Isoprenoid biosynthesis regulation in poplars by methylerythritol phosphate and mevalonic acid pathways

Remodeling of the terpenoid metabolism during prolonged phosphate depletion in the marine diatom Phaeodactylum tricornutum

Terpenoids are a diverse class of naturally occurring organic compounds, which derive from five-carbon isoprene units and play crucial roles in physiology, ecological interactions such as defense mechanisms, or adaptation to environmental stresses. In Phaeodactylum tricornutum, some of the most important isoprenoids are sterols and pigments, derived from precursors of the cytosolic mevalonate and the plastidial methyl-erythritol 4-phosphate pathway, respectively. However, the regulation of isoprenoid metabolism in P. tricornutum has not yet been characterized, presenting a major gap in our understanding of its ecological functions and adaptations. By leveraging metabolic, photosynthetic, and transcriptomic analyses, we characterized the dynamic remodeling of the isoprenoid pathways during prolonged nutrient stress in wild-type diatoms. We observed the down-regulation of the methylerythritol 4-phosphate and pigment biosynthesis pathways and the upregulation of key genes in the mevalonate and sterol biosynthesis pathways. At the metabolite level, we observed an overall decrease in pigment and no changes in sterol levels. Using a genetically engineered diatom strain to produce a heterologous monoterpenoid to monitor the availability of one of the main terpenoid precursors, geranyl diphosphate (GPP), we suggest that cytosolic GPP pools increase during prolonged phosphate depletion. Our results have demonstrated how the biosynthesis of isoprenoid metabolites and the pools of prenyl phosphate are vastly remodeled during phosphate depletion. We anticipate that the knowledge generated in this study can serve as a foundation for understanding ecological responses and adaptations of diatoms to nutrient stress, contributing to our broader comprehension of marine ecosystem dynamics and design strategies for producing high-value compounds in diatoms.

Developing Light-Emitting Plants (LEPs) with SrAl2O4: Eu2+, Dy3+ by Using Pressure Infiltration, Optimal Conditions for Glowing and Plant Stress Response

Developing light-emitting plants (LEPs) using SrAl2O4 has been working for the past few years because SrAl2O4 is a phosphorescent material with long-lasting and bright glowing properties. The six plant species (Episcia cupreata, Tabebuia argentea, Syngonium hybrid, Mimusops elengi, Schefflera arboricola, and Pilea cadierei) were infused with SrAl2O4, which has a particle size of 2.7 µm. The E. cupreata exhibited the highest phosphorescence (a relative phosphorescence value of 36.93) compared to other plant species. The optimal pressure to infuse SrAl2O4 into the plant is 7 × 104 N/m2 exposed for 60 min while 17.5 g/L SrAl2O4 is the best concentration. After infusion, the plants did not show physical abnormalities. However, the amount of MDA and antioxidants in plants was increased. Based on metabolomics analysis, SrAl2O4 might stress plants, but plants might be able to respond by producing antioxidant compounds. Therefore, using SrAl2O4 to LEPs did not kill the plants and provided high light output.

Metabolomics and Transcriptomics Reveal the Role of the Terpene Biosynthetic Pathway in the Mechanism of Insect Resistance in Solanum habrochaites

Terpenes are a large variety of natural organic compounds that can enhance the resistance of plants to phytophagous insects through induction. In this study, differential expression genes and metabolites of Alice Craig (AC) and Solanum habrochaite (SH) were screened and analyzed by transcriptomics and metabolomics. The results show that terpene biosynthesis is one of the most crucial secondary metabolic pathways in plants. SH significantly accumulates more terpenes than AC by up regulating the expression of relevant genes. It is worth noting that virus-induced SlHDR silencing not only reduces the expression of downstream genes (SlTPS3, SlFPP, and SlGGPPS) in the terpene biosynthesis pathway, but also significantly affects the synthesis of related terpenoids, there by reducing the insect resistance of tomatoes. The results will be beneficial for understanding the synthesis mechanism of terpenoids in tomatoes and supply new genetic resources for the development of insect-resistant tomatoes.

The MYC Gene RrbHLH105 Contributes to Salt Stress-Induced Geraniol in Rose by Regulating Trehalose-6-Phosphate Signalling

Rose (Rosa rugosa) is an important perfume plant, but its cultivation is significantly constrained by salt stress. Terpenes represent the most abundant volatile aromatic compounds in roses, yet little is known about how terpene metabolism responds to salt stress. In this study, salt-treated rose petals presented significant accumulation of monoterpenes, including geraniol, due to the disruption of jasmonic acid (JA) biosynthesis and signalling. Overexpression and silencing analyses revealed a MYC transcription factor involved in JA signalling (RrbHLH105) as a repressor of geraniol biosynthesis. RrbHLH105 was shown to activate the trehalose-6-phosphate synthase genes RrTPS5 and RrTPS8 by binding to the E-box (5'-CANNTG-3'). The increased trehalose-6-phosphate content and decreased geraniol content in rose petals overexpressing TPS5 or RrTPS8, along with the high accumulation of geraniol in petals where both RrbHLH105 and TPSs were cosilenced, indicate that trehalose signalling plays a role in the negative regulation of geraniol accumulation via the RrbHLH105-TPS module. In summary, the suppression of RrbHLH105 by salt stress leads to excessive geraniol accumulation through the inhibition of both RrbHLH105-mediated JA signalling and RrTPS-mediated trehalose signalling in rose petals. Additionally, this study highlights the emerging role of RrbHLH105 as a critical integrator of JA and trehalose signalling crosstalk.

Integrated Analysis of Terpenoid Profiles and Full-Length Transcriptome Reveals the Central Pathways of Sesquiterpene Biosynthesis in Atractylodes chinensis (DC.) Koidz

Atractylodes chinensis (DC.) Koidz. is an aromatic and medicinal plant in East Asia. The primary bioactive compounds in this species are sesquiterpenes, particularly β-eudesmol, hinesol, and atractylon. Cultivation techniques require improvement to meet the medicinal demands of this species. In this study, gas chromatography-mass spectrometry analysis of an A. chinensis germplasm showed its essential oil contained various sesquiterpenes, including a high relative ratio of β-eudesmol. Full-length transcriptome profiling of A. chinensis revealed 26 genes related to terpenoid biosynthesis. These genes belonged to 13 gene families, including five in the isopentenyl pyrophosphate synthase gene family and four in the terpene synthase gene family. The functions of the four terpene synthase genes were proposed based on gene expression patterns and phylogenetic relationships: one was thought to encode monoterpene synthase and three to encode sesquiterpene synthase. Based on the results, the central biosynthesis pathways of the major sesquiterpenes in the A. chinensis rhizome were proposed, and three sesquiterpene synthase genes were identified as expressed in the rhizome for the first time. AcHMGR, AcFPPS, and the three sesquiterpene synthase genes were proposed as potential targets for molecular breeding in A. chinensis to enhance its sesquiterpene content.

Research on using Aquilaria sinensis callus to evaluate the agarwood-inducing potential of fungi

Agarwood is a precious resinous heartwood highly valued for its cultural, religious, and medicinal significance. With the increasing market demand, natural agarwood resources are rapidly depleting, making the development of effective artificial induction methods for agarwood highly significant. This study aims to explore the feasibility of using callus tissue to assess the ability of fungi to induce agarwood formation. We selected two fungi isolated from Aquilaria sinensis, W-1 (Podospora setosa) and W-15 (Alternaria alstroemeriae), and used the known agarwood-inducing fungi YMY (Pestalotiopsis sp.) as a positive control, by treating A. sinensis callus with their fermented filtrates. The experimental results showed that W-1 and W-15 treatments significantly enhanced the activity of Superoxide dismutase (SOD) and Peroxidase (POD) in the callus tissue and upregulated the expression of 3-hydroxy-3-methylglutaryl-CoA synthase (HMGS), 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), and sesquiterpene synthase (ASS-1). GC-MS analysis further confirmed that the contents of sesquiterpenes and aromatic compounds in A. sinensis treated with W-1 and W-15 were significantly elevated, suggesting that these fungi possess the capacity to induce the formation of agarwood. This study demonstrates that using callus tissue to screen fungi capable of inducing agarwood is feasible and effective, providing new insights for screening fungi resources that efficiently induce agarwood formation in the future.

Integrated Transcriptomic and Metabolomic Analyses Reveal Changes in Aroma- and Taste-Related Substances During the Withering Process of Black Tea

Withering is one of the major processing steps critical for the quality of black tea. In this study, we investigated the mechanisms underlying the physicochemical changes in metabolites and gene expression during the withering process of black tea using metabolomic and transcriptomic approaches, respectively. Based on gas chromatography/mass spectrometry non-targeted metabolomic approaches (GC-MS) and ultra-high performance liquid chromatograph-tandem mass spectrometry (UHPLC-MS/MS), a total of 76 volatile compounds and 160 non-volatile compounds were identified from tea leaves, respectively. RNA-seq analysis revealed that the number of differentially expressed genes (DEGs) for the comparative combination of withering time (i.e., W4h, W6h, W8h, W10h, and W12h) compared with CK (i.e., fresh leaves) were 3634, 2906, 4127, 5736, and 7650, respectively. The core genes in starch metabolism, namely alpha-amylase (AMY) and beta-amylase (BAM), were upregulated as withering time increased. AMY and BAM contributed to the decomposition of starch to increase the soluble sugars. The content of tea leaf alcohols and aldehydes, which are the vital contributors for greenish aroma, gradually decreased as withering time increased due to the downregulation of associated genes while the compounds related to sweet and fruity characteristics increased due to the upregulated expression of related genes. Most DEGs involved in amino acids were significantly upregulated, leading to the increase in free amino acids content. However, DEGs involved in catechins metabolism were generally downregulated during withering, and resulted in a reduction in catechins content and the accumulation of theaflavins. The same trend was observed in alpha-linolenic acid metabolism-related genes that were downregulated and enhanced the reduction in grassy aroma in black tea. The weighted gene co-expression network analysis (WGCNA) of DEGs showed that one module can be associated with more components and one component can be regulated by various modules. Our findings provide new insights into the quality formation of black tea during the withering process.

Functional Analysis of PsHMGR1 and PsTPS1 Related to Floral Terpenoids Biosynthesis in Tree Peony

Tree peony (Paeonia suffruticosa), as a popular ornamental plant worldwide, has a unique floral fragrance, and it is important in the pollination, ornamental, food, and fragrance product industries. However, the underlying molecular mechanisms for the synthesis of floral fragrance terpenoids in tree peony are not well understood, constraining their exploitation. P. suffruticosa 'Oukan' produces strong floral fragrance terpenoids with high ornamental value and excellent stress resistance and is considered a valuable model for studying tree peony floral fragrance formation. Based on transcriptome data analysis, the PsHMGR1 and PsTPS1 genes associated with floral terpene synthesis were cloned. Then, PsHMGR1 and PsTPS1 were functionally characterized by amino acid sequence analysis, multiple sequence alignment, phylogenetic tree construction, qRT-PCR, and transgenic assay. PsHMGR1 contains two transmembrane structures and a conserved HMG-CoA_reductase_class I domain, and PsTPS1 belongs to TPS-a subfamily. The qRT-PCR analysis showed that the expression levels of PsHMGR1 and PsTPS1 increased and then decreased at different flower development stages, and both were significantly higher in flowers than in roots, stems, and leaves. In addition, the linalool content in PsHMGR1 transgenic lines was significantly higher than that of WT. Germacrene D, which was not found in WT, was detected in the flowers of PsTPS1 transgenic lines. These results indicate that PsHMGR1 and PsTPS1 promote terpene synthesis in plants and provide ideas for the molecular mechanism of enhancing terpene synthesis in tree peony floral fragrance.

Novel Differentially Expressed LncRNAs Regulate Artemisinin Biosynthesis in Artemisia annua

Long non-coding RNAs (lncRNAs) are crucial in regulating secondary metabolite production in plants, but their role in artemisinin (ART) biosynthesis, a key anti-malarial compound from Artemisia annua, remains unclear. Here, by investigating high-artemisinin-producing (HAP) and lowartemisinin-producing (LAP) genotypes, we found that the final artemisinin content in A. annua is influenced by the quantity of the precursor compounds. We report on RNA deep sequencing in HAP and LAP genotypes. Based on the application of a stringent pipeline, 1419 novel lncRNAs were identified. Moreover, we identified 256 differentially expressed lncRNAs between HAP and LAP. We then established correlations between lncRNAs and artemisinin biosynthesis genes in order to identify a molecular framework for the differential expression of the pathway between the two genotypes. Three potential lncRNAs (MSTRG.33718.2, MSTRG.30396.1 and MSTRG.2697.4) linked to the key artemisinin biosynthetic genes (ADS: Amorpha-4,11-diene synthase, DXS: 1-deoxy-D-xylulose-5-phosphate synthase, and HMGS: 3-hydroxyl-3-methyglutaryl CoA synthase) were detected. Importantly, we observed that up-regulation of these lncRNAs positively modulates the target artemisinin biosynthetic genes, potentially leading to high artemisinin biosynthesis in HAP. In contrast, BAS (beta-amyrin synthase), which is involved in the artemisinin competing pathway, was strongly down-regulated in HAP compared to LAP, in line with the expression pattern of the linked lncRNA MSTRG.30396.1. By identifying and characterizing lncRNAs that are potentially linked to the regulation of key biosynthetic genes, this work provides new insights into the complex regulatory networks governing artemisinin production in A. annua. Such findings could pave the way for innovative approaches in metabolic engineering, potentially enhancing artemisinin yields and addressing challenges in sustainable production.

Biosynthesis of bridged tricyclic sesquiterpenes in Inula lineariifolia

Presilphiperfolane-type sesquiterpenes represent a unique group of atypical sesquiterpenoids characterized by their distinctive tricyclic structure. They have significant potential as lead compounds for pharmaceutical and agrochemical development. Herein, we utilized a transcriptomic approach to identify a terpene synthase (TPS) gene responsible for the biosynthesis of rare presilphiperfolane-type sesquiterpenes in Inula lineariifolia, designated as IlTPS1. Through phylogenetic analysis, we have identified the evolutionary conservation of key motifs, including RR(x)8W, DDxxD, and NSE/DTE in IlTPS1, which are shared with other tricyclic sesquiterpene synthases in the TPS-a subfamily of Asteraceae plants. Subsequent biochemical characterization of recombinant IlTPS1 revealed it to be a multiproduct enzyme responsible for the synthesis of various tricyclic sesquiterpene alcohols from farnesyl diphosphate (FPP), resulting in production of seven distinct sesquiterpenes. Mass spectrometry and nuclear magnetic resonance (NMR) spectrometry identified presilphiperfolan-8β-ol and presilphiperfol-7-ene as predominant products. Furthermore, biological activity assays revealed that the products from IlTPS1 exhibited a potent antifungal activity against Nigrospora oryzae. Our study represents a significant advancement as it not only functionally identifies the first step enzyme in presilphiperfolane biosynthesis but also establishes the heterologous bioproduction of these unique sesquiterpenes.

A Light-Driven In Vitro Enzymatic Biosystem for the Synthesis of α-Farnesene from Methanol

Terpenoids of substantial industrial interest are mainly obtained through direct extraction from plant sources. Recently, microbial cell factories or in vitro enzymatic biosystems have emerged as promising alternatives for terpenoid production. Here, we report a route for the synthesis of α-farnesene based on an in vitro enzyme cascade reaction using methanol as an inexpensive and renewable C1 substrate. Thirteen biocatalytic reactions divided into 2 modules were optimized and coupled to achieve methanol-to-α-farnesene conversion via integration with natural thylakoid membranes as a green energy engine. This in vitro enzymatic biosystem driven by light enabled the production of 1.43 and 2.40 mg liter-1 α-farnesene using methanol and the intermediate glycolaldehyde as substrates, respectively. This work could provide a promising strategy for developing light-powered in vitro biosynthetic platforms to produce more natural compounds synthesized from C1 substrates.

Revelation of enzyme/transporter-mediated metabolic regulatory model for high-quality terpene accumulation in developing fruits of Lindera glauca

Lindera glauca with rich resource and fruit terpene has emerged as potential material for utilization in China, but different germplasms show a variation for essential oil content and volatile profiling. This work aimed to determine key regulators (enzymes or transporters) and unravel mechanism of governing high production of essential oil of L. glauca fruit (EO-LGF). Temporal analysis of fruit growth and EO-LGF accumulation (yield, volatile compounds and contents) during development revealed a notable change in the contents of EO-LGF and its 45 compounds in developing fruits, and the major groups were monoterpene and sesquiterpene, showing good antioxidant and antimicrobial activities. To highlight molecular mechanism that govern such difference in terpene content and compound in developing fruits, Genome-wide assay was used to annotate 104 genes for terpene-synthesis pathway based on recent transcriptome data, and the comparative associations of terpene accumulative amount with gene transcriptional level were conducted on developing fruits to identify some crucial determinants (enzymes and transporters) with metabolic regulation model for high-quality terpene accumulation, involving in carbon allocation (sucrose cleavage, glycolysis and OPP pathway), metabolite transport, isoprene precursor production, C5-unit formation (MEP and MVA pathways), and mono-/sesqui-terpene synthesis. Our findings may present strategy for engineering terpene accumulation for utilization.

Interactions with microbial consortia have variable effects in organic carbon and production of exometabolites among genotypes of Populus trichocarpa

Poplar is a short-rotation woody crop frequently studied for its significance as a sustainable bioenergy source. The successful establishment of a poplar plantation partially depends on its rhizosphere-a dynamic zone governed by complex interactions between plant roots and a plethora of commensal, mutualistic, symbiotic, or pathogenic microbes that shape plant fitness. In an exploratory endeavor, we investigated the effects of a consortium consisting of ectomycorrhizal fungi and a beneficial Pseudomonas sp. strain GM41 on plant growth (including height, stem girth, leaf, and root growth) and as well as growth rate over time, across four Populus trichocarpa genotypes. Additionally, we compared the level of total organic carbon and plant exometabolite profiles across different poplar genotypes in the presence of the microbial consortium. These data revealed no significant difference in plant growth parameters between the treatments and the control across four different poplar genotypes at 7 weeks post-inoculation. However, total organic carbon and exometabolite profiles were significantly different between the genotypes and the treatments. These findings suggest that this microbial consortium has the potential to trigger early signaling responses in poplar, influencing its metabolism in ways crucial for later developmental processes and stress tolerance.

De Novo Transcriptome Profiling for the Generation and Validation of Microsatellite Markers, Transcription Factors, and Database Development for Andrographis paniculata

Andrographis paniculata belongs to the family Acanthaceae and is known for its medicinal properties owing to the presence of unique constituents belonging to the lactones, diterpenoids, diterpene glycosides, flavonoids, and flavonoid glycosides groups of chemicals. Andrographolide, a major therapeutic constituent of A. paniculata, is extracted primarily from the leaves of this plant and exhibits antimicrobial and anti-inflammatory activities. Using 454 GS-FLX pyrosequencing, we have generated a whole transcriptome profile of entire leaves of A. paniculata. A total of 22,402 high-quality transcripts were generated, with an average transcript length and N50 of 884 bp and 1007 bp, respectively. Functional annotation revealed that 19,264 (86%) of the total transcripts showed significant similarity with the NCBI-Nr database and were successfully annotated. Out of the 19,264 BLAST hits, 17,623 transcripts were assigned GO terms and distributed into three major functional categories: molecular function (44.62%), biological processes (29.19%), and cellular component (26.18%) based on BLAST2GO. Transcription factor analysis showed 6669 transcripts, belonging to 57 different transcription factor families. Fifteen TF genes that belong to the NAC, MYB, and bHLH TF categories were validated by RT PCR amplification. In silico analysis of gene families involved in the synthesis of biochemical compounds having medicinal values, such as cytochrome p450, protein kinases, heat shock proteins, and transporters, was completed and a total of 102 different transcripts encoding enzymes involved in the biosynthesis of terpenoids were predicted. Out of these, 33 transcripts belonged to terpenoid backbone biosynthesis. This study also identified 4254 EST-SSRs from 3661 transcripts, representing 16.34% of the total transcripts. Fifty-three novel EST-SSR markers generated from our EST dataset were used to assess the genetic diversity among eighteen A. paniculata accessions. The genetic diversity analysis revealed two distinct sub-clusters and all accessions based on the genetic similarity index were distinct from each other. A database based on EST transcripts, EST-SSR markers, and transcription factors has been developed using data generated from the present study combined with available transcriptomic resources from a public database using Meta transcriptome analysis to make genomic resources available in one place to the researchers working on this medicinal plant.

Overexpression of 1-deoxy-D-xylulose-5-phosphate reductoisomerase enhances the monoterpene content in Litsea cubeba

Monoterpenes are important components of plant essential oils and have long been used as raw materials for spices and food flavorings. Litsea cubeba is an economically aromatic plant species, the fruits of which produce essential oil with monoterpenes as the dominant components. As a branch point of carbon flow in the methyl erythritol phosphate (MEP) biosynthesis pathway, 1-deoxy-D-xylo-5-phosphate reductoisomerase (DXR) is a key rate-limiting enzyme that catalyzes the MEP pathway's second committed step. Therefore, DXR has become an effective regulation target to improve the biosynthesis of plant monoterpenes. In this study, we identified a DXR from L. cubeba, which was highly expressed in fruits, induced by MeJA and repressed by darkness. An enzyme assay showed that recombination LcDXR protein catalyzed DXP with NADPH as the cofactor. Transient overexpression of LcDXR significantly increased the content of monoterpenes in L. cubeba. Furthermore, LcDXR-overexpressing tobaccos were conducted and showed almost 5.9-fold increase in monoterpenes production, including limonene, α-pinene, eucalyptol, linalool, terpineol and camphor. Overexpression of LcDXR activated the metabolic flux of monoterpene biosynthesis through crosstalk and feedback mechanism. In addition, LcDXR-overexpressing tobaccos had no effect on phenotype of transgenic tobaccos. Our results demonstrate that LcDXR is a critical regulator of the monoterpene production in L. cubeba and other plants.

Biosynthesis and the Transcriptional Regulation of Terpenoids in Tea Plants (Camellia sinensis)

Terpenes, especially volatile terpenes, are important components of tea aroma due to their unique scents. They are also widely used in the cosmetic and medical industries. In addition, terpene emission can be induced by herbivory, wounding, light, low temperature, and other stress conditions, leading to plant defense responses and plant-plant interactions. The transcriptional levels of important core genes (including HMGR, DXS, and TPS) involved in terpenoid biosynthesis are up- or downregulated by the MYB, MYC, NAC, ERF, WRKY, and bHLH transcription factors. These regulators can bind to corresponding cis-elements in the promoter regions of the corresponding genes, and some of them interact with other transcription factors to form a complex. Recently, several key terpene synthesis genes and important transcription factors involved in terpene biosynthesis have been isolated and functionally identified from tea plants. In this work, we focus on the research progress on the transcriptional regulation of terpenes in tea plants (Camellia sinensis) and thoroughly detail the biosynthesis of terpene compounds, the terpene biosynthesis-related genes, the transcription factors involved in terpene biosynthesis, and their importance. Furthermore, we review the potential strategies used in studying the specific transcriptional regulation functions of candidate transcription factors that have been discriminated to date.

Metabolite Profiling to Evaluate Metabolic Changes in Genetically Modified Protopanaxadiol-Enriched Rice

Event DS rice producing protopanaxadiol (PPD) has been previously developed by inserting Panax ginseng dammarenediol-II synthase gene (PgDDS) and PPD synthase gene (CYP716A47). We performed a gas chromatography-mass spectrometry (GC-MS)-based metabolomics of the DS rice to identify metabolic alterations as the effects of genetic engineering by measuring the contents of 65 metabolites in seeds and 63 metabolites in leaves. Multivariate analysis and one-way analysis of variance between DS and non-genetically modified (GM) rice showed that DS rice accumulated fewer tocotrienols, tocopherols, and phytosterols than non-GM rice. These results may be due to competition for the same precursors because PPDs in DS rice are synthesized from the same precursors as those of phytosterols. In addition, multivariate analysis of metabolic data from rice leaves revealed that composition differed by growth stage rather than genetic modifications. Our results demonstrate the potential of metabolomics for identifying metabolic alterations in response to genetic modifications.