Versatile CYP98A enzymes catalyse meta-hydroxylation reveals diversity of salvianolic acids biosynthesis

Ecotype-specific phenolic acid accumulation and root softness in Salvia miltiorrhiza are driven by environmental and genetic factors

Salvia miltiorrhiza Bunge, a renowned medicinal herb in traditional Chinese medicine, displays distinctive root texture and high phenolic acid content, traits influenced by genetic and environmental factors. However, the underlying regulatory networks remain unclear. Here, we performed multi-omics analyses on ecotypes from four major Chinese regions, focusing on environmental impacts on root structure, phenolic acid accumulation and lignin composition. Lower temperatures and increased UV-B radiation were associated with elevated rosmarinic acid (RA) and salvianolic acid B (SAB) levels, particularly in the Sichuan ecotype. Structural models indicated that the radial arrangement of xylem conduits contributes to greater root hardness. Genomic assembly and comparative analysis of the Sichuan ecotype revealed a unique phenolic acid metabolism gene cluster, including SmWRKY40, a WRKY transcription factor essential for RA and SAB biosynthesis. Overexpression of SmWRKY40 enhanced phenolic acid levels and lignin content, whereas its knockout reduced root hardness. Integrating high-throughput (DNA affinity purification sequencing) and point-to-point (Yeast One-Hybrid, Dual-Luciferase and Electrophoretic Mobility Shift Assay) protein-DNA interaction detection platform further identified SmWRKY40 binding sites across ecotypes, revealing specific regulatory networks. Our findings provide insights into the molecular basis of root texture and bioactive compound accumulation, advancing breeding strategies for quality improvement in S. miltiorrhiza.

CYP98A monooxygenases: a key enzyme family in plant phenolic compound biosynthesis

Phenolic compounds are derived from the phenylpropanoid metabolic pathways of plants and include phenylpropionic acids, lignins, coumarins, and flavonoids. These compounds are among the most abundant and diverse classes of secondary metabolites found throughout the plant kingdom. Phenolic compounds play critical roles in the growth, development, and stress resistance of horticultural plants. Moreover, some phenolic compounds exhibit substantial biological activities, and they are widely utilized across various sectors, such as the pharmaceutical and food industries. The cytochrome P450 monooxygenase 98A subfamily (CYP98A) is involved mainly in the biosynthesis of phenolic compounds, mediating the meta-hydroxylation of aromatic rings in the common phenylpropane biosynthesis pathways of phenolic compounds. However, research on this family of oxidases is currently fragmented, and a systematic and comprehensive review has not yet been conducted. This review offers an exhaustive summary of the molecular features of the CYP98A family and the functions of CYP98A monooxygenases in the biosynthesis of different types of phenolic compounds. In addition, this study provides a reference for the exploration and functional study of plant CYP98A family enzymes. An enhanced understanding of CYP98A monooxygenases can help in the cultivation of high-quality horticultural plants with increased resistance to biotic and abiotic stresses and enhanced accumulation of natural bioactive compounds via metabolic engineering strategies. Moreover, the structural optimization and modification of CYP98A monooxygenases can provide additional potential targets for synthetic biology, enabling the efficient in vitro production of important phenolic compounds to address production supply conflicts.

The chromosome-scale assembly of the Salvia plebeia genome provides insight into the biosynthesis and regulation of rosmarinic acid

Salvia plebeia is an important traditional Chinese medicinal herb, with flavonoids and phenolic acids as its primary bioactive components. However, the absence of a reference genome hinders our understanding of genetic basis underlying the synthesis of these components. Here, we present a high-quality, chromosome-scale genome assembly of S. plebeia, spanning 1.22 Gb, with a contig N50 of 91.72 Mb and 36 861 annotated protein-coding genes. Leveraging the genome data, we identified four catalytic enzymes-one rosmarinic acid synthase (RAS) and three cytochrome P450 monooxygenases (CYP450s) -in S. plebeia, which are involved in rosmarinic acid biosynthesis. We demonstrate that SpRAS catalyses the conjugation of various acyl donors and acceptors, resulting in the formation of rosmarinic acid and its precursor compounds. SpCYP98A75, SpCYP98A77 and SpCYP98A78 catalyse the formation of rosmarinic acid from its precursors at either the C-3 or the C-3' position. Notably, SpCYP98A75 exhibited a stronger hydroxylation capacity at the C-3' position, whereas SpCYP98A77 and SpCYP98A78 demonstrate greater hydroxylation efficiency at the C-3 position. Furthermore, SpCYP98A75 hydroxylated both the C-3 and C-3' positions simultaneously, promoting the conversion of 4-coumaroyl-4'-hydroxyphenyllactic acid to rosmarinic acid. Next, using a hairy root genetic transformation system for S. plebeia, we identified a basic helix-loop-helix protein type transcription factor, SpbHLH54, which positively regulates the biosynthesis of rosmarinic acid and homoplantaginin in S. plebeia. These findings provide a valuable genomic resource for elucidating the mechanisms of rosmarinic acid biosynthesis and its regulation and improve the understanding of evolutionary patterns within the Lamiaceae family.

Isolation of Endophytic Fungi and Effects on Secondary Metabolites in Hairy Roots of Salvia miltiorrhiza

The slow growth rate of medicinal plants has made them unable to meet people's needs, and the use of biotechnology to obtain natural products from medicinal plants can alleviate this problem. This study isolated and identified 42 endophytic fungi from the roots, stems, and leaves of Salvia miltiorrhiza, belonging to 13 genera. The endophytic fungi that promote the accumulation of secondary metabolites in the hairy roots of S. miltiorrhiza were screened by co-culture and elicitors preparation. Among them, 15 endophytic fungi presented relatively high crude polysaccharide yields. Co-culture experiments showed that endophytic strains had different effects on the biomass and the accumulation of secondary metabolites in the hairy roots of S. miltiorrhiza, with strain KLBMPSM237 being the most effective. The contents of tanshinone I, salvianolic acid B and rosmarinic acid in the hairy roots of S. miltiorrhiza were significantly increased by KLBMPSM237 polysaccharide inducers at different concentrations. This study provides new microbial resources and technical methods for increasing the natural products in hairy roots of S. miltiorrhiza.

Phenolic metabolism in Sarcandra glabra is mediated by distinct BAHD hydroxycinnamoyltransferases

Sarcandra glabra (Chloranthaceae) has an elaborate phenolic metabolism, encompassing various hydroxycinnamic acid esters. This may imply that multiple hydroxycinnamoyltransferases are involved in establishing this spectrum of natural compounds. Five coding sequences from S. glabra, belonging to the superfamily of BAHD acyltransferases, have been amplified from S. glabra cDNA, and the proteins were expressed in Escherichia coli. By assaying the proteins biochemically, the main substrates of these enzymes were identified as p-coumaroyl- and caffeoyl-CoA as donor substrates together with varying acceptor substrates. SgHST mainly forms p-coumaroyl- and caffeoylshikimic acid, but also the corresponding quinic acid esters as well as amides with 3- and 5-hydroxyanthranilic acids. SgHQT1 predominantly catalyzes the formation of p-coumaroyl- and caffeoyl-5-O-quinic acid, while SgHQT2 correspondingly forms p-coumaroyl- and caffeoyl-4-O-quinic acid. To our knowledge, this is the first characterized enzyme forming cryptochlorogenic acid and its precursor p-coumaroyl-4-O-quinic acid. SgRAS synthesizes rosmarinic acid and its precursors (caffeoyl-4'-hydroxyphenyllactic, p-coumaroyl-4'-hydroxyphenyllactic, p-coumaroyl-3',4'-dihydroxyphenyllactic acids) as well as amides with aromatic d-amino acids. No substrates could be identified for the fifth sequence, SgHCT-F, which phylogenetically groups with benzyl alcohol O-benzoyltransferases. All enzymes, except SgHCT-F, were fully kinetically characterized, and their expression in different tissues of S. glabra was assessed.

Enhancing active ingredient biosynthesis in Chinese herbal medicine: biotechnological strategies and molecular mechanisms

Background

Chinese herbal medicine (CHM) is a fundamental component of traditional Chinese medical practice, offering a rich source of natural remedies with significant therapeutic potential. However, the scarcity of active ingredients and complex extraction procedures present substantial challenges to their widespread clinical application. This review aims to address this gap by exploring the potential of modern biotechnological advancements in enhancing the biosynthesis of these valuable compounds.

Methodology

The study takes a comprehensive approach, delving into the chemical composition of CHM's active ingredients and elucidating their biosynthetic pathways and molecular regulatory mechanisms. Additionally, it surveys recent progress in extraction methodologies and evaluates engineering strategies aimed at synthetic production. This multifaceted analysis forms the foundation for examining the role of synthetic biology in augmenting CHM's active ingredient synthesis.

Results

Our examination provides insights into the intricate biosynthetic pathways governing the formation of CHM's active ingredients, as well as the complex molecular regulatory networks that underlie these processes. Furthermore, the review highlights advancements in extraction techniques, demonstrating their ability to streamline and enhance the isolation of these compounds. Engineering approaches for synthetic production, including metabolic engineering and synthetic biology tools, are assessed for their potential to overcome natural limitations and scale up production.

Conclusions

By integrating insights from biosynthesis, molecular regulation, extraction methodologies, and synthetic biology, this review establishes a robust theoretical framework for enhancing the production of CHM's active ingredients. The proposed strategies and practical guidance aim to facilitate their broader utilization in modern medicine while promoting sustainability and accessibility within this invaluable medicinal heritage.

Elucidating the wedelolactone biosynthesis pathway from Eclipta prostrata (L.) L.: a comprehensive analysis integrating de novo comparative transcriptomics, metabolomics, and molecular docking of targeted proteins

Eclipta prostrata belongs to the Asteraceae family. The plant contains bioactive compounds like wedelolactone (WDL) and demethylwedelolactone (DW). Its transcriptomic information engaged with secondary metabolite biosynthesis is not available. Based on differential accumulation of WDL and DW in root, shoot of the mature plant, we performed comparative de novo transcriptome of root and shoot tissue in three independent biological replicates and generated 49820 unique transcripts. Annotation resulted in significant matches for 43,015 unigenes. Based on differential gene expression data, we found WDL biosynthesis-related transcripts, which were mainly upregulated in shoot. Finally, 13 selected differentially expressed transcripts related to WDL biosynthesis that were validated by qRT-PCR. Detailed tissue-specific metabolite and transcript profiling revealed that DW highly accumulated in root and WDL accumulation was high in aerial part along with transcripts. For WDL pathway exploration, we did integrated profiling of 08 metabolites and 13 transcripts and witnessed that only naringenin, apigenin, DW, and WDL were detected in different developmental stages. Taking leads from the findings, we postulated that naringenin to apigenin pathway is one potential route for WDL biosynthesis. Moreover, wound stress led to accumulation of DW and WDL and related biosynthetic transcripts. Furthermore, the selected enzymes were subjected to molecular docking and binding studies for the predicted substrates involved in crucial and advance steps of WDL biosynthesis. A comprehensive analysis integrating de novo transcriptomics, metabolomics, and molecular docking of targeted proteins paves the way for the elucidation of the putative wedelolactone biosynthesis pathway from E. prostrata.

The total biosynthesis route of rosmarinic acid in Sarcandra glabra based on transcriptome sequencing

Sarcandra glabra is a widely distributed and valuable plant in food and daily chemical industries, and is also a common-used medicinal plant for treating inflammatory diseases and tumors. Rosmarinic acid (RA) with significant pharmacological activity is an abundant and important constituent in S. glabra, however, little information about key enzymes involving the biosynthesis of RA in S. glabra is available and the underlying biosynthesis mechanisms of RA in S. glabra remain undeciphered. Therefore, in this study, by full-length transcriptome sequencing analyses of S. glabra, we screened the RA biosynthesis candidate genes based on sequence similarity and conducted enzymatic function characterization in vitro and in vivo. As a result, a complete set of 7 kinds of enzymes (SgPALs, SgC4H, Sg4CL, SgTATs, SgHPPRs, SgRAS and SgC3H) involving the biosynthesis route of RA from phenylalanine and tyrosine, were identified and fully characterized. This research systematically revealed the complete biosynthesis route of RA in S. glabra, which helps us better understand the process of RA synthesis and accumulation, especially the substrate promiscuities of SgRAS and SgC3H provide the molecular biological basis for the efficient biosynthesis of specific and abundant RA in S. glabra. The 7 kinds of key enzymes revealed in this study can be utilized as tool enzymes for production of RA by synthetic biology methods.

UHPLC-QTOF-MS-Based Targeted Metabolomics Provides Novel Insights into the Accumulative Mechanism of Soil Types on the Bioactive Components of Salvia miltiorrhiza

The root of Salvia miltiorrhiza Bunge (SMB) has been widely used to treat cardiovascular diseases. However, the contents of secondary metabolites in the roots from different production areas are significantly different, and the impact of soil factors on this accumulation remains unclear. Therefore, this study aimed to elucidate the regularity of variation between the active components and soil factors through targeted metabolomics and chemical dosimetry. Soils were collected from five different cities (A, B, C, D, and E) and transplanted into the study area. The results showed that there were significant differences in the soil fertility characteristics and heavy metal pollution levels in different soils. Ten water- and twelve lipid-soluble metabolites were identified in SMBs grown in all soil types. SMBs from D cities exhibited the highest total tanshinone content (p < 0.05). The salvianolic acid B content in SMBs from E cities was the highest (p < 0.05). Interestingly, correlation analysis revealed a significant negative correlation between the accumulation of lipid-soluble and water-soluble metabolites. Double-matrix correlation analysis demonstrated that available potassium (AK) was significantly negatively correlated with salvianolic acid B (r = -0.80, p = 0.0004) and positively correlated with tanshinone IIA (r = 0.66, p = 0.008). Conversely, cadmium (Cd) and cuprum (Cu) were significantly positively and negatively correlated with salvianolic acid B (r = 0.96, p < 0.0001 and r = 0.72, p = 0.0024) and tanshinone IIA (r = 0.40, p = 0.14 and r = 0.73, p = 0.0018), respectively. Mantel's test indicated that AK (r > 0.52, p < 0.001), Cu (r > 0.60, p < 0.005), and Cd (r > 0.31, p < 0.05) were the primary drivers of the differences in the active components of SMBs. These findings provide a theoretical framework for modulating targeted metabolites of SMB through soil factors, with significant implications for the cultivation and quality control of medicinal plants.