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The Krebs cycle in cells that contain mitochondria is necessary for both energy production and anabolic processes. In given cell/condition, the Krebs cycle is dynamic but remains at a steady state. In this article, we first aimed at comparing the properties of a closed cycle versus the same metabolism in a linear array. The main finding is that, unlike a linear metabolism, the closed cycle can reach a steady state (SS) regardless of the nature and magnitude of the disturbance. When the cycle is modeled with input and output reactions, the "open" cycle is robust and reaches a steady state but with exceptions that lead to sustained accumulation of intermediate metabolites, i.e., conditions at which no SS can be achieved. The modeling of the cycle in cancer, trying to obtain marked reductions in flux, shows that these reductions are limited and therefore the Warburg effect is moderate at most. In general, our results of modeling the cycle in different conditions and looking for the achievement, or not, of SS, suggest that the cycle may have a regulation, not yet discovered, to go from an open cycle to a closed one. Said regulation could allow for reaching the steady state, thus avoiding the unwanted effects derived from the aberrant accumulation of metabolites in the mitochondria. The information in this paper might be useful to evaluate metabolism-modifying medicines. [ABSTRACT FROM AUTHOR]

Background: Salt stress is one of the main constraints determining crop productivity, and therefore one of the main limitations for food production. The aim of this study was to characterize the salt stress response at the physiological and molecular level of different Broccoli (Brassica oleracea L. var. Italica Plenck) cultivars that were previously characterized in field and greenhouse trials as salt sensitive or salt tolerant. This study aimed to identify functional and molecular traits capable of predicting the ability of uncharacterized lines to cope with salt stress. For this purpose, this study measured different physiological parameters, hormones and metabolites under control and salt stress conditions. Results: This study found significant differences among cultivars for stomatal conductance, transpiration, methionine, proline, threonine, abscisic acid, jasmonic acid and indolacetic acid. Salt tolerant cultivars were shown to accumulate less sodium and potassium in leaves and have a lower sodium to potassium ratio under salt stress. Analysis of primary metabolites indicated that salt tolerant cultivars have higher concentrations of several intermediates of the Krebs cycle and the substrates of some anaplerotic reactions. Conclusions: This study has found that the energetic status of the plant, the sodium extrusion and the proline content are the limiting factors for broccoli tolerance to salt stress. Our results establish physiological and molecular traits useful as distinctive markers to predict salt tolerance in Broccoli or to design novel biotechnological or breeding strategies for improving broccoli tolerance to salt stress. [ABSTRACT FROM AUTHOR]

The Krebs cycle in cells that contain mitochondria is necessary for both energy production and anabolic processes. In given cell/condition, the Krebs cycle is dynamic but remains at a steady state. In this article, we first aimed at comparing the properties of a closed cycle versus the same metabolism in a linear array. The main finding is that, unlike a linear metabolism, the closed cycle can reach a steady state (SS) regardless of the nature and magnitude of the disturbance. When the cycle is modeled with input and output reactions, the “open” cycle is robust and reaches a steady state but with exceptions that lead to sustained accumulation of intermediate metabolites, i.e., conditions at which no SS can be achieved. The modeling of the cycle in cancer, trying to obtain marked reductions in flux, shows that these reductions are limited and therefore the Warburg effect is moderate at most. In general, our results of modeling the cycle in different conditions and looking for the achievement, or not, of SS, suggest that the cycle may have a regulation, not yet discovered, to go from an open cycle to a closed one. Said regulation could allow for reaching the steady state, thus avoiding the unwanted effects derived from the aberrant accumulation of metabolites in the mitochondria. The information in this paper might be useful to evaluate metabolism-modifying medicines.

Dark, that is, nonphototrophic, microbial CO2 fixation occurs in a large range of soils. However, it is still not known whether dark microbial CO2 fixation substantially contributes to the C balance of soils and what factors control this process. Therefore, the objective of this study was to quantitate dark microbial CO2 fixation in temperate forest soils, to determine the relationship between the soil CO2 concentration and dark microbial CO2 fixation, and to estimate the relative contribution of different microbial groups to dark CO2 fixation. For this purpose, we conducted a 13C‐CO2 labeling experiment. We found that the rates of dark microbial CO2 fixation were positively correlated with the CO2 concentration in all soils. Dark microbial CO2 fixation amounted to up to 320 µg C kg−1 soil day−1 in the Ah horizon. The fixation rates were 2.8–8.9 times higher in the Ah horizon than in the Bw1 horizon. Although the rates of dark microbial fixation were small compared to the respiration rate (1.2%–3.9% of the respiration rate), our findings suggest that organic matter formed by microorganisms from CO2 contributes to the soil organic matter pool, especially given that microbial detritus is more stable in soil than plant detritus. Phospholipid fatty acid analyses indicated that CO2 was mostly fixed by gram‐positive bacteria, and not by fungi. In conclusion, our study shows that the dark microbial CO2 fixation rate in temperate forest soils increases in periods of high CO2 concentrations, that dark microbial CO2 fixation is mostly accomplished by gram‐positive bacteria, and that dark microbial CO2 fixation contributes to the formation of soil organic matter. [ABSTRACT FROM AUTHOR]

Pyruvate carboxylase of Corynebacterium glutamicum serves as anaplerotic enzyme when cells are growing on carbohydrates and plays an important role in the industrial production of metabolites derived from the tricarboxylic acid cycle, such as l-glutamate or l-lysine. Previous studies suggested that the enzyme from C. glutamicum is very labile, as activity could only be measured in permeabilized cells, but not in cell-free extracts. In this study, we established conditions allowing activity measurements in cell-free extracts of C. glutamicum and purification of the enzyme by avidin affinity chromatography and gel filtration. Using a coupled enzymatic assay with malate dehydrogenase, Vmax values between 20 and 25 μmol min−1 mg−1 were measured for purified pyruvate carboxylase corresponding to turnover numbers of 160 – 200 s−1 for the tetrameric enzyme. The concentration dependency for pyruvate and ATP followed Michaelis-Menten kinetics with Km values of 3.76 ± 0.72 mM and 0.61 ± 0.13 mM, respectively. For bicarbonate, concentrations ≥5 mM were required to obtain activity and half-maximal rates were found at 13.25 ± 4.88 mM. ADP and aspartate inhibited PCx activity with apparent Ki values of 1.5 mM and 9.3 mM, respectively. Acetyl-CoA had a weak inhibitory effect, but only at low concentrations up to 50 μM. The results presented here enable further detailed biochemical and structural studies of this enzyme. [ABSTRACT FROM AUTHOR]

It has been established that in cells of Nocardia vaccinii IMB B-7405 (surfactant producer) glucose catabolism is performed through pentose phosphate cycle as well as through gluconate (activi­ty of NAD+-dependent glucose-6- phosphate dehydrogenase and FAD+-dependent glucose dehydrogenase 835 ± 41 and 698 ± 35 nmol∙min-1∙mg-1 of protein respectively). 6-Phosphogluconate formed in the gluconokinase reaction is involved in the pentose phosphate cycle (activity of constitutive NADP+-dependent 6-phosphogluconate dehydrogenase 357 ± 17 nmol∙min-1∙mg-1 of protein). Glyce­rol catabolism to dihydroxyacetonephosphate (the intermediate of glycolysis) may be performed in two ways: through glycerol-3-phosphate (glycerol kinase activity 244 ± 12 nmol∙min-1∙mg-1 of protein) and through dihydroxyacetone. Replenishment of the C4-dicarboxylic acids pool in N. vaccinii IMV B-7405 grown on glucose and glycerol occurs in the phosphoenolpyruvate(PEP)carboxylase reaction (714–803 nmol∙min-1∙mg-1 of protein). 2-Oxoglutara­te was involved in tricarboxylic acid cycle by alternate pathway with the participation of 2-oxoglutarate synthase. The observed activity of both key enzymes of gluconeogenesis (PEP- carboxykinase and PEP-synthase), trehalose phosphate synthase and NADP+-dependent glutamate dehydrogenase confirmed the ability of IMV B-7405 strain to the synthesis of surface active glyco- and aminolipids, respectively.

Covering two-thirds of our planet, the global deep ocean plays a central role in supporting life on Earth. Among other processes, this biggest ecosystem buffers the rise of atmospheric CO2. Despite carbon sequestration in the deep ocean has been known for a long time, microbial activity in the meso- and bathypelagic realm via the “assimilation of bicarbonate in the dark” (ABD) has only recently been described in more details. Based on recent findings, this process seems primarily the result of chemosynthetic and anaplerotic reactions driven by different groups of deep-sea prokaryoplankton. We quantified bicarbonate assimilation in relation to total prokaryotic abundance, prokaryotic heterotrophic production and respiration in the meso- and bathypelagic Mediterranean Sea. The measured ABD values, ranging from 133 to 370 μg C m−3 d−1, were among the highest ones reported worldwide for similar depths, likely due to the elevated temperature of the deep Mediterranean Sea (13–14°C also at abyssal depths). Integrated over the dark water column (≥200 m depth), bicarbonate assimilation in the deep-sea ranged from 396 to 873 mg C m−2 d−1. This quantity of produced de novo organic carbon amounts to about 85–424% of the phytoplankton primary production and covers up to 62% of deep-sea prokaryotic total carbon demand. Hence, the ABD process in the meso- and bathypelagic Mediterranean Sea might substantially contribute to the inorganic and organic pool and significantly sustain the deep-sea microbial food web. To elucidate the ABD key-players, we established three actively nitrifying and CO2-fixing prokaryotic enrichments. Consortia were characterized by the co-occurrence of chemolithoautotrophic Thaumarchaeota and chemoheterotrophic proteobacteria. One of the enrichments, originated from Ionian bathypelagic waters (3,000 m depth) and supplemented with low concentrations of ammonia, was dominated by the Thaumarchaeota “low-ammonia-concentration” deep-sea ecotype, an enigmatic and ecologically important group of organisms, uncultured until this study.

Covering two-thirds of our planet, the global deep ocean plays a central role in supporting life on Earth. Among other processes, this biggest ecosystem buffers the rise of atmospheric CO2. Despite carbon sequestration in the deep ocean has been known for a long time, microbial activity in the meso- and bathypelagic realm via the "assimilation of bicarbonate in the dark" (ABD) has only recently been described in more details. Based on recent findings, this process seems primarily the result of chemosynthetic and anaplerotic reactions driven by different groups of deep-sea prokaryoplankton. We quantified bicarbonate assimilation in relation to total prokaryotic abundance, prokaryotic heterotrophic production and respiration in the meso- and bathypelagic Mediterranean Sea. The measured ABD values, ranging from 133 to 370 μg Cm-3 d-1, were among the highest ones reported worldwide for similar depths, likely due to the elevated temperature of the deepMediterranean Sea (13-14°C also at abyssal depths). Integrated over the dark water column (≥200m depth), bicarbonate assimilation in the deep-sea ranged from 396 to 873mg C m-2 d-1. This quantity of produced de novo organic carbon amounts to about 85-424% of the phytoplankton primary production and covers up to 62% of deep-sea prokaryotic total carbon demand. Hence, the ABD process in the meso- and bathypelagic Mediterranean Sea might substantially contribute to the inorganic and organic pool and significantly sustain the deep-sea microbial food web. To elucidate the ABD key-players, we established three actively nitrifying and CO2-fixing prokaryotic enrichments. Consortia were characterized by the co-occurrence of chemolithoautotrophic Thaumarchaeota and chemoheterotrophic proteobacteria. One of the enrichments, originated from Ionian bathypelagic waters (3,000m depth) and supplemented with low concentrations of ammonia, was dominated by the Thaumarchaeota "low-ammonia-concentration" deep-sea ecotype, an enigmatic and ecologically important group of organisms, uncultured until this study. [ABSTRACT FROM AUTHOR]

The metabolite profile changes induced by Fe-deficiency in leaves and xylem sap of several Strategy I plant species have been characterized. We have confirmed that Fe deficiency causes consistent changes both in the xylem sap and leaf metabolite profiles. The main changes in the xylem sap metabolite profile in response to Fe deficiency include consistent decreases in aminoacids, N-related metabolites and carbohydrates and increases in TCA cycle metabolites. In tomato, Fe-resupply causes a transitory flush of xylem sap carboxylates, but within one day the metabolite profile of the xylem sap from Fe-deficient plants becomes similar to that of Fe-sufficient controls. The main changes in the metabolite profile of leaf extracts in response to Fe deficiency include consistent increases in aminoacids and N-related metabolites, carbohydrates and TCA cycle metabolites. In leaves, selected pairs of aminoacids and TCA cycle metabolites show high correlations, with the sign depending of the Fe status. These data suggest that in low photosynthesis, C-starved Fe-deficient plants anaplerotic reactions involving aminoacids can be crucial for survival in the short-term.

Aims: Detailed knowledge about the enzymes responsible for conversion of C3 and C4 compounds will be helpful to establish the bacterial strain Ralstonia eutropha as platform for the production of biotechnologically interesting compounds. Although various studies about these enzymes were accomplished in the past, some contradicting information about the enzyme pattern in this bacterium still exists. To resolve these discrepancies, the C3/C4 metabolism was reinvestigated after the genome sequence of this bacterium became available. Methods and Results: In silico analysis of genome sequence revealed putative genes coding for NAD(P)+-dependent malic enzymes (Mae), phoshoenolpyruvate carboxykinase (Pck), phosphoenolpyruvate carboxylase (Ppc), phosphoenolpyruvate synthase (Pps) and pyruvate carboxylase (Pyc). Reverse transcription PCR revealed constitutive expression of mae and pck genes, whereas no transcripts of pyc and ppc were found. Expression of active NADP+-dependent MaeB and Pck and absence of Pyc and Ppc was confirmed by spectrophotometric enzyme assays. Conclusions: The data reported in this study suggest that two enzymes, (i) MaeB and (ii) Pck, mediate between the C3 and C4 intermediates in R. eutropha H16. The enzymatic conversion of pyruvate into phosphoenolpyruvate (PEP) is catalysed by Pps, and an NADH+-dependent Mdh mediates the reversible conversion of malate and oxaloacetate. Significance and Impact of the Study: An increased knowledge of the enzymes mediating between C3 and C4 intermediates in R. eutropha will facilitate metabolic engineering. [ABSTRACT FROM AUTHOR]

The gene encoding pyruvate carboxylase (pyc) was isolated from a Sinorhizobium meliloti Rm1021 cosmid bank by complementation of a Rhizobium tropici pyc mutant. PYC-negative mutants of S. meliloti Rm1021 were isolated by transposon mutagenesis and were unable to grow with glucose or pyruvate as sole carbon sources, but were symbiotically competent in combination with alfalfa plants. PYC activity assays, pyc::lacZ gene fusion studies and an in vivo biotinylation assay showed that PYC activity in S. meliloti was dependent mainly on biotin availability and not on changes in gene transcription. The subunit and holo-enzyme molecular masses of the S. meliloti PYC indicated that the enzyme was an α4 homotetramer. The S. meliloti PYC had a high apparent Ka (0.23 mM) for the allosteric activator acetyl-CoA and was product-inhibited by sub-millimolar concentrations of oxaloacetate. In contrast to other bacterial α4-PYCs which have been characterized, the S. meliloti enzyme was not strongly inhibited by L-aspartate. [ABSTRACT FROM AUTHOR]

A prototrophic pyruvate-carboxylase-negative (Pyc-) mutant was constructed by deleting the PYC1 and PYC2 genes in a CEN.PK strain of Saccharomyces cerevisiae. Its maximum specific growth rate on ethanol was identical to that of the isogenic wild type but it was unable to grow in batch cultures in glucose-ammonia media. Consistent with earlier reports, growth on glucose could be restored by supplying aspartate as a sole nitrogen source. Ethanol could not replace aspartate as a source of oxaloacetate in batch cultures. To investigate whether alleviation of glucose repression allowed expression of alternative pathways for oxaloacetate synthesis, the Pyc- strain and an isogenic wild-type strain were grown in aerobic carbon-limited chemostat cultures at a dilution rate of 0.10 h-1 on mixtures of glucose and ethanol. In such mixed-substrate chemostat cultures of the Pyc- strain, steady-state growth could only be obtained when ethanol contributed 30% or more of the substrate carbon in the feed. Attempts to further decrease the ethanol content of the feed invariably resulted in washout. In Pyc- as well as in wild-type cultures, levels of isocitrate lyase, malate synthase and phospho-enol-pyruvate carboxykinase in cell extracts decreased with a decreasing ethanol content in the feed. Nevertheless, at the lowest ethanol fraction that supported growth of the Pyc- mutant, activities of the glyoxylate cycle enzymes in cell extracts were still sufficient to meet the requirement for C4-compounds in biomass synthesis. This suggests that factors other than glucose repression of alternative routes for oxaloacetate synthesis prevent growth of Pyc-mutants on glucose. [ABSTRACT FROM AUTHOR]

The strict anaerobe Desulfobacter postgatei oxidizes acetate to CO with sulfate as electron acceptor. During growth at 28°C with a doubling time of 16 h the oxidation and assimilation rate of acetate were 280 nmol and 20 nmol per min and mg protein, respectively. In cell extracts all the enzymes of the citric acid cycle were found (numbers in brackets=specific activities in nmol per min and mg protein at 28°C): Citrate (si)-synthase (250); aconitase (200); NADP-dependent isocitrate dehydrogenase (8500); 2-oxoglutarate: ferredoxin oxidoreductase (300); succinyl-CoA: acetate CoA transferase (160); membrane bound succinate dehydrogenase (3500); and membrane bound malate dehydrogenase with 2,3-dimethyl-1,4-naphthoquinone as artificial electron acceptor (54). The following enzymes catalyzing the synthesis of oxaloacetate from acetate and CO were also present: Acetyl-CoA synthetase (10); ferredoxin dependent pyruvate synthase (30); phosphoenolpyruvate synthetase (10); and phosphoenolpyruvate carboxylase (24). The key enzymes of the glyoxylate cycle were not detected. The order of magnitude of the observed enzyme activities was sufficient to account for an oxidation of acetate via the citric acid cycle and for a synthesis of oxaloacetate from acetate and CO as anaplerotic reaction. The membranes of D. postgatei contained menaquinone (0.35 nmol per mg cell dry weight) rather than ubiquinone or demethylmenaquinone. The cytoplasmic fraction contained ferredoxin (0.09 nmol per mg cell dry weight). [ABSTRACT FROM AUTHOR]

All the enzymes required for the oxidation of acetate to CO via the citric acid cycle were found in Desulfobacter postgatei. To obtain in vivo evidence for the operation of this cycle, the sulfate reducing bacterium was grown on [C]acetate in the presence of a large pool of CO and the incorporation of C into glutamate (≙ 2-oxoglutarate), aspartate (≙ oxaloacetate), and alanine (≙ pyruvate) was studied. The labelling data were found to be consistent with (i) the oxidation of acetate to CO via the reactions of the citric acid cycle, (ii) the synthesis of citrate via a citrate (si)-synthase, and (iii) the anaplerotic synthesis of oxaloacetate from acetate and 2 CO via pyruvate as intermediate. [ABSTRACT FROM AUTHOR]

Anaplerotic reactions replenish TCA cycle intermediates during growth. In Saccharomyces cerevisiae , pyruvate carboxylase and the glyoxylate cycle have been experimentally identified to be the main anaplerotic routes during growth on glucose (C6) and ethanol (C2), respectively. The current study investigates the importance of the two isoenzymes of pyruvate carboxylase (PYC1 and PYC2) and one of the key enzymes of the glyoxylate cycle (ICL1) for growth on glycerol (C3) as a sole carbon source. As the wild-type strains of the CEN.PK family are unable to grow in pure synthetic glycerol medium, a reverse engineered derivative showing a maximum specific growth rate of 0.14 h−1 was used as the reference strain. While the deletion of PYC1 reduced the maximum specific growth rate by about 38%, the deletion of PYC2 had no significant impact, neither in the reference strain nor in the pyc1 Δ mutant. The deletion of ICL1 only marginally reduced growth of the reference strain but further decreased the growth rate of the pyc1 deletion strain by 20%. Interestingly, the triple deletion (pyc1 Δ pyc2 Δ icl1 Δ) did not show any growth. Therefore, both the pyruvate carboxylase and the glyoxylate cycle are involved in anaplerosis during growth on glycerol. [ABSTRACT FROM AUTHOR]