Melatonin-mediated metabolic reprogramming and stress adaptation in plants.

key messageMelatonin acts as a multifunctional regulator of plant stress adaptation by reprogramming primary and secondary metabolism and coordinating ROS, nitric oxide, and phytohormone signalling. Integrating metabolomics with transcriptomics and proteomics provides new insights into these mechanisms and highlights melatonin as a promising strategy for enhancing crop resilience and productivity under diverse environmental stresses. Plants, being sessile, are continuously exposed to diverse environmental challenges, which disrupt cellular homeostasis and reduce crop productivity. To survive under such conditions, plants have evolved complex defence mechanisms involving metabolic reprogramming and coordinated molecular signalling networks. Among the regulatory molecules involved in stress adaptation, melatonin (N-acetyl-5-methoxytryptamine) has emerged as a multifunctional signalling compound that plays a pivotal role in plant growth, development, and stress tolerance. Acting as a potent antioxidant and signalling regulator, melatonin modulates multiple metabolic pathways associated with energy metabolism, amino acid biosynthesis, carbohydrate metabolism, and secondary metabolite production. These metabolic adjustments enhance the accumulation of osmoprotectants, antioxidants, and defence-related metabolites, thereby improving plant resilience under stress. Recent advances in metabolomics, together with transcriptomics and proteomics, have provided deeper insights into melatonin-mediated metabolic regulation in plants. High-throughput analytical platforms such as liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), and nuclear magnetic resonance (NMR) enable comprehensive profiling of stress-responsive metabolites and reveal how melatonin orchestrates metabolic network reprogramming. Emerging evidence indicates that melatonin interacts with reactive oxygen species, nitric oxide, and multiple phytohormones to regulate gene expression, protein abundance, and metabolite accumulation, thereby integrating stress perception with physiological adaptation. This review summarises current knowledge on melatonin biosynthesis, signalling pathways, cross-talk and its role in regulating primary and secondary metabolism under diverse stresses. Emphasis has been laid on metabolomics-driven insights and multi-omics integration to elucidate the molecular mechanisms underlying melatonin-mediated stress tolerance and to support strategies to improve crop resilience and productivity.