Targeted metabolomics of Physaria fendleri, an industrial crop producing hydroxy fatty acids

13C-labeling reveals non-conventional pathways providing carbon for hydroxy fatty acid synthesis in Physaria fendleri

Physaria fendleri is a member of the Brassicaceae that produces in its embryos hydroxy fatty acids, constituents of oils that are very valuable and widely used by industry for cosmetics, lubricants, biofuels, etc. Free of toxins and rich in hydroxy fatty acids, Physaria provides a promising alternative to imported castor oil and is on the verge of being commercialized. This study aims to identify important biochemical step(s) for oil synthesis in Physaria, which may serve as target(s) for future crop improvement. To advance towards this goal, the endosperm composition was analysed by LC-MS/MS to develop and validate culture conditions that mimic the development of the embryos in planta. Using developing Physaria embryos in culture and 13C-labeling, our studies revealed that: (i) Physaria embryos metabolize carbon into biomass with an efficiency significantly lower than other photosynthetic embryos; (ii) the plastidic malic enzyme provides 42% of the pyruvate used for de novo fatty acid synthesis, which is the highest measured so far in developing 'green' oilseed embryos; and (iii) Physaria uses non-conventional pathways to channel carbon into oil, namely the Rubisco shunt, which fixes CO2 released in the plastid, and the reversibility of isocitrate dehydrogenase, which provides additional carbon for fatty acid elongation.

Time-resolved systems analysis of the induction of high photosynthetic capacity in Arabidopsis during acclimation to high light

Induction of high photosynthetic capacity is a key acclimation response to high light (HL) for many herbaceous dicot plants; however, the signaling pathways that control this response remain largely unknown. Here, a systems biology approach was utilized to characterize the induction of high photosynthetic capacity in strongly and weakly acclimating Arabidopsis thaliana accessions. Plants were grown for 5 wk in a low light (LL) regime, and time-resolved photosynthetic physiological, metabolomic, and transcriptomic responses were measured during subsequent exposure to HL. The induction of high nitrogen (N) assimilation rates early in the HL shift was strongly predictive of the induction of photosynthetic capacity later in the HL shift. Accelerated N assimilation rates depended on the mobilization of existing organic acid (OA) reserves and increased de novo OA synthesis during the induction of high photosynthetic capacity. Enhanced sucrose biosynthesis capacity increased in tandem with the induction of high photosynthetic capacity, and increased starch biosynthetic capacity was balanced by increased starch catabolism. This systems analysis supports a model in which the efficient induction of N assimilation early in the HL shift begins the cascade of events necessary for the induction of high photosynthetic capacity acclimation in HL.

Metabolic and transcriptomic study of pennycress natural variation identifies targets for oil improvement

Pennycress (Thlaspi arvense L.), a member of the Brassicaceae family, produces seed oil high in erucic acid, suitable for biodiesel and aviation fuel. Although pennycress, a winter annual, could be grown as a dedicated bioenergy crop, an increase in its seed oil content is required to improve its economic competitiveness. The success of crop improvement relies upon finding the right combination of biomarkers and targets, and the best genetic engineering and/or breeding strategies. In this work, we combined biomass composition with metabolomic and transcriptomic studies of developing embryos from 22 pennycress natural variants to identify targets for oil improvement. The selected accession collection presented diverse levels of fatty acids at maturity ranging from 29% to 41%. Pearson correlation analyses, weighted gene co-expression network analysis and biomarker identifications were used as complementary approaches to detect associations between metabolite level or gene expression and oil content at maturity. The results indicated that improving seed oil content can lead to a concomitant increase in the proportion of erucic acid without affecting the weight of embryos. Processes, such as carbon partitioning towards the chloroplast, lipid metabolism, photosynthesis, and a tight control of nitrogen availability, were found to be key for oil improvement in pennycress. Besides identifying specific targets, our results also provide guidance regarding the best timing for their modification, early or middle maturation. Thus, this work lays out promising strategies, specific for pennycress, to accelerate the successful development of lines with increased seed oil content for biofuel applications.

Elevated CO2 increases biomass of Sorghum bicolor green prop roots under drought conditions via soluble sugar accumulation and photosynthetic activity

Elevated [CO2 ] (E[CO2 ]) mitigates agricultural losses of C4 plants under drought. Although several studies have described the molecular responses of the C4 plant species Sorghum bicolor during drought exposure, few have reported the combined effects of drought and E[CO2 ] (E[CO2 ]/D) on the roots. A previous study showed that, among plant organs, green prop roots (GPRs) under E[CO2 ]/D presented the second highest increase in biomass after leaves compared with ambient [CO2 ]/D. GPRs are photosynthetically active and sensitive to drought. To understand which mechanisms are involved in the increase in biomass of GPRs, we performed transcriptome analyses of GPRs under E[CO2 ]/D. Whole-transcriptome analysis revealed several pathways altered under E[CO2 ]/D, among which photosynthesis was strongly affected. We also used previous metabolome data to support our transcriptome data. Activities associated with photosynthesis and central metabolism increased, as seen by the upregulation of photosynthesis-related genes, a rise in glucose and polyol contents, and increased contents of chlorophyll a and carotenoids. Protein-protein interaction networks revealed that proliferation, biogenesis, and homeostasis categories were enriched and contained mainly upregulated genes. The findings suggest that the previously reported increase in GPR biomass of plants grown under E[CO2 ]/D is mainly attributed to glucose and polyol accumulation, as well as photosynthesis activity and carbon provided by respiratory CO2 refixation. Our findings reveal that an intriguing and complex metabolic process occurs in GPRs under E[CO2 ]/D, showing the crucial role of these organs in plant drought /tolerance.

Physaria fendleri FAD3-1 overexpression increases ɑ-linolenic acid content in Camelina sativa seeds

Camelina (Camelina sativa) is an oil crop with a short growing period, resistance to drought and cold, low fertilizer requirements, and can be transformed using floral dipping. Seeds have a high content of polyunsaturated fatty acids, especially ɑ-linolenic acid (ALA), at 32-38%. ALA is an omega-3 fatty acid that is a substrate for eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) in the human body. In this study, ALA content was further enhanced by the seed-specific expression of Physaria fendleri FAD3-1 (PfFAD3-1) in camelina. The ALA content increased up to 48% in T2 seeds and 50% in T3 seeds. Additionally, size of the seeds increased. The expression of fatty acid metabolism-related genes in PfFAD3-1 OE transgenic lines was different from that in the wild type, where the expression of CsFAD2 decreased and CsFAD3 increased. In summary, we developed a high omega-3 fatty acid-containing camelina with up to 50% ALA content by introducing PfFAD3-1. This line can be used for genetic engineering to obtain EPA and DHA from seeds.

Seasonal turnover and insights into the overwintering biology of wireworms (Coleoptera: Elateridae) in the Canadian Prairies

BACKGROUND

The long-lived terricolous larvae of click beetles, colloquially called wireworms, pose a significant threat to agriculture worldwide. Several economically important pest species have been documented in the Canadian Prairies, including Hypnoidus bicolor, Limonius californicus and Hypnoidus abbreviatus. However, most monitoring activities are performed in the early spring and there is evidence from other geographical regions of seasonal shifts in wireworm species composition and prevalence. Further, little is known about the overwintering physiology or behaviors of wireworms, which undoubtedly contribute to their population dynamics.

RESULTS

We surveyed wireworm populations from four Manitoban fields six times throughout the 2020 and 2021 growing seasons. Both Hypnoidus species were active throughout the spring and summer; however, L. californicus did not become active until later in the spring. Chill-coma recovery assays indicated Hypnoidus species recovered quicker than L. californicus from cold acclimation. Vertical migration assays simulating progressively lower ambient temperatures experienced by overwintering larvae identified H. bicolor throughout the soil profile, with L. californicus preferentially found at cooler, shallower depths. We speculate that these differences in species distribution within the soil column are due to the higher levels of putative cryoprotectants (for example, trehalose, sorbitol, glucose, glycerol) in L. californicus, as identified by targeted liquid chromatography tandem mass spectrometry.

CONCLUSION

Our findings of a stark seasonal turnover in wireworm species prevalence and composition in the Canadian Prairies should be incorporated into future integrated pest management and surveillance activities. This study also advances our understanding of wireworm overwintering biology, which should be factored into current management approaches. © 2022 His Majesty the King in Right of Canada. Pest Management Science © 2022 Society of Chemical Industry. Reproduced with the permission of the Minister of Agriculture and Agri-Food Canada.

A metabolomic platform to identify and quantify polyphenols in coffee and related species using liquid chromatography mass spectrometry

INTRODUCTION

Products of plant secondary metabolism, such as phenolic compounds, flavonoids, alkaloids, and hormones, play an important role in plant growth, development, stress resistance. The plant family Rubiaceae is extremely diverse and abundant in Central America and contains several economically important genera, e.g. Coffea and other medicinal plants. These are known for the production of bioactive polyphenols (e.g. caffeine and quinine), which have had major impacts on human society. The overall goal of this study was to develop a high-throughput workflow to identify and quantify plant polyphenols.

METHODS

First, a method was optimized to extract over 40 families of phytochemicals. Then, a high-throughput metabolomic platform has been developed to identify and quantify 184 polyphenols in 15 min.

RESULTS

The current metabolomics study of secondary metabolites was conducted on leaves from one commercial coffee variety and two wild species that also belong to the Rubiaceae family. Global profiling was performed using liquid chromatography high-resolution time-of-flight mass spectrometry. Features whose abundance was significantly different between coffee species were discriminated using statistical analysis and annotated using spectral databases. The identified features were validated by commercially available standards using our newly developed liquid chromatography tandem mass spectrometry method.

DISCUSSION

Caffeine, trigonelline and theobromine were highly abundant in coffee leaves, as expected. Interestingly, wild Rubiaceae leaves had a higher diversity of phytochemicals in comparison to commercial coffee: defense-related molecules, such as phenylpropanoids (e.g., cinnamic acid), the terpenoid gibberellic acid, and the monolignol sinapaldehyde were found more abundantly in wild Rubiaceae leaves.

Effective Mechanisms for Improving Seed Oil Production in Pennycress (Thlaspi arvense L.) Highlighted by Integration of Comparative Metabolomics and Transcriptomics

Pennycress is a potentially lucrative biofuel crop due to its high content of long-chain unsaturated fatty acids, and because it uses non-conventional pathways to achieve efficient oil production. However, metabolic engineering is required to improve pennycress oilseed content and make it an economically viable source of aviation fuel. Research is warranted to determine if further upregulation of these non-conventional pathways could improve oil production within the species even more, which would indicate these processes serve as promising metabolic engineering targets and could provide the improvement necessary for economic feasibility of this crop. To test this hypothesis, we performed a comparative biomass, metabolomic, and transcriptomic analyses between a high oil accession (HO) and low oil accession (LO) of pennycress to assess potential factors required to optimize oil content. An evident reduction in glycolysis intermediates, improved oxidative pentose phosphate pathway activity, malate accumulation in the tricarboxylic acid cycle, and an anaplerotic pathway upregulation were noted in the HO genotype. Additionally, higher levels of threonine aldolase transcripts imply a pyruvate bypass mechanism for acetyl-CoA production. Nucleotide sugar and ascorbate accumulation also were evident in HO, suggesting differential fate of associated carbon between the two genotypes. An altered transcriptome related to lipid droplet (LD) biosynthesis and stability suggests a contribution to a more tightly-packed LD arrangement in HO cotyledons. In addition to the importance of central carbon metabolism augmentation, alternative routes of carbon entry into fatty acid synthesis and modification, as well as transcriptionally modified changes in LD regulation, are key aspects of metabolism and storage associated with economically favorable phenotypes of the species.

Expression of AtWRI1 and AtDGAT1 during soybean embryo development influences oil and carbohydrate metabolism

Soybean oil is one of the most consumed vegetable oils worldwide. Genetic improvement of its concentration in seeds has been historically pursued due to its direct association with its market value. Engineering attempts aiming to increase soybean seed oil presented different degrees of success that varied with the genetic design and the specific variety considered. Understanding the embryo's responses to the genetic modifications introduced, is a critical step to successful approaches. In this work, the metabolic and transcriptional responses to AtWRI1 and AtDGAT1 expression in soybean seeds were evaluated. AtWRI1 is a master regulator of fatty acid (FA) biosynthesis, and AtDGAT1 encodes an enzyme catalysing the final and rate-limiting step of triacylglycerides biosynthesis. The events expressing these genes in the embryo did not show an increase in total FA content, but they responded with changes in the oil and carbohydrate composition. Transcriptomic studies revealed a down-regulation of genes putatively encoding for oil body packaging proteins, and a strong induction of genes annotated as lipases and FA biosynthesis inhibitors. Novel putative AtWRI1 targets, presenting an AW-box in the upstream region of the genes, were identified by comparison with an event that harbours only AtWRI1. Lastly, targeted metabolomics analysis showed that carbon from sugar phosphates could be used for FA competing pathways, such as starch and cell wall polysaccharides, contributing to the restriction in oil accumulation. These results allowed the identification of key cellular processes that need to be considered to break the embryo's natural restriction to uncontrolled seed lipid increase.

Suppression of Physaria fendleri SDP1 Increased Seed Oil and Hydroxy Fatty Acid Content While Maintaining Oil Biosynthesis Through Triacylglycerol Remodeling

Physaria fendleri is a burgeoning oilseed crop that accumulates the hydroxy fatty acid (HFA), lesquerolic acid, and can be a non-toxic alternative crop to castor for production of industrially valuable HFA. Recently, P. fendleri was proposed to utilize a unique seed oil biosynthetic pathway coined "triacylglycerol (TAG) remodeling" that utilizes a TAG lipase to remove common fatty acids from TAG allowing the subsequent incorporation of HFA after initial TAG synthesis, yet the lipase involved is unknown. SUGAR DEPENDENT 1 (SDP1) has been characterized as the dominant TAG lipase involved in TAG turnover during oilseed maturation and germination. Here, we characterized the role of a putative PfeSDP1 in both TAG turnover and TAG remodeling. In vitro assays confirmed that PfeSDP1 is a TAG lipase and demonstrated a preference for HFA-containing TAG species. Seed-specific RNAi knockdown of PfeSDP1 resulted in a 12%-16% increase in seed weight and 14%-19% increase in total seed oil content with no major effect on seedling establishment. The increase in total oil content was primarily due to ~4.7% to ~14.8% increase in TAG molecular species containing two HFA (2HFA-TAG), and when combined with a smaller decrease in 1HFA-TAG content the proportion of total HFA in seed lipids increased 4%-6%. The results are consistent with PfeSDP1 involved in TAG turnover but not TAG remodeling to produce 2HFA-TAG. Interestingly, the concomitant reduction of 1HFA-TAG in PfeSDP1 knockdown lines suggests PfeSDP1 may have a role in reverse TAG remodeling during seed maturation that produces 1HFA-TAG from 2HFA-TAG. Overall, our results provide a novel strategy to enhance the total amount of industrially valuable lesquerolic acid in P. fendleri seeds.

Dynamic nutrient acquisition from a hydrated apoplast supports biotrophic proliferation of a bacterial pathogen of maize

Plant pathogens perturb their hosts to create environments suitable for their proliferation, including the suppression of immunity and promotion of water and nutrient availability. Although necrotrophs obtain water and nutrients by disrupting host-cell integrity, it is unknown whether hemibiotrophs, such as the bacterial pathogen Pantoea stewartii subsp. stewartii (Pnss), actively liberate water and nutrients during the early, biotrophic phase of infection. Here, we show that water and metabolite accumulation in the apoplast of Pnss-infected maize leaves precedes the disruption of host-cell integrity. Nutrient acquisition during this biotrophic phase is a dynamic process; the partitioning of metabolites into the apoplast rate limiting for their assimilation by proliferating Pnss cells. The formation of a hydrated and nutritive apoplast is driven by an AvrE-family type III effector, WtsE. Given the broad distribution of AvrE-family effectors, this work highlights the importance of actively acquiring water and nutrients for the proliferation of phytopathogenic bacteria during biotrophy.

Metabolite shift in Medicago truncatula occurs in phosphorus deprivation

Symbiotic nitrogen (N) fixation entails successful interaction between legume hosts and rhizobia that occur in specialized organs called nodules. N-fixing legumes have a higher demand for phosphorus (P) than legumes grown on mineral N. Medicago truncatula is an important model plant for characterization of effects of P deficiency at the molecular level. Hence, a study was carried out to address the alteration in metabolite levels of M. truncatula grown aeroponically and subjected to 4 weeks of P stress. First, GC-MS-based untargeted metabolomics initially revealed changes in the metabolic profile of nodules, with increased levels of amino acids and sugars and a decline in amounts of organic acids. Subsequently, LC-MS/MS was used to quantify these compounds including phosphorylated metabolites in the whole plant. Our results showed a drastic reduction in levels of organic acids and phosphorylated compounds in -P leaves, with a moderate reduction in -P roots and nodules. Additionally, sugars and amino acids were elevated in the whole plant under P deprivation. These findings provide evidence that N fixation in M. truncatula is mediated through a N feedback mechanism that in parallel is related to carbon and P metabolism.

Fat on plastic: Metabolic consequences of an LDPE diet in the fat body of the greater wax moth larvae (Galleria mellonella)

The caterpillar larvae of the greater wax moth (Galleria mellonella) are avid plastivores, as when provided a diet of low-density polyethylene (LDPE) they actively feed on it. Recent work has highlighted the importance of their microbiome in the putative biodegradation of this plastic polymer, though the impact of plastic metabolism on the insect host is less clear. In the present study, we undertook an integrative approach spanning all levels of biological organization to explore the effects of a plastic diet on the metabolic physiology of this animal model of plastic biodegradation. We demonstrate that an LDPE diet is not sufficient to maintain optimal larval growth and survival. In addition, we confirm that plastic fed waxworms retain their fat body lipid stores in a manner proportional to their individual polyethylene consumption suggesting a direct effect of LDPE biodegradation. At the functional level, the oxidative capacity of the fat body of LDPE-fed larvae is maintained reflecting unaltered metabolic function of the tissue. Finally, metabolomic analyses confirmed fat body lipid stores maintenance in LDPE-fed worms, but uncovered various other nutritional deficiencies. Overall, this work unveils novel insights in the complex interplay between LDPE biodegradation and the metabolic physiology of this model plastivore.

MYO-Inositol In Fermented Sugar Matrix Improves Human Macrophage Function

SCOPE

Reactive oxygen species production by innate immune cells plays a central role in host defense against invading pathogens at wound-site. A weakened hos-defense results in persistent infection leading to wound chronicity. Fermented Papaya Preparation (FPP), a complex sugar matrix, bolstered respiratory burst activity and improved wound healing outcomes in chronic wound patients. The objective of the current study was to identify underlying molecular factor/s responsible for augmenting macrophage host defense mechanisms following FPP supplementation.

METHODS AND RESULTS

In depth LC-MS/MS analysis of cells supplemented with FPP led to identification of myo-inositol as a key determinant of FPP activity towards improving macrophage function. Myo-inositol, in quantities that is present in FPP, significantly improved macrophage respiratory burst and phagocytosis via de novo synthesis pathway of ISYNA1. Additionally, myo-inositol transporters, HMIT and SMIT1, played a significant role in such activity. Blocking these pathways using siRNA attenuated FPP-induced improved macrophage host defense activities. FPP supplementation emerges as a novel approach to increase intracellular myo-inositol levels. Such supplementation also modified wound microenvironment in chronic wound patients to augment myo-inositol levels in wound fluid.

CONCLUSION

These observations indicate that myo-inositol in FPP influences multiple aspects of macrophage function critical for host defense against invading pathogens. This article is protected by copyright. All rights reserved.

The Evolution of Leaf Function during Development Is Reflected in Profound Changes in the Metabolic Composition of the Vacuole

During its development, the leaf undergoes profound metabolic changes to ensure, among other things, its growth. The subcellular metabolome of tomato leaves was studied at four stages of leaf development, with a particular emphasis on the composition of the vacuole, a major actor of cell growth. For this, leaves were collected at different positions of the plant, corresponding to different developmental stages. Coupling cytology approaches to non-aqueous cell fractionation allowed to estimate the subcellular concentrations of major compounds in the leaves. The results showed major changes in the composition of the vacuole across leaf development. Thus, sucrose underwent a strong allocation, being mostly located in the vacuole at the beginning of development and in the cytosol at maturity. Furthermore, these analyses revealed that the vacuole, rather rich in secondary metabolites and sugars in the growth phases, accumulated organic acids thereafter. This result suggests that the maintenance of the osmolarity of the vacuole of mature leaves would largely involve inorganic molecules.

Review of the recent developments in metabolomics-based phytochemical research

Phytochemicals are important bioactive components present in natural products. Although the health benefits of many food products are well-known and accepted as a common knowledge, the identity of the main bioactive molecules and the mechanism by which they interact in the body of human are often unknown. It was only in the last 30 years when the field of metabolomics had matured that the identification of such molecules with bioactivity has been made possible through the development of instruments to separate and computational techniques to characterize complex samples. This in turn has enabled in vitro studies to quantify the biological activity of the respective phytochemical either in mice models or in humans. In this review, the importance of key dietary phytochemicals such as phenolic acids, flavonoids, carotenoids, resveratrol, curcumin, and capsaicinoids are discussed together with their potential functions for human health. Untargeted metabolomics, in particular, liquid chromatography mass spectrometry, is the most used method to isolate, identify and profile bioactive compounds in the study of phytochemicals in foods. The application of metabolomics in drug discovery is a common practice nowadays and has boosted the drug and/or supplement manufacturing sector.HighlightsPhytochemicals are beneficial compounds for human healthPhytochemicals are plant-based bioactive and obtainable from natural productsUntargeted metabolomics has boosted the discovery of phytochemicals from foodTargeted metabolomics is key in the authentication and screening of phytochemicalsMetabolomics of phytochemicals is reshaping the road to drug and supplement manufacture.

Triacylglycerol remodeling in Physaria fendleri indicates oil accumulation is dynamic and not a metabolic endpoint

Oilseed plants accumulate triacylglycerol (TAG) up to 80% of seed weight with the TAG fatty acid composition determining its nutritional value or use in the biofuel or chemical industries. Two major pathways for production of diacylglycerol (DAG), the immediate precursor to TAG, have been identified in plants: de novo DAG synthesis and conversion of the membrane lipid phosphatidylcholine (PC) to DAG, with each pathway producing distinct TAG compositions. However, neither pathway fits with previous biochemical and transcriptomic results from developing Physaria fendleri seeds for accumulation of TAG containing >60% lesquerolic acid (an unusual 20 carbon hydroxylated fatty acid), which accumulates at only the sn-1 and sn-3 positions of TAG. Isotopic tracing of developing P. fendleri seed lipid metabolism identified that PC-derived DAG is utilized to initially produce TAG with only one lesquerolic acid. Subsequently a nonhydroxylated fatty acid is removed from TAG (transiently reproducing DAG) and a second lesquerolic acid is incorporated. Thus, a dynamic TAG remodeling process involving anabolic and catabolic reactions controls the final TAG fatty acid composition. Reinterpretation of P. fendleri transcriptomic data identified potential genes involved in TAG remodeling that could provide a new approach for oilseed engineering by altering oil fatty acid composition after initial TAG synthesis; and the comparison of current results to that of related Brassicaceae species in the literature suggests the possibility of TAG remodeling involved in incorporation of very long-chain fatty acids into the TAG sn-1 position in various plants.

Metabolomics, a Powerful Tool for Understanding Plant Abiotic Stress

Metabolomics is a technology that generates large amounts of data and contributes to obtaining wide and integral explanations of the biochemical state of a living organism. Plants are continuously affected by abiotic stresses such as water scarcity, high temperatures and high salinity, and metabolomics has the potential for elucidating the response-to-stress mechanisms and develop resistance strategies in affected cultivars. This review describes the characteristics of each of the stages of metabolomic studies in plants and the role of metabolomics in the characterization of the response of various plant species to abiotic stresses.

Targeted Metabolic Profiles of the Leaves and Xylem Sap of Two Sugarcane Genotypes Infected with the Vascular Bacterial Pathogen Leifsonia xyli subsp. xyli

Ratoon stunt (RS) is a worldwide disease that reduces biomass up to 80% and is caused by the xylem-dwelling bacterium Leifsonia xyli subsp. xyli. This study identified discriminant metabolites between a resistant (R) and a susceptible (S) sugarcane variety at the early stages of pathogen colonization (30 and 120 days after inoculation—DAI) by untargeted and targeted metabolomics of leaves and xylem sap using gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively. Bacterial titers were quantified in sugarcane extracts at 180 DAI through real-time polymerase chain reaction. Bacterial titers were at least four times higher on the S variety than in the R one. Global profiling detected 514 features in the leaves and 68 in the sap, while 119 metabolites were quantified in the leaves and 28 in the sap by targeted metabolomics. Comparisons between mock-inoculated treatments indicated a greater abundance of amino acids in the leaves of the S variety and of phenolics, flavonoids, and salicylic acid in the R one. In the xylem sap, fewer differences were detected among phenolics and flavonoids, but also included higher abundances of the signaling molecule sorbitol and glycerol in R. Metabolic changes in the leaves following pathogen inoculation were detected earlier in R than in S and were mostly related to amino acids in R and to phosphorylated compounds in S. Differentially represented metabolites in the xylem sap included abscisic acid. The data represent a valuable resource of potential biomarkers for metabolite-assisted selection of resistant varieties to RS.

Workflow for the Quantification of Soluble and Insoluble Carbohydrates in Soybean Seed

Soybean seed composition has a profound impact on its market value and commercial use as an important commodity. Increases in oil and protein content have been historically pursued by breeders and genetic engineers; consequently, rapid methods for their quantification are well established. The interest in complete carbohydrate profiles in mature seeds, on the other hand, has recently increased due to numerous attempts to redirect carbohydrates into oil and protein or to offer specialty seed with a specific sugar profile to meet animal nutritional requirements. In this work, a sequential protocol for quantifying reserve and structural carbohydrates in soybean seed was developed and validated. Through this procedure, the concentrations of soluble sugars, sugar alcohols, starch, hemicellulose, and crystalline cellulose can be determined in successive steps from the same starting material using colorimetric assays, LC-MS/MS, and GC-MS. The entire workflow was evaluated using internal standards to estimate the recovery efficiency. Finally, it was successfully applied to eight soybean genotypes harvested from two locations, and the resulting correlations of carbohydrate and oil or protein are presented. This methodology has the potential not only to guide soybean cultivar optimization processes but also to be expanded to other crops with only slight modifications.

Non-conventional pathways enable pennycress (Thlaspi arvense L.) embryos to achieve high efficiency of oil biosynthesis

Pennycress (Thlaspi arvense L.) accumulates oil up to 35% of the total seed biomass, and its overall fatty acid composition is suitable for aviation fuel. However, for this plant to become economically viable, its oil production needs to be improved. In vivo culture conditions that resemble the development of pennycress embryos in planta were developed based on the composition of the liquid endosperm. Then, substrate uptake rates and biomass accumulation were measured from cultured pennycress embryos, revealing a biosynthetic efficiency of 93%, which is one of the highest in comparison with other oilseeds to date. Additionally, the ratio of carbon in oil to CO2 indicated that non-conventional pathways are likely to be responsible for such a high carbon conversion efficiency. To identify the reactions enabling this phenomenon, parallel labeling experiments with 13C-labeled substrates were conducted in pennycress embryos. The main findings of these labeling experiments include: (i) the occurrence of the oxidative reactions of the pentose phosphate pathway in the cytosol; (ii) the reversibility of isocitrate dehydrogenase; (iii) the operation of the plastidic NADP-dependent malic enzyme; and (iv) the refixation of CO2 by Rubisco. These reactions are key providers of carbon and reductant for fatty acid synthesis and elongation.

Differential Metabolic Responses Caused by the Most Important Insect Pest of Coffee Worldwide, the Coffee Berry Borer (Hypothenemus hampei)

The world's coffee supply is threatened by the coffee berry borer, Hypothenemus hampei, the most destructive pest affecting coffee production and quality. This study hypothesized that coffee berry borer infestation induces distinct metabolic responses in the green coffee seeds of Coffea arabica and Coffea canephora (robusta). A targeted metabolomics approach was conducted using liquid chromatography tandem mass spectrometry to quantify intracellular metabolites in infested and uninfested arabica and robusta green seeds. In parallel, the seed biomass content and composition were assessed for the same conditions. Coffee berry borer attack induced increases in the levels of chlorogenic acids in arabica seeds, whereas organic acids and sugar alcohols were more abundant in infested robusta seeds. Most importantly, a set of compounds was identified as biomarkers differentiating the metabolic response of these taxa to the coffee berry borer.

Metabolomics as an Emerging Tool for the Study of Plant-Pathogen Interactions

Plants defend themselves from most microbial attacks via mechanisms including cell wall fortification, production of antimicrobial compounds, and generation of reactive oxygen species. Successful pathogens overcome these host defenses, as well as obtain nutrients from the host. Perturbations of plant metabolism play a central role in determining the outcome of attempted infections. Metabolomic analyses, for example between healthy, newly infected and diseased or resistant plants, have the potential to reveal perturbations to signaling or output pathways with key roles in determining the outcome of a plant-microbe interaction. However, application of this -omic and its tools in plant pathology studies is lagging relative to genomic and transcriptomic methods. Thus, it is imperative to bring the power of metabolomics to bear on the study of plant resistance/susceptibility. This review discusses metabolomics studies that link changes in primary or specialized metabolism to the defense responses of plants against bacterial, fungal, nematode, and viral pathogens. Also examined are cases where metabolomics unveils virulence mechanisms used by pathogens. Finally, how integrating metabolomics with other -omics can advance plant pathology research is discussed.

Liquid Chromatography Tandem Mass Spectrometry Quantification of 13C-Labeling in Sugars

Subcellular compartmentation has been challenging in plant ¹³C-metabolic flux analysis. Indeed, plant cells are highly compartmented: they contain vacuoles and plastids in addition to the regular organelles found in other eukaryotes. The distinction of reactions between compartments is possible when metabolites are synthesized in a particular compartment or by a unique pathway. Sucrose is an example of such a metabolite: it is specifically produced in the cytosol from glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P). Therefore, determining the ¹³C-labeling in the fructosyl and glucosyl moieties of sucrose directly informs about the labeling of cytosolic F6P and G6P, respectively. To date, the most commonly used method to monitor sucrose labeling is by nuclear magnetic resonance, which requires substantial amounts of biological sample. This study describes a new methodology that accurately measures the labeling in free sugars using liquid chromatography tandem mass spectrometry (LC-MS/MS). For this purpose, maize embryos were pulsed with [U-¹³C]-fructose, intracellular sugars were extracted, and their time-course labeling was analyzed by LC-MS/MS. Additionally, extracts were enzymatically treated with hexokinase to remove the soluble hexoses, and then invertase to cleave sucrose into fructose and glucose. Finally, the labeling in the glucosyl and fructosyl moieties of sucrose was determined by LC-MS/MS.

Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis

BACKGROUND

Ricinoleic acid is a high-value hydroxy fatty acid with broad industrial applications. Hiptage benghalensis seed oil contains a high amount of ricinoleic acid (~ 80%) and represents an emerging source of this unusual fatty acid. However, the mechanism of ricinoleic acid accumulation in H. benghalensis is yet to be explored at the molecular level, which hampers the exploration of its potential in ricinoleic acid production.

RESULTS

To explore the molecular mechanism of ricinoleic acid biosynthesis and regulation, H. benghalensis seeds were harvested at five developing stages (13, 16, 19, 22, and 25 days after pollination) for lipid analysis. The results revealed that the rapid accumulation of ricinoleic acid occurred at the early-mid-seed development stages (16-22 days after pollination). Subsequently, the gene transcription profiles of the developing seeds were characterized via a comprehensive transcriptome analysis with second-generation sequencing and single-molecule real-time sequencing. Differential expression patterns were identified in 12,555 transcripts, including 71 enzymes in lipid metabolic pathways, 246 putative transcription factors (TFs) and 124 long noncoding RNAs (lncRNAs). Twelve genes involved in diverse lipid metabolism pathways, including fatty acid biosynthesis and modification (hydroxylation), lipid traffic, triacylglycerol assembly, acyl editing and oil-body formation, displayed high expression levels and consistent expression patterns with ricinoleic acid accumulation in the developing seeds, suggesting their primary roles in ricinoleic acid production. Subsequent co-expression network analysis identified 57 TFs and 35 lncRNAs, which are putatively involved in the regulation of ricinoleic acid biosynthesis. The transcriptome data were further validated by analyzing the expression profiles of key enzyme-encoding genes, TFs and lncRNAs with quantitative real-time PCR. Finally, a network of genes associated with ricinoleic acid accumulation in H. benghalensis was established.

CONCLUSIONS

This study was the first step toward the understating of the molecular mechanisms of ricinoleic acid biosynthesis and oil accumulation in H. benghalensis seeds and identified a pool of novel genes regulating ricinoleic acid accumulation. The results set a foundation for developing H. benghalensis into a novel ricinoleic acid feedstock at the transcriptomic level and provided valuable candidate genes for improving ricinoleic acid production in other plants.

Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis

BACKGROUND

Ricinoleic acid is a high-value hydroxy fatty acid with broad industrial applications. Hiptage benghalensis seed oil contains a high amount of ricinoleic acid (~ 80%) and represents an emerging source of this unusual fatty acid. However, the mechanism of ricinoleic acid accumulation in H. benghalensis is yet to be explored at the molecular level, which hampers the exploration of its potential in ricinoleic acid production.

RESULTS

To explore the molecular mechanism of ricinoleic acid biosynthesis and regulation, H. benghalensis seeds were harvested at five developing stages (13, 16, 19, 22, and 25 days after pollination) for lipid analysis. The results revealed that the rapid accumulation of ricinoleic acid occurred at the early-mid-seed development stages (16-22 days after pollination). Subsequently, the gene transcription profiles of the developing seeds were characterized via a comprehensive transcriptome analysis with second-generation sequencing and single-molecule real-time sequencing. Differential expression patterns were identified in 12,555 transcripts, including 71 enzymes in lipid metabolic pathways, 246 putative transcription factors (TFs) and 124 long noncoding RNAs (lncRNAs). Twelve genes involved in diverse lipid metabolism pathways, including fatty acid biosynthesis and modification (hydroxylation), lipid traffic, triacylglycerol assembly, acyl editing and oil-body formation, displayed high expression levels and consistent expression patterns with ricinoleic acid accumulation in the developing seeds, suggesting their primary roles in ricinoleic acid production. Subsequent co-expression network analysis identified 57 TFs and 35 lncRNAs, which are putatively involved in the regulation of ricinoleic acid biosynthesis. The transcriptome data were further validated by analyzing the expression profiles of key enzyme-encoding genes, TFs and lncRNAs with quantitative real-time PCR. Finally, a network of genes associated with ricinoleic acid accumulation in H. benghalensis was established.

CONCLUSIONS

This study was the first step toward the understating of the molecular mechanisms of ricinoleic acid biosynthesis and oil accumulation in H. benghalensis seeds and identified a pool of novel genes regulating ricinoleic acid accumulation. The results set a foundation for developing H. benghalensis into a novel ricinoleic acid feedstock at the transcriptomic level and provided valuable candidate genes for improving ricinoleic acid production in other plants.

Beyond the wall: High-throughput quantification of plant soluble and cell-wall bound phenolics by liquid chromatography tandem mass spectrometry

Plants accumulate several thousand of phenolic compounds, including lignins and flavonoids, which are mainly synthesized through the phenylpropanoid pathway, and play important roles in plant growth and adaptation. A novel high-throughput ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method was established to quantify the levels of 19 flavonoids and 15 other phenolic compounds, including acids, aldehydes, and alcohols. The chromatographic separation was performed in 10 min, allowing for the resolution of isomers such as 3-, 4-, and 5-chlorogenic acids, 4-hydroxybenzoic and salicylic acids, isoorientin and orientin, and luteolin and kaempferol. The linearity range for each compound was found to be in the low fmol to the high pmol. Furthermore, this UHPLC-MS/MS approach was shown to be very sensitive with limits of detection between 1.5 amol to 300 fmol, and limits of quantification between 5 amol to 1000 fmol. Extracts from maize seedlings were used to assess the robustness of the method in terms of recovery efficiency, matrix effect, and accuracy. The biological matrix did not suppress the signal for 32 out of the 34 metabolites under investigation. Additionally, the majority of the analytes were recovered from the biological samples with an efficiency above 75%. All flavonoids and other phenolic compounds had an intra- and inter-day accuracy within a ±20% range, except for coniferyl alcohol and vanillic acid. Finally, the quantification of flavonoids, free and cell wall-bound phenolics in seedlings from two maize lines with contrasting phenolic content was successfully achieved using this methodology.

A liquid chromatography tandem mass spectroscopy approach for quantification of protein methylation stoichiometry

Post-translational modifications are biologically important and wide-spread modulators of protein function. Although methods for detecting the presence of specific modifications are becoming established, approaches for quantifying their mol modification/mol protein stoichiometry are less well developed. Here we introduce a ratiometric, label-free, targeted liquid chromatography tandem mass spectroscopy-based method for estimating Lys and Arg methylation stoichiometry on post-translationally modified proteins. Methylated Lys and Arg were detected with limits of quantification at low fmol and with linearity extending from 20 to 5000 fmol. This level of sensitivity allowed estimation of methylation stoichiometry from microgram quantities of various proteins, including those derived from either recombinant or tissue sources. The method also disaggregated total methylation stoichiometry into its elementary mono-, di-, and tri-methylated residue components. In addition to being compatible with kinetic experiments of protein methylation, the approach will be especially useful for characterizing methylation states of proteins isolated from cells and tissues.

Metabotype variation in a field population of tansy plants influences aphid host selection

It is well known that plant volatiles influence herbivores in their selection of a host plant; however, less is known about how the nonvolatile metabolome affects herbivore host selection. Metabolic diversity between intraspecific plants can be characterized using non-targeted mass spectrometry that gives us a snapshot overview of all metabolic processes occurring within a plant at a particular time. Here, we show that non-targeted metabolomics can be used to reveal links between intraspecific chemical diversity and ecological processes in tansy (Tanacetum vulgare). First, we show that tansy plants can be categorized into five subgroups based up on their metabolic profiles, and that these "metabotypes" influenced natural aphid colonization in the field. Second, this grouping was not due to induced metabolomic changes within the plant due to aphid feeding but rather resulted from constitutive differences in chemical diversity between plants. These findings highlight the importance of intraspecific chemical diversity within one plant population and provide the first report of a non-targeted metabolomic field study in chemical ecology.

May Dietary Supplementation Augment Respiratory Burst in Wound-Site Inflammatory Cells?

Persistent infection contributes to wound chronicity. At the wound site, NADPH oxidase (NOX) activity in immune cells fights infection to enable the healing process. Fermented papaya preparation (FPP) is a carbohydrate-rich nutritional supplement that has demonstrated ability to bolster respiratory burst in experimental rodent systems. In FPP, glucose coexists with fructose and maltose in addition to multiple other sugar alcohols such as inositol. We have previously reported that FPP supplementation augments wound healing in diabetic mice via improvement of respiratory burst activity of wound innate immune cells. In this clinical study ( clinicaltrials.gov : NCT02332993), chronic wound patients were orally supplemented with FPP daily. Inducible production of reactive oxygen species was significantly higher in wound-site immune cells from patients supplemented with FPP and on standard of care (SoC) for wound management compared with those patients receiving SoC alone. Wound closure in FPP-supplemented patients showed improvement. Importantly, the consumption of this mixture of carbohydrates, including significant amounts of glucose, did not increase HbA1c. These observations warrant a full-length clinical trial testing the hypothesis that FPP improves wound closure by augmenting NOX activity in immune cells at the wound site. Antioxid. Redox Signal. 28, 401-405.

Impact of Environment on the Biomass Composition of Soybean (Glycine max) seeds

Factors including genetics, fertilization, and climatic conditions, can alter the biomass composition of soybean seeds, consequently impacting their market value and usage. This study specifically determined the content of protein and oil, as well as the composition of proteinogenic amino acids and fatty acids in seeds from 10 diverse soybean cultivars grown in four different sites. The results highlighted that different environments produce a different composition for the 10 cultivars under investigation. Specifically, the levels of oleic and linoleic acids, important contributors to oil stability, were negatively correlated. Although the protein and oil contents were higher in some locations, their "quality" was lower in terms of composition of essential amino acids and oleic acid, respectively. Finally, proteinogenic histidine and glutamate were the main contributors to the separation between Central and Northern growing sites. Taken together, these results can guide future breeding and engineering efforts aiming to develop specialized soybean lines.

Disruptions in valine degradation affect seed development and germination in Arabidopsis

We have functionally characterized the role of two putative mitochondrial enzymes in valine degradation using insertional mutants. Prior to this study, the relationship between branched-chain amino acid degradation (named for leucine, valine and isoleucine) and seed development was limited to leucine catabolism. Using a reverse genetics approach, we show that disruptions in the mitochondrial valine degradation pathway affect seed development and germination in Arabidopsis thaliana. A null mutant of 3-hydroxyisobutyryl-CoA hydrolase (CHY4, At4g31810) resulted in an embryo lethal phenotype, while a null mutant of methylmalonate semialdehyde dehydrogenase (MMSD, At2g14170) resulted in seeds with wrinkled coats, decreased storage reserves, elevated valine and leucine, and reduced germination rates. These data highlight the unique contributions CHY4 and MMSD make to the overall growth and viability of plants. It also increases our knowledge of the role branched-chain amino acid catabolism plays in seed development and amino acid homeostasis.

A sweet story: Bean pod mottle virus transmission dynamics by Mexican bean beetles (Epilachna varivestis)

Worldwide crop losses due to plant diseases exceed $60 billion annually. Next to fungi, viruses represent the greatest contributor to those losses, and these are transmitted in nature primarily by insects. Mexican bean beetles (Epilachna varivestis ) are formidable pests of soybean, as well as efficient vectors of several soybean-infecting viruses, including Bean pod mottle virus (BPMV). Beetle-borne viruses have a unique mode of transmission, though their interactions with host plants and vectors remain poorly understood. In these studies, we implemented targeted metabolite profiling and high throughput RNA sequencing approaches to explore metabolic and molecular changes in soybean leaves infected with BPMV. The virus-infected plants showed altered defence signaling and amino acid concentrations—and most strikingly—had dramatically higher sucrose levels. Based on the results, we performed a series of E. varivestis behavioral bioassays using near-isogenic soybean lines of differing foliar sucrose levels in an attempt to more directly associate sucrose content and E. varivestis feeding preferences. Choice assays revealed E. varivestis is more attracted to BPMV-infected soybean than to healthy plants. Moreover, no-choice assays indicated that beetles consume less foliage per plant but ultimately feed on more plants in a given time period if they are higher in sucrose. Importantly, these virus-driven changes to beetle feeding preferences are likely to increase BPMV spread in natural environments.

High-throughput quantification of the levels and labeling abundance of free amino acids by liquid chromatography tandem mass spectrometry

Accurate assessment of mass isotopomer distributions (MIDs) of intracellular metabolites, such as free amino acids (AAs), is crucial for quantifying in vivo fluxes. To date, the majority of studies that measured AA MIDs have relied on the analysis of proteinogenic rather than free AAs by: i) GC-MS, which involved cumbersome process of derivatization, or ii) NMR, which requires large quantities of biological sample. In this work, the development and validation of a high-throughput LC-MS/MS method allowing the quantification of the levels and labeling of free AAs is described. Sensitivity in the order of the femtomol was achieved using multiple reaction monitoring mode (MRM). The MIDs of all free AAs were assessed without the need of derivatization, and were validated (except for Trp) on a mixture of unlabeled AA standards. Finally, this method was applied to the determination of the ¹³C-labeling abundance in free AAs extracted from maize embryos cultured with ¹³C-glutamine or ¹³C-glucose. Although Cys was below the limit of detection in these biological samples, the MIDs of a total of 18 free AAs were successfully determined. Due to the increased application of tandem mass spectrometry for ¹³C-Metabolic Flux Analysis, this novel method will enable the assessment of more complete and accurate labeling information of intracellular AAs, and therefore a better definition of the fluxes.

Mass spectrometry-based plant metabolomics: Metabolite responses to abiotic stress

Metabolomics is one omics approach that can be used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include analysis of a wide range of chemical species with diverse physical properties, from ionic inorganic compounds to biochemically derived hydrophilic carbohydrates, organic and amino acids, and a range of hydrophobic lipid-related compounds. This complexitiy brings huge challenges to the analytical technologies employed in current plant metabolomics programs, and powerful analytical tools are required for the separation and characterization of this extremely high compound diversity present in biological sample matrices. The use of mass spectrometry (MS)-based analytical platforms to profile stress-responsive metabolites that allow some plants to adapt to adverse environmental conditions is fundamental in current plant biotechnology research programs for the understanding and development of stress-tolerant plants. In this review, we describe recent applications of metabolomics and emphasize its increasing application to study plant responses to environmental (stress-) factors, including drought, salt, low oxygen caused by waterlogging or flooding of the soil, temperature, light and oxidative stress (or a combination of them). Advances in understanding the global changes occurring in plant metabolism under specific abiotic stress conditions are fundamental to enhance plant fitness and increase stress tolerance. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 35:620-649, 2016.

Ehrlichia secretes Etf-1 to induce autophagy and capture nutrients for its growth through RAB5 and class III phosphatidylinositol 3-kinase

Ehrlichia chaffeensis is an obligatory intracellular bacterium that causes a potentially fatal emerging zoonosis, human monocytic ehrlichiosis. E. chaffeensis has a limited capacity for biosynthesis and metabolism and thus depends mostly on host-synthesized nutrients for growth. Although the host cell cytoplasm is rich with these nutrients, as E. chaffeensis is confined within the early endosome-like membrane-bound compartment, only host nutrients that enter the compartment can be used by this bacterium. How this occurs is unknown. We found that ehrlichial replication depended on autophagy induction involving class III phosphatidylinositol 3-kinase (PtdIns3K) activity, BECN1 (Beclin 1), and ATG5 (autophagy-related 5). Ehrlichia acquired host cell preincorporated amino acids in a class III PtdIns3K-dependent manner and ehrlichial growth was enhanced by treatment with rapamycin, an autophagy inducer. Moreover, ATG5 and RAB5A/B/C were routed to ehrlichial inclusions. RAB5A/B/C siRNA knockdown, or overexpression of a RAB5-specific GTPase-activating protein or dominant-negative RAB5A inhibited ehrlichial infection, indicating the critical role of GTP-bound RAB5 during infection. Both native and ectopically expressed ehrlichial type IV secretion effector protein, Etf-1, bound RAB5 and the autophagy-initiating class III PtdIns3K complex, PIK3C3/VPS34, and BECN1, and homed to ehrlichial inclusions. Ectopically expressed Etf-1 activated class III PtdIns3K as in E. chaffeensis infection and induced autophagosome formation, cleared an aggregation-prone mutant huntingtin protein in a class III PtdIns3K-dependent manner, and enhanced ehrlichial proliferation. These data support the notion that E. chaffeensis secretes Etf-1 to induce autophagy to repurpose the host cytoplasm and capture nutrients for its growth through RAB5 and class III PtdIns3K, while avoiding autolysosomal killing.

Identification of multiple lipid genes with modifications in expression and sequence associated with the evolution of hydroxy fatty acid accumulation in Physaria fendleri

Two Brassicaceae species, Physaria fendleri and Camelina sativa, are genetically very closely related to each other and to Arabidopsis thaliana. Physaria fendleri seeds contain over 50% hydroxy fatty acids (HFAs), while Camelina sativa and Arabidopsis do not accumulate HFAs. To better understand how plants evolved new biochemical pathways with the capacity to accumulate high levels of unusual fatty acids, transcript expression and protein sequences of developing seeds of Physaria fendleri, wild-type Camelina sativa, and Camelina sativa expressing a castor bean (Ricinus communis) hydroxylase were analyzed. A number of potential evolutionary adaptations within lipid metabolism that probably enhance HFA production and accumulation in Physaria fendleri, and, in their absence, limit accumulation in transgenic tissues were revealed. These adaptations occurred in at least 20 genes within several lipid pathways from the onset of fatty acid synthesis and its regulation to the assembly of triacylglycerols. Lipid genes of Physaria fendleri appear to have co-evolved through modulation of transcriptional abundances and alterations within protein sequences. Only a handful of genes showed evidence for sequence adaptation through gene duplication. Collectively, these evolutionary changes probably occurred to minimize deleterious effects of high HFA amounts and/or to enhance accumulation for physiological advantage. These results shed light on the evolution of pathways for novel fatty acid production in seeds, help explain some of the current limitations to accumulation of HFAs in transgenic plants, and may provide improved strategies for future engineering of their production.

Metabolite fingerprinting of pennycress (Thlaspi arvense L.) embryos to assess active pathways during oil synthesis

Pennycress (Thlaspi arvense L.), a plant naturalized to North America, accumulates high levels of erucic acid in its seeds, which makes it a promising biodiesel and industrial crop. The main carbon sinks in pennycress embryos were found to be proteins, fatty acids, and cell wall, which respectively represented 38.5, 33.2, and 27.0% of the biomass at 21 days after pollination. Erucic acid reached a maximum of 36% of the total fatty acids. Together these results indicate that total oil and erucic acid contents could be increased to boost the economic competitiveness of this crop. Understanding the biochemical basis of oil synthesis in pennycress embryos is therefore timely and relevant to guide future breeding and/or metabolic engineering efforts. For this purpose, a combination of metabolomics approaches was conducted to assess the active biochemical pathways during oil synthesis. First, gas chromatography-mass spectrometry (GC-MS) profiling of intracellular metabolites highlighted three main families of compounds: organic acids, amino acids, and sugars/sugar alcohols. Secondly, these intermediates were quantified in developing pennycress embryos by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in multiple reaction monitoring mode. Finally, partitional clustering analysis grouped the intracellular metabolites that shared a similar pattern of accumulation over time into eight clusters. This study underlined that: (i) sucrose might be stored rather than cleaved into hexoses; (ii) glucose and glutamine would be the main sources of carbon and nitrogen, respectively; and (iii) glycolysis, the oxidative pentose phosphate pathway, the tricarboxylic acid cycle, and the Calvin cycle were active in developing pennycress embryos.