Plants have long been recognized as biochemical powerhouses, producing a vast array of compounds through their secondary metabolic pathways [1]. Although historically referred to as ‘secondary’ due to their perceived non-essential role in basic plant survival, it is now understood that these metabolites are integral to plant growth, development and adaptation to environmental challenges. Secondary metabolites, such as alkaloids, terpenoids, phenolics and flavonoids, serve as critical mediators of plant-environment interactions, conferring resistance to biotic and abiotic stressors [2]. Beyond their ecological functions, these compounds are invaluable to humans, supporting industries ranging from pharmaceuticals and nutrition to agrochemicals and chemical additives.

The biosynthesis of secondary metabolites in plants is a complex, highly regulated process involving intricate metabolic pathways and molecular machinery. Secondary metabolites are derived from primary metabolic precursors, such as amino acids, sugars, and fatty acids, through specialized enzymatic pathways [3]. These pathways are often compartmentalized within specific tissues or organelles, reflecting their spatiotemporal regulation [4]. Advances in understanding these regulatory networks have revealed that secondary metabolite production is not a static process but a dynamic response to internal and external stimuli, enabling plants to adapt to changing environments [5]. These discoveries provide a foundation for manipulating biosynthetic pathways to enhance the production of valuable secondary metabolites.

By integrating data from multiple biological layers, researchers can construct comprehensive models of metabolic networks, identify key regulatory nodes, and uncover novel biosynthetic genes. Genomics has been instrumental in identifying gene clusters responsible for secondary metabolite biosynthesis [6]. Transcriptomics has enabled the identification of differentially expressed genes under various environmental conditions [7]. Proteomics complements transcriptomics by giving us information about the functional proteins involved in secondary metabolism. Mass spectrometry-based proteomics has enabled the identification of enzymes and regulatory proteins that are post-translationally modified, offering a deeper understanding of pathway dynamics [8]. The integration of multi-omics data, facilitated by bioinformatics tools and machine learning, has enabled the construction of predictive models for secondary metabolism. Systems biology approaches, such as network analysis, have identified key regulatory hubs that control metabolic flux, paving the way for targeted metabolic engineering [9,10].

Synthetic biology has emerged as a powerful tool for reconstructing and optimizing metabolic pathways, enabling the large-scale production of valuable secondary metabolites. In plants, metabolic engineering strategies often involve the overexpression or silencing of key biosynthetic genes [11]. Heterologous expression systems, such as bacteria, yeast, or plant cell cultures, offer an alternative approach for producing secondary metabolites [12]. Synthetic biology has also enabled the creation of novel metabolic pathways by combining enzymes from different species, leading to the production of non-natural analogs with enhanced bioactivity. CRISPR/Cas9-based gene editing has further revolutionized metabolic engineering by enabling precise modifications to biosynthetic genes [13,14].

The physiological regulation of secondary metabolism is tightly linked to stress response pathways, allowing plants to dynamically adjust their metabolic output. Biotic stressors, such as herbivory and pathogen attack, trigger the production of defense-related secondary metabolites, such as glucosinolates, terpenoids, and phytoalexins [15]. Abiotic stressors, such as drought, salinity, and temperature extremes, induce the accumulation of secondary metabolites with protective functions [16]. The physiological regulation of secondary metabolism involves complex signaling networks, including phytohormones like jasmonic acid, salicylic acid, and abscisic acid [17]. These hormones act as master regulators, coordinating the expression of biosynthetic genes in response to stress. These hormones act as master regulators, coordinating the expression of biosynthetic genes in response to stress [18]. Recent studies have also revealed the role of secondary metabolites in plant growth and development, challenging their “secondary” classification [19,20].

Despite their significance, the low natural abundance of many secondary metabolites poses a challenge for large-scale production, limiting their commercial and therapeutic potential. Recent advances in plant biology, particularly in understanding the biosynthesis, regulation, and functional roles of these compounds, have provided fresh prospects for overcoming these limitations. This editorial investigates the various facets of plant secondary metabolism, focusing on biosynthesis and molecular control, multi-omics approaches, metabolic engineering through synthetic biology, and the role of secondary metabolites in stress tolerance and physiological regulation. By probing these areas, we aim to highlight the transformative potential of secondary metabolites in both plant biology and human applications.

The study of plant secondary metabolism is at a pivotal juncture, with significant opportunities and challenges ahead. Advancements in multi-omics, synthetic biology, and gene editing have yielded sophisticated tools that facilitate the elucidation of intricate secondary metabolic pathways and the augmentation of their production. However, several challenges persist, including the scalability of metabolic engineering approaches, the ecological impact of genetically modified plants, and the ethical considerations of synthetic biology [30,31]. Future research endeavors should prioritize the integration of multi-omics data to develop predictive models of metabolic flux, thereby facilitating the design of efficient biosynthetic pathways. Furthermore, an exploration of the ecological and evolutionary roles of secondary metabolites will facilitate a more profound comprehension of their adaptive significance, thereby informing conservation and agricultural strategies. The development of sustainable production platforms, such as plant cell cultures and microbial factories, will be critical for meeting the growing demand for secondary metabolites in medicine, agriculture, and industry. Addressing public perception and regulatory frameworks surrounding genetically modified organisms and synthetic biology is imperative to ensure the safe and equitable application of these technologies [32,33]. The translation of scientific advances into practical solutions will require collaborative efforts between researchers, policymakers, and industry stakeholders.

Jiang Y, Liu L, Wang K, Zhao M, Chen P, Lei J, et al. Response of the ginseng C₂H₂-type zinc finger protein family PgZFPs gene to methyl jasmonate regulation. Phyton-Int J Exp Bot. 2024;93(11):3055–71. doi:10.32604/phyton.2024.056384.