Metabolic control and regulation of the tricarboxylic acid cycle in photosynthetic and heterotrophic plant tissues

Leaf day respiration involves multiple carbon sources and depends on previous dark metabolism

Day respiration (Rd) is the metabolic, nonphotorespiratory process by which illuminated leaves liberate CO2 during photosynthesis. Rd is used routinely in photosynthetic models and is thus critical for calculations. However, metabolic details associated with Rd are poorly known, and this can be problematic to predict how Rd changes with environmental conditions and relates to night respiration. It is often assumed that day respiratory CO2 release just reflects 'ordinary' catabolism (glycolysis and Krebs 'cycle'). Here, we carried out a pulse-chase experiment, whereby a 13CO2 pulse in the light was followed by a chase period in darkness and then in the light. We took advantage of nontargeted, isotope-assisted metabolomics to determine non-'ordinary' metabolism, detect carbon remobilisation and compare light and dark 13C utilisation. We found that several concurrent metabolic pathways ('ordinary' catabolism, oxidative pentose phosphates pathway, amino acid production, nucleotide biosynthesis and secondary metabolism) took place in the light and participated in net CO2 efflux associated with day respiration. Flux reconstruction from metabolomics leads to an underestimation of Rd, further suggesting the contribution of a variety of CO2-evolving processes. Also, the cornerstone of the Krebs 'cycle', citrate, is synthetised de novo from photosynthates mostly in darkness, and remobilised or synthesised from stored material in the light. Collectively, our data provides direct evidence that leaf day respiration (i) involves several CO2-producing reactions and (ii) is fed by different carbon sources, including stored carbon disconnected from current photosynthates.

Energy metabolism analysis of exogenous glutamate on promoting co-accumulation of astaxanthin yield and biomass in Phaffia rhodozyma D3

Effective metabolic regulators play an essential role in regulating astaxanthin biosynthesis in Phaffia rhodozyma. In this study, it was found that 5 mM glutamate increased the astaxanthin yield and biomass of P. rhodozyma D3 to 22.34 mg/L and 6.12 g/L, which were 1.22 and 1.33 times higher than the control group, respectively. Meanwhile, glucose uptake was increased and the level of reactive oxygen species (ROS) was reduced with 5 mM glutamate. To further explore the interrelationship between glutamate and astaxanthin synthesis, the energy metabolism of P. rhodozyma D3 with and without glutamate was analysed. Glutamate promoted the Embden-Meyerhof-Parnas pathway (EMP) metabolic flux, modulated the tricarboxylic acid (TCA) cycle and the pentose phosphate pathway (PPP), activated the ornithine cycle and purine metabolism, and provided more ATP and NADPH for astaxanthin accumulation. This study clarified the possible mechanism by which glutamate promoted astaxanthin accumulation in P. rhodozyma.

Comparative proteomic and metabolomic analyses reveal stress responses of hemp to salinity

KEY MESSAGE

Integrated omics analyses outline the cellular and metabolic events of hemp plants in response to salt stress and highlight several photosynthesis and energy metabolism related pathways as key regulatory points. Soil salinity affects many physiological processes of plants and leads to crop yield losses worldwide. For hemp, a crop that is valued for multiple aspects, such as its medical compounds, fibre, and seed, a comprehensive understanding of its salt stress responses is a prerequisite for resistance breeding and tailoring its agronomic performance to suit certain industrial applications. Here, we first observed the phenotype of salt-stressed hemp plants and found that under NaCl treatment, hemp plants displayed pronounced growth defects, as indicated by the significantly reduced average height, number of leaves, and chlorophyll content. Next, we conducted comparative proteomics and metabolomics to dissect the complex salt-stress response mechanisms. A total of 314 proteins and 649 metabolites were identified to be differentially behaving upon NaCl treatment. Functional classification and enrichment analysis unravelled that many differential proteins were proteases associated with photosynthesis. Through metabolic pathway enrichment, several energy-related pathways were found to be altered, such as the biosynthesis and degradation of branched-chain amino acids, and our network analysis showed that many ribosomal proteins were involved in these metabolic adaptations. Taken together, for hemp plants, influences on chloroplast function probably represent a major toxic effect of salinity, and modulating several energy-producing pathways possibly through translational regulation is presumably a key protective mechanism against the negative impacts. Our data and analyses provide insights into our understanding of hemp's stress biology and may lay a foundation for future functional genomics studies.

Selenium Nanomaterials Enhance Sheath Blight Resistance and Nutritional Quality of Rice: Mechanisms of Action and Human Health Benefit

In the current work, the foliar application of selenium nanomaterials (Se0 NMs) suppressed sheath blight in rice (Oryza sativa). The beneficial effects were nanoscale specific and concentration dependent. Specifically, foliar amendment of 5 mg/L Se0 NMs decreased the disease severity by 68.8% in Rhizoctonia solani-infected rice; this level of control was 1.57- and 2.20-fold greater than that of the Se ions with equivalent Se mass and a commercially available pesticide (Thifluzamide). Mechanistically, (1) the controlled release ability of Se0 NMs enabled a wider safe concentration range and greater bioavailability to Se0 NMs, and (2) transcriptomic and metabolomic analyses demonstrated that Se0 NMs simultaneously promoted the salicylic acid- and jasmonic-acid-dependent acquired disease resistance pathways, antioxidative system, and flavonoid biosynthesis. Additionally, Se0 NMs improved rice yield by 31.1%, increased the nutritional quality by 6.4-7.2%, enhanced organic Se content by 44.8%, and decreased arsenic and cadmium contents by 38.7 and 42.1%, respectively, in grains as compared with infected controls. Human simulated gastrointestinal tract model results showed that the application of Se0 NMs enhanced the bioaccessibility of Se in grains by 22.0% and decreased the bioaccessibility of As and Cd in grains by 20.3 and 13.4%, respectively. These findings demonstrate that Se0 NMs can serve as an effective and sustainable strategy to increase food quality and security.

Thioredoxins o1 and h2 jointly adjust mitochondrial dihydrolipoamide dehydrogenase-dependent pathways towards changing environments

Thioredoxins (TRXs) are central to redox regulation, modulating enzyme activities to adapt metabolism to environmental changes. Previous research emphasized mitochondrial and microsomal TRX o1 and h2 influence on mitochondrial metabolism, including photorespiration and the tricarboxylic acid (TCA) cycle. Our study aimed to compare TRX-based regulation circuits towards environmental cues mainly affecting photorespiration. Metabolite snapshots, phenotypes and CO2 assimilation were compared among single and multiple TRX mutants in the wild-type and the glycine decarboxylase T-protein knockdown (gldt1) background. Our analyses provided evidence for additive negative effects of combined TRX o1 and h2 deficiency on growth and photosynthesis. Especially metabolite accumulation patterns suggest a shared regulation mechanism mainly on mitochondrial dihydrolipoamide dehydrogenase (mtLPD1)-dependent pathways. Quantification of pyridine nucleotides, in conjunction with 13C-labelling approaches, and biochemical analysis of recombinant mtLPD1 supported this. It also revealed mtLPD1 inhibition by NADH, pointing at an additional measure to fine-tune it's activity. Collectively, we propose that lack of TRX o1 and h2 perturbs the mitochondrial redox state, which impacts on other pathways through shifts in the NADH/NAD+ ratio via mtLPD1. This regulation module might represent a node for simultaneous adjustments of photorespiration, the TCA cycle and branched chain amino acid degradation under fluctuating environmental conditions.

Impact of Heavy Metal Pollution in the Environment on the Metabolic Profile of Medicinal Plants and Their Therapeutic Potential

The paper provides a comprehensive examination of heavy metal stress on medicinal plants, focusing on its impact on antioxidant capacity and biosynthetic pathways critical to their therapeutic potential. It explores the complex relationship between heavy metals and the physiological and biochemical responses of medicinal plants, highlighting how metal stress disrupts biosynthetic pathways, altering concentrations of secondary metabolites. This disruption may compromise the overall quality and efficacy of medicinal plants, requiring a holistic understanding of its cumulative impacts. Furthermore, the study discusses the potential of targeted genetic editing to enhance plant resilience against heavy metal stress by manipulating genes associated with antioxidant defenses. This approach represents a promising frontier in safeguarding medicinal plants in metal-contaminated environments. Additionally, the research investigates the role of phytohormone signaling in plant adaptive mechanisms to heavy metal stress, revealing its influence on biochemical and physiological responses, thereby adding complexity to plant adaptation. The study underscores the importance of innovative technologies and global cooperation in protecting medicinal plants' therapeutic potential and highlights the need for mitigation strategies to address heavy metal contamination effectively.

Drought Stress Responses in Arabica Coffee Genotypes: Physiological and Metabolic Insights

Understanding the impact of drought stress on Arabica coffee physiology and metabolism is essential in the pursuit of developing drought-resistant varieties. In this study, we explored the physiological and metabolite changes in coffee genotypes exhibiting varying degrees of tolerance to drought-namely, the relatively tolerant Ca74110 and Ca74112, and the sensitive Ca754 and CaJ-19 genotypes-under well-watered conditions and during terminal drought stress periods at two time points (0 and 60 days following the onset of stress). The metabolite profiling uncovered significant associations between the growth and the physiological characteristics of coffee genotypes with distinct drought tolerance behaviors. Initially, no marked differences were observed among the genotypes or treatments. However, at the 60-day post-drought onset time point, notably higher shoot growth, biomass, CO2 assimilation, pigments, and various physiological parameters were evident, particularly in the relatively tolerant genotypes. The metabolite profiling revealed elevations in glucose, maltose, amino acids, and organic acids, and decreases in other metabolites. These alterations were more pronounced in the drought-tolerant genotypes, indicating a correlation between enhanced compatible solutes and energy-associated metabolites crucial for drought tolerance mechanisms. This research introduces GC-MS-based metabolome profiling to the study of Ethiopian coffee, shedding light on its intricate responses to drought stress and paving the way for the potential development of drought-resistant coffee seedlings in intensified agro-ecological zones.

Oxalic acid secretion alleviates saline-alkali stress in alfalfa by improving photosynthetic characteristics and antioxidant activity

Saline-alkali stress significantly affects the growth and yield of alfalfa (Medicago sativa L.). Organic acid secretion is crucial in alleviating abiotic stress-induced damage in plants. In this study, we evaluated the contents of the major organic acids secreted by the roots of tolerant (ZD) and sensitive (LYL) varieties of alfalfa under saline-alkali stress and investigated the effects of these organic acids on the growth, and physiological functions of alfalfa. Our results indicated that the oxalic acid (OA) content was the highest among the organic acids secreted from alfalfa roots under saline-alkali stress, and oxalic acid content was the most significantly different between the two varieties, ZD and LYL, compared to the contents of the other organic acids. Oxalic acid alleviated the inhibition of alfalfa growth caused by saline-alkali stress, improved photosynthetic characteristics, reduced the accumulation of reactive oxygen species, and increased the activity of antioxidant enzymes and content of osmoregulatory substances. Furthermore, oxalic acid resulted in significantly increased expression of genes involved in photosynthesis and antioxidant system in alfalfa under saline-alkali stress. This study revealed the effects of oxalic acid secreted by the root system on stress-related physiological processes, providing valuable insights into the functions of root secretions in plant saline-alkali resistance.

Tissue distribution of metabolites in Cordyceps cicadae determined by DESI-MSI analysis

In this paper, we establish an in situ visualization analysis method to image the spatial distribution of metabolites in different parts (sclerotium, coremium) and different microregions of Cordyceps cicadae (C. cicadae) to achieve the in situ visual characterization of tissues for a variety of metabolites such as nucleosides, amino acids, polysaccharides, organic acids, fatty acids, and so on. The study included LC-MS chemical composition identification, preparation of C. cicadae tissue sections, DEDI-MSI analysis, DESI combined with Q-TOF/MS to obtain high-resolution imaging of mass-to-charge ratio and space, imaging of C. cicadae in positive-negative ion mode with a spatial resolution of 100 μm, and localizing and identifying its chemical compositions based on its precise mass. A total of 62 compounds were identified; nucleosides were mainly distributed in the coremium, L-threonine and DL-isoleucine, and other essential amino acids; peptides were mainly distributed in the sclerotium of C. cicadae; and the rest of the amino acids did not have a clear pattern; sugars and sugar alcohols were mainly distributed in the coremium of C. cicadae; organic acids and fatty acids were distributed in the nucleus of C. cicadae more than in the sclerotium, and the mass spectrometry imaging method is established in the research. The mass spectrometry imaging method established in this study is simple and fast and can visualize and analyse the spatial distribution of metabolites of C. cicadae, which is of great significance in characterizing the metabolic network of C. cicadae, and provides support for the quality evaluation of C. cicadae and the study of the temporal and spatial metabolic network of chemical compounds.

Dynamics of organic acid exudation and rhizobacteria in maize rhizosphere respond to N-CDs

To sustainably feed the growing global population, it is essential to increase crop yields on limited land while reducing the use of fertilizers and agrochemicals. The rhizosphere regulation shows significant potential to address this challenge. Here, foliar applied doping of nitrogen in carbon dots (N-CDs) entered maize leaves, and were transported to the stems and roots. The internalized N-CDs significantly increased the biomass (26.4-93.8%) and photosynthesis (17.0-20.3 %) of maize seedling during the three-week application of N-CDs, providing the substrate for tricarboxylic acid cycle (TCA) in shoots and roots. Correspondingly, more organic acids involved in TCA cycle, such as citric acid (14.0-fold), succinic acid (4.4-fold) and malic acid (3.4-fold), were synthesized and then secreted into rhizosphere after exposed to N-CDs for one day. As the exposure time increased, greater secretion of above organic acids by the roots was induced. However, no significant change was observed in the relative abundance of rhizobacteria after foliar application with N-CDs for one day. After one week, the relative abundances of Azotobacter, Bacillus, Lysobacter, Mucilaginibacter, and Sphingomonas increased by 0.8-3.8 folds. The relative abundance of more beneficial rhizobacteria (Sphingomonas, Lysobacter, Rhizobium, Azotobacter, Pseudomonas, Mucilaginibacter and Bacillus) enriched by 0.3-6.0 folds after two weeks, and Sphingomonas, Flavisolibacter and Bacillus improved by 0.6-3.2 folds after three weeks. These dynamic changes suggested that N-CDs initiate the synthesis and secretion of organic acids and then recruited beneficial rhizobacteria. The hierarchical partitioning analysis further indicated that N-CDs-induced secretion of organic acids from the roots was the main drivers of rhizobacteria community dynamics. The differential microbes altered by N-CDs were mainly involved in nitrogen (N) and phosphorus (P) cycles, which are beneficial for N and P uptake, and maize growth. These results provide insights into understanding the rhizosphere regulation of nanomaterials to improve plant productivity and nutrient-use efficiency.

Tripogon loliiformis tolerates rapid desiccation after metabolic and transcriptional priming during initial drying

Crop plants and undomesticated resilient species employ different strategies to regulate their energy resources and growth. Most crop species are sensitive to stress and prioritise rapid growth to maximise yield or biomass production. In contrast, resilient plants grow slowly, are small, and allocate their resources for survival in challenging environments. One small group of plants, termed resurrection plants, survive desiccation of their vegetative tissue and regain full metabolic activity upon watering. However, the precise molecular mechanisms underlying this extreme tolerance remain unknown. In this study, we employed a transcriptomics and metabolomics approach, to investigate the mechanisms of desiccation tolerance in Tripogon loliiformis, a modified desiccation-tolerant plant, that survives gradual but not rapid drying. We show that T. loliiformis can survive rapid desiccation if it is gradually dried to 60% relative water content (RWC). Furthermore, the gene expression data showed that T. loliiformis is genetically predisposed for desiccation in the hydrated state, as evidenced by the accumulation of MYB, NAC, bZIP, WRKY transcription factors along with the phytohormones, abscisic acid, salicylic acid, amino acids (e.g., proline) and TCA cycle sugars during initial drying. Through network analysis of co-expressed genes, we observed differential responses to desiccation between T. loliiformis shoots and roots. Dehydrating shoots displayed global transcriptional changes across broad functional categories, although no enrichment was observed during drying. In contrast, dehydrating roots showed distinct network changes with the most significant differences occurring at 40% RWC. The cumulative effects of the early stress responses may indicate the minimum requirements of desiccation tolerance and enable T. loliiformis to survive rapid drying. These findings potentially hold promise for identifying biotechnological solutions aimed at developing drought-tolerant crops without growth and yield penalties.

Effects of Vine Water Status on Malate Metabolism and γ-Aminobutyric Acid (GABA) Pathway-Related Amino Acids in Marselan (Vitis vinifera L.) Grape Berries

Malic acid is the predominant organic acid in grape berries, and its content is affected by abiotic factors such as temperature (fruit zone microclimate) and water (vine water status). The objectives of this study were to explore the potential mechanisms behind the effects of vine water status on the biosynthesis and degradation of berry malic acid and the potential downstream effects on berry metabolism. This study was conducted over two growing seasons in 2021 and 2022, comprising three watering regimes: no water stress (CK), light water stress (LWS), and moderate water stress (MWS). Compared to CK, a significantly higher level of malic acid was found in berries from the MWS treatment when the berry was still hard and green (E-L 33) in both years. However, water stress reduced the malic acid content at the ripe berry harvest (E-L 38) stage. The activities of NAD-malate dehydrogenase (NAD-MDH) and pyruvate kinase (PK) were enhanced by water stress. Except for the E-L 33 stage, the activity of phosphoenolpyruvate carboxylase (PEPC) was reduced by water stress. The highest phosphoenolpyruvate carboxykinase (PEPCK) activity was observed at the berry veraison (E-L 35) stage and coincided with the onset of a decrease in the malate content. Meanwhile, the expression of VvPEPCK was consistent with its enzyme activity. This study showed that water stress changed the content of some free amino acids (GABA, proline, leucine, aspartate, and glutamate), two of which (glutamate and GABA) are primary metabolites of the GABA pathway.

Physiological and metabolomic responses of the ethylene insensitive squash mutant etr2b to drought

The squash gain-of-function mutant etr2b disrupts the ethylene-binding domain of ethylene receptor CpETR2B, conferring partial ethylene insensitivity, changes in flower and fruit development, and enhanced salt tolerance. In this paper, we found that etr2b also confers a growth advantage as well as a physiological and metabolomic response that make the mutant better adapted to drought. Mutant plants had a higher root and leaf biomass than WT under both well-watered and drought conditions, but the reduction in growth parameters in response to drought was similar in WT and etr2b. Water deficit reduced all gas-exchange parameters in both WT and etr2b, but under moderate drought the mutant increased photosynthesis rate in comparison with control conditions, and showed a higher leaf CO2 concentration, transpiration rate, and stomata conductance than WT. The response of etr2b to drought indicates that ethylene is a negative regulator of plant growth under both control and drought. Since etr2b increased ABA content in well-watered plant, but prevented the induction of ABA production in response to drought, it is likely that the etr2b response under drought is not mediated by ABA. A 1H NMR metabolomic analysis revealed that etr2b enhances the accumulation of osmolytes (soluble sugars and trigonelline), unsaturated and polyunsaturated fatty acids, and phenolic compounds under drought, concomitantly with a reduction of malic- and fumaric-acid. The role of CpETR2B and ethylene in the regulation of these drought-protective metabolites is discussed.

Metabolome and transcriptome reprogramming underlying tomato drought resistance triggered by a Pseudomonas strain

Although amelioration of drought stress by Plant Growth Promoting Rhizobacteria (PGPR) is a well-documented phenomenon, the combined molecular and metabolic mechanisms governing this process remain unclear. In these lines, the present study aimed to provide new insights in the underlying drought attenuating mechanisms of tomato plants inoculated with a PGP Pseudomonas putida strain, by using a combination of metabolomic and transcriptomic approaches. Following Differentially Expressed Gene analysis, it became evident that inoculation resulted in a less disturbed plant transcriptome upon drought stress. Untargeted metabolomics highlighted the differential metabolite accumulation upon inoculation, as well as the less metabolic reprograming and the lower accumulation of stress-related metabolites for inoculated stressed plants. These findings were in line with morpho-physiological evidence of drought stress mitigation in the inoculated plants. The redox state modulation, the more efficient nitrogen assimilation, as well as the differential changes in amino acid metabolism, and the induction of the phenylpropanoid biosynthesis pathway, were the main drought-attenuating mechanisms in the SAESo11-inoculated plants. Shifts in pathways related to hormonal signaling were also evident upon inoculation at a transcript level and in conjunction with carbon metabolism regulation, possibly contributed to a drought-attenuation preconditioning. The identified signatory molecules of SAESo11-mediated priming against drought included aspartate, myo-inositol, glutamate, along with key genes related to trehalose, tryptophan and cysteine synthesis. Taken together, SAESo11-inoculation provides systemic effects encompassing both metabolic and regulatory functions, supporting both seedling growth and drought stress amelioration.

Identification of Two Flip-Over Genes in Grass Family as Potential Signature of C4 Photosynthesis Evolution

In flowering plants, C4 photosynthesis is superior to C3 type in carbon fixation efficiency and adaptation to extreme environmental conditions, but the mechanisms behind the assembly of C4 machinery remain elusive. This study attempts to dissect the evolutionary divergence from C3 to C4 photosynthesis in five photosynthetic model plants from the grass family, using a combined comparative transcriptomics and deep learning technology. By examining and comparing gene expression levels in bundle sheath and mesophyll cells of five model plants, we identified 16 differentially expressed signature genes showing cell-specific expression patterns in C3 and C4 plants. Among them, two showed distinctively opposite cell-specific expression patterns in C3 vs. C4 plants (named as FOGs). The in silico physicochemical analysis of the two FOGs illustrated that C3 homologous proteins of LHCA6 had low and stable pI values of ~6, while the pI values of LHCA6 homologs increased drastically in C4 plants Setaria viridis (7), Zea mays (8), and Sorghum bicolor (over 9), suggesting this protein may have different functions in C3 and C4 plants. Interestingly, based on pairwise protein sequence/structure similarities between each homologous FOG protein, one FOG PGRL1A showed local inconsistency between sequence similarity and structure similarity. To find more examples of the evolutionary characteristics of FOG proteins, we investigated the protein sequence/structure similarities of other FOGs (transcription factors) and found that FOG proteins have diversified incompatibility between sequence and structure similarities during grass family evolution. This raised an interesting question as to whether the sequence similarity is related to structure similarity during C4 photosynthesis evolution.

5-ALA Improves the Low Temperature Tolerance of Common Bean Seedlings through a Combination of Hormone Transduction Pathways and Chlorophyll Metabolism

Low-temperature stress is a key factor limiting the yield and quality of the common bean. 5-aminolevulinic acid (5-ALA), an antioxidant in plants, has been shown to modulate plant cold stress responses. However, the molecular mechanisms of 5-ALA-induced physiological and chemical changes in common bean seedlings under cold stress remains unknown. This study explored the physiological and transcriptome changes of common bean seedlings in response to cold stress after 5-ALA pretreatment. Physiological results showed that exogenous 5-ALA promotes the growth of common bean plants under cold stress, increases the activity of antioxidant enzymes (superoxide dismutase: 23.8%; peroxidase: 10.71%; catalase: 9.09%) and proline content (24.24%), decreases the relative conductivity (23.83%), malondialdehyde (33.65%), and active oxygen content, and alleviates the damage caused by cold to common bean seedlings. Transcriptome analysis revealed that 214 differentially expressed genes (DEGs) participate in response to cold stress. The DEGs are mainly concentrated in indole alkaloid biosynthesis, carotenoid biosynthesis, porphyrin, and chlorophyll metabolism. It is evident that exogenous 5-ALA alters the expression of genes associated with porphyrin and chlorophyll metabolism, as well as the plant hormone signal transduction pathway, which helps to maintain the energy supply and metabolic homeostasis under low-temperature stress. The results reveal the effect that applying exogenous 5-ALA has on the cold tolerance of the common bean and the molecular mechanism of its response to cold tolerance, which provides a theoretical basis for exploring and improving plant tolerance to low temperatures.

Lanthanum Silicate Nanomaterials Enhance Sheath Blight Resistance in Rice: Mechanisms of Action and Soil Health Evaluation

In the current study, foliar spray with lanthanum (La) based nanomaterials (La10Si6O27 nanorods, La10Si6O27 nanoparticle, La(OH)3 nanorods, and La2O3 nanoparticle) suppressed the occurrence of sheath blight (Rhizoctonia solani) in rice. The beneficial effects were morphology-, composition-, and concentration-dependent. Foliar application of La10Si6O27 nanorods (100 mg/L) yielded the greatest disease suppression, significantly decreasing the disease severity by 62.4% compared with infected controls; this level of control was 2.7-fold greater than the commercially available pesticide (Thifluzamide). The order of efficacy was as follows: La10Si6O27 nanorods > La10Si6O27 nanoparticle > La(OH)3 nanorods > La2O3 nanoparticle. Mechanistically, (1) La10Si6O27 nanorods had greater bioavailability, slower dissolution, and simultaneous Si nutrient benefits; (2) transcriptomic and metabolomic analyses revealed that La10Si6O27 nanorods simultaneously strengthened rice systemic acquired resistance, physical barrier formation, and antioxidative systems. Additionally, La10Si6O27 nanorods improved rice yield by 35.4% and promoted the nutritional quality of the seeds as compared with the Thifluzamide treatment. A two-year La10Si6O27 nanorod exposure had no effect on soil health based on the evaluated chemical, physical, and biological soil properties. These findings demonstrate that La based nanomaterials can serve as an effective and sustainable strategy to safeguard crops and highlight the importance of nanomaterial composition and morphology in terms of optimizing benefit.

The Role of TCA Cycle Enzymes in Plants

As one of the iconic pathways in plant metabolism, the tricarboxylic acid (TCA) cycle is commonly thought to not only be responsible for the oxidization of respiratory substrate to drive ATP synthesis but also provide carbon skeletons to anabolic processes and contribute to carbon-nitrogen interaction and biotic stress responses. The functions of the TCA cycle enzymes are characterized by a saturation transgenesis approach, whereby the constituent expression of proteins is knocked out or reduced in order to investigate their function in vivo. The alteration of TCA cycle enzyme expression results in changed plant growth and photosynthesis under controlled conditions. Moreover, improvements in plant performance and postharvest properties are reported by overexpression of either endogenous forms or heterologous genes of a number of the enzymes. Given the importance of the TCA cycle in plant metabolism regulation, here, the function of each enzyme and its roles in different tissues are discussed. This article additionally highlights the recent finding that the plant TCA cycle, like that of mammals and microbes, dynamically assembles functional substrate channels or metabolons and discusses the implications of this finding to the current understanding of the metabolic regulation of the plant TCA cycle.

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.

Unveiling the dark side of guard cell metabolism

Evidence suggests that guard cells have higher rate of phosphoenolpyruvate carboxylase (PEPc)-mediated dark CO2 assimilation than mesophyll cells. However, it is unknown which metabolic pathways are activated following dark CO2 assimilation in guard cells. Furthermore, it remains unclear how the metabolic fluxes throughout the tricarboxylic acid (TCA) cycle and associated pathways are regulated in illuminated guard cells. Here we carried out a13C-HCO3 labelling experiment in tobacco guard cells harvested under continuous dark or during the dark-to-light transition to elucidate principles of metabolic dynamics downstream of CO2 assimilation. Most metabolic changes were similar between dark-exposed and illuminated guard cells. However, illumination altered the metabolic network structure of guard cells and increased the 13C-enrichment in sugars and metabolites associated to the TCA cycle. Sucrose was labelled in the dark, but light exposure increased the 13C-labelling and leads to more drastic reductions in the content of this metabolite. Fumarate was strongly labelled under both dark and light conditions, while illumination increased the 13C-enrichment in pyruvate, succinate and glutamate. Only one 13C was incorporated into malate and citrate in either dark or light conditions. Our results indicate that several metabolic pathways are redirected following PEPc-mediated CO2 assimilation in the dark, including gluconeogenesis and the TCA cycle. We further showed that the PEPc-mediated CO2 assimilation provides carbons for gluconeogenesis, the TCA cycle and glutamate synthesis and that previously stored malate and citrate are used to underpin the specific metabolic requirements of illuminated guard cells.

Exploring Exogenous Indole-3-acetic Acid's Effect on the Growth and Biochemical Profiles of Synechocystis sp. PAK13 and Chlorella variabilis

Microalgae have garnered scientific interest for their potential to produce bioactive compounds. However, the large-scale industrial utilization of microalgae faces challenges related to production costs and achieving optimal growth conditions. Thus, this study aimed to investigate the potential role of exogenous indole-3-acetic acid (IAA) application in improving the growth and production of bioactive metabolites in microalgae. To this end, the study employed different concentrations of exogenously administered IAA ranging from 0.36 µM to 5.69 µM to assess its influence on the growth and biochemical composition of Synechocystis and Chlorella. IAA exposure significantly increased IAA levels in both strains. Consequentially, improved biomass accumulation in parallel with increased total pigment content by approximately eleven-fold in both strains was observed. Furthermore, the application of IAA stimulated the accumulation of primary metabolites. Sugar levels were augmented, providing a carbon source that facilitated amino acid and fatty acid biosynthesis. As a result, amino acid levels were enhanced as well, leading to a 1.55-fold increase in total amino acid content in Synechocystis and a 1.42-fold increase in Chlorella. Total fatty acids content increased by 1.92-fold in Synechocystis and by 2.16-fold in Chlorella. Overall, the study demonstrated the effectiveness of exogenously adding IAA as a strategy for enhancing the accumulation of microalgae biomass and biomolecules. These findings contribute to the advancement of microalgae-based technologies, opening new avenues to produce economically important compounds derived from microalgae.

Virtual Cold Chain Method to Evaluate the Effect of Rising Temperature on the Quality Evolution of Peach Fruit

Poor temperature management along a cold chain leads to fruit quality deterioration and loss. In order to determine the threshold value of temperature fluctuation in a cold chain, peach fruits were stored in four different virtual cold chains applying different temperature-time scenarios. Core temperature profiling, the physicochemical qualities, and the activities of the peaches' antioxidant enzymes were monitored during cold storage and shelf life. Abusive temperature management (temperature increased to 20 and 15 °C three times) resulted in a significant increase in a peach's core temperature to the highest temperature measured: 17.6 °C. The ethylene production rate at the end of the shelf life of peaches under these temperatures was 21.03-28.16% higher than the constant-temperature group and accompanied by significantly lower levels of flesh firmness, titratable acid content, total phenol and flavonoid content, and peroxidase (POD) and catalase (CAT) activities (p < 0.05). The results of a principal component analysis (PCA) and heatmap confirmed the results. Limited temperature increases (10 °C) in a cold chain had little impact on the quality of the peaches, while temperature increases higher than 15 °C three times would negatively affect the quality of the peaches significantly. The temperature of a cold chain needs to be controlled precisely to reduce the loss of peaches.

Morphological and metabolomics profiling of intraspecific Arabidopsis hybrids in relation to biomass heterosis

Heterosis contributes greatly to the worldwide agricultural yield. However, the molecular mechanism underlying heterosis remains unclear. This study took advantage of Arabidopsis intraspecific hybrids to identify heterosis-related metabolites. Forty-six intraspecific hybrids were used to examine parental effects on seed area and germination time. The degree of heterosis was evaluated based on biomass: combinations showing high heterosis of F₁ hybrids exhibited a biomass increase from 6.1 to 44% over the better parent value (BPV), whereas that of the low- and no-heterosis hybrids ranged from - 19.8 to 9.8% over the BPV. Metabolomics analyses of F₁ hybrids with high heterosis and those with low one suggested that changes in TCA cycle intermediates are key factors that control growth. Notably, higher fumarate/malate ratios were observed in the high heterosis F₁ hybrids, suggesting they provide metabolic support associated with the increased biomass. These hybrids may produce more energy-intensive biomass by speeding up the efficiency of TCA fluxes. However, the expression levels of TCA-process-related genes in F₁ hybrids were not associated with the intensity of heterosis, suggesting that the post-transcriptional or post-translational regulation of these genes may affect the productivity of the intermediates in the TCA cycle.

Metabolomic analysis reveals astaxanthin biosynthesis in heterotrophic microalga Chromochloris zofingiensis

The utilization of gibberellic acid-3, high carbon/nitrogen ratio and salinity concentration can effectively enhance astaxanthin biosynthesis in Chromochloris zofingiensis under the heterotrophic conditions, but the underlying mechanisms remained yet to be investigated. The metabolomics analysis revealed that enhancement of the glycolysis, pentose phosphate pathways (PPP), and tricarboxylic acid (TCA) cycle led to astaxanthin accumulation under the induction conditions. The increased fatty acids can significantly increase astaxanthin esterification. The addition of appropriate concentrations of glycine (Gly) and γ-aminobutyric acid (GABA) promoted astaxanthin biosynthesis in C. zofingiensis, as well as benefiting for biomass yield. With the addition of 0.5 mM GABA, the astaxanthin yield increased to 0.35 g·L^-1, which was 1.97-fold higher than that of the control. This study advanced understanding about astaxanthin biosynthesis in heterotrophic microalga, and provided novel strategies for enhanced astaxanthin production in C. zofingiensis.

Comparative metabolomic profiling of Arabidopsis thaliana roots and leaves reveals complex response mechanisms induced by a seaweed extract

Seaweed extracts are a prominent class of biostimulants that enhance plant health and tolerance to biotic and abiotic stresses due to their unique bioactive components. However, the mechanisms of action of biostimulants are still unknown. Here, we have used a metabolomic approach, a UHPLC-MS method, to uncover the mechanisms induced following application to Arabidopsis thaliana of a seaweed extract derived from Durvillaea potatorum and Ascophyllum nodosum. We have identified, following the application of the extract, key metabolites and systemic responses in roots and leaves across 3 timepoints (0, 3, 5 days). Significant alterations in metabolite accumulation or reduction were found for those belonging to broad groups of compounds such as lipids, amino acids, and phytohormones; and secondary metabolites such as phenylpropanoids, glucosinolates, and organic acids. Strong accumulations of TCA cycle and N-containing and defensive metabolites such as glucosinolates were also found revealing the enhancement of carbon and nitrogen metabolism and defence systems. Our study has demonstrated that application of seaweed extract dramatically altered the metabolomic profiles of Arabidopsis and revealed differences in roots and leaves that varied across the timepoints tested. We also show clear evidence of systemic responses that were initiated in the roots and resulted in metabolic alterations in the leaves. Collectively, our results suggest that this seaweed extract promotes plant growth and activates defence systems by altering various physiological processes at the individual metabolite level.

Integrated metabolite analysis and health-relevant in vitro functionality of white, red, and orange maize (Zea mays L.) from the Peruvian Andean race Cabanita at different maturity stages

The high maize (Zea mays L.) diversity in Peru has been recognized worldwide, but the investigation focused on its integral health-relevant and bioactive characterization is limited. Therefore, this research aimed at studying the variability of the primary and the secondary (free and dietary fiber-bound phenolic, and carotenoid compounds) metabolites of three maize types (white, red, and orange) from the Peruvian Andean race Cabanita at different maturity stages (milk-S1, dough-S2, and mature-S3) using targeted and untargeted methods. In addition, their antioxidant potential, and α-amylase and α-glucosidase inhibitory activities relevant for hyperglycemia management were investigated using in vitro models. Results revealed a high effect of the maize type and the maturity stage. All maize types had hydroxybenzoic and hydroxycinnamic acids in their free phenolic fractions, whereas major bound phenolic compounds were ferulic acid, ferulic acid derivatives, and p-coumaric acid. Flavonoids such as luteolin derivatives and anthocyanins were specific in the orange and red maize, respectively. The orange and red groups showed higher phenolic ranges (free + bound) (223.9-274.4 mg/100 g DW, 193.4- 229.8 mg/100 g DW for the orange and red maize, respectively) than the white maize (162.2-225.0 mg/100 g DW). Xanthophylls (lutein, zeaxanthin, neoxanthin, and a lutein isomer) were detected in all maize types. However, the orange maize showed the highest total carotenoid contents (3.19-5.87 μg/g DW). Most phenolic and carotenoid compounds decreased with kernel maturity in all cases. In relation to the primary metabolites, all maize types had similar fatty acid contents (linoleic acid > oleic acid > palmitic acid > α-linolenic acid > stearic acid) which increased with kernel development. Simple sugars, alcohols, amino acids, free fatty acids, organic acids, amines, and phytosterols declined along with grain maturity and were overall more abundant in white maize at S1. The in vitro functionality was similar among Cabanita maize types, but it decreased with the grain development, and showed a high correlation with the hydrophilic free phenolic fraction. Current results suggest that the nutraceutical characteristics of orange and white Cabanita maize are better at S1 and S2 stages while the red maize would be more beneficial at S3.

Desiccation Stress Tolerance in Porphyra and Pyropia Species: A Latitudinal Analysis along the Chilean Coast

One of the most important factors regulating the distribution and abundance of seaweeds is desiccation, triggered mainly by tidal changes and climatic variation. Porphyra and Pyropia species have evolved multiple strategies to tolerate desiccation stress; however, how these tolerance strategies differ in these species inhabiting different latitudes is still unknown. In this context, we analyzed, in situ, the physiological responses of these species (collected from 18° S to 41° S along the Chilean coast) to desiccation stress using biochemical and molecular analyses. The hyper-arid terrestrial climate of northern Chile, with high evaporation and lack of constant rain determines a very steep increase in desiccation stress in the upper intertidal during low tide for these species. Accordingly, the results showed that, in comparison with the southernmost populations, the Porphyra/Pyropia species from the north zone of Chile (18°-30° S) exhibited higher contents of lipoperoxide and carbonyls (1.6-1.9 fold) together with higher enzymatic activities, including ascorbate peroxidase, catalase, peroxiredoxin, and thioredoxin (2-3-fold). In addition, a substantial expression of cat, prx, and trx transcripts during desiccation was demonstrated, mainly in the northernmost populations. These results provide evidence of (i) significant activation of antioxidant enzymes and transcripts (principally cat and prx); (ii) participation of phenolic antioxidant compounds as a highly plastic physiological strategy to cope with desiccation; and (iii) the activation of the tolerance responses was affected by species latitudinal distribution. Thus, for the first time, this study integrated the biochemical and genetic responses of diverse Porphyra/Pyropia species to better understand their physiological dynamics of tolerance over a wide latitudinal range.

Changes in Metabolic Profile of Rice Leaves Induced by Humic Acids

The use of humic substances in agriculture as a biostimulant emerged as one of the promising methods to promote sustainable production. Different molecular, biochemical, and physiological processes are triggered, resulting in nutrient efficiency use and protection against abiotic stress. Understanding plant changes promoted by humic substances is essential for innovative and tailored biostimulation technologies. Cell metabolites are the final target of the response chain, and the metabolomic approach can be helpful in unveiling pathways related to plant response. This study aimed to evaluate a global metabolic alteration of rice leaves induced by humic acids (HA) applied in a hydroponics system. Using ¹H NMR and GC-TOF/MS analysis, we observed a significant decrease in all main metabolites classes in leaves treated with HA, including lipids, organic acids, amino acids, and carbohydrates. Metabolites in higher concentrations in HA-treated plants are candidates as markers of HA bioactivity, including amino acids, intermediates of tricarboxylic acid cycle, and lipids, and aromatic compounds related to plant-stress response.

Self-regulation mechanism difference of Chlorella vulgaris and Scenedesmus obliquus in toxic sludge extract caused by hydroquinone biodegradation

Chlorella vulgaris (C. vulgaris) and Scenedesmus obliquus (S. obliquus) were compared to remove toxicity under conditions of sludge extract cultivation for 30 days. The toxicity of sludge extract, the growth characteristics, photosynthetic pigment, superoxide dismutase (SOD) enzyme and catalase (CAT) enzyme activities of the two microalgae were studied by contrast. The results showed that small molecular organic matter (<500 Da) was more easily utilized by microalgae. The toxicity in the toxic group of C. vulgaris and S. obliquus on the 30^th day decreased to 56.8 ± 1.2% and 60.7 ± 2.8%, respectively. In the toxic group, the maximal SOD enzyme activity of C. vulgaris and S. obliquus were 2.02 U/mg proteins and 8.21 U/mg proteins, respectively, demonstrating that toxicity caused more oxidative damage to S. obliquus than to C. vulgaris. Proteomics analysis revealed that C. vulgaris mainly regulates energy synthesis and distribution primarily through sugar metabolism, and biomass synthesis primarily through carbon metabolism, whereas S. obliquus mainly regulates energy synthesis and distribution primarily through sugar metabolism and oxidative phosphorylation, resulting in sludge toxicity stress regulation.

Physiological and protein profiling analysis provides insight into the underlying molecular mechanism of potato tuber development regulated by jasmonic acid in vitro

BACKGROUND

Jasmonates (JAs) are one of important phytohormones regulating potato tuber development. It is a complex process and the underlying molecular mechanism regulating tuber development by JAs is still limited. This study attempted to illuminate it through the potential proteomic dynamics information about tuber development in vitro regulated by exogenous JA.

RESULTS

A combined analysis of physiological and iTRAQ (isobaric tags for relative and absolute quantification)-based proteomic approach was performed in tuber development in vitro under exogenous JA treatments (0, 0.5, 5 and 50 μΜ). Physiological results indicated that low JA concentration (especially 5 μM) promoted tuber development, whereas higher JA concentration (50 μM) showed inhibition effect. A total of 257 differentially expressed proteins (DEPs) were identified by iTRAQ, which provided a comprehensive overview on the functional protein profile changes of tuber development regulated by JA. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that low JA concentration (especially 5 μM) exhibited the promotion effects on tuber development in various cellular processes. Some cell wall polysaccharide synthesis and cytoskeleton formation-related proteins were up-regulated by JA to promote tuber cell expansion. Some primary carbon metabolism-related enzymes were up-regulated by JA to provide sufficient metabolism intermediates and energy for tuber development. And, a large number of protein biosynthesis, degradation and assembly-related were up-regulated by JA to promote tuber protein biosynthesis and maintain strict protein quality control during tuber development.

CONCLUSIONS

This study is the first to integrate physiological and proteomic data to provide useful information about the JA-signaling response mechanism of potato tuber development in vitro. The results revealed that the levels of a number of proteins involved in various cellular processes were regulated by JA during tuber development. The proposed hypothetical model would explain the interaction of these DEPs that associated with tuber development in vitro regulated by JA.

Genetic and Biochemical Investigation of Seed Fatty Acid Accumulation in Arabidopsis

As a vegetable oil, consisting principally of triacylglycerols, is the major storage form of photosynthetically-fixed carbon in oilseeds which are of significant agricultural and industrial value. Photosynthesis in chlorophyll-containing green seeds, along with photosynthesis in leaves and other green organs, generates ATP and reductant (NADPH and NADH) needed for seed fatty acid production. However, contribution of seed photosynthesis to fatty acid accumulation in seeds have not been well-defined. Here, we report the contribution of seed-photosynthesis to fatty acid production by probing segregating green (photosynthetically-competent) and non-green or yellow (photosynthetically-non-competent) seeds in siliques of an Arabidopsis chlorophyll synthase mutant. Using this mutant, we found that yellow seeds lacking photosynthetic capacity reached 80% of amounts of oil in green seeds at maturity. Combining this with studies using shaded siliques, we determined that seed-photosynthesis accounts for 20% and silique and leaf/stem photosynthesis each account for ~40% of the ATP and reductant for seed oil production. Transmission electron microscopy (TEM) and pyridine nucleotides and ATP analyses revealed that seed photosynthesis provides ATP and reductant for oil production mostly during early development, as evidenced by delayed oil accumulation in non-green seeds. Transcriptomic analyses suggests that the oxidative pentose phosphate pathway could be the source of carbon, energy and reductants required for fatty acid synthesis beyond the early stages of seed development.

Genome and transcriptome analysis of rock-dissolving Pseudomonas sp. NLX-4 strain

Microbial weathering processes can significantly promote soil properties and reduce rock-to-soil ratio. Some soil-inhabiting bacteria exhibit efficient rock-dissolution abilities by releasing organic acids and other chemical elements from the silicate rocks. However, our understanding of the molecular mechanisms involved during bacterial rock-dissolution is still limited. In this study, we performed silicate rock-dissolution experiments on a Pseudomonas sp. NLX-4 strain isolated from an over-exploited mining site. The results revealed that Pseudomonas sp. NLX-4 strain efficiently accelerates the dissolution of silicate rocks by secreting amino acids, exopolysaccharides, and organic acids. Through employing genome and transcriptome sequencing (RNA-seq), we identified the major regulatory genes. Specifically, 15 differentially expressed genes (DEGs) encoding for siderophore transport, EPS and amino acids synthesis, organic acids metabolism, and bacterial resistance to adverse environmental conditions were highly up-regulated in silicate rock cultures of NLX-4 strain. Our study reports a potential bacterial based approach for improving the ecological restoration of over-exploited rock mining sites.

Can biochemical traits bridge the gap between genomics and plant performance? A study in rice under drought

The possibility of introducing metabolic/biochemical phenotyping to complement genomics-based predictions in breeding pipelines has been considered for years. Here we examine to what extent and under what environmental conditions metabolic/biochemical traits can effectively contribute to understanding and predicting plant performance. In this study, multivariable statistical models based on flag leaf central metabolism and oxidative stress status were used to predict grain yield (GY) performance for 271 indica rice (Oryza sativa) accessions grown in the field under well-watered and reproductive stage drought conditions. The resulting models displayed significantly higher predictability than multivariable models based on genomic data for the prediction of GY under drought (Q2 = 0.54-0.56 versus 0.35) and for stress-induced GY loss (Q2 = 0.59-0.64 versus 0.03-0.06). Models based on the combined datasets showed predictabilities similar to metabolic/biochemical-based models alone. In contrast to genetic markers, models with enzyme activities and metabolite values also quantitatively integrated the effect of physiological differences such as plant height on GY. The models highlighted antioxidant enzymes of the ascorbate-glutathione cycle and a lipid oxidation stress marker as important predictors of rice GY stability under drought at the reproductive stage, and these stress-related variables were more predictive than leaf central metabolites. These findings provide evidence that metabolic/biochemical traits can integrate dynamic cellular and physiological responses to the environment and can help bridge the gap between the genome and the phenome of crops as predictors of GY performance under drought.

Metabolic and DNA checkpoints for the enhancement of Al tolerance

Acidic soils are a major limiting factor for food production in many developing countries. High concentrations of soluble Al cations, particularly Al³⁺, inhibit cell division and root elongation in plants. Al³⁺ damages several biomolecules, including DNA, impairing gene expression and cell cycle progression. Notably, the loss-of-function mutants of DNA checkpoints may mediate Al tolerance. Furthermore, mitochondrial organic acids play key roles in neutralizing Al³⁺ within the cell and around the rhizosphere. Here, we provide knowledge synthesis on interactions between checkpoints related to mitochondrial organic acid homeostasis and DNA integrity mediating Al tolerance in land plants. These interactions, coupled with remarkable advances in tools related to metabolism and cell cycle, may facilitate the development of next-generation productive crops under Al toxicity.

Transcriptome changes in the developing sugarcane culm associated with high yield and early-season high sugar content

Sugarcane, with its exceptional carbon dioxide assimilation, biomass and sugar yield, has a high potential for the production of bio-energy, bio-plastics and high-value products in the food and pharmaceutical industries. A crucial challenge for long-term economic viability and environmental sustainability is also to optimize the production of biomass composition and carbon sequestration. Sugarcane varieties such as KQ228 and Q253 are highly utilized in the industry. These varieties are characterized by a high early-season sugar content associated with high yield. In order to investigate these correlations, 1,440 internodes were collected and combined to generate a set of 120 samples in triplicate across 24 sugarcane cultivars at five different development stages. Weighted gene co-expression network analysis (WGCNA) was used and revealed for the first time two sets of co-expressed genes with a distinct and opposite correlation between fibre and sugar content. Gene identification and metabolism pathways analysis was used to define these two sets of genes. Correlation analysis identified a large number of interconnected metabolic pathways linked to sugar content and fibre content. Unsupervised hierarchical clustering of gene expression revealed a stronger level of segregation associated with the genotypes than the stage of development, suggesting a dominant genetic influence on biomass composition and facilitating breeding selection. Characterization of these two groups of co-expressed key genes can help to improve breeding program for high fibre, high sugar species or plant synthetic biology.

GWAS on multiple traits identifies mitochondrial ACONITASE3 as important for acclimation to submergence stress

Flooding causes severe crop losses in many parts of the world. Genetic variation in flooding tolerance exists in many species; however, there are few examples for the identification of tolerance genes and their underlying function. We conducted a genome-wide association study (GWAS) in 387 Arabidopsis (Arabidopsis thaliana) accessions. Plants were subjected to prolonged submergence followed by desubmergence, and seven traits (score, water content, Fv/Fm, and concentrations of nitrate, chlorophyll, protein, and starch) were quantified to characterize their acclimation responses. These traits showed substantial variation across the range of accessions. A total of 35 highly significant single-nucleotide polymorphisms (SNPs) were identified across the 20 GWA datasets, pointing to 22 candidate genes, with functions in TCA cycle, DNA modification, and cell division. Detailed functional characterization of one candidate gene, ACONITASE3 (ACO3), was performed. Chromatin immunoprecipitation followed by sequencing showed that a single nucleotide polymorphism in the ACO3 promoter co-located with the binding site of the master regulator of retrograde signaling ANAC017, while subcellular localization of an ACO3-YFP fusion protein confirmed a mitochondrial localization during submergence. Analysis of mutant and overexpression lines determined changes in trait parameters that correlated with altered submergence tolerance and were consistent with the GWAS results. Subsequent RNA-seq experiments suggested that impairing ACO3 function increases the sensitivity to submergence by altering ethylene signaling, whereas ACO3 overexpression leads to tolerance by metabolic priming. These results indicate that ACO3 impacts submergence tolerance through integration of carbon and nitrogen metabolism via the mitochondrial TCA cycle and impacts stress signaling during acclimation to stress.

Metabolites in Cherry Buds to Detect Winter Dormancy

Winter dormancy is still a “black box” in phenological models, because it evades simple observation. This study presents the first step in the identification of suitable metabolites which could indicate the timing and length of dormancy phases for the sweet cherry cultivar ‘Summit’. Global metabolite profiling detected 445 named metabolites in flower buds, which can be assigned to different substance groups such as amino acids, carbohydrates, phytohormones, lipids, nucleotides, peptides and some secondary metabolites. During the phases of endo- and ecodormancy, the energy metabolism in the form of glycolysis and the tricarboxylic acid (TCA) cycle was shut down to a minimum. However, the beginning of ontogenetic development was closely related to the up-regulation of the carbohydrate metabolism and thus to the generation of energy for the growth and development of the sweet cherry buds. From the 445 metabolites found in cherry buds, seven were selected which could be suitable markers for the ecodormancy phase, whose duration is limited by the date of endodormancy release (t₁) and the beginning of ontogenetic development (t₁*). With the exception of abscisic acid (ABA), which has been proven to control bud dormancy, all of these metabolites show nearly constant intensity during this phase.

Enhancement of astaxanthin accumulation in Haematococcus pluvialis by exogenous oxaloacetate combined with nitrogen deficiency

Effective inducers and stress conditions play an essential role in the regulation of astaxanthin biosynthesis. This study reports a strategy developed by combining exogenous addition of oxaloacetate (OA) with nitrogen deficiency to facilitate astaxanthin production in Haematococcus pluvialis. Significantly, addition of 10 mM-OA enhanced the cellular astaxanthin content about 7.18-fold under nitrogen deficiency on day 7, with the content of astaxanthin esters increased concomitantly. To further elucidate the role and mechanism of OA on astaxanthin synthesis, the physiological and metabolic analyses of H. pluvialis treated with exogenous OA were performed. The results showed that exogenous OA promoted respiration over photosynthesis. Concurrently, the metabolite levels in the Embden-Meyerhof-Parnas pathway, pentose phosphate pathway and tricarboxylic acid cycle obviously increased. The enhancement of respiratory metabolic pathways led to elevated levels of substrates, thus directly promoted astaxanthin synthesis. The present findings provide a new and effective approach for optimizing astaxanthin production.

Differential Physiological, Transcriptomic, and Metabolomic Responses of Paspalum wettsteinii Under High-Temperature Stress

Global warming has far-reaching effects on plant growth and development. As a warm-season forage grass, Paspalum wettsteinii is highly adaptable to high temperatures. However, the response mechanism of P. wettsteinii under high-temperature stress is still unclear. Therefore, we investigated the physiological indicators, transcriptome and metabolome of P. wettsteinii under different heat stress treatments. Plant height, the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), and the contents of soluble sugar, proline, chlorophyll a, and chlorophyll b increased and then decreased, while the malondialdehyde (MDA) content decreased and then increased with increasing heat stress. Transcriptomic analysis revealed that genes related to energy and carbohydrate metabolism, heat shock proteins (HSPs), and transcription factors (TFs), secondary metabolite biosynthesis and the antioxidant system significantly changed to varying degrees. Metabolomic analysis showed that only free fatty acids were downregulated, while amino acids and their derivatives, organic acids, flavonoids, and sugars were both up- and downregulated under heat stress. These combined analyses revealed that growth was promoted at 25-40°C, while at 45°C, excess reactive oxygen species (ROS) damage reduced antioxidant and osmoregulatory effects and inactivated genes associated with the light and electron transport chains (ETCs), as well as damaged the PS II system and inhibited photosynthesis. A small number of genes and metabolites were upregulated to maintain the basic growth of P. wettsteinii. The physiological and biochemical changes in response to high-temperature stress were revealed, and the important metabolites and key genes involved in the response to high temperature were identified, providing an important reference for the physiological and molecular regulation of high-temperature stress in plants.

Mitochondrial proteomic analysis reveals the regulation of energy metabolism and reactive oxygen species production in Clematis terniflora DC. leaves under high-level UV-B radiation followed by dark treatment

Clematis terniflora DC. is an important medicinal plant from the family Ranunculaceae. A previous study has shown that active ingredients in C. terniflora, such as flavonoids and coumarins, are increased under ultraviolet B radiation (UV-B) and dark treatment and that the numbers of genes related to the tricarboxylic acid cycle and mitochondrial electron transport chain (mETC) are changed. To uncover the mechanism of the response to UV-B radiation and dark treatment in C. terniflora, mitochondrial proteomics was performed. The results showed that proteins related to photorespiration, mitochondrial membrane permeability, the tricarboxylic acid cycle, and the mETC mainly showed differential expression profiles. Moreover, the increase in alternative oxidase indicated that another oxygen-consuming respiratory pathway in plant mitochondria was induced to minimize mitochondrial reactive oxygen species production. These results suggested that respiration and mitochondrial membrane permeability were deeply influenced to avoid energy consumption and maintain energy balance under UV-B radiation and dark treatment in C. terniflora leaf mitochondria. Furthermore, oxidative phosphorylation was able to regulate intracellular oxygen balance to resist oxidative stress. This study improves understanding of the function of mitochondria in response to UV-B radiation and dark treatment in C. terniflora. SIGNIFICANCE: C. terniflora was an important traditional Chinese medicine for anti-inflammatory. Previous study showed that the contents of coumarins which were the main active ingredient in C. terniflora were induced by UV-B radiation and dark treatment. In the present study, to uncover the regulatory mechanism of metabolic changes in C. terniflora, mitochondrial proteomics analysis of leaves was performed. The results showed that photorespiration and oxidative phosphorylation pathways were influenced under UV-B radiation and dark treatment. Mitochondria in C. terniflora leaf played a crucial role in energy mechanism and regulation of cellular oxidation-reduction to maintain cell homeostasis under UV-B radiation followed with dark treatment.

Impact of Potassium Pre-Harvest Applications on Fruit Quality and Condition of Sweet Cherry (Prunus avium L.) Cultivated under Plastic Covers in Southern Chile Orchards

In rainy locations, sweet cherry is cultivated under plastic covers, which are useful to prevent fruit cracking but decrease cherry quality such as firmness and acidity. Here we evaluate the impact of pre-harvest K foliar applications on harvest and post-harvest fruit quality and condition of sweet cherry cultivated under plastic covers in southern Chile orchards. The study was performed on two commercial orchards (cv. Regina), located in different regions, during two consecutive seasons. In all cases, a conventional K regime (four sprays) was compared to an intensive K regimen (seven sprays). Results showed that cherries from the most southern region revealed lower acidity but higher soluble solids content weight and size. The intensive K regime improved the firmness and acidity of fruits of covered trees at harvest and post-harvest. Moreover, we found that condition defects were higher in fruits from un-covered trees and that trees grown under intensive K regime showed lower levels of cracking at harvest and pitting at post-harvest compared to trees treated with the conventional K regime. Otherwise, pedicel browning was inconsistently affected by K sprays. Our results revealed that an intensive K regime could improve the quality and condition of fruits at harvest and post-harvest in covered orchards of sweet cherry cv. Regina; however, the impacts can significantly vary depending on season and locality.

Exogenous sodium fumarate enhances astaxanthin accumulation in Haematococcus pluvialis by enhancing the respiratory metabolic pathway

Improvement of astaxanthin yield is a continuing objective in Haematococcus pluvialis cultivation. In this study, a new strategy combining exogenous sodium fumarate (SF) with nitrogen deficiency was demonstrated to promote astaxanthin accumulation in H. pluvialis. SF significantly accelerated astaxanthin synthesis over cell growth. Notably, under nitrogen deficiency, 10 mM SF increased the cellular astaxanthin content by 1.75-fold and 1.47-fold on day 7 and 12, respectively. Further studies indicated that SF increased the level of respiratory metabolites in the Embden-Meyerhof-Parnas pathway, tricarboxylic acid cycle and pentose phosphate pathway. An enhanced substrate pool due to the acceleration of respiratory metabolic pathways directly induced astaxanthin synthesis. Meanwhile, the accumulation of C18:1, C18:2 and C18:3 fatty acids enhanced astaxanthin synthesis indirectly by promoting the process of esterification. This study not only helps to elucidate the role of respiratory metabolic pathways in astaxanthin synthesis but also provides a new effective technique to improve astaxanthin production.

Comparative genomic analysis of the tricarboxylic acid cycle members in four Solanaceae vegetable crops and expression pattern analysis in Solanum tuberosum

Background

The tricarboxylic acid (TCA) cycle is crucial for energy supply in animal, plant, and microbial cells. It is not only the main pathway of carbohydrate catabolism but also the final pathway of lipid and protein catabolism. Some TCA genes have been found to play important roles in the growth and development of tomato and potato, but no comprehensive study of TCA cycle genes in Solanaceae crops has been reported.

Results

In this study, we analyzed TCA cycle genes in four important Solanaceae vegetable crops (potato (Solanum tuberosum), tomato (Solanum lycopersicum), eggplant (Solanum melongena), and pepper (Capsicum annuum)) based on comparative genomics. The four Solanaceae crops had a total of 180 TCA cycle genes: 43 in potato, 44 in tomato, 40 in eggplant, and 53 in pepper. Phylogenetic analysis, collinearity analysis, and tissue expression patterns revealed the conservation of and differences in TCA cycle genes between the four Solanaceae crops and found that there were unique subgroup members in Solanaceae crops that were independent of Arabidopsis genes. The expression analysis of potato TCA cycle genes showed that (1) they were widely expressed in various tissues, and some transcripts like Soltu.DM.01G003320.1(SCoAL) and Soltu.DM.04G021520.1 (SDH) mainly accumulate in vegetative organs, and some transcripts such as Soltu.DM.12G005620.3 (SDH) and Soltu.DM.02G007400.4 (MDH) are preferentially expressed in reproductive organs; (2) several transcripts can be significantly induced by hormones, such as Soltu.DM.08G023870.2 (IDH) and Soltu.DM.06G029290.1 (SDH) under ABA treatment, and Soltu.DM.07G021850.2 (CSY) and Soltu.DM.09G026740.1 (MDH) under BAP treatment, and Soltu.DM.02G000940.1 (IDH) and Soltu.DM.01G031350.4 (MDH) under GA treatment; (3) Soltu.DM.11G024650.1 (SDH) can be upregulated by the three disease resistance inducers including Phytophthora infestans, acibenzolar-S-methyl (BTH), and DL-β-amino-n-butyric acid (BABA); and (4) the levels of Soltu.DM.01G045790.1 (MDH), Soltu.DM.01G028520.3 (CSY), and Soltu.DM.12G028700.1 (CSY) can be activated by both NaCl and mannitol. The subcellular localization results of three potato citrate synthases showed that Soltu.DM.01G028520.3 was localized in mitochondria, while Soltu.DM.12G028700.1 and Soltu.DM.07G021850.1 were localized in the cytoplasm.

Conclusions

This study provides a scientific foundation for the comprehensive understanding and functional studies of TCA cycle genes in Solanaceae crops and reveals their potential roles in potato growth, development, and stress response.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08109-9.

Metabolomics Analyses Reveal Metabolites Affected by Plant Growth-Promoting Endophytic Bacteria in Roots of the Halophyte Mesembryanthemum crystallinum

Mesembryanthemum crystallinum L. (common ice plant) is an edible halophyte. However, if ice plants are used to phytoremediate salinity soil, there are problems of slow initial growth, and a long period before active NaCl uptake occurs under higher salinity conditions. Application of endophytic bacteria may improve the problem, but there remain gaps in our understanding of how endophytic bacteria affect the growth and the biochemical and physiological characteristics of ice plants. The aims of this study were to identify growth-promoting endophytic bacteria from the roots of ice plants and to document the metabolomic response of ice plants after application of selected endophytic bacteria. Two plant growth-promoting endophytic bacteria were selected on the basis of their ability to promote ice plant growth. The two strains putatively identified as Microbacterium spp. and Streptomyces spp. significantly promoted ice plant growth, at 2-times and 2.5-times, respectively, compared with the control and also affected the metabolome of ice plants. The strain of Microbacterium spp. resulted in increased contents of metabolites related to the tricarboxylic acid cycle and photosynthesis. The effects of salt stress were alleviated in ice plants inoculated with the endobacterial strains, compared with uninoculated plants. A deeper understanding of the complex interplay among plant metabolites will be useful for developing microbe-assisted soil phytoremediation strategies, using Mesembryanthemum species.

Use Chou's 5-steps rule to identify protein post-translational modification and its linkage to secondary metabolism during the floral development of Lonicera japonica Thunb

Lonicera japonica Thunb. is widely used in traditional medicine systems of East Asian and attracts a large amount of studies on the biosynthesis of its active components. Currently, there is little understanding regarding the regulatory mechanisms behind the accumulation of secondary metabolites during its developmental stages. In this study, published transcriptomic and proteomic data were mined to evaluate potential linkage between protein modification and secondary metabolism during the floral development. Stronger correlations were observed between differentially expressed genes (DEGs) and their corresponding differentially abundant proteins (DAPs) in the comparison of juvenile bud stage (JBS)/third green stage (TGS) vs. silver flowering stage (SFS). Seventy-five and 76 cor-rDEGs and cor-rDAPs (CDDs) showed opposite trends at both transcriptional and translational levels when comparing their levels at JBS and TGS relative to those at SFS. CDDs were mainly involved in elements belonging to the protein metabolism and the TCA cycle. Protein-protein interaction analysis indicated that the interacting proteins in the major cluster were primarily involved in TCA cycle and protein metabolism. In the simple phenylpropanoids biosynthetic pathway of SFS, both phospho-2-dehydro-3-deoxyheptonate aldolase (PDA) and glutamate/aspartate-prephenate aminotransferase (AAT) were decreased at the protein level, but increased at the gene level. A confirmatory experiment indicated that protein ubiquitination and succinylation were more prominent during the early floral developmental stages, in correlation with simple phenylpropanoids accumulation. Taken together, those data indicates that phenylpropanoids metabolism and floral development are putatively regulated through the ubiquitination and succinylation modifications of PDA, AAT, and TCA cycle proteins in L. japonica.

Downregulation of the E2 Subunit of 2-Oxoglutarate Dehydrogenase Modulates Plant Growth by Impacting Carbon-Nitrogen Metabolism in Arabidopsis thaliana

In Arabidopsis thaliana, two genes encode the E2 subunit of the 2-oxoglutarate dehydrogenase (2-OGDH), a multimeric complex composed of three subunits. To functionally characterize the isoforms of E2 subunit, we isolated Arabidopsis mutant lines for each gene encoding the E2 subunit and performed a detailed molecular and physiological characterization of the plants under controlled growth conditions. The functional lack of expression of E2 subunit isoforms of 2-OGDH increased plant growth, reduced dark respiration and altered carbohydrate metabolism without changes in the photosynthetic rate. Interestingly, plants from e2-ogdh lines also exhibited reduced seed weight without alterations in total seed number. We additionally observed that downregulation of 2-OGDH activity led to minor changes in the levels of tricarboxylic acid cycle intermediates without clear correlation with the reduced expression of specific E2-OGDH isoforms. Furthermore, the e2-ogdh mutant lines exhibited a reduction by up to 25% in the leaf total amino acids without consistent changes in the amino acid profile. Taken together, our results indicate that the two isoforms of E2 subunit play a similar role in carbon-nitrogen metabolism, in plant growth and in seed weight.

Thioredoxin-mediated regulation of (photo)respiration and central metabolism

Thioredoxins (TRXs) are ubiquitous proteins engaged in the redox regulation of plant metabolism. Whilst the light-dependent TRX-mediated activation of Calvin-Benson cycle enzymes is well documented, the role of extraplastidial TRXs in the control of the mitochondrial (photo)respiratory metabolism has been revealed relatively recently. Mitochondrially located TRX o1 has been identified as a regulator of alternative oxidase, enzymes of, or associated with, the tricarboxylic acid (TCA) cycle, and the mitochondrial dihydrolipoamide dehydrogenase (mtLPD) involved in photorespiration, the TCA cycle, and the degradation of branched chain amino acids. TRXs are seemingly a major point of metabolic regulation responsible for activating photosynthesis and adjusting mitochondrial photorespiratory metabolism according to the prevailing cellular redox status. Furthermore, TRX-mediated (de)activation of TCA cycle enzymes contributes to explain the non-cyclic flux mode of operation of this cycle in illuminated leaves. Here we provide an overview on the decisive role of TRXs in the coordination of mitochondrial metabolism in the light and provide in silico evidence for other redox-regulated photorespiratory enzymes. We further discuss the consequences of mtLPD regulation beyond photorespiration and provide outstanding questions that should be addressed in future studies to improve our understanding of the role of TRXs in the regulation of central metabolism.

The mitochondrial pyruvate carrier (MPC) complex mediates one of three pyruvate-supplying pathways that sustain Arabidopsis respiratory metabolism

Malate oxidation by plant mitochondria enables the generation of both oxaloacetate and pyruvate for tricarboxylic acid (TCA) cycle function, potentially eliminating the need for pyruvate transport into mitochondria in plants. Here, we show that the absence of the mitochondrial pyruvate carrier 1 (MPC1) causes the co-commitment loss of its putative orthologs, MPC3/MPC4, and eliminates pyruvate transport into Arabidopsis thaliana mitochondria, proving it is essential for MPC complex function. While the loss of either MPC or mitochondrial pyruvate-generating NAD-malic enzyme (NAD-ME) did not cause vegetative phenotypes, the lack of both reduced plant growth and caused an increase in cellular pyruvate levels, indicating a block in respiratory metabolism, and elevated the levels of branched-chain amino acids at night, a sign of alterative substrate provision for respiration. 13C-pyruvate feeding of leaves lacking MPC showed metabolic homeostasis was largely maintained except for alanine and glutamate, indicating that transamination contributes to the restoration of the metabolic network to an operating equilibrium by delivering pyruvate independently of MPC into the matrix. Inhibition of alanine aminotransferases when MPC1 is absent resulted in extremely retarded phenotypes in Arabidopsis, suggesting all pyruvate-supplying enzymes work synergistically to support the TCA cycle for sustained plant growth.

Stress response of lettuce (Lactuca sativa) to environmental contamination with selected pharmaceuticals: A proteomic study

Pharmaceutical compounds have been found in rivers and treated wastewaters. They often contaminate irrigation waters and consequently accumulate in edible vegetables, causing changes in plants metabolism. The main objective of this work is to understand how lettuce plants cope with the contamination from three selected pharmaceuticals using a label free proteomic analysis. A lettuce hydroponic culture, grown for 36 days, was exposed to metformin, acetaminophen and carbamazepine (at 1 mg/L), during 8 days, after which roots and leaves were sampled and analysed using a liquid chromatography-mass spectrometry proteomics-based approach. In roots, a total of 612 proteins showed differentially accumulation while in leaves 237 proteins were identified with significant differences over controls. Carbamazepine was the contaminant that most affected protein abundance in roots, while in leaves the highest number of differentially accumulated proteins was observed for acetaminophen. In roots under carbamazepine, stress related protein species such as catalase, superoxide dismutase and peroxidases presented higher abundance. Ascorbate peroxidase increased in roots under metformin. Cell respiration protein species were affected by the presence of the three pharmaceuticals suggesting possible dysregulation of the Krebs cycle. Acetaminophen caused the main differences in respiration pathways, with more emphasis in leaves. Lettuce plants revealed different tolerance levels when contaminants were compared, being more tolerant to metformin presence and less tolerant to carbamazepine. SIGNIFICANCE: The significant increase of emerging contaminants in ecosystems makes essential to understand how these compounds may affect the metabolism of different organisms. Our study contributes with a detailed approach of the main interactions that may occur in plant metabolism when subjected to the stress induced by three different pharmaceuticals (acetaminophen, carbamazepine and metformin).

Two mitochondrial phosphatases, PP2c63 and Sal2, are required for posttranslational regulation of the TCA cycle in Arabidopsis

Protein phosphorylation is a well-established post-translational mechanism that regulates protein functions and metabolic pathways. It is known that several plant mitochondrial proteins are phosphorylated in a reversible manner. However, the identities of the protein kinases/phosphatases involved in this mechanism and their roles in the regulation of the tricarboxylic acid (TCA) cycle remain unclear. In this study, we isolated and characterized plants lacking two mitochondrially targeted phosphatases (Sal2 and PP2c63) along with pyruvate dehydrogenase kinase (PDK). Protein-protein interaction analysis, quantitative phosphoproteomics, and enzymatic analyses revealed that PDK specifically regulates pyruvate dehydrogenase complex (PDC), while PP2c63 nonspecifically regulates PDC. When recombinant PP2c63 and Sal2 proteins were added to mitochondria isolated from mutant plants, protein-protein interaction and enzymatic analyses showed that PP2c63 directly phosphorylates and modulates the activity of PDC, while Sal2 only indirectly affects TCA cycle enzymes. Characterization of steady-state metabolite levels and fluxes in the mutant lines further revealed that these phosphatases regulate flux through the TCA cycle, and that altered metabolism in the sal2 pp2c63 double mutant compromises plant growth. These results are discussed in the context of current models of the control of respiration in plants.