Phytochemical drivers of insect herbivory: a functional toolbox to support agroecological diversification.

Plant metabolism is a key feature of biodiversity that remains underexploited in functional frameworks used in agroecology. Here, we study how phytochemical diversity considered at three organizational levels can promote pest control. In a factorial field experiment, we manipulated plant diversity in three monocultures and three mixed crops of oilseed rape to explore how intra- and interspecific phytochemical diversity affects pest infestation. We combined recent progress in metabolomics with classic metrics used in ecology to test a box of hypotheses grounded in plant defence theory. According to the hypothesis of 'phytochemically mediated coevolution', our study stresses the relationships between herbivore infestation and particular classes of specialized metabolites like glucosinolates. Among 178 significant relationships between metabolites and herbivory rates, only 20% were negative. At the plant level, phytochemical abundance and richness had poor predictive power on pest regulation. This challenges the hypothesis of 'synergistic effects'. At the crop cover level, in line with the hypothesis of 'associational resistance', the phytochemical dissimilarity between neighbouring plants limited pest infestation. We discuss the intricate links between associational resistance and bottom-up pest control. Bridging different levels of organization in agroecosystems helps to dissect the multi-scale relationships between phytochemistry and insect herbivory.

6-Phosphogluconate dehydrogenase 2 bridges the OPP and shikimate pathways to enhance aromatic amino acid production in plants.

The oxidative pentose phosphate (OPP) pathway provides metabolic intermediates for the shikimate pathway and directs carbon flow to the biosynthesis of aromatic amino acids (AAAs), which serve as basic protein building blocks and precursors of numerous metabolites essential for plant growth. However, genetic evidence linking the two pathways is largely unclear. In this study, we identified 6-phosphogluconate dehydrogenase 2 (PGD2), the rate-limiting enzyme of the cytosolic OPP pathway, through suppressor screening of arogenate dehydrogenase 2 (adh2) in Arabidopsis. Our data indicated that a single amino acid substitution at position 63 (glutamic acid to lysine) of PGD2 enhanced its enzyme activity by facilitating the dissociation of products from the active site of PGD2, thus increasing the accumulation of AAAs and partially restoring the defective phenotype of adh2. Phylogenetic analysis indicated that the point mutation occurred in a well-conserved amino acid residue. Plants with different amino acids at this conserved site of PGDs confer diverse catalytic activities, thus exhibiting distinct AAAs producing capability. These findings uncover the genetic link between the OPP pathway and AAAs biosynthesis through PGD2. The gain-of-function point mutation of PGD2 identified here could be considered as a potential engineering target to alter the metabolic flux for the production of AAAs and downstream compounds.

Ecological risk of per-and polyfluorinated alkyl substances in the phytoremediation process: a case study for ecologically keystone species across two generations.

The potential ecological risk of per- and polyfluorinated alkyl substances (PFASs) in phytoremediation has raised social concerns, promoting a need to better understand their distribution and risks in the recovery process of aquatic plants. Herein, we aim to fill this knowledge gap by investigating the distribution and ecotoxicological effects of PFASs on the structure and function of water-macrophyte-sediment microcosm systems. Among the entire system, 63.0 %-73.1 % PFOA was found in sediments and submerged plants, however, 52.5 %-53.0 % of PFPeA and 47.0 %-47.5 % of PFBS remained in the water under different treatments. PFOA was more bioavailable than the other substances, as demonstrated by the bioaccumulation factors (BAF) with ranges exposed to PFPeA and PFBS. Bioaccumulation PFASs induced plant oxidative stress which generates enzymes to suppress superoxide, and disturbed the processes of lysine biosynthesis, in which allysine, meso-2,6-diaminoheptanedioate, and Nsuccinyl-2-amino-6-ketopimelate were downregulated. PFASs were detected in the propagator (turions) of an ecological restoration species, where short-chain PFASs (70.1 % and 45.7 % for 2 or 20 µg/L PFAS exposure, respectively) were found to spread further into new individuals and profoundly influence ecological processes shaping populations. PFASs significantly enhanced the number of microbial species in the sediment, but the degree of differentiation in the microbial community structure was not significantly different. This study enhances our understanding of the ecological mechanisms of PFASs in the water-macrophyte-sediment systems and potential threats to the recovery process of macrophytes.

Efficient and Powerful Integration of Targeted Metabolomics and Transcriptomics for Analyzing the Metabolism Behind Desirable Traits in Plants.

Through current mass spectrometry methods and multiple RNA-Seq technologies, large metabolomics and transcriptomics datasets are readily obtainable, which provide a powerful and global perspective on metabolism. Indeed, one "omics" method is often not enough to draw strong conclusions about metabolism. Combining and interpreting multiple "omics" datasets remains a challenging task that requires careful statistical considerations and pre-planning. Here we describe a protocol for obtaining high-quality metabolomics and transcriptomics datasets in developing plant embryos followed by a robust approach to integration of the two. This protocol is readily adjustable and scalable to any other metabolically active organ or tissue.

Common metabolism and transcription responses of low-cadmium-accumulative wheat (Triticum aestivum L.) cultivars sprayed with nano-selenium.

Cadmium (Cd) contamination in soils threatens food security, while cultivating low-Cd-accumulative varieties, coupled with agro-nanotechnology, offers a potential solution to reduce Cd accumulation in crops. Herein, foliar application of selenium nanoparticles (SeNPs) was performed on seedlings of two low-Cd-accumulative wheat (Triticum aestivum L.) varieties grown in soil spiked with Cd at 3 mg/kg. Results showed that foliar application of SeNPs at 0.16 mg/plant (SeNPs-M) significantly decreased the Cd content in leaves of XN-979 and JM-22 by 46.4 and 40.8 %, and alleviated oxidative damage. The wheat leaves treated with SeNPs-M underwent significant metabolic and transcriptional reprogramming. On one hand, four specialized antioxidant metabolites such as L-Tyrosine, beta-N-acetylglucosamine, D-arabitol, and monolaurin in response to SeNPs in JM-22 and XN-979 is the one reason for the decrease of Cd in wheat leaves. Moreover, alleviation of stress-related kinases, hormones, and transcription factors through oxidative post-translational modification, subsequently regulates the expression of defense genes via Se-enhanced glutathione peroxidase. These findings indicate that combining low-Cd-accumulative cultivars with SeNPs spraying is an effective strategy to reduce Cd content in wheat and promote sustainable agricultural development.

Study of pesticide transformation processes in different wheat varieties and their effects on plant metabolism.

BACKGROUND: This study aims to obtain systematic understanding of the way by which pesticides are metabolized in plants and the influence of this process on plants' metabolism as this process has a key impact on plant-based food safety and quality. The research was conducted under field conditions, which enabled to capture metabolic processes taking place in plants grown under multihectare cultivation conditions. RESULTS: Research was conducted on three wheat varieties cultivated under field conditions and treated by commercially available preparations (fungicides, herbicides, insecticides, and growth regulator). Plant tissues with distinctions in roots, green parts, and ears were collected periodically during spring-summer vegetation period, harvested grains were also investigated. Sample extracts were examined by chromatographic techniques coupled with tandem mass spectrometry for: dissipation kinetics study, identification of pesticide metabolites, and fingerprint-based assessment of metabolic changes. CONCLUSION: Tissue type and wheat varieties influenced pesticide dissipation kinetics and resulting metabolites. Metabolic changes of plants were influenced by type of applied pesticide and its concentration in plants tissues. Despite differences in plant metabolic response to pesticide stress during cultivation, grain metabolomes of all investigated wheat varieties were statistically similar. 4-[cyclopropyl(hydroxy)methylidene]-3,5-dioxocyclo-hexanecarboxylic acid and trans-chrysantemic acid - metabolites of crop-applied trinexapac-ethyl and lambda-cyhalothrin, respectively, were identified in cereal grains. These compounds were not considered to be present in cereal grains up to now. The research was conducted under field conditions, enabling the measurement of metabolic processes taking place in plants grown under large-scale management conditions. © 2024 Society of Chemical Industry.

Isotopically nonstationary metabolic flux analysis of plants: recent progress and future opportunities.

Metabolic flux analysis (MFA) is a valuable tool for quantifying cellular phenotypes and to guide plant metabolic engineering. By introducing stable isotopic tracers and employing mathematical models, MFA can quantify the rates of metabolic reactions through biochemical pathways. Recent applications of isotopically nonstationary MFA (INST-MFA) to plants have elucidated nonintuitive metabolism in leaves under optimal and stress conditions, described coupled fluxes for fast-growing algae, and produced a synergistic multi-organ flux map that is a first in MFA for any biological system. These insights could not be elucidated through other approaches and show the potential of INST-MFA to correct an oversimplified understanding of plant metabolism.

A Practical Guide to the Representation of Protein Regulation in the Web Application ChloroKB.

ChloroKB ( http://chlorokb.fr ) is a knowledge base providing synoptic representations of the metabolism of the model plant Arabidopsis thaliana and its regulation. Initially focused on plastid metabolism, ChloroKB now accounts for the metabolism throughout the cell. ChloroKB is based on the CellDesigner formalism. CellDesigner supports graphical notation and listing of the corresponding symbols based on the Systems Biology Graphical Notation. Thus, this formalism allows biologists to represent detailed biochemical processes in a way that can be easily understood and shared, facilitating communication between researchers. In this chapter, we will focus on a specificity of ChloroKB, the representation of multilayered regulation of protein activity. Information on regulation of protein activity is indeed central to understanding the plant response to fluctuating environmental conditions. However, the intrinsic diversity of the regulatory modes and the abundance of detail may hamper comprehension of the regulatory processes described in ChloroKB. With this chapter, ChloroKB users will be guided through the representation of these sophisticated biological processes of prime importance to understanding metabolism or for applied purposes. The descriptions provided, which summarize years of work and a broad bibliography in a few pages, can help speed up the integration of regulatory processes in kinetic models of plant metabolism.

Comprehensive LC-MS/MS analysis of nitrogen-related plant metabolites.

We have developed and validated a novel LC-MS/MS method for simultaneously analyzing amino acids, biogenic amines, and their acetylated and methylated derivatives in plants. This method involves a one-step extraction of 2-5 mg of lyophilized plant material followed by fractionation of different biogenic amine forms, and exploits an efficient combination of hydrophilic interaction liquid chromatography (HILIC), reversed phase (RP) chromatography with pre-column derivatization, and tandem mass spectrometry (MS). This approach enables high-throughput processing of plant samples, significantly reducing the time needed for analysis and its cost. We also present a new synthetic route for deuterium-labeled polyamines. The LC-MS/MS method was rigorously validated by quantifying levels of nitrogen-related metabolites in seedlings of seven plant species, including Arabidopsis, maize, and barley, all of which are commonly used model organisms in plant science research. Our results revealed substantial variations in the abundance of these metabolites between species, developmental stages, and growth conditions, particularly for the acetylated and methylated derivatives and the various polyamine fractions. However, the biological relevance of these plant metabolites is currently unclear. Overall, this work contributes significantly to plant science by providing a powerful analytical tool and setting the stage for future investigations into the functions of these nitrogen-related metabolites in plants.

Uptake, translocation, and metabolization of amitriptyline, lidocaine, orphenadrine, and tramadol by cress and pea.

The uptake, translocation, and metabolization of four widely used drugs, amitriptyline, orphenadrine, lidocaine, and tramadol, were investigated in a laboratory study. Cress (Lepidium sativum L.) and pea (Pisum sativum L.) were employed as model plants. These plants were grown in tap water containing the selected pharmaceuticals at concentrations ranging from 0.010 to 10 mg L-1, whereby the latter concentration was employed for the (tentative) identification of drug-related metabolites formed within the plant. Thereby, mainly phase I metabolites were detected. Time-resolved uptake studies, with sampling after 1, 2, 4, 8, and 16 days, revealed that all four pharmaceuticals were taken up by the roots and further relocated to plant stem and leaves. Also in these studies, the corresponding phase I metabolites could be detected, and their translocation from root to stem (pea only) and finally leaves could be investigated.

Methylation and Demethylation of Emerging Contaminants in Plants.

Many contaminants of emerging concern (CECs) have reactive functional groups and may readily undergo biotransformations, such as methylation and demethylation. These transformations have been reported to occur during human metabolism and wastewater treatment, leading to the propagation of CECs. When treated wastewater and biosolids are used in agriculture, CECs and their transformation products (TPs) are introduced into soil-plant systems. However, little is known about whether transformation cycles, such as methylation and demethylation, take place in higher plants and hence affect the fate of CECs in terrestrial ecosystems. In this study, we explored the interconversion between four common CECs (acetaminophen, diazepam, methylparaben, and naproxen) and their methylated or demethylated TPs in Arabidopsis thaliana cells and whole wheat seedlings. The methylation-demethylation cycle occurred in both plant models with demethylation generally taking place at a greater degree than methylation. The transformation rate of demethylation or methylation was dependent on the bond strength of R-CH3, with demethylation of methylparaben or methylation of acetaminophen being more pronounced. Although not explored in this study, these interconversions may exert influences on the behavior and biological activity of CECs, particularly in terrestrial ecosystems. The study findings demonstrated the prevalence of transformation cycles between CECs and their methylated or demethylated TPs in higher plants, contributing to a more complete understanding of risks of CECs in the human-wastewater-soil-plant continuum.

Multifunctional 5-hydroxyconiferaldehyde O-methyltransferases (CAldOMTs) in plant metabolism.

Lignin, flavonoids, melatonin, and stilbenes are plant specialized metabolites with diverse physiological and biological functions, supporting plant growth and conferring stress resistance. Their biosynthesis requires O-methylations catalyzed by 5-hydroxyconiferaldehyde O-methyltransferase (CAldOMT; also called caffeic acid O-methyltransferase, COMT). CAldOMT was first known for its roles in syringyl (S) lignin biosynthesis in angiosperm cell walls and later found to be multifunctional. This enzyme also catalyzes O-methylations in flavonoid, melatonin, and stilbene biosynthetic pathways. Phylogenetic analysis indicated the convergent evolution of enzymes with OMT activities towards the monolignol biosynthetic pathway intermediates in some gymnosperm species that lack S-lignin and Selaginella moellendorffii, a lycophyte which produces S-lignin. Furthermore, neofunctionalization of CAldOMTs occurred repeatedly during evolution, generating unique O-methyltransferases (OMTs) with novel catalytic activities and/or accepting novel substrates, including lignans, 1,2,3-trihydroxybenzene, and phenylpropenes. This review summarizes multiple aspects of CAldOMTs and their related proteins in plant metabolism and discusses their evolution, molecular mechanism, and roles in biorefineries, agriculture, and synthetic biology.

MFP1 defines the subchloroplast location of starch granule initiation.

Starch is one of the major carbohydrate storage compounds in plants. The biogenesis of starch granules starts with the formation of initials, which subsequently expand into granules. Several coiled-coil domain-containing proteins have been previously implicated with the initiation process, but the mechanisms by which they act remain largely elusive. Here, we demonstrate that one of these proteins, the thylakoid-associated MAR-BINDING FILAMENT-LIKE PROTEIN 1 (MFP1), specifically determines the subchloroplast location of initial formation. The expression of MFP1 variants "mis"-targeted to specific locations within chloroplasts in Arabidopsis results in distinctive shifts in not only how many but also where starch granules are formed. Importantly, "re" localizing MFP1 to the stromal face of the chloroplast's inner envelope is sufficient to generate starch granules in this aberrant position. These findings provide compelling evidence that a single protein MFP1 possesses the capacity to direct the initiation and biosynthesis machinery of starch granules.

Metabolome regulation and restoration mechanism of different varieties of rice (Oryza sativa L.) after lindane stress.

There is a lack of studies on the ability of plants to metabolize chlorinated organic pollutants (COPs) and the dynamic expression changes of metabolic molecules during degradation. In this study, hybrid rice Chunyou 927 (CY) and Zhongzheyou 8 (ZZY), traditional rice subsp. Indica Baohan 1 (BH) and Xiangzaoxian 45 (XZX), and subsp. Japonica Yangjing 687 (YJ) and Longjing 31 (LJ) were stressed by a typical COPs of lindane and then transferred to a lindane-free culture to incubate for 9 days. The cumulative concentrations in the roots of BH, XZX, CY, ZZY, YJ and LJ were 71.46, 65.42, 82.06, 80.11, 47.59 and 56.10 mg·kg-1, respectively. And the degradation ratios on day 9 were 87.89 %, 86.92 %, 94.63 %, 95.49 %, 72.04 % and 82.79 %, respectively. On the 0 day after the release of lindane stress, the accumulated lindane inhibited the normal physiological activities of rice by affecting lipid metabolism in subsp. Indica BH, amino acid metabolism and synthesis and nucleotide metabolism in hybrid CY. Carbohydrate metabolism of subsp. Japonica YJ also was inhibited, but with low accumulation of lindane, YJ regulated amino acid metabolism to resist stress. With the degradation of lindane in rice, the amino acid metabolism of BH and CY, which had high degradation ratios on day 9, was activated to compound biomolecules required for the organism to recover from the damage. Amino acid metabolism and carbohydrate metabolism were disturbed and inhibited mainly in YJ with low degradation ratios. This study provides the difference of the metabolic capacity of the metabolic capacity of different rice varieties to lindane, and changes at the molecular level and metabolic response mechanism of rice during the metabolism of lindane.

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.

A simulation model (PostPLANT-Soil) for predicting pesticide concentrations in succeeding leafy vegetables: II. Validation with experimental data on plant uptake in a growth chamber.

We validated a simulation model (PostPLANT-Soil) for predicting pesticide concentrations in succeeding leafy vegetables reported in our first paper in this series, which includes the pesticide sorption process into plant roots. As a result of the model validation with the measured data from a plant uptake study in a growth chamber, the model successfully simulated the concentration changes of pesticides in a plant shoot. However, the simulated shoot concentrations for several pesticides were overestimated compared to the measured values. The leafy vegetable (Brassica rapa) used in this study probably has a high metabolic ability for the fungicide flutolanil from the result of the uptake study under a hydroponic condition.

Uptake and metabolization of four sartan drugs by eight different plants: Targeted and untargeted analyses by HPLC-drift-tube-ion-mobility quadrupole time-of-flight mass spectrometry.

In this study, we investigated the uptake and metabolization of four drugs (plus the associated prodrugs) from the sartan family by eight edible plants. Growing the plants hydroponically in a medium containing the respective drug, more than 40 phases I and II metabolites derived from the four sartan drugs could be tentatively identified. To demonstrate the suitability of the proposed analytical approach for actual environmental samples, garden cress (Lepidium sativum) selected as a model plant was grown in water drawn from the effluent of two local wastewater treatment plants. Thereby, three of the sartans, namely, olmesartan, candesartan, and valsartan, could be found in the plant extracts at concentrations of 3.1, 10.4, and 14.4 ng g-1 , respectively. Additionally, for candesartan and valsartan, a glycosylated transformation product could be detected. In order to extend the present (targeted) workflow also toward the analysis of unknown transformation products (i.e., those not listed in the custom-made database used for this research), a nontargeted approach for the analysis of plant extracts with respect to the presence of drug-related metabolites was developed. Comparison of the targeted and the nontargeted workflows led to the finding of two additional, so far unidentified, transformation products originating from azilsartan.

An Arabidopsis mutant line lacking the mitochondrial calcium transport regulator MICU shows an altered metabolite profile.

Plant metabolism is constantly changing and requires input signals for efficient regulation. The mitochondrial calcium uniporter (MCU) couples organellar and cytoplasmic calcium oscillations leading to oxidative metabolism regulation in a vast array of species. In Arabidopsis thaliana, genetic deletion of AtMICU leads to altered mitochondrial calcium handling and ultrastructure. Here we aimed to further assess the consequences upon genetic deletion of AtMICU. Our results confirm that AtMICU safeguards intracellular calcium transport associated with carbohydrate, amino acid, and phytol metabolism modifications. The implications of such alterations are discussed.

Meloidogyne enterolobii MeMSP1 effector targets the glutathione-S-transferase phi GSTF family in Arabidopsis to manipulate host metabolism and promote nematode parasitism.

Meloidogyne enterolobii is an emerging root-knot nematode species that overcomes most of the nematode resistance genes in crops. Nematode effector proteins secreted in planta are key elements in the molecular dialogue of parasitism. Here, we show the MeMSP1 effector is secreted into giant cells and promotes M. enterolobii parasitism. Using co-immunoprecipitation and bimolecular fluorescent complementation assays, we identified glutathione-S-transferase phi GSTFs as host targets of the MeMSP1 effector. This protein family plays important roles in plant responses to abiotic and biotic stresses. We demonstrate that MeMSP1 interacts with all Arabidopsis GSTF. Moreover, we confirmed that the N-terminal region of AtGSTF9 is critical for its interaction, and atgstf9 mutant lines are more susceptible to root-knot nematode infection. Combined transcriptome and metabolome analyses showed that MeMSP1 affects the metabolic pathways of Arabidopsis thaliana, resulting in the accumulation of amino acids, nucleic acids, and their metabolites, and organic acids and the downregulation of flavonoids. Our study has shed light on a novel effector mechanism that targets plant metabolism, reducing the production of plant defence-related compounds while favouring the accumulation of metabolites beneficial to the nematode, and thereby promoting parasitism.

Physiological and metabolic changes in response to Boron levels are mediated by ethylene affecting tomato fruit yield.

Boron (B) is an essential nutrient for the plant, and its stress (both deficiency and toxicity) are major problems that affect crop production. Ethylene metabolism (both signaling and production) is important to plants' differently responding to nutrient availability. To better understand the connections between B and ethylene, here we investigate the function of ethylene in the responses of tomato (Solanum lycopersicum) plants to B stress (deficiency, 0 µM and toxicity, 640 µM), using ethylene related mutants, namely nonripening (nor), ripening-inhibitor (rin), never ripe (Nr), and epinastic (Epi). Our results show that B stress does not necessarily inhibit plant growth, but both B stress and ethylene signaling severely affected physiological parameters, such as photosynthesis, stomatal conductance, and chlorophyll a fluorescence. Under B toxicity, visible symptoms of toxicity appeared in the roots and margins of the older leaves through necrosis, caused by the accumulation of B which stimulated ethylene biosynthesis in the shoots. Both nor and rin (ethylene signaling) mutants presented similar responses, being these genotypes more sensitive and displaying several morphophysiological alterations, including fruit productivity reductions, in response to the B toxicity conditions. Therefore, our results suggest that physiological and metabolic changes in response to B fluctuations are likely mediated by ethylene signaling.