The ancient CYP716 family is a major contributor to the diversification of eudicot triterpenoid biosynthesis

Integrated Metabolomics and Transcriptomics Analysis Reveals New Insights into Triterpene Biosynthesis in Rosa rugosa

Rosa rugosa is highly regarded for its aesthetic and therapeutic qualities. In particular, R. rugosa's flowers are known to produce essential oils containing a mixture of volatile terpenes, phenylpropanoids, and other compounds. Despite this, extensive research exists on volatile terpenes in flowers, while the knowledge of non-volatile terpenes in distinct tissues is still limited. Using UPLC-ESI-MS/MS, a comprehensive analysis of the terpene metabolites in five different tissues of R. rugosa was conducted. These metabolites accumulated in distinct tissues, and the majority of them were triterpenoids. Transcriptome data were collected from five tissues using RNA-seq. Transcriptomics and metabolomics were utilized to evaluate the triterpene biosynthesis pathway, resulting in new insights into its regulation and biosynthesis. The RrOSC10 was identified as a key enzyme in converting 2,3-oxidosqualene into α-amyrin, potentially contributing to the triterpene biosynthesis pathway. Furthermore, the expression of the RrOSC10 gene was upregulated by salinity for 0.5 h and 1 h, with subsequent downregulation at 2 h. This study lays a foundation for future research on the biosynthesis and accumulation of triterpenes in R. rugosa.

Chemoproteomics reveals the epoxidase enzyme for the biosynthesis of camptothecin in Ophiorrhiza pumila

The downstream biosynthetic route of camptothecin has remained unclear for more than half a century. Here, we discovered a P450 enzyme involved in camptothecin biosynthesis from plant by chemoproteomics, which lays the foundation for synthesis of camptothecin and highlights the effectiveness of chemoproteomic profiling for discovering unknown enzymes.

Combined Metabolite and Transcriptomic Profiling Unveil a Potential Gene Network Involved in the Triterpenoid Metabolism of Rose roxburghii

Rose roxburghii, a horticulturally significant species within the Rosa genus of the Rosaceae family, is renowned for its abundance of secondary metabolites and ascorbate, earning it the title 'king of vitamin C'. Despite this recognition, the mechanisms underlying the biosynthesis and regulation of triterpenoid compounds in R. roxburghii remain largely unresolved. In this study, we conducted high-performance liquid chromatography profiling across various organs of R. roxburghii, including fruit, root, stem, and leaves, revealing distinct distributions of triterpenoid compounds among different plant parts. Notably, the fruit exhibited the highest total triterpenoid content, followed by root and stem, with leaf containing the lowest levels, with leaf containing the lowest levels. Transcriptomic analysis unveiled preferential expression of members from the cytochrome P450 (CYP) and glycosyltransferase (UGT) families, likely contributing to the higher accumulation of both ascorbate and triterpenoid compounds in the fruits of R. roxburghii compared to other tissues of R. roxburghii. Transcriptomic analysis unveiled a potential gene network implicated in the biosynthesis of both ascorbate and triterpenoid compounds in R. roxburghii. These findings not only deepen our understanding of the metabolic pathways in this species but also have implications for the design of functional foods enriched with ascorbate and triterpenoids in R. roxburghii.

Chromosome-level genome assembly of Prunella vulgaris L. provides insights into pentacyclic triterpenoid biosynthesis

Prunella vulgaris is one of the bestselling and widely used medicinal herbs. It is recorded as an ace medicine for cleansing and protecting the liver in Chinese Pharmacopoeia and has been used as the main constitutions of many herbal tea formulas in China for centuries. It is also a traditional folk medicine in Europe and other countries of Asia. Pentacyclic triterpenoids are a major class of bioactive compounds produced in P. vulgaris. However, their biosynthetic mechanism remains to be elucidated. Here, we report a chromosome-level reference genome of P. vulgaris using an approach combining Illumina, ONT, and Hi-C technologies. It is 671.95 Mb in size with a scaffold N50 of 49.10 Mb and a complete BUSCO of 98.45%. About 98.31% of the sequence was anchored into 14 pseudochromosomes. Comparative genome analysis revealed a recent WGD in P. vulgaris. Genome-wide analysis identified 35 932 protein-coding genes (PCGs), of which 59 encode enzymes involved in 2,3-oxidosqualene biosynthesis. In addition, 10 PvOSC, 358 PvCYP, and 177 PvUGT genes were identified, of which five PvOSCs, 25 PvCYPs, and 9 PvUGTs were predicted to be involved in the biosynthesis of pentacyclic triterpenoids. Biochemical activity assay of PvOSC2, PvOSC4, and PvOSC6 recombinant proteins showed that they were mixed amyrin synthase (MAS), lupeol synthase (LUS), and β-amyrin synthase (BAS), respectively. The results provide a solid foundation for further elucidating the biosynthetic mechanism of pentacyclic triterpenoids in P. vulgaris.

A century of studying plant secondary metabolism-From "what?" to "where, how, and why?"

Over the past century, early advances in understanding the identity of the chemicals that collectively form a living plant have led scientists to deeper investigations exploring where these molecules localize, how they are made, and why they are synthesized in the first place. Many small molecules are specific to the plant kingdom and have been termed plant secondary metabolites, despite the fact that they can play primary and essential roles in plant structure, development, and response to the environment. The past 100 yr have witnessed elucidation of the structure, function, localization, and biosynthesis of selected plant secondary metabolites. Nevertheless, many mysteries remain about the vast diversity of chemicals produced by plants and their roles in plant biology. From early work characterizing unpurified plant extracts, to modern integration of 'omics technology to discover genes in metabolite biosynthesis and perception, research in plant (bio)chemistry has produced knowledge with substantial benefits for society, including human medicine and agricultural biotechnology. Here, we review the history of this work and offer suggestions for future areas of exploration. We also highlight some of the recently developed technologies that are leading to ongoing research advances.

Comparative transcriptome and metabolite profiling reveal diverse pattern of CYP-TS gene expression during corosolic acid biosynthesis in Lagerstroemia speciosa (L.) Pers

KEY MESSAGE

Extensive leaf transcriptome profiling and differential gene expression analysis of field grown and elicited shoot cultures of L. speciosa suggest that differential synthesis of CRA is mediated primarily by CYP and TS genes, showing functional diversity. Lagerstroemia speciosa L. is a tree species with medicinal and horticultural attributes. The pentacyclic triterpene, Corosolic acid (CRA) obtained from this species is widely used for the management of diabetes mellitus in traditional medicine. The high mercantile value of the compound and limited availability of innate resources entail exploration of alternative sources for CRA production. Metabolic pathway engineering for enhanced bioproduction of plant secondary metabolites is an attractive proposition for which, candidate genes in the pathway need to be identified and characterized. Therefore, in the present investigation, we focused on the identification of cytochrome P450 (CYP450) and oxidosqualene cyclases (OSC) genes and their differential expression during biosynthesis of CRA. The pattern of differential expression of these genes in the shoot cultures of L. speciosa, elicited with different epigenetic modifiers (azacytidine (AzaC), sodium butyrate (NaBu) and anacardic acid (AA)), was studied in comparison with field grown plant. Further, in vitro cultures with varying (low to high) concentrations of CRA were systematically assessed for the expression of CYP-TS and associated genes involved in CRA biosynthesis by transcriptome sequencing. The sequenced samples were de novo assembled into 180,290 transcripts of which, 92,983 transcripts were further annotated by UniProt. The results are collectively given in co-occurrence heat maps to identify the differentially expressed genes. The combined transcript and metabolite profiles along with RT-qPCR analysis resulted in the identification of CYP-TS genes with high sequence variation. Further, instances of concordant/discordant relation between CRA biosynthesis and CYP-TS gene expression were observed, indicating functional diversity in genes.

Minor Hydroxylated Triterpenoids Produced in Engineered Yeast by the Enzymes OSC and CYP716s from the Plant Enkianthus chinensis and Their Anti-Inflammatory and Hepatoprotective Activities

Triterpenoids are a type of specialized metabolites that exhibit a wide range of biological activities. However, the availability of some minor triterpenoids in nature is limited, which has hindered our understanding of their pharmacological potential. To overcome this limitation, heterologous biosynthesis of triterpenoids in yeast has emerged as a promising and time-efficient production platform for obtaining these minor compounds. In this study, we analyzed the transcriptomic data of Enkianthus chinensis to identify one oxidosqualene cyclase (EcOSC) gene and four CYP716s. Through heterologous expression of these genes in yeast, nine natural pentacyclic triterpenoids, including three skeleton products (1-3) produced by one multifunctional OSC and six minor oxidation products (4-9) catalyzed by CYP716s, were obtained. Of note, we discovered that CYP716E60 could oxidize ursane-type and oleanane-type triterpenoids to produce 6β-OH derivatives, marking the first confirmed C-6β hydroxylation in an ursuane-type triterpenoid. Compound 9 showed moderate inhibitory activity against NO production and dose-dependently reduced IL-1β and IL-6 production at the transcriptional and protein levels. Compounds 1, 2, 8, and 9 exhibited moderate hepatoprotective activity with the survival rates of HepG2 cells from 61% to 68% at 10 μM.

Cuticular wax biosynthesis in blueberries (Vaccinium corymbosum L.): Transcript and metabolite changes during ripening and storage affect key fruit quality traits

In fruits, cuticular waxes affect fruit quality traits such as surface color at harvest and water loss during postharvest storage. This study investigated the transcriptional regulation of cuticular wax deposition in northern highbush blueberries (Vaccinium corymbosum L.) in relation to fruit water loss and surface color during ripening and postharvest storage, as well as the effects of abscisic acid (ABA)-mediated changes in cuticular wax deposition on these fruit quality traits. Total cuticular wax content (μg∙cm-2) decreased during fruit ripening and increased during postharvest storage. Transcriptome analysis revealed a transcript network for cuticular wax deposition in blueberries. Particularly, five OSC-Likes were identified as putative genes for triterpene alcohol production, with OSC-Like1 and OSC-Like2 encoding mixed amyrin synthases, OSC-Like3 encoding a lupeol synthase, and OSC-Like4 and OSC-Like5 encoding cycloartenol synthases. The expression of three CYP716A-like genes correlated to the accumulation of two triterpene acids oleanolic acid and ursolic acid, the major wax compounds in blueberries. Exogenous ABA application induced the expression of triterpenoid biosynthetic genes and the accumulation of β-amyrin and oleanolic acid, as well as increased the ratio of oleanolic acid to ursolic acid. These changes were associated with reduced fruit water loss. The content of β-diketones was also increased by ABA application, and this increase was associated with increased fruit lightness (measured as L* using CIELAB Color Space by a colorimeter). This study provided key insights on the molecular basis of cuticular wax deposition and its implications on fruit quality traits in blueberries.

Integrated metabolome and transcriptome analysis identifies candidate genes involved in triterpenoid saponin biosynthesis in leaves of Centella asiatica (L.) Urban

Centella asiatica (L.) Urban is a well-known medicinal plant which has multiple pharmacological properties. Notably, the leaves of C. asiatica contain large amounts of triterpenoid saponins. However, there have only been a few studies systematically elucidating the metabolic dynamics and transcriptional differences regarding triterpenoid saponin biosynthesis during the leaf development stages of C. asiatica. Here, we performed a comprehensive analysis of the metabolome and transcriptome to reveal the dynamic patterns of triterpenoid saponin accumulation and identified the key candidate genes associated with their biosynthesis in C. asiatica leaves. In this study, we found that the key precursors in the synthesis of terpenoids, including DMAPP, IPP and β-amyrin, as well as 22 triterpenes and eight triterpenoid saponins were considered as differentially accumulated metabolites. The concentrations of DMAPP, IPP and β-amyrin showed significant increases during the entire stage of leaf development. The levels of 12 triterpenes decreased only during the later stages of leaf development, but five triterpenoid saponins rapidly accumulated at the early stages, and later decreased to a constant level. Furthermore, 48 genes involved in the MVA, MEP and 2, 3-oxidosqualene biosynthetic pathways were selected following gene annotation. Then, 17 CYP450s and 26 UGTs, which are respectively responsible for backbone modifications, were used for phylogenetic-tree construction and time-specific expression analysis. From these data, by integrating metabolomics and transcriptomics analyses, we identified CaHDR1 and CaIDI2 as the candidate genes associated with DMAPP and IPP synthesis, respectively, and CaβAS1 as the one regulating β-amyrin synthesis. Two genes from the CYP716 family were confirmed as CaCYP716A83 and CaCYP716C11. We also selected two UGT73 families as candidate genes, associated with glycosylation of the terpenoid backbone at C-3 in C. asiatica. These findings will pave the way for further research on the molecular mechanisms associated with triterpenoid saponin biosynthesis in C. asiatica.

A review of structural modification and biological activities of oleanolic acid

Oleanolic acid (OA), a pentacyclic triterpenoid, exhibits a broad spectrum of biological activities, including antitumor, antiviral, antibacterial, anti-inflammatory, hepatoprotective, hypoglycemic, and hypolipidemic effects. Since its initial isolation and identification, numerous studies have reported on the structural modifications and pharmacological activities of OA and its derivatives. Despite this, there has been a dearth of comprehensive reviews in the past two decades, leading to challenges in subsequent research on OA. Based on the main biological activities of OA, this paper comprehensively summarized the modification strategies and structure-activity relationships (SARs) of OA and its derivatives to provide valuable reference for future investigations into OA.

Stressing the importance of plant specialized metabolites: omics-based approaches for discovering specialized metabolism in plant stress responses

Plants produce a diverse range of specialized metabolites that play pivotal roles in mediating environmental interactions and stress adaptation. These unique chemical compounds also hold significant agricultural, medicinal, and industrial values. Despite the expanding knowledge of their functions in plant stress interactions, understanding the intricate biosynthetic pathways of these natural products remains challenging due to gene and pathway redundancy, multifunctionality of proteins, and the activity of enzymes with broad substrate specificity. In the past decade, substantial progress in genomics, transcriptomics, metabolomics, and proteomics has made the exploration of plant specialized metabolism more feasible than ever before. Notably, recent advances in integrative multi-omics and computational approaches, along with other technologies, are accelerating the discovery of plant specialized metabolism. In this review, we present a summary of the recent progress in the discovery of plant stress-related specialized metabolites. Emphasis is placed on the application of advanced omics-based approaches and other techniques in studying plant stress-related specialized metabolism. Additionally, we discuss the high-throughput methods for gene functional characterization. These advances hold great promise for harnessing the potential of specialized metabolites to enhance plant stress resilience in the future.

Deciphering triterpenoid saponin biosynthesis by leveraging transcriptome response to methyl jasmonate elicitation in Saponaria vaccaria

Methyl jasmonate (MeJA) is a known elicitor of plant specialized metabolism, including triterpenoid saponins. Saponaria vaccaria is an annual herb used in traditional Chinese medicine, containing large quantities of oleanane-type triterpenoid saponins with anticancer properties and structural similarities to the vaccine adjuvant QS-21. Leveraging the MeJA-elicited saponin biosynthesis, we identify multiple enzymes catalyzing the oxidation and glycosylation of triterpenoids in S. vaccaria. This exploration is aided by Pacbio full-length transcriptome sequencing and gene expression analysis. A cellulose synthase-like enzyme can not only glucuronidate triterpenoid aglycones but also alter the product profile of a cytochrome P450 monooxygenase via preference for the aldehyde intermediate. Furthermore, the discovery of a UDP-glucose 4,6-dehydratase and a UDP-4-keto-6-deoxy-glucose reductase reveals the biosynthetic pathway for the rare nucleotide sugar UDP-D-fucose, a likely sugar donor for fucosylation of plant natural products. Our work enables the production and optimization of high-value saponins in microorganisms and plants through synthetic biology approaches.

Recent advances in triterpenoid pathway elucidation and engineering

Triterpenoids are among the most assorted class of specialized metabolites found in all the taxa of living organisms. Triterpenoids are the leading active ingredients sourced from plant species and are utilized in pharmaceutical and cosmetic industries. The triterpenoid precursor 2,3-oxidosqualene, which is biosynthesized via the mevalonate (MVA) pathway is structurally diversified by the oxidosqualene cyclases (OSCs) and other scaffold-decorating enzymes such as cytochrome P450 monooxygenases (P450s), UDP-glycosyltransferases (UGTs) and acyltransferases (ATs). A majority of the bioactive triterpenoids are harvested from the native hosts using the traditional methods of extraction and occasionally semi-synthesized. These methods of supply are time-consuming and do not often align with sustainability goals. Recent advancements in metabolic engineering and synthetic biology have shown prospects for the green routes of triterpenoid pathway reconstruction in heterologous hosts such as Escherichia coli, Saccharomyces cerevisiae and Nicotiana benthamiana, which appear to be quite promising and might lead to the development of alternative source of triterpenoids. The present review describes the biotechnological strategies used to elucidate complex biosynthetic pathways and to understand their regulation and also discusses how the advances in triterpenoid pathway engineering might aid in the scale-up of triterpenoid production in engineered hosts.

Characterization of the horse chestnut genome reveals the evolution of aescin and aesculin biosynthesis

Horse chestnut (Aesculus chinensis) is an important medicinal tree that contains various bioactive compounds, such as aescin, barrigenol-type triterpenoid saponins (BAT), and aesculin, a glycosylated coumarin. Herein, we report a 470.02 Mb genome assembly and characterize an Aesculus-specific whole-genome duplication event, which leads to the formation and duplication of two triterpenoid biosynthesis-related gene clusters (BGCs). We also show that AcOCS6, AcCYP716A278, AcCYP716A275, and AcCSL1 genes within these two BGCs along with a seed-specific expressed AcBAHD6 are responsible for the formation of aescin. Furthermore, we identify seven Aesculus-originated coumarin glycoside biosynthetic genes and achieve the de novo synthesis of aesculin in E. coli. Collinearity analysis shows that the collinear BGC segments can be traced back to early-diverging angiosperms, and the essential gene-encoding enzymes necessary for BAT biosynthesis are recruited before the splitting of Aesculus, Acer, and Xanthoceras. These findings provide insight on the evolution of gene clusters associated with medicinal tree metabolites.

Enhancing Centelloside Production in Centella asiatica Hairy Root Lines through Metabolic Engineering of Triterpene Biosynthetic Pathway Early Genes

Centella asiatica is a medicinal plant with a rich tradition of use for its therapeutic properties. Among its bioactive compounds are centellosides, a group of triterpenoid secondary metabolites whose potent pharmacological activities have attracted significant attention. Metabolic engineering has emerged as a powerful biotechnological tool to enhance the production of target compounds. In this study, we explored the effects of overexpressing the squalene synthase (SQS) gene and transcription factor TSAR2 on various aspects of C. asiatica hairy root lines: the expression level of centelloside biosynthetic genes, morphological traits, as well as squalene, phytosterol, and centelloside content. Three distinct categories of transformed lines were obtained: LS, harboring At-SQS; LT, overexpressing TSAR2; and LST, simultaneously carrying both transgenes. These lines displayed noticeable alterations in morphological traits, including changes in branching rate and biomass production. Furthermore, we observed that the expression of T-DNA genes, particularly aux2 and rolC genes, significantly modulated the expression of pivotal genes involved in centelloside biosynthesis. Notably, the LS lines boasted an elevated centelloside content but concurrently displayed reduced phytosterol content, a finding that underscores the intriguing antagonistic relationship between phytosterol and triterpene pathways. Additionally, the inverse correlation between the centelloside content and morphological growth values observed in LS lines was countered by the action of TSAR2 in the LST and LT lines. This difference could be attributed to the simultaneous increase in the phytosterol content in the TSAR2-expressing lines, as these compounds are closely linked to root development. Overall, these discoveries offer valuable information for the biotechnological application of C. asiatica hairy roots and their potential to increase centelloside production.

Discovery of unique CYP716C oxidase involved in pentacyclic triterpene biosynthesis from Camptotheca acuminata

Dozens of triterpenes have been isolated from Camptotheca acuminata, however, triterpene metabolism in this plant remains poorly understood. The common C28 carboxy located in the oleanane-type and ursane-type triterpenes indicates the existence of a functionally active triterpene, C28 oxidase, in this plant. Thorough mining and screening of the CYP716 genes were initiated using the multi-omics database for C. acuminata. Two CYP716A (CYP716A394 and CYP716A395) and three CYP716C (CYP716C80-CYP716C82) were identified based on conserved domain analyses and hierarchical cluster analyses. CYP716 microsomal proteins were prepared and their enzymatic activities were evaluated in vitro. The CYP716 classified into the CYP716C subfamily displays β-amyrin oxidation activity, and CYP716A displays α-amyrin and lupeol oxidation activity, based on gas chromatography-mass spectrometry analyses. The oxidation products were determined based on their mass and nuclear magnetic resonance spectrums. The optimum reaction conditions and kinetic parameters for CYP716C were determined, and functions were verified in Nicotiana benthaminana. Relative quantitative analyses revealed that these CYP716C genes were enriched in the leaves of C. acuminata plantlets after 60 d. These results indicate that CYP716C plays a dominant role in oleanane-type triterpene metabolism in the leaves of C. acuminata via a substrate-specific manner, and CYP716A is responsible for ursane- and lupane-type triterpene metabolism in fruit. This study provides valuable insights into the unique CYP716C-mediated oxidation step of pentacyclic triterpene biosynthesis in C. acuminata.

Construction of a UDP-Arabinose Regeneration System for Efficient Arabinosylation of Pentacyclic Triterpenoids

Glycosylation is an important method of modifying natural products and is usually catalyzed by uridine 5'-diphosphate (UDP)-glycosyltransferase. UDP-β-l-arabinose (UDP-Ara) confers specific functions to natural products such as pentacyclic triterpenoids. However, UDP-arabinosyltransferase with high regioselectivity toward pentacyclic triterpenoids has rarely been reported. In addition, UDP-Ara is mainly biosynthesized from UDP-α-d-glucose (UDP-Glc) through several reaction steps, resulting in the high cost of UDP-Ara. Herein, UGT99D1 was systematically characterized for specifically transferring one moiety of arabinose to the C-3 position of typical pentacyclic triterpenoids. Subsequently, 15 enzymes from plants, mammals, and microorganisms were characterized, and a four-enzyme cascade comprising sucrose synthase, UDP-Glc dehydrogenase, UDP-α-d-glucuronic acid decarboxylase, and UDP-Glc 4-epimerase was constructed to transform sucrose into UDP-Ara with UDP recycling. This system was demonstrated to efficiently produce the arabinosylated derivative (Ara-BA) of typical pentacyclic triterpenoid betulinic acid (BA). Finally, the in vitro cytotoxicity tests indicated that Ara-BA showed much higher anticancer activities than BA. The established arabinosylation platform shows the potential to enhance the pharmacological activity of natural products.

Natural products of pentacyclic triterpenoids: from discovery to heterologous biosynthesis

Covering: up to 2022Pentacyclic triterpenoids are important natural bioactive substances that are widely present in plants and fungi. They have significant medicinal efficacy, play an important role in reducing blood glucose and protecting the liver, and have anti-inflammatory, anti-oxidation, anti-fatigue, anti-viral, and anti-cancer activities. Pentacyclic triterpenoids are derived from the isoprenoid biosynthetic pathway, which generates common precursors of triterpenes and steroids, followed by cyclization with oxidosqualene cyclases (OSCs) and decoration via cytochrome P450 monooxygenases (CYP450s) and glycosyltransferases (GTs). Many biosynthetic pathways of triterpenoid saponins have been elucidated by studying their metabolic regulation network through the use of multiomics and identifying their functional genes. Unfortunately, natural resources of pentacyclic triterpenoids are limited due to their low content in plant tissues and the long growth cycle of plants. Based on the understanding of their biosynthetic pathway and transcriptional regulation, plant bioreactors and microbial cell factories are emerging as alternative means for the synthesis of desired triterpenoid saponins. The rapid development of synthetic biology, metabolic engineering, and fermentation technology has broadened channels for the accumulation of pentacyclic triterpenoid saponins. In this review, we summarize the classification, distribution, structural characteristics, and bioactivity of pentacyclic triterpenoids. We further discuss the biosynthetic pathways of pentacyclic triterpenoids and involved transcriptional regulation. Moreover, the recent progress and characteristics of heterologous biosynthesis in plants and microbial cell factories are discussed comparatively. Finally, we propose potential strategies to improve the accumulation of triterpenoid saponins, thereby providing a guide for their future biomanufacturing.

Structural and functional diversity in plant specialized metabolism signals and products: The case of oxylipins and triterpenes

Metabolic enzymes tend to evolve towards catalytic efficacy, precision and speed. This seems particularly true for ancient and conserved enzymes involved in fundamental cellular processes that are present virtually in every cell and organism and converting and producing relatively limited metabolite numbers. Nevertheless, sessile organisms like plants have an astonishing repertoire of specific (specialized) metabolites that, by numbers and chemical complexity, by far exceed primary metabolites. Most theories agree that early gene duplication, subsequent positive selection and diversifying evolution have allowed relaxed selection of duplicated metabolic genes, thus facilitating the accumulation of mutations that could broaden substrate/product specificity and lower activation barriers and kinetics. Here, we use oxylipins, oxygenated fatty acids of plastidial origin to which the phytohormone jasmonate belongs, and triterpenes, a large group of specialized metabolites whose biosynthesis is often elicited by jasmonates, to showcase the structural and functional diversity of chemical signals and products in plant metabolism.

OeBAS and CYP716C67 catalyze the biosynthesis of health-beneficial triterpenoids in olive (Olea europaea) fruits

The bioactive properties of olive (Olea europaea) fruits and olive oil are largely attributed to terpenoid compounds, including diverse triterpenoids such as oleanolic, maslinic and ursolic acids, erythrodiol, and uvaol. They have applications in the agri-food, cosmetics, and pharmaceutical industries. Some key steps involved in the biosynthesis of these compounds are still unknown. Genome mining, biochemical analysis, and trait association studies have been used to identify major gene candidates controlling triterpenoid content of olive fruits. Here, we identify and functionally characterize an oxidosqualene cyclase (OeBAS) required for the production of the major triterpene scaffold β-amyrin, the precursor of erythrodiol, oleanolic and maslinic acids, and a cytochrome P450 (CYP716C67) that mediates 2α oxidation of the oleanane- and ursane-type triterpene scaffolds to produce maslinic and corosolic acids, respectively. To confirm the enzymatic functions of the entire pathway, we have reconstituted the olive biosynthetic pathway for oleanane- and ursane-type triterpenoids in the heterologous host, Nicotiana benthamiana. Finally, we have identified genetic markers associated with oleanolic and maslinic acid fruit content on the chromosomes carrying the OeBAS and CYP716C67 genes. Our results shed light on the biosynthesis of olive triterpenoids and provide new gene targets for germplasm screening and breeding for high triterpenoid content.

Whole-genome Duplication Reshaped Adaptive Evolution in A Relict Plant Species, Cyclocarya paliurus

Cyclocarya paliurus is a relict plant species that survived the last glacial period and shows a population expansion recently. Its leaves have been traditionally used to treat obesity and diabetes with the well-known active ingredient cyclocaric acid B. Here, we presented three C. paliurus genomes from two diploids with different flower morphs and one haplotype-resolved tetraploid assembly. Comparative genomic analysis revealed two rounds of recent whole-genome duplication events and identified 691 genes with dosage effects that likely contribute to adaptive evolution through enhanced photosynthesis and increased accumulation of triterpenoids. Resequencing analysis of 45 C. paliurus individuals uncovered two bottlenecks, consistent with the known events of environmental changes, and many selectively swept genes involved in critical biological functions, including plant defense and secondary metabolite biosynthesis. We also proposed the biosynthesis pathway of cyclocaric acid B based on multi-omics data and identified key genes, in particular gibberellin-related genes, associated with the heterodichogamy in C. paliurus species. Our study sheds light on evolutionary history of C. paliurus and provides genomic resources to study the medicinal herbs.

A developmental gradient reveals biosynthetic pathways to eukaryotic toxins in monocot geophytes

Numerous eukaryotic toxins that accumulate in geophytic plants are valuable in the clinic, yet their biosynthetic pathways have remained elusive. A lead example is the >150 Amaryllidaceae alkaloids (AmAs) including galantamine, an FDA-approved treatment for Alzheimer's disease. We show that while AmAs accumulate to high levels in many tissues in daffodils, biosynthesis is localized to nascent, growing tissue at the base of leaves. A similar trend is found for the production of steroidal alkaloids (e.g. cyclopamine) in corn lily. This model of active biosynthesis enabled elucidation of a complete set of biosynthetic genes for the production of AmAs. Taken together, our work sheds light on the developmental and enzymatic logic of diverse alkaloid biosynthesis in daffodil. More broadly, it suggests a paradigm for biosynthesis regulation in monocot geophytes where plants are protected from herbivory through active charging of newly formed cells with eukaryotic toxins that persist as aboveground tissue develops.

Elucidation of the pathway for biosynthesis of saponin adjuvants from the soapbark tree

The Chilean soapbark tree (Quillaja saponaria) produces soap-like molecules called QS saponins that are important vaccine adjuvants. These highly valuable compounds are sourced by extraction from the bark, and their biosynthetic pathway is unknown. Here, we sequenced the Q. saponaria genome. Through genome mining and combinatorial expression in tobacco, we identified 16 pathway enzymes that together enable the production of advanced QS pathway intermediates that represent a bridgehead for adjuvant bioengineering. We further identified the enzymes needed to make QS-7, a saponin with excellent therapeutic properties and low toxicity that is present in low abundance in Q. saponaria bark extract. Our results enable the production of Q. saponaria vaccine adjuvants in tobacco and open the way for new routes to access and engineer natural and new-to-nature immunostimulants.

Cytochrome P450s in plant terpenoid biosynthesis: discovery, characterization and metabolic engineering

As the largest family of natural products, terpenoids play valuable roles in medicine, agriculture, cosmetics and food. However, the traditional methods that rely on direct extraction from the original plants not only produce low yields, but also result in waste of resources, and are not applicable at all to endangered species. Modern heterologous biosynthesis is considered a promising, efficient, and sustainable production method, but it relies on the premise of a complete analysis of the biosynthetic pathway of terpenoids, especially the functionalization processes involving downstream cytochrome P450s. In this review, we systematically introduce the biotech approaches used to discover and characterize plant terpenoid-related P450s in recent years. In addition, we propose corresponding metabolic engineering approaches to increase the effective expression of P450 and improve the yield of terpenoids, and also elaborate on metabolic engineering strategies and examples of heterologous biosynthesis of terpenoids in Saccharomyces cerevisiae and plant hosts. Finally, we provide perspectives for the biotech approaches to be developed for future research on terpenoid-related P450.

Biosynthesis of mushroom-derived type II ganoderic acids by engineered yeast

Type II ganoderic acids (GAs) produced by the traditional medicinal mushroom Ganoderma are a group of triterpenoids with superior biological activities. However, challenges in the genetic manipulation of the native producer, low level of accumulation in the farmed mushroom, the vulnerabilities of the farming-based supply chain, and the elusive biosynthetic pathway have hindered the efficient production of type II GAs. Here, we assemble the genome of type II GAs accumulating G. lucidum accession, screen cytochrome P450 enzymes (CYPs) identified from G. lucidum in baker's yeast, identify key missing CYPs involved in type II GAs biosynthesis, and investigate the catalytic reaction sequence of a promiscuous CYP. Then, we engineer baker's yeast for bioproduciton of GA-Y (3) and GA-Jb (4) and achieve their production at higher level than those from the farmed mushroom. Our findings facilitate the further deconvolution of the complex GA biosynthetic network and the development of microbial cell factories for producing GAs at commercial scale.

By-Product of the Red Ginseng Manufacturing Process as Potential Material for Use as Cosmetics: Chemical Profiling and In Vitro Antioxidant and Whitening Activities

Red ginseng (RG), which is obtained from heated Panax ginseng and is produced by steaming followed by drying, is a valuable herb in Asian countries. Steamed ginseng dew (SGD) is a by-product produced in processing red ginseng. In the present study, phytochemical profiling of extracts of red ginseng and steamed ginseng dew was carried out using gas chromatography-mass spectrometry (GC-MS) and rapid resolution liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (RRLC-Q-TOF-MS) analysis. Additionally, antioxidant activities (DPPH, ·OH, and ABTS scavenging ability) and whitening activities (tyrosinase and elastase inhibitory activity) were analyzed. Phytochemical profiling revealed the presence of 66 and 28 compounds that were non-saponin components in chloroform extracts of red ginseng and steamed ginseng dew (RG-CE and SGD-CE), respectively. Meanwhile, there were 20 ginsenosides identified in n-butanol extracts of red ginseng and steamed ginseng dew (RG-NBE and SGD-NBE). By comparing the different polar extracts of red ginseng and steamed ginseng dew, it was found that the ethyl acetate extract of red ginseng (RG-EAE) had the best antioxidant capacity and whitening effect, the water extract of steamed ginseng dew (SGD-WE) had stronger antioxidant capacity, and the SGD-NBE and SGD-CE had a better whitening effect. This study shows that RG and SGD have tremendous potential to be used in the cosmetic industries.

Engineering medicinal plant-derived CYPs: a promising strategy for production of high-valued secondary metabolites

Cytochorme P450s (CYPs) play a critical role in the catalysis of secondary metabolite biosynthetic pathways. For their commercial use, various strategies for metabolic pathway engineering using CYP as a potential target have been explored. Plants produce a vast diversity of secondary metabolites which are being used to treat various ailments and diseases. Some of these metabolites are difficult to obtain in large quantities limiting their industrial use. Cytochrome P450 enzymes (CYPs) are important catalysts in the biosynthesis of highly valued secondary metabolites, and are found in all domains of life. With the development of high-throughput sequencing and high-resolution mass spectrometry, new biosynthetic pathways and associated CYPs are being identified. In this review, we present CYPs identified from medicinal plants as a potential game changer in the metabolic engineering of secondary metabolic pathways. We present the achievements made so far in enhancing the production of important bioactivities through pathway engineering, giving some popular examples. At last, current challenges and possible strategies to overcome the limitations associated with CYP engineering to enhance the biosynthesis of target secondary metabolites are also highlighted.

Plant Specialised Glycosides (PSGs): their biosynthetic enzymatic machinery, physiological functions and commercial potential

Plants, the primary producers of our planet, have evolved from simple aquatic life to very complex terrestrial habitat. This habitat transition coincides with evolution of enormous chemical diversity, collectively termed as 'Plant Specialised Metabolisms (PSMs)', to cope the environmental challenges. Plant glycosylation is an important process of metabolic diversification of PSMs to govern their in planta stability, solubility and inter/intra-cellular transport. Although, individual category of PSMs (terpenoids, phenylpropanoids, flavonoids, saponins, alkaloids, phytohormones, glucosinolates and cyanogenic glycosides) have been well studied; nevertheless, deeper insights of physiological functioning and genomic aspects of plant glycosylation/deglycosylation processes including enzymatic machinery (CYPs, GTs, and GHs) and regulatory elements are still elusive. Therefore, this review discussed the paradigm shift on genomic background of enzymatic machinery, transporters and regulatory mechanism of 'Plant Specialised Glycosides (PSGs)'. Current efforts also update the fundamental understanding about physiological, evolutionary and adaptive role of glycosylation/deglycosylation processes during the metabolic diversification of PSGs. Additionally, futuristic considerations and recommendations for employing integrated next-generation multi-omics (genomics, transcriptomics, proteomics and metabolomics), including gene/genome editing (CRISPR-Cas) approaches are also proposed to explore commercial potential of PSGs.

Cytochrome P450 monooxygenase-mediated tailoring of triterpenoids and steroids in plants

The cytochrome P450 monooxygenase (CYP) superfamily comprises hemethiolate enzymes that perform remarkable regio- and stereospecific oxidative chemistry. As such, CYPs are key agents for the structural and functional tailoring of triterpenoids, one of the largest classes of plant natural products with widespread applications in pharmaceuticals, food, cosmetics, and agricultural industries. In this review, we provide a full overview of 149 functionally characterised CYPs involved in the biosynthesis of triterpenoids and steroids in primary as well as in specialised metabolism. We describe the phylogenetic distribution of triterpenoid- and steroid-modifying CYPs across the plant CYPome, present a structure-based summary of their reactions, and highlight recent examples of particular interest to the field. Our review therefore provides a comprehensive up-to-date picture of CYPs involved in the biosynthesis of triterpenoids and steroids in plants as a starting point for future research.

The chromosome-level holly (Ilex latifolia) genome reveals key enzymes in triterpenoid saponin biosynthesis and fruit color change

The Ilex L. (hollies) genus of Aquifoliaceae shows high species diversity in tropical and subtropical regions of Asia and South America. Throughout the range of the genus, Ilex species have been widely used in beverage and medicine production and as ornamentals. Here, we assembled a high-quality, chromosome-level genome of Ilex latifolia, which has extremely high economic value because of its useful secondary metabolite production and the high ornamental value of its decorative red berries. The 99.8% genome sequence was anchored to 20 pseudochromosomes, with a total length of 766.02 Mb and a scaffold N50 of 33.45 Mb. Based on the comparative genomic analysis of 14 angiosperm species, we recovered I. latifolia as the sister group to all other campanulids. Two whole-genome duplication (WGD) events were identified in hollies: one shared ancient WGD in the ancestor of all eudicots and a recent and independent WGD in hollies. We performed a genome-wide search to screen candidate genes involved in the biosynthesis of pentacyclic triterpenoid saponins in I. latifolia. Three subfamilies of CYP450 (CYP71A, CYP72A, and CYP716A) appear to have expanded. The transcriptomic analysis of I. latifolia leaves at five developmental stages revealed that two CYP716A genes and one CYP72A gene probably play important roles in this biosynthetic pathway. In addition, we totally identified 12 genes in the biosynthesis pathways of pelargonidin and cyanidin and observed their differential expression in green and red fruit pericarps, suggesting an association between pelargonidin and cyanidin biosynthesis and fruit pericarp color change. The accumulation of pelargonidin and cyanidin is expected to play an important role in the ornamental value of I. latifolia. Altogether, this study elucidated the molecular basis of the medicinal and ornamental value of I. latifolia, providing a data basis and promising clues for further applications.

Identification of key amino acid residues toward improving the catalytic activity and substrate specificity of plant-derived cytochrome P450 monooxygenases CYP716A subfamily enzyme for triterpenoid production in Saccharomyces cerevisiae

Triterpenoids constitute a group of specialized plant metabolites with wide structural diversity and high therapeutic value for human health. Cytochrome P450 monooxygenases (CYP) are a family of enzymes important for generating the structural diversity of triterpenoids by catalyzing the site-specific oxidization of the triterpene backbone. The CYP716 enzyme family has been isolated from various plant families as triterpenoid oxidases; however, their experimental crystal structures are not yet available and the detailed catalytic mechanism remains elusive. Here, we address this challenge by integrating bioinformatics approaches with data from other CYP families. Medicago truncatula CYP716A12, the first functionally characterized CYP716A subfamily enzyme, was chosen as the model for this study. We performed homology modeling, structural alignment, in silico site-directed mutagenesis, and molecular docking analysis to search and screen key amino acid residues relevant to the catalytic activity and substrate specificity of the CYP716A subfamily enzyme in triterpenoid biosynthesis. An in vivo functional analysis using engineered yeast that endogenously produced plant-derived triterpenes was performed to elucidate the results. When the amino acids in the signature region and substrate recognition sites (SRSs) were substituted, the product profile of CYP716A12 was modified. We identified amino acid residues that control the substrate contraction of the enzyme (D292) and engineered the enzyme to improve its catalytic activity and substrate specificity (D122, I212, and Q358) for triterpenoid biosynthesis. In addition, we demonstrated the versatility of this strategy by changing the properties of key residues in SRSs to improve the catalytic activity of Arabidopsis thaliana CYP716A1 (S356) and CYP716A2 (M206, F210) at C-28 on the triterpene backbone. This research has the potential to help in the production of desired triterpenoids in engineered yeast by increasing the catalytic activity and substrate specificity of plant CYP716A subfamily enzymes.

Heterologous Expression of Three Transcription Factors Differently Regulated Astragalosides Metabolic Biosynthesis in Astragalus membranaceus Hairy Roots

Astragalus membranaceus has been used as a highly popular Chinese herbal medicine for centuries. Triterpenoids, namely astragalosides I, II, III, and IV, represent the main active compounds in this plant species. Transcription factors have a powerful effect on metabolite biosynthesis in plants. We investigated the effect of the Arabidopsis MYB12, production of anthocyanin pigment 1 (PAP1), and maize leaf color (LC) transcription factors in regulating the synthesis of astragaloside metabolites in A. membranaceus. Overexpression of these transcription factors in hairy roots differentially up-regulated these active compounds. Specifically, the overexpression of LC resulted in the accumulation of astragalosides I–IV. The content of astragalosides I and IV were, in particular, more highly accumulated. Overexpression of MYB12 increased the accumulation of astragaloside I in transgenic hairy roots, followed by astragaloside IV, and overexpression of PAP1 resulted in the increased synthesis of astragalosides I and IV. In addition, we found that overexpression of PAP1 together with LC increased astragaloside III levels. At the transcriptional level, several key genes of the mevalonate biosynthetic pathway, especially HMGR1, HMGR2, and HMGR3, were up-regulated differentially in response to these transcription factors, resulting in astragaloside synthesis in the hairy roots of A. membranaceus. Overall, our results indicated that heterologous expression of Arabidopsis MYB12, PAP1, and maize LC differentially affected triterpenoids biosynthesis, leading to the increased biosynthesis of active compounds in A. membranaceus.

Metabolome and Transcriptome Analysis Reveals the Transcriptional Regulatory Mechanism of Triterpenoid Saponin Biosynthesis in Soapberry (Sapindus mukorossi Gaertn.)

Soapberry (Sapindus mukorossi Gaertn.) pericarps are rich in valuable bioactive triterpenoid saponins. However, the saponin content dynamics and the molecular regulatory network of saponin biosynthesis in soapberry pericarps remain largely unclear. Here, we performed combined metabolite profiling and transcriptome analysis to identify saponin accumulation kinetic patterns, investigate gene networks, and characterize key candidate genes and transcription factors (TFs) involved in saponin biosynthesis in soapberry pericarps. A total of 54 saponins were tentatively identified, including 25 that were differentially accumulated. Furthermore, 49 genes putatively involved in sapogenin backbone biosynthesis and some candidate genes assumed to be responsible for the backbone modification, including 41 cytochrome P450s and 45 glycosyltransferases, were identified. Saponin-specific clusters/modules were identified by Mfuzz clustering and weighted gene coexpression network analysis, and one TF-gene regulatory network underlying saponin biosynthesis was proposed. The results of yeast one-hybrid assay and electrophoretic mobility shift assay suggested that SmbHLH2, SmTCP4, and SmWRKY27 may play important roles in the triterpenoid saponin biosynthesis by directly regulating the transcription of SmCYP71D-3 in the soapberry pericarp. Overall, these findings provide valuable information for understanding the molecular regulatory mechanism of saponin biosynthesis, enriching the gene resources, and guiding further research on triterpenoid saponin accumulation in soapberry pericarps.

Whole-Genome Identification and Analysis of Multiple Gene Families Reveal Candidate Genes for Theasaponin Biosynthesis in Camellia oleifera

Camellia oleifera is an economically important oilseed tree. Seed meals of C. oleifera have a long history of use as biocontrol agents in shrimp farming and as cleaning agents in peoples’ daily lives due to the presence of theasaponins, the triterpene saponins from the genus Camellia. To characterize the biosynthetic pathway of theasaponins in C. oleifera, members of gene families involved in triterpenoid biosynthetic pathways were identified and subjected to phylogenetic analysis with corresponding members in Arabidopsis thaliana, Camellia sinensis, Actinidia chinensis, Panax ginseng, and Medicago truncatula. In total, 143 triterpenoid backbone biosynthetic genes, 1169 CYP450s, and 1019 UGTs were identified in C. oleifera. The expression profiles of triterpenoid backbone biosynthetic genes were analyzed in different tissue and seed developmental stages of C. oleifera. The results suggested that MVA is the main pathway for triterpenoid backbone biosynthesis. Moreover, the candidate genes for theasaponin biosynthesis were identified by WGCNA and qRT-PCR analysis; these included 11 CYP450s, 14 UGTs, and eight transcription factors. Our results provide valuable information for further research investigating the biosynthetic and regulatory network of theasaponins.

Chromosome-level genome of Entada phaseoloides provides insights into genome evolution and triterpenoid saponins biosynthesis

As a medicinal herbal plant, Entada phaseoloides has high levels of secondary metabolites, particularly triterpenoid saponins, which are important resources for scientific research and medical applications. However, the lack of a reference genome for this genus has limited research on its evolution and utilization of its medicinal potential. In this study, we report a chromosome-scale genome assembly for E. phaseoloides using Illumina, Nanopore long reads, and high-throughput chromosome conformation capture technology. The assembled reference genome is 456.18 Mb (scaffold N50=30.9 Mb; contig N50=6.34 Mb) with 95.71 % of the sequences anchored onto 14 pseudochromosomes. E. phaseoloides was estimated to diverge from the Leguminosae lineage at approximately 72.0 million years ago. With the integration of transcriptomic and metabolomic data, gene expression patterns and metabolite profiling of E. phaseoloides were determined in different tissues. The pattern of gene expression and metabolic profile of the kernel were distinct from those of other tissues. Furthermore, the evolution of certain gene families involved in the biosynthesis of triterpenoid saponins and terpenes was analyzed and offer new insights into the formation of these two metabolites. Four CYP genes, one UGT gene and related transcription factors were identified as candidate genes contributing to regulation of triterpenoid saponins biosynthesis. As the first high-quality assembled reference genome in the genus Entada, it will not only provide new information for the evolutionary study of this genus and conservation biology of E. phaseoloides but also lay a foundation for the formation and utilization of secondary metabolites in medicinal plants.

Engineering of Yarrowia lipolytica for the production of plant triterpenoids: Asiatic, madecassic, and arjunolic acids

Several plant triterpenoids have valuable pharmaceutical properties, but their production and usage is limited since extraction from plants can burden natural resources, and result in low yields and purity. Here, we engineered oleaginous yeast Yarrowia lipolytica to produce three valuable plant triterpenoids (asiatic, madecassic, and arjunolic acids) by fermentation. First, we established the recombinant production of precursors, ursolic and oleanolic acids, by expressing plant enzymes in free or fused versions in a Y. lipolytica strain previously optimized for squalene production. Engineered strains produced up to 11.6 mg/g DCW ursolic acid or 10.2 mg/g DCW oleanolic acid. The biosynthetic pathway from ursolic acid was extended by expressing the Centella asiatica cytochrome P450 monoxygenases CaCYP716C11p, CaCYP714E19p, and CaCYP716E41p, resulting in the production of trace amounts of asiatic acid and 0.12 mg/g DCW madecassic acid. Expressing the same C. asiatica cytochromes P450 in oleanolic acid-producing strain resulted in the production of oleanane triterpenoids. Expression of CaCYP716C11p in the oleanolic acid-producing strain yielded 8.9 mg/g DCW maslinic acid. Further expression of a codon-optimized CaCYP714E19p resulted in 4.4 mg/g DCW arjunolic acid. Lastly, arjunolic acid production was increased to 9.1 mg/g DCW by swapping the N-terminal domain of CaCYP714E19p with the N-terminal domain from a Kalopanax septemlobus cytochrome P450. In summary, we have demonstrated the production of asiatic, madecassic, and arjunolic acids in a microbial cell factory. The strains and fermentation processes need to be further improved before the production of these molecules by fermentation can be industrialized.

Assessment of major centelloside ratios in Centella asiatica accessions grown under identical ecological conditions, bioconversion clues and identification of elite lines

Centellosides viz., asiatic acid, madecassic acid, asiaticoside, madecassoside, are the major bioactive molecules in Centella asiatica. In this study madecassic acid:asiatic acid, madecassoside:asiaticoside (C6-hydroxylation versus non-hydroxylation) and asiaticoside:asiatic acid, madecassoside:madecassic acid (C28-glycoside versus aglycone) ratios in 50 C. asiatica accessions originally collected from their natural habitats in south India and grown under identical ecological conditions for six generations were determined using validated HPTLC-densitometry protocols. Asiatic acid, madecassic acid, asiaticoside and madecassoside contents ranged from 0.00-0.29% (average 0.03 ± 0.06%; 28 accessions recorded asiatic acid content as zero), 0.02-0.72% (0.12 ± 0.13%), 0.04-2.41% (0.44 ± 0.52%) and 0.15-5.27% (1.59 ± 1.26%), respectively. Distinctly, C6-hydroxylated (madecassic acid:asiatic acid 4.00, madecassoside:asiaticoside 3.61) and C28-glycosylated (asiaticoside:asiatic acid 14.67, madecassoside: madecassic acid 13.25) centellosides dominated over the respective non-derivatized entities. Our results infer that both C6-hydroxylation by CYP450-dependent monooxygenases and C28-glycosylation by UDP-Glc glucosyltransferases are dominant bioconversion steps in C. asiatica. Besides, this study discovered six elite lines of C. asiatica, with their (asiaticoside + madecassoside) contents above the industrial benchmark (≥ 4%) from south India. Two elite clones with asiaticoside contents ≥ 2% were also identified. Standardization of the agrotechniques of these elite lines could lead to their industrial applications. Further, this study emphasizes the need for standardizing all four centellosides as biomarkers in C. asiatica raw drugs, pharmaceutical and cosmetic products.

Genome-wide transcriptome analysis and characterization of the cytochrome P450 flavonoid biosynthesis genes in pigeon pea (Cajanus cajan)

226 CcCYP450 genes were identified at the genomic level and were classified into 45 clades based on phylogenetic analysis. CcCYP75B165 gene was found that might play important roles in the biosynthesis of flavonoids in pigeon pea, and was significantly induced by methyl jasmonate (MeJA). The cytochrome P450 mono-oxygenase (CYP450) superfamily plays a key role in the flavonoid biosynthesis pathway and resists different kinds of stresses. Several CYP450 genes have been identified to be involved in the biosynthesis of crop protection agents. However, the CcCYP450 genes from pigeon pea have not been identified. Here, 226 CcCYP450 genes were identified at the genomic level by analysing the gene structure, distribution on chromosomes, gene duplication, and conserved motifs and were classified into 45 clades based on phylogenetic analysis. RNA-seq analysis revealed clear details of CcCYP450 genes that varied with time of MeJA (methyl jasmonate) induction. Among them, six CcCYP450 subfamily genes were found that might play important roles in the biosynthesis of flavonoids in pigeon pea. The overexpression of CcCYP75B165 in pigeon pea significantly induced the accumulation of genistin and downregulated the contents of cajaninstilbene acid, apigenin, isovitexin, and genistein and the expression of flavonoid synthase genes. This study provides theoretical guidance and plant genetic resources for cultivating new pigeon pea varieties with high flavonoid contents and exploring the molecular mechanisms of the biosynthesis of flavonoids under MeJA treatment.

Chromosomal level genome of Ilex asprella and insight into antiviral triterpenoid pathway

Ilex asprella is a widely used herbs in Traditional Chinese Medicine for treating viral infection and relieving inflammation. Due to the earlier fruiting period of I. asprella, it is the major food source for frugivores in summer. Despite its pharmacological and ecological importance, a reference genome for I. asprella is lacking. By using Illumina, stLFR and Omni-C sequencing data, we present the first chromosomal-level assembly for I. asprella. The genome assembly size is 804 Mbp, with Benchmarking Universal Single-Copy Orthologs (BUSCO) score 94.4% for eudicotyledon single copy genes. Transcriptomes of leaves, stems, flowers, premature fruits and roots were analyzed, providing 39,215 gene models. The complete set of genes involved in the triterpenoids production is disclosed for the first time. We have also found the oxidosqualene cyclases (OSCs), CYP716s and UDP-glycosyltransferases (UGTs), which are responsible for the modification of triterpenoid backbones, resulting in the high variety of triterpenoid saponins.

Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax

All extant core-eudicot plants share a common ancestral genome that has experienced cyclic polyploidizations and (re)diploidizations. Reshuffling of the ancestral core-eudicot genome generates abundant genomic diversity, but the role of this diversity in shaping the hierarchical genome architecture, such as chromatin topology and gene expression, remains poorly understood. Here, we assemble chromosome-level genomes of one diploid and three tetraploid Panax species and conduct in-depth comparative genomic and epigenomic analyses. We show that chromosomal interactions within each duplicated ancestral chromosome largely maintain in extant Panax species, albeit experiencing ca. 100–150 million years of evolution from a shared ancestor. Biased genetic fractionation and epigenetic regulation divergence during polyploidization/(re)diploidization processes generate remarkable biochemical diversity of secondary metabolites in the Panax genus. Our study provides a paleo-polyploidization perspective of how reshuffling of the ancestral core-eudicot genome leads to a highly dynamic genome and to the metabolic diversification of extant eudicot plants.

The role of polyploidization generated genomic diversity in shaping the hierarchical genome architecture remains unclear. Here, the authors show that repatterning of the ancestral eudicot genome has resulted in multi-dimensional genome plasticity and secondary metabolite diversification via comparisons of Panax genomes.

De Novo Biosynthesis of Oleanane-Type Ginsenosides in Saccharomyces cerevisiae Using Two Types of Glycosyltransferases from Panax ginseng

Oleanane-type ginsenosides are highly biologically active substances in Panax ginseng, a popular Chinese dietary plant. Lack of key enzymes for glycosylation reactions has hindered de novo synthesis of these bioactive molecules. We mined candidate glycosyltransferases (GTs) of the ginseng database by combining key metabolites and transcriptome coexpression analyses and verified their function using in vitro enzymatic assays. The PgCSyGT1, a cellulose synthase-like GT rather than a UDP-dependent glucuronosyltransferase (UGT), was verified as the key enzyme for transferring a glucuronosyl moiety to the free C3-OH of oleanolic acid to synthesize calenduloside E. Two UGTs (PgUGT18 and PgUGT8) were first identified as, respectively, catalyzing the glycosylation reaction of the second sugar moiety of C3 and the C28 in the oleanane-type ginsenoside biosynthetic pathway. Then, we integrated these GTs in combinations into Saccharomyces cerevisiae genome and realized de novo biosynthesis of oleanane-type ginsenosides with a yield of 1.41 μg/L ginsenoside Ro in shake flasks. This report provides a basis for effective biosynthesis of diverse oleanane-type ginsenosides in microbial cell factories.

CRISPR-Cas system in microbial hosts for terpenoid production

Terpenoids represent the largest group of secondary metabolites with variable structures and functions. Terpenoids are well known for their beneficial application in human life, such as pharmaceutical products, vitamins, hormones, anticancer drugs, cosmetics, flavors and fragrances, foods, agriculture, and biofuels. Recently, engineering microbial cells have been provided with a sustainable approach to produce terpenoids with high yields. Noticeably, the clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) system has emerged as one of the most efficient genome-editing technologies to engineer microorganisms for improving terpenoid production. In this review, we summarize the application of the CRISPR-Cas system for the production of terpenoids in microbial hosts such as Escherichia coli, Saccharomyces cerevisiae, Corynebacterium glutamicum, and Pseudomonas putida. CRISPR-Cas9 deactivated Cas9 (dCas9)-based CRISPR (CRISPRi), and the dCas9-based activator (CRISPRa) have been used in either individual or combinatorial systems to control the metabolic flux for enhancing the production of terpenoids. Finally, the prospects of using the CRISPR-Cas system in terpenoid production are also discussed.

High-yield bioactive triterpenoid production by heterologous expression in Nicotiana benthamiana using the Tsukuba system

Oleanolic acid is a pentacyclic triterpenoid found in numerous plant species and is a precursor to several bioactive triterpenoids with commercial potential. However, oleanolic acid accumulates at low levels in plants, and its chemical synthesis is challenging. Here, we established a method for producing oleanolic acid in substantial quantities via heterologous expression of pathway enzymes in Nicotiana benthamiana. The "Tsukuba system" is one of the most efficient agroinfiltration-based transient protein expression systems using the vector pBYR2HS, which contains geminiviral replication machinery and a double terminator for boosting expression. Additionally, the pBYR2HS vector contains an expression cassette for the gene-silencing suppressor p19 protein from tomato bushy stunt virus, which can also contribute to enhancing the expression of target proteins. In this study, we evaluated the applicability of this system to heterologous triterpenoid production in N. benthamiana. Medicago truncatula cytochrome P450 monooxygenase (CYP) 716A12 is the first enzyme to be functionally characterized as β-amyrin C-28 oxidase producing oleanolic acid. A mutant CYP716A12 (D122Q) with improved catalytic activity engineered in our previous study was co-expressed with other enzymes in N. benthamiana leaves. Using pBYR2HS, oleanolic acid yield was increased 13.1-fold compared with that using the conventional binary vector, indicating the advantage of the Tsukuba system. We also demonstrated the efficacy of co-expressing a mutant Arabidopsis thaliana HMGR1 catalytic domain, additional NADPH-cytochrome P450 reductase (CPR) transferring electrons to heterologous CYPs, and application of ascorbic acid for preventing leaf necrosis after agroinfiltration, to improve product yield. As a result, the product yields of both simple (β-amyrin) and oxidized (oleanolic acid and maslinic acid) triterpenoids were significantly improved compared with the previously reported yield in heterologous triterpenoid production in N. benthamiana leaves.

Transcriptome and metabolome analysis to reveal major genes of saikosaponin biosynthesis in Bupleurum chinense

BACKGROUND

Bupleurum chinense DC. is a widely used traditional Chinese medicinal plant. Saikosaponins are the major bioactive constituents of B. chinense, but relatively little is known about saikosaponin biosynthesis. In the present study, we performed an integrated analysis of metabolic composition and the expressed genes involved in saikosaponin biosynthetic pathways among four organs (the root, flower, stem, and leaf) of B. chinense to discover the genes related to the saikosaponin biosynthetic pathway.

RESULTS

Transcript and metabolite profiles were generated through high-throughput RNA-sequencing (RNA-seq) data analysis and liquid chromatography tandem mass spectrometry, respectively. Evaluation of saikosaponin contents and transcriptional changes showed 152 strong correlations (P < 0.05) over 3 compounds and 77 unigenes. These unigenes belonged to eight gene families: the acetoacetyl CoA transferase (AACT) (6), HMG-CoA synthase (HMGS) (2), HMG-CoA reductase (HMGR) (2), mevalonate diphosphate decarboxylase (MVD) (1), 1-deoxy-D-xylulose-5-phosphate synthase (DXS) (3), farnesyl diphosphate synthase (FPPS) (11), β-amyrin synthase (β-AS) (13) and cytochrome P450 enzymes (P450s) (39) families.

CONCLUSIONS

Our results investigated the diversity of the saikosaponin triterpene biosynthetic pathway in the roots, stems, leaves and flowers of B. chinese by integrated transcriptomic and metabolomic analysis, implying that manipulation of P450s genes such as Bc95697 and Bc35434 might improve saikosaponin biosynthesis. This is a good candidate for the genetic improvement of this important medicinal plant.

Advances in production and structural derivatization of the promising molecule ursolic acid

Ursolic acid (UA) is a ursane-type pentacyclic triterpenoid compound, naturally produced in plants via specialized metabolism and exhibits vast range of remarkable physiological activities and pharmacological manifestations. Owing to significant safety and efficacy in different medical conditions, UA may serve as a backbone to produce its derivatives with novel therapeutic functions. This review aims to provide ideas for exploring more diverse structures to improve UA pharmacological activity and increasing its biological yield to meet the industrial requirements by systematically reviewing the current research progress of UA. We first provides an overview of the pharmacological activities, acquisition methods and structural modifications of UA. Among them, we focused on the synthetic modifications of UA to yield valuable derivatives with enhanced therapeutic potential. Furthermore, harnessing the essential advances for green synthesis of UA and its derivatives by advent of metabolic engineering and synthetic biology are of great concern. In this regard, all pivotal advances for enhancing the production of UA have been discussed. In combination with the advantages of UA biosynthesis and transformation strategy, large-scale microbial production of UA is a promising platform for further exploration.

Immunostimulatory 6/6/6/6 Tetracyclic Triterpenoid Saponins with the Methyl-30 Incorporated Cyclization from the Root of Colquhounia elegans

Two novel triterpenoid saponins, colqueleganoids A (1) and B (2), with the first methyl-30 incorporated 6/6/6/6-cyclized carbon skeleton (named colquelegane), were isolated from the root of Colquhounia elegans. Their structures including absolute configuration were determined by spectroscopic methods and X-ray crystallographic analyses. Interestingly, both compounds significantly enhanced TNF-α production and 1 also increased the IL-6 production in RAW264.7 macrophages stimulated with lipopolysaccharide (LPS), suggesting their potential application as immunostimulants in immunotherapy and vaccination.

Cytochrome P450 catalyses the 29-carboxyl group formation of celastrol

Celastrol, a potent anticancer and anti-obesity drug, was first isolated from Tripterygium wilfordii Hook. f. and it is produced in small quantities in many members of the Celastraceae family. The heterologous reconstitution of celastrol biosynthesis could be a promising method for the efficient production of celastrol and natural and unnatural derivatives thereof, yet only part of the biosynthetic pathway is known. Here, we report a cytochrome P450 monooxygenase (TwCYP712K1) from T. wilfordii that performs the three-step oxidation of friedelin to polpunonic acid in the celastrol pathway. Heterologous expression of TwCYP712K1 showed that TwCYP712K1 catalyses not only the transformation of friedelin to polpunonic acid but also the oxidation of β-amyrin or α-amyrin. The role of TwCYP712K1 in the biosynthesis of celastrol was further revealed via RNA interference. Some key residues of TwCYP712K1 were also screened by molecular docking and site-directed mutagenesis. Our results lay a solid foundation for further elucidating the biosynthesis of celastrol and related triterpenoids.

BAHD acetyltransferase contributes to wound-induced biosynthesis of oleo-gum resin triterpenes in Boswellia

Triterpenes (30-carbon isoprene compounds) represent a large and highly diverse class of natural products that play various physiological functions in plants. The triterpene biosynthetic enzymes, particularly those catalyzing the late-stage regio-selective modifications are not well characterized. The bark of select Boswellia trees, e.g., B. serrata exudes specialized oleo-gum resin in response to wounding, which is enriched with boswellic acids (BAs), a unique class of C3α-epimeric pentacyclic triterpenes with medicinal properties. The bark possesses a network of resin secretory structures comprised of vertical and horizontal resin canals, and amount of BAs in bark increases considerably in response to wounding. To investigate BA biosynthetic enzymes, we conducted tissue-specific transcriptome profiling and identified a wound-responsive BAHD acetyltransferase (BsAT1) of B. serrata catalyzing the late-stage C3α-O-acetylation reactions in the BA biosynthetic pathway. BsAT1 catalyzed C3α-O-acetylation of αBA, βBA, and 11-keto-βBA in vitro and in planta assays to produce all the major C3α-O-acetyl-BAs (3-acetyl-αBA, 3-acetyl-βBA, and 3-acetyl-11-keto-βBA) found in B. serrata bark and oleo-gum resin. BsAT1 showed strict specificity for BA scaffold, whereas it did not acetylate the more common C3β-epimeric pentacyclic triterpenes. The analysis of steady-state kinetics using various BAs revealed distinct substrate affinity and catalytic efficiency. BsAT1 transcript expression coincides with increased levels of C3α-O-acetyl-BAs in bark in response to wounding, suggesting a role of BsAT1 in wound-induced biosynthesis of C3α-O-acetyl-BAs. Overall, the results provide new insights into the biosynthesis of principal chemical constituents of Boswellia oleo-gum resin.