Integrative analysis of the steroidal alkaloids distribution and biosynthesis of bulbs Fritillariae Cirrhosae through metabolome and transcriptome analyses

Comparative metabolomics of two nettle species unveils distinct high-altitude adaptation mechanisms on the Tibetan Plateau

BACKGROUND

The extreme high-altitude conditions of the Tibetan Plateau, characterized by intense solar radiation, low temperatures, and reduced oxygen levels, poses significant challenges to plant survival. Plants inhabiting this region have evolved specialized mechanisms to adapt to high-altitude environments. While most studies have focused on genomic and ecological perspectives, few have explored adaptive mechanisms in a metabolic context. In particular, comparative studies examining similarities and differences in the metabolomes of closely related species are exceedingly rare. As sister species, the nettle species Urtica hyperborea and U. dioica are distributed above 4000 m above sea level, with a sympatric distribution on the Tibetan Plateau, they provide an ideal system to investigate the aforementioned question.

RESULTS

In this study, we conducted non-targeted metabolic profiling of the leaves from U. hyperborea and U. dioica collected at three sympatric sites on the Tibetan Plateau. A total of 2906 annotated metabolites were detected. Differential metabolites at Sites 1 (4697 m) and 3 (4465 m) were enriched in pathways for flavonoid, flavone and flavonol, and phenylpropanoid biosynthesis. In contrast, Site 2, located at the highest altitude (5007 m), primarily exhibited enrichment in carbon metabolism pathways. Regarding the altitudinal variation of the same species, common metabolic pathways between the two groups included fructose and mannose metabolism, α-linolenic acid metabolism, and glycerophospholipid metabolism. The metabolic pathways enriched only inU. hyperboreaincluded starch and sucrose metabolism, galactose metabolism, and phenylpropanoid biosynthesis. The metabolically enriched pathways specific toU. dioicaincluded pantothenate and coenzyme A biosynthesis, as well as glutathione metabolism.

CONCLUSIONS

We found that the metabolic differences between the two sympatric species are primarily in carbohydrate and phenylpropanoid contents. The differential metabolites of the same species across different altitudes were enriched mainly in carbon metabolism pathways and lipid metabolism pathways. Thus, our study revealed that the high-altitude adaptation mechanisms of sympatric species are not identical. Moreover, adaptation strategies within the same species were generally consistent across altitudes, exhibiting only slight variations. This study provide novel insights into the adaptive metabolic strategies of U. hyperborea and U. dioica, contributing to a deeper understanding of the mechanisms underlying plant adaptation to extreme high-altitude conditions.

Cellular strategies for surviving the alpine extremes: methylerythritol phosphate pathway-driven isoprenoid biosynthesis and stress resilience

High altitude conditions pose a significant challenge to all earth's inhabitants including flora. Low atmospheric pressure (thin air), intense ultraviolet (UV) light, and ultra-low temperatures combine to cause oxidative stress in plants. In these abiotic stress conditions, plants exhibit various ecophysiological, morphological, and biochemical adaptations to cope with stress. Morphologically, plants may develop smaller, thicker leaves with protective trichomes or waxy cuticles against intense UV radiation, and minimize water loss in the thin, dry air. However biochemically, plants increase the production of UV-absorbing compounds like flavonoids and phenolic acids along with antioxidant enzymes for neutralizing reactive oxygen species (ROS). To protect against these stress conditions plants start producing specialized metabolites, i.e., isoprenoids, phenolic acids, flavonoids, sterols, carotenoids, etc. The production of these specialized metabolites occurs through MEP (methylerythritol phosphate) and MVA (mevalonic acid) pathways. Although, this article aims to review the scientific complexities of high-altitude plants by providing an in-depth explanation of the MEP pathway, including its regulation, sources and causes of oxidative stress in plants, functions and roles of isoprenoids in stress tolerance, and the adaptation strategies that support alpine plant survival and acclimation. The MEP pathway's products, several carotenoids, viz., phytoene, lycopene, β-carotene, etc., and terpenoids, viz., geraniol, citral, phytol, etc., act as potent scavengers of ROS, providing defense against oxidative damage. Also, phytohormones, viz., abscisic acid, salicylic acid, and jasmonic acid play crucial roles in modulating plant responses to oxidative stress. To date, little scientific literature is available specifically on high-altitude plants with respect to MEP pathway and oxidative stress management. Understanding the interaction between the MEP pathway and oxidative stress in high-altitude plants can provide insight into the implications for improving crop resilience and producing bioactive chemicals with potential human health benefits.

UDP-glucosyltransferases from UGT73 family catalyze 3-O-glucosylation of isosteroidal and steroidal alkaloids in Fritillaria unibracteata var. wabuensis

Fritillaria unibracteata var. wabuensis is an important resource plant for the famous traditional Chinese medicine Fritillariae cirrhosae bulbus ("Chuanbeimu" in Chinese). F. cirrhosae bulbus is the dried bulbs of several species from Fritillaria genus, with isosteroidal alkaloids components assumed as the bioactive ingredients. However, the biosynthesis pathway of isosteroidal alkaloids remains elusive. Here, we adopted F. unibracteata var. wabuensis as a material to identify genes involved in the biosynthesis of isosteroidal alkaloids. We first constructed the multi-tissue metabolome and transcriptome dataset of F. unibracteata var. wabuensis. Interestingly, imperialine-3-β-d-glucoside, an isosteroidal glycoalkaloid, was found to be the major tissue-specific accumulated alkaloid. Through phylogenetic and co-expression analysis, we identified two UDP-glucosyltransferases from UGT73 family catalyzing 3-O-glucosylation of isosteroidal and steroidal alkaloids: imperialine 3-O-glucosyltransferase (FuwI3GT) can use both isosteroidal alkaloid imperialine and steroidal alkaloid solanidine as substrates, while solanidine 3-O-glucosyltransferase (FuwS3GT) can only use steroidal alkaloid solanidine as a substrate. We further approved that the W201 residue of FuwI3GT determined its substrate preference of isosteroidal alkaloids. Overall, our results identified enzymes involved in 3-O-glucosylation of isosteroidal and steroidal alkaloids in F. unibracteata var. wabuensis and paved the way to fully elucidate the isosteroidal alkaloid biosynthesis pathway in Fritillaria species.

Isolation and Identification of Alkaloid Genes from the Biomass of Fritillaria taipaiensis P.Y. Li

BACKGROUND/OBJECTIVES

Fritillaria taipaiensis P.Y. Li is a valuable traditional Chinese medicinal herb that utilizes bulbs as medicine, which contain multiple alkaloids. Biomass, as a sustainable resource, has promising applications in energy, environmental, and biomedical fields. Recently, the biosynthesis and regulatory mechanisms of the main biomass components of biomass have become a prominent research topic.

METHODS

In this article, we explored the differences in the heterosteroidal alkaloid components of F. taipaiensis biomass using liquid chromatography-mass spectrometry and high-throughput transcriptome sequencing.

RESULTS

The experimental results demonstrated significant differences in the eight types of heterosteroidal alkaloid components among the biomass of F. taipaiensis, including peimisine, imperialine, peimine, peiminine, ebeinone, ebeiedine, ebeiedinone, and forticine. Transcriptomic analysis revealed substantial significant differences in gene expression patterns in the various samples. Three catalytic enzyme-coding genes, 3-hydroxy-3-methylglutaryl coenzyme A synthase (HMGS), 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR), and terpene synthase (TPS), were speculated to contribute to the regulation of the differential accumulation of alkaloid synthesis in F. taipaiensis bulbs. A strong positive correlation was observed between the transcriptional level of the TPS gene and the alkaloid content of F. taipaiensis biomass, suggesting that TPS may be a key gene in the biosynthesis pathway of alkaloids. This finding can be used for subsequent gene function verification and molecular regulatory network analysis.

CONCLUSIONS

This work provides fundamental data and novel insights for the subsequent research on alkaloid biosynthesis in F. taipaiensis.

Transcriptomic analysis reveals effects of fertilization towards growth and quality of Fritillariae thunbergii bulbus

Fritillariae thunbergii Bulbus (FTB) is a traditional Chinese medicine that has been widely cultivated for its expectorant, antitussive, antiasthmatic, antiviral, and anticancer properties. The yield and quality of F. thunbergii are influenced by cultivation conditions, such as the use of fertilizers. However, the optimal type of fertilizers for maximum quality and yield and underlying mechanisms are not clear. We collected F. thunbergii using raw chicken manure (RC), organic fertilizer (OF), and plant ash (PA) as the base fertilizer in Pan'an County, Jinhua City, Zhejiang Province as experimental materials. The combined results of HPLC-ELSD detection and yield statistics showed that the F. thunbergii with OF application was the best, with the content of peimine and peiminine reaching 0.0603% and 0.0502%, respectively. In addition, the yield was 2.70 kg/m2. Transcriptome analysis indicated that up-regulation of the ABA signaling pathway might promote bulb yield. Furthermore, putative key genes responsible for steroidal alkaloid accumulation were identified. These results provided guiding significance for the rational fertilization conditions of F. thunbergii as well as the basis for the exploration of functional genes related to the alkaloid biosynthesis pathway.

Integrative analysis of metabolome and transcriptome provides new insights into functional components of Lilii Bulbus

Objective

Lilium brownii var. viridulum (LB) and L. lancifolium (LL) are the main sources of medicinal lily (Lilii Bulbus, Baihe in Chinese) in China. However, the functional components of these two species responsible for the treatment efficacy are yet not clear. In order to explore the therapeutic material basis of Lilii Bulbus, we selected L. davidii var. willmottiae (LD) only used for food as the control group to analyze the differences between LD and the other two (LB and LL).

Methods

Metabolome and transcriptome were carried out to investigate the differences of active components in LD vs LB and LD vs LL. Data of metabolome and transcriptome was analysed using various analysis methods, such as principal component analysis (PCA), hierarchical cluster analysis (HCA), and so on. Differentially expressed genes (DEGs) were enriched through KEGG and GO enrichment analysis.

Results

The PCA and HCA of the metabolome indicated the metabolites were clearly separated and varied greatly in LL and LB contrasted with LD. There were 318 significantly differential metabolites (SDMs) in LD vs LB group and 298 SDMs in LD vs LL group. Compared with LD group, the significant up-regulation of steroidal saponins and steroidal alkaloids were detected both in LB and LL groups, especially in LB group. The HCA of transcriptome indicated that there was significant difference in LB vs LD group, while the difference between LL and LD varied slightly. Additionally, 47 540 DEGs in LD vs LB group and 18 958 DEGs in LD vs LL group were identified. Notably, CYP450s involving in the biosynthesis of steroidal saponins and steroidal alkaloids were detected, and comparing with LD, CYP724, CYP710A, and CYP734A1 in LB and CYP90B in LL were all up-regulated.

Conclusion

This study suggested that steroidal saponins and steroidal alkaloids maybe the representative functional components of Lilii Bulbus, which can provide new insights for Lilii Bulbus used in the research and development of classic famous formula.

Integrative analysis of the metabolome and transcriptome provides insights into the mechanisms of lignan biosynthesis in Herpetospermum pedunculosum (Cucurbitaceae)

BACKGROUND

Herpetospermum pedunculosum (Ser.) C. B. Clarke is a traditional Chinese herbal medicine that heavily relies on the lignans found in its dried ripe seeds (Herpetospermum caudigerum), which have antioxidant and hepatoprotective functions. However, little is known regarding the lignan biosynthesis in H. pedunculosum. In this study, we used metabolomic (non-targeted UHPLC-MS/MS) and transcriptome (RNA-Seq) analyses to identify key metabolites and genes (both structural and regulatory) associated with lignan production during the green mature (GM) and yellow mature (YM) stages of H. pedunculosum.

RESULTS

The contents of 26 lignan-related metabolites and the expression of 30 genes involved in the lignan pathway differed considerably between the GM and YM stages; most of them were more highly expressed in YM than in GM. UPLC-Q-TOF/MS confirmed that three Herpetospermum-specific lignans (including herpetrione, herpetotriol, and herpetin) were found in YM, but were not detected in GM. In addition, we proposed a lignan biosynthesis pathway for H. pedunculosum based on the fundamental principles of chemistry and biosynthesis. An integrated study of the transcriptome and metabolome identified several transcription factors, including HpGAF1, HpHSFB3, and HpWOX1, that were highly correlated with the metabolism of lignan compounds during seed ripening. Furthermore, functional validation assays revealed that the enzyme 4-Coumarate: CoA ligase (4CL) catalyzes the synthesis of hydroxycinnamate CoA esters.

CONCLUSION

These results will deepen our understanding of seed lignan biosynthesis and establish a theoretical basis for molecular breeding of H. pedunculosum.

Metabolite profiling and transcriptomic analyses demonstrate the effects of biocontrol agents on alkaloid accumulation in Fritillaria thunbergii

BACKGROUND

During Fritillaria thunbergii planting, pests and diseases usually invade the plant, resulting in reduced yield and quality. Previous studies have demonstrated that using biocontrol agents can effectively control grubs and affect the steroid alkaloids content in F. thunbergii. However, the molecular regulatory mechanisms underlying the differences in the accumulation of steroid alkaloids in response to biocontrol agents remain unclear.

RESULTS

Combined transcriptomic and metabolic analyses were performed by treating the bulbs of F. thunbergii treated with biocontrol agents during planting. Otherwise, 48 alkaloids including 32 steroid alkaloids, 6 indole alkaloids, 2 scopolamine-type alkaloids, 1 isoquinoline alkaloid, 1 furoquinoline alkaloid, and 6 other alkaloids were identified. The content of steroidal alkaloids particularly peimine, peiminine, and veratramine, increased significantly in the group treated with the biocontrol agents. Transcriptome sequencing identified 929 differential genes using biocontrol agents, including 589 upregulated and 340 downregulated genes. Putative biosynthesis networks of steroid alkaloids have been established and combined with differentially expressed structural unigenes, such as acetyl-CoA C-acetyl-transferase, acelyl-CoAC-acetyltransferase3-hydroxy-3-methylglutaryl-coenzyme A synthase, 1-deoxy-D-xylulose-5-phosphate reductor-isomerase, 2-C-methyl-D-erythritol-4-phosphate cytidylyltransferase and 4-hydroxy-3-methylbut-2-enyl diphosphate reductase. In addition, biological processes such as amino acid accumulation and oxidative phosphorylation were predicted to be related to the synthesis of steroid alkaloids. Cytochrome P450 enzymes also play crucial roles in the steroid alkaloid synthesis. The transcription factor families MYB and bHLH were significantly upregulated after using biocontrol agents.

CONCLUSIONS

Biocontrol agents increased the steroid alkaloids accumulation of steroid alkaloids by affecting key enzymes in the steroid alkaloid synthesis pathway, biological processes of oxidative phosphorylation and amino acid synthesis, cytochrome P450 enzymes, and transcription factors. This study revealed the mechanism underlying the difference in steroidal alkaloids in F. thunbergii after using biocontrol agents, laying the groundwork for future industrial production of steroid alkaloids and ecological planting of medicinal materials in the future.

Rapid Test for Adulteration of Fritillaria Thunbergii in Fritillaria Cirrhosa by Laser-Induced Breakdown Spectroscopy

Fritillaria has a long history in China, and it can be consumed as medicine and food. Owing to the high cost of Fritillaria cirrhosa, traders sometimes mix it with the cheaper Fritillaria thunbergii powder to make profit. Herein, we proposed a laser-induced breakdown spectroscopy (LIBS) technique to test the adulteration present in the sample of Fritillaria cirrhosa powder. Experimental samples with different adulteration levels were prepared, and their LIBS spectra were obtained. Partial least squares regression (PLSR) was adopted as the quantitative analysis model to compare the effects of four data standardization methods, namely, mean centring, normalization by total area, standard normal variable, and normalization by the maximum, on the performance of the PLSR model. Principal component analysis and least absolute shrinkage and selection operator (LASSO) were utilized for feature extraction and feature selection, and the performance of the PLSR model was determined based on its quantitative analysis. Subsequently, the optimal number of features was determined. The residuals were corrected using support vector regression (SVR). The mean absolute error and root mean square error of prediction obtained from the quantitative analysis results of the combined LASSO-PLSR-SVR model for the test set data were 5.0396% and 7.2491%, respectively, and the coefficient of determination R² was 0.9983. The results showed that the LIBS technique can be adopted to test adulteration in the sample of Fritillaria cirrhosa powder and has potential applications in drug quality control.

Transcriptome and metabolome profiling of the medicinal plant Veratrum mengtzeanum reveal key components of the alkaloid biosynthesis

Veratrum mengtzeanum is the main ingredient for Chinese folk medicine known as "Pimacao" due to its unique alkaloids. A diverse class of plant-specific metabolites having key pharmacological activities. There are limited studies on alkaloid synthesis and its metabolic pathways in plants. To elucidate the alkaloid pathway and identify novel biosynthetic enzymes and compounds in V. mengtzeanum, transcriptome and metabolome profiling has been conducted in leaves and roots. The transcriptome of V. mengtzeanum leaves and roots yielded 190,161 unigenes, of which 33,942 genes expressed differentially (DEGs) in both tissues. Three enriched regulatory pathways (isoquinoline alkaloid biosynthesis, indole alkaloid biosynthesis and tropane, piperidine and pyridine alkaloid biosynthesis) and a considerable number of genes such as AED3-like, A4U43, 21 kDa protein-like, 3-O-glycotransferase 2-like, AtDIR19, MST4, CASP-like protein 1D1 were discovered in association with the biosynthesis of alkaloids in leaves and roots. Some transcription factor families, i.e., AP2/ERF, GRAS, NAC, bHLH, MYB-related, C3H, FARI, WRKY, HB-HD-ZIP, C2H2, and bZIP were also found to have a prominent role in regulating the synthesis of alkaloids and steroidal alkaloids in the leaves and roots of V. mengtzeanum. The metabolome analysis revealed 74 significantly accumulated metabolites, with 55 differentially accumulated in leaves compared to root tissues. Out of 74 metabolites, 18 alkaloids were highly accumulated in the roots. A novel alkaloid compound viz; 3-Vanilloylygadenine was discovered in root samples. Conjoint analysis of transcriptome and metabolome studies has also highlighted potential genes involved in regulation and transport of alkaloid compounds. Here, we have presented a comprehensive metabolic and transcriptome profiling of V. mengtzeanum tissues. In earlier reports, only the roots were reported as a rich source of alkaloid biosynthesis, but the current findings revealed both leaves and roots as significant manufacturing factories for alkaloid biosynthesis.

Transcriptome Analysis of CYP450 Family Members in Fritillaria cirrhosa D. Don and Profiling of Key CYP450s Related to Isosteroidal Alkaloid Biosynthesis

Fritillaria cirrhosa D. Don (known as Chuan-Bei-Mu in Chinese) can synthesize isosteroidal alkaloids (ISA) with excellent medicinal value, and its bulb has become an indispensable ingredient in many patented drugs. Members of the cytochrome P450 (CYP450) gene superfamily have been shown to play essential roles in regulating steroidal alkaloids biosynthesis. However, little information is available on the P450s in F. cirrhosa. Here, we performed full-length transcriptome analysis and discovered 48 CYP450 genes belonging to 10 clans, 25 families, and 46 subfamilies. By combining phylogenetic trees, gene expression, and key F. cirrhosa ISA content analysis, we presumably identify seven FcCYP candidate genes, which may be hydroxylases active at the C-22, C-23, or C-26 positions in the late stages of ISA biosynthesis. The transcript expression levels of seven FcCYP candidate genes were positively correlated with the accumulation of three major alkaloids in bulbs of different ages. These data suggest that the candidate genes are most likely to be associated with ISA biosynthesis. Finally, the subcellular localization prediction of FcCYPs and transient expression analysis within Nicotiana benthamiana showed that the FcCYPs were mainly localized in the chloroplast. This study presents a systematic analysis of the CYP450 gene family in F. cirrhosa and provides a foundation for further functional characterization of the CYPs involved in ISA biosynthesis.