HDR, the last enzyme in the MEP pathway, differently regulates isoprenoid biosynthesis in two woody plants

Iron-Sulfur Cluster Enzymes of the Methylerythritol Phosphate Pathway: IspG and IspH

Iron-sulfur cluster (Fe-S) enzymes catalyze important biological processes in cellular metabolism. They evolved in the preoxic world and are oxygen sensitive; biology has therefore evolved a range of mechanisms to protect them from oxidative damage. The 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis has two Fe-S enzymes: IspG and IspH. Both enzymes utilize 3:1 site-differentiated [4Fe-4S] clusters to perform rather unique dehydroxylation reactions. They may play roles in facilitating oxidative stress sensing and signaling. While bacterial IspG and IspH are well characterized, plant IspG and IspH are not. A particularly fascinating aspect of these enzymes is their ability to balance both their biosynthetic catalytic roles and their presumptive signaling roles in metabolism. Here we review current knowledge about the mechanism, structures, and function of IspG and IspH, and we propose future research directions to help answer the many remaining questions about them. We also provide a primer for investigators keen to start working with these enzymes, as they share with the Fe-S family a set of unique handling and experimental challenges.

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.

Photoproduction of Aviation Fuel β-Caryophyllene From the Eukaryotic Green Microalga Chlamydomonas reinhardtii

β-caryophyllene is a plant-derived sesquiterpene and is regarded as a promising ingredient for aviation fuels. Microalgae can convert CO2 into energy-rich bioproducts through photosynthesis, making them potential platforms for the sustainable production of sesquiterpenes. However, heterologous sesquiterpene engineering in microalgae is still in its infancy, and β-caryophyllene production in eukaryotic photosynthetic microorganisms has not been reported. In this study, we succeeded in producing β-caryophyllene in the model eukaryotic microalga Chlamydomonas reinhardtii by heterologously expressing a β-caryophyllene synthase (QHS). Furthermore, overexpressing the key enzyme of the 2-C-methyl-D-erythritol 4-phosphate pathway in the QHS-expressing strain (QHS-DXS-HDR-18) resulted in a 17-fold higher β-caryophyllene production compared to the single expression of QHS (QHS-28). Additionally, when isopentenyl diphosphate isomerase (CrIDI) was overexpressed, the β-caryophyllene production was up to 480.6 μg/L in QHS-DXS-HDR-CrIDI-16 and increased by 1.8-fold compared to the parental strain QHS-DXS-HDR-18. Under photoautotrophic and photomixotrophic conditions in photobioreactors, the β-caryophyllene production in QHS-DXS-HDR-CrIDI-16 reached 854.7 and 1016.8 μg/L, respectively. Noticeably, all the β-caryophyllene-producing strains generated in this study did not exhibit adverse effects on cell growth and photosynthesis activity compared to the untransformed strain. This study demonstrates the first successful attempt to produce β-caryophyllene in the eukaryotic microalga C. reinhardtii and develops a novel strategy for increasing sesquiterpene production in eukaryotic photosynthetic microorganisms.

Time-series transcriptome analysis reveals the cascade mechanism of biological processes following the perturbation of the MVA pathway in Salvia miltiorrhiza

Various biological processes are interconnected in plants. Transcription factors (TFs) often act as regulatory hubs to regulate plant growth and responses to stress by integrating various biological pathways. Despite extensive studies on TFs functions in various plant species, our understanding of the details of TFs regulation remains limited. In this study, clonal seedlings of Salvia miltiorrhiza were exposed to specific inhibitors for 12 h. Time-series transcriptome data, sampled hourly, were used to construct co-expression networks and gene regulatory networks (GRNs). Transcriptome dynamic analysis was utilized to capture the gene expression dynamics of various biological processes and decipher the potential molecular mechanisms that regulate these processes. The perturbation results showed the growth and development processes of S.miltiorrhiza were primarily affected at the early stage, whereas stress response-related biological processes were mainly influenced at the later stage. And there was a correlation between the series of key differentially expressed genes in terpenoid biosynthesis pathways and the topological distribution of these pathways. Furthermore, the GRNs based on TFs indicate that TFs play a crucial role in connecting various biological processes. In the cytoplasmic lysate gene regulatory module, SmWRKY48-SmTCP4-SmWRKY28 constituted a regulation hub regulating S.miltiorrhiza responses to perturbation of the MVA pathway. The regulation hub mediated various pathways, including pyruvate metabolism, glycolysis/gluconeogenesis, amino acid metabolism, and ubiquinone and other terpenoid-quinone biosynthesis.Our findings suggest that perturbation of a key biological pathway in S.miltiorrhiza has time-dependent effects on other biological processes. And SmWRKY48-SmTCP4-SmWRKY28 constitutes the regulatory hub in S.miltiorrhiza responses to perturbation of MVA pathway.

Unveiling Anthraquinones: Diverse Health Benefits of an Essential Secondary Metabolite

Since ancient times, plants have been used as a remedy for numerous diseases. The pharmacological properties of plants are due to the presence of secondary metabolites like terpenoids, flavonoids, alkaloids, etc. Anthraquinones represent a group of naturally occurring quinones found generously across various plant species. Anthraquinones attract a significant amount of attention due to their reported efficacy in treating a wide range of diseases. Their complex chemical structures, combined with inherent medicinal properties, underscore their potential as agents for therapy. They demonstrate several therapeutic properties such as laxative, antitumor, antimalarial, antibacterial, antifungal, antioxidant, etc. Anthraquinones are found in different forms (derivatives) in plants, and they exhibit various medicinal properties due to their structure and chemical nature. The precursors for the biosynthesis of anthraquinones in higher plants are provided by different pathways such as plastidic hemiterpenoid 2-C-methyl-D-erthriol4-phosphate (MEP), mevalonate (MVA), isochorismate synthase and polyketide. Anthraquinones possess several medicinal properties and a complex biosynthetic pathway, making them good candidates for patenting new products, synthesis methods, and biotechnological production advancements. By conducting a thorough analysis of scientific literature, this review provides insights into the intricate interplay between anthraquinone biosynthesis and its broad-ranging contributions to human health.

Proteomics: An Essential Tool to Study Plant-Specialized Metabolism

Plants are a valuable source of specialized metabolites that provide a plethora of therapeutic applications. They are natural defenses that plants use to adapt and respond to their changing environment. Decoding their biosynthetic pathways and understanding how specialized plant metabolites (SPMs) respond to biotic or abiotic stress will provide vital knowledge for plant biology research and its application for the future sustainable production of many SPMs of interest. Here, we focus on the proteomic approaches and strategies that help with the study of plant-specialized metabolism, including the: (i) discovery of key enzymes and the clarification of their biosynthetic pathways; (ii) study of the interconnection of both primary (providers of carbon and energy for SPM production) and specialized (secondary) metabolism; (iii) study of plant responses to biotic and abiotic stress; (iv) study of the regulatory mechanisms that direct their biosynthetic pathways. Proteomics, as exemplified in this review by the many studies performed to date, is a powerful tool that forms part of omics-driven research. The proteomes analysis provides an additional unique level of information, which is absent from any other omics studies. Thus, an integrative analysis, considered versus a single omics analysis, moves us more closely toward a closer interpretation of real cellular processes. Finally, this work highlights advanced proteomic technologies with immediate applications in the field.

A comprehensive review of the molecular and genetic mechanisms underlying gum and resin synthesis in Ferula species

Ferula spp. are plants that produce oleo-gum-resins (OGRs), which are plant exudates with various colors. These OGRs have various industrial applications in pharmacology, perfumery, and food. The main constituents of these OGRs are terpenoids, a diverse group of organic compounds with different structures and functions. The biosynthesis of OGRs in Ferula spp., particularly galbanum, holds considerable economic and ecological importance. However, the molecular and genetic underpinnings of this biosynthetic pathway remain largely enigmatic. This review provides an overview of the current state of knowledge on the biosynthesis of OGRs in Ferula spp., highlighting the major enzymes, genes, and pathways involved in the synthesis of different terpenoid classes, such as monoterpenes, sesquiterpenes, and triterpenes. It also examines the potential of using omics techniques, such as transcriptomics and metabolomics, and genome editing tools, such as CRISPR/Cas, to increase the yield and quality of Ferula OGRs, as well as to create novel bioactive compounds with enhanced properties. Moreover, this review addresses the current challenges and opportunities of applying gene editing in Ferula spp., and suggests some directions for future research and development.

Deoxyxylulose 5-Phosphate Synthase Does Not Play a Major Role in Regulating the Methylerythritol 4-Phosphate Pathway in Poplar

The plastidic 2-C-methylerythritol 4-phosphate (MEP) pathway supplies the precursors of a large variety of essential plant isoprenoids, but its regulation is still not well understood. Using metabolic control analysis (MCA), we examined the first enzyme of this pathway, 1-deoxyxylulose 5-phosphate synthase (DXS), in multiple grey poplar (Populus × canescens) lines modified in their DXS activity. Single leaves were dynamically labeled with 13CO2 in an illuminated, climate-controlled gas exchange cuvette coupled to a proton transfer reaction mass spectrometer, and the carbon flux through the MEP pathway was calculated. Carbon was rapidly assimilated into MEP pathway intermediates and labeled both the isoprene released and the IDP+DMADP pool by up to 90%. DXS activity was increased by 25% in lines overexpressing the DXS gene and reduced by 50% in RNA interference lines, while the carbon flux in the MEP pathway was 25-35% greater in overexpressing lines and unchanged in RNA interference lines. Isoprene emission was also not altered in these different genetic backgrounds. By correlating absolute flux to DXS activity under different conditions of light and temperature, the flux control coefficient was found to be low. Among isoprenoid end products, isoprene itself was unchanged in DXS transgenic lines, but the levels of the chlorophylls and most carotenoids measured were 20-30% less in RNA interference lines than in overexpression lines. Our data thus demonstrate that DXS in the isoprene-emitting grey poplar plays only a minor part in controlling flux through the MEP pathway.

Hydroxymethylbutenyl diphosphate accumulation reveals MEP pathway regulation for high CO2-induced suppression of isoprene emission

Isoprene is emitted by some plants and is the most abundant biogenic hydrocarbon entering the atmosphere. Multiple studies have elucidated protective roles of isoprene against several environmental stresses, including high temperature, excessive ozone, and herbivory attack. However, isoprene emission adversely affects atmospheric chemistry by contributing to ozone production and aerosol formation. Thus, understanding the regulation of isoprene emission in response to varying environmental conditions, for example, elevated CO2, is critical to comprehend how plants will respond to climate change. Isoprene emission decreases with increasing CO2 concentration; however, the underlying mechanism of this response is currently unknown. We demonstrated that high-CO2-mediated suppression of isoprene emission is independent of photosynthesis and light intensity, but it is reduced with increasing temperature. Furthermore, we measured methylerythritol 4-phosphate (MEP) pathway metabolites in poplar leaves harvested at ambient and high CO2 to identify why isoprene emission is reduced under high CO2. We found that hydroxymethylbutenyl diphosphate (HMBDP) was increased and dimethylallyl diphosphate (DMADP) decreased at high CO2. This implies that high CO2 impeded the conversion of HMBDP to DMADP, possibly through the inhibition of HMBDP reductase activity, resulting in reduced isoprene emission. We further demonstrated that although this phenomenon appears similar to abscisic acid (ABA)-dependent stomatal regulation, it is unrelated as ABA treatment did not alter the effect of elevated CO2 on the suppression of isoprene emission. Thus, this study provides a comprehensive understanding of the regulation of the MEP pathway and isoprene emission in the face of increasing CO2.

Automatization of metabolite extraction for high-throughput metabolomics: case study on transgenic isoprene-emitting birch

Metabolomics studies are becoming increasingly common for understanding how plant metabolism responds to changes in environmental conditions, genetic manipulations and treatments. Despite the recent advances in metabolomics workflow, the sample preparation process still limits the high-throughput analysis in large-scale studies. Here, we present a highly flexible robotic system that integrates liquid handling, sonication, centrifugation, solvent evaporation and sample transfer processed in 96-well plates to automatize the metabolite extraction from leaf samples. We transferred an established manual extraction protocol performed to a robotic system, and with this, we show the optimization steps required to improve reproducibility and obtain comparable results in terms of extraction efficiency and accuracy. We then tested the robotic system to analyze the metabolomes of wild-type and four transgenic silver birch (Betula pendula Roth) lines under unstressed conditions. Birch trees were engineered to overexpress the poplar (Populus × canescens) isoprene synthase and to emit various amounts of isoprene. By fitting the different isoprene emission capacities of the transgenic trees with their leaf metabolomes, we observed an isoprene-dependent upregulation of some flavonoids and other secondary metabolites as well as carbohydrates, amino acid and lipid metabolites. By contrast, the disaccharide sucrose was found to be strongly negatively correlated to isoprene emission. The presented study illustrates the power of integrating robotics to increase the sample throughput, reduce human errors and labor time, and to ensure a fully controlled, monitored and standardized sample preparation procedure. Due to its modular and flexible structure, the robotic system can be easily adapted to other extraction protocols for the analysis of various tissues or plant species to achieve high-throughput metabolomics in plant research.