Complete pathway elucidation and heterologous reconstitution of (+)-nootkatone biosynthesis from Alpinia oxyphylla

Characterization and functional reconstruction of a highly productive germacrene A synthase from Liriodendron chinense

Plants produce a large array of natural products which play important roles in flavours, fragrances and medicines. However, some high-value plant intermediate metabolites cannot be directly extracted from plants. The tulip tree (Liriodendron chinense) in the Magnoliaceae family is rich in sesquiterpenes. Upon characterizing the functions of 11 Liriodendron chinense terpene synthases, we discovered that LcTPS3 could produce high yields of (+)-germacrene A, which was shown to be a central scaffold in sesquiterpene biosynthesis. This compound can be completely transformed into β-elemene at high temperature, a broad-spectrum antitumor drug widely used in clinical treatment. By expressing LcTPS3 in a precursor-providing Saccharomyces cerevisiae chassis and with the aid of metabolic engineering, the fermentation yield of (+)-germacrene A has been achieved at 14.71 g/L. Site-directed mutagenesis experiments and molecular dynamics simulations revealed that the A280V suppresses the cyclization of substrate by influencing the conformation of the enzyme-substrate. The Y282L facilitates secondary cyclization to produce α-guaiene by shortening the distance between the catalytic residue Y531 and the substrate. These insights underscore the high plasticity of LcTPS3 and suggest that its targeted engineering could unlock the synthesis of a wider array of valuable sesquiterpenes.

Genome-wide identification and expression analyses of CYP450 genes in Chrysanthemum indicum

BACKGROUND

The cytochrome P450 superfamily comprises a large group of enzymes crucial for the biosynthesis and metabolism of diverse endogenous and exogenous secondary metabolites in plants. Chrysanthemum, an ornamental genus with considerable medicinal value, is one of the most economically important floricultural crops in the world. The characteristics and functions of CYP450 genes in Chrysanthemum species, however, remain largely unknown.

RESULTS

In this study, we identified 371 CYP450 genes in the Chrysanthemum indicum genome, and categorized them into 8 clans and 44 families through phylogenetic analysis. Gene duplication analysis revealed 111 genes in 47 tandem duplicated clusters and 28 genes in 15 syntenic blocks, suggesting that extensive duplication events may account for the rapid expansion of CiCYP450 superfamily. Additionally, extensive variations in gene structure, motif composition, and cis-regulatory element likely enhance the functional diversity of CiCYP450 proteins. Volatile metabolomic analysis detected a total of 53 distinct volatile organic compounds across the leaves, stems, and roots of C. indicum, with 19 and 16 compounds being exclusive to leaves and stems, respectively. Transcriptomic analysis identified 248 expressed CiCYP450 genes, with 31, 40, and 88 specifically or preferentially expressed in leaves, stems, and roots, respectively. Further correlation analyses between gene expression levels and compound contents highlighted 36 candidate CiCYP450 genes potentially responsible for the biosynthesis of 47 volatile organic compounds.

CONCLUSIONS

The genome-wide analyses of cytochrome P450 superfamily offers essential genomic resources for functional studies of CiCYP450 genes, and is significant for the molecular breeding of Chrysanthemum.

Nootkatone Alleviates Type 2 Diabetes in db/db Mice Through AMPK Activation and ERK Inhibition: An Integrated In Vitro and In Vivo Study

Type 2 diabetes mellitus (T2DM) is a common chronic metabolic disorder that imposes a substantial healthcare burden globally. Recent advances highlight the potential of natural products in ameliorating T2DM. In this study, we investigated the therapeutic efficacy of nootkatone (Nok), a natural sesquiterpene ketone, in T2DM and elucidated its underlying mechanisms. In vivo experiments demonstrated that Nok administration markedly improved dysregulated glucose metabolism and ameliorated serum biochemical abnormalities in db/db mice. Leveraging a network pharmacology-based approach, we identified putative molecular targets of Nok. Subsequent in vitro analyses revealed that Nok significantly enhanced glucose consumption in cultured cells. Mechanistically, Nok robustly activated AMP-activated protein kinase (AMPK) while suppressing mitogen-activated protein kinase (MAPK) signaling. Western blot validation further indicated that Nok downregulated the phosphorylation of MAPK1/3 (ERK2/1), attenuating MAPK pathway activation and thereby alleviating metabolic dysfunction-associated fatty liver disease (MAFLD) progression in the diabetic model. Collectively, our findings suggest that Nok exerts anti-diabetic effects via dual modulation of AMPK activation and MAPK inhibition, effectively restoring metabolic homeostasis and mitigating inflammation in T2DM. This study positions Nok as a promising natural compound for therapeutic intervention in T2DM and associated metabolic disorders.

Integrated analysis of transcriptome and metabolome reveals the molecular basis of quality differences in Alpinia oxyphylla Miq. From geo-authentic and non-authentic areas

Alpinia oxyphylla Miq., a well-accepted medicinal and edible plant in south China. The primary ingredients of this medicine vary significantly depending on their origin, which profoundly impacts its quality. In this study, a principal component analysis was performed on 17 different planting areas of A. oxyphylla, with nootkatone and kaempferol identified as representative sesquiterpenoids and flavonoids, respectively. To investigate the genes involved in nootkatone and kaempferol biosynthesis, a combined transcriptome and metabolome profiling was carried out on materials sourced from geo-authentic and non-authentic areas. The transcriptome analysis of these two types of accessions identified 96,691 unigenes, with 13,589 genes showing differential expression in both regions. Metabolome analysis revealed 2859 differentially accumulated metabolites across the four pairwise comparisons. Correlation analysis uncovered a number of genes, that associated with the differential biosynthesis of nootkatone and kaempferol in A. oxyphylla fruits from geo-authentic and non-authentic areas. Further investigation highlighted the candidate gene AoFMO1's ability to heterologously biosynthesize nootkatone in Arabidopsis thaliana leaves. This research lays the groundwork for a deeper understanding of the molecular mechanisms behind the authentication of A. oxyphylla's quality synthesis, and presents a comprehensive list of candidate genes for future functional studies to enhance the development of high-quality A. oxyphylla varieties rich in medicinal ingredients.

Biosynthesis of Edible Terpenoids: Hosts and Applications

Microbial foods include microbial biomass, naturally fermented foods, and heterologously synthesized food ingredients derived from microbial fermentation. Terpenoids, using isoprene as the basic structure, possess various skeletons and functional groups. They exhibit diverse physicochemical properties and physiological activities, such as unique flavor, anti-bacterial, anti-oxidant, anti-cancer, and hypolipemic, making them extensively used in the food industry, such as flavor, fragrance, preservatives, dietary supplements, and medicinal health food. Compared to traditional strategies like direct extraction from natural species and chemical synthesis, microbial cell factories for edible terpenoids have higher titers and yields. They can utilize low-cost raw materials and are easily scaling-up, representing a novel green and sustainable production mode. In this review, we briefly introduce the synthetic pathway of terpenoids and the applications of microbial cell factories producing edible terpenoids. Secondly, we highlight several typical and non-typical microbial chassis in edible terpenoid-producing cell factories. In addition, we reviewed the recent advances of representative terpenoid microbial cell factories with a gram-scale titer in food flavor, food preservation, nutritional enhancers, and medicinal health foods. Finally, we predict the future directions of microbial cell factories for edible terpenoids and their commercialization process.

Innovative approaches in the discovery of terpenoid natural products

As a class of natural compounds ubiquitous in nature, diverse terpenoids exhibit a broad spectrum of applications in human endeavors. The efficient discovery of novel terpenoids and the establishment of a terpene library for broad utilization represent pressing challenges in terpenoid natural product research. Various microbial platforms offer abundant precursors for terpene biosynthesis from diverse sources. Leveraging artificial intelligence for enzyme function prediction and screening can facilitate the identification of terpenoid synthesis components with innovative mechanisms. Automated high-throughput bio-foundry workstations can expedite the construction of terpenoid libraries, providing substantial time and labor savings. The integration of multiple strategies promises to yield substantial advancements in the exploration of valuable terpenoids.

Spatiotemporal analysis of microstructure, sensory attributes, and full-spectrum metabolomes reveals the relationship between bitterness and nootkatone in Alpinia oxyphylla miquel fruit peel and seeds

The Alpinia oxyphylla fruit (AOF) is a popular condiment and traditional Chinese medicine in Asia, known for its neuroprotective compound nootkatone. However, there has not been a comprehensive study of its flavor or the relationship between sensory and bioactive compounds. To address this issue, we examined AOF's microstructure, flavor, and metabolomic profiles during fruit maturation. The key markers used to distinguish samples included fruit expansion, testa pigmentation, aril liquefaction, oil cell expansion, peel spiciness, aril sweetness, and seed bitterness. A full-spectrum metabolomic analysis, combining a nontargeted metabolomics approach for volatile compounds and a widely targeted metabolomics approach for nonvolatile compounds, identified 1,448 metabolites, including 1,410 differentially accumulated metabolites (DAMs). Notably, 31 DAMs, including nootkatone, were associated with spicy peel, sweet aril, and bitter seeds. Correlational analysis indicated that bitterness intensity is an easy-to-use biomarker for nootkatone content in seeds. KEGG enrichment analysis linked peel spiciness to phenylpropanoid and capsaicin biosynthesis, seed bitterness to terpenoid (especially nootkatone) biosynthesis, and aril sweetness to starch and sucrose metabolism. This investigation advances the understanding of AOF's complex flavor chemistry and underlying bioactive principle, encapsulating the essence of the adage: "no bitterness, no intelligence" within the realm of phytochemistry.

Application of valencene and prospects for its production in engineered microorganisms

Valencene, a sesquiterpene with the odor of sweet and fresh citrus, is widely used in the food, beverage, flavor and fragrance industry. Valencene is traditionally obtained from citrus fruits, which possess low concentrations of this compound. In the past decades, the great market demand for valencene has attracted considerable attention from researchers to develop novel microbial cell factories for more efficient and sustainable production modes. This review initially discusses the biosynthesis of valencene in plants, and summarizes the current knowledge of the key enzyme valencene synthase in detail. In particular, we highlight the heterologous production of valencene in different hosts including bacteria, fungi, microalgae and plants, and focus on describing the engineering strategies used to improve valencene production. Finally, we propose potential engineering directions aiming to further increase the production of valencene in microorganisms.

Cutting-edge plant natural product pathway elucidation

Plant natural products (PNPs) play important roles in plant physiology and have been applied across diverse fields of human society. Understanding their biosynthetic pathways informs plant evolution and meanwhile enables sustainable production through metabolic engineering. However, the discovery of PNP biosynthetic pathways remains challenging due to the diversity of enzymes involved and limitations in traditional gene mining approaches. In this review, we will summarize state-of-the-art strategies and recent examples for predicting and characterizing PNP biosynthetic pathways, respectively, with multiomics-guided tools and heterologous host systems and share our perspectives on the systematic pipelines integrating these various bioinformatic and biochemical approaches.