Biosynthesis-based spatial metabolome of Salvia miltiorrhiza Bunge by combining metabolomics approaches with mass spectrometry-imaging

Promising mass spectrometry imaging: exploring microscale insights in food

This review focused on mass spectrometry imaging (MSI), a powerful tool in food analysis, covering its ion source schemes and procedures and their applications in food quality, safety, and nutrition to provide detailed insights into these aspects. The review presented a detailed introduction to both commonly used and emerging ionization sources, including nanoparticle laser desorption/ionization (NPs-LDI), air flow-assisted ionization (AFAI), desorption ionization with through-hole alumina membrane (DIUTHAME), plasma-assisted laser desorption ionization (PALDI), and low-temperature plasma (LTP). In the MSI process, particular emphasis was placed on quantitative MSI (QMSI) and super-resolution algorithms. These two aspects synergistically enhanced MSI's analytical capabilities: QMSI enabled accurate relative and absolute quantification, providing reliable data for composition analysis, while super-resolution algorithms improved molecular spatial imaging resolution, facilitating biomarker and trace substance detection. MSI outperformed conventional methods in comprehensively exploring food functional factors, biomarker discovery, and monitoring processing/storage effects by discerning molecular species and their spatial distributions. However, challenges such as immature techniques, complex data processing, non-standardized instruments, and high costs existed. Future trends in instrument enhancement, multispectral integration, and data analysis improvement were expected to deepen our understanding of food chemistry and safety, highlighting MSI's revolutionary potential in food analysis and research.

Exploring natural product biosynthesis in plants with mass spectrometry imaging

The biosynthesis of natural products (NPs) is a complex dynamic spatial and temporal process that requires the collaboration of multiple disciplines to explore the underlying mechanisms. Mass spectrometry imaging (MSI) is a powerful technique for studying NPs due to its high molecular coverage and sensitivity without the need for labeling. To date, many analysts still use MSI primarily for visualizing the distribution of NPs in heterogeneous tissues, although studies have proved that it can provide crucial insights into the specialized spatial metabolic process of NPs. In this review we strive to bring awareness of the importance of MSI, and we advocate further exploitation of the spatial information obtained from MSI to establish metabolite-gene expression relationships.

Desorption Electrospray Ionization-Mass Spectrometry Imaging-Based Spatial Metabolomics for Visualizing and Comparing Ginsenosides and Lipids among Multiple Parts and Positions of the Panax ginseng Root

Ginsenosides and lipids are both bioactive ingredients for ginseng. Targeting these two categories of components, this study was designed to develop desorption electrospray ionization-mass spectrometry imaging approaches and spatial metabolomics strategies, achieving the visualization and differentiation among different parts of Panax ginseng root (e.g., rhizome, main root, lateral root, fibrous root, and adventitious root). Potential chemical markers were identified by searching an in-house ginsenoside library and online Lipid Maps database, together with high-resolution MS2 data analysis. Six ginsenosides and 11 lipids were diagnostic to differentiate five different parts of the P. ginseng root. Additionally, three ginsenosides and 20 lipids were identified as differential markers among the six positions of the main root of P. ginseng. High-abundance malonyl- and oleanolic acid-ginsenosides were observed in the rhizome. These results assist in understanding the accumulation of bioactive molecules all through the root of P. ginseng, which can benefit its quality control and rational use.

A holistic visualization for quality of Chinese materia medica: Structural and metabolic visualization by magnetic resonance imaging

The quality of Chinese materia medica (CMM) is a challenging and focused topic in the modernization of traditional Chinese medicine (TCM). A profound comprehension of the morphology, structure, active constituents, and dynamic changes during the whole process of CMM growth is essential, which needs highly precise contemporary techniques for in-depth elucidation. Magnetic resonance imaging (MRI) is a cutting-edge tool integrating the benefits of both nuclear magnetic resonance (NMR) spectroscopy and imaging technology. With real-time, non-destructive, and in situ detection capabilities, MRI has been previously used for monitoring internal and external structures of plants alongside compounds during physiological processes in vivo. Here, factors involved in the holistic quality evaluation of CMMs were investigated. Given the applications of MRI in various plants, several representative CMMs were used as examples to demonstrate a methodology of quality visualization by MRI, embodying holistically monitoring the real-time macroscopic morphology, mesoscopic structure, and microscopic metabolites non-destructively in situ. Taken together, the review not only presents a pioneering application mode for utilizing MRI for CMM quality visualization but also holds promise for advancing the quality control and evaluation of CMMs.

Effect of soil and community factors on the yield and medicinal quality of Artemisia argyi growth at different altitudes of the Funiu mountain

Altitude and ecological factors significantly influence plant growth and the accumulation of secondary metabolites. However, current research on the impact of altitude and ecological factors on the yield and medicinal quality of Artemisia argyi (A. argyi) is limited. This study established sampling sites in wild populations of A. argyi across seven altitude ranges on Funiu Mountain. We quantified the yield, output rate of moxa, and key medicinal ingredients. Additionally, we analyzed the response of yield and medicinal quality of wild A. argyi populations to various ecological factors at different altitudes. The results showed that wild populations of A. argyi exhibited higher yields and medicinal quality at altitudes below 500 m. Yield was positively correlated with higher soil total nitrogen (TN) content and lower soil total phosphorus (TP) content, while the improvements in medicinal quality were positively associated with higher population density and lower contents of both soil TN and TP. The variation in soil C/N, C/P, and N/P ratios across different altitudes was substantial, affecting soil mineralization and subsequently influencing the absorption of mineral elements by A. argyi. Notably, the phosphorus content in leaves and stems was negatively correlated with yield and medicinal quality, respectively. In contrast, the accumulation of nitrogen, phosphorus, and potassium in leaves was positively correlated with yield. The differences in the primary medicinal ingredients between the leaves and stems of A. argyi were maximum at altitudes below 500 m. The contents of neochlorogenic acid and cryptochlorogenic acid in both leaves and stems showed a significant positive correlation. In the principal component analysis, the primary medicinal ingredients from the leaves contributed more significantly to the overall quality than those from stems. These results suggest that A. argyi is best suited for cultivation at altitudes below 500 m. Population density and the soil's TN and TP contents play a crucial role in determining the yield and medicinal quality of A. argyi. Futhermore, the medicinal quality of A. argyi is more indicative of the main medicinal ingredients found in the leaves, while the stems also serve as a key organ for accumulating flavonoids and phenolic acids.

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.

Recent Advances and New Insights in Genome Analysis and Transcriptomic Approaches to Reveal Enzymes Associated with the Biosynthesis of Dendrobine-Type Sesquiterpenoid Alkaloids (DTSAs) from the Last Decade

Dendrobium species, which are perennial herbs widely distributed in tropical and subtropical regions, are notable for their therapeutic properties attributed to various bioactive compounds, including dendrobine-type sesquiterpenoid alkaloids (DTSAs). The objective of this review article is to provide a comprehensive overview of recent advances in the biosynthesis of DTSAs, including their extraction from Dendrobium species and endophytes, elucidation of associated genes through genomic and transcriptomic sequencing in both Dendrobium spp. and endophytes, exploration of the biosynthetic pathways of DTSAs, and drawing conclusions and outlining future perspectives in this field. Alkaloids, predominantly nitrogen-containing compounds found in medicinal orchids, include over 140 types discovered across more than 50 species. DTSAs, identified in 37 picrotoxane alkaloids, have a distinctive five-membered nitrogen heterocyclic ring. This review highlights endophytic fungi as alternative sources of DTSAs, emphasizing their potential in pharmaceutical applications when plant-derived compounds are scarce or complex. Genomic and transcriptomic sequencing of Dendrobium spp. and their endophytes has identified key genes involved in DTSAs biosynthesis, elucidating pathways such as the mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways. Genes encoding enzymes, such as acetyl-CoA C-acetyltransferase and diphosphomevalonate decarboxylase, are positively associated with dendrobine production. Despite significant advancements, the complexity of terpenoid biosynthesis in different subcellular compartments remains a challenge. Future research should focus on leveraging high-quality genomic data and omics technologies to further understand and manipulate the biosynthetic pathways of DTSAs and enhance their medicinal use.

Mass spectrometry imaging as a promising analytical technique for herbal medicines: an updated review

Herbal medicines (HMs) have long played a pivotal role in preventing and treating various human diseases and have been studied widely. However, the complexities present in HM metabolites and their unclear mechanisms of action have posed significant challenges in the modernization of traditional Chinese medicine (TCM). Over the past two decades, mass spectrometry imaging (MSI) has garnered increasing attention as a robust analytical technique that enables the simultaneous execution of qualitative, quantitative, and localization analyses without complex sample pretreatment. With advances in technical solutions, MSI has been extensively applied in the field of HMs. MSI, a label-free ion imaging technique can comprehensively map the spatial distribution of HM metabolites in plant native tissues, thereby facilitating the effective quality control of HMs. Furthermore, the spatial dimension information of small molecule endogenous metabolites within animal tissues provided by MSI can also serve as a supplement to uncover pharmacological and toxicological mechanisms of HMs. In the review, we provide an overview of the three most common MSI techniques. In addition, representative applications in HM are highlighted. Finally, we discuss the current challenges and propose several potential solutions. We hope that the summary of recent findings will contribute to the application of MSI in exploring metabolites and mechanisms of action of HMs.

Identification of Plant Compounds with Mass Spectrometry Imaging (MSI)

The presence and localization of plant metabolites are indicative of physiological processes, e.g., under biotic and abiotic stress conditions. Further, the chemical composition of plant parts is related to their quality as food or for medicinal applications. Mass spectrometry imaging (MSI) has become a popular analytical technique for exploring and visualizing the spatial distribution of plant molecules within a tissue. This review provides a summary of mass spectrometry methods used for mapping and identifying metabolites in plant tissues. We present the benefits and the disadvantages of both vacuum and ambient ionization methods, considering direct and indirect approaches. Finally, we discuss the current limitations in annotating and identifying molecules and perspectives for future investigations.

Drying enhances the antioxidant activity of Allium mongolicum Regel through the phenylpropane and AA-MA pathway as shown by metabolomics

Fresh Allium mongolicum Regel (FA) and dried A. mongolicum Regel (DA) are significantly different in antioxidant activity. However, the relevant mechanisms have not yet been explored. We evaluated the antioxidant activities of two varieties of FA and DA and characterized their metabolites using targeted metabolomics. The effect of different metabolites on the antioxidant activity of A. mongolicum Regel was investigated by multivariate analysis. A total of 713 metabolites were detected in all samples. Pearson correlation analysis demonstrated that the key primary metabolites were directly and significantly correlated with the total phenolic content (TPC) and total flavonoid content (TFC), while the secondary metabolites were directly correlated with antioxidant activity. The higher antioxidant activity of DA may be mainly attributed to the higher TPC and TFC. This study revealed the potential mechanism by which drying enhances the antioxidant activity of A. mongolicum Regel.

Spatial metabolome of biosynthesis and metabolism in Cyclocarya paliurus leaves

A large number of plant metabolites were discovered, but their biosynthetic and metabolic pathways are still largely unknown. However, the spatial distribution of metabolites and their changes in metabolic pathways can be supplemented by mass spectrometry imaging (MSI) techniques. For this purpose, the combination of desorption electrospray ionization (DESI)-MSI and non-targeted metabolomics was used to obtain the spatial distribution information of metabolites in the leaves of Cyclocarya paliurus (Batal.) Iljinskaja (C. paliurus). The sample pretreatment method was optimized to have higher detection sensitivity in DESI. The changes of metabolites in C. paliurus were analyzed in depth with the integration of the spatial distribution information of metabolites. The main pathways for biosynthesis of flavonoid precursor and the effect of changes in compound structure on the spatial distribution were found. Spatial metabolomics can provide more metabolite information and a platform for the in-depth understanding of the biosynthesis and metabolism in plants.

Nontargeted metabolomics and enzyme inhibitory and antioxidant activities for chemical and biological characterization of jujube (Ziziphus jujuba) extracts

The chemical and biologically active characterization of jujube samples (fruits, cores, and leaves) were carried out by the integrated nontargeted metabolomics and bioassay. Firstly, collision cross-section values of active compounds in jujubes were determined by ultrahigh-performance liquid chromatography coupled with ion mobility quadrupole time-of-flight mass spectrometry. Then, a multidimensional statistical analysis that contained principal component analysis, partial least squares-discriminant analysis and hierarchical clustering analysis was employed to effectively cluster different tissues and types of jujubes, making identification more scientific. Furthermore, angiotensin-converting enzyme (ACE) and 2, 2-diphenyl-1-picrylhydrazyl (DPPH) were used to evaluate the quality of jujubes from a double activity dimension. The analytical results obtained by using ACE and DPPH to evaluate the quality of jujube were different from multivariate statistics, providing a reference for the application of jujube. Therefore, integrating chemical and biological perspectives to evaluate the quality of jujube provided a more comprehensive evaluation and effective reference for clinical needs.

Imaging plant metabolism in situ

Mass spectrometry imaging (MSI) has emerged as an invaluable analytical technique for investigating the spatial distribution of molecules within biological systems. In the realm of plant science, MSI is increasingly employed to explore metabolic processes across a wide array of plant tissues, including those in leaves, fruits, stems, roots, and seeds, spanning various plant systems such as model species, staple and energy crops, and medicinal plants. By generating spatial maps of metabolites, MSI has elucidated the distribution patterns of diverse metabolites and phytochemicals, encompassing lipids, carbohydrates, amino acids, organic acids, phenolics, terpenes, alkaloids, vitamins, pigments, and others, thereby providing insights into their metabolic pathways and functional roles. In this review, we present recent MSI studies that demonstrate the advances made in visualizing the plant spatial metabolome. Moreover, we emphasize the technical progress that enhances the identification and interpretation of spatial metabolite maps. Within a mere decade since the inception of plant MSI studies, this robust technology is poised to continue as a vital tool for tackling complex challenges in plant metabolism.

Combined Widely Targeted Metabolomic, Transcriptomic, and Spatial Metabolomic Analysis Reveals the Potential Mechanism of Coloration and Fruit Quality Formation in Actinidia chinensis cv. Hongyang

Postharvest kiwifruit (Actinidia chinensis cv. Hongyang) pulp is mainly composed of outer yellow-flesh (LR) and inner red-flesh (HR). However, information about the differences in coloration and fruit quality between these two parts are limited. In this study, widely targeted metabolomic, transcriptomic, and spatial metabolomic analyses were used to reveal the potential mechanism of coloration and fruit quality formation. The results show that a total of 1001 metabolites were identified in Hongyang kiwifruit, and the accumulation of 211 metabolites were significantly higher in the HR than LR, including 69 flavonoids, 53 phenolic acids, and 38 terpenoids. There were no significant differences in the content of citric acid, quinic acid, glucose, fructose, or sucrose between the LR and HR. These results were consistent with the results from the RNA-seq profile and spatial metabolomic analysis. In addition, a total of 23 key candidate genes related to flesh color and fruit quality formation were identified and validated by qRT-PCR analysis. This study provides a theoretical basis for elucidating the underlying mechanism of the formation of kiwifruit flesh color and fruit quality.

Identification and characterization of a novel tyrosine aminotransferase gene (SmTAT3-2) promotes the biosynthesis of phenolic acids in Salvia miltiorrhiza Bunge

Rosmarinic acid (RA) and salvianolic acid B (SAB) are main phenolic acids in Salvia miltiorrhiza Bunge have been widely used in the treatment of cardiovascular and cerebrovascular diseases due to their excellent pharmacological activity. RA is a precursor of SAB, and tyrosine transaminase (TAT, EC 2.6.1.5) is a crucial rate-limiting enzyme in their metabolism pathway. This study identified a novel TAT gene, SmTAT3-2, and found that it is a new transcript derived from unconventional splicing of SmTAT3. We used different substrates for enzymatic reaction with SmTAT1, SmTAT3 and SmTAT3-2. Subcellular localization of SmTAT1 and SmTAT3-2 was completed based on submicroscopic techniques. In addition, they were overexpressed and CRISPR/Cas9 gene edited in hairy roots of S. miltiorrhiza. Revealed SmTAT3-2 and SmTAT1 showed a stronger affinity for L-tyrosine than SmTAT3, localized in the cytoplasm, and promoted the synthesis of phenolic acid. In overexpressed SmTAT3-2 hairy roots, the content of RA and SAB was significantly increased by 2.53 and 3.38 fold, respectively, which was significantly higher than that of overexpressed SmTAT1 strain compared with EV strain. These findings provide a valuable key enzyme gene for the phenolic acids metabolism pathway and offer a theoretical basis for the clinical application.

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.

Comparative metabolomic and transcriptomic analysis of Saccharomyces cerevisiae W303a and CEN.PK2-1C

Saccharomyces cerevisiae is a health microorganism closely related to human life, especially in food and pharmaceutical industries. S. cerevisiae W303a and CEN.PK2-1C are two commonly used strains for synthetic biology-based natural product production. Yet, the metabolomic and transcriptomic differences between these two strains have not been compared. In this study, metabolomics and transcriptomics were applied to analyze the differential metabolites and differential expression genes (DEGs) between W303a and CEN.PK2-1C cultured in YPD and SD media. The growth rate of W303a in YPD medium was the lowest compared with other groups. When cultured in YPD medium, CEN.PK2-1C produced more phenylalanine than W303a; when cultured in SD medium, W303a produced more phospholipids than CEN.PK2-1C. Transcriptomic analysis revealed that 19 out of 22 genes in glycolysis pathway were expressed at higher levels in CEN.PK2-1C than that in W303a no matter which media were used, and three key genes related to phenylalanine biosynthesis including ARO9, ARO7 and PHA2 were up-regulated in CEN.PK2-1C compared with W303a when cultured in YPD medium, whereas seven DEGs associated with phospholipid biosynthesis were up-regulated in W303a compared with CEN.PK2-1C when cultured in SD medium. The high phenylalanine produced by CEN.PK2-1C and high phospholipids produced by W303a indicated that CEN.PK2-1C may be more suitable for synthesis of natural products with phenylalanine as precursor, whereas W303a may be more appropriate for synthesis of phospholipid metabolites. This finding provides primary information for strain selection between W303a and CEN.PK2-1C for synthetic biology-based natural product production.

Applications of ambient ionization mass spectrometry in 2022: An annual review

The development of ambient ionization mass spectrometry (AIMS) has transformed analytical science, providing the means of performing rapid analysis of samples in their native state, both in and out of the laboratory. The capacity to eliminate sample preparation and pre-MS separation techniques, leading to true real-time analysis, has led to AIMS naturally gaining a broad interest across the scientific community. Since the introduction of the first AIMS techniques in the mid-2000s, the field has exploded with dozens of novel ion sources, an array of intriguing applications, and an evident growing interest across diverse areas of study. As the field continues to surge forward each year, ambient ionization techniques are increasingly becoming commonplace in laboratories around the world. This annual review provides an overview of AIMS techniques and applications throughout 2022, with a specific focus on some of the major fields of research, including forensic science, disease diagnostics, pharmaceuticals and food sciences. New techniques and methods are introduced, demonstrating the unwavering drive of the analytical community to further advance this exciting field and push the boundaries of what analytical chemistry can achieve.

Desorption electrospray ionization and matrix-assisted laser desorption/ionization as imaging approaches for biological samples analysis

The imaging of biological tissues can offer valuable information about the sample composition, which improves the understanding of analyte distribution in such complex samples. Different approaches using mass spectrometry imaging (MSI), also known as imaging mass spectrometry (IMS), enabled the visualization of the distribution of numerous metabolites, drugs, lipids, and glycans in biological samples. The high sensitivity and multiple analyte evaluation/visualization in a single sample provided by MSI methods lead to various advantages and overcome drawbacks of classical microscopy techniques. In this context, the application of MSI methods, such as desorption electrospray ionization-MSI (DESI-MSI) and matrix-assisted laser desorption/ionization-MSI (MALDI-MSI), has significantly contributed to this field. This review discusses the evaluation of exogenous and endogenous molecules in biological samples using DESI and MALDI imaging. It offers rare technical insights not commonly found in the literature (scanning speed and geometric parameters), making it a comprehensive guide for applying these techniques step-by-step. Furthermore, we provide an in-depth discussion of recent research findings on using these methods to study biological tissues.

Time-series transcriptome provides insights into the gene regulation network involved in the icariin-flavonoid metabolism during the leaf development of Epimedium pubescens

Herba Epimedii (Epimedium) leaves are rich in prenylated flavonol glycosides (PFGs) with high medicinal value. However, the dynamics and regulatory network of PFG biosynthesis remain largely unclear. Here, we combined metabolite profiling (targeted to PFGs) and a high-temporal-resolution transcriptome to elucidate PFGs' regulatory network in Epimedium pubescens and identified key candidate structural genes and transcription factors (TFs) involved in PFG accumulation. Chemical profile analysis revealed that PFG content was quite different between buds and leaves and displayed a continuous decline with leaf development. The structural genes are the determinant reasons, and they are strictly regulated by TFs under temporal cues. We further constructed seven time-ordered gene co-expression networks (TO-GCNs) of PFG biosynthesis genes (including EpPAL2, EpC4H, EpCHS2, EpCHI2, EpF3H, EpFLS3, and EpPT8), and three flavonol biosynthesis routines were then predicted. The TFs involved in TO-GCNs were further confirmed by WGCNA analysis. Fourteen hub genes, comprising 5 MYBs, 1 bHLH, 1 WD40, 2 bZIPs, 1 BES1, 1 C2H2, 1 Trihelix, 1 HD-ZIP, and 1 GATA were identified as candidate key TFs. The results were further validated by TF binding site (TFBS) analysis and qRT-PCR. Overall, these findings provide valuable information for understanding the molecular regulatory mechanism of PFGs biosynthesis, enriching the gene resources, which will guide further research on PFG accumulation in Epimedium.

Seeing plants as never before

Imaging has long supported our ability to understand the inner life of plants, their development, and response to a dynamic environment. While optical microscopy remains the core tool for imaging, a suite of novel technologies is now beginning to make a significant contribution to visualize plant metabolism. The purpose of this review was to provide the scientific community with an overview of current imaging methods, which rely variously on either nuclear magnetic resonance (NMR), mass spectrometry (MS) or infrared (IR) spectroscopy, and to present some examples of their application in order to illustrate their utility. In addition to providing a description of the basic principles underlying these technologies, the review discusses their various advantages and limitations, reveals the current state of the art, and suggests their potential application to experimental practice. Finally, a view is presented as to how the technologies will likely develop, how these developments may encourage the formulation of novel experimental strategies, and how the enormous potential of these technologies can contribute to progress in plant science.

Spatially resolved metabolomics combined with bioactivity analyses to evaluate the pharmacological properties of two Radix Puerariae species

ETHNOPHARMACOLOGICAL RELEVANCE

P. lobata and P. thomsonii are medicinal plants with similar pharmacological functions but different therapeutic effects. A novel method is presented herein to investigate metabolites in terms of their distribution and qualification, quantification is necessary to elucidate the different therapeutic effects of the two Puerariae species.

AIM OF THE STUDY

The aim of the present study was to perform spatially resolved metabolomics combined with bioactivity analyses to systematically compare the metabolite differences in P. lobata and P. thomsonii by distribution, qualification, quantification, and biological activity to evaluate their pharmacological properties.

MATERIALS AND METHODS

Air flow-assisted desorption electrospray ionization-mass spectrometry imaging (AFADESI-MSI) was performed to characterize the differences in the metabolite distributions of P. lobata and P. thomsonii. Further qualitative and quantitative analyses of the differential metabolites were performed using liquid chromatography-mass spectrometry (LC-MS). Biological activities correlated with the differences in the metabolites were validated by MTT assays.

RESULTS

Some metabolites showed complementary distributions of the phloem and xylem in the two species, saccharide, vitamin, and inosine levels were higher in the phloem of P. thomsonii but higher in the xylem of P. lobata. The 3'-hydroxyl puerarin level was higher in the xylem of P. thomsonii but higher in the phloem of P. lobata. Qualitative and quantitative analyses of the metabolites revealed a total of 52 key differential metabolites. MTT assays showed that daidzein, daidzin, puerarin, ononin, genistin, formononetin, 3'-hydroxy puerarin, 3'-methoxy puerarin, mirificin, and 3'-methoxy daidzin exerted protective effects on H9c2 cells against hypoxia/reoxygenation injury. P. lobata extracts exhibited a significantly better protective efficacy than P. thomsonii extracts.

CONCLUSIONS

In this study, AFADESI-MSI combined with LC-MS and biological activities comprehensively elucidated metabolite differences in the distribution, qualification, quantification, and pharmacological properties of P. lobata and P. thomsonii. The results of this study could provide a novel strategy for species identification and quality assessment of similar Chinese herbal medicines.

Comparative analysis of the metabolites in Pinellia ternata from two producing regions using ultra-high-performance liquid chromatography–electrospray ionization–tandem mass spectrometry

The rhizomes of Pinellia ternata have a long history of being used as a traditional Chinese herb. To determine the chemical constituents of Pinelliae rhizome, Xi banxia and Jing banxia were collected from two different producing regions and subjected to analysis using ultra-high-performance liquid chromatography–electrospray ionization–tandem mass spectrometry. A total of 573 metabolites were identified in 12 different categories. Next, cluster analysis and principal component analysis were performed, which revealed a distinct separation between the two species. The analysis of the differential metabolites revealed that among the 155 metabolites in Xi banxia, 68 metabolites were upregulated, and 87 metabolites were downregulated. The relative concentration of flavonoids in Xi banxia was higher than that in Jing banxia, while the relative concentrations of alkaloids, phenolic acids, and terpenoids were higher in Jing banxia. These results would provide a theoretical basis for the pharmacological activity analysis and functional study of P. ternata.

Matrix-assisted laser-desorption/ionization-mass spectrometric imaging of psilocybin and its analogues in psychedelic mushrooms using a cesium chloride-coated target plate

Fungi with hallucinogenic properties and neurotoxicity have been listed as prohibited drugs in recent years, but there is a lack of in situ quantification of psilocybin and analogues in these samples to avoid the decomposition of these psychoactive tryptamines in time-consuming sample preparation. In this study, matrix-assisted laser-desorption/ionization (MALDI)-Fourier transform ion cyclotron resonance (FT ICR) mass spectrometric imaging (MSI) was used to analyze the distribution of psilocybin and its analogues in hallucinogenic Psilocybe mushrooms. A cesium chloride (CsCl)-coated target plate was prepared to improve the detection sensitivity and reduce the interference of other compounds or decomposition products with very similar m/z values in MALDI-FT ICR MS analysis. Psilocybin and other tryptamines with structurally similar compounds, including psilocin, baeocystin, tryptophan, tryptamine, and aeruginascin, were identified and imaged in the psilocybe tissue section; the semiquantitative analysis of the distribution of psilocybin was also investigated using a homemade 75-well CsCl-coated plate; and the target plate can be placed on the mass spectrometry target carrier along with the indium-tin oxide (ITO) conductive slide, which can simultaneously carry out matrix vapor deposition, thus ensuring the parallelism between the standards and samples in the pretreatment experiment and MSI. The contents of psilocybin and its analogues in the psilocybe tissue section can be evaluated from the color changes corresponding to different concentration standard curves. Furthermore, a comprehensive comparison between MALDI-FT ICR MS and ultra-performance liquid chromatography-quadrupole time of flight mass spectrometry (UPLC-Q/TOF MS) analysis was performed for quantification and validation. This study reduces the decomposition in time-consuming sample pretreatment and provides a powerful tool for drug abuse control and forensic analysis.

Rapid authentication of different herbal medicines by heating online extraction electrospray ionization mass spectrometry

The rapid and accurate authentication of traditional Chinese medicines (TCMs) has always been a key scientific and technical problem in the field of pharmaceutical analysis. Herein, a novel heating online extraction electrospray ionization mass spectrometry (H-oEESI-MS) was developed for the rapid and direct analysis of extremely complex substances without the requirement for any sample pretreatment or pre-separation steps. The overall molecular profile and fragment structure features of various herbal medicines could be completely captured within 10-15 s, with minimal sample (<0.5 mg) and solvent consumption (<20 μL for one sample). Furthermore, a rapid differentiation and authentication strategy for TCMs based on H-oEESI-MS was proposed, including metabolic profile characterization, characteristic marker screening and identification, and multivariate statistical analysis model validation. In an analysis of 52 batches of seven types of Aconitum medicinal materials, 20 and 21 key compounds were screened out as the characteristic markers of raw and processed Aconitum herbal medicines, respectively, and the possible structures of all the characteristic markers were comprehensively identified based on Compound Discoverer databases. Finally, multivariate statistical analysis showed that all the different types of herbal medicines were well differentiated and identified (R²X > 0.87, R²Y > 0.91, and Q² > 0.72), which further verified the feasibility and reliability of this comprehensive strategy for the rapid authentication of different TCMs based on H-oEESI-MS. In summary, this rapid authentication strategy realized the ultra-high-throughput, low-cost, and standardized detection of various complex TCMs for the first time, thereby demonstrating wide applicability and value for the development of quality standards for TCMs.

Metabolic profiling, in-situ spatial distribution, and biosynthetic pathway of functional metabolites in Dendrobium nobile stem revealed by combining UPLC-QTOF-MS with MALDI-TOF-MSI

The stem of Dendrobium nobile Lindl. (Orchidaceae), called "Shihu" in traditional Chinese medicine, is a well-known medicinal and edible plant material in China. It is used as an antipyretic, analgesic, and tonic to nourish the stomach and Yin (i.e., to improve the production of body fluids). These therapeutic properties are attributed to its alkaloids, sesquiterpenoids, bibenzyls, fluorenones, and phenanthrenes. However, a comprehensive understanding of these metabolites and their spatial distribution in stems is lacking. In this study, ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) was performed to obtain detailed metabolites information about D. nobile stems. Then, the spatial distributions of diverse metabolites, including alkaloids and sesquiterpenoids, were characterized and visualized by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry imaging (MALDI-TOF-MSI). Based on the spatial and metabolic profiling data, sesquiterpene alkaloid dendrobine was chosen for the exhaustive study of a biosynthetic pathway in D. nobile. This is the first report on mass spectrometry imaging for Dendrobium species. As a result, critical bioactive metabolites such as 11 alkaloids, 10 sesquiterpenes, and 13 other metabolites were putatively identified and relatively quantified. The identified alkaloids were distributed in the parenchyma or vascular bundle, and sesquiterpenes were present in all regions of the stem with higher abundance in the vascular bundle and cuticle, or in the cuticle and epidermis. The biosynthetic pathway and accumulation pattern of dendrobine in D. nobile stem were also proposed. Our findings not only provided a critical methodology for the thorough understanding of physiological changes in metabolites and precise utilization of D. nobile stem, but also displayed an effective strategy for insight into the biosynthesis of bioactive metabolites in plants.

Mass spectrometry imaging: new eyes on natural products for drug research and development

Natural products (NPs) and their structural analogs represent a major source of novel drug development for disease prevention and treatment. The development of new drugs from NPs includes two crucial aspects. One is the discovery of NPs from medicinal plants/microorganisms, and the other is the evaluation of the NPs in vivo at various physiological and pathological states. The heterogeneous spatial distribution of NPs in medicinal plants/microorganisms or in vivo can provide valuable information for drug development. However, few molecular imaging technologies can detect thousands of compounds simultaneously on a label-free basis. Over the last two decades, mass spectrometry imaging (MSI) methods have progressively improved and diversified, thereby allowing for the development of various applications of NPs in plants/microorganisms and in vivo NP research. Because MSI allows for the spatial mapping of the production and distribution of numerous molecules in situ without labeling, it provides a visualization tool for NP research. Therefore, we have focused this mini-review on summarizing the applications of MSI technology in discovering NPs from medicinal plants and evaluating NPs in preclinical studies from the perspective of new drug research and development (R&D). Additionally, we briefly reviewed the factors that should be carefully considered to obtain the desired MSI results. Finally, the future development of MSI in new drug R&D is proposed.

A mass spectrometry imaging approach on spatiotemporal distribution of multiple alkaloids in Gelsemium elegans

Gelsemium elegans contains multiple alkaloids with pharmacological effects, thus researchers focus on the identification and application of alkaloids extracted from G. elegans. Regretfully, the spatiotemporal distribution of alkaloids in G. elegans is still unclear. In this study, the desorption electrospray ionization mass spectrometry imaging (DESI-MSI) was applied to simultaneously analyze the distribution of pharmacologically important alkaloids in different organ/tissue sections of G. elegans at different growth stages. Finally, 23 alkaloids were visualized in roots, stems and leaves at seedling stage and 19 alkaloids were observed at mature stage. In mature G. elegans, 16 alkaloids were distributed in vascular bundle region of mature roots, 15 alkaloids were mainly located in the pith region of mature stems and 2 alkaloids were enriched in epidermis region of mature stems. A total of 16 alkaloids were detected in leaf veins of mature leaves and 17 alkaloids were detected in shoots. Interestingly, diffusion and transfer of multiple alkaloids in tissues have been observed along with the development and maturation. This study comprehensively characterized the spatial metabolomics of G. elegans alkaloids, and the spatiotemporal distribution of alkaloid synthesis. In addition, the results also have reference value for the development and application of Gelsemium elegans and other medicinal plants.

Spatiotemporal and Transcriptional Characterization on Tanshinone Initial Synthesis in Salvia miltiorrhiza Roots

Tanshinones are the bioactive constituents of Danshen (Salvia miltiorrhiza Bunge), which is used in Traditional Chinese Medicine to treat cardiovascular and other diseases, and they synthesize and accumulate in the root periderm of S. miltiorrhiza. However, there is no relevant report on the initial stage of tanshinone synthesis, as well as the root structure and gene expression characteristics. The present study aims to provide new insights into how these bioactive principles begin to synthesize by characterizing possible differences in their biosynthesis and accumulation during early root development from both spatial and temporal aspects. The morphological characteristics and the content of tanshinones in roots of S. miltiorrhiza were investigated in detail by monitoring the seedlings within 65 days after germination (DAGs). The ONT transcriptome sequencing was applied to investigate gene expression patterns. The periderm of the S. miltiorrhiza storage taproot initially synthesized tanshinone on about 30 DAGs. Three critical stages of tanshinone synthesis were preliminarily determined: preparation, the initial synthesis, and the continuous rapid synthesis. The difference of taproots in the first two stages was the smallest, and the differentially expressed genes (DEGs) were mainly enriched in terpene synthesis. Most genes involved in tanshinone synthesis were up regulated during the gradual formation of the red taproot. Plant hormone signal transduction and ABC transport pathways were widely involved in S. miltiorrhiza taproot development. Five candidate genes that may participate in or regulate tanshinone synthesis were screened according to the co-expression pattern. Moreover, photosynthetic ferredoxin (FD), cytochrome P450 reductase (CPR), and CCAAT binding transcription factor (CBF) were predicted to interact with the known downstream essential enzyme genes directly. The above results provide a necessary basis for analyzing the initial synthesis and regulation mechanism of Tanshinones.

Transgelin-2 Involves in the Apoptosis of Colorectal Cancer Cells Induced by Tanshinone-IIA

Tanshinone IIA (TanIIA) is the main active ingredient in the fat-soluble components isolated from Salvia miltiorrhiza Bunge. Our previous studies have convincingly proved that TanIIA is an effective drug against human colorectal carcinoma cells. In order to further demonstrate the effect of TanIIA on CRC, we carried out exploratory research about it in vivo and in vitro. The results demonstrated that TanIIA were observably more effective than control group in preventing tumor growth, and it has increased the survival time. Cancer cells viability and proliferation were accompanied by concentration and time dependent decline reached with TanIIA. We found that TanIIA altered the morphology of cytoskeleton and it could obviously induce apoptosis of colorectal cancer cells and block the cells in the G0/G1 phase. TanIIA also increased phosphorylation of p38MAPK, upregulated ATF-2 expression and downregulated Transgelin-2 expression, which could be reversed by SB203580, a p38MAPK-specific inhibitor. Our results suggested that TanIIA could induce apoptosis of colorectal cancer and block the cells in G0/G1 phase involved in downregulating the expression of Transgelin-2 through p38MAPK signal pathway.

Untargeted LC-MS/MS-Based Metabolomic Profiling for the Edible and Medicinal Plant Salvia miltiorrhiza Under Different Levels of Cadmium Stress

Salvia miltiorrhiza, a medicinal and edible plant, has been extensively applied to treat cardiovascular diseases and chronic hepatitis. Cadmium (Cd) affects the quality of S. miltiorrhiza, posing serious threats to human health. To reveal the metabolic mechanisms of S. miltiorrhiza's resistance to Cd stress, metabolite changes in S. miltiorrhiza roots treated with 0 (CK), 25 (T1), 50 (T2) and 100 (T3) mg kg-1 Cd by liquid chromatography coupled to mass spectrometry (LC-MS/MS) were investigated. A total of 305 metabolites were identified, and most of them were amino acids, organic acids and fatty acids, which contributed to the discrimination of CK from the Cd-treated groups. Among them, S. miltiorrhiza mainly upregulated o-tyrosine, chorismate and eudesmic acid in resistance to 25 mg kg-1 Cd; DL-tryptophan, L-aspartic acid, L-proline and chorismite in resistance to 50 mg kg-1 Cd; and L-proline, L-serine, L-histidine, eudesmic acid, and rosmarinic acid in resistance to 100 mg kg-1 Cd. It mainly downregulated unsaturated fatty acids (e.g., oleic acid, linoleic acid) in resistance to 25, 50, and 100 mg kg-1 Cd and upregulated saturated fatty acids (especially stearic acid) in resistance to 100 mg kg-1 Cd. Biosynthesis of unsaturated fatty acids, isoquinoline alkaloid, betalain, aminoacyl-tRNA, and tyrosine metabolism were the significantly enriched metabolic pathways and the most important pathways involved in the Cd resistance of S. miltiorrhiza. These data elucidated the crucial metabolic mechanisms involved in S. miltiorrhiza Cd resistance and the crucial metabolites that could be used to improve resistance to Cd stress in medicinal plant breeding.

Desorption Electrospray Ionization Mass Spectrometry Imaging Illustrates the Quality Characters of Isatidis Radix

For a long history, herbal medicines have made significant contributions to human health all around the world. However, the exploration of an effective approach to illustrate their inner quality remains a challenge. So, it is imperative to develop new methods and technologies to characterize and identify quality markers of herbal medicines. Taking Isatidis Radix, the dried root of Isatis indigotica as an example, desorption electrospray ionization (DESI), in combination with quadrupole-time-of-flight mass spectrometry (Q-TOF/MS), was applied in this work for the first time to reveal the comprehensive spatial distribution of metabolites and, further, to illustrate quality characters of this herbal medicine. After simple pretreatment, 102 metabolites including alkaloids, sulfur-containing compounds, phenylpropanoids, nucleosides, amino acids, organic acids, flavonoids, phenols, terpenes, saccharides, peptides, and sphingolipids were characterized, some of which were successfully localized and visualized in the transverse section of the root. Based on the ion images, samples with different quality characters were distinguished unambiguously by the pattern recognition method of orthogonal partial least squares discrimination analysis (OPLS-DA). Simultaneously, 11 major influencing components exerting higher ion intensities in superior samples were identified as the potential quality markers of Isatidis Radix. Desorption electrospray ionization (DESI) mass spectrometry imaging (MSI), together with chemometric analysis could not only improve the understanding of the plant biology of herbal medicines but also be beneficial in the identification of quality markers, so as to carry out better quality control of herbal medicines.

Computational Workflow to Study the Diversity of Secondary Metabolites in Fourteen Different Isatis Species

The screening of real features among thousands of ions remains a great challenge in the study of metabolomics. In this research, a workflow designed based on the MetaboFR tool and “feature-rating” rule was developed to screen the real features in large-scale data analyses. Seventy-four reference standards were used to test the feasibility, with 83.21% of real features being obtained after MetaboFR processing. Moreover, the full workflow was applied for systematic characterization of 14 species of the genus Isatis, with the result that 87.72% of real features were retained and 69.19% of the in-source fragments were removed. To gain insights into metabolite diversity within this plant family, 1697 real features were tentatively identified, including lipids, phenylpropanoids, organic acids, indole derivatives, etc. Indole derivatives were demonstrated to be the best chemical markers with which to differentiate different species. The rare existence of indole derivatives in Isatis cappadocica (cap) and Isatis cappadocica subsp. Steveniana (capS) indicates that the biosynthesis of indole derivatives could play a key role in driving the chemical diversity and evolution of genus Isatis. Our workflow provides the foundations for the exploration of real features in metabolomics, and has the potential to reveal the chemical composition and marker metabolites of secondary metabolites in plant fields.