Citrate Pool Research Articles

High-level biosynthesis of enantiopure germacrene D in yeast.

Germacrene D, a sesquiterpenoid compound found mainly in plant essential oils at a low level as (+) and/or (-) enantiomeric forms, is an ingredient for the fragrance industry, but a process for the sustainable supply of enantiopure germacrene D is not yet established. Here, we demonstrate metabolic engineering in yeast (Saccharomyces cerevisiae) achieving biosynthesis of enantiopure germacrene D at a high titer. To boost farnesyl pyrophosphate (FPP) flux for high-level germacrene D biosynthesis, a background yeast chassis (CENses5C) was developed by genomic integration of the expression cassettes for eight ergosterol pathway enzymes that sequentially converted acetyl-CoA to FPP and by replacing squalene synthase promoter with a copper-repressible promoter, which restricted FPP flux to the competing pathway. Galactose-induced expression of codon-optimized plant germacrene D synthases led to 13-30 fold higher titers of (+) or (-)-germacrene D in CENses5C than the parent strain CEN.PK2.1C. Furthermore, genomic integration of germacrene D synthases in GAL80, LPP1 and rDNA loci generated CENses8(+D) and CENses8(-D) strains, which produced 41.36µg/ml and 728.87µg/ml of (+) and (-)-germacrene D, respectively, without galactose supplementation. Moreover, coupling of mitochondrial citrate pool to the cytosolic acetyl-CoA, by expressing a codon-optimized ATP-citrate lyase of oleaginous yeast, resulted in 137.71µg/ml and 815.81µg/ml of (+) or (-)-germacrene D in CENses8(+D)* and CENses8(-D)* strains, which were 67-120 fold higher titers than in CEN.PK2.1C. In fed-batch fermentation, CENses8(+D)* and CENses8(-D)* produced 290.28µg/ml and 2519.46µg/ml (+) and (-)-germacrene D, respectively, the highest titers in shake-flask fermentation achieved so far. KEY POINTS: • Engineered S. cerevisiae produced enantiopure (+) and (-)-germacrene D at high titers • Engineered strain produced up to 120-fold higher germacrene D than the parental strain • Highest titers of enantiopure (+) and (-)-germacrene D achieved so far in shake-flask.

Pyruvate dehydrogenase fuels a critical citrate pool that is essential for Th17 cell effector functions

Pyruvate dehydrogenase (PDH) is the central enzyme connecting glycolysis and the tricarboxylic acid (TCA) cycle. The importance of PDH function in T helper 17 (Th17) cells still remains to be studied. Here, we show that PDH is essential for the generation of a glucose-derived citrate pool needed for Th17 cell proliferation, survival, and effector function. Invivo, mice harboring a Tcell-specific deletion of PDH are less susceptible to developing experimental autoimmune encephalomyelitis. Mechanistically, the absence of PDH in Th17 cells increases glutaminolysis, glycolysis, and lipid uptake in a mammalian target of rapamycin (mTOR)-dependent manner. However, cellular citrate remains critically low in mutant Th17 cells, which interferes with oxidative phosphorylation (OXPHOS), lipid synthesis, and histone acetylation, crucial for transcription of Th17 signature genes. Increasing cellular citrate in PDH-deficient Th17 cells restores their metabolism and function, identifying a metabolic feedback loop within the central carbon metabolism that may offer possibilities for therapeutically targeting Th17 cell-driven autoimmunity.

Increased Fatty Acid Synthesis and Catabolism Supports Metastatic Breast Cancer Cell Migration

Lipid accumulation is positively associated with breast cancer aggressiveness and poorer clinical outcomes. Despite this observation, mechanisms underlying the increase and role of stored lipid in breast cancer progression remain incompletely understood. The accumulation of triacylglycerol (TAG) is dependent on the balance of uptake, synthesis, and utilization of fatty acids (FAs). In the current study, we utilized non‐metastatic MCF10A‐ras and metastatic MCF10CA1a human breast cancer cells to determine differences in TAG storage and catabolism for sustaining migration—a critical step in the metastatic cascade. Our results demonstrate that MCF10CA1a cells have 90% more TAG than MCF10A‐ras (TAG Assay and Transmission Electron Microscopy), although no significant difference in 14C‐palmitate uptake. MCF10CA1a cells have greater FA synthesis as shown by greater incorporation of 13C‐acetate (60%), 13C‐glucose (65%), and 13C‐glutamine (50%) into palmitate compared to the MCF10A‐ras cells (LC‐MS/MS), as well as higher protein levels of FA synthase (FASN). Additionally, MCF10CA1a cells display greater flux of uniformly‐labeled 13C‐glucose and 13C‐glutamine to the FA synthesis precursor, citrate, and lower intracellular citrate pool size compared to MCF10A‐ras. In addition to increased FA anabolism, MCF10CA1a cells rely on FA oxidation (FAO) for cellular migration compared to MCF10A‐ras cells, as determined by inhibiting the rate‐limiting enzyme of FAO, carnitine palmitoyltransferase 1, with etomoxir (transwell and wound‐healing assays). Pretreatment with the FASN inhibitor TVB‐3166 (3 d) significantly reduced TAG levels and subsequent migration by 67% compared to vehicle‐treated cells. Similarly, pretreatment with inhibitors of the TAG‐synthesizing enzymes diacylglycerol O‐acyltransferase 1 and 2 reduced TAG accumulation and subsequent migration (75%) of MCF10CA1a cells compared to vehicle. Together, the data suggest that FA synthesis may contribute to TAG storage necessary to sustain breast cancer migration. To test this hypothesis, we inhibited the initial enzyme of the TAG lipolysis pathway, adipose triacylglycerol lipase (ATGL; inhibitor ATGListatin), and measured migration. Inhibition of ATGL alone reduced MCF10CA1a cell migration (20% decrease compared to vehicle), and addition of the FAO inhibitor (etomoxir) provided no further effect. Our study indicates that metastatic MCF10CA1a cells accumulate FAs by increasing de novo lipogenesis, store them as TAG, and that catabolism of these stores drives FAO‐dependent migration.

Metabolic engineering to guide evolution – Creating a novel mode for L-valine production with Corynebacterium glutamicum

Evolutionary approaches are often undirected and mutagen-based yielding numerous mutations, which need elaborate screenings to identify relevant targets. We here apply Metabolic engineering to Guide Evolution (MGE), an evolutionary approach evolving and identifying new targets to improve microbial producer strains. MGE is based on the idea to impair the cell's metabolism by metabolic engineering, thereby generating guided evolutionary pressure. It consists of three distinct phases: (i) metabolic engineering to create the evolutionary pressure on the applied strain followed by (ii) a cultivation phase with growth as straightforward screening indicator for the evolutionary event, and (iii) comparative whole genome sequencing (WGS), to identify mutations in the evolved strains, which are eventually re-engineered for verification. Applying MGE, we evolved the PEP and pyruvate carboxylase-deficient strain C. glutamicum Δppc Δpyc to grow on glucose as substrate with rates up to 0.31 ± 0.02 h−1 which corresponds to 80% of the growth rate of the wildtype strain. The intersection of the mutations identified by WGS revealed isocitrate dehydrogenase (ICD) as consistent target in three independently evolved mutants. Upon re-engineering in C. glutamicum Δppc Δpyc, the identified mutations led to diminished ICD activities and activated the glyoxylate shunt replenishing oxaloacetate required for growth. Intracellular relative quantitative metabolome analysis showed that the pools of citrate, isocitrate, cis-aconitate, and L-valine were significantly higher compared to the WT control. As an alternative to existing L-valine producer strains based on inactivated or attenuated pyruvate dehydrogenase complex, we finally engineered the PEP and pyruvate carboxylase-deficient C. glutamicum strains with identified ICD mutations for L-valine production by overexpression of the L-valine biosynthesis genes. Among them, C. glutamicum Δppc Δpyc ICDG407S (pJC4ilvBNCE) produced up to 8.9 ± 0.4 g L-valine L−1, with a product yield of 0.22 ± 0.01 g L-valine per g glucose.

Metabolic changes in cancer cells upon suppression of MYC

BackgroundCancer cells engage in aerobic glycolysis and glutaminolysis to fulfill their biosynthetic and energetic demands in part by activating MYC. Previous reports have characterized metabolic changes in proliferating cells upon MYC loss or gain of function. However, metabolic differences between MYC-dependent cancer cells and their isogenic differentiated counterparts have not been characterized upon MYC suppression in vitro.ResultsHere we report metabolic changes between MYC-dependent mouse osteogenic sarcomas and differentiated osteoid cells induced upon MYC suppression. While osteogenic sarcoma cells increased oxygen consumption and spare respiratory capacity upon MYC suppression, they displayed minimal changes in glucose and glutamine consumption as well as their respective contribution to the citrate pool. However, glutamine significantly induced oxygen consumption in the presence of MYC which was dependent on aminotransferases. Furthermore, inhibition of aminotransferases selectively diminished cell proliferation and survival of osteogenic sarcoma MYC-expressing cells. There were minimal changes in ROS levels and cell death sensitivity to reactive oxygen species (ROS)-inducing agents between osteoid cells and osteogenic sarcoma cells. Nevertheless, the mitochondrial-targeted antioxidant Mito-Vitamin E still diminished proliferation of MYC-dependent osteogenic sarcoma cells.ConclusionThese data highlight that aminotransferases and mitochondrial ROS might be attractive targets for cancer therapy in MYC-driven tumors.

Transcriptomic analysis reveals differential gene expression in response to aluminium in common bean (Phaseolus vulgaris) genotypes

Aluminium (Al) resistance in common bean is known to be due to exudation of citrate from the root after a lag phase, indicating the induction of gene transcription and protein synthesis. The aims of this study were to identify Al-induced differentially expressed genes and to analyse the expression of candidate genes conferring Al resistance in bean. The suppression subtractive hybridization (SSH) method was used to identify differentially expressed genes in an Al-resistant bean genotype ('Quimbaya') during the induction period. Using quantitative real-time PCR the expression patterns of selected genes were compared between an Al-resistant and an Al-sensitive genotype ('VAX 1') treated with Al for up to 24 h. Short-term Al treatment resulted in up-regulation of stress-induced genes and down-regulation of genes involved in metabolism. However, the expressions of genes encoding enzymes involved in citrate metabolism were not significantly affected by Al. Al treatment dramatically increased the expression of common bean expressed sequence tags belonging to the citrate transporter gene family MATE (multidrug and toxin extrusion family protein) in both the Al-resistant and -sensitive genotype in close agreement with Al-induced citrate exudation. The expression of a citrate transporter MATE gene is crucial for citrate exudation in common bean. However, although the expression of the citrate transporter is a prerequisite for citrate exudation, genotypic Al resistance in common bean particularly depends on the capacity to sustain the synthesis of citrate for maintaining the cytosolic citrate pool that enables exudation.

Light Stress Is Not Effective to Enhanced Crassulacean Acid Metabolism

Clusia minor L., a C3-CAM intermediate, and Clusia multiflora H. B. K., a C3 obligate, present two physiotypes of a similar morphotype occurring sympatrically in the field. Both species, exposed 2 days to high light, show similar responses to this kind of stress: (i) the level of xanthophyll pigments in tested plants during the daycourse adapts to stress, (ii) the levels of antheraxanthin and zeaxanthin clearly increase during the afternoon showing increased de-epoxidation, (iii) the changes in the xanthophyll cycle are similar. Exposure to high light increases the malate levels in C. minor during the afternoon while decreases the day/night changes of the malate levels, and hence the Crassulacean Acid Metabolism (CAM) expression. It can be concluded that strong light applied as a single stress factor to well-watered plants is not effective in strengthing the CAM metabolism in a C3-CAM intermediate plant but rather suppresses the CAM activity despite exposure to high light energy. It is suggested that, when water supply is not limiting and other stresses do not prevail, C3 allows to use up the citrate pool, especially in the afternoon and enables a superior daily photon utilization.

Aluminum resistance in common bean (Phaseolus vulgaris) involves induction and maintenance of citrate exudation from root apices

Two common bean (Phaseolus vulgaris L.) genotypes differing in aluminum (Al) resistance, Quimbaya (Al-resistant) and VAX-1 (Al-sensitive) were grown in hydroponics for up to 25 h with or without Al, and several parameters related to the exudation of organic acids anions from the root apex were investigated. Al treatment enhanced the exudation of citrate from the root tips of both genotypes. However, its dynamic offers the most consistent relationship between Al-induced inhibition of root elongation and Al accumulation in and exclusion from the root apices. Initially, in both genotypes the short-term (4 h) Al-injury period was characterized by the absence of citrate efflux independent of the citrate content of the root apices, and reduction of cytosolic turnover of citrate conferred by a reduced Nicotinamide adenine dinucleotide phosphate-isocitrate dehydrogenase (EC 1.1.1.42) activity. Transient recovery from initial Al stress (4-12 h) was found to be dependent mainly on the capacity to utilize internal citrate pools (Al-resistant genotype Quimbaya) or enhanced citrate synthesis [increased activities of NAD-malate dehydrogenase (EC 1.1.1.37) and ATP-phosphofructokinase (EC 2.7.1.11) in Al-sensitive VAX-1]. Sustained recovery from Al stress through citrate exudation in genotype Quimbaya after 24 h Al treatment relied on restoring the internal citrate pool and the constitutive high activity of citrate synthase (CS) (EC 4.1.3.7) fuelled by high phosphoenolpyruvate carboxylase (EC 4.1.1.31) activity. In the Al-sensitive genotype VAX-1 the citrate exudation and thus Al exclusion and root elongation could not be maintained coinciding with an exhaustion of the internal citrate pool and decreased CS activity.

Regulation of citB expression in Bacillus subtilis: integration of multiple metabolic signals in the citrate pool and by the general nitrogen regulatory system

The tricarboxylic acid (TCA) cycle is one of the major routes of carbon catabolism in Bacillus subtilis. The syntheses of the enzymes performing the initial reactions of the cycle, citrate synthase, and aconitase, are synergistically repressed by rapidly metabolizable carbon sources and glutamine. This regulation involves the general transcription factor CcpA and the specific repressor CcpC. In this study, we analyzed the expression and intracellular localization of CcpC. The synthesis of citrate, the effector of CcpC, requires acetyl-CoA. This metabolite is located at a branching point in metabolism. It can be converted to acetate in overflow metabolism or to citrate. Manipulations of the fate of acetyl-CoA revealed that efficient citrate synthesis is required for the expression of the citB gene encoding aconitase and that control of the two pathways utilizing acetyl-CoA converges in the control of citrate synthesis for the induction of the TCA cycle. The citrate pool seems also to be controlled by arginine catabolism. The presence of arginine results in a severe CcpC-dependent repression of citB. In addition to regulators involved in sensing the carbon status of the cell, the pleiotropic nitrogen-related transcription factor, TnrA, activates citB transcription in the absence of glutamine.

CitI, a Transcription Factor Involved in Regulation of Citrate Metabolism in Lactic Acid Bacteria

A large variety of lactic acid bacteria (LAB) can utilize citrate under fermentative conditions. Although much information concerning the metabolic pathways leading to citrate utilization by LAB has been gathered, the mechanisms regulating these pathways are obscure. In Weissella paramesenteroides (formerly called Leuconostoc paramesenteroides), transcription of the citMDEFCGRP citrate operon and the upstream divergent gene citI is induced by the presence of citrate in the medium. Although genetic experiments have suggested that CitI is a transcriptional activator whose activity can be modulated in response to citrate availability, specific details of the interaction between CitI and DNA remained unknown. In this study, we show that CitI recognizes two A+T-rich operator sites located between citI and citM and that the DNA-binding affinity of CitI is increased by citrate. Subsequently, this citrate signal propagation leads to the activation of the cit operon through an enhanced recruitment of RNA polymerase to its promoters. Our results indicate that the control of CitI by the cellular pools of citrate provides a mechanism for sensing the availability of citrate and adjusting the expression of the cit operon accordingly. In addition, this is the first reported example of a transcription factor directly functioning as a citrate-activated switch allowing the cell to optimize the generation of metabolic energy.

Multiple compartments with different metabolic characteristics are involved in biosynthesis of intracellular and released glutamine and citrate in astrocytes.

The metabolism of glucose and lactate was investigated in cultured mouse cerebellar astrocytes, a culture preparation consisting of a homogeneous population of cells, by incubating the cells in a medium containing either [U-(13)C]glucose or [U-(13)C]lactate in combination with unlabeled lactate and glucose, respectively. After the incubation, cell extracts and media were analyzed by GC/MS (gas chromatography/mass spectrometry) for labeling patterns in aspartate, glutamate, and glutamine, as well as the tricarboxylic acid (TCA) cycle constituents citrate and fumarate. Triple labeling of extracellular citrate exceeded that of double labeling from [U-(13)C]glucose. This was not the case when lactate was the labeled precursor. These results indicate that pyruvate carboxylation in biosynthesis of releasable citrate was less prominent from lactate compared with glucose. As observed in the case of extracellular citrate, triple labeling of intracellular aspartate was higher than double labeling when [U-(13)C]glucose was the precursor, but not with [U-(13)C]lactate as precursor. The pattern of labeling in citrate was different intra- and extracellularly and the extent of labeling extracellularly was 10 times higher using [U-(13)C]glucose compared with [U-(13)C]lactate. However, the intracellular citrate labeling from [U-(13)C]glucose only exceeded that originating from labeled lactate by a factor of two. This is in contrast to the labeling pattern obtained for glutamine, since intracellularly this was equally prominent using [U-(13)C]glucose and [U-(13)C]lactate as substrates. Moreover, extracellularly the labeling was only slightly higher when using [U-(13)C]glucose compared with [U-(13)C]lactate. Intracellular glutamate and extracellular glutamine exhibited similar incorporation patterns with regard to double compared with triple labeling and the extent of incorporation of label from [U-(13)C]lactate compared with [U-(13)C]glucose. It should be noted that the main intracellular pools of citrate and glutamine were compartmentalized; i.e., releasable citrate and glutamine exhibited a labeling pattern distinctly different from that of their intracellular pools. Moreover, carboxylation of pyruvate using glucose as the precursor was more important for biosynthesis of releasable glutamine and citrate, compared with their intracellular pools. Based on the results a model of multiple compartments is suggested. The compartments differ with regard to utilization of lactate and glucose, synthetic pathways for TCA cycle intermediates and amino acids, particularly citrate and glutamine, as well as the contents of different metabolites.

Role of glutamate dehydrogenase reaction in the control of citrate pool in yeast

1.1. Role of NADP-glutamate dehydrogenase in the depletion of citrate was analyzed using permeabilized yeast cells.2.2. Citrate was converted to 2-oxoglutarate, which was then metabolized to glutamate by NADP-glutamate dehydrogenase in the presence of ammonium ion.3.3. Formation of 2-oxoglutarate plus glutamate was in good agreement with the concentration of citrate decreased. Glutamate formation can be a good indicator of the depletion of citrate, because 70% of the citrate decreased was converted to glutamate.4.4. Glycolytic activity was closely correlated with the decrease in citrate under the in situ conditions.5.5. NADP-glutamate dehydrogenase increased in anaerobically grown yeast cells.6.6. An effective depletion of citrate by increased synthesis of NADP-glutamate dehydrogenase can explain the lowered mechanism of citrate causing glycolytic stimulation under the anaerobic growth conditions of yeast.

A Preliminary Study of the Source and Fate of Carbon Acquired Via CAM inLittorella unifloravar.americana(Fern.) G1.

ABSTRACT The aquatic Crassulacean Acid Metabolism (CAM) plant, Littorella uniflora var. americana (Fern.) G1., was the subject of some preliminary investigations to determine (1) if the source of the nocturnally accumulated carbon is endogenous, from respiration, or is exogenous, (2) if this carbon was stored primarily as malic acid, as is typical for the CAM pathway and (3) if the nocturnally accumulated carbon was photosynthetically incorporated during the subsequent light period. Littorella plants were collected from the field and held in the labor-atory under different levels of CO2, light, and temperature. The diurnal malic acid rhythm in leaves ranged from 46 to 60 μmoles · g−1 fresh wt., Radiocarbon studies showed that endogenous CO2 (from dark respiration) accounted for 30 to 99% of the nocturnal carbon accumulation. Paper chromatography revealed that the nocturnally incorporated, labelled carbon was primarily in the malate pool, with some labeling of the citrate pool. All of the nocturnally acqui...

Turnover rates and intracellular pool size distribution of citrate cycle intermediates in normal, diabetic and fat-fed rats estimated by computer analysis from specific activity decay data of 14C-labeled citrate cycle acids.

Specific radioactivity curves of citrate, malate, glutamate and aspartate were measured in vivo in liver from normal, fat‐fed and diabetic rats with [1‐14C]acetate as precursor at time intervals of 0.1 to 20 min. A mathematical model of 14 pools and 40 interconnecting flux rates been constructed and by computer analysis on the Univac 1108 flux rates and intra‐ and extra‐mitochondrial metabolite pool distribution calculated from the measured specific radioactivity curves. Flux rates and pool distributions were varied by using an automatic minimization routine to minimize the difference between observed and theoretical values until an acceptable fit of computer generated specific radioactivity time curves to experimentally observed specific radioactivities was obtained. Steady state kinetics were assumed, i.e. the model was fixed with no change in pool sizes over the measured time interval. The main conclusions were: A state of non‐equilibration of isotope exists for the acetyl‐CoA and acetylcarnitine, citrate, malate, aspartate, glutamate and α‐ketoglutarate pools distributed between cytoplasmic and mitochondrial compartments. Cytoplasmic pools of citrate, acetyl‐CoA and acetylcarnitine account for the slow rate of radioactivity decay observed for these metabolites in vivo. Key flux rates were acetate entry into the citrate cycle of 0.36, 0.28 and 1.05 μmoles × min−1× g liver−1 in normal, fat‐fed and diabetic rats. Citrate turnover rates were 1.21, 0.37 and 1.94 μmoles × min−1× g liver−1 for normal, fat‐fed and diabetic rats. The acetate pool was 0.23 μmoles/g liver in normal, 0.44 μmoles/g liver in fat‐fed and 0.38 μmoles/g liver in diabetic rats. Metabolite pool distribution was greater in the extra‐ than intramitochondrial space: the shift was most marked in the diabetic rat where the intra‐ to extramitochondrial malate distribution was in the ratio of 1:21.5.

Fe and Ca Uptake as Related to Root‐Sap and Stem‐Exudate Citrate in Soybeans

AbstractTwo soybean varieties that differentially absorb and translocate iron were used to compare root‐sap citrate with stem‐exudate citrate as they are involved in the uptake of Fe and Ca. The status of Fe and PO4 in the prenutrient solution determined the citrate concentration in the root sap and the citrate translocated in the stem exudate. There was a parallel between the iron and the citrate translocated in the stem exudate, but this relationship did not appear to exist for the citrate and Fe concentrations in the root sap.Iron stress (deficiency) promoted the accumulation of citrate in the root‐sap, but there was not a concomitant increase of citrate in the stem exudate. In iron‐deficient soybeans, phosphate stress also promoted the accumulation of citrate in the root sap, and here, stem‐exudate citrate and root‐sap citrate more nearly followed the same trends. The citrate pool in the root appears to result from a deficiency of iron and may not be directly involved in the absorption and translocation of iron from the growth medium. Increasing amounts of phosphate in the prenutrient decreased both the citrate and Fe in the root sap and stem exudate.The factors controlling the uptake of Fe are rather specific and are not related to the uptake of radioactive Ca 45 in soybeans regardless of soybean variety, degree of iron stress, or citrate concentration in the root.

Utilization of citrate by epiphyseal cartilage of rachitic and normal rats

1. 1. The citrate concentration is reduced in tibial epiphyseal cartilage from rats made rachitic with diets low in phosphate and vitamin D. Addition of vitamin D to the diet for 3 to 7 days raises the citrate level without otherwise altering the rickets histologically. 2. 2. Citrate utilization by slices of tibial epiphyseal cartilage incubated in vitro was measured by determining the production of 14CO 2 from [6- 14C]citrate. The epiphyseal tissues from rachitic rats produced 14CO 2 at a rate several-fold that of tissue from normal rats or rachitic rats given vitamin D and/or inorganic phosphate. This difference was not accounted for by the variation in the apparent size of the citrate pool. 3. 3. One explanation for the decrease in the citrate content of rachitic epiphyses is increased utilization of this substrate by the cartilage.