Plant metabolism and synthetic biology

Plants possess an intricate network of metabolic pathways that govern their growth, development, and responses to environmental stimuli. By combining the principles of engineering and biology, synthetic biology offers a powerful toolkit to decipher and manipulate these complex metabolic processes. The special issue showcases recent research efforts and innovative engineering strategies aimed at unraveling the secrets of plant metabolism and the potential applications of plant metabolites. Through the intersection of engineering and biology, this collection of articles illuminates the transformative potential of synthetic biology in unraveling the intricacies of plant metabolism and leveraging its immense value for various industries.

1. Unraveling plant metabolism: harnessing multi-omics strategy and synthetic biology

Plant secondary metabolites are of immense pharmaceutical importance. Currently, more than 11% of basic and essential drugs recognized by the World Health Organization (WHO) are derived from flowering plants. These compounds, synthesized by plants for various ecological purposes, have demonstrated remarkable therapeutic properties and continue to be a valuable source of novel drugs and treatments. However, our understanding of plant metabolism is still incomplete and limited in many ways.

One of the emerging directions is to elucidate plant metabolic pathway or investigate biosynthetic enzyme using multi-omics techniques. By integrating various omics approaches such as genomics, proteomics, and metabolomics, we may gain a comprehensive understanding of the molecular mechanisms underlying the synthesis, regulation, and function of plant secondary metabolites. Using tandem MS-based targeted metabolomics analysis, Pu et al. was able to provide an extensive repertoire of flavonoids produced by Camptotheca acuminate, including some that are previously unknown [1]. Further spatial analysis of these flavonoids in C. acuminate derived a comprehensive metabolic map for the synthesis of all the identified flavonoids in C. acuminate with some of the keys biosynthetic genes proposed from co-expression analysis. Similarly, through coupling metabolomic and transcriptomic analysis of Curcuma wenyujin, Chen et al. were able to depict the metabolic pathway of curcuminoids and identified the key polyketide synthase in C. wenyujin [2]. In another work, Yao et al. integrate comprehensive genomic and transcriptomic analysis of Epimedium pubescens Maxim, proposed candidate genes putatively encoding a UDP-glycosyltransferase, a key enzyme responsible for the glycosylation of flavonoid glycosides, and likely involved in flavonoid biosynthesis, which were validated through functional verification of one gene in the synthesis of baohuoside II [3]. In addition to compound discovery and gene identification, omics-analysis can also provide insights into the regulatory mechanisms of plant metabolism. Through integrative analysis of transcriptome and metabolome coupled with bisulfite sequencing-based DNA methylation mapping, Lin et al. were able to reveal the role of DNA methylation in the promoter region of the chalcone isomerase (CHI) gene, a key gene in the Lithocarpus polystachyus Rehd flavonoid biosynthesis, to flavonoid biosynthesis and accumulation [4].

Functional genomics coupled with heterologous expression in model plant such as Nicotiana benthamiana, or in workhouse microorganisms such as Escherichia coli or baker's yeast has emerged as a widely employed strategy to elucidate plant secondary metabolism. Using this strategy, Huang et al. reported the discovery of a novel and promiscuous C-glycosyltransferase from Anemarrhena asphodeloides that can function on a broad array of metabolites, and its catalytic capacity can be further expanded through rational protein engineering [5]. Using similar strategy, Fan et al. identified a novel oxidosqualene cyclase from maize from genomic and bioinformatic analysis and validated its function with an engineered yeast strain that accumulate high level of 2,3-oxidosqualene [6]. In another article, Xia et al. discovered a new dual function cytochrome P450 from soybean through transcriptomic analysis coupled with functional characterizations in yeast and soybean [7].

2. Potential agricultural applications of plant metabolites

Beyond their pharmaceutical importance and nutritional value, plant metabolites exhibit vast agricultural potentials. This special issue also explores the multifaceted roles of plant metabolites and delves into their potential applications in agriculture from the lens of synthetic biology. The detrimental effects of excessive synthetic pesticide and fertilizer usage in agriculture have prompted a growing interest in natural alternatives. In their review, Panda et al. highlight recent advancements in engineering microorganisms to produce natural agrochemicals, particularly plant-derived ones, and address the challenges associated with developing and implementing these strategies to meet market demands while mitigating environmental and health concerns [8]. In a more specific example, to address the significant crop losses caused by fungal pathogens and the drawbacks of chemical-based fungicides, there is an urgent need for environmentally friendly and effective agricultural fungicides, and Chiu et al. discussed the potential of plant antifungal proteins for future agricultural applications, exploring their diverse functionality and discussing their utilization as alternative fungicides [9].

3. Advancing biological production of plant metabolites through synthetic biology

Recognizing the immense potential of plant metabolites in pharmaceutical, food, and agricultural domains, many endeavors are focused on harnessing synthetic biology to fulfill the market demand for these valuable compounds. By combining microbial cell factories (MCFs) and cell-free systems (CFSs), Yu et al. successfully achieved the highest reported titer of agroclavine (AC), a structurally complex ergot alkaloid, at 1209 mg/L [1]. This work underscores the potential of employing such a strategy to overcome the limitations associated with both microbial cell factories (MCFs) and cell-free systems (CFSs). Researchers are also investigating the potential of non-conventional microbial hosts as alternative chassis to produce plant metabolites, with the aim of finding hosts that possess unique properties and characteristics. In one commentary, Yu et al. highlighted a recent synthetic biology effort in which Pichia pastoris, a methylotrophic yeast, was engineered to successfully produce catharanthine, a precursor to vinblastine, showcasing the potential of this non-model yeast as a chassis for the biosynthesis of complex plant natural products [10]. In addition to heterologous bioproduction, direct engineering of native plants can also be a valuable approach to enhance the accumulation of specific metabolites. An illustrative example is presented in this issue, where Wu et al. engineered carotenoid biosynthesis in tomato by expressing the four involved synthetic genes using fruit-specific promoters [11]. The engineered tomatoes exhibited enhanced antioxidant capacity and extended shelf life. This work exemplifies accurate metabolic engineering and highlight the potential of synthetic biology to improve crop traits and explore the health benefits of carotenoid derivatives.