Expansion within the CYP71D subfamily drives the heterocyclization of tanshinones synthesis in Salvia miltiorrhiza

Molecular mechanism of SmMYB53 activates the expression of SmCYP71D375, thereby modulating tanshinone accumulation in Salvia miltiorrhiza

Tanshinones are bioactive diterpenoid chemicals of the herb Salvia miltiorrhiza with a characteristic furan D-ring. As a newly identified downstream enzyme, SmCYP71D375, catalyzes hydroxylation by 14,16-ether (hetero)cyclization to form the furan D-ring from the precursor of the phenolic abietane-type diterpenoids that exist widely in Lamiaceae plants. However, its transcriptional regulatory network, with SmCYP71D375 as the direct target gene, remains unclear. In the present study, the promoter of SmCYP71D375 was employed as the bait to mine the upstream regulatory protein using the cDNA yeast library of S. miltiorrhiza. An R2R3-MYB transcription factor gene, SmMYB53, was identified. Overexpressing SmMYB53 in transgenic hairy roots upregulated SmCYP71D375 expression, thereby accelerating tanshinone accumulation, whereas tanshinone accumulation was inhibited in SmMYB53-RNAi transgenic hairy root lines. To dissect the regulatory network of SmMYB53, SmbZIP51 was captured using SmMYB53 as the bait to prey for its potential interacting proteins in the cDNA yeast library. Yeast two-hybrid, glutathione S-transferase pull-down, and bimolecular fluorescence complementation assays were independently used to verify the interaction between the SmMYB53 and SmbZIP51 proteins . We further verified that the upregulation of SmCYP71D375 activated by SmMYB53 would be inhibited by the interaction of SmMYB53 and SmbZIP51. The present findings uncover the molecular regulatory network underlying SmCYP71D375 as the direct target regulating tanshinone biosynthesis and offer a basis for the genetic improvement of medicinal substance biosynthesis in S. miltiorrhiza.

Telomere-to-telomere gap-free genome assembly provides genetic insight into the triterpenoid saponins biosynthesis in Platycodon grandiflorus

Platycodon grandiflorus has been widely used in Asia as a medicinal herb and food because of its anti-inflammatory and hepatoprotective properties. P. grandiflorus has important clinical value because of the active triterpenoid saponins in its roots. However, the biosynthetic pathway of triterpenoid saponins in P. grandiflorus remains unclear, and the related genes remain unknown. Therefore, in this study, we assembled a high-quality and integrated telomere-to-telomere P. grandiflorus reference genome and combined time-specific transcriptome and metabolome profiling to identify the cytochrome P450s (CYPs) responsible for the hydroxylation processes involved in triterpenoid saponin biosynthesis. Nine chromosomes were assembled without gaps or mismatches, and nine centromeres and 18 telomere regions were identified. This genome eliminated redundant sequences from previous genome versions and incorporated structural variation information. Comparative analysis of the P. grandiflorus genome revealed that P. grandiflorus underwent a core eudicot γ-WGT event. We screened 211 CYPs and found that tandem and proximal duplications may be crucial for the expansion of CYP families. We outlined the proposed hydroxylation steps, likely catalyzed by the CYP716A/72A/749A families, in platycodin biosynthesis and identified three PgCYP716A, seven PgCYP72A, and seven PgCYP749A genes that showed a positive correlation with platycodin biosynthesis. By establishing a T2T assembly genome, transcriptome, and metabolome resource for P. grandiflorus, we provide a foundation for the complete elucidation of the platycodins biosynthetic pathway, which consequently leads to heterologous bioproduction, and serves as a fundamental genetic resource for molecular-assisted breeding and genetic improvement of P. grandiflorus.

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.

CRISPR-Cas9 Mediated Gene Editing Platform Through Callus-to-Plant Regeneration and Functional Analysis of DoALA4─DoALA6 in Dendrobium officinale

Dendrobium orchids are well known for their great horticultural and medicinal values; however, the CRISPR/Cas9 gene editing system for Dendrobium species still needs to be improved. Therefore, this study aims to establish a CRISPR/Cas9-based functional validation system using Dendrobium officinale as a model species for the Dendrobium genus and to validate the DoALA4─DoALA6 genes, which may relate to growth and disease resistance. We first conducted a bioinformatics analysis of the P-type ATPase gene family in D. officinale, revealing the evolutionary diversity of P-type ATPase genes in orchids. Second, we inserted the GFP gene into the vector of CRISPR/Cas9 gene editing system to enhance the selection efficiency of genome-edited plants. Comparative analysis showed that different explants exhibited varying transformation efficiencies, ranging from 5% to 46.2%. Considering the regeneration capability, survival rate and gene editing efficiency, we selected callus as the transformation explant. Third, we used this editing system to generate DoALA4─DoALA6 mutants. Phenotypic observations of the mutants and inoculation of D. officinale with Sclerotium rolfsii indicated that DoALA4─DoALA6 are crucial for the growth of D. officinale and its resistance to southern blight disease. This efficient and stable CRISPR/Cas9 platform offers a foundation for further gene studies and Dendrobium breeding.

The high-quality chromosome-level genome assembly of Dracocephalum rupestre Hance

Dracocephalum rupestre Hance is China's traditional herbal medicine in the family Labiatae with numerous health benefits, including anti-inflammatory, antiviral and anti-tumor activities. However, the genus Dracocephalum has no reference genome currently, which restricts the research on the breeding, cultivation and exploration of medicinal properties in D. rupestre. Thus, we present the high-quality chromosome-level genome assembly of D. rupestre using a combination of Pacbio HiFi sequencing and Hi-C scaffolding technologies. The final genome was 435.45 Mb with a contig N50 of 49.83 Mb and a scaffold N50 of 59.06 Mb. The assembled sequences were anchored to 7 chromosomes with an integration efficiency of 96.96%. Furthermore, we predicted 25,865 protein-coding genes, 98.23% of which were functionally annotated. These results offer valuable resources for understanding the genetic basis of the unique phenotypes of D. rupestre and will facilitate further study of the functional genomics of this species.

Bacterial biosynthesis of abietane-type diterpene ferruginol from glucose

BACKGROUND

Microbial supply of plant extracts is a promising biomanufacturing strategy that requires engineering of metabolic pathways and enzymes. This study presents the engineering of Corynebacterium glutamicum for heterologous production of diterpenes miltiradiene and ferruginol.

RESULTS

Through targeted metabolic pathway modifications, including inactivation of pyruvate carboxylase and phytoene synthase, the HL01 strain was optimized to enhance pyruvate and geranylgeranyl pyrophosphate (GGPP) pools. Overexpression of key MEP pathway enzymes (Dxs and Idi) and implementation of three GGPP synthase modules further boosted diterpene synthesis. Then, combining those modules with diterpene synthase (DiTPS) and intact P450 reductase modules (CYP76AH1 and CPR1) enabled production of miltiradiene (ferruginol equivalent) at 237.46 ± 34.8 mg/L and ferruginol at 107.34 ± 1.2 mg/L under constant glucose feeding, respectively.

CONCLUSIONS

Modular gene expression for heterologous metabolic pathway can be optimized for bacterial biosynthesis. This is the first demonstration of ferruginol production in bacteria. These findings pave the way for further optimization of diterpene biosynthesis through pathway engineering and module integration in bacterial systems.

Genome-wide identification of the SmPHR gene family in Salvia miltiorrhiza and SmPHR7-mediated response to phosphate starvation in Arabidopsis thaliana

KEY MESSAGE

This study reveals the transcripts of S. miltiorrhiza in response to phosphate deficiency, identifies 18 SmPHRs in the genome, and tentatively establishes a role for SmPHR7 in regulating phosphate starvation. Phosphorus is essential for plant growth and development, and phosphate deficiency is a common nutritional stress. Salvia miltiorrhiza (Danshen) is a traditional Chinese herb whose main active medicinal secondary metabolite is used in the treatment of heart disease. However, the physiological and molecular effects of phosphate starvation in S. miltiorrhiza have not been well studied. Here, we first investigated the effect of phosphate starvation on the growth and major medicinal compounds. Biomass decreased with lower phosphate concentrations, while the accumulation of compounds varied in S. miltiorrhiza. Transcriptome analysis showed that phosphate starvation affected the expression of genes involved in processes such as glycolysis/gluconeogenesis, glycerolipid metabolism, and phenylpropanoid biosynthesis. Phosphate starvation response (PHR) transcription factors play an important role in the phosphate starvation response, and we identified 18 PHR family genes in S. miltiorrhiza, distributed across 8 chromosomes. The expression levels of different SmPHR family members in roots and shoots differ in response to phosphate starvation. SmPHR7, which is highly expressed in response to phosphate starvations, was selected for further functional characterization. SmPHR7 has transcriptional activation activity and is localized in the nucleus. Furthermore, the expression of SmPHR7 in the Arabidopsis thaliana mutant phr (SmPHR7-OX) is shown to partially rescue the phosphate starvation phenotype. The expression of the Pi starvation-induced (PSI) gene in SmPHR7-OX showed a significant induction compared to the phr mutant under phosphate starvation. The identification of the SmPHR gene family significantly contributes to a broader understanding of phosphate starvation signaling in S. miltiorrhiza.

A long road ahead to reliable and complete medicinal plant genomes

Long-read DNA sequencing has propelled medicinal plant genomics forward, with over 400 genomes from 203 plants sequenced by February 2025. However, many genomes still have assembly and annotation flaws, with only 11 gapless telomere-to-telomere assemblies. The core challenge remains identifying genes linked to secondary metabolite biosynthesis, regulation and evolution. High-quality complete genomes are essential for characterizing biosynthetic gene clusters and for enabling robust functional genomics and synthetic biology applications. We propose to focus on achieving more complete genome assemblies in diverse varieties on the basis of refining the currently available ones, leverage lessons from crop genomics research, and apply the cutting-edge genomics technologies in research of medicinal plant genomics.

New insights of advanced biotechnological engineering strategies for tanshinone biosynthesis in Salvia miltiorrhiza

Salvia miltiorrhiza Bunge, a well-known traditional Chinese herbal medicine, has been served as not only medicine for human ailments, but also health care products. As one of major bioactive ingredients, tanshinones are widely used to treat cardiovascular and cerebrovascular diseases, and also possess different pharmacological activities including anti-tumor, anti-inflammatory, anti-fibrotic and others. However, the content of tanshinones is relatively low in S. miltiorrhiza plants. Recently, multiple biotechnological strategies have been applied to improve tanshinone production. In this review, advances in bioactivities, biosynthesis pathway and regulation, transcriptional regulatory network, epigenetic modification and synthetic biology are summarized, and future perspectives are discussed, which will help develop high-quality S. miltiorrhiza resources.

Mining the Candidate Transcription Factors Modulating Tanshinones' and Phenolic Acids' Biosynthesis Under Low Nitrogen Stress in Salvia miltiorrhiza

Mining valuable genes is helpful to breed high-quality Salvia miltiorrhiza exhibiting efficient nitrogen fertilizer utilization efficiency. In the present study, transcriptome sequencing was introduced to select the candidate transcription factors (TFs) involved in tanshinones' (TAs) and phenolic acids' (PHAs) biosynthesis as well as low nitrogen (LN) stress. In totally, 97.71 Gb clean data was obtained from fifteen sequencing samples and 30,975 unigenes were assembled. Among of them, 27,843 unigenes were successfully annotated. Overall, 8663 differential expression genes (DEGs) were identified, among of which 5034 unigenes were up-regulated, and 3629 unigenes were down-regulated. By enrichment of DEGs together with gene co-expression network construction, 10 candidate TFs including HSFB2b, LBD12, ERF1A, ERF98, LBD25, HSF24, RAM1, HSFA4B, TCP8, and WRKY24 were finally retrieved, which are predicted to participate in modulating TA and PHA biosynthesis under LN stress. Quantitative real-time polymerase chain reaction (qRT-PCR) detection was introduced to further detect the expression profile of candidate TFs under LN stress. These findings offer a valuable resource for in-depth study of TAs 'and PHAs' biosynthesis under LN stress in S. miltiorrhiza.

Three cytochrome P450 enzymes consecutively catalyze the biosynthesis of furanoclerodane precursors in Salvia species

Salvia species native to the Americas are rich in valuable bioactive furanoclerodanes like the psychoactive salvinorin A found in Salvia divinorum, which is used in the treatment of opioid addiction. However, relatively little is known about their biosynthesis. To address this, we investigated the biosynthesis of salviarin, the most abundant furanoclerodane structure in the ornamental sage Salvia splendens. Using a self-organizing map and mutual rank analysis of RNA-seq co-expression data, we identified three cytochrome P450 enzymes responsible for the consecutive conversion of kolavenol into the salviarin precursors: annonene, hardwickiic acid, and hautriwaic acid. Annonene and hardwickiic acid have been proposed as intermediates in the biosynthesis of salvinorin A, and we therefore tested for a common evolutionary origin of the furanoclerodane pathway in these Salvia species by searching for homologous genes in available data for S. divinorum. The enzymes encoded by orthologous genes from S. divinorum displayed kolavenol synthase, annonene synthase, and hardwickiic acid synthase activity, respectively, supporting the view that these are intermediate steps in the biosynthesis of salvinorin A. We further investigated the origin of annonene synthase and the role of gene duplication in the evolution of this specific activity. Our work shows how S. splendens can serve as a model species for the study of furanoclerodane biosynthesis in Salvia species, contributes to understanding the evolution of specialized metabolism in plants, and provides new tools for the production of salvinorin A in biotechnological chassis.

Abscisic acid enhances SmAPK1-mediated phosphorylation of SmbZIP4 to positively regulate tanshinone biosynthesis in Salvia miltiorrhiza

Tanshinones, isolated from Salvia miltiorrhiza, is efficient to treat cardiovascular and cerebrovascular diseases. Abscisic acid (ABA) treatment is found to promote tanshinone biosynthesis; however, the underlying mechanism has not been fully elucidated. A protein kinase namely SmAPK1 was identified as an important positive regulator of ABA-induced tanshinone accumulation in S. miltiorrhiza. Using SmAPK1 as bait, a basic region leucine zipper (bZIP) family transcription factor SmbZIP4 was screened from the cDNA library. Functional identification reveals that SmbZIP4 negatively regulates tanshinone biosynthesis in hairy roots and transgenic plants through directly targeting SmGGPPS and SmCYP76AK1. SmAPK1 phosphorylates the Ser97 and Thr99 site of SmbZIP4, leading to its degradation via the 26S proteasome pathway, which is promoted by ABA-induced enhancement of SmAPK1 kinase activity. Degradation of SmbZIP4 upregulates the expression levels of SmGGPPS and SmCYP76AK1, resulting in increased tanshinone content. Taken together, our results reveal new molecular mechanism by which SmAPK1-SmbZIP4 module plays a crucial role in ABA-induced tanshinone accumulation. This study sheds new insights in the biosynthesis of bioactive compounds in medicinal plants.

BrCYP71 mutation resulted in stay-green in pak choi (Brassica rapa L. ssp. chinensis)

KEY MESSAGE

BrCYP71 encoding multifunctional oxidase was mapped using BSA-Seq and linkage analysis, and its function in stay-green of pak choi was verified through Arabidopsis heterologous transgenic experiment. Stay-green refers to the phenomenon that plant leaves remain green during senescence and even after death, which is of great significance for improving the commerciality of leafy vegetables during storage or transportation and extending their shelf life. In this study, we identified a stay-green mutant of pak choi and named it nye2. Genetic analysis showed that the stay-green trait was controlled by a recessive nuclear gene. We obtained a 550 kb candidate region on chromosome A03 using BSA-Seq and linkage analysis. In this interval, BraA03g049920.3.5C, named BrCYP71, was identified as a candidate gene using sequence variation analysis. BrCYP71 is an ortholog of Arabidopsis AT4G13290, which encodes a multifunctional oxidase. A 4 bp insertion from T to TGATC in the first exon of BrCPY71 in the mutant led to the formation of a stop codon, TAA. Ectopic overexpression of BrCYP71 in Arabidopsis cyp71 could restored the wild-type phenotype. These results indicate that BrCYP71 contributes to the stay-green of nye2. The expression levels of chlorophyll catabolism-related genes in nye2 were significantly reduced compared to those in the wild-type, suggesting that BrCPY71 affected chlorophyll catabolism. Our achievement provides a novel genetic resource for breeding the stay-green varieties of Brassica rapa.

Deciphering the biosynthetic pathway of triterpene saponins in Prunella vulgaris

The traditional Chinese medicinal plant Prunella vulgaris contains numerous triterpene saponin metabolites, notably ursolic and oleanolic acid saponins, which have significant pharmacological values. Despite their importance, the genes responsible for synthesizing these triterpene saponins in P. vulgaris remain unidentified. This study used a comprehensive screening methodology, combining phylogenetic analysis, gene expression assessment, metabolome-transcriptome correlation and co-expression analysis, to identify candidate genes involved in triterpene saponins biosynthesis. Nine candidate genes - two OSCs, three CYP716s and four UGT73s - were precisely identified from large gene families comprising hundreds of members. These genes were subjected to heterologous expression and functional characterization, with enzymatic activity assays confirming their roles in the biosynthetic pathway, aligning with bioinformatics predictions. Analysis revealed that these genes originated from a whole-genome duplication (WGD) event in P. vulgaris, highlighting the potential importance of WGD for plant metabolism. This study addresses the knowledge gap in the biosynthesis of triterpene saponins in P. vulgaris, establishing a theoretical foundation for industrial production via synthetic biology. Additionally, we present an efficient methodological protocol that integrates evolutionary principles and bioinformatics techniques in metabolite biosynthesis research. This approach holds significant value for studies focused on unraveling various biosynthetic pathways.

The ABC transporter SmABCG1 mediates tanshinones export from the peridermic cells of Salvia miltiorrhiza root

Plants have mechanisms to transport secondary metabolites from where they are biosynthesized to the sites where they function, or to sites such as the vacuole for detoxification. However, current research has mainly focused on metabolite biosynthesis and regulation, and little is known about their transport. Tanshinone, a class diterpenoid with medicinal properties, is biosynthesized in the periderm of Salvia miltiorrhiza roots. Here, we discovered that tanshinone can be transported out of peridermal cells and secreted into the soil environment and that the ABC transporter SmABCG1 is involved in the efflux of tanshinone ⅡA and tanshinone Ⅰ. The SmABCG1 gene is adjacent to the diterpene biosynthesis gene cluster in the S. miltiorrhiza genome. The temporal-spatial expression pattern of SmABCG1 is consistent with tanshinone accumulation profiles. SmABCG1 is located on the plasma membrane and preferentially accumulates in the peridermal cells of S. miltiorrhiza roots. Heterologous expression in Xenopus laevis oocytes demonstrated that SmABCG1 can export tanshinone ⅡA and tanshinone Ⅰ. CRISPR/Cas9-mediated mutagenesis of SmABCG1 in S. miltiorrhiza hairy roots resulted in a significant decrease in tanshinone contents in both hairy roots and the culture medium, whereas overexpression of this gene resulted in increased tanshinone contents. CYP76AH3 transcript levels increased in hairy roots overexpressing SmABCG1 and decreased in knockout lines, suggesting that SmABCG1 may affect the expression of CYP76AH3, indirectly regulating tanshinone biosynthesis. Finally, tanshinone ⅡA showed cytotoxicity to Arabidopsis roots. These findings offer new perspectives on plant diterpenoid transport and provide a new genetic tool for metabolic engineering and synthetic biology research.

Genome-Wide Identification and Expression Analysis of Carotenoid Cleavage Dioxygenase Genes in Salvia miltiorrhiza

In the process of catalyzing carotenoids into various apocarotenoids and other derivatives, carotenoid cleavage dioxygenases (CCDs) play key roles. However, little information on CCDs has been reported in regard to Salvia miltiorrhiza. In this study, a total of 21 CCD genes were identified in the whole genome of S. miltiorrhiza, mainly distributed between five chromosomes. Phylogenetic relationship analysis revealed that 21 SmCCD genes were classified into four subfamilies, including SmCCD4, 7, 8, and NCED; the members of the same subfamily show similar gene structures and tertiary structures. The interspecific collinearity with other plant species, such as Arabidopsis thaliana and Oryza sativa was analyzed. Cis-elements analysis demonstrated that the majority were stress response-, light response-, growth-, and development-related. The expression pattern of the SmCCD genes was expressed in the analyzed tissues. Furthermore, the majority of the SmCCD4 subfamily members varied in their expression levels under the treatment of MeJA, YE, and ABA, indicating the potential function of SmCCD4 in the metabolism process of S. miltiorrhiza. In general, this study provides a systematic analysis of SmCCD genes and lays the foundation for uncovering the regulation and function of SmCCD genes in S. miltiorrhiza.

SmJAZ1/8 inhibits the stimulation of SmbHLH59, which limits the accumulation of salvianolic acids and tanshinones in Salvia miltiorrhiza

Salvia miltiorrhiza is a model medicinal plant that is typically used to treat cardiovascular and cerebrovascular diseases. The primary active medicinal ingredients of S. miltiorrhiza are salvianolic acids and tanshinones. Jasmonate (JA) is a vital phytohormone that regulates secondary metabolism. The exogenous application of methyl jasmonate (MeJA) can promote the accumulation of active ingredients in S. miltiorrhiza. Here, we identified a MeJA-responsive SmbHLH59 gene that encodes for a bHLH IIIe family transcription factor. The overexpression of SmbHLH59 in S. miltiorrhiza increased the contents of salvianolic acids and tanshinones, while the opposite effect was observed when SmbHLH59 was knocked out via CRISPR. Meanwhile, SmbHLH59 was observed to activate the expressions of SmPAL1, SmC4H1, SmHPPR1, SmCPS1, and SmKSL1 genes by binding to the E/G-box elements of their promoters. Further investigations demonstrated that SmJAZ1 and SmJAZ8 interacted with SmbHLH59 to inhibit its activation of these five genes. In summary, a JA signaling pathway component (SmbHLH59) was identified that strongly enhanced the accumulation of salvianolic acids and tanshinones through the direct activation of multiple enzyme genes in their biosynthetic pathways. Consequently, this study enriches our knowledge toward further elucidating the molecular mechanisms behind the regulation of JA in the secondary metabolism of S. miltiorrhiza.

Quantitative Trait Locus Mapping and Candidate Gene Analysis of the Contents of Three Tanshinone Components in Salvia miltiorrhiza Bunge

Tanshinones are abietane diterpenoid quinone compounds with diverse biological activities and pharmacological effects found in Salvia miltiorrhiza. Leveraging the high-density genetic map established through our prior research endeavors, we conducted a quantitative trait locus (QTL) analysis pertaining to the concentrations of three major tanshinone components, cryptotanshinone, tanshinone I, and tanshinone IIA, in S. miltiorrhiza. This extensive investigation was conducted across three distinct planting environments, ultimately identifying a comprehensive repertoire of 27 discernible QTLs. These QTLs were mapped onto four distinct linkage groups (LG), namely LG1, LG5, LG6, and LG7, which explained 3.11%-37.85% phenotypic variation. Candidate genes were projected based on consistent QTLs detected for each active ingredient in three environments. Nineteen putative candidate genes involved in the regulation of tanshinone biosynthesis were identified. These genes participate in primary metabolic and multiple branching terpenoid biosynthesis pathways, forming a complex regulatory network. Our findings have the potential to offer novel insights into advancing the understanding of the regulatory mechanisms governing tanshinone biosynthesis. Furthermore, these results establish crucial groundwork for gene discovery, marker-assisted selection breeding, and map-based cloning of functional genes associated with tanshinone content in S. miltiorrhiza.

Integration of CRISPR/Cas9 with multi-omics technologies to engineer secondary metabolite productions in medicinal plant: Challenges and Prospects

Plants acts as living chemical factories that may create a large variety of secondary metabolites, most of which are used in pharmaceutical products. The production of these secondary metabolites is often much lower. Moreover, the primary constraint after discovering potential metabolites is the capacity to manufacture sufficiently for use in industrial and therapeutic contexts. The development of omics technology has brought revolutionary discoveries in various scientific fields, including transcriptomics, metabolomics, and genome sequencing. The metabolic pathways leading to the utilization of new secondary metabolites in the pharmaceutical industry can be identified with the use of these technologies. Genome editing (GEd) is a versatile technology primarily used for site-directed DNA insertions, deletions, replacements, base editing, and activation/repression at the targeted locus. Utilizing GEd techniques such as clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 (CRISPR-associated protein 9), metabolic pathways engineered to synthesize bioactive metabolites optimally. This article will briefly discuss omics and CRISPR/Cas9-based methods to improve secondary metabolite production in medicinal plants.

Chromosome-Scale Genome and Transcriptomic Analyses Reveal Differential Regulation of Terpenoid Secondary Metabolites in Hericium coralloides

Construction of the genome of Hericium coralloides, a species of edible mushroom, and identification of the genes involved in terpenoid biosynthesis can determine the biology and genetics of terpenoids. The present study describes the assembly of a high-quality chromosome-scale genome of H. coralloides using Pacbio HiFi sequencing and Hi-C technology. This genome consisted of 13 chromosomes, a total size of 43.6 Mb, contigs of N50 3.6 Mb, GC content at 54%, and BUSCOs integrity of 96.9%. Genes associated with terpenoid biosynthesis were predicted by KEGG enrichment analysis and homologous alignment. The Her011461 and Her008335 genes, encoding proteins in the terpenoid backbone synthesis pathway, were found to encode geranylgeranyl pyrophosphate and farnesyl diphosphate synthases, key enzymes in the biosynthesis of geranylgeranyl diphosphate, a precursor of several diterpenoids. Her011463 was found to be involved in regulating diterpene cyclase. The Her005433, Her006724, Her010605, and Her010608 genes were found to encode sesquiterpene synthesis. Most of these genes were more highly expressed in dikaryotic mycelia than in the primordium and fruiting bodies, indicating that terpenoids may be more abundant in dikaryotic mycelia. To our knowledge, this study is the first to assemble the H. coralloides genome at the chromosome scale and to identify the genes involved in terpenoid biosynthesis.

Genome-Wide Identification and Characterization of Diterpenoid Pathway CYPs in Andrographis paniculata and Analysis of Their Expression Patterns under Low Temperature Stress

Andrographis paniculata is known for its diterpenoid medicinal compounds with antibacterial and anti-inflammatory properties. However, it faces production and cultivation challenges due to low temperatures (LTs). Cytochrome P450 monooxygenases (CYPs) are key enzymes in diterpenoid accumulation. Nevertheless, the functions and LT-related expression patterns of diterpenoid pathway CYPs in Andrographis paniculata remain poorly understood. In this study, 346 CYPs were discovered in Andrographis paniculata. Among them, 328 CYPs belonged to 42 known subfamilies. The remaining 17 CYPs might have represented novel subfamilies unique to this species. A total of 65 candidate CYPs associated with diterpenoid modification were identified. Of these, 50 were transmembrane proteins, and 57 were localized to chloroplasts. The CYP71 subfamily was the most abundant and had the highest motif diversity. Promoters of all candidate CYPs commonly contained elements responsive to gibberellins (GAs), methyl jasmonate (MeJA), and abiotic stresses. Notably, the XP_051152769 protein, corresponding to a CYP gene over 40,000 bp in length, featured an extraordinarily long intron (40,751 nts). Functional elements within this intron were related to LT, GAs, and dehydration pathways. Based on the promoter element arrangement and subfamily classification, 10 representative candidate CYPs were selected. Under LT stress, significant expression changes were observed in three representative CYPs: CYP71D, ent-kaurenoic acid oxidase (KAO), and ent-kaurene oxidase (KO). KAO and KO were significantly upregulated during early LT stress. KAO and KO interacted with each other and jointly interacted with GA20OX2-like. CYP71D acted as a negative response factor to LT stress. Among the 37 proteins interacting with CYP71D, 95% were CYPs. This study provides a critical preliminary foundation for investigating the functions of diterpenoid pathway CYPs in Andrographis paniculata, thereby facilitating the development of LT-tolerant cultivars.

Integrated Transcriptomics and Metabolomics Reveal Key Insights into Iridoid Biosynthesis in Gentiana crassicaulis Seeds during Germination

Background:Gentiana crassicaulis Duthie ex Burk., a key species used in traditional Chinese medicine for treating rheumatic pain and stroke, contains iridoids as its primary active component. However, the biosynthetic mechanisms underlying iridoid production are not fully understood. Methods: This study focused on iridoid biosynthesis during the germination of G. crassicaulis seeds, integrating metabolomic and transcriptomic analyses to uncover the underlying pathways and key candidate genes. Results: 196,132 unigenes and 10 iridoid compounds were identified through RNA-seq and ultra performance liquid chromatography-quadrupole time of flight-mass spectrometer (UPLC-Q-TOF-MS), respectively. The intersection of results from Pearson correlation analysis and weighted gene co-expression network analysis (WGCNA) revealed a significant correlation between 26 genes and iridoid levels, suggesting their potential role in the iridoid metabolism. Notably, six highly expressed candidate genes (DL7H, SLS, CYP76, CYP72A2, CYP84A1, and 13-LOX3) and five iridoids (loganic acid, sweroside, swertiamarin, gentiopicroside, and 6'-O-β-D-glucosyl-gentiopicroside) responded to methyl jasmonate stimulation in G. crassicaulis seedlings. Conclusions: by combining the known functions of candidate gene families, It is hypothesized that the CYP716 and LOX families exert indirect influences on iridoid metabolism, while the CYP71, CYP81, CYP72, CYP76, CYP710 families, 2OG-FeII family, and the glucosyltransferase family are likely to play direct roles in the biosynthetic transformations of the five iridoids. This study provides a theoretical basis for further functional gene validation and metabolic engineering aimed at enhancing iridoid production. The insights gained could lead to improved iridoid production efficiency in medicinal plants, ultimately benefiting the quality and efficacy of medicinal materials.

(±)-Salvicatone A: A Pair of C27-Meroterpenoid Enantiomers with Skeletons from the Roots and Rhizomes of Salvia castanea Diels f. tomentosa Stib

(±)-Salvicatone A (1), a C27-meroterpenoid featuring a unique 6/6/6/6/6-pentacyclic carbon skeleton with a 7,8,8a,9,10,10a-hexahydropyren-1 (6H)-one motif, was isolated from the roots and rhizomes of Salvia castanea Diels f. tomentosa Stib. Its structure was characterized by comprehensive spectroscopic analyses along with computer-assisted structure elucidation, including ACD/structure elucidator and quantum chemical calculations with 1H/13C NMR and electronic circular dichroism. Biogenetically, compound 1 was constructed from decarboxylation following [4 + 2] Diels-Alder cycloaddition reaction between caffeic acid and miltirone analogue. Bioassays showed that (-)-1 and (+)-1 inhibited nitric oxide production in lipopolysaccharide-induced RAW264.7 macrophage cells with an IC50 value of 6.48 ± 1.25 and 15.76 ± 5.55 μM, respectively. The structure-based virtual screening based on the pharmacophores in ePharmaLib, as well as the molecular docking and molecular dynamics simulations study, implied that (-)-1 and (+)-1 may potentially bind to retinoic acid receptor-related orphan receptor C to exert anti-inflammatory activities.

The genomes of seven economic Caesalpinioideae trees provide insights into polyploidization history and secondary metabolite biosynthesis

The Caesalpinioideae subfamily contains many well-known trees that are important for economic sustainability and human health, but a lack of genomic resources has hindered their breeding and utilization. Here, we present chromosome-level reference genomes for the two food and industrial trees Gleditsia sinensis (921 Mb) and Biancaea sappan (872 Mb), the three shade and ornamental trees Albizia julibrissin (705 Mb), Delonix regia (580 Mb), and Acacia confusa (566 Mb), and the two pioneer and hedgerow trees Leucaena leucocephala (1338 Mb) and Mimosa bimucronata (641 Mb). Phylogenetic inference shows that the mimosoid clade has a much higher evolutionary rate than the other clades of Caesalpinioideae. Macrosynteny comparison suggests that the fusion and breakage of an unstable chromosome are responsible for the difference in basic chromosome number (13 or 14) for Caesalpinioideae. After an ancient whole-genome duplication (WGD) shared by all Caesalpinioideae species (CWGD, ∼72.0 million years ago [MYA]), there were two recent successive WGD events, LWGD-1 (16.2-19.5 MYA) and LWGD-2 (7.1-9.5 MYA), in L. leucocephala. Thereafter, ∼40% gene loss and genome-size contraction have occurred during the diploidization process in L. leucocephala. To investigate secondary metabolites, we identified all gene copies involved in mimosine metabolism in these species and found that the abundance of mimosine biosynthesis genes in L. leucocephala largely explains its high mimosine production. We also identified the set of all potential genes involved in triterpenoid saponin biosynthesis in G. sinensis, which is more complete than that based on previous transcriptome-derived unigenes. Our results and genomic resources will facilitate biological studies of Caesalpinioideae and promote the utilization of valuable secondary metabolites.

The methyl jasmonate-responsive transcription factor SmERF106 promotes tanshinone accumulation in Salvia miltiorrhiza

Understanding the regulatory biosynthesis mechanisms of active compounds in herbs is vital for the preservation and sustainable use of natural medicine resources. Diterpenoids, which play a key role in plant growth and resistance, also serve as practical products for humans. Tanshinone, a class of abietane-type diterpenes unique to the Salvia genus, such as Salvia miltiorrhiza, is an excellent model for studying diterpenoids. In this study, we discovered that a transcription factor, SmERF106, responds to MeJA induction and is located in the nucleus. It exhibits a positive correlation with the expression of SmKSL1 and SmIDI1, which are associated with tanshinone biosynthesis. We performed DNA affinity purification sequencing (DAP-seq) to predict genes that may be transcriptionally regulated by SmERF106. Our cis-elements analysis suggested that SmERF106 might bind to GCC-boxes in the promoters of SmKSL1 and SmIDI1. This indicates that SmKSL1 and SmIDI1 could be potential target genes regulated by SmERF106 in the tanshinone biosynthesis pathway. Their interaction was then demonstrated through a series of in vitro and in vivo binding experiments, including Y1H, EMSA, and Dual-LUC. Overexpression of SmERF106 in the hairy root of S. miltiorrhiza led to a significant increase in tanshinone content and the transcriptional levels of SmKSL1 and SmIDI1. In summary, we found that SmERF106 can activate the transcription of SmKSL1 and SmIDI1 in response to MeJA induction, thereby promoting tanshinone biosynthesis. This discovery provides new insights into the regulatory mechanisms of tanshinones in response to JA and offers a potential gene tool for tanshinone metabolic engineering strategy.

Advances in the Structures, Pharmacological Activities, and Biosynthesis of Plant Diterpenoids

More and more diterpenoids have attracted extensive attention due to the diverse chemical structures and excellent biological activities, and have been developed into clinical drugs or consumer products. The vast majority of diterpenoids are derived from plants. With the long-term development of plant medicinal materials, the natural resources of many plant diterpenoids are decreasing, and the biosynthetic mechanism of key active components has increasingly become a research hotspot. Using synthetic biology to engineer microorganisms into "cell factories" to produce the desired compounds is an essential means to solve these problems. In this review, we depict the plant-derived diterpenoids from chemical structure, biological activities, and biosynthetic pathways. We use representative plant diterpenes as examples to expound the research progress on their biosynthesis, and summarize the heterologous production of plant diterpenoids in microorganisms in recent years, hoping to lay the foundation for the development and application of plant diterpenoids in the future.

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.

Microalgae: towards human health from urban areas to space missions

Space exploration and interstellar migration are important strategies for long-term human survival. However, extreme environmental conditions, such as space radiation and microgravity, can cause adverse effects, including DNA damage, cerebrovascular disease, osteoporosis, and muscle atrophy, which would require prophylactic and remedial treatment en route. Production of oral drugs in situ is therefore critical for interstellar travel and can be achieved through industrial production utilizing microalgae, which offers high production efficiency, edibility, resource minimization, adaptability, stress tolerance, and genetic manipulation ease. Synthetic biological techniques using microalgae as a chassis offer several advantages in producing natural products, including availability of biosynthetic precursors, potential for synthesizing natural metabolites, superior quality and efficiency, environmental protection, and sustainable development. This article explores the advantages of bioproduction from microalgal chassis using synthetic biological techniques, suitability of microalgal bioreactor-based cell factories for producing value-added natural metabolites, and prospects and applications of microalgae in interstellar travel.

Alendronate Functionalized Bone-Targeting Pomolic Acid Liposomes Restore Bone Homeostasis for Osteoporosis Treatment

Introduction

Osteoporosis, characterized by dysregulation of osteoclastic bone resorption and osteoblastic bone formation, severely threatens human health during aging. However, there is still no good therapy for osteoporosis, so this direction requires our continuous attention, and there is an urgent need for new drugs to solve this problem.

Methods

Traditional Chinese Medicine Salvia divinorum monomer pomolic acid (PA) could effectively inhibit osteoclastogenesis and ovariectomized osteoporosis. However, its poor solubility and lack of targeting severely limits its further application. A novel bone-targeting nanomedicine (PA@TLipo) has been developed to reconstruct the osteoporotic microenvironment by encapsulating pomolic acid in alendronate-functionalized liposomes. Through a series of operations such as synthesis, purification, encapsulation, and labeling, the PA@TLipo have been prepared. Moreover, the cytotoxicity, bone targeting and anti-osteoporosis effect was verified by cell and animal experiments.

Results

In the aspect of targeting, the PA@TLipo can effectively aggregate on the bone tissue to reduce bone loss, and in terms of toxicity, PA@TLipo could increase the bone target ability in comparison to nontargeted liposome, thereby mitigating systemic cytotoxicity. Moreover, PA@TLipo inhibited osteoclast formation and bone resorption in vitro and reduced bone loss in ovariectomy-induced osteoporotic mice.

Conclusion

In this study, a novel therapeutic agent was designed and constructed to treat osteoporosis, consisting of a liposome material as the drug pocket, PA as the anti-osteoporosis drug, and ALN as the bone-targeting molecule. And our study is the first to employ a bone-targeted delivery system to deliver PA for OVX-induced bone loss, providing an innovative solution for treating osteoporosis.

Biosynthesis and signal transduction of plant growth regulators and their effects on bioactive compound production in Salvia miltiorrhiza (Danshen)

Plant growth regulators (PGRs) are involved in multiple aspects of plant life, including plant growth, development, and response to environmental stimuli. They are also vital for the formation of secondary metabolites in various plants. Salvia miltiorrhiza is a famous herbal medicine and has been used commonly for > 2000 years in China, as well as widely used in many other countries. S. miltiorrhiza is extensively used to treat cardiovascular and cerebrovascular diseases in clinical practices and has specific merit against various diseases. Owing to its outstanding medicinal and commercial potential, S. miltiorrhiza has been extensively investigated as an ideal model system for medicinal plant biology. Tanshinones and phenolic acids are primary pharmacological constituents of S. miltiorrhiza. As the growing market for S. miltiorrhiza, the enhancement of its bioactive compounds has become a research hotspot. S. miltiorrhiza exhibits a significant response to various PGRs in the production of phenolic acids and tanshinones. Here, we briefly review the biosynthesis and signal transduction of PGRs in plants. The effects and mechanisms of PGRs on bioactive compound production in S. miltiorrhiza are systematically summarized and future research is discussed. This article provides a scientific basis for further research, cultivation, and metabolic engineering in S. miltiorrhiza.

High-quality chromosome-level genome assembly and multi-omics analysis of rosemary (Salvia rosmarinus) reveals new insights into the environmental and genome adaptation

High-quality genome of rosemary (Salvia rosmarinus) represents a valuable resource and tool for understanding genome evolution and environmental adaptation as well as its genetic improvement. However, the existing rosemary genome did not provide insights into the relationship between antioxidant components and environmental adaptability. In this study, by employing Nanopore sequencing and Hi-C technologies, a total of 1.17 Gb (97.96%) genome sequences were mapped to 12 chromosomes with 46 121 protein-coding genes and 1265 non-coding RNA genes. Comparative genome analysis reveals that rosemary had a closely genetic relationship with Salvia splendens and Salvia miltiorrhiza, and it diverged from them approximately 33.7 million years ago (MYA), and one whole-genome duplication occurred around 28.3 MYA in rosemary genome. Among all identified rosemary genes, 1918 gene families were expanded, 35 of which are involved in the biosynthesis of antioxidant components. These expanded gene families enhance the ability of rosemary adaptation to adverse environments. Multi-omics (integrated transcriptome and metabolome) analysis showed the tissue-specific distribution of antioxidant components related to environmental adaptation. During the drought, heat and salt stress treatments, 36 genes in the biosynthesis pathways of carnosic acid, rosmarinic acid and flavonoids were up-regulated, illustrating the important role of these antioxidant components in responding to abiotic stresses by adjusting ROS homeostasis. Moreover, cooperating with the photosynthesis, substance and energy metabolism, protein and ion balance, the collaborative system maintained cell stability and improved the ability of rosemary against harsh environment. This study provides a genomic data platform for gene discovery and precision breeding in rosemary. Our results also provide new insights into the adaptive evolution of rosemary and the contribution of antioxidant components in resistance to harsh environments.

Metabolomic and transcriptomic analyses highlight metabolic regulatory networks of Salvia miltiorrhiza in response to replant disease

BACKGROUND

Salvia miltiorrhiza, a well-known traditional Chinese medicine, frequently suffers from replant diseases that adversely affect its quality and yield. To elucidate S. miltiorrhiza's metabolic adaptations to replant disease, we analyzed its metabolome and transcriptome, comparing normal and replant diseased plants for the first time.

RESULTS

We identified 1,269 metabolites, 257 of which were differentially accumulated metabolites, and identified 217 differentially expressed genes. Integrated transcriptomic and metabolomic analyses revealed a significant up-regulation and co-expression of metabolites and genes associated with plant hormone signal transduction and flavonoid biosynthesis pathways in replant diseases. Within plant hormone signal transduction pathway, plants afflicted with replant disease markedly accumulated indole-3-acetic acid and abscisic acid, correlating with high expression of their biosynthesis-related genes (SmAmidase, SmALDH, SmNCED, and SmAAOX3). Simultaneously, changes in hormone concentrations activated plant hormone signal transduction pathways. Moreover, under replant disease, metabolites in the local flavonoid metabolite biosynthetic pathway were significantly accumulated, consistent with the up-regulated gene (SmHTC1 and SmHTC2). The qRT-PCR analysis largely aligned with the transcriptomic results, confirming the trends in gene expression. Moreover, we identified 10 transcription factors co-expressed with differentially accumulated metabolites.

CONCLUSIONS

Overall, we revealed the key genes and metabolites of S. miltiorrhiza under replant disease, establishing a robust foundation for future inquiries into the molecular responses to combat replant stress.

Genome-Wide Identification and Functional Analysis of Salvia miltiorrhiza MicroRNAs Reveal the Negative Regulatory Role of Smi-miR159a in Phenolic Acid Biosynthesis

MicroRNAs (miRNAs) are a group of endogenous small non-coding RNAs in plants. They play critical functions in various biological processes during plant growth and development. Salvia miltiorrhiza is a well-known traditional Chinese medicinal plant with significant medicinal, economic, and academic values. In order to elucidate the role of miRNAs in S. miltiorrhiza, six small RNA libraries from mature roots, young roots, stems, mature leaves, young leaves and flowers of S. miltiorrhiza and one degradome library from mixed tissues were constructed. A total of 184 miRNA precursors, generating 137 known and 49 novel miRNAs, were genome-widely identified. The identified miRNAs were predicted to play diversified regulatory roles in plants through regulating 891 genes. qRT-PCR and 5' RLM-RACE assays validated the negative regulatory role of smi-miR159a in SmMYB62, SmMYB78, and SmMYB80. To elucidate the function of smi-miR159a in bioactive compound biosynthesis, smi-miR159a transgenic hairy roots were generated and analyzed. The results showed that overexpression of smi-miR159a caused a significant decrease in rosmarinic acid and salvianolic acid B contents. qRT-PCR analysis showed that the targets of smi-miR159a, including SmMYB62, SmMYB78, and SmMYB80, were significantly down-regulated, accompanied by the down-regulation of SmPAL1, SmC4H1, Sm4CL1, SmTAT1, SmTAT3, SmHPPR1, SmRAS, and SmCYP98A14 genes involved in phenolic acid biosynthesis. It suggests that smi-miR159a is a significant negative regulator of phenolic acid biosynthesis in S. miltiorrhiza.

The Smi-miR858a-SmMYB module regulates tanshinone and phenolic acid biosynthesis in Salvia miltiorrhiza

Tanshinones and phenolic acids are two major classes of bioactive compounds in Salvia miltiorrhiza. Revealing the regulatory mechanism of their biosynthesis is crucial for quality improvement of S. miltiorrhiza medicinal materials. Here we demonstrated that Smi-miR858a-Smi-miR858c, a miRNA family previously known to regulate flavonoid biosynthesis, also played critical regulatory roles in tanshinone and phenolic acid biosynthesis in S. miltiorrhiza. Overexpression of Smi-miR858a in S. miltiorrhiza plants caused significant growth retardation and tanshinone and phenolic acid reduction. Computational prediction and degradome and RNA-seq analyses revealed that Smi-miR858a could directly cleave the transcripts of SmMYB6, SmMYB97, SmMYB111, and SmMYB112. Yeast one-hybrid and transient transcriptional activity assays showed that Smi-miR858a-regulated SmMYBs, such as SmMYB6 and SmMYB112, could activate the expression of SmPAL1 and SmTAT1 involved in phenolic acid biosynthesis and SmCPS1 and SmKSL1 associated with tanshinone biosynthesis. In addition to directly activating the genes involved in bioactive compound biosynthesis pathways, SmMYB6, SmMYB97, and SmMYB112 could also activate SmAOC2, SmAOS4, and SmJMT2 involved in the biosynthesis of methyl jasmonate, a significant elicitor of plant secondary metabolism. The results suggest the existence of dual signaling pathways for the regulation of Smi-miR858a in bioactive compound biosynthesis in S. miltiorrhiza.

Genome-Wide Identification and Expression Analysis of Sucrose Nonfermenting 1-Related Protein Kinase (SnRK) Genes in Salvia miltiorrhiza in Response to Hormone

The SnRK gene family is the chief component of plant stress resistance and metabolism through activating the phosphorylation of downstream proteins. S. miltiorrhiza is widely used for the treatment of cardiovascular diseases in Asian countries. However, information about the SnRK gene family of S. miltiorrhiza is not clear. The aim of this study is to comprehensively analyze the SnRK gene family of S. miltiorrhiza and its response to phytohormone. Here, 33 SmSnRK genes were identified and divided into three subfamilies (SmSnRK1, SmSnRK2 and SmSnRK3) according to phylogenetic analysis and domain. SmSnRK genes within same subgroup shared similar protein motif composition and were unevenly distributed on eight chromosomes of S. miltiorrhiza. Cis-acting element analysis showed that the promoter of SmSnRK genes was enriched with ABRE motifs. Expression pattern analysis revealed that SmSnRK genes were preferentially expressed in leaves and roots. Most SmSnRK genes were induced by ABA and MeJA treatment. Correlation analysis showed that SmSnRK3.15 and SmSnRK3.18 might positively regulate tanshinone biosynthesis; SmSnRK3.10 and SmSnRK3.12 might positively regulate salvianolic acid biosynthesis. RNAi-based silencing of SmSnRK2.6 down-regulated the biosynthesis of tanshinones and biosynthetic genes expression. An in vitro phosphorylation assay verified that SmSnRK2.2 interacted with and phosphorylated SmAREB1. These findings will provide a valuable basis for the functional characterization of SmSnRK genes and quality improvement of S. miltiorrhiza.

Endophytic fungus Penicillium steckii DF33 promoted tanshinones biosynthesis in Salvia miltiorrhiza by regulating the expression of CYP450 genes

Salvia miltiorrhiza, a prominent traditional Chinese medicinal resource, has been extensively employed in the management of cardiovascular and cerebrovascular ailments. Ensuring the consistency of S. miltiorrhiza raw materials revolves around the imperative task of maintaining stable tanshinones content and composition. An effective approach in this regard involves the utilization of endophytic fungi as inducers. Within this context, our study spotlights an endophytic fungus, Penicillium steckii DF33, isolated from the roots of S. miltiorrhiza. Remarkably, this fungus has demonstrated a significant capacity to boost the biosynthesis and accumulation of tanshinones. The primary objective of this investigation is to elucidate the underlying regulatory mechanism by which DF33 enhances and regulates the biosynthesis and accumulation of tanshinones. This is achieved through its influence on the differential expression of crucial CYP450 genes within the S. miltiorrhiza hairy roots system. The results revealed that the DF33 elicitor not only promotes the growth of hairy roots but also enhances the accumulation of tanshinones. Notably, the content of cryptotanshinone was reached 1.6452 ± 0.0925 mg g-1, a fourfold increase compared to the control group. Our qRT-PCR results further demonstrate that the DF33 elicitor significantly up-regulates the expression of most key enzyme genes (GGPPS, CPS1, KSL1, CYP76AH1, CYP76AH3, CYP76AK1, CYP71D411) involved in the tanshinone biosynthesis pathway. This effect is particularly pronounced in certain critical CYP450 genes and Tanshinone ⅡA synthase (SmTⅡAS), with their expression levels peaking at 7 days or 14 days, respectively. In summary, endophytic P. steckii DF33 primarily enhances tanshinone biosynthesis by elevating the expression levels of pivotal enzyme genes associated with the modification and transformation stages within the tanshinone biosynthesis pathway. These findings underscore the potential of employing plant probiotics, specifically endophytic and root-associated microbes, to facilitate the biosynthesis and transformation of vital constituents in medicinal plants, and this approach holds promise for enhancing the quality of traditional Chinese medicinal materials.

Characterization of CYP82 genes involved in the biosynthesis of structurally diverse benzylisoquinoline alkaloids in Corydalis yanhusuo

Benzylisoquinoline alkaloids (BIAs) represent a significant class of secondary metabolites with crucial roles in plant physiology and substantial potential for clinical applications. CYP82 genes are involved in the formation and modification of various BIA skeletons, contributing to the structural diversity of compounds. In this study, Corydalis yanhusuo, a traditional Chinese medicine rich in BIAs, was investigated to identify the catalytic function of CYP82s during BIA formation. Specifically, 20 CyCYP82-encoding genes were cloned, and their functions were identified in vitro. Ten of these CyCYP82s were observed to catalyze hydroxylation, leading to the formation of protopine and benzophenanthridine scaffolds. Furthermore, the correlation between BIA accumulation and the expression of CyCYP82s in different tissues of C. yanhusuo was assessed their. The identification and characterization of CyCYP82s provide novel genetic elements that can advance the synthetic biology of BIA compounds such as protopine and benzophenanthridine, and offer insights into the biosynthesis of BIAs with diverse structures in C. yanhusuo.

Molecular regulation of the key specialized metabolism pathways in medicinal plants

The basis of modern pharmacology is the human ability to exploit the production of specialized metabolites from medical plants, for example, terpenoids, alkaloids, and phenolic acids. However, in most cases, the availability of these valuable compounds is limited by cellular or organelle barriers or spatio-temporal accumulation patterns within different plant tissues. Transcription factors (TFs) regulate biosynthesis of these specialized metabolites by tightly controlling the expression of biosynthetic genes. Cutting-edge technologies and/or combining multiple strategies and approaches have been applied to elucidate the role of TFs. In this review, we focus on recent progress in the transcription regulation mechanism of representative high-value products and describe the transcriptional regulatory network, and future perspectives are discussed, which will help develop high-yield plant resources.

Genome-Wide Identification and Characterization of the Salvia miltiorrhiza Histone Deacetylase (HDAC) Family in Response to Multiple Abiotic Stresses

Salvia miltiorrhiza is a plant commonly used in traditional Chinese medicine. Its material bases for treating diseases are tanshinones and phenolic acids, including salvianolic acids. Histone deacetylase proteins (HDACs) are a class of specific functional enzymes that interact with acetylation groups on the N-terminal lysine of histone proteins further regulate gene transcription through structural changes at the chromatin level. HDACs involved in the growth and development of various plants, and induced by plant hormones to regulate the internal environment of plants to resist stress, at the same time affect the accumulation of some secondary metabolites. However, the role of SmHDACs on the accumulation of salvianolic acid in S. miltiorrhiza remains unclear. In this study, 16 SmHDACs genes were identified from the high-quality S. miltiorrhiza genome, their physicochemical properties were predicted. In phylogenetic trees co-constructed with HDACs proteins from other plants, SmHDACs was divided into three subfamilies, each with similar motif and conserved domain composition. The distribution of the three subfamilies is similar to that of dicotyledonous plants. Chromosome localization analysis showed that SmHDACs genes were randomly located. Cis-acting element analysis predicted that SmHDACs gene expression may be related to and induced by various phytohormones, such as MeJA and ABA. By combining the expression pattern and co-expression network induced by phytohormones, we speculate that SmHDACs may further influence the synthesis of salvianolic acid, and identified SmHDA5, a potential functional gene, then speculate its downstream target based on the co-expression network. In summary, we analyzed the SmHDACs gene family of S. miltiorrhiza and screened out the potential functional gene SmHDA5. From the perspective of epigenetics, we proposed the molecular mechanism of plant hormone promoting salvianolic acid synthesis, which filled the gap in the subdivision of histone deacetylase in S. miltiorrhiza research, provided a theoretical basis for the culture and transformation of S. miltiorrhiza germplasm resources.

Comparative transcriptomics of two Salvia subg. Perovskia species contribute towards molecular background of abietane-type diterpenoid biosynthesis

Tanshinones, are a group of diterpenoid red pigments present in Danshen - an important herbal drug of Traditional Chinese Medicine which is a dried root of Salvia miltiorrhiza Bunge. Some of the tanshinones are sought after as pharmacologically active natural products. To date, the biosynthetic pathway of tanshinones has been only partially elucidated. These compounds are also present in some of the other Salvia species, i.a. from subgenus Perovskia, such as S. abrotanoides (Kar.) Sytsma and S. yangii B.T. Drew. Despite of the close genetic relationship between these species, significant qualitative differences in their diterpenoid profile have been discovered. In this work, we have used the Liquid Chromatography-Mass Spectrometry analysis to follow the content of diterpenoids during the vegetation season, which confirmed our previous observations of a diverse diterpenoid profile. As metabolic differences are reflected in different transcript profile of a species or tissues, we used metabolomics-guided transcriptomic approach to select candidate genes, which expression possibly led to observed chemical differences. Using an RNA-sequencing technology we have sequenced and de novo assembled transcriptomes of leaves and roots of S. abrotanoides and S. yangii. As a result, 134,443 transcripts were annotated by UniProt and 56,693 of them were assigned as Viridiplantae. In order to seek for differences, the differential expression analysis was performed, which revealed that 463, 362, 922 and 835 genes indicated changes in expression in four comparisons. GO enrichment analysis and KEGG functional analysis of selected DEGs were performed. The homology and expression of two gene families, associated with downstream steps of tanshinone and carnosic acid biosynthesis were studied, namely: cytochromes P-450 and 2-oxoglutarate-dependend dioxygenases. Additionally, BLAST analysis revealed existence of 39 different transcripts related to abietane diterpenoid biosynthesis in transcriptomes of S. abrotanoides and S. yangii. We have used quantitative real-time RT-PCR analysis of selected candidate genes, to follow their expression levels over the vegetative season. A hypothesis of an existence of a multifunctional CYP76AH89 in transcriptomes of S. abrotanoides and S. yangii is discussed and potential roles of other CYP450 homologs are speculated. By using the comparative transcriptomic approach, we have generated a dataset of candidate genes which provides a valuable resource for further elucidation of tanshinone biosynthesis. In a long run, our investigation may lead to optimization of diterpenoid profile in S. abrotanoides and S. yangii, which may become an alternative source of tanshinones for further research on their bioactivity and pharmacological therapy.

IMP: bridging the gap for medicinal plant genomics

Medicinal plants have garnered significant attention in ethnomedicine and traditional medicine due to their potential antitumor, anti-inflammatory and antioxidant properties. Recent advancements in genome sequencing and synthetic biology have revitalized interest in natural products. Despite the availability of sequenced genomes and transcriptomes of these plants, the absence of publicly accessible gene annotations and tabular formatted gene expression data has hindered their effective utilization. To address this pressing issue, we have developed IMP (Integrated Medicinal Plantomics), a freely accessible platform at https://www.bic.ac.cn/IMP. IMP curated a total of 8 565 672 genes for 84 high-quality genome assemblies, and 2156 transcriptome sequencing samples encompassing various organs, tissues, developmental stages and stimulations. With the integrated 10 analysis modules, users could simply examine gene annotations, sequences, functions, distributions and expressions in IMP in a one-stop mode. We firmly believe that IMP will play a vital role in enhancing the understanding of molecular metabolic pathways in medicinal plants or plants with medicinal benefits, thereby driving advancements in synthetic biology, and facilitating the exploration of natural sources for valuable chemical constituents like drug discovery and drug production.

Multiomics analyses of two Leonurus species illuminate leonurine biosynthesis and its evolution

The Lamiaceae family is renowned for its terpenoid-based medicinal components, but Leonurus, which has traditional medicinal uses, stands out for its alkaloid-rich composition. Leonurine, the principal active compound found in Leonurus, has demonstrated promising effects in reducing blood lipids and treating strokes. However, the biosynthetic pathway of leonurine remains largely unexplored. Here, we present the chromosome-level genome sequence assemblies of Leonurus japonicus, known for its high leonurine production, and Leonurus sibiricus, characterized by very limited leonurine production. By integrating genomics, RNA sequencing, metabolomics, and enzyme activity assay data, we constructed the leonurine biosynthesis pathway and identified the arginine decarboxylase (ADC), uridine diphosphate glucosyltransferase (UGT), and serine carboxypeptidase-like (SCPL) acyltransferase enzymes that catalyze key reactions in this pathway. Further analyses revealed that the UGT-SCPL gene cluster evolved by gene duplication in the ancestor of Leonurus and neofunctionalization of SCPL in L. japonicus, which contributed to the accumulation of leonurine specifically in L. japonicus. Collectively, our comprehensive study illuminates leonurine biosynthesis and its evolution in Leonurus.

Cytotoxic diterpenoids from Salvia glutinosa and comparison with the tanshinone profile of danshen (Salvia miltiorrhiza)

The roots of Salvia miltiorrhiza are the source of the traditional Chinese medicine danshen and the class of tanshinones, particular quinoid nor-diterpenoids of the abietane type. Of these compounds, cryptotanshinone, dihydrotanshinone I, tanshinone I, and tanshinone IIA, have been extensively studied for their anticancer potential, not only but as well because of their high abundance in S. miltiorrhiza and their thus easy availability. However, also additional Salvia species are known to contain tanshinones, mainly such of the subgenus Glutinaria, of which S. glutinosa is the only species widely occurring in Europe. Using UHPLC-DAD-MS, the tanshinone profile of S. glutinosa roots collected from two different locations was compared to the profile in S. miltiorrhiza roots. In addition, tanshinone IIA and another six diterpenoids from S. glutinosa were investigated for their antiproliferative and cytotoxic potential against MDA-MB-231 and HL-60 cells. Apart from dihydrotanshinone I, which has been previously characterized due to its anticancer properties, we determined danshenol A as a highly antiproliferative and cytotoxic agent, significantly surpassing the effects of dihydrotanshinone I. With regard to the diterpenoid profile, S. miltiorrhiza showed a higher concentration for most of the tanshinones, except for (+)-danshexinkun A, which was present in comparable amounts in both species. Danshenol A, in contrast, was only present in S. glutinosa as were dehydroabietic acid and (+)-pisiferic acid. The results of our study underlines the long traditional use of danshen due to its high amount on tanshinones, but also demonstrates the potential value of investigating closely related species for the discovery of new biologically active lead compounds.

Functional characterization of CYP81C16 involved in the tanshinone biosynthetic pathway in Salvia miltiorrhiza

Danshen, the dried roots and rhizomes of Salvia miltiorrhiza Bunge (S. miltiorrhiza), is widely used in the treatment of cardiovascular and cerebrovascular diseases. Tanshinones, the bioactive compounds from Danshen, exhibit a wide spectrum of pharmacological properties, suggesting their potential for future therapeutic applications. Tanshinone biosynthesis is a complex process involving at least six P450 enzymes that have been identified and characterized, most of which belong to the CYP76 and CYP71 families. In this study, CYP81C16, a member of the CYP71 clan, was identified in S. miltiorrhiza. An in vitro assay revealed that it could catalyze the hydroxylation of four para-quinone-type tanshinones, namely neocryptotanshinone, deoxyneocryptotanshinone, and danshenxinkuns A and B. SmCYP81C16 emerged as a potential broad-spectrum oxidase targeting the C-18 position of para-quinone-type tanshinones with an impressive relative conversion rate exceeding 90%. Kinetic evaluations andin vivo assays underscored its highest affinity towards neocryptotanshinone among the tested substrates. The overexpression of SmCYP81C16 promoted the accumulation of (iso)tanshinone in hairy root lines. The characterization of SmCYP81C16 in this study accentuates its potential as a pivotal tool in the biotechnological production of tanshinones, either through microbial or plant metabolic engineering.

Functions of Representative Terpenoids and Their Biosynthesis Mechanisms in Medicinal Plants

Terpenoids are the broadest and richest group of chemicals obtained from plants. These plant-derived terpenoids have been extensively utilized in various industries, including food and pharmaceuticals. Several specific terpenoids have been identified and isolated from medicinal plants, emphasizing the diversity of biosynthesis and specific functionality of terpenoids. With advances in the technology of sequencing, the genomes of certain important medicinal plants have been assembled. This has improved our knowledge of the biosynthesis and regulatory molecular functions of terpenoids with medicinal functions. In this review, we introduce several notable medicinal plants that produce distinct terpenoids (e.g., Cannabis sativa, Artemisia annua, Salvia miltiorrhiza, Ginkgo biloba, and Taxus media). We summarize the specialized roles of these terpenoids in plant-environment interactions as well as their significance in the pharmaceutical and food industries. Additionally, we highlight recent findings in the fields of molecular regulation mechanisms involved in these distinct terpenoids biosynthesis, and propose future opportunities in terpenoid research, including biology seeding, and genetic engineering in medicinal plants.

Advanced application of nanotechnology in active constituents of Traditional Chinese Medicines

Traditional Chinese Medicines (TCMs) have been used for centuries for the treatment and management of various diseases. However, their effective delivery to targeted sites may be a major challenge due to their poor water solubility, low bioavailability, and potential toxicity. Nanocarriers, such as liposomes, polymeric nanoparticles, inorganic nanoparticles and organic/inorganic nanohybrids based on active constituents from TCMs have been extensively studied as a promising strategy to improve the delivery of active constituents from TCMs to achieve a higher therapeutic effect with fewer side effects compared to conventional formulations. This review summarizes the recent advances in nanocarrier-based delivery systems for various types of active constituents of TCMs, including terpenoids, polyphenols, alkaloids, flavonoids, and quinones, from different natural sources. This review covers the design and preparation of nanocarriers, their characterization, and in vitro/vivo evaluations. Additionally, this review highlights the challenges and opportunities in the field and suggests future directions for research. Nanocarrier-based delivery systems have shown great potential in improving the therapeutic efficacy of TCMs, and this review may serve as a comprehensive resource to researchers in this field.

CYP72D19 from Tripterygium wilfordii catalyzes C-2 hydroxylation of abietane-type diterpenoids

KEY MESSAGE

CYP72D19, the first functional gene of the CYP72D subfamily, catalyzes the C-2 hydroxylation of abietane-type diterpenoids. The abietane-type diterpenoids, e.g., triptolide, tripdiolide, and 2-epitripdiolide, are the main natural products for the anti-tumor, anti-inflammatory, and immunosuppressive activities of Tripterygium wilfordii, while their biosynthetic pathways are not resolved. Here, we cloned and characterized the CYP72D19-catalyzed C-2 hydroxylation of dehydroabietic acid, a compound that has been proven to be a biosynthetic intermediate in triptolide biosynthesis. Through molecular docking and site-directed mutagenesis, L386, L387, and I493 near the active pocket were found to have an important effect on the enzyme activity, which also indicates that steric hindrance of residues plays an important role in function. In addition, CYP72D19 also catalyzed a variety of abietane-type diterpenoids with benzene ring, presumably because the benzene ring of the substrate molecule stabilized the C-ring, allowing the protein and the substrate to form a relatively stable spatial structure. This is the first demonstration of CYP72D subfamily gene function. Our research provides important genetic elements for the structural modification of active ingredients and the heterologous production of other 2-hydroxyl abietane-type natural products.

Identification of novel flavin-dependent monooxygenase from Strobilanthes Cusia reveals molecular basis of indoles' biosynthetic logic

BACKGROUND

Strobilanthes cusia (Nees) Kuntze is a traditional medical plant distributed widely in south China. The indole compounds that originated from the plant are responsible for its pharmacological activities. However, the reason why indole ingredients are accumulated in this herb and how it is biosynthesized has remained largely unknown.

RESULTS

In this study, metabolic and transcriptional profiling measurement experiments of different S. cusia organs were carried out to understand the underlying molecular basis of indoles' biosynthetic logic. A metabolic investigation demonstrated that the indoles are primarily accumulated mainly in aerial parts, particularly in leaves. RNA-seq was employed to reveal the organ specific accumulation of indoles in different S. cusia organs. Meanwhile, a flavin-dependent monooxygenase gene (ScFMO1) was found in S. cusia, and it has capacity to produce indoxyl from indole by the fermentation assay. Finally, we assessed the outcomes of transient expression experiment in tobacco and confirmed that ScFMO1 localizes in cytoplasm.

CONCLUSIONS

Our results suggest that ScFMO1 plays a key role in biosynthesis of indoles (Indigo, indirubin, indican, etc.), it will be useful for illuminating the molecular basis of the medicinal indoles' biosynthesis and developing strategies for improving their yields.

Phenotyping of Salvia miltiorrhiza Roots Reveals Associations between Root Traits and Bioactive Components

Plant phenomics aims to perform high-throughput, rapid, and accurate measurement of plant traits, facilitating the identification of desirable traits and optimal genotypes for crop breeding. Salvia miltiorrhiza (Danshen) roots possess remarkable therapeutic effect on cardiovascular diseases, with huge market demands. Although great advances have been made in metabolic studies of the bioactive metabolites, investigation for S. miltiorrhiza roots on other physiological aspects is poor. Here, we developed a framework that utilizes image feature extraction software for in-depth phenotyping of S. miltiorrhiza roots. By employing multiple software programs, S. miltiorrhiza roots were described from 3 aspects: agronomic traits, anatomy traits, and root system architecture. Through K-means clustering based on the diameter ranges of each root branch, all roots were categorized into 3 groups, with primary root-associated key traits. As a proof of concept, we examined the phenotypic components in a series of randomly collected S. miltiorrhiza roots, demonstrating that the total surface of root was the best parameter for the biomass prediction with high linear regression correlation (R2 = 0.8312), which was sufficient for subsequently estimating the production of bioactive metabolites without content determination. This study provides an important approach for further grading of medicinal materials and breeding practices.