The Glycerate and Phosphorylated Pathways of Serine Synthesis in Plants: The Branches of Plant Glycolysis Linking Carbon and Nitrogen Metabolism

Growth conditions trigger genotype-specific metabolic responses that affect the nutritional quality of kale cultivars

Kales (Brassica oleracea convar. acephala) are fast-growing, nutritious leafy vegetables ideal for year-round indoor farming. However, selection of the best cultivars for growth under artificial lighting necessitates a deeper understanding of leaf metabolism in different kale types. Here we examined a curly-leaved cultivar, Half Tall, and a lacinato-type cultivar, Black Magic, under moderate light (130 µmol photons m-2 s-1/22 °C) and high light (800 µmol photons m-2 s-1/26 °C) conditions. These conditions induced genotype-dependent differences in nutritionally important metabolites, especially anthocyanins and glucosinolates (GSLs), in kale cultivars. In the pale green Half Tall, growth under high light conditions did not induce changes in either pigmentation or total GSL content. In contrast, the purple pigmentation of Black Magic intensified due to increased anthocyanin accumulation. Black Magic showed reduced contents of indole GSLs and increased contents of aliphatic GSLs under high light conditions, with notable cultivar-specific adjustments in individual GSL species. Correlation analysis of metabolite profiles suggested cultivar-specific metabolic interplay between serine biosynthesis and the production of indole GSLs. RNA sequencing identified candidate genes encoding metabolic enzymes and regulatory components behind anthocyanin and GSL biosynthesis. These findings improve our understanding of leaf metabolism and its effects on the nutritional quality of kale cultivars.

Soybean tolerance to waterlogging is achieved by detoxifying root lactate via lactate dehydrogenase in leaves and metabolizing malate and succinate

Waterlogging is a significant stressor for crops, particularly in lowland regions where soil conditions exacerbate the problem. Waterlogged roots experience hypoxia, disrupting oxidative phosphorylation and triggering metabolic reorganization to sustain energy production. Here, we investigated the metabolic aspects that differentiate two soybean sister lines contrasting for waterlogging tolerance. After 11 days of waterlogging, roots of the tolerant line (PELBR15-7015C) modulated their fermentative metabolism by exporting key metabolites (lactate, malate, and succinate) to the shoot. These metabolites were metabolized in the leaves, supporting photosynthesis and facilitating sugar export to the roots, sustaining a root-shoot-root cycling process. In contrast, the sensitive line (PELBR15-7060) entered a quiescent state, depleting its carbon stock and accumulating protective metabolites. Our study reveals that long-term waterlogging tolerance is primarily achieved through lactate detoxification in the leaves, along with malate and succinate metabolism, enabling root metabolism to withstand hypoxia. This mechanism offers new insights into crop resilience under waterlogged conditions, with implications for modern agriculture as climate change intensifies the frequency and duration of such stress events.

The Cyclin-Dependent Kinase activity modulates the central carbon metabolism in maize during germination

The cell cycle is predominantly controlled by Cyclins/Cyclin-Dependent Kinases (Cyc/CDK) complexes, which phosphorylate targets involved in cellular proliferation. Evidence suggests that Cyc/CDK targets extend beyond traditional proteins and include enzymes that regulate the central carbon metabolism. Maize embryo axes rapidly internalize and metabolize glucose. After 24 h of imbibition in glucose-rich media, axes exhibited increased length and weight, with more pronounced effects at 72 h. This morphology enhancement was impaired when RO-3306, a specific CDK inhibitor, was added. The protein profile of maize embryo extracts at 18 and 24 h indicated altered phosphorylation patterns following CDK activity inhibition. Metabolomic analysis at 24 h of imbibition revealed that maize embryos without sugar in the media, with or without RO-3306, had a decreased sugar and amino acid content. Conversely, axes exposed to glucose demonstrated increased conversion into various mono and di-saccharides such as fructose, mannitol, galactose, and maltose but not sucrose. This pattern was reversed upon the addition of RO-3306. Glucose promoted the accumulation of amino acids such as cysteine, valine, leucine, and intermediates of the tricarboxylic acid (TCA) cycle, such as malate and citrate. The CDK inhibitor redirected the glucose metabolism toward increased serine levels, followed by other amino acids like phenylalanine, valine, and leucine. Additionally, TCA cycle intermediates and sterols significantly decreased. Overall, these results contribute to understanding the role of CDK in maize morphogenesis during germination and underscore its impact on modulating various central carbon pathways, including glycolysis, amino acid catabolism/anabolism, TCA cycle, and sterols biosynthesis.

Natural variation in the chickpea metabolome under drought stress

Chickpea is the world's fourth largest grown legume crop, which significantly contributes to food security by providing calories and dietary protein globally. However, the increased frequency of drought stress has significantly reduced chickpea production in recent years. Here, we have performed a field experiment with 36 diverse chickpea genotypes to evaluate grain yield, photosynthetic activities and molecular traits related to drought stress. For metabolomics analysis, leaf tissue was collected at three time points representing different pod-filling stages. We identified L-threonic acid, fructose and sugar alcohols involved in chickpea adaptive drought response within the mid-pod-filling stage. A stress susceptibility index for each genotype was calculated to identify tolerance capacity under drought, distributing the 36 genotypes into four categories from best to worst performance. To understand how biochemical mechanisms control different traits for genetic improvement, we performed a differential Jacobian analysis, which unveiled the interplay between various metabolic pathways across three time points, including higher flux towards inositol interconversions, glycolysis for high-performing genotypes, fumarate to malate conversion, and carbon and nitrogen metabolism perturbations. Metabolic GWAS (mGWAS) analysis uncovered gene candidates involved in glycolysis and MEP pathway corroborating with the differential biochemical Jacobian results. Accordingly, this proposed data analysis strategy bridges the gap from pure statistical association to causal biochemical relations by exploiting natural variation. Our study offers new perspectives on the genetic and metabolic understanding of drought tolerance-associated diversity in the chickpea metabolome and led to the identification of metabolic control points that can be also tested in other legume crops.

The Role of Glutamate Metabolism and the GABA Shunt in Bypassing the Tricarboxylic Acid Cycle in the Light

Glutamate is an essential amino acid in both the energy and biosynthetic processes in plant cells. The aim of this work was to study changes in glutamate metabolism upon irradiation of maize (Zea mays L.) leaves with light of different spectral compositions, as well as to identify mechanisms regulating the work of enzymes involved in the studied process. A study was conducted of light-induced changes in glutamate metabolism in maize leaves, mediated by redirecting the glutamate flow to the γ-aminobutyric acid (GABA) shunt. Glutamate dehydrogenase (GDH) was more active in darkness, and the irradiation by red light inhibited the expression of both the Gdh1 and Gdh2 genes. EGTA and ruthenium red abolished the effects of light, indicating the participation of Ca2+ ions in phytochrome signal transduction. Contrary to GDH, glutamate decarboxylase (GAD) activity was moderately higher in the light, stimulated by red light, while far-red light reversed the effect. The effect of light on Gad expression was more pronounced than on GAD activity. Irradiation by red light also resulted in the increase in activity of GABA transaminase (GTA), which was abolished by far-red light. The third enzyme of the GABA shunt, succinic semialdehyde dehydrogenase (SSADH), was also activated by light. The effect of light on the expression of Ssadh1, but not on Ssadh2, was phytochrome-dependent. It is concluded that irradiation by light shifts glutamate metabolism from GDH to GAD with the activation of GABA transaminase and SSADH. This suggests that the GABA pathway plays a role in the maintenance of the tricarboxylic acid cycle in the light via bypassing its reactions when the 2-oxoglutarate dehydrogenase complex is inhibited and the cycle switches to the open mode.

Photorespiratory Metabolism and Its Regulatory Links to Plant Defence Against Pathogens

When plants face biotic stress, the induction of defence responses imposes a massive demand for carbon and energy resources, which could decrease the reserves allocated towards growth. These growth-defence trade-offs have important implications for plant fitness and productivity and influence the outcome of plant-pathogen interactions. Biotic stress strongly affects plant cells' primary metabolism, including photosynthesis and respiration, the main source of energy and carbon skeletons for plant growth, development, and defence. Although the nature of photosynthetic limitations imposed by pathogens is variable, infection often increases photorespiratory pressure, generating conditions that promote ribulose-1,5-bisphosphate oxygenation, leading to a metabolic shift from assimilation to photorespiration. Photorespiration, the significant metabolic flux following photosynthesis, protects the photosynthetic apparatus from photoinhibition. However, recent studies reveal that its role is far beyond photoprotection. The intermediates of the photorespiratory cycle regulate photosynthesis, and photorespiration interacts with the metabolic pathways of nitrogen and sulphur, shaping the primary metabolism for stress responses. This work aims to present recent insights into the integration of photorespiration within the network of primary metabolism under biotic stress. It also explores the potential implications of regulating photosynthetic-photorespiratory metabolism for plant defence against bacterial and fungal pathogens.

The phototoxicity of sulfamethoxazole stress on pakchoi cabbage (Brassica rapa var. chinensis) seedlings: From the perspective of photoreaction and omics analysis

The increasing use of antibiotics has attracted widespread attention to their environmental risks. However, the phototoxicity of sulfonamide antibiotics to plants remain unclear. In this study, the mechanism of the effect of sulfamethoxazole on photosynthesis of pakchoi cabbage (Brassica rapa var. chinensis) was investigated. The results showed that sulfamethoxazole inhibited the growth of pakchoi cabbage and produced photosynthetic toxicity. The growth inhibition rates increased with concentration, the root and shoot weight were 76.02 % and 47.04 % of the control, respectively, with stay-greens phenomenon in 4 mg·L-1 sulfamethoxazole treatment. Chlorophyll precursors (protoporphyrin IX (Proto IX), Mg-proto IX, and protochlorophyllide (Pchlide), 5-aminolevulinic acid (ALA), and porphobilinogen (PBG)) were 1.38-, 1.26-, 1.12-, 1.71-, and 0.96-fold of the control, respectively; photosynthetic pigments (chlorophyll a, chlorophyll b, and carotenoids) were 1.26-, 1.39-, and 1.03-fold of the control, respectively. Respiration rate was 271.42 % of the control, whereas the net photosynthetic rate was 50.50 % of the control. The maximum photochemical quantum yield of PSII (Fv/Fm), the actual photosynthetic efficiency (Y(II)), the quantum yield of non-regulated energy dissipation (Y(NO)), the apparent electron transfer efficiency of PSII (ETR) under actual light intensity were affected, and chloroplast swelling was observed. Proteomic analysis showed that photosynthesis-related pathways were significantly up-regulated, biological processes such as light response, carbohydrates, and reactive oxygen species were activated. Metabolomic analysis revealed that the tricarboxylic acid cycle (TCA cycle) and carbohydrate catabolism were stimulated significantly (p < 0.05), sugars and amino acids were increased to regulate and enhance the resilience of photosynthesis. While folate biosynthesis and ribosomal pathways were significantly down-regulated, the synthesis and translation processes of amino acids and nucleotides were inhibited.

Effects of Decabromodiphenyl Ethane and Cadmium Coexposure on Their Bioaccumulation, Oxidative Stress, Root Metabolism, and Rhizosphere Soil Microorganisms in a Soil-Rice System

Decabromodiphenyl ethane (DBDPE) and cadmium (Cd) are typical pollutants in e-waste, seriously threatening crop growth. This study investigated the bioaccumulation and toxicity mechanisms of DBDPE and Cd in a soil-rice system. The results showed that 50 mg/kg DBDPE could reduce the level of accumulation of Cd in rice roots. DBDPE and Cd induced the antioxidant system (SOD, POD, and MDA) in rice seedlings. The combined exposure reduced the contents of carbohydrates, lipids, amino acids, and organic acids. Phenylalanine and phenylpropanoid metabolisms were identified as the key detoxification metabolic pathways under combined exposure. DBDPE and Cd disrupted the functional cycling of carbon and nitrogen in rhizosphere soil, while Gemmatimonadetes, Actinobacteria, and Bacteroidetes were the key bacterial groups responding to DBDPE and Cd stress. This work provides data for the toxicity risk evaluation of DBDPE and Cd combined exposure to food crops.

Enhanced photorespiratory and TCA pathways by elevated CO2 to manage ammonium nutrition in tomato leaves

Plants grown under exclusive ammonium (NH4+) nutrition have high carbon (C) demand to sustain proper nitrogen (N) assimilation and energy required for plant growth, generally impaired when compared to nitrate (NO3-) nutrition. Thereby, the increment of the atmospheric carbon dioxide (CO2) concentration, in the context of climate change, will potentially allow plants to better face ammonium nutrition. In this work, tomato (Solanum lycopersicum L.) plants were grown under ammonium or nitrate nutrition in conditions of ambient (aCO2, 400 ppm) or elevated CO2 (eCO2, 800 ppm) atmosphere. Elevated CO2 increased photosynthesis rate and tomato shoot growth regardless of the N source. In the case of NH4+-fed leaves the positive effect of elevated CO2 occurred despite of the high tissue NH4+ accumulation. Under eCO2 ammonium nutrition triggered, among others, the modulation of genes related to C provision pathways (including carbonic anhydrase and glyoxylate cycle), antioxidant response and cell membranes protection. The enhanced photosynthate production at eCO2 facilitated C skeleton provision through the TCA cycle and anaplerotic pathways to promote amino acid synthesis. Moreover, photorespiratory activity was stimulated by eCO2 and contributed to yield serine as additional sink for NH4+ excess. Overall, these changes denote a connection between the respiratory and the photorespiratory pathways linked to ammonium nutrition. This metabolic strategy may allow crops to grow efficiently using ammonium as fertilizer in a future climate change scenario, while mitigating N losses.

Impact of microplastic residues from polyurethane films on crop growth: Unraveling insights through transcriptomics and metabolomics analysis

The utilisation of coated controlled-release fertilizers (CRFs) leads to the persistence of residual plastic films in agricultural soils, posing a potential threat to crop health. This study investigates the impacts of four residual films (0.39 %, w/w) derived from CRFs in soil, including petrochemical polyether, bio-based polyether, castor oil polyester, and wheat straw polyester polyurethane on wheat growth. This study found that PecPEUR significantly reduced wheat plant height, stem diameter, leaf area, and aboveground fresh weight by 24.8 %, 20.2 %, and 25.7 %. Through an in-depth exploration of transcriptomics and metabolomics, it has been discovered that all residual films disrupted glycolysis-related metabolic pathways in wheat roots, affecting seedling growth. Among them, PecPEUR significantly reduced the fresh weight of aboveground parts by 20.5 %. In contrast, polyester polyurethane residue had no discernible impact on aboveground wheat growth. This was attributed to the enrichment of wheat root genes in jasmonic acid and γ-aminobutyric acid metabolic pathways, thus mitigating oxidative stress, enhancing stress resistance, and ensuring normal plant growth. This study, for the first time, provides comprehensive insights into the effects of polyurethane film residue on wheat seedling growth, underscoring its potential as a promising alternative to conventional plastics in soil.

Deciphering the Impact of ZnO Nanoparticles and a Sunscreen Product Containing ZnO on Phosphorus Dynamics and Release in Chlorella pyrenoidosa in Aquatic Systems

Zinc oxide nanoparticles (ZnO NPs) expedite the conversion of organic phosphorus (OP) into PO4-P (Pi), facilitating phosphorus (P) absorption by algae. Our study explored the mechanisms of converting OP (2-aminoethylphosphonic acid (AEP) and β-glycerol phosphate (β-GP)) into Pi in Chlorella pyrenoidosa under P deficiency with sunscreen and ZnO NPs. Cell density followed the order of K2HPO4 > β-GP+ZnO > β-GP > AEP+ZnO > AEP > P-free. ZnO NPs promoted the conversion of β-GP, containing C-O-P bonds (0.028-0.041 mg/L), into Pi more efficiently than AEP, which possesses C-P bonds (0.022-0.037 mg/L). Transcriptomics revealed Pi transport/metabolism (phoB (3.99-12.01 fold), phoR (2.20-5.50 fold), ppa (4.49-10.40 fold), and ppk (2.50-5.40 fold)) and phospholipid metabolism (SQD1 (1.85-2.79 fold), SQD2 (2.60-6.53 fold), MGD (2.13-3.21 fold), and DGD (4.08-7.56 fold)) were up-regulated compared to K2HPO4. 31P nuclear magnetic resonance spectroscopy identified intracellular P as polyphosphate, orthophosphate, and pyrophosphate. Synchrotron radiation-based X-ray near-edge structure spectroscopy indicated that K2HPO4 and Zn3(PO4)2 in β-GP+ZnO were increased by 8.09% and 7.28% compared to AEP+ZnO, suggesting superior P storage in β-GP+ZnO. Overall, ZnO NPs improved photoinduced electron-hole pair separation and charge separation efficiency and amplified the ·OH and ·O2- levels, promoting OP photoconversion into Pi and algae growth.

Tomato and mini-cucumber tolerance to photoperiodic injury involves photorespiration and the engagement of nighttime cyclic electron flow from dynamic LEDs

Controlled environment agriculture (CEA) is critical for achieving year-round food security in many regions of the world. CEA is a resource-intensive endeavor, with lighting consuming a large fraction of the energy. To lessen the burden on the grid and save costs, an extended photoperiod strategy can take advantage of off-peak time-of-day options from utility suppliers. However, extending the photoperiod limits crop production morphologically and physiologically if pushed too long. Here, we present a continuous-light dynamic light-emitting diode (LED) strategy (involving changes in spectra, intensity, and timing), that overcomes these limitations. We focused on tomato, a well described photoperiodic injury-sensitive species, and mini-cucumber, a photoperiodic injury-tolerant species to first assess morphological responses under control (16-h photoperiod, unchanging spectrum), constant (24-h photoperiod, unchanging spectrum), and two variations of a dynamic LED strategy, dynamic 1 (16-h "day", 3-h "peak", 8-h "night" spectra) and dynamic 2 (20-h "day", 5-h "peak", 4-h "night" spectra). Next, we tested the hypothesis of photorespiration's involvement in photoperiodic injury by using a leaf gas exchange coupled with chlorophyll fluorescence protocol. We further explored Adenosine triphosphate (ATP): Nicotinamide adenine dinucleotide phosphate (NADPH) ratio supply/demand responses by probing photosynthetic electron flow and proton flow with the MultispeQ instrument. We found canopy architecture can be tuned by minor variations of the same dynamic LED strategy, and we highlight dynamic 1 as the optimal choice for both tomato and mini-cucumber as it improved biomass/architecture and first-yield, respectively. A central discovery was that dynamic 1 had a significantly higher level of photorespiration than control, for both species. Unexpectedly, photorespiration was comparable between species under the same treatments, except under constant. However, preliminary data on a fully tolerant tomato genotype grown under constant treatment upregulated photorespiration similar to mini-cucumber. These results suggest that photoperiodic injury tolerance involves a sustained higher level of photorespiration under extended photoperiods. Interestingly, diurnal MultispeQ measurements point to the importance of cyclic electron flow at subjective nighttime that may also partially explain why dynamic LED strategies mitigate photoperiodic injury. We propose an ontology of photoperiodic injury involving photorespiration, triose phosphate utilization, peroxisomal H2O2-catalase balance, and a circadian external coincidence model of sensitivity that initiates programmed cell death.

Preventive effect of Cleome spinosa against cucumber Fusarium wilt and improvement on cucumber growth and physiology

Cucumber wilt is an important soil borne disease in cucumber production, which seriously affects the development of the cucumber industry. Cleome spinosa also has pharmacological effects such as antibacterial, analgesic, anti-inflammatory, and insect repellent. To study the control effect and mechanism of Cleome spinosa fumigation on cucumber wilt disease, different concentrations of Cleome spinosa fragments were applied on cucumber plants infected with Fusarium oxysporum. Cleome spinosa fumigation significantly reduced the incidence rate of cucumber Fusarium wilt. Under the fumigation treatment of 7.5 g kg-1 Cleome spinosa fragments, the preventive effects were 74.7%. Cleome spinosa fragments fumigation can promote cucumber growth and synthesis of photosynthetic pigments, thereby improving individual plant yield and fruit quality. At 7.5 g kg-1 Cleome spinosa fragments fumigation treatment, the plant height and individual plant yield of cucumber increased by 20.3% and 34.3%, respectively. Cleome spinosa fumigation can enhance the activity of antioxidant enzymes in cucumber, maintain a balance of reactive oxygen species metabolism, and enhance the plant disease resistance. Moreover, Cleome spinosa can also regulate the activities of Mg2+-ATPase and Ca2+-ATPase, enhancing its resistance to Fusarium oxysporum. Moreover, number of bacteria and fungi significantly decreased under Cleome spinosa fumigation. Those results suggested that Cleome spinosa could effectively restrain cucumber Fusarium wilt. This study will provide a new idea for the further use of biological fumigation to prevent soil-borne diseases.

Evaluation of Cellular Responses by Chlamydomonas reinhardtii in Media Containing Dairy-Processing Residues Derived from Cheese as Nutrients by Analyzing Cell Growth Activity and Comprehensive Gene Transcription Levels

Utilities of whey powder (WP) and whey protein concentrate 34% powder (WPC34) prepared as dairy-processing residues were evaluated using a green alga Chlamydomonas reinhardtii. Analysis of C. reinhardtii growth showed that the strain used WP and WPC34 as nitrogen sources. Its specific growth rate and maximum cell density in WP-containing medium were higher than those in WPC34-containing medium; growth with WPC34 was improved by adding KCl or K2HPO4, which content was decreased as a result of WPC34's preparation from WP. Although the lipid contents in media containing dairy-processing residues were 2.72 ± 0.31 wt% and 2.62 ± 0.20 wt% with no significant difference, the composition ratio of fatty acid C14 with WPC34 was higher than that with WP and the composition ratio of the sum of fatty acid-C16 and -C18 with WPC34 tended to be lower than that with WP. Additionally, analyses of gene transcription showed that the transcription level of acetyl-CoA carboxylase biotin carboxyl carrier protein in WPC34-containing medium was lower than that in WP-containing medium, possibly affecting the ratios of the chain lengths of fatty acids. The transcription of genes involved in glycolysis and the TCA cycle was outstandingly lower in algae grown in WPC34-containing medium when compared to those cultivated in the presence of WP, resulting in differences in energy production for cell proliferation.

Mitochondrial atp1 mRNA knockdown by a custom-designed pentatricopeptide repeat protein alters ATP synthase

Spontaneous mutations are rare in mitochondria and the lack of mitochondrial transformation methods has hindered genetic analyses. We show that a custom-designed RNA-binding pentatricopeptide repeat (PPR) protein binds and specifically induces cleavage of ATP synthase subunit1 (atp1) mRNA in mitochondria, significantly decreasing the abundance of the Atp1 protein and the assembled F1Fo ATP synthase in Arabidopsis (Arabidopsis thaliana). The transformed plants are characterized by delayed vegetative growth and reduced fertility. Five-fold depletion of Atp1 level was accompanied by a decrease in abundance of other ATP synthase subunits and lowered ATP synthesis rate of isolated mitochondria, but no change to mitochondrial electron transport chain complexes, adenylates, or energy charge in planta. Transcripts for amino acid transport and a variety of stress response processes were differentially expressed in lines containing the PPR protein, indicating changes to achieve cellular homeostasis when ATP synthase was highly depleted. Leaves of ATP synthase-depleted lines showed higher respiratory rates and elevated steady-state levels of numerous amino acids, most notably of the serine family. The results show the value of using custom-designed PPR proteins to influence the expression of specific mitochondrial transcripts to carry out reverse genetic studies on mitochondrial gene functions and the consequences of ATP synthase depletion on cellular functions in Arabidopsis.

Comparative Metabolomics and Transcriptome Studies of Two Forms of Rhododendron chrysanthum Pall. under UV-B Stress

Rhododendron chrysanthum Pall. (R. chrysanthum), a plant with UV-B resistance mechanisms that can adapt to alpine environments, has gained attention as an important plant resource with the ability to cope with UV-B stress. In this experiment, R. chrysanthums derived from the same origin were migrated to different culture environments (artificial climate chamber and intelligent artificial incubator) to obtain two forms of R. chrysanthum. After UV-B irradiation, 404 metabolites and 93,034 unigenes were detected. Twenty-six of these different metabolites were classified as UV-B-responsive metabolites. Glyceric acid is used as a potential UV-B stress biomarker. The domesticated Rhododendron chrysanthum Pall. had high amino acid and SOD contents. The study shows that the domesticated Rhododendron chrysanthum Pall. has significant UV-B resistance. The transcriptomics results show that the trends of DEGs after UV-B radiation were similar for both forms of R. chrysanthum: cellular process and metabolic process accounted for a higher proportion in biological processes, cellular anatomical entity accounted for the highest proportion in the cellular component, and catalytic activity and binding accounted for the highest proportion in the molecular function category. Through comparative study, the forms of metabolites resistant to UV-B stress in plants can be reflected, and UV-B radiation absorption complexes can be screened for application in future specific practices. Moreover, by comparing the differences in response to UV-B stress between the two forms of R. chrysanthum, references can be provided for cultivating domesticated plants with UV-B stress resistance characteristics. Research on the complex mechanism of plant adaptation to UV-B will be aided by these results.

Regulation and mechanism of pyrite and humic acid on the toxicity of arsenate in lettuce

Pyrite and humic acid are common substances in nature, and the combined effects of pyrite and humic acid on arsenic phytotoxicity are more widespread in the actual environments than that of a single substance, but have received less attention. In this study, the interaction between pyrite and humic acid in arsenate solution was studied, and the effects of pyrite and humic acid on plant toxicity of arsenate were evaluated. The results showed that arsenate + pyrite + fulvic acid (V-PF) treatment immobilized more arsenic by forming chemical bonds such as AsS and Fe-As-O and reduced the migration of arsenic to plants. Compared to the arsenate + fulvic acid (VF), arsenate + pyrite (VP) and arsenate (V) group, the inorganic arsenic content of lettuce leaves in the V- PF group was reduced by 19.8 %, 13.4 % and 13.4 %, respectively. In addition, the V-PF group increased the absorption of Ca, Fe and Cu in plant roots, and improved the activity of superoxide dismutase (SOD) in plant leaves. Compared to the VF group, SOD and MDA in the V-PF group increased by 34.1 % in 30 days and decreased by 47.3 % in 40 days, respectively. The biomass of lettuce in V-PF group was increased by 29.3 % compared with that in VF group on day 50. The protein content of the V-PF group was 58.3 % higher than that of the VF group and 23.1 % higher than that of the VP group. Furthermore, metabolomics analysis showed that the V-PF group promoted glycolysis by up-regulating glyoxylic acid and dicarboxylic acid metabolism, thus reducing carbohydrate accumulation. Phosphocreatine metabolism was also up-regulated, which decreased the oxidative damage in lettuce induced by arsenic. This study will provide new ideas for scientifically and rationally assessing the ecological environmental risks of arsenic and regulating its toxicity.

γ-Aminobutyric acid (GABA) in N2-fixing-legume symbiosis: Metabolic flux and carbon/nitrogen homeostasis in responses to abiotic constraints

Nodule symbiosis is an energetic process that demands a tremendous carbon (C) cost, which massively increases in responses to environmental stresses. Notably, most common respiratory pathways (e.g., glycolysis and Krebs cycle) that sustain nitrogenase activity and subsequent nitrogen (N) assimilation (amino acid formation) display a noncyclic mode of C flux. In such circumstances, the nodule's energy charge could markedly decrease, leading to a lower symbiotic activity under stresses. The host plant then attempts to induce alternative robust metabolic pathways to minimize the C expenditure and compensate for the loss in respiratory substrates. GABA (γ-aminobutyric acid) shunt appears to be among the highly conserved metabolic bypass induced in responses to stresses. Thus, it can be suggested that GABA, via its primary biosynthetic pathway (GABA shunt), is simultaneously induced to circumvent stress-susceptible decarboxylating portion of the Krebs cycle and to replenish symbiosome with energy and C skeletons for enhancing nitrogenase activity and N assimilation besides the additional C costs expended in the metabolic stress acclimations (e.g., biosynthesis of secondary metabolites and excretion of anions). The GABA-mediated C/N balance is strongly associated with interrelated processes, including pH regulation, oxygen (O2) protection, osmoregulation, cellular redox control, and N storage. Furthermore, it has been anticipated that GABA could be implicated in other functions beyond its metabolic role (i.e., signaling and transport). GABA helps plants possess remarkable metabolic plasticity, which might thus assist nodules in attenuating stressful events.

The phosphorylated pathway of serine biosynthesis affects sperm, embryo, and sporophyte development, and metabolism in Marchantia polymorpha

Serine metabolism is involved in various biological processes. Here we investigate primary functions of the phosphorylated pathway of serine biosynthesis in a non-vascular plant Marchantia polymorpha by analyzing knockout mutants of MpPGDH encoding 3-phosphoglycerate dehydrogenase in this pathway. Growth phenotypes indicate that serine from the phosphorylated pathway in the dark is crucial for thallus growth. Sperm development requires serine from the phosphorylated pathway, while egg formation does not. Functional MpPGDH in the maternal genome is necessary for embryo and sporophyte development. Under high CO2 where the glycolate pathway of serine biosynthesis is inhibited, suppressed thallus growth of the mutants is not fully recovered by exogenously-supplemented serine, suggesting the importance of serine homeostasis involving the phosphorylated and glycolate pathways. Metabolomic phenotypes indicate that the phosphorylated pathway mainly influences the tricarboxylic acid cycle, the amino acid and nucleotide metabolism, and lipid metabolism. These results indicate the importance of the phosphorylated pathway of serine biosynthesis in the dark, in the development of sperm, embryo, and sporophyte, and metabolism in M. polymorpha.

U-13C-glucose incorporation into source leaves of Brassica napus highlights light-dependent regulations of metabolic fluxes within central carbon metabolism

Plant central carbon metabolism comprises several important metabolic pathways acting together to support plant growth and yield establishment. Despite the emergence of 13C-based dynamic approaches, the regulation of metabolic fluxes between light and dark conditions has not yet received sufficient attention for agronomically relevant plants. Here, we investigated the impact of light/dark conditions on carbon allocation processes within central carbon metabolism of Brassica napus after U-13C-glucose incorporation into leaf discs. Leaf gas-exchanges and metabolite contents were weakly impacted by the leaf disc method and the incorporation of glucose. 13C-analysis by GC-MS showed that U-13C-glucose was converted to fructose for de novo biosynthesis of sucrose at similar rates in both light and dark conditions. However, light conditions led to a reduced commitment of glycolytic carbons towards respiratory substrates (pyruvate, alanine, malate) and TCA cycle intermediates compared to dark conditions. Analysis of 13C-enrichment at the isotopologue level and metabolic pathway isotopic tracing reconstructions identified the contribution of multiple pathways to serine biosynthesis in light and dark conditions. However, the direct contribution of the glucose-6-phosphate shunt to serine biosynthesis was not observed. Our results also provided isotopic evidences for an active metabolic connection between the TCA cycle, glycolysis and photorespiration in light conditions through a rapid reallocation of TCA cycle decarboxylations back to the TCA cycle through photorespiration and glycolysis. Altogether, these results suggest the active coordination of core metabolic pathways across multiple compartments to reorganize C-flux modes.

Uncovering the dominant role of root metabolism in shaping rhizosphere metabolome under drought in tropical rainforest plants

Plant-soil-microbe interactions are crucial for driving rhizosphere processes that contribute to metabolite turnover and nutrient cycling. With the increasing frequency and severity of water scarcity due to climate warming, understanding how plant-mediated processes, such as root exudation, influence soil organic matter turnover in the rhizosphere is essential. In this study, we used 16S rRNA gene amplicon sequencing, rhizosphere metabolomics, and position-specific 13C-pyruvate labeling to examine the effects of three different plant species (Piper auritum, Hibiscus rosa sinensis, and Clitoria fairchildiana) and their associated microbial communities on soil organic carbon turnover in the rhizosphere. Our findings indicate that in these tropical plants, the rhizosphere metabolome is primarily shaped by the response of roots to drought rather than direct shifts in the rhizosphere bacterial community composition. Specifically, the reduced exudation of plant roots had a notable effect on the metabolome of the rhizosphere of P. auritum, with less reliance on neighboring microbes. Contrary to P. auritum, H. rosa sinensis and C. fairchildiana experienced changes in their exudate composition during drought, causing alterations to the bacterial communities in the rhizosphere. This, in turn, had a collective impact on the rhizosphere's metabolome. Furthermore, the exclusion of phylogenetically distant microbes from the rhizosphere led to shifts in its metabolome. Additionally, C. fairchildiana appeared to be associated with only a subset of symbiotic bacteria under drought conditions. These results indicate that plant species-specific microbial interactions systematically change with the root metabolome. As roots respond to drought, their associated microbial communities adapt, potentially reinforcing the drought tolerance strategies of plant roots. These findings have significant implications for maintaining plant health and preference during drought stress and improving plant performance under climate change.

Photorespiration: regulation and new insights on the potential role of persulfidation

Photorespiration has been considered a 'futile' cycle in C3 plants, necessary to detoxify and recycle the metabolites generated by the oxygenating activity of Rubisco. However, several reports indicate that this metabolic route plays a fundamental role in plant metabolism and constitutes a very interesting research topic. Many open questions still remain with regard to photorespiration. One of these questions is how the photorespiratory process is regulated in plants and what factors contribute to this regulation. In this review, we summarize recent advances in the regulation of the photorespiratory pathway with a special focus on the transcriptional and post-translational regulation of photorespiration and the interconnections of this process with nitrogen and sulfur metabolism. Recent findings on sulfide signaling and protein persulfidation are also described.

Metabolic Profiling in Tuberous Roots of Ranunculus asiaticus L. as Influenced by Vernalization Procedure

Ranunculus asiaticus L. is an ornamental geophyte. In commercial practice, it is mainly propagated by rehydrated tuberous roots. Vernalization before planting is a common practice to overcome the natural dormancy of tuberous roots; however, little is known about the mechanisms underlying the plant's response to low temperatures. We investigated the influence of three preparation procedures of tuberous roots, only rehydration (control, C), and rehydration plus vernalization at 3.5 °C for 2 weeks (V2) and for 4 weeks (V4), on plant growth, leaf photosynthesis, flowering, and metabolism in plants of two hybrids, MBO (early flowering, pale orange flower) and MDR (medium earliness, bright orange flower), grown in pots in an unheated greenhouse. We reported the responses observed in the aerial part in a previous article in this journal. In this paper, we show changes in the underground organs in carbohydrate, amino acids, polyphenols, and protein levels throughout the growing cycle in the different plant stages: pre-planting, vegetative growth, and flowering. The metabolic profile revealed that the two hybrids had different responses to the root preparation procedure. In particular, MBO synthesized GABA and alanine after 2 weeks and sucrose after 4 weeks of vernalization. In contrast, MDR was more sensitive to vernalization; in fact, a higher synthesis of polyphenols was observed. However, both hybrids synthesized metabolites that could withstand exposure to low temperatures.

Genome-Wide Association Studies Using 3VmrMLM Model Provide New Insights into Branched-Chain Amino Acid Contents in Rice Grains

Rice (Oryza sativa L.) is a globally important food source providing carbohydrates, amino acids, and dietary fiber for humans and livestock. The branched-chain amino acid (BCAA) level is a complex trait related to the nutrient quality of rice. However, the genetic mechanism underlying the BCAA (valine, leucine, and isoleucine) accumulation in rice grains remains largely unclear. In this study, the grain BCAA contents and 239,055 SNPs of a diverse panel containing 422 rice accessions were adopted to perform a genome-wide association study (GWAS) using a recently proposed 3VmrMLM model. A total of 357 BCAA-content-associated main-effect quantitative trait nucleotides (QTNs) were identified from 15 datasets (12 BCAA content datasets and 3 BLUP datasets of BCAA). Furthermore, the allelic variation of two novel candidate genes, LOC_Os01g52530 and LOC_Os06g15420, responsible for the isoleucine (Ile) content alteration were identified. To reveal the genetic basis of the potential interactions between the gene and environmental factor, 53 QTN-by-environment interactions (QEIs) were detected using the 3VmrMLM model. The LOC_Os03g24460, LOC_Os01g55590, and LOC_Os12g31820 were considered as the candidate genes potentially contributing to the valine (Val), leucine (Leu), and isoleucine (Ile) accumulations, respectively. Additionally, 10 QTN-by-QTN interactions (QQIs) were detected using the 3VmrMLM model, which were putative gene-by-gene interactions related to the Leu and Ile contents. Taken together, these findings suggest that the implementation of the 3VmrMLM model in a GWAS may provide new insights into the deeper understanding of BCAA accumulation in rice grains. The identified QTNs/QEIs/QQIs serve as potential targets for the genetic improvement of rice with high BCAA levels.

Possibility to Apply Strontium Aluminate to Produce Light-Emitting Plants: Efficiency and Safety

Light-emitting plants (LEPs) provides light in areas without electricity. The phosphorescent compound was used as a lighting material for LEP development. However, using the phosphorescent compound for LEPs development required optimization and phytotoxicity evaluation. Strontium aluminate (SrAl2 O4 ) is a phosphorescent compound that can glow for a long time and is easily recharged by visible light. In this study, using SrAl2 O4 to develop LEPs was evaluated. Additionally, plant stress under SrAl2 O4 was investigated. Metabolomic analysis can explain the possible mechanism of plants' stress under SrAl2 O4 . After, injecting 3 mL of 5 % (w/v) SrAl2 O4 products 1, 2, and 3 into the stem of Ipomoea aquatica, the result showed that SrAl2 O4 products 2 and 3 caused oxidative stress. The metabolomic analysis also indicated that I. aquatica responded to SrAl2 O4 product 1 by increasing pipecolic acid and salicylic acid, while I. aquatica injected with SrAl2 O4 products 2 and 3 showed a decrease in salicylic acid around 0.005 and 0.061-fold, respectively, compared to control plants. and an excess accumulation of MDA around 10.00-12.00 μmol g-1 FW. A 15 % concentration of SrAl2 O4 can be used for LEPs development, enabling photoemission 18-fold for 50 min. SrAl2 O4 product 1 has the potential to be a material for LEPs.

Effects of exogenous glycine betaine and cycloleucine on photosynthetic capacity, amino acid composition, and hormone metabolism in Solanum melongena L

Although exogenous glycine betaine (GB) and cycloleucine (Cyc) have been reported to affect animal cell metabolism, their effects on plant growth and development have not been studied extensively. Different concentrations of exogenous glycine betaine (20, 40, and 60 mmol L^-1) and cycloleucine (10, 20, and 40 mmol L^-1), with 0 mmol L^-1 as control, were used to investigate the effects of foliar spraying of betaine and cycloleucine on growth, photosynthesis, chlorophyll fluorescence, Calvin cycle pathway, abaxial leaf burr morphology, endogenous hormones, and amino acid content in eggplant. We found that 40 mmol L^-1 glycine betaine had the best effect on plant growth and development; it increased the fresh and dry weight of plants, increased the density of abaxial leaf hairs, increased the net photosynthetic rate and Calvin cycle key enzyme activity of leaves, had an elevating effect on chlorophyll fluorescence parameters, increased endogenous indoleacetic acid (IAA) content and decreased abscisic acid (ABA) content, and increased glutamate, serine, aspartate, and phenylalanine contents. However, cycloleucine significantly inhibited plant growth; plant apical dominance disappeared, plant height and dry and fresh weights decreased significantly, the development of abaxial leaf hairs was hindered, the net photosynthetic rate and Calvin cycle key enzyme activities were inhibited, the endogenous hormones IAA and ABA content decreased, and the conversion and utilization of glutamate, arginine, threonine, and glycine were affected. Combined with the experimental results and plant growth phenotypes, 20 mmol L^-1 cycloleucine significantly inhibited plant growth. In conclusion, 40 mmol L^-1 glycine betaine and 20 mmol L^-1 cycloleucine had different regulatory effects on plant growth and development.

The diversity of substrates for plant respiration and how to optimize their use

Plant respiration is a foundational biological process with the potential to be optimized to improve crop yield. To understand and manipulate the outputs of respiration, the inputs of respiration-respiratory substrates-need to be probed in detail. Mitochondria house substrate catabolic pathways and respiratory machinery, so transport into and out of these organelles plays an important role in committing substrates to respiration. The large number of mitochondrial carriers and catabolic pathways that remain unidentified hinder this process and lead to confusion about the identity of direct and indirect respiratory substrates in plants. The sources and usage of respiratory substrates vary and are increasing found to be highly regulated based on cellular processes and environmental factors. This review covers the use of direct respiratory substrates following transport through mitochondrial carriers and catabolism under normal and stressed conditions. We suggest the introduction of enzymes not currently found in plant mitochondria to enable serine and acetate to be direct respiratory substrates in plants. We also compare respiratory substrates by assessing energetic yields, availability in cells, and their full or partial oxidation during cell catabolism. This information can assist in decisions to use synthetic biology approaches to alter the range of respiratory substrates in plants. As a result, respiration could be optimized by introducing, improving, or controlling specific mitochondrial transporters and mitochondrial catabolic pathways.

Transcriptome dynamics provides insights into divergences of the photosynthesis pathway between Saccharum officinarum and Saccharum spontaneum

Saccharum spontaneum and Saccharum officinarum contributed to the genetic background of modern sugarcane cultivars. Saccharum spontaneum has shown a higher net photosynthetic rate and lower soluble sugar than S. officinarum. Here, we analyzed 198 RNA-sequencing samples to investigate the molecular mechanisms for the divergences of photosynthesis and sugar accumulation between the two Saccharum species. We constructed gene co-expression networks based on differentially expressed genes (DEGs) both for leaf developmental gradients and diurnal rhythm. Our results suggested that the divergence of sugar accumulation may be attributed to the enrichment of major carbohydrate metabolism and the oxidative pentose phosphate pathway. Compared with S. officinarum, S. spontaneum DEGs showed a high enrichment of photosynthesis and contained more complex regulation of photosynthesis-related genes. Noticeably, S. spontaneum lacked gene interactions with sulfur assimilation stimulated by photorespiration. In S. spontaneum, core genes related to clock and photorespiration displayed a sensitive regulation by the diurnal rhythm and phase-shift. Small subunit of Rubisco (RBCS) displayed higher expression in the source tissues of S. spontaneum. Additionally, it was more sensitive under a diurnal rhythm, and had more complex gene networks than that in S. officinarum. This indicates that the differential regulation of RBCS Rubisco contributed to photosynthesis capacity divergence in both Saccharum species.

Changes in the Rhizosphere Prokaryotic Community Structure of Halodule wrightii Monospecific Stands Associated to Submarine Groundwater Discharges in a Karstic Costal Area

Belowground seagrass associated microbial communities regulate biogeochemical dynamics in the surrounding sediments and influence seagrass physiology and health. However, little is known about the impact of environmental stressors upon interactions between seagrasses and their prokaryotic community in coastal ecosystems. Submerged groundwater discharges (SGD) at Dzilam de Bravo, Yucatán, Mexico, causes lower temperatures and salinities with higher nutrient loads in seawater, resulting in Halodule wrightii monospecific stands. In this study, the rhizospheric archaeal and bacterial communities were characterized by 16S rRNA Illumina sequencing along with physicochemical determinations of water, porewater and sediment in a 400 m northwise transect from SGD occurring at 300 m away from coastline. Core bacterial community included Deltaproteobacteria, Bacteroidia and Planctomycetia, possibly involved in sulfur metabolism and organic matter degradation while highly versatile Bathyarchaeia was the most abundantly represented class within the archaeal core community. Beta diversity analyses revealed two significantly different clusters as result of the environmental conditions caused by SGD. Sites near to SGD presented sediments with higher redox potentials and sand contents as well as lower organic matter contents and porewater ammonium concentrations compared with the furthest sites. Functional profiling suggested that denitrification, aerobic chemoheterotrophy and environmental adaptation processes could be better represented in these sites, while sulfur metabolism and genetic information processing related profiles could be related to SGD uninfluenced sites. This study showed that the rhizospheric prokaryotic community structure of H. wrightii and their predicted functions are shaped by environmental stressors associated with the SGD. Moreover, insights into the archaeal community composition in seagrasses rhizosphere are presented.

Evolutionary implications of C2 photosynthesis: how complex biochemical trade-offs may limit C4 evolution

The C2 carbon-concentrating mechanism increases net CO2 assimilation by shuttling photorespiratory CO2 in the form of glycine from mesophyll to bundle sheath cells, where CO2 concentrates and can be re-assimilated. This glycine shuttle also releases NH3 and serine into the bundle sheath, and modelling studies suggest that this influx of NH3 may cause a nitrogen imbalance between the two cell types that selects for the C4 carbon-concentrating mechanism. Here we provide an alternative hypothesis outlining mechanisms by which bundle sheath NH3 and serine play vital roles to not only influence the status of C2 plants along the C3 to C4 evolutionary trajectory, but to also convey stress tolerance to these unique plants. Our hypothesis explains how an optimized bundle sheath nitrogen hub interacts with sulfur and carbon metabolism to mitigate the effects of high photorespiratory conditions. While C2 photosynthesis is typically cited for its intermediary role in C4 photosynthesis evolution, our alternative hypothesis provides a mechanism to explain why some C2 lineages have not made this transition. We propose that stress resilience, coupled with open flux tricarboxylic acid and photorespiration pathways, conveys an advantage to C2 plants in fluctuating environments.

Metabolomics and proteomics reveal the toxicological mechanisms of florfenicol stress on wheat (Triticum aestivum L.) seedlings

Although the ecological impacts of antibiotics have received attention worldwide, research on the toxicity of florfenicol is still limited. We conducted a metabolomic and proteomic study on wheat (Triticum aestivum L.) seedlings to reveal the toxicological mechanism of florfenicol. The growth of the wheat seedlings was found to be inhibited by florfenicol. Antioxidant enzyme activities (superoxide dismutase, peroxidase and catalase), malondialdehyde content and membrane permeability increased with increasing florfenicol concentration. The contents of chlorophyll and chlorophyll synthesis precursor substances (Proto IX, Mg-proto IX and Pchlide), photosynthetic and respiration rates, and chlorophyll fluorescence parameters decreased, indicating that photosynthesis was inhibited. The ultrastructure of chloroplasts was destroyed, as evidenced by the blurred membrane surface, irregular grana arrangement, irregular thylakoid lamella structure, and increased plastoglobuli number. Proteome analysis revealed that up-regulated proteins were highly involved in protein refolding, translation, oxidation-reduction, tricarboxylic acid cycle (TCA cycle), reactive oxygen species metabolic process, cellular oxidant detoxification, and response to oxidative stress. The down-regulated proteins were mainly enriched in photosynthesis-related pathways. In the metabolome analysis, the content of most of the metabolites in wheat leaves, such as carbohydrates and amino acids increased significantly (p < 0.05). Combined pathway analysis showed that florfenicol stress stimulated the TCA cycle pathway and downregulated the photosynthesis pathway.

Analysis of proteomic changes in cassava cv. Kasetsart 50 caused by Sri Lankan cassava mosaic virus infection

BACKGROUND

Sri Lankan cassava mosaic virus (SLCMV) is a plant virus causing significant economic losses throughout Southeast Asia. While proteomics has the potential to identify molecular markers that could assist the breeding of virus resistant cultivars, the effects of SLCMV infection in cassava have not been previously explored in detail.

RESULTS

Liquid Chromatography-Tandem Mass Spectrometry (LC/MS-MS) was used to identify differentially expressed proteins in SLCMV infected leaves, and qPCR was used to confirm changes at mRNA levels. LC/MS-MS identified 1,813 proteins, including 479 and 408 proteins that were upregulated in SLCMV-infected and healthy cassava plants respectively, while 109 proteins were detected in both samples. Most of the identified proteins were involved in biosynthetic processes (29.8%), cellular processes (20.9%), and metabolism (18.4%). Transport proteins, stress response molecules, and proteins involved in signal transduction, plant defense responses, photosynthesis, and cellular respiration, although present, only represented a relatively small subset of the detected differences. RT-qPCR confirmed the upregulation of WRKY 77 (A0A140H8T1), WRKY 83 (A0A140H8T7), NAC 6 (A0A0M4G3M4), NAC 35 (A0A0M5JAB4), NAC 22 (A0A0M5J8Q6), NAC 54 (A0A0M4FSG8), NAC 70 (A0A0M4FEU9), MYB (A0A2C9VER9 and A0A2C9VME6), bHLH (A0A2C9UNL9 and A0A2C9WBZ1) transcription factors. Additional upregulated transcripts included receptors, such as receptor-like serine/threonine-protein kinase (RSTK) (A0A2C9UPE4), Toll/interleukin-1 receptor (TIR) (A0A2C9V5Q3), leucine rich repeat N-terminal domain (LRRNT_2) (A0A2C9VHG8), and cupin (A0A199UBY6). These molecules participate in innate immunity, plant defense mechanisms, and responses to biotic stress and to phytohormones.

CONCLUSIONS

We detected 1,813 differentially expressed proteins infected cassava plants, of which 479 were selectively upregulated. These could be classified into three main biological functional groups, with roles in gene regulation, plant defense mechanisms, and stress responses. These results will help identify key proteins affected by SLCMV infection in cassava plants.

Effect of Light Quality on Metabolomic, Ionomic, and Transcriptomic Profiles in Tomato Fruit

Light quality affects plant growth and the functional component accumulation of fruits. However, there is little knowledge of the effects of light quality based on multiomics profiles. This study combined transcriptomic, ionomic, and metabolomic analyses to elucidate the effects of light quality on metabolism and gene expression in tomato fruit. Micro-Tom plants were grown under blue or red light-emitting diode light for 16 h daily after anthesis. White fluorescent light was used as a reference. The metabolite and element concentrations and the expression of genes markedly changed in response to blue and red light. Based on the metabolomic analysis, amino acid metabolism and secondary metabolite biosynthesis were active in blue light treatment. According to transcriptomic analysis, differentially expressed genes in blue and red light treatments were enriched in the pathways of secondary metabolite biosynthesis, carbon fixation, and glycine, serine, and threonine metabolism, supporting the results of the metabolomic analysis. Ionomic analysis indicated that the element levels in fruits were more susceptible to changes in light quality than in leaves. The concentration of some ions containing Fe in fruits increased under red light compared to under blue light. The altered expression level of genes encoding metal ion-binding proteins, metal tolerance proteins, and metal transporters in response to blue and red light in the transcriptomic analysis contributes to changes in the ionomic profiles of tomato fruit.

UV-B Irradiation to Amino Acids and Carbohydrate Metabolism in Rhododendron chrysanthum Leaves by Coupling Deep Transcriptome and Metabolome Analysis

Under natural environmental conditions, excess UV-B stress can cause serious injuries to plants. However, domestication conditions may allow the plant to better cope with the upcoming UV-B stress. The leaves of Rhododendron chrysanthum are an evergreen plant that grows at low temperatures and high altitudes in the Changbai Mountains, where the harsh ecological environment gives it different UV resistance properties. Metabolites in R. chrysanthum have a significant impact on UV-B resistance, but there are few studies on the dynamics of their material composition and gene expression levels. We used a combination of gas chromatography time-of-flight mass spectrometry and transcriptomics to analyze domesticated and undomesticated R. chrysanthum under UV-B radiation. A total of 404 metabolites were identified, of which amino acids were significantly higher and carbohydrates were significantly lower in domesticated R. chrysanthum. Transcript profiles throughout R. chrysanthum under UV-B were constructed and analyzed, with an emphasis on sugar and amino acid metabolism. The transcript levels of genes associated with sucrose and starch metabolism during UV-B resistance in R. chrysanthum showed a consistent trend with metabolite content, while amino acid metabolism was the opposite. We used metabolomics and transcriptomics approaches to obtain dynamic changes in metabolite and gene levels during UV-B resistance in R. chrysanthum. These results will provide some insights to elucidate the molecular mechanisms of UV tolerance in plants.

Over-Expression of Phosphoserine Aminotransferase-Encoding Gene (AtPSAT1) Prompts Starch Accumulation in L. turionifera under Nitrogen Starvation

It has been demonstrated that the phosphorylation pathway of L-serine (Ser) biosynthesis (PPSB) is very important in plant growth and development, but whether and how PPSB affects nitrogen metabolism and starch accumulation has not been fully elucidated. In this study, we took the energy plant duckweed (strain Lemna turionifera 5511) as the research object and used a stable genetic transformation system to heterologously over-expressing Arabidopsis AtPSAT1 (the gene encoding phosphoserine aminotransferase, the second enzyme of PPSB). Our results showed that, under nitrogen starvation, the transgenic plants grew faster, with higher values of Fv/Fm, rETR, and Y(II), as well as fresh and dry weight, than the wild-type. More promisingly, the accumulation of starch was also found to be significantly improved when over-expressing AtPSAT1 in the transgenic plants. qRT-PCR analysis results showed that the expression of genes related to nitrogen assimilation, carbon metabolism, and starch biosynthesis was up-regulated, while the expression of starch degradation-related genes was down-regulated by AtPSAT1 over-expression. We propose that the increased starch accumulation caused by AtPSAT1 over-expression may result from both elevated photosynthetic capacity and nitrogen utilization efficiency. This research sheds new light on the mechanism underlying the ability of PPSB to coordinate nitrogen and carbon metabolism, and provides a feasible way to improve starch production, that is, through engineering PPSB in crops.

Position-specific carbon isotope analysis of serine by gas chromatography/Orbitrap mass spectrometry, and an application to plant metabolism

RATIONALE

Position-specific ¹³ C/¹² C ratios within amino acids remain largely unexplored in environmental samples due to methodological limitations. We hypothesized that natural-abundance isotope patterns in serine may serve as a proxy for plant metabolic fluxes including photorespiration. Here we describe an Orbitrap method optimized for the position-specific carbon isotope analysis of serine to test our hypothesis and discuss the generalizability of this method to other amino acids.

METHODS

Position-specific carbon isotope ratios of serine were measured using a Thermo Scientific™ Q Exactive™ GC Orbitrap™. Amino acids were hydrolyzed from Arabidopsis biomass, purified from potential matrix interferences, and derivatized alongside standards. Derivatized serine (N,O-bis(trifluoroacetyl)methyl ester) was isolated using gas chromatography, trapped in a reservoir, and purged into the electron ionization source over tens of minutes, producing fragment ions containing different combinations of atoms from the serine-derivative molecule. The ¹³ C/¹² C ratios of fragments with monoisotopic masses of 110.0217, 138.0166, and 165.0037 Da were monitored in the mass analyzer and used to calculate position-specific δ¹³ C values relative to a working standard.

RESULTS

This methodology constrains position-specific δ¹³ C values for nanomole amounts of serine isolated from chemically complex mixtures. The δ¹³ C values of fragment ions of serine were characterized with ≤1‰ precisions, leading to propagated standard errors of 0.7-5‰ for each carbon position. Position-specific δ¹³ C values differed by up to ca 28 ± 5‰ between serine molecules hydrolyzed from plants grown under contrasting pCO₂ , selected to promote different fluxes through photosynthesis and photorespiration. The method was validated using pure serine standards characterized offline.

CONCLUSIONS

This study presents the first Orbitrap-based measurements of natural-abundance, position-specific carbon isotope variation in an amino acid isolated from a biological matrix. We present a method for the precise characterization of isotope ratios in serine and propose applications probing metabolism in plants. We discuss the potential for extending these approaches to other amino acids, paving the way for novel applications.

Differential sensitivity of metabolic pathways in sugar beet roots to combined salt, heat, and light stress

Plants in nature commonly encounter combined stress scenarios. The response to combined stressors is often unpredictable from the response to single stresses. To address stress interference in roots, we applied salinity, heat, and high light to hydroponically grown sugar beet. Two main patterns of metabolomic acclimation were apparent. High salt of 300 mM NaCl considerably lowered metabolite amounts, for example, those of most amino acids, γ-amino butyric acid (GABA), and glucose. Very few metabolites revealed the opposite trend with increased contents at high salts, mostly organic acids such as citric acid and isocitric acid, but also tryptophan, tyrosine, and the compatible solute proline. High temperature (31°C vs. 21°C) also frequently lowered root metabolite pools. The individual effects of salinity and heat were superimposed under combined stress. Under high light and high salt conditions, there was a significant decline in root chloride, mannitol, ribulose 5-P, cysteine, and l-aspartate contents. The results reveal the complex interaction pattern of environmental parameters and urge researchers to elaborate in much more detail and width on combinatorial stress effects to bridge work under controlled growth conditions to growth in nature, and also to better understand acclimation to the consequences of climate change.

Additive effects of heatwave and water stresses on soybean seed yield is caused by impaired carbon assimilation at pod formation but not at flowering

Heatwave (HW) combined with water stress (WS) are critical environmental factors negatively affecting crop development. This study aimed to quantify the individual and combined effects of HW and WS during early reproductive stages on leaf and nodule functioning and their relation with final soybean seed yield (SY). For this purpose, during flowering (R2) and pod formation (R4) soybean (Glycine max L. Merr.) plants were exposed to different temperature (ambient[25ºC] versus HW[40ºC]) and water availability (full capacity versus WS[20% field capacity]). HW, WS and their combined impact on yield depended on the phenological stage at which stress was applied being more affected at R4. For gas exchange, WS severely impaired photosynthetic machinery, especially when combined with HS. Impaired photoassimilate supply at flowering caused flower abortion and a significant reduction in final SY due to interacting stresses and WS. On the other hand, at pod formation (R4), decreased leaf performance caused additive effect on SY by decreasing pod setting and seed size with combined stresses. At the nodule level, WS (alone or in combination with HW) caused nodule impairment, which was reflected by lower leaf N. Such response was linked with a poor malate supply to bacteroids and feed-back inhibition caused by nitrogenous compounds accumulation. In summary, our study noted that soybean sensitivity to interacting heat and water stresses was highly conditioned by the phenological stage at which it occurs with, R4 stage being the critical moment. To our knowledge this is the first soybean work integrating combined stresses at early reproductive stages.

An Arabidopsis GCMS chemical ionization technique to quantify adaptive responses in central metabolism

We present a methodology to survey central metabolism in 13CO2-labeled Arabidopsis (Arabidopsis thaliana) rosettes by ammonia positive chemical ionization-gas chromatography-mass spectrometry. This technique preserves the molecular ion cluster of methyloxime/trimethylsilyl-derivatized analytes up to 1 kDa, providing unambiguous nominal mass assignment of >200 central metabolites and 13C incorporation rates into a subset of 111 from the tricarboxylic acid (TCA) cycle, photorespiratory pathway, amino acid metabolism, shikimate pathway, and lipid and sugar metabolism. In short-term labeling assays, we observed plateau labeling of ∼35% for intermediates of the photorespiratory cycle except for glyoxylate, which reached only ∼4% labeling and was also present at molar concentrations several fold lower than other photorespiratory intermediates. This suggests photorespiratory flux may involve alternate intermediate pools besides the generally accepted route through glyoxylate. Untargeted scans showed that in illuminated leaves, noncyclic TCA cycle flux and citrate export to the cytosol revert to a cyclic flux mode following methyl jasmonate (MJ) treatment. MJ also caused a block in the photorespiratory transamination of glyoxylate to glycine. Salicylic acid treatment induced the opposite effects in both cases, indicating the antagonistic relationship of these defense signaling hormones is preserved at the metabolome level. We provide complete chemical ionization spectra for 203 Arabidopsis metabolites from central metabolism, which uniformly feature the unfragmented pseudomolecular ion as the base peak. This unbiased, soft ionization technique is a powerful screening tool to identify adaptive metabolic trends in photosynthetic tissue and represents an important advance in methodology to measure plant metabolic flux.

Unique metabolite profiles of Indonesian cocoa beans from different origins and their correlation with temperature

Chocolate flavors vary depending on the origin of the cocoa beans used. Differences in soil, microorganisms, and environmental factors contribute to the formation of flavor precursors in cocoa beans. During cocoa bean fermentation, environmental temperature has been shown to alter metabolite concentrations. However, the correlation between the metabolite profile of cocoa beans and the temperature of their region of origin has not been fully defined. In this study, the metabolite profiles of Indonesian cocoa beans of various origins were evaluated using gas chromatography/mass spectrometry-based analysis, and were found to differ depending on the origin of the bean. Subsequently, the correlation between metabolite profile and environmental temperature of the origin was assessed using orthogonal projection to latent structure regression (OPLS-R) analysis. The analysis revealed that seven metabolites were associated with temperature: γ-aminobutyric acid (GABA), ethanolamine, glycerol, isocitric acid + citric acid, succinic acid, malic acid, and saccharic acid. The findings of this study will be valuable to chocolate industries for the production of single-origin chocolates.

Effects of citric acid on antioxidant system and carbon-nitrogen metabolism of Elymus dahuricus under Cd stress

Exogenous citric acid (CA), which acts as an important intermediate product of the tricarboxylic acid (TCA) cycle, can enhance the TCA cycle activity and activate the branched operation of the TCA cycle, thus providing energy required for resistance to adverse conditions. However, the effects of CA application on TCA cycle-related metabolism under cadmium (Cd) were less reported. To investigate the effects of CA on the Cd tolerance of Dahurian wildrye grass (Elymus dahuricus), the growth, Cd accumulation, antioxidant systems and metabolic pathways of leaves and roots were investigated by a potted soil experiment with Cd (50 mg/kg) and CA (4 mmol/L) treatments. The results showed that Cd stress seriously affected growth and induced the production of reactive oxygen in clover leaves and roots, leading to membrane peroxidation and activation of the antioxidant defense system. Exogenous CA could not only effectively relieve the inhibition of Cd stress on growth and reduce the amount of reactive oxygen by increasing the antioxidant capacities but could also promote an increase in root Cd content. Metabolomic results showed that the application of CA increased the contents of sugars, sugar alcohols, and resistant substances, and promoted the metabolism of amino acids including γ-aminobutyric acid (GABA). These alterations contributed the significant enhancement of the Cd resistance, which may be related to the changes in the TCA cycle activity and the metabolism of the shikimic acid pathway in leaves and roots as well as GABA shunt in roots.

Molecular and Metabolic Changes under Environmental Stresses: The Biosynthesis of Quality Components in Preharvest Tea Shoots

Severe environments impose various abiotic stresses on tea plants. Although much is known about the physiological and biochemical responses of tea (Camellia sinensis L.) shoots under environmental stresses, little is known about how these stresses impact the biosynthesis of quality components. This review summarizes and analyzes the changes in molecular and quality components in tea shoots subjected to major environmental stresses during the past 20 years, including light (shade, blue light, green light, and UV-B), drought, high/low temperature, CO2, and salinity. These studies reveal that carbon and nitrogen metabolism is critical to the downstream biosynthesis of quality components. Based on the molecular responses of tea plants to stresses, a series of artificial methods have been suggested to treat the pre-harvest tea plants that are exposed to inhospitable environments to improve the quality components in shoots. Furthermore, many pleiotropic genes that are up- or down-regulated under both single and concurrent stresses were analyzed as the most effective genes for regulating multi-resistance and quality components. These findings deepen our understanding of how environmental stresses affect the quality components of tea, providing novel insights into strategies for balancing plant resistance, growth, and quality components in field-based cultivation and for breeding plants using pleiotropic genes.

Age-Associated Changes of Nasal Bacterial Microbiome in Patients With Chronic Rhinosinusitis

Age-related changes in nasal bacterial microbiota of patients with chronic rhinosinusitis (CRS) remains unclear. In this study, we aimed to identify distinct characteristics of nasal bacterial microbiota between aged and younger patients with CRS through 16S rDNA gene sequencing. Patients with CRS undergoing endoscopic sinus surgery were recruited and separated into aged (≥60 years, median age = 66 years, N = 17) and younger (<60 years, median age = 35.5 years, N = 14) patients. Diversity, bacterial composition and metabolic activities of nasal microbiota between aged and younger patients were compared. Results have shown that levels of OTUs (p = 0.0173) and microbiota diversity (all p < 0.05) decreased significantly in aged patients. The abundance of phylum Actinobacteria, and genus Corynebacterium were significantly higher in aged patients, while the abundance of phylum Bacteroidetes, Fusobacteria, and genus Fusobacterium, Peptoniphilus were significantly higher in younger patients. In addition, predicted functional profiles have revealed that 41 KEGG pathways involving in 12 metabolic pathways, 4 genetic information processing, 3 environmental information processing, 4 cellular processes, 8 organismal systems, 6 human diseases, and 4 unclassified pathways were identified. Among which, the vast majority of metabolic activities are involved in replication and repair, membrane transport, translation, and the metabolism of amino acid, carbohydrate, energy, cofactors and vitamins, and nucleotide. On the level of the thirdly bacterial metabolic pathways, purine metabolism, glycine, serine and threonine metabolism, valine, leucine and isoleucine biosynthesis, glycolysis/gluconeogenesis and phenylalanine, tyrosine and tryptophan biosynthesis are significantly up-regulated while carbon fixation pathways in prokaryotesand methane metabolism are significantly down-regulated in aged patients. Overall, our analysis revealed that age-related physiological and pathological changes on the nasal mucosal surface may alter the host immune response and be highly associated with the nasal bacterial microbiota of patients with CRS. However, future studies are needed to elucidate the causal relationship.

The changes in Lemna minor metabolomic profile: A response to diclofenac incubation

Metabolomics is an emerging approach that investigates the changes in the metabolome profile. In the present study, Lemna minor -considered as an experimental aquatic plant model- was incubated with 10 and 100 μM diclofenac (DCF) for 96 h, respectively. Knowing that DCF is internationally often problematic in wastewater effluents and that it might affect particularly the metabolic profiles in aquatic plants, mainly the oxidoreductase, dehydrogenase, peroxidase, and glutathione reductase activities, here it was hypothesized (H) that in the common duckweed, DCF might increase the phenolic and flavonoids pathways, as an antioxidant response to this stress (H1). Also, it was expected DCF to alternate the physiological characteristics, especially the molecular interaction and biochemical properties, of Lemna (H2). Metabolic changes were investigated with target and untargeted screening analysis using RPLC-HILIC-ESI-TOF-MS. Twelve amino acids were identified in all treatments, together with three organic acids (p-coumaric, cinnamic, and sinapic acids). In untargeted screening, the important metabolites to discriminate between different treatments were assigned to Lemna such as organic acids, lignin, sugars, amino acids, dipeptides, flavonoids, biflavonoids, fatty acids, among others. In resume, Lemna responded to both DCF concentrations, showing different stress patterns. A similar metabolic response had already been identified in other studies in exposing Lemna to other anthropogenic stressors (like pesticides).

Hydrogel Alginate Seed Coating as an Innovative Method for Delivering Nutrients at the Early Stages of Plant Growth

Seed coating containing fertilizer nutrients and plant growth biostimulants is an innovative technique for precision agriculture. Nutrient delivery can also be conducted through multilayer seed coating. For this purpose, sodium alginate with NPK, which was selected in a preliminary selection study, crosslinked with divalent ions (Cu(II), Mn(II), Zn(II)) as a source of fertilizer micronutrients, was used to produce seed coating. The seeds were additionally coated with a solution containing amino acids derived from high-protein material. Amino acids can be obtained by alkaline hydrolysis of mealworm larvae (Gly 71.2 ± 0.6 mM, Glu 55.8 ± 1.3 mM, Pro 48.8 ± 1.5 mM, Ser 31.4 ± 1.5 mM). The formulations were applied in different doses per 100 g of seeds: 35 mL, 70 mL, 105 mL, and 140 mL. SEM-EDX surface analysis showed that 70 mL of formulation/100 g of seeds formed a continuity of coatings but did not result in a uniform distribution of components on the surface. Extraction tests proved simultaneous low leaching of nutrients into water (max. 10%), showing a slow release pattern. There occurred high bioavailability of fertilizer nutrients (even up to 100%). Pot tests on cucumbers (Cornichon de Paris) confirmed the new method’s effectiveness, yielding a 50% higher fresh sprout weight and four times greater root length than uncoated seeds. Seed coating with hydrogel has a high potential for commercial application, stimulating the early growth of plants and thus leading to higher crop yields.

Genotype- and tissue-specific metabolic networks and hub genes involved in water-induced distinct sweet cherry fruit cracking phenotypes

Sweet cherry fruit cracking is a complex physiological disorder that causes significant economic losses. Despite many years of research there is a lack of understanding of the mechanisms involved in cracking. Here, skin and flesh tissue from the cracking susceptible 'Early Bigi’ and the cracking tolerant ‘Regina’ cultivars were sampled prior and just after water dipping treatment to identify water-affected metabolic networks that putatively involved in fruit cracking. Primary metabolites, most strongly those involved in sugars and amino acid metabolism, such as glucose and asparagine, shifted in 'Early Bigi’ compared with ‘Regina’ tissues following water exposure. Comparisons between cultivars, tissues and dipping points identified significant differentially expressed genes. Particularly, genes related to abscisic acid, ethylene biosynthesis, pectin metabolism, expansins and aquaporins were altered in water-exposed tissues. To further characterize the role of these genes in cracking, their single nucleotide variants of the coding regions was studied in another eight sweet cherry cultivars, which differ in their sensitivity to cracking, revealing a strong link mainly between pectin metabolism-related genes and cracking-phenotypes. Integrated metabolomic and transcriptomic profiling uncovered genotypic- and tissue-specific metabolic pathways, including tricarboxylic acid cycle, cell enlargement, lipid and ethanol biosynthesis, and plant defense that putatively are involved in fruit cracking. Based on these results, a model which describes the skin and flesh metabolic reprogramming during water-induced fruit cracking in the susceptible 'Early Bigi’ cultivar is presented. Τhis study can help to explore novel candidate genes and metabolic pathways for cracking tolerance in sweet cherry.

Characterization and Comparison of Bacterial Communities of an Invasive and Two Native Caribbean Seagrass Species Sheds Light on the Possible Influence of the Microbiome on Invasive Mechanisms

Invasive plants, including marine macrophytes, are one of the most important threats to biodiversity by displacing native species and organisms depending on them. Invasion success is dependent on interactions among living organisms, but their study has been mostly limited to negative interactions while positive interactions are mostly underlooked. Recent studies suggested that microorganisms associated with eukaryotic hosts may play a determinant role in the invasion process. Along with the knowledge of their structure, taxonomic composition, and potential functional profile, understanding how bacterial communities are associated with the invasive species and the threatened natives (species-specific/environmentally shaped/tissue-specific) can give us a holistic insight into the invasion mechanisms. Here, we aimed to compare the bacterial communities associated with leaves and roots of two native Caribbean seagrasses (Halodule wrightii and Thalassia testudinum) with those of the successful invader Halophila stipulacea, in the Caribbean island Curaçao, using 16S rRNA gene amplicon sequencing and functional prediction. Invasive seagrass microbiomes were more diverse and included three times more species-specific core OTUs than the natives. Associated bacterial communities were seagrass-specific, with higher similarities between natives than between invasive and native seagrasses for both communities associated with leaves and roots, despite their strong tissue differentiation. However, with a higher number of OTUs in common, the core community (i.e., OTUs occurring in at least 80% of the samples) of the native H. wrightii was more similar to that of the invader H. stipulacea than T. testudinum, which could reflect more similar essential needs (e.g., nutritional, adaptive, and physiological) between native and invasive, in contrast to the two natives that might share more environment-related OTUs. Relative to native seagrass species, the invasive H. stipulacea was enriched in halotolerant bacterial genera with plant growth-promoting properties (like Halomonas sp. and Lysinibacillus sp.) and other potential beneficial effects for hosts (e.g., heavy metal detoxifiers and quorum sensing inhibitors). Predicted functional profiles also revealed some advantageous traits on the invasive species such as detoxification pathways, protection against pathogens, and stress tolerance. Despite the predictive nature of our findings concerning the functional potential of the bacteria, this investigation provides novel and important insights into native vs. invasive seagrasses microbiome. We demonstrated that the bacterial community associated with the invasive seagrass H. stipulacea is different from native seagrasses, including some potentially beneficial bacteria, suggesting the importance of considering the microbiome dynamics as a possible and important influencing factor in the colonization of non-indigenous species. We suggest further comparison of H. stipulacea microbiome from its native range with that from both the Mediterranean and Caribbean habitats where this species has a contrasting invasion success. Also, our new findings open doors to a more in-depth investigation combining meta-omics with bacterial manipulation experiments in order to confirm any functional advantage in the microbiome of this invasive seagrass.

Transcriptome Variations in Verticillium dahliae in Response to Two Different Inorganic Nitrogen Sources

The fungus Verticillium dahliae causes vascular wilt disease on hundreds of plant species. The main focus of the research to control this fungus has been aimed at infection processes such as penetration peg formation and effector secretion, but the ability of the fungus to acquire and utilize nutrients are often overlooked and may hold additional potential to formulate new disease control approaches. Little is known about the molecular mechanisms of nitrogen acquisition and assimilation processes in V. dahliae. In this present study, RNA sequencing and gene expression analysis were used to examine differentially expressed genes in response to the different nitrogen sources, nitrate and ammonium, in V. dahliae. A total of 3244 and 2528 differentially expressed genes were identified in response to nitrate and ammonium treatments, respectively. The data indicated nitrate metabolism requires additional energy input while ammonium metabolism is accompanied by reductions in particular cellular processes. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of DEGs during nitrate metabolism revealed that many of the genes encoded those involved in protein biosynthetic and metabolic processes, especially ribosome and RNA polymerase biosynthesis, but also other processes including transport and organonitrogen compound metabolism. Analysis of DEGs in the ammonium treatment indicated that cell cycle, oxidoreductase, and certain metabolic activities were reduced. In addition, DEGs participating in the utilization of both nitrate and ammonium were related to L-serine biosynthesis, energy-dependent multidrug efflux pump activity, and glycerol transport. We further showed that the mutants of three differentially expressed transcription factors (VdMcm1, VdHapX, and VDAG_08640) exhibited abnormal phenotypes under nitrate and ammonium treatment compared with the wild type strain. Deletion of VdMcm1 displayed slower growth when utilizing both nitrogen sources, while deletion of VdHapX and VDAG_08640 only affected nitrate metabolism, inferring that nitrogen assimilation required regulation of bZIP transcription factor family and participation of cell cycle. Taken together, our findings illustrate the convergent and distinctive regulatory mechanisms between preferred (ammonium) and alternative nitrogen (nitrate) metabolism at the transcriptome level, leading to better understanding of inorganic nitrogen metabolism in V. dahliae.

Diversified amino acid-mediated allosteric regulation of phosphoglycerate dehydrogenase for serine biosynthesis in land plants

The phosphorylated pathway of serine biosynthesis is initiated with 3-phosphoglycerate dehydrogenase (PGDH). The liverwort Marchantia polymorpha possesses an amino acid-sensitive MpPGDH which is inhibited by l-serine and activated by five proteinogenic amino acids, while the eudicot Arabidopsis thaliana has amino acid-sensitive AtPGDH1 and AtPGDH3 as well as amino acid-insensitive AtPGDH2. In this study, we analyzed PGDH isozymes of the representative land plants: the monocot Oryza sativa (OsPGDH1–3), basal angiosperm Amborella trichopoda (AmtriPGDH1–2), and moss Physcomitrium (Physcomitrella) patens (PpPGDH1–4). We demonstrated that OsPGDH1, AmtriPGDH1, PpPGDH1, and PpPGDH3 were amino acid-sensitive, whereas OsPGDH2, OsPGDH3, AmtriPGDH2, PpPGDH2, and PpPGDH4 were either sensitive to only some of the six effector amino acids or insensitive to all effectors. This indicates that PGDH sensitivity to effectors has been diversified among isozymes and that the land plant species examined, except for M. polymorpha, possess different isozyme types in terms of regulation. Phylogenetic analysis suggested that the different sensitivities convergently evolved in the bryophyte and angiosperm lineages. Site-directed mutagenesis of AtPGDH1 revealed that Asp⁵³⁸ and Asn⁵⁵⁶ residues in the ACT domain are involved in allosteric regulation by the effectors. These findings provide insight into the evolution of PGDH isozymes, highlighting the functional diversification of allosteric regulation in land plants.