scholarly journals Imaging and modelling of poly(3-hydroxybutyrate) synthesis in Paracoccus denitrificans

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sergio Bordel ◽  
Rob J. M. van Spanning ◽  
Fernando Santos-Beneit
Keyword(s):  
Exponential Growth ◽  
Laser Scanning ◽  
Paracoccus Denitrificans ◽  
Tca Cycle ◽  
Metabolic Model ◽  
Acetyl Coa ◽  
Granule Formation ◽  
The Tca Cycle ◽  
A Genome ◽  
Phb Production

AbstractPoly(3-hydroxybutyrate) (PHB) granule formation in Paracoccus denitrificans Pd1222 was investigated by laser scanning confocal microscopy (LSCM) and gas chromatography analysis. Cells that had been starved for 2 days were free of PHB granules but resynthesized them within 30 min of growth in fresh medium with succinate. In most cases, the granules were distributed randomly, although in some cases they appeared in a more organized pattern. The rates of growth and PHB accumulation were analyzed within the frame of a Genome-Scale Metabolic Model (GSMM) containing 781 metabolic genes, 1403 reactions and 1503 metabolites. The model was used to obtain quantitative predictions of biomass yields and PHB synthesis during aerobic growth on succinate as sole carbon and energy sources. The results revealed an initial fast stage of PHB accumulation, during which all of the acetyl-CoA originating from succinate was diverted to PHB production. The next stage was characterized by a tenfold lower PHB production rate and the simultaneous onset of exponential growth, during which acetyl-CoA was predominantly drained into the TCA cycle. Previous research has shown that PHB accumulation correlates with cytosolic acetyl-CoA concentration. It has also been shown that PHB accumulation is not transcriptionally regulated. Our results are consistent with the mentioned findings and suggest that, in absence of cell growth, most of the cellular acetyl-CoA is channeled to PHB synthesis, while during exponential growth, it is drained to the TCA cycle, causing a reduction of the cytosolic acetyl-CoA pool and a concomitant decrease of the synthesis of acetoacetyl-CoA (the precursor of PHB synthesis).

scholarly journals Imaging and modelling of poly(3-hydroxybutyrate) synthesis in Paracoccus denitrificans

2021 ◽  
Author(s):  
Sergio Bordel ◽  
Rob J. M. van Spanning ◽  
Fernando Santos-Beneit
Keyword(s):  
Exponential Growth ◽  
Laser Scanning ◽  
Paracoccus Denitrificans ◽  
Tca Cycle ◽  
Metabolic Model ◽  
Acetyl Coa ◽  
Granule Formation ◽  
The Tca Cycle ◽  
A Genome ◽  
Phb Production

Abstract Poly(3-hydroxybutyrate) (PHB) granule formation in Paracoccus denitrificans Pd1222 was investigated by laser scanning confocal microscopy (LSCM) and gas chromatography analysis. Cells that had been starved for 2 days were free of PHB granules but resynthesized them within 30 minutes of growth in fresh medium with succinate. In most cases, the granules were distributed randomly, although in some cases they appeared in a more organized pattern. The rates of growth and PHB accumulation were analyzed within the frame of a Genome-Scale Metabolic Model (GSMM) containing 781 metabolic genes, 1403 reactions and 1503 metabolites. The model was used to obtain quantitative predictions of biomass yields and PHB synthesis during aerobic growth on succinate as sole carbon and energy sources. The results revealed an initial fast stage of PHB accumulation, during which all of the acetyl-CoA originating from succinate was diverted to PHB production. The next stage was characterized by a tenfold lower PHB production rate and the simultaneous onset of exponential growth, during which acetyl-CoA was predominantly drained into the TCA cycle. Previous research has shown that PHB accumulation correlates with cytosolic acetyl-CoA concentration. It has also been shown that PHB accumulation is not transcriptionally regulated. Our results are consistent with the mentioned findings and suggest that, in absence of cell growth, most of the cellular acetyl-CoA is channeled to PHB synthesis, while during exponential growth, it is drained to the TCA cycle, causing a reduction of the cytosolic acetyl-CoA pool and a concomitant decrease of the synthesis of acetoacetyl-CoA (the precursor of PHB synthesis).

Gluconeogenesis from labeled carbon: estimating isotope dilution

1986 ◽  
Vol 250 (3) ◽  
pp. E296-E305 ◽  
Author(s):  
J. K. Kelleher
Keyword(s):  
Steady State ◽  
Isotope Dilution ◽  
Experimental Tests ◽  
Tca Cycle ◽  
Tricarboxylic Acid ◽  
Complex Model ◽  
Acetyl Coa ◽  
The Tca Cycle ◽  
Carbon Compounds ◽  
Mathematical Techniques

To estimate the rate of gluconeogenesis from steady-state incorporation of labeled 3-carbon precursors into glucose, isotope dilution must be considered so that the rate of labeling of glucose can be quantitatively converted to the rate of gluconeogenesis. An expression for the value of this isotope dilution can be derived using mathematical techniques and a model of the tricarboxylic acid (TCA) cycle. The present investigation employs a more complex model than that used in previous studies. This model includes the following pathways that may affect the correction for isotope dilution: 1) flux of 3-carbon precursor to the oxaloacetate pool via acetyl-CoA and the TCA cycle; 2) flux of 4- or 5-carbon compounds into the TCA cycle; 3) reversible flux between oxaloacetate (OAA) and pyruvate and between OAA and fumarate; 4) incomplete equilibrium between OAA pools; and 5) isotope dilution of 3-carbon tracers between the experimentally measured pool and the precursor for the TCA-cycle OAA pool. Experimental tests are outlined which investigators can use to determine whether these pathways are significant in a specific steady-state system. The study indicated that flux through these five pathways can significantly affect the correction for isotope dilution. To correct for the effects of these pathways an alternative method for calculating isotope dilution is proposed using citrate to relate the specific activities of acetyl-CoA and OAA.

Pattern of substrate utilization in vascular smooth muscle using 13C isotopomer analysis of glutamate

1998 ◽  
Vol 275 (6) ◽  
pp. H2227-H2235 ◽  
Author(s):  
Tara M. Allen ◽  
Christopher D. Hardin
Keyword(s):  
Smooth Muscle ◽  
Vascular Smooth Muscle ◽  
Tca Cycle ◽  
Tricarboxylic Acid ◽  
Acetyl Coa ◽  
Contractile State ◽  
The Tca Cycle ◽  
Direct Measurements ◽  
Isotopomer Analysis ◽  
13C Isotopomer Analysis

Although vascular smooth muscle (VSM) derives the majority of its energy from oxidative phosphorylation, controversy exists concerning which substrates are utilized by the tricarboxylic acid (TCA) cycle. We used 13C isotopomer analysis of glutamate to directly measure the entry of exogenous [13C]glucose and acetate and unlabeled endogenous sources into the TCA cycle via acetyl-CoA. Hog carotid artery segments denuded of endothelium were superfused with 5 mM [1-13C]glucose and 0–5 mM [1,2-13C]acetate at 37°C for 3–12 h. We found that both resting and contracting VSM preferentially utilize [1,2-13C]acetate compared with [1-13C]glucose and unlabeled substrates. The entry of glucose into the TCA cycle (30–60% of total entry via acetyl-CoA) exhibited little change despite alterations in contractile state or acetate concentrations ranging from 0 to 5 mM. We conclude that glucose and nonglucose substrates are important oxidative substrates for resting and contracting VSM. These are the first direct measurements of relative substrate entry into the TCA cycle of VSM during activation and may provide a useful method to measure alterations in VSM metabolism under physiological and pathophysiological conditions.

scholarly journals Modeling the Interplay between Photosynthesis, CO2 Fixation, and the Quinone Pool in a Purple Non-Sulfur Bacterium

2019 ◽  
Author(s):  
Adil Alsiyabi ◽  
Cheryl Immethun ◽  
Rajib Saha
Keyword(s):  
Organic Compounds ◽  
Redox State ◽  
Rhodopseudomonas Palustris ◽  
Tca Cycle ◽  
Metabolic Model ◽  
Hydrogen Gas ◽  
A Genome ◽  
Feed Forward Controller ◽  
Quinone Pool

AbstractRhodopseudomonas palustris CGA009 is a purple non-sulfur bacterium (PNSB) that can fix CO2 and nitrogen or break down organic compounds for its carbon and nitrogen requirements. Light, inorganic, and organic compounds can all be used for its source of energy. Excess electrons produced during its metabolic processes can be exploited to produce hydrogen gas or biodegradable polyesters (polyhydroxybutyrate). A genome-scale metabolic model of the bacterium was reconstructed to study the interactions between photosynthesis, carbon dioxide fixation, and the redox state of the quinone pool. A comparison of model-predicted flux values with published in vivo MFA fluxes resulted in predicted errors of 5-19% across four different growth substrates. The model predicted the presence of an unidentified sink responsible for the oxidation of excess quinols generated by the TCA cycle. Furthermore, light-dependent energy production was found to be highly dependent on the rate of quinol oxidation. Finally, the extent of CO2 fixation was predicted to be dependent on the amount of ATP generated through the electron transport cycle, with excess ATP going toward the energy-demanding CBB pathway. Based on this analysis, it is hypothesized that the quinone redox state acts as a feed-forward controller of the CBB pathway, signaling the amount of ATP available.

scholarly journals Massively parallel fitness profiling reveals multiple novel enzymes inPseudomonas putidalysine metabolism

2018 ◽  
Author(s):  
Mitchell G. Thompson ◽  
Jacquelyn M. Blake-Hedges ◽  
Pablo Cruz-Morales ◽  
Jesus F. Barajas ◽  
Samuel C. Curran ◽  
...  
Keyword(s):  
Tca Cycle ◽  
Central Metabolism ◽  
It Use ◽  
Catabolic Genes ◽  
Genome Wide ◽  
The Tca Cycle ◽  
A Genome ◽  
Domains Of Life ◽  
Lysine Degradation ◽  
Lysine Metabolism

AbstractDespite intensive study for 50 years, the biochemical and genetic links between lysine metabolism and central metabolism inPseudomonas putidaremain unresolved. To establish these biochemical links, we leveraged Random Barcode Transposon Sequencing (RB-TnSeq), a genome-wide assay measuring the fitness of thousands of genes in parallel, to identify multiple novel enzymes in both L- and D-lysine metabolism. We first describe three pathway enzymes that catabolize L-2-aminoadipate (L-2AA) to 2-ketoglutarate (2KG), connecting D-lysine to the TCA cycle. One of these enzymes, PP_5260, contains a DUF1338 domain, a family with no previously described biological function. Our work also identified the recently described CoA independent route of L-lysine degradation that metabolizes to succinate. We expanded on previous findings by demonstrating that glutarate hydroxylase CsiD is promiscuous in its 2-oxoacid selectivity. Proteomics of select pathway enzymes revealed that expression of catabolic genes is highly sensitive to particular pathway metabolites, implying intensive local and global regulation. This work demonstrates the utility of RB-TnSeq for discovering novel metabolic pathways in even well-studied bacteria, as well as a powerful tool for validating previous research.ImportanceP. putidalysine metabolism can produce multiple commodity chemicals, conferring great biotechnological value. Despite much research, connecting lysine catabolism to central metabolism inP. putidaremained undefined. Herein we use Random Barcode Transposon Sequencing to fill in the gaps of lysine metabolism inP. putida. We describe a route of 2-oxoadipate (2OA) catabolism in bacteria, which utilizes DUF1338 containing protein PP_5260. Despite its prevalence in many domains of life, DUF1338 containing proteins had no known biochemical function. We demonstrate PP_5260 is a metalloenzyme which catalyzes an unusual 2OA to D-2HG decarboxylation. Our screen also identified a recently described novel glutarate metabolic pathway. We validate previous results, and expand the understanding of glutarate hydroxylase CsiD by showing can it use either 2OA or 2KG as a cosubstrate. Our work demonstrates biological novelty can be rapidly identified using unbiased experimental genetics, and that RB-TnSeq can be used to rapidly validate previous results.

scholarly journals Lipogenesis and Redox Balance in Nitrogen-Fixing Pea Bacteroids

2016 ◽  
Vol 198 (20) ◽  
pp. 2864-2875 ◽  
Author(s):  
Jason J. Terpolilli ◽  
Shyam K. Masakapalli ◽  
Ramakrishnan Karunakaran ◽  
Isabel U. C. Webb ◽  
Rob Green ◽  
...  
Keyword(s):  
Direct Reduction ◽  
Root Nodules ◽  
Dicarboxylic Acids ◽  
Tca Cycle ◽  
Redox Potentials ◽  
Acetyl Coa ◽  
Content Type ◽  
The Tca Cycle ◽  
Redox Poise ◽  
Phb Synthase

ABSTRACTWithin legume root nodules, rhizobia differentiate into bacteroids that oxidize host-derived dicarboxylic acids, which is assumed to occur via the tricarboxylic acid (TCA) cycle to generate NAD(P)H for reduction of N2. Metabolic flux analysis of laboratory-grownRhizobium leguminosarumshowed that the flux from [13C]succinate was consistent with respiration of an obligate aerobe growing on a TCA cycle intermediate as the sole carbon source. However, the instability of fragile pea bacteroids prevented their steady-state labeling under N2-fixing conditions. Therefore, comparative metabolomic profiling was used to compare free-livingR. leguminosarumwith pea bacteroids. While the TCA cycle was shown to be essential for maximal rates of N2fixation, levels of pyruvate (5.5-fold reduced), acetyl coenzyme A (acetyl-CoA; 50-fold reduced), free coenzyme A (33-fold reduced), and citrate (4.5-fold reduced) were much lower in bacteroids. Instead of completely oxidizing acetyl-CoA, pea bacteroids channel it into both lipid and the lipid-like polymer poly-β-hydroxybutyrate (PHB), the latter via a type III PHB synthase that is active only in bacteroids. Lipogenesis may be a fundamental requirement of the redox poise of electron donation to N2in all legume nodules. Direct reduction by NAD(P)H of the likely electron donors for nitrogenase, such as ferredoxin, is inconsistent with their redox potentials. Instead, bacteroids must balance the production of NAD(P)H from oxidation of acetyl-CoA in the TCA cycle with its storage in PHB and lipids.IMPORTANCEBiological nitrogen fixation by symbiotic bacteria (rhizobia) in legume root nodules is an energy-expensive process. Within legume root nodules, rhizobia differentiate into bacteroids that oxidize host-derived dicarboxylic acids, which is assumed to occur via the TCA cycle to generate NAD(P)H for reduction of N2. However, direct reduction of the likely electron donors for nitrogenase, such as ferredoxin, is inconsistent with their redox potentials. Instead, bacteroids must balance oxidation of plant-derived dicarboxylates in the TCA cycle with lipid synthesis. Pea bacteroids channel acetyl-CoA into both lipid and the lipid-like polymer poly-β-hydroxybutyrate, the latter via a type II PHB synthase. Lipogenesis is likely to be a fundamental requirement of the redox poise of electron donation to N2in all legume nodules.

scholarly journals Glutamatergic and GABAergic TCA Cycle and Neurotransmitter Cycling Fluxes in Different Regions of Mouse Brain

2013 ◽  
Vol 33 (10) ◽  
pp. 1523-1531 ◽  
Author(s):  
Vivek Tiwari ◽  
Susmitha Ambadipudi ◽  
Anant B Patel
Keyword(s):  
Cerebral Cortex ◽  
Mouse Brain ◽  
Ex Vivo ◽  
Tca Cycle ◽  
Metabolic Model ◽  
Nmr Studies ◽  
Inhibitory Function ◽  
The Tca Cycle ◽  
The Brain ◽  
C Nmr

The 13C nuclear magnetic resonance (NMR) studies together with the infusion of 13C-labeled substrates in rats and humans have provided important insight into brain energy metabolism. In the present study, we have extended a three-compartment metabolic model in mouse to investigate glutamatergic and GABAergic tricarboxylic acid (TCA) cycle and neurotransmitter cycle fluxes across different regions of the brain. The 13C turnover of amino acids from [1,6-13C2]glucose was monitored ex vivo using qH-[13C]-NMR spectroscopy. The astroglial glutamate pool size, one of the important parameters of the model, was estimated by a short infusion of [2-13C]acetate. The ratio Vcyc/VTCA was calculated from the steady-state acetate experiment. The 13C turnover curves of [4-13C]/[3-13C]glutamate, [4-13C]glutamine, [2-13C]/[3-13C]GABA, and [3-13C]aspartate from [1,6-13C2]glucose were analyzed using a three-compartment metabolic model to estimate the rates of the TCA cycle and neurotransmitter cycle associated with glutamatergic and GABAergic neurons. The glutamatergic TCA cycle rate was found to be highest in the cerebral cortex (0.91±0.05 μmol/g per minute) and least in the hippocampal region (0.64±0.07 μmol/g per minute) of the mouse brain. In contrast, the GABAergic TCA cycle flux was found to be highest in the thalamus-hypothalamus (0.28±0.01 μmol/g per minute) and least in the cerebral cortex (0.24±0.02 μmol/g per minute). These findings indicate that the energetics of excitatory and inhibitory function is distinct across the mouse brain.

scholarly journals N-acetyltaurine and Acetylcarnitine Production for the Mitochondrial Acetyl-CoA Regulation in Skeletal Muscles during Endurance Exercises

Metabolites ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 522
Author(s):  
Teruo Miyazaki ◽  
Yuho Nakamura-Shinya ◽  
Kei Ebina ◽  
Shoichi Komine ◽  
Song-Gyu Ra ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Palmitic Acid ◽  
Skeletal Muscles ◽  
Metabolic Flux ◽  
Human Subjects ◽  
Tca Cycle ◽  
Blood Levels ◽  
Acetyl Coa ◽  
The Tca Cycle ◽  
Human Skeletal Muscle Cells

During endurance exercises, a large amount of mitochondrial acetyl-CoA is produced in skeletal muscles from lipids, and the excess acetyl-CoA suppresses the metabolic flux from glycolysis to the TCA cycle. This study evaluated the hypothesis that taurine and carnitine act as a buffer of the acetyl moiety of mitochondrial acetyl-CoA derived from the short- and long-chain fatty acids of skeletal muscles during endurance exercises. In human subjects, the serum concentrations of acetylated forms of taurine (NAT) and carnitine (ACT), which are the metabolites of acetyl-CoA buffering, significantly increased after a full marathon. In the culture medium of primary human skeletal muscle cells, NAT and ACT concentrations significantly increased when they were cultured with taurine and acetate or with carnitine and palmitic acid, respectively. The increase in the mitochondrial acetyl-CoA/free CoA ratio induced by acetate and palmitic acid was suppressed by taurine and carnitine, respectively. Elevations of NAT and ACT in the blood of humans during endurance exercises might serve the buffering of the acetyl-moiety in mitochondria by taurine and carnitine, respectively. The results suggest that blood levels of NAT and ACT indicate energy production status from fatty acids in the skeletal muscles of humans undergoing endurance exercise.

Growth of Paracoccus denitrificans on [2, 3- 13 C]succinate and [1, 4- 13 C]succinate IIl. Biosynthetic pathways

1988 ◽  
Vol 233 (1270) ◽  
pp. 1-15 ◽  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acids ◽  
Gas Chromatography ◽  
Paracoccus Denitrificans ◽  
Tca Cycle ◽  
Gas Chromatography Mass Spectrometry ◽  
Biosynthetic Pathways ◽  
The Tca Cycle ◽  
Phosphoenol Pyruvate

The biosynthesis in vivo of a number of amino acids, sugars, and purines in Paracoccus denitrificans grown on either [2, 3- 13 C]succinate or [1, 4- 13 C]succinate was investigated by using gas chromatography–mass spectrometry. The distribution of label in the TCA-cycle-related amino acids indicated that carbon intermediates of energy metabolism were utilized as precursors for the biosynthesis of these amino acids in vivo . The biosynthesis of glycine, serine, phenylalanine and glycerol from labelled succinate in vivo were consistent with phosphoenol pyruvate as an intermediate. A mechanism for the formation of C 4 , C 5 and C 6 sugars without the use of fructose-1, 6-bisphosphate aldolase (which has not been detected in P. denitrificans ) is proposed. The 13 C-enrichments of ribose in the bacterium indicate that there are at least three routes of ribose biosynthesis operating during growth on labelled succinate. The probability distribution of labelled purine molecules was successfully predicted for adenine, guanine and adenosine, thus confirming their generally accepted route of biosynthesis in vivo .

Growth of Paracoccus denitrificans on [2, 3- 13 C]succinate and [1, 4- 13 C]succinate. I. The flux of carbon in energy metabolism and the operation of the TCA cycle

1987 ◽  
Vol 231 (1264) ◽  
pp. 339-347 ◽  
Keyword(s):  
Mass Spectrometry ◽  
Energy Metabolism ◽  
Malic Enzyme ◽  
Paracoccus Denitrificans ◽  
Tca Cycle ◽  
Labelling Pattern ◽  
Carboxyl Groups ◽  
The Tca Cycle ◽  
Tca Cycle Intermediates

The metabolism of Paracoccus denitrificans , grown on either [2, 3- 13 C]- succinate or [1, 4- 13 C]succinate, was investigated by using gas chromato­graphy-mass spectrometry. The distribution of label in a group of metabolites closely related to the TCA-cycle intermediates showed that the flux of carbon from succinate in energy metabolism in vivo was via pyruvate (malic enzyme) and acetyl CoA. The labelling pattern of the carboxyl groups showed that one fifth of the succinate pool was formed by the regeneration of succinate via the TCA cycle, and four fifths was supplied externally as substrate from the medium.

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