, selenocompound/sulfur metabolism, and lipid remodeling. Key antioxidant enzymes, glutathione and thioredoxin systems, Fe-S cluster assembly proteins, oxidoreductases, and membrane transporters were significantly upregulated under Se(IV) stress. Four major metabolic modules-glutathione, thioredoxin, iron-sulfur cluster, and lipid metabolism-coordinated to maintain redox homeostasis, mitigate oxidative damage, and drive Se(IV) detoxification. While core redox responses are conserved across microbes, our multi-omics integration in a filamentous fungus reveals a dose-stratified deployment of fungal wall/lipid remodeling and transporter control that refines existing models. This study provides a mechanistic basis for the application of PM2 in selenium bioremediation and the green biosynthesis of Se nanoparticles (SeNPs).