Multi-Omics Analyses of Lettuce (Lactuca sativa) Reveals Primary Metabolism Reorganization Supporting Distinct Features of Secondary Metabolism Induced by Supplementing UV-A Radiation.

UV can serve as an effective light spectrum for regulating plant secondary metabolites, while relevant studies on UV-A are much less extensive than those on UV-B. A comprehensive understanding of the selective effects of UV-A on different secondary metabolites and the specific features of primary metabolism that drive these effects is still lacking. To address this knowledge gap, we conducted a study to analyze the dynamic changes in the metabolome and transcriptome of lettuce leaves irradiated with red plus UV-A light (monochromatic red light as control). Generally, UV-A promoted the synthesis of most phenylpropanoids and terpenoids originating from the shikimate and methylerythritol phosphate (MEP) pathway in plastids but sacrificed the synthesis of terpenoids derived from the mevalonate (MVA) pathway, particularly sesquiterpenes. Increased precursors supply for the shikimate and MEP pathway under UV-A was directly supported by the activation of the Calvin-Benson cycle and phosphoenolpyruvate transport. Whereas, along with phosphoenolpyruvate transport, the TCA cycle was restrained, causing deprivation of the MVA pathway precursor. In addition, UV-A also activated the plastidic oxidative branch of the pentose phosphate pathway, photorespiration, and malate shuttle, to ensure a sufficient supply of nitrogen, circulation homeostasis of the Calvin-Benson cycle, and energy balance, thus indirectly supporting UV-A-induced specific secondary metabolic output. This study provides a comprehensive framework for understanding the flexible primary-secondary metabolism interactions that are able to produce specific metabolites favorable for adaptation to environmental stimuli.

Machine learning enables identification of an alternative yeast galactose utilization pathway.

How genomic differences contribute to phenotypic differences is a major question in biology. The recently characterized genomes, isolation environments, and qualitative patterns of growth on 122 sources and conditions of 1,154 strains from 1,049 fungal species (nearly all known) in the yeast subphylum Saccharomycotina provide a powerful, yet complex, dataset for addressing this question. We used a random forest algorithm trained on these genomic, metabolic, and environmental data to predict growth on several carbon sources with high accuracy. Known structural genes involved in assimilation of these sources and presence/absence patterns of growth in other sources were important features contributing to prediction accuracy. By further examining growth on galactose, we found that it can be predicted with high accuracy from either genomic (92.2%) or growth data (82.6%) but not from isolation environment data (65.6%). Prediction accuracy was even higher (93.3%) when we combined genomic and growth data. After the GALactose utilization genes, the most important feature for predicting growth on galactose was growth on galactitol, raising the hypothesis that several species in two orders, Serinales and Pichiales (containing the emerging pathogen Candida auris and the genus Ogataea, respectively), have an alternative galactose utilization pathway because they lack the GAL genes. Growth and biochemical assays confirmed that several of these species utilize galactose through an alternative oxidoreductive D-galactose pathway, rather than the canonical GAL pathway. Machine learning approaches are powerful for investigating the evolution of the yeast genotype-phenotype map, and their application will uncover novel biology, even in well-studied traits.

Unraveling the impact of nanopollution on plant metabolism and ecosystem dynamics.

Nanopollution (NPOs), a burgeoning consequence of the widespread use of nanoparticles (NPs) across diverse industrial and consumer domains, has emerged as a critical environmental issue. While extensive research has scrutinized the repercussions of NPs pollution on ecosystems and human health, scant attention has been directed towards unraveling its implications for plant life. This comprehensive review aims to bridge this gap by delving into the nuanced interplay between NPOs and plant metabolism, encompassing both primary and secondary processes. Our exploration encompasses an in-depth analysis of the intricate mechanisms governing the interaction between plants and NPs. This involves a thorough examination of how physicochemical properties such as size, shape, and surface characteristics influence the uptake and translocation of NPs within plant tissues. The impact of NPOs on primary metabolic processes, including photosynthesis, respiration, nutrient uptake, and water transport. Additionally, this study explored the multifaceted alterations in secondary metabolism, shedding light on the synthesis and modulation of secondary metabolites in response to NPs exposure. In assessing the consequences of NPOs for plant life, we scrutinize the potential implications for plant growth, development, and environmental interactions. The intricate relationships revealed in this review underscore the need for a holistic understanding of the plant-NPs dynamics. As NPs become increasingly prevalent in ecosystems, this investigation establishes a fundamental guide that underscores the importance of additional research to shape sustainable environmental management strategies and address the extensive effects of NPs on the development of plant life and environmental interactions.

The timing of bacterial mesophyll infection shapes the leaf chemical landscape.

Chemistry in eukaryotic intercellular spaces is shaped by both hosts and symbiotic microorganisms such as bacteria. Pathogenic microorganisms like barley-associated Xanthomonas translucens (Xt) swiftly overtake the inner leaf tissue becoming the dominant microbial community member during disease development. The dynamic metabolic changes due to Xt pathogenesis in the mesophyll spaces remain unknown. Genomic group I of Xt consists of two barley-infecting lineages: pathovar translucens (Xtt) and pathovar undulosa (Xtu). Xtu and Xtt, although genomically distinct, cause similar water-soaked lesions. To define the metabolic signals associated with inner leaf colonization, we used untargeted metabolomics to characterize Xtu and Xtt metabolism signatures associated with mesophyll growth. We found that mesophyll apoplast fluid from infected tissue yielded a distinct metabolic profile and shift from catabolic to anabolic processes over time compared to water-infiltrated control. The pathways with the most differentially expressed metabolites by time were glycolysis, tricarboxylic acid cycle, sucrose metabolism, pentose interconversion, amino acids, galactose, and purine metabolism. Hierarchical clustering and principal component analysis showed that metabolic changes were more affected by the time point rather than the individual colonization of the inner leaves by Xtt compared to Xtu. Overall, in this study, we identified metabolic pathways that explain carbon and nitrogen usage during host-bacterial interactions over time for mesophyll tissue colonization. This foundational research provides initial insights into shared metabolic strategies of inner leaf colonization niche occupation by related but phylogenetically distinct phyllosphere bacteria. IMPORTANCE: The phyllosphere is a habitat for microorganisms including pathogenic bacteria. Metabolic shifts in the inner leaf spaces for most plant-microbe interactions are unknown, especially for Xanthomonas species in understudied plants like barley (Hordeum vulgare). Xanthomonas translucens pv. translucens (Xtt) and Xanthomonas translucens pv. undulosa (Xtu) are phylogenomically distinct, but both colonize barley leaves for pathogenesis. In this study, we used untargeted metabolomics to shed light on Xtu and Xtt metabolic signatures. Our findings revealed a dynamic metabolic landscape that changes over time, rather than exhibiting a pattern associated with individual pathovars. These results provide initial insights into the metabolic mechanisms of X. translucens inner leaf pathogenesis.

Imaging plant metabolism in situ.

Mass spectrometry imaging (MSI) has emerged as an invaluable analytical technique for investigating the spatial distribution of molecules within biological systems. In the realm of plant science, MSI is increasingly employed to explore metabolic processes across a wide array of plant tissues, including those in leaves, fruits, stems, roots, and seeds, spanning various plant systems such as model species, staple and energy crops, and medicinal plants. By generating spatial maps of metabolites, MSI has elucidated the distribution patterns of diverse metabolites and phytochemicals, encompassing lipids, carbohydrates, amino acids, organic acids, phenolics, terpenes, alkaloids, vitamins, pigments, and others, thereby providing insights into their metabolic pathways and functional roles. In this review, we present recent MSI studies that demonstrate the advances made in visualizing the plant spatial metabolome. Moreover, we emphasize the technical progress that enhances the identification and interpretation of spatial metabolite maps. Within a mere decade since the inception of plant MSI studies, this robust technology is poised to continue as a vital tool for tackling complex challenges in plant metabolism.

Quinoa panicles contribute to carbon assimilation and are more tolerant to salt stress than leaves.

Contribution of inflorescences to seed filling have attracted great attention given the resilience of this photosynthetic organ to stressful conditions. However, studies have been almost exclusively focused to small grain cereals. In this study, we aimed to explore these responses in quinoa, as a climate resilient seed crop of elevated economic and nutritious potential. We compared the physiological and metabolic performance of panicles and leaves of two quinoa cultivars growing under contrasting salinity levels. Plant growth, photosynthetic and transpiratory gas exchange and chlorophyll fluorescence were monitored in inflorescences and leaves throughout the experiment. At flowering stage, young and mature leaves and panicles were sampled for key metabolic markers related to carbon, nitrogen and secondary metabolisms. When subjected to salt stress, panicles showed attenuated declines on photosynthesis, water use, pigments, amino acids, and protein levels as compared to leaves. In fact, the assimilation rates, together with a high hexose content evidenced an active photosynthetic role of the panicle under optimal and salt stress conditions. Moreover, we also found significant genotypic variability for physiological and metabolic traits of panicles and leaves, which emphasizes the study of genotype-dependent stress responses at the whole plant level. We conclude that quinoa panicles are less affected by salt stress than leaves, which encourages further research and exploitation of this organ for crop improvement and stress resilience considering the high natural diversity.

Adjusting function of camphor on primary metabolism in Cinnamomum camphora stressed by high temperature.

Cinnamomum camphora has great economic value for its wide utilization in traditional medicine and furniture material, and releases lots of monoterpenes to tolerate high temperature. To uncover the adjusting function of monoterpenes on primary metabolism and promoting their utilization as anti-high temperature agents, the photosynthetic capacities, primary metabolite levels, cell ultrastructure and associated gene expression were surveyed in C. camphora when it was blocked monoterpene biosynthesis with fosmidomycin (Fos) and fumigated with camphor (a typical monoterpene in the plant) under high temperature (Fos+38 °C+camphor). Compared with the control (28 °C), high temperature at 38 °C decreased the starch content and starch grain size, and increased the fructose, glucose, sucrose and soluble sugar content. Meanwhile, high temperature also raised the lipid content, with the increase of lipid droplet size and numbers. These variations were further intensified in Fos+ 38 °C treatment. Compared with Fos+ 38 °C treatment, Fos+ 38 °C+camphor treatment improved the starch accumulation by promoting 4 gene expression in starch biosynthesis, and lowered the sugar content by suppressing 3 gene expression in pentose phosphate pathway and promoting 15 gene expression in glycolysis and tricarboxylic acid cycle. Meanwhile, Fos+ 38 °C+camphor treatment also lowered the lipid content, which may be caused by the down-regulation of 2 genes in fatty acid formation and up-regulation of 4 genes in fatty acid decomposition. Although Fos+ 38 °C+camphor treatment improved the photosynthetic capacities in contrast to Fos+ 38 °C treatment, it cannot explain the variations of these primary metabolite levels. Therefore, camphor should adjust related gene expression to maintain the primary metabolism in C. camphora tolerating high temperature.

The nitrogen-dependent GABA pathway of tomato provides resistance to a globally invasive fruit fly.

Introduction: The primary metabolism of plants, which is mediated by nitrogen, is closely related to the defense response to insect herbivores. Methods: An experimental system was established to examine how nitrogen mediated tomato resistance to an insect herbivore, the oriental fruit fly (Bactrocera dorsalis). All tomatoes were randomly assigned to the suitable nitrogen (control, CK) treatment, nitrogen excess (NE) treatment and nitrogen deficiency (ND) treatment. Results: We found that nitrogen excess significantly increased the aboveground biomass of tomato and increased the pupal biomass of B. dorsalis. Metabolome analysis showed that nitrogen excess promoted the biosynthesis of amino acids in healthy fruits, including γ-aminobutyric acid (GABA), arginine and asparagine. GABA was not a differential metabolite induced by injury by B. dorsalis under nitrogen excess, but it was significantly induced in infested fruits at appropriate nitrogen levels. GABA supplementation not only increased the aboveground biomass of plants but also improved the defensive response of tomato. Discussion: The biosynthesis of GABA in tomato is a resistance response to feeding by B. dorsalis in appropriate nitrogen, whereas nitrogen excess facilitates the pupal weight of B. dorsalis by inhibiting synthesis of the GABA pathway. This study concluded that excess nitrogen inhibits tomato defenses in plant-insect interactions by inhibiting GABA synthesis, answering some unresolved questions about the nitrogen-dependent GABA resistance pathway to herbivores.

Transcriptomics and metabolomics reveal the primary and secondary metabolism changes in Glycyrrhiza uralensis with different forms of nitrogen utilization.

The roots and rhizomes of Glycyrrhiza uralensis Fisch. represent the oldest and most frequently used herbal medicines in Eastern and Western countries. However, the quality of cultivated G. uralensis has not been adequate to meet the market demand, thereby exerting increased pressure on wild G. uralensis populations. Nitrogen, vital for plant growth, potentially influences the bioactive constituents of plants. Yet, more information is needed regarding the effect of different forms of nitrogen on G. uralensis. G. uralensis seedlings were exposed to a modified Hoagland nutrient solution (HNS), varying concentrations of nitrate (KNO3), or ammonium (NH4)2SO4. We subsequently obtained the roots of G. uralensis for physiology, transcriptomics, and metabolomics analyses. Our results indicated that medium-level ammonium nitrogen was more effective in promoting G. uralensis growth compared to nitrate nitrogen. However, low-level nitrate nitrogen distinctly accelerated the accumulation of flavonoid ingredients. Illumina sequencing of cDNA libraries prepared from four groups-treated independently with low/medium NH4 + or NO3 - identified 364, 96, 103, and 64 differentially expressed genes (DEGs) in each group. Our investigation revealed a general molecular and physiological metabolism stimulation under exclusive NH4 + or NO3 - conditions. This included nitrogen absorption and assimilation, glycolysis, Tricarboxylic acid (TCA) cycle, flavonoid, and triterpenoid metabolism. By creating and combining putative biosynthesis networks of nitrogen metabolism, flavonoids, and triterpenoids with related structural DEGs, we observed a positive correlation between the expression trend of DEGs and flavonoid accumulation. Notably, treatments with low-level NH4 + or medium-level NO3 - positively improved primary metabolism, including amino acids, TCA cycle, and glycolysis metabolism. Meanwhile, low-level NH4 + and NO3 - treatment positively regulated secondary metabolism, especially the biosynthesis of flavonoids in G. uralensis. Our study lays the foundation for a comprehensive analysis of molecular responses to varied nitrogen forms in G. uralensis, which should help understand the relationships between responsive genes and subsequent metabolic reactions. Furthermore, our results provide new insights into the fundamental mechanisms underlying the treatment of G. uralensis and other Glycyrrhiza plants with different nitrogen forms.

Copper boosts the biostimulant activity of a vegetal-derived protein hydrolysate in basil: morpho-physiological and metabolomics insights.

In addition to be used as a plant protection agent, copper (Cu) is also an essential micronutrient for plant growth and development. The bioavailability of Cu in agricultural systems can be limited due to its specific physical-chemical characteristics, leading to imbalances in plant production. To address this issue, an experimental trial was conducted on Genovese basil (Ocimum basilicum L.) in protected conditions to comparatively evaluate the effects of a vegetable protein hydrolysate (VPH), free Cu and Cu complexed with peptides and amino acids of vegetal origin (Cu and Cu-VPH, respectively), and a combination of VPH and Cu-VPH (VPH+Cu-VPH). The study showed that the combined application of VPH+Cu-VPH led to a significant average increase of 16.3% in fresh yield compared to the untreated Control and Cu treatment. This finding was supported by an improved photosynthetic performance in ACO2 (+29%) and Fv/Fm (+7%). Furthermore, mineral analysis using ICP OES demonstrated that Cu and Cu-VPH treatments determined, on average, a 15.1-, 16.9-, and 1.9-fold increase in Cu in plant tissues compared to control, VPH, and VPH+Cu-VPH treatments, respectively. However, the VPH+Cu-VPH treatment induced the highest contents of the other analyzed ions, except for P. In particular, Mg, Mn, Ca, and Fe, which take part in the constitution of chlorophylls, water splitting system, and photosynthetic electron transport chain, increased by 23%, 21%, 25%, and 32% compared to respective controls. Indeed, this improved the photosynthetic efficiency and the carboxylation capacity of the plants, and consequently, the physiological and productive performance of Genovese basil, compared to all other treatments and control. Consistently, the untargeted metabolomics also pointed out a distinctive modulation of phytochemical signatures as a function of the treatment. An accumulation of alkaloids, terpenoids, and phenylpropanoids was observed following Cu treatment, suggesting an oxidative imbalance upon metal exposure. In contrast, a mitigation of oxidative stress was highlighted in Cu-VPH and VPH+Cu-VPH, where the treatments reduced stress-related metabolites. Overall, these results highlight an interaction between Cu and VPH, hence paving the way towards the combined use of Cu and biostimulants to optimize agronomic interventions.

Denoising Autoencoder Normalization for Large-Scale Untargeted Metabolomics by Gas Chromatography-Mass Spectrometry.

Large-scale metabolomics assays are widely used in epidemiology for biomarker discovery and risk assessments. However, systematic errors introduced by instrumental signal drifting pose a big challenge in large-scale assays, especially for derivatization-based gas chromatography-mass spectrometry (GC-MS). Here, we compare the results of different normalization methods for a study with more than 4000 human plasma samples involved in a type 2 diabetes cohort study, in addition to 413 pooled quality control (QC) samples, 413 commercial pooled plasma samples, and a set of 25 stable isotope-labeled internal standards used for every sample. Data acquisition was conducted across 1.2 years, including seven column changes. In total, 413 pooled QC (training) and 413 BioIVT samples (validation) were used for normalization comparisons. Surprisingly, neither internal standards nor sum-based normalizations yielded median precision of less than 30% across all 563 metabolite annotations. While the machine-learning-based SERRF algorithm gave 19% median precision based on the pooled quality control samples, external cross-validation with BioIVT plasma pools yielded a median 34% relative standard deviation (RSD). We developed a new method: systematic error reduction by denoising autoencoder (SERDA). SERDA lowered the median standard deviations of the training QC samples down to 16% RSD, yielding an overall error of 19% RSD when applied to the independent BioIVT validation QC samples. This is the largest study on GC-MS metabolomics ever reported, demonstrating that technical errors can be normalized and handled effectively for this assay. SERDA was further validated on two additional large-scale GC-MS-based human plasma metabolomics studies, confirming the superior performance of SERDA over SERRF or sum normalizations.

Comparative constraint-based modelling of fruit development across species highlights nitrogen metabolism in the growth-defence trade-off.

Although primary metabolism is well conserved across species, it is useful to explore the specificity of its network to assess the extent to which some pathways may contribute to particular outcomes. Constraint-based metabolic modelling is an established framework for predicting metabolic fluxes and phenotypes and helps to explore how the plant metabolic network delivers specific outcomes from temporal series. After describing the main physiological traits during fruit development, we confirmed the correlations between fruit relative growth rate (RGR), protein content and time to maturity. Then a constraint-based method is applied to a panel of eight fruit species with a knowledge-based metabolic model of heterotrophic cells describing a generic metabolic network of primary metabolism. The metabolic fluxes are estimated by constraining the model using a large set of metabolites and compounds quantified throughout fruit development. Multivariate analyses showed a clear common pattern of flux distribution during fruit development with differences between fast- and slow-growing fruits. Only the latter fruits mobilise the tricarboxylic acid cycle in addition to glycolysis, leading to a higher rate of respiration. More surprisingly, to balance nitrogen, the model suggests, on the one hand, nitrogen uptake by nitrate reductase to support a high RGR at early stages of cucumber and, on the other hand, the accumulation of alkaloids during ripening of pepper and eggplant. Finally, building virtual fruits by combining 12 biomass compounds shows that the growth-defence trade-off is supported mainly by cell wall synthesis for fast-growing fruits and by total polyphenols accumulation for slow-growing fruits.

Primary Metabolite Screening Shows Significant Differences between Embryogenic and Non-Embryogenic Callus of Tamarillo (Solanum betaceum Cav.).

Tamarillo is a solanaceous tree that has been extensively studied in terms of in vitro clonal propagation, namely somatic embryogenesis. In this work, a protocol of indirect somatic embryogenesis was applied to obtain embryogenic and non-embryogenic callus from leaf segments. Nuclear magnetic resonance spectroscopy was used to analyze the primary metabolome of these distinct calli to elucidate possible differentiation mechanisms from the common genetic background callus. Standard multivariate analysis methods were then applied, and were complemented by univariate statistical methods to identify differentially expressed primary metabolites and related metabolic pathways. The results showed carbohydrate and lipid metabolism to be the most relevant in all the calli assayed, with most discriminant metabolites being fructose, glucose and to a lesser extent choline. The glycolytic rate was higher in embryogenic calli, which shows, overall, a higher rate of sugar catabolism and a different profile of phospholipids with a choline/ethanolamine analysis. In general, our results show that a distinct primary metabolome between embryogenic and non-embryogenic calli occurs and that intracellular levels of fructose and sucrose and the glucose to sucrose ratio seem to be good candidates as biochemical biomarkers of embryogenic competence.

A comprehensive view of metabolic responses to CYP98 perturbation in ancestral plants.

Cytochrome P450 monooxygenase 98 (CYP98) is a critical rate-limiting enzyme of the phenylpropanoid pathway. One of the end-product of the phenylpropanoid pathway is a lignin monomer, although the occurrence of lignin in bryophytes is controversial. Here we investigated the functions of PpCYP98 in Physcomitrium patens by transcriptome and metabolome analyses. We identified 5266 differentially expressed genes (DEGs) and 68 differentially abundant secondary metabolites between wild-type and ΔPpCYP98 gametophores. Of the identified metabolites, 23 phenolic acids were identified, with only one showing upregulation. Among the phenolic acids, 4-coumaroyl tartaric acid and chlorogenic acid showed significant decreases. Declines were also observed in coniferylaldehyde and coniferin, precursor substances and downstream products of the lignin monomer coniferyl alcohol, respectively. Thus, the pre-lignin synthesis pathway already exists in bryophytes, and PpCYP98 plays vital roles in this pathway. Besides, most flavonoids show significant reductions, including eriodyctiol, dihydroquecetin, and dihydromyricetin, whereas naringenin chalone and dihydrokaempferol were increased after PpCYP98 knockout. Therefore, the synthesis of flavonoids shares the core pathway with phenylpropanoids and mainly starts from caffeoyl-CoA, that is the compound of divergence between the two pathways in moss. PpCYP98 showed systemic effects on metabolisms, including carbohydrate, fatty acid, and hormonal signaling transductions, suggesting that PpCYP98 might indirectly regulate carbon influx allocation. Our results demonstrated roles of PpCYP98 were essential for the development of the early landing plant.

H2 S works synergistically with rhizobia to modify photosynthetic carbon assimilation and metabolism in nitrogen-deficient soybeans.

Hydrogen sulfide (H2 S) performs a crucial role in plant development and abiotic stress responses by interacting with other signalling molecules. However, the synergistic involvement of H2 S and rhizobia in photosynthetic carbon (C) metabolism in soybean (Glycine max) under nitrogen (N) deficiency has been largely overlooked. Therefore, we scrutinised how H2 S drives photosynthetic C fixation, utilisation, and accumulation in soybean-rhizobia symbiotic systems. When soybeans encountered N deficiency, organ growth, grain output, and nodule N-fixation performance were considerably improved owing to H2 S and rhizobia. Furthermore, H2 S collaborated with rhizobia to actively govern assimilation product generation and transport, modulating C allocation, utilisation, and accumulation. Additionally, H2 S and rhizobia profoundly affected critical enzyme activities and coding gene expressions implicated in C fixation, transport, and metabolism. Furthermore, we observed substantial effects of H2 S and rhizobia on primary metabolism and C-N coupled metabolic networks in essential organs via C metabolic regulation. Consequently, H2 S synergy with rhizobia inspired complex primary metabolism and C-N coupled metabolic pathways by directing the expression of key enzymes and related coding genes involved in C metabolism, stimulating effective C fixation, transport, and distribution, and ultimately improving N fixation, growth, and grain yield in soybeans.

Deep Proteogenomics of a Photosynthetic Cyanobacterium.

Cyanobacteria, the evolutionary ancestors of plant chloroplasts, contribute substantially to the Earth's biogeochemical cycles and are of great interest for a sustainable economy. Knowledge of protein expression is the key to understanding cyanobacterial metabolism; however, proteome studies in cyanobacteria are limited and cover only a fraction of the theoretical proteome. Here, we performed a comprehensive proteogenomic analysis of the model cyanobacterium Synechocystis sp. PCC 6803 to characterize the expressed (phospho)proteome, re-annotate known and discover novel open reading frames (ORFs). By mapping extensive shotgun mass spectrometry proteomics data onto a six-frame translation of the Synechocystis genome, we refined the genomic annotation of 64 ORFs, including eight completely novel ORFs. Our study presents the largest reported (phospho)proteome dataset for a unicellular cyanobacterium, covering the expression of about 80% of the theoretical proteome under various cultivation conditions, such as nitrogen or carbon limitation. We report 568 phosphorylated S/T/Y sites that are present on numerous regulatory proteins, including the transcriptional regulators cyAbrB1 and cyAbrB2. We also catalogue the proteins that have never been detected under laboratory conditions and found that a large portion of them is plasmid-encoded. This dataset will serve as a resource, providing dedicated information on growth condition-dependent protein expression and phosphorylation.

Non-canonical and developmental roles of the TCA cycle in plants.

Over recent years, our understanding of the tricarboxylic acid cycle (TCAC) in living organisms has expanded beyond its canonical role in cellular energy production. In plants, TCAC metabolites and related enzymes have important roles in physiology, including vacuolar function, chelation of metals and nutrients, photorespiration, and redox regulation. Research in other organisms, including animals, has demonstrated unexpected functions of the TCAC metabolites in a number of biological processes, including signaling, epigenetic regulation, and cell differentiation. Here, we review the recent progress in discovery of non-canonical roles of the TCAC. We then discuss research on these metabolites in the context of plant development, with a focus on research related to tissue-specific functions of the TCAC. Additionally, we review research describing connections between TCAC metabolites and phytohormone signaling pathways. Overall, we discuss the opportunities and challenges in discovering new functions of TCAC metabolites in plants.

Inhibition of nitrogen assimilation promotes carbon-based secondary metabolism in callus of Cyclocarya paliurus.

The biosynthesis and accumulation of secondary metabolites are critical important to quality formation of medicinal plants, which are usually give way to primary processes and growth. Here, methionine sulfoximine (MSO) was used to inhibit the nitrogen assimilation in callus of Cyclocarya paliurus. The newly assimilated nitrogen characterized by 15N atom percentage excess, and the levels of amino acid and protein were reduced. The other primary processes such as carbohydrate metabolism and lipid metabolism were also repressed. In addition, the expression of the growth-related target of rapamycin (TOR) signaling was repressed, indicating nitrogen assimilation inhibition led to a systematic down-regulated primary metabolisms and resulted in a disruption of growth. In contrast, the biosynthesis of flavonoids and triterpenoids, antioxidase system, and the SnRK2-mediated abscisic acid (ABA) and jasmonic acid (JA) signaling were induced, which can improve plant stress resistance and defense. Nitrogen assimilation inhibition led to the carbon metabolic flux redirection from primary processes to secondary pathways, and facilitated the biosynthesis of flavonoids and triterpenoids in calluses of C. paliurus. Our results provide a comprehensive understanding of metabolic flux redirection between primary and secondary metabolic pathways and a potential means to improve the quality of medicinal plants.

Nutrient availability regulates Deschampsia antarctica photosynthetic and stress tolerance performance in Antarctica.

Deschampsia antarctica is one of the only two native vascular plants in Antarctica, mostly located in the ice-free areas of the Peninsula's coast and adjacent islands. This region is characterized by a short growing season, frequent extreme climatic events, and soils with reduced nutrient availability. However, it is unknown whether its photosynthetic and stress tolerance mechanisms are affected by the availability of nutrients to deal with this particular environment. We studied the photosynthetic, primary metabolic, and stress tolerance performance of D. antarctica plants growing on three close sites (<500 m) with contrasting soil nutrient conditions. Plants from all sites showed similar photosynthetic rates, but mesophyll conductance and photobiochemistry were more limiting (~25%) in plants growing on low-nutrient availability soils. Additionally, these plants showed higher stress levels and larger investments in photoprotection and carbon pools, most probably driven by the need to stabilize proteins and membranes, and remodel cell walls. In contrast, when nutrients were readily available, plants shifted their carbon investment towards amino acids related to osmoprotection, growth, antioxidants, and polyamines, leading to vigorous plants without appreciable levels of stress. Taken together, these findings demonstrate that D. antarctica displays differential physiological performances to cope with adverse conditions depending on resource availability, allowing it to maximize stress tolerance without jeopardizing photosynthetic capacity.

Unravelling the Phytotoxic Effects of Glyphosate on Sensitive and Resistant Amaranthus palmeri Populations by GC-MS and LC-MS Metabolic Profiling.

Glyphosate, the most successful herbicide in history, specifically inhibits the activity of the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS; EC 2.5.1.19), one of the key enzymes in the shikimate pathway. Amaranthus palmeri is a driver weed in agriculture today that has evolved glyphosate-resistance through increased EPSPS gene copy number and other mechanisms. Non-targeted GC-MS and LC-MS metabolomic profiling was conducted to examine the innate physiology and the glyphosate-induced perturbations in one sensitive and one resistant (by EPSPS amplification) population of A. palmeri. In the absence of glyphosate treatment, the metabolic profile of both populations was very similar. The comparison between the effects of sublethal and lethal doses on sensitive and resistant populations suggests that lethality of the herbicide is associated with an amino acid pool imbalance and accumulation of the metabolites of the shikimate pathway upstream from EPSPS. Ferulic acid and its derivatives were accumulated in treated plants of both populations, while quercetin and its derivative contents were only lower in the resistant plants treated with glyphosate.