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

Harnessing the dynamics of plant organic acids metabolism following abiotic stresses

Plants encounter various environmental stresses throughout development, including shade, high light, drought, hypoxia, extreme temperatures, and metal toxicity, all of which adversely affect growth and productivity. Organic acids (OAs), besides serving as intermediates in the tricarboxylic acid (TCA) cycle, play crucial roles in multiple metabolic pathways and cellular compartments, including mitochondrial metabolism, amino acid metabolism, the glyoxylate cycle, and the photosynthetic mechanisms of C4 and CAM plants. OAs contribute to stress tolerance by acting as root chelating agents, regulating ATP production, and providing reducing power for detoxifying reactive oxygen species (ROS). They also participate in the biosynthesis of solutes involved in stress signaling and osmoregulation, particularly during stomatal movements. This review explores how OAs regulate plant metabolism in response to specific abiotic stresses, emphasizing the increased production of malate, citrate, and succinate, which enhance resilience to water deficits, metal toxicity, and flooding. Since these mechanisms involve intricate metabolic networks, changes in OA metabolism present promising and underexplored potential for agriculture. Understanding these mechanisms could lead to innovative strategies for developing crops with greater resilience to climate change, whether through genetic manipulation or by selecting varieties with favorable metabolic responses to stress.

Epigenetic control of gene expression by cellular metabolisms in plants

Covalent modifications on DNA and histones can regulate eukaryotic gene expression and are often referred to as epigenetic modifications. These chemical reactions require various metabolites as donors or co-substrates, such as acetyl coenzyme A, S-adenosyl-l-methionine, and α-ketoglutarate. Metabolic processes that take place in the cytoplasm, nucleus, or other cellular compartments may impact epigenetic modifications in the nucleus. Here, we review recent advances on metabolic control of chromatin modifications and thus gene expression in plants, with a focus on the functions of nuclear compartmentalization of metabolic processes and enzymes in DNA and histone modifications. Furthermore, we discuss the functions of cellular metabolisms in fine-tuning gene expression to facilitate the responses or adaptation to environmental changes in plants.

Biochemical and Epigenetic Regulation of Glutamate Metabolism in Maize (Zea mays L.) Leaves under Salt Stress

The effect of salt stress (150 mM NaCl) on the expression of genes, methylation of their promoters, and enzymatic activity of glutamate dehydrogenase (GDH), glutamate decarboxylase (GAD), and the 2-oxoglutarate (2-OG)-dehydrogenase (2-OGDH) complex was studied in maize (Zea mays L.). GDH activity increased continuously under salt stress, being 3-fold higher after 24 h. This was accompanied by the appearance of a second isoform with lower electrophoretic mobility. The expression of the Gdh1 gene strongly increased after 6-12 h of incubation, which corresponded to the demethylation of its promoter, while Gdh2 gene expression slightly increased after 2-6 h and then decreased. GAD activity gradually increased in the first 12 h, and then returned to the control level. This corresponded to the increase of Gad expression and its demethylation. Salt stress led to a 2-fold increase in the activity of 2-OGDH during the first 6 h of NaCl treatment, then the activity returned to the control level. Expression of the genes Ogdh1 and Ogdh3 peaked after 1-2 h of incubation. After 6-8 h with NaCl, the expression of these genes declined below the control levels, which correlated with the higher methylation of their promoters. We conclude that salt stress causes a redirection of the 2-OG flux to the γ-aminobutyric acid shunt via its amination to glutamate, by altering the expression of the Gdh1 and Gdh2 genes, which likely promotes the assembly of the native GDH molecule having a different subunit composition and greater affinity for 2-OG.

Comparative transcriptome and coexpression network analysis revealed the regulatory mechanism of Astragalus cicer L. in response to salt stress

BACKGROUND

Astragalus cicer L. is a perennial rhizomatous legume forage known for its quality, high biomass yield, and strong tolerance to saline-alkaline soils. Soil salinization is a widespread environmental pressure. To use A. cicer L. more scientifically and environmentally in agriculture and ecosystems, it is highly important to study the molecular response mechanism of A. cicer L. to salt stress.

RESULTS

In this study, we used RNA-seq technology and weighted gene coexpression network analysis (WGCNA) were performed. The results showed 4 key modules were closely related to the physiological response of A. cicer. L. to salt stress. The differentially expressed genes (DEGs) of key modules were mapped into the KEGG database, and found that the most abundant pathways were the plant hormone signal transduction pathway and carbon metabolism pathway. The potential regulatory networks of the cytokinin signal transduction pathway, the ethylene signal transduction pathway, and carbon metabolism related pathways were constructed according to the expression pathways of the DEGs. Seven hub genes in the key modules were selected and distributed among these pathways. They may involved in the positive regulation of cytokinin signaling and carbon metabolism in plant leaves, but limited the positive expression of ethylene signaling. Thus endowing the plant with salt tolerance in the early stage of salt stress.

CONCLUSIONS

Based on the phenotypic and physiological responses of A. cicer L. to salt stress, this study constructed the gene coexpression network of potential regulation to salt stress in key modules, which provided a new reference for exploring the response mechanism of legumes to abiotic stress.

Biological nitrogen fixation maintains carbon/nitrogen balance and photosynthesis at elevated CO2

Understanding crop responses to elevated CO2 is necessary to meet increasing agricultural demands. Crops may not achieve maximum potential yields at high CO2 due to photosynthetic downregulation, often associated with nitrogen limitation. Legumes have been proposed to have an advantage at elevated CO2 due to their ability to exchange carbon for nitrogen. Here, the effects of biological nitrogen fixation (BNF) on the physiological and gene expression responses to elevated CO2 were examined at multiple nitrogen levels by comparing alfalfa mutants incapable of nitrogen fixation to wild-type. Elemental analysis revealed a role for BNF in maintaining shoot carbon/nitrogen (C/N) balance under all nitrogen treatments at elevated CO2, whereas the effect of BNF on biomass was only observed at elevated CO2 and the lowest nitrogen dose. Lower photosynthetic rates at were associated with the imbalance in shoot C/N. Genome-wide transcriptional responses were used to identify carbon and nitrogen metabolism genes underlying the traits. Transcription factors important to C/N signalling were identified from inferred regulatory networks. This work supports the hypothesis that maintenance of C/N homoeostasis at elevated CO2 can be achieved in plants capable of BNF and revealed important regulators in the underlying networks including an alfalfa (Golden2-like) GLK ortholog.

Identification of the succinate-CoA ligase protein gene family reveals that TaSUCL1-1 positively regulate cadmium resistance in wheat

The Succinate-CoA ligase (SUCL1) gene family is involved in energy metabolism, phytohormone signaling, and plant growth, development, and tolerance to stress. This is the first study to analyze the SUCL1 gene family in wheat (Triticum aestivum). 17 TaSUCL1 genes were identified in the complete genome sequence and classified into five subfamilies based on related genes found in three other species. The 17 TaSUCL1 genes were unevenly distributed across 11 chromosomes, and the collinearity of these genes was further investigated. Through using real-time qPCR (RT-qPCR) analysis, we identified the expression patterns of the TaSUCL1 genes under various tissues and different heavy metal stress conditions. The functions of selected TaSUCL1-1 gene were investigated by RNA interference (RNAi). This study provided a comprehensive analysis of the TaSUCL1 gene family. Within the TaSUCL1 genes, the exon-intron structure and motif composition exhibited significant similarity among members of the same evolutionary branch. Homology analysis and phylogenetic comparison of the SUCL1 genes in different plants offered valuable insights for studying the evolutionary characteristics of the SUCL1 genes. The expression levels of the TaSUCL1 genes in different tissues and under various metal stress conditions reveal its important role in plant growth and development. Gene function analysis demonstrated that TaSUCL1-1 silenced wheat plants exhibited a decrease in the total cadmium (Cd) concentrations and gene expression levels compared to the wild type (WT). Additionally, TaSUCL1-1 belonging to class c physically interacts with the β-amylase protein TaBMY1 as verified by yeast two-hybridization. This research provides a useful resource for further study of the function and molecular genetic mechanism of the SUCL1 gene family members.

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.

Control of histone demethylation by nuclear-localized α-ketoglutarate dehydrogenase

Methylations on nucleosomal histones play fundamental roles in regulating eukaryotic transcription. Jumonji C domain-containing histone demethylases (JMJs) dynamically control the level of histone methylations. However, how JMJ activity is generally regulated is unknown. We found that the tricarboxylic acid cycle-associated enzyme α-ketoglutarate (α-KG) dehydrogenase (KGDH) entered the nucleus, where it interacted with various JMJs to regulate α-KG-dependent histone demethylations by JMJs, and thus controlled genome-wide gene expression in plants. We show that nuclear targeting is regulated by environmental signals and that KGDH is enriched at thousands of loci in Arabidopsis thaliana. Chromatin-bound KGDH catalyzes α-KG decarboxylation and thus may limit its local availability to KGDH-coupled JMJs, inhibiting histone demethylation. Thus, our results uncover a regulatory mechanism for histone demethylations by JMJs.

Mitochondria in photosynthetic cells: Coordinating redox control and energy balance

In photosynthetic tissues in the light, the function of energy production is associated primarily with chloroplasts, while mitochondrial metabolism adjusts to balance ATP supply, regulate the reduction level of pyridine nucleotides, and optimize major metabolic fluxes. The tricarboxylic acid cycle in the light transforms into a noncyclic open structure (hemicycle) maintained primarily by the influx of malate and the export of citrate to the cytosol. The exchange of malate and citrate forms the basis of feeding redox energy from the chloroplast into the cytosolic pathways. This supports the level of NADPH in different compartments, contributes to the biosynthesis of amino acids, and drives secondary metabolism via a supply of substrates for 2-oxoglutarate-dependent dioxygenase and for cytochrome P450-catalyzed monooxygenase reactions. This results in the maintenance of redox and energy balance in photosynthetic plant cells and in the formation of numerous bioactive compounds specific to any particular plant species. The noncoupled mitochondrial respiration operates in coordination with the malate and citrate valves and supports intensive fluxes of respiration and photorespiration. The metabolic system of plants has features associated with the remarkable metabolic plasticity of mitochondria that permit the use of energy accumulated during photosynthesis in a way that all anabolic and catabolic pathways become optimized and coordinated.

Leonurine hydrochloride-a new drug for the treatment of menopausal syndrome: Synthesis, estrogen-like effects and pharmacokinetics

This research aimed to investigate the estrogen-like effects of Leonurine hydrochloride (Leo). First, we developed a total synthesis of Leo from 3,4,5-trimethoxy-benzoic acid and the structure was confirmed through 1H NMR and mass spectrometry (MS). Then the estrogenic activity of Leo in vitro and in vivo was studied. The proliferation and proliferation inhibitory effects of Leo on MCF-7 cells and MDA-MB-231 cells indicate that Leo exerts estrogen-like effects through estrogen receptor α (ERα) and estrogen receptor β((ERβ) in vitro. Uterotrophic assay in juvenile mice showed that Leo has an estrogen-like effect in vivo, as it can promote the development of the uterus of juvenile mice, increase its uterine coefficient and the size of the uterine cavity, as well as the increased number of uterine glands and the thickened uterine wall. For further research, cyclophosphamide (CTX) was used to establish a mouse model of ovarian function decline. Through this model, we found that Leo can restore the estrous cycle of mice, increase the number of primordial and primary follicles in the ovaries of mice, and regulate the disordered hypothalamic-pituitary-ovarian (HPOA) axis of mice. Finally, the pharmacokinetics of Leo was studied and oral bioavailability of Leo was calculated to be 2.21%. Leo was synthesized and the estrogen-like effect in vitro and in vivo was confirmed as well as its pharmacokinetics.

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.

The knowns and unknowns of intracellular partitioning of carbon and nitrogen, with focus on the organic acid-mediated interplay between mitochondrion and chloroplast

The presence of specialized cellular compartments in higher plants express an extraordinary degree of intracellular organization, which provides efficient mechanisms to avoid misbalancing of the metabolism. This offers the flexibility by which plants can quickly acclimate to fluctuating environmental conditions. For that, a fine temporal and spatial regulation of metabolic pathways is required and involves several players e.g. organic acids. In this review we discuss different facets of the organic acid metabolism within plant cells with special focus to those related to the interactions between organic acids compartmentalization and the partitioning of carbon and nitrogen. The connections between organic acids and CO₂ assimilation, tricarboxylic acid (TCA) cycle, amino acids metabolism, and redox status are highlighted. Moreover, the key enzymes and transporters as well as their function on the coordination of interorganellar metabolic exchanges are discussed.