Carbon Metabolites Research Articles

Response of nitrate reductase activity and NIA genes expression in roots of Arabidopsis hxk1 mutant treated with selected carbon and nitrogen metabolites

In plants sugar sensing and signal transduction involves pathways dependent or independent on HXK1 as a glucose sensor. Research was conducted to determine which pathway is responsible for regulation of the nitrate reduction. The effect of selected carbon and nitrogen metabolites on nitrate reductase (NR) activity in Arabidopsis thaliana wild type (WT) and hxk1 mutant roots was studied. Exogenously supplied sugar, sucrose (Suc) and organic acid, 2-oxoglutarate (2-OG) led to an increase in the total and actual activity of NR. It was due to both the increase in expression of NIA genes and NR activation state. The stimulatory effect of Suc and 2-OG on nitrate reduction was less pronounced in hxk1 mutant roots with T-DNA insertion in the AtHXK1 gene encoding hexokinase1 (HXK1) and characterized by reduced hexokinase activity and root level of G6P and F6P. On the other hand, it was shown that exogenous glucose did not mimic Suc-mediated NR activation in Arabidopsis roots. Taken together, this data suggest that the Suc signaling pathway might be independent from hexose's sensor dependent mechanism.

Inactivation of Phaeodactylum tricornutum urease gene using transcription activator-like effector nuclease-based targeted mutagenesis.

Diatoms are unicellular photosynthetic algae with promise for green production of fuels and other chemicals. Recent genome-editing techniques have greatly improved the potential of many eukaryotic genetic systems, including diatoms, to enable knowledge-based studies and bioengineering. Using a new technique, transcription activator-like effector nucleases (TALENs), the gene encoding the urease enzyme in the model diatom, Phaeodactylum tricornutum, was targeted for interruption. The knockout cassette was identified within the urease gene by PCR and Southern blot analyses of genomic DNA. The lack of urease protein was confirmed by Western blot analyses in mutant cell lines that were unable to grow on urea as the sole nitrogen source. Untargeted metabolomic analysis revealed a build-up of urea, arginine and ornithine in the urease knockout lines. All three intermediate metabolites are upstream of the urease reaction within the urea cycle, suggesting a disruption of the cycle despite urea production. Numerous high carbon metabolites were enriched in the mutant, implying a breakdown of cellular C and N repartitioning. The presented method improves the molecular toolkit for diatoms and clarifies the role of urease in the urea cycle.

Mechanisms of physiological adjustment of N2 fixation in Cicer arietinum L. (chickpea) during early stages of water deficit: single or multi-factor controls.

Drought negatively impacts symbiotic nitrogen fixation (SNF) in Cicer arietinumL. (chickpea), thereby limiting yield potential. Understanding how drought affects chickpea nodulation will enable the development of strategies to biotechnologically engineer chickpea varieties with enhanced SNF under drought conditions. By analyzing carbon and nitrogen metabolism, we studied the mechanisms of physiological adjustment of nitrogen fixation in chickpea plants nodulated with Mesorhizobium ciceri during both drought stress and subsequent recovery. The nitrogenase activity, levels of several key carbon (in nodules) and nitrogen (in both nodules and leaves) metabolites and antioxidant compounds, as well as the activity of related nodule enzymes were examined in M.ciceri-inoculated chickpea plants under early drought stress and subsequent recovery. Results indicated that drought reduced nitrogenase activity, and that this was associated with a reduced expression of the nifK gene. Furthermore, drought stress promoted an accumulation of amino acids, mainly asparagine in nodules (but not in leaves), and caused a cell redox imbalance in nodules. An accumulation of organic acids, especially malate, in nodules, which coincided with the decline of nodulated root respiration, was also observed under drought stress. Taken together, our findings indicate that reduced nitrogenase activity occurring at early stages of drought stress involves, at least, the inhibition of respiration, nitrogen accumulation and an imbalance in cell redox status in nodules. The results of this study demonstrate the potential that the genetic engineering-based improvement of SNF efficiency could be applied to reduce the impact of drought on the productivity of chickpea, and perhaps other legume crops.

Microcirculation of skeletal muscle adapts differently to a resistive exercise intervention with and without superimposed whole-body vibrations.

Whole-body vibration (WBV) training is commonly practiced and may enhance peripheral blood flow. Here, we investigated muscle morphology and acute microcirculatory responses before and after a 6-week resistive exercise training intervention without (RE) or with (RVE) simultaneous whole-body vibrations (20 Hz, 6 mm peak-to-peak amplitude) in 26 healthy men in a randomized, controlled parallel-design study. Total haemoglobin (tHb) and tissue oxygenation index (TOI) were measured in gastrocnemius muscle (GM) with near-infrared spectroscopy (NIRS). Whole-body oxygen consumption (VO2 ) was measured via spirometry, and skeletal muscle morphology was determined in soleus (SOL) muscle biopsies. Our data reveal that exercise-induced muscle deoxygenation both before and after 6 weeks training was similar in RE and RVE (P = 0.76), although VO2 was 20% higher in the RVE group (P < 0.001). The RVE group showed a 14%-point increase in reactive hyperaemia (P = 0.007) and a 27% increase in blood volume (P < 0.01) in GM after 6 weeks of training. The number of capillaries around fibres was increased by 15% after 6 weeks training in both groups (P < 0.001) with no specific effect of superimposed WBV (P = 0.61). Neither of the training regimens induced fibre hypertrophy in SOL. The present findings suggest an increased blood volume and vasodilator response in GM as an adaptation to long-term RVE, which was not observed after RE alone. We conclude that RVE training enhances vasodilation of small arterioles and possibly capillaries. This effect might be advantageous for muscle thermoregulation and the delivery of oxygen and nutrients to exercising muscle and removal of carbon dioxide and metabolites.

Modulation of auxin content in Arabidopsis confers improved drought stress resistance

Auxin is a well-known plant phytohormone that is involved in multiple plant growth processes and stress responses. In this study, auxin response was significantly modulated under drought stress condition. The iaaM-OX transgenic lines with higher endogenous indole-3-acetic acid (IAA) level and IAA pre-treated wild type (WT) plants exhibited enhanced drought stress resistance, while the yuc1yuc2yuc6 triple mutants with lower endogenous IAA level showed decreased stress resistance in comparison to non-treated WT plants. Additionally, endogenous and exogenous auxin positively modulated the expression levels of multiple abiotic stress-related genes (RAB18, RD22, RD29A, RD29B, DREB2A, and DREB2B), and positively affected reactive oxygen species (ROS) metabolism and underlying antioxidant enzyme activities. Moreover, auxin significantly modulated some carbon metabolites including amino acids, organic acids, sugars, sugar alcohols and aromatic amines. Notably, endogenous and exogenous auxin positively modulated root architecture especially the lateral root number. Taken together, this study demonstrated that auxin might participate in the positive regulation of drought stress resistance, through regulation of root architecture, ABA-responsive genes expression, ROS metabolism, and metabolic homeostasis, at least partially.

C2 photosynthesis generates about 3-fold elevated leaf CO2 levels in the C3-C4 intermediate species Flaveria pubescens.

Formation of a photorespiration-based CO2-concentrating mechanism in C3-C4 intermediate plants is seen as a prerequisite for the evolution of C4 photosynthesis, but it is not known how efficient this mechanism is. Here, using in vivo Rubisco carboxylation-to-oxygenation ratios as a proxy to assess relative intraplastidial CO2 levels is suggested. Such ratios were determined for the C3-C4 intermediate species Flaveria pubescens compared with the closely related C3 plant F. cronquistii and the C4 plant F. trinervia. To this end, a model was developed to describe the major carbon fluxes and metabolite pools involved in photosynthetic-photorespiratory carbon metabolism and used quantitatively to evaluate the labelling kinetics during short-term (14)CO2 incorporation. Our data suggest that the photorespiratory CO2 pump elevates the intraplastidial CO2 concentration about 3-fold in leaves of the C3-C4 intermediate species F. pubescens relative to the C3 species F. cronquistii.

Targeted profiling of polar intracellular metabolites using ion-pair-high performance liquid chromatography and -ultra high performance liquid chromatography coupled to tandem mass spectrometry: Applications to serum, urine and tissue extracts

The effective analysis of polar ionic metabolites by LC–MS, such as those encountered in central carbon metabolism, represents a major problem for metabolic profiling that is not adequately addressed using strategies based on either reversed-phase or HILIC methods. Here we have compared analysis of central carbon metabolites on optimized methods using HILIC, porous graphitic carbon or ion pair chromatography (IPC) using tributyl ammonium as IP reagent. Of the 3 chromatographic approaches examined only IPC enabled us to obtain a robust analytical methodology. This system was used to profile more than a hundred endogenous metabolic intermediates in urine, serum and tissue samples. However, whilst we found IPC to be the best of the approaches examined considerable care was still needed to obtain robust data. Thus, in excess of 40 of representative biological samples were needed to “condition” a new analytical column and further 10 matrix injections were then required at the beginning of each analytical batch in order to obtain robust and reproducible chromatographic separations. An additional limitation that we have found was that, for a small number of phosphorylated and poly carboxylic acid metabolites, measurement was only possible if the analytes were present in relatively high concentrations. We also found that, whilst this methodology could be used for the analysis of both in vitro cell culture media, cell extracts, tissue, and biological fluids (blood, urine), for the best results columns should only be used to analyze a single matrix. However, despite the need for extensive column conditioning, and the manifold disadvantages resulting from the contamination of the separation system and mass spectrometer with the ion pair reagent, IPC-MS currently provides the best means of analyzing these polar, ionic and problematic metabolites.

Metabolic switching of central carbon metabolism in response to nitrate: Application to autofermentative hydrogen production in cyanobacteria

Nitrate removal from culture media is widely used to enhance autofermentative hydrogen production in cyanobacteria during dark anaerobiosis. Here we have performed a systematic inventory of carbon and nitrogen metabolites, redox pools, and excreted product fluxes which show that addition of nitrate to cultures of Synechococcus sp. PCC 7002 has no influence on glycogen catabolic rate, but shifts the distribution of excreted products from predominantly lactate and H2 to predominantly CO2 and nitrite, while increasing the total consumption of intracellular reducing equivalents (mainly glycogen) by 3-fold. Together with LC–MS derived metabolite pool sizes these data show that glycogen catabolism is redirected from the upper-glycolytic (EMP) pathway to the oxidative pentose phosphate (OPP) pathway upon nitrate addition. This metabolic switch in carbon catabolism is shown to temporally correlate with the pyridine nucleotide redox-poise (NAD(P)H/NAD(P)+) and demonstrates the reductant availability controls H2 evolution in cyanobacteria.

Comparative proteomic and metabolomic analyses reveal mechanisms of improved cold stress tolerance in bermudagrass (Cynodon dactylon (L.) Pers.) by exogenous calcium

As an important second messenger, calcium is involved in plant cold stress response, including chilling (<20 °C) and freezing (<0 °C). In this study, exogenous application of calcium chloride (CaCl2 ) improved both chilling and freezing stress tolerances, while ethylene glycol-bis-(β-aminoethyl) ether-N,N,N,N-tetraacetic acid (EGTA) reversed CaCl2 effects in bermudagrass (Cynodon dactylon (L.) Pers.). Physiological analyses showed that CaCl2 treatment alleviated the reactive oxygen species (ROS) burst and cell damage triggered by chilling stress, via activating antioxidant enzymes, non-enzymatic glutathione antioxidant pool, while EGTA treatment had the opposite effects. Additionally, comparative proteomic analysis identified 51 differentially expressed proteins that were enriched in redox, tricarboxylicacid cycle, glycolysis, photosynthesis, oxidative pentose phosphate pathway, and amino acid metabolisms. Consistently, 42 metabolites including amino acids, organic acids, sugars, and sugar alcohols were regulated by CaCl2 treatment under control and cold stress conditions, further confirming the common modulation of CaCl2 treatment in carbon metabolites and amino acid metabolism. Taken together, this study reported first evidence of the essential and protective roles of endogenous and exogenous calcium in bermudagrass response to cold stress, partially via activation of the antioxidants and modulation of several differentially expressed proteins and metabolic homeostasis in the process of cold acclimation.

CO2-enriched atmosphere and supporting material impact the growth, morphophysiology and ultrastructure of in vitro Brazilian-ginseng [Pfaffia glomerata (Spreng.) Pedersen] plantlets

This study aimed to evaluate under photoautotrophic conditions the effect of CO2-enriched atmosphere (360 or 1,000 μmol CO2 mol−1 air) combined with two substrate types (agar or Florialite®) in vitro on plants of Pfaffia glomerata, an endangered medicinal species with promising applications in phytotherapy and phytomedicine. The effects of the treatments on the growth, stomatal density, Rubisco activity, carbon isotopic discrimination, metabolite accumulation, photosynthetic pigments and ultrastructural characteristics were investigated. After a 35-day cultivation period, the in vitro-growth of P. glomerata nodal segments under the different treatments resulted in plants with substantial differences in relation to their growth, photosynthetic pigments, stomatal density and leaf ultrastructural characteristics. The enrichment with CO2 coupled with a porous substrate increased the growth of P. glomerata. The stomatal density in the abaxial epidermis more than doubled in response to the high CO2 supply in both supporting types, whereas the Rubisco activity and activation state were both unresponsive to the treatments. Regardless of the CO2 supply, the plants grown in agar displayed higher carbon isotope discrimination than their counterparts grown in Florialite®. We propose that the long-term photosynthetic performance was improved using Florialite® as a growth support in combination with a high CO2 supply. No apparent signs of photosynthetic down-regulation could be found under elevated CO2 conditions. The enrichment of in vitro atmospheres with CO2 coupled with a porous substrate offers new possibilities for improving the growth and production on a commercial scale of high morphological and physiological quality Pfaffia plants.

Genetic Basis of Metabolome Variation in Yeast

Metabolism, the conversion of nutrients into usable energy and biochemical building blocks, is an essential feature of all cells. The genetic factors responsible for inter-individual metabolic variability remain poorly understood. To investigate genetic causes of metabolome variation, we measured the concentrations of 74 metabolites across 100 segregants from a Saccharomyces cerevisiae cross by liquid chromatography-tandem mass spectrometry. We found 52 quantitative trait loci for 34 metabolites. These included linkages due to overt changes in metabolic genes, e.g., linking pyrimidine intermediates to the deletion of ura3. They also included linkages not directly related to metabolic enzymes, such as those for five central carbon metabolites to ira2, a Ras/PKA pathway regulator, and for the metabolites, S-adenosyl-methionine and S-adenosyl-homocysteine to slt2, a MAP kinase involved in cell wall integrity. The variant of ira2 that elevates metabolite levels also increases glucose uptake and ethanol secretion. These results highlight specific examples of genetic variability, including in genes without prior known metabolic regulatory function, that impact yeast metabolism.

Carbon in airway macrophages from children with asthma

BackgroundAirway macrophage (AM) phagocytosis is impaired in severe asthma. Prostaglandin (PG) E2 and D2 are increased in severe asthma and suppress AM phagocytic function in vitro. In this study, we...

Evaluation of Carbon and Nitrogen Metabolism in the Leaves of Some Creeper Weed Legumes Growing Wild in Tripura

Leguminous cover crops provide permanent soil cover, reduce erosion, increase soil nutrient level and organic matter. More than 35 weed legumes are luxuriantly growing in different localities of Tripura. In the present paper carbon metabolites such as chlorophyll-a, b, total chlorophyll and carotenoid and various nitrogen metabolites (soluble protein, total protein and total free amino acid) in the leaves of four creeper weed legumes have been studied. As the levels of the various carbon and nitrogen metabolites were found in higher these weed plants can be used for tea garden, rubber plantation forests and agricultural fields to enrich soil nitrogen level.

Vitamin K metabolism: Current knowledge and future research

Vitamin K is an essential fat-soluble micronutrient that is required for the post-translational γ-carboxylation of specific glutamic acid residues in hepatic and extra-hepatic proteins involved in blood coagulation and preventing cartilage and vasculature calcification. In humans, sources of vitamin K are derived from plants as phylloquinone and bacteria as the menaquinones. Menadione is a synthetic product used as a pharmaceutical but also represents an intermediate in the tissue-specific conversion of vitamin K to menaquinone-4, which preferentially resides in tissues such as brain. Research into vitamin K metabolism is essential for the understanding of vitamin K biology in health and disease. Progress in this area, driven by knowledge of vitamin K and the availability of markers of vitamin K status, has already proved beneficial in many areas of medicine and further opportunities present themselves. Areas of interest discussed in this review include prophylactic administration of vitamin K1 in term and preterm neonates, interactions between vitamins K and E, the industrial conversion of vitamin K to dihydro-vitamin K in foods, tissue-specific conversion of vitamin K to menaquinone-4, the biological activity of the five and seven carbon metabolites of vitamin K and circadian variations.

Chemical and technical challenges in the analysis of central carbon metabolites by liquid-chromatography mass spectrometry

This review deals with chemical and technical challenges in the analysis of small-molecule metabolites involved in central carbon and energy metabolism via liquid-chromatography mass-spectrometry (LC-MS). The covered analytes belong to the prominent pathways in biochemical carbon oxidation such as glycolysis or the tricarboxylic acid cycle and, for the most part, share unfavorable properties such as a high polarity, chemical instability or metal-affinity. The topic is introduced by selected examples on successful applications of metabolomics in the clinic. In the core part of the paper, the structural features of important analyte classes such as nucleotides, coenzyme A thioesters or carboxylic acids are linked to "problematic hotspots" along the analytical chain (sample preparation and-storage, separation and detection). We discuss these hotspots from a chemical point of view, covering issues such as analyte degradation or interactions with metals and other matrix components. Based on this understanding we propose solutions wherever available. A major notion derived from these considerations is that comprehensive carbon metabolomics inevitably requires multiple, complementary analytical approaches covering different chemical classes of metabolites.

THE ROLE OF SOME SOLUBLE METABOLITES IN OSMOTIC ADJUSTMENT TO REDUCED MATRIC AND OSMOTIC WATER POTENTIAL IN TWO SOYBEAN CULTIVARS دور بعض المواد الايضيه الذائبة في الانضباط الاسموزي لسلالتين من نبات فول الصويا تحت النقص في الجهد المائي للتربة

This work aimed to study the effect of reduced matric- and osmotic water potential on changes of some parameters affecting plant water potential related to metabolism. The experimental plants are two cultivars of soybean (Giza 111 and Giza 21). The study is concerned mainly with internal adjustment in soluble metabolites affecting plant water relation. Such as soluble sugars (SS), hydrolysable carbohydrates (HC) among carbon metabolites and total free amino acids (AA) as nitrogenous components as well as soluble proteins which contribute water conservation in the plant. Statistical treatment of data helped much in clarifying the role of each of the four metabolic components in adjusting to the reduced water potential in the soil (water stress).

Resolving the Role of Plant Glutamate Dehydrogenase: II. Physiological Characterization of Plants Overexpressing the Two Enzyme Subunits Individually or Simultaneously

Glutamate dehydrogenase (GDH; EC 1.4.1.2) is able to carry out the deamination of glutamate in higher plants. In order to obtain a better understanding of the physiological function of GDH in leaves, transgenic tobacco (Nicotiana tabacum L.) plants were constructed that overexpress two genes from Nicotiana plumbaginifolia (GDHA and GDHB under the control of the Cauliflower mosiac virus 35S promoter), which encode the α- and β-subunits of GDH individually or simultaneously. In the transgenic plants, the GDH protein accumulated in the mitochondria of mesophyll cells and in the mitochondria of the phloem companion cells (CCs), where the native enzyme is normally expressed. Such a shift in the cellular location of the GDH enzyme induced major changes in carbon and nitrogen metabolite accumulation and a reduction in growth. These changes were mainly characterized by a decrease in the amount of sucrose, starch and glutamine in the leaves, which was accompanied by an increase in the amount of nitrate and Chl. In addition, there was an increase in the content of asparagine and a decrease in proline. Such changes may explain the lower plant biomass determined in the GDH-overexpressing lines. Overexpressing the two genes GDHA and GDHB individually or simultaneously induced a differential accumulation of glutamate and glutamine and a modification of the glutamate to glutamine ratio. The impact of the metabolic changes occurring in the different types of GDH-overexpressing plants is discussed in relation to the possible physiological function of each subunit when present in the form of homohexamers or heterohexamers.

Capillary electrophoresis–mass spectrometry reveals the distribution of carbon metabolites during nitrogen starvation in Synechocystis sp. PCC 6803

Nitrogen availability is one of the most important factors for the survival of cyanobacteria. Previous studies on Synechocystis revealed a contradictory situation with regard to metabolism during nitrogen starvation; that is, glycogen accumulated even though the expressions of sugar catabolic genes were widely upregulated. Here, we conducted transcript and metabolomic analyses using capillary electrophoresis-mass spectrometry on Synechocystis sp. PCC 6803 under nitrogen starvation. The levels of some tricarboxylic acid cycle intermediates (succinate, malate and fumarate) were greatly increased by nitrogen deprivation. Purine and pyrimidine nucleotides were markedly downregulated under nitrogen depletion. The levels of 19 amino acids changed under nitrogen deprivation, especially those of amino acids synthesized from pyruvate and phosphoenolpyruvate, which showed marked increases. Liquid chromatography-mass spectrometry analysis demonstrated that the amount of NADPH and the NADPH/NADH ratio decreased under nitrogen depletion. These data demonstrate that there are increases in not only glycogen but also in metabolites downstream of sugar catabolism in Synechocystis sp. PCC 6803 under nitrogen starvation, resolving the contradiction between glycogen accumulation and induction of sugar catabolic gene expression in this unicellular cyanobacterium.

Growth and nodulation of symbiotic Medicago truncatula at different levels of phosphorus availability.

Medicago truncatula is an important model plant for characterization of P deficiency on leguminous plants at the physiological and molecular levels. Growth optimization of this plant with regard to P supply is the first essential step for elucidation of the role of P in regulation of nodulation. Hence, a study was carried out to address the growth pattern of M. truncatula hydroponically grown at different gradual increases in P levels. The findings revealed that M. truncatula had a narrow P regime, with an optimum P level (12 μM P) which is relatively close to the concentration that induces P toxicity. The accumulated P concentration (2.7 mg g–1 dry matter), which is normal for other crops and legumes, adversely affected the growth of M. truncatula plants. Under P deficiency, M. truncatula showed a higher symbiotic efficiency with Sinorhizobium meliloti 2011 in comparison with S. meliloti 102F51, partially as a result of higher electron allocation to N2 versus H+. The total composition of free amino acids in the phloem was significantly affected by P deprivation. This pattern was found to be almost exclusively the result of the increase in the asparagine level, suggesting that asparagine might be the shoot-derived signal that translocates to the nodules and exerts the down-regulation of nitrogenase activity. Additionally, P deprivation was found to have a strong influence on the contents of the nodule carbon metabolites. While levels of sucrose and succinate tended to decrease, a higher accumulation of malate was observed. These findings have provided evidence that N2 fixation of M. truncatula is mediated through an N feedback mechanism which is closely related to nodule carbon metabolism.

Online-Based Kinetic Analysis of Higher Alcohol and Ester Synthesis During Winemaking Fermentations

The production of the major volatile carbon compounds corresponding to the predominant higher alcohols and esters synthesized during wine alcoholic fermentation was monitored using an online GC system. The accuracy and frequency of measurements made it possible to calculate kinetic parameters, in particular rates and specific rates of production. Using this original GC system and a model describing the evolution of the gas–liquid ratio during the fermentation process, kinetic gas–liquid balances of the synthesis of volatile compounds could be followed. This showed that, for esters—substantial proportions of which are lost in the off-gas (up to 40 % of the total production at 20 °C)—measurements of the liquid concentration, rather than of the total production (liquid content + losses), can lead to misinterpretations of yeast metabolism. The specific production rate of individual higher alcohols reached their maximum values before the exhaustion of the corresponding precursor amino acids. Isobutanol and isoamyl alcohol were formed from carbon metabolites and nitrogen metabolites and consequently were produced continuously throughout the fermentation process. In contrast, propanol synthesis was strongly correlated with the presence of assimilable nitrogen, during both the growth and stationary phases. Therefore, propanol appears to be a highly pertinent marker of nitrogen metabolism. Acetate ester concentrations correlated linearly with the concentrations of the corresponding higher alcohols, indicating that the availability of the precursors is the main limiting factor for the production of these esters. These results open possibilities for innovative approaches based on metabolic flux analysis and taking their dynamics into account.