Transcriptional coordination of metabolic reprogramming in chlorogenic- and gamma aminobutyric acid-treated pepper during postharvest storage

Pepper ( Capsicum annuum L.) fruits rapidly deteriorate during postharvest storage, necessitating innovative preservation strategies. Chlorogenic acid (CGA) and gamma-aminobutyric acid (GABA) are bioactive compounds that extend storage life; however, the molecular mechanisms through which they produce this effect remain largely unexplored. We used integrated untargeted metabolomic and transcriptomic approaches to thoroughly clarify the molecular mechanisms governing the pepper fruit responses to CGA, GABA, and combined CGA + GABA treatments during 12 days of postharvest storage. Metabolomic analysis identified 717 differentially accumulated metabolites (DAMs) across 11 superclasses, with amino acids, organic acids, and phospholipids emerging as the predominant categories. Transcriptomic profiling revealed 2477 differentially expressed genes (DEGs), and the combined treatment induced the most transcriptional changes (1737 DEGs). Lipid metabolism was a central regulatory target, with 123 distinct lipid species among the total metabolites and coordinated upregulation of fatty acid biosynthesis enzymes ( LACS , KCR , and HCD ) following treatment. Amino acid metabolism constitutes another pivotal network, with 152 amino acid-related DAMs spanning seven biosynthesis families and enhancing glutamate dehydrogenase (GAD) expression, promoting GABA accumulation. Phenylpropanoid pathway analysis revealed sophisticated regulation, with early enzyme levels downregulated and downstream enzyme ( CHS and CYP450 families) levels upregulated, indicating selective metabolic flux redirection toward flavonoid biosynthesis. Correlation analysis identified five key transcription factors ( CaRAP2.7 , CabHLH93 , CaHSF30 , CaTCP19 , and CaGATA8 ) that were strongly associated with core metabolites; nuclear-localized CaGATA8 showed strong correlations with amino acid and phenylpropanoid metabolism. These findings reveal that CGA and GABA treatments enhance pepper fruit storage tolerance through the coordinated regulation of lipid membrane stabilization, amino- acid-mediated stress protection, and secondary antioxidant metabolite biosynthesis, providing molecular insights for developing effective postharvest preservation strategies. • CGA+GABA extends pepper fruit shelf life via lipid and amino acid reprogramming. • Combined CGA+GABA induces 1737 DEGs and upregulates LACS, KCR , and HCD. • Enhanced GAD and 152 amino acid DAMs promote stress tolerance. • Upregulated CHS and CYP450 redirect flux toward flavonoid synthesis. • CaGATA8 correlates with amino acid and phenylpropanoid metabolism genes.