scholarly journals Conditional iron and pH-dependent activity of a non-enzymatic glycolysis and pentose phosphate pathway

2016 ◽  
Vol 2 (1) ◽  
pp. e1501235 ◽  
Author(s):  
Markus A. Keller ◽  
Andre Zylstra ◽  
Cecilia Castro ◽  
Alexandra V. Turchyn ◽  
Julian L. Griffin ◽  
...  
Keyword(s):  
Pentose Phosphate Pathway ◽  
Metabolic Networks ◽  
Reaction Rates ◽  
Structural Features ◽  
Pentose Phosphate ◽  
Resonance Spectroscopy ◽  
Enzymatic Reactions ◽  
Evolutionary Origins ◽  
Sugar Phosphates ◽  
Neutral Conditions

Little is known about the evolutionary origins of metabolism. However, key biochemical reactions of glycolysis and the pentose phosphate pathway (PPP), ancient metabolic pathways central to the metabolic network, have non-enzymatic pendants that occur in a prebiotically plausible reaction milieu reconstituted to contain Archean sediment metal components. These non-enzymatic reactions could have given rise to the origin of glycolysis and the PPP during early evolution. Using nuclear magnetic resonance spectroscopy and high-content metabolomics that allowed us to measure several thousand reaction mixtures, we experimentally address the chemical logic of a metabolism-like network constituted from these non-enzymatic reactions. Fe(II), the dominant transition metal component of Archean oceanic sediments, has binding affinity toward metabolic sugar phosphates and drives metabolism-like reactivity acting as both catalyst and cosubstrate. Iron and pH dependencies determine a metabolism-like network topology and comediate reaction rates over several orders of magnitude so that the network adopts conditional activity. Alkaline pH triggered the activity of the non-enzymatic PPP pendant, whereas gentle acidic or neutral conditions favored non-enzymatic glycolytic reactions. Fe(II)-sensitive glycolytic and PPP-like reactions thus form a chemical network mimicking structural features of extant carbon metabolism, including topology, pH dependency, and conditional reactivity. Chemical networks that obtain structure and catalysis on the basis of transition metals found in Archean sediments are hence plausible direct precursors of cellular metabolic networks.

scholarly journals The Pentose Phosphate Pathway and Pyruvate Carboxylation after Neonatal Hypoxic-Ischemic Brain Injury

2014 ◽  
Vol 34 (4) ◽  
pp. 724-734 ◽  
Author(s):  
Eva MF Brekke ◽  
Tora S Morken ◽  
Marius Widerøe ◽  
Asta K Håberg ◽  
Ann-Mari Brubakk ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Glucose Metabolism ◽  
Pentose Phosphate Pathway ◽  
De Novo ◽  
Pentose Phosphate ◽  
Adult Brain ◽  
Resonance Spectroscopy ◽  
Neonatal Brain ◽  
Artery Ligation ◽  
Pyruvate Carboxylation

The neonatal brain is vulnerable to oxidative stress, and the pentose phosphate pathway (PPP) may be of particular importance to limit the injury. Furthermore, in the neonatal brain, neurons depend on de novo synthesis of neurotransmitters via pyruvate carboxylase (PC) in astrocytes to increase neurotransmitter pools. In the adult brain, PPP activity increases in response to various injuries while pyruvate carboxylation is reduced after ischemia. However, little is known about the response of these pathways after neonatal hypoxia-ischemia (HI). To this end, 7-day-old rats were subjected to unilateral carotid artery ligation followed by hypoxia. Animals were injected with [1,2-13C]glucose during the recovery phase and extracts of cerebral hemispheres ipsi- and contralateral to the operation were analyzed using 1H- and 13C-NMR (nuclear magnetic resonance) spectroscopy and high-performance liquid chromatography (HPLC). After HI, glucose levels were increased and there was evidence of mitochondrial hypometabolism in both hemispheres. Moreover, metabolism via PPP was reduced bilaterally. Ipsilateral glucose metabolism via PC was reduced, but PC activity was relatively preserved compared with glucose metabolism via pyruvate dehydrogenase. The observed reduction in PPP activity after HI may contribute to the increased susceptibility of the neonatal brain to oxidative stress.

scholarly journals Further observations on the Mg-protoporphyrin IX monomethyl ester (oxidative) cyclase system

1993 ◽  
Vol 290 (2) ◽  
pp. 355-359 ◽  
Author(s):  
B J Whyte ◽  
P A Castelfranco
Keyword(s):  
Pentose Phosphate Pathway ◽  
Protoporphyrin Ix ◽  
Companion Paper ◽  
Pentose Phosphate ◽  
Chloroplast Pigments ◽  
Cyclization Process ◽  
Reconstituted System ◽  
Sugar Phosphates ◽  
Cytochrome P 450 ◽  
Monomethyl Ester

The Mg-protoporphyrin IX monomethyl ester (oxidative) cyclase was strongly inhibited by CN- and N3- in a reconstituted system, but was inhibited slightly or not at all by the same reagents in intact developing chloroplasts. Known inhibitors of cytochrome P-450 processes showed no consistent effect. Benzoquinone and quinol, which can give rise to the same semiquinone by one-electron redox events, were strong inhibitors of the cyclase. It was previously shown that O2 and a source of electrons are required in the cyclization process. The substrates for the dehydrogenases of the pentose phosphate pathway (glucose 6-phosphate and 6-phosphogluconate) were effective reductants in the reconstituted system with supernatant that had been dialysed or passed through Sephadex G-50, in the absence of added NADP+. However, inhibitor studies suggested that the electrons from these sugar phosphates reached the cyclase system via NADPH. Therefore we infer the presence of protein-bound NADP+ that can be reduced by glucose 6-phosphate and 6-phosphogluconate and donate reducing equivalents to the cyclase system. This bound NADPH pool may be particularly effective in the cyclization process, owing to channeling. These findings are discussed in relation to the results of a companion paper [Whyte and Castelfranco (1993) Biochem. J. 290, 361-367] on the breakdown of chloroplast pigments in the same reconstituted system.

scholarly journals The pentose phosphate pathway constitutes a major metabolic hub in pathogenic Francisella

2021 ◽  
Vol 17 (8) ◽  
pp. e1009326
Author(s):  
Héloise Rytter ◽  
Anne Jamet ◽  
Jason Ziveri ◽  
Elodie Ramond ◽  
Mathieu Coureuil ◽  
...  
Keyword(s):  
Pentose Phosphate Pathway ◽  
Metabolic Pathways ◽  
Pathogenic Bacteria ◽  
Metabolic Networks ◽  
Tricarboxylic Acid Cycle ◽  
Sulfur Metabolism ◽  
Time Lapse ◽  
Pentose Phosphate ◽  
Francisella Novicida

Metabolic pathways are now considered as intrinsic virulence attributes of pathogenic bacteria and thus represent potential targets for antibacterial strategies. Here we focused on the role of the pentose phosphate pathway (PPP) and its connections with other metabolic pathways in the pathophysiology of Francisella novicida. The involvement of the PPP in the intracellular life cycle of Francisella was first demonstrated by studying PPP inactivating mutants. Indeed, we observed that inactivation of the tktA, rpiA or rpe genes severely impaired intramacrophage multiplication during the first 24 hours. However, time-lapse video microscopy demonstrated that rpiA and rpe mutants were able to resume late intracellular multiplication. To better understand the links between PPP and other metabolic networks in the bacterium, we also performed an extensive proteo-metabolomic analysis of these mutants. We show that the PPP constitutes a major bacterial metabolic hub with multiple connections to glycolysis, the tricarboxylic acid cycle and other pathways, such as fatty acid degradation and sulfur metabolism. Altogether our study highlights how PPP plays a key role in the pathogenesis and growth of Francisella in its intracellular niche.

scholarly journals In silico study of peculiarities of metabolism of erythrocytes with glucosephosphate isomerase deficiency

2019 ◽  
Vol 10 (3) ◽  
pp. 306-313
Author(s):  
O. I. Dotsenko
Keyword(s):  
Alternative Energy ◽  
Metabolic Networks ◽  
Experimental Studies ◽  
Supportive Therapy ◽  
Pentose Phosphate ◽  
Premature Aging ◽  
Enzymatic Reactions ◽  
Theoretical Substantiation ◽  
Evaluation Approach ◽  
Balance Analysis

Glucose phosphate isomerase (GPI) deficiency, the third most common cause of hereditary nonspherocytic hemolytic anemia, is associated with the mutation of the GPI gene. The results of the GPI deficiency are premature aging of erythrocytes, macrocytosis, reticulocytosis, minor splenomegaly, hyperbilirubinemia and hyperferritinemia, and hemolytic crisis under the influence of exogenous oxidants such as infections or drugs. Regarding the the lack of GPI correction drugs, the theoretical substantiation of supportive therapy based on system biology approaches that would allow the analysis of the relationships between numerical metabolic processes in a cell would be beneficial. The stoichiometric model of erythrocytes’ steady state metabolism, including the pathways of Embden-Meyerhof and pentose phosphate (PPP), purine metabolism cycles and glutathione synthesis, has been developed. To predict the redistribution of metabolic flows in erythrocytes under conditions of GPI deficiency, we used the flux balance analysis (FBA). In this approach, calculations of the elementary flux modes (EFMs) and the control-effective flux (CEF) have been performed. Using the CEF evaluation approach, effective profiles of enzymatic reactions depending on the degree of enzyme deficiency were obtained. It has been shown that these relationships can be the basis for future experimental studies. Analysis of the profiles of enzymatic reactions of metabolic networks suggests that erythrocytes are capable of metabolizing other substrates that contribute to overcoming the effects of energy stress in the case of enzymopathies. So, it is shown that erythrocytes can effectively use SAM and adenosine as alternative energy sources. It has been established that the GPI enzymopathy results in a decrease in the flow through the glycolysis and pentose phosphate pathway, resulting in a decrease in the content of such reducing agents as NADPH and GSH, ATP. The processes of the GSH synthesis from amino acids in the cell are shown to be suppressed. Decreased content of NADPH and GSH cause the premature aging of erythrocytes. The target therapeutic approaches that influence the behaviour of the metabolic network of erythrocytes are discussed.

scholarly journals Profiling of Pentose Phosphate Pathway Intermediates in Blood Spots by Tandem Mass Spectrometry: Application to Transaldolase Deficiency

2003 ◽  
Vol 49 (8) ◽  
pp. 1375-1380 ◽  
Author(s):  
Jojanneke H J Huck ◽  
Eduard A Struys ◽  
Nanda M Verhoeven ◽  
Cornelis Jakobs ◽  
Marjo S van der Knaap
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Pentose Phosphate Pathway ◽  
Multiple Reaction Monitoring ◽  
Pentose Phosphate ◽  
Dihydroxyacetone Phosphate ◽  
Tandem Mass ◽  
Sugar Phosphate ◽  
Blood Spots ◽  
Sugar Phosphates

Abstract Background: Recently, several patients with abnormal polyol profiles in body fluids have been reported, but the origins of these polyols are unknown. We hypothesized that they are derived from sugar phosphate intermediates of the pentose phosphate pathway (PPP), and we developed a semiquantitative method for profiling of pentose phosphate pathway intermediates. Methods: Sugar phosphates in blood spots were simultaneously analyzed by liquid chromatography–tandem mass spectrometry using an ion-pair-loaded C18 HPLC column. The tandem mass spectrometer was operated in the multiple-reaction monitoring mode. Enzymatically prepared d-[13C6]glucose 6-phosphate was used as internal standard. The method was used to study sugar phosphates abnormalities in a patient affected with a deficiency of transaldolase (TALDO1; EC 2.2.1.2). Results: In control blood spots, dihydroxyacetone phosphate, pentulose 5-phosphates, pentose 5-phosphates, hexose 6-phosphates, and sedoheptulose 7-phosphate were detected. Detection limits ranged from ∼100 to ∼500 nmol/L. Glyceraldehyde 3-phosphate and erythrose 4-phosphate were undetectable. Intra- and interassay imprecision (CVs) were 10–17% and 12–21%, respectively. In blood from the TALDO1-deficient patient, sedoheptulose 7-phosphate was increased. Conclusions: The new method allows investigation of patients in whom a defect in the PPP is suspected. Measurements of sugar phosphate intermediates of the PPP may provide new insights into metabolic defects underlying the accumulating polyols.

[5-3H]glucose overestimates glycolytic flux in isolated working rat heart: role of the pentose phosphate pathway

2001 ◽  
Vol 280 (3) ◽  
pp. E502-E508 ◽  
Author(s):  
Gary W. Goodwin ◽  
David M. Cohen ◽  
Heinrich Taegtmeyer
Keyword(s):  
Steady State ◽  
Pentose Phosphate Pathway ◽  
Rat Heart ◽  
Physiological State ◽  
Pentose Phosphate ◽  
Glycolytic Flux ◽  
Precursor Pool ◽  
Rat Hearts ◽  
Extracellular Glucose ◽  
Sugar Phosphates

We set out to study the pentose phosphate pathway (PPP) in isolated rat hearts perfused with [5-3H]glucose and [1-14C]glucose or [6-14C]glucose (crossover study with 1- then 6- or 6- then 1-14C-labeled glucose). To model a physiological state, hearts were perfused under working conditions with Krebs-Henseleit buffer containing 5 mM glucose, 40 μU/ml insulin, 0.5 mM lactate, 0.05 mM pyruvate, and 0.4 mM oleate/3% albumin. The steady-state C1/C6 ratio (i.e., the ratio from [1-14C]glucose to [6-14C]glucose) of metabolites released by the heart, an index of oxidative PPP, was not different from 1 (1.06 ± 0.19 for14CO2, and 1.00 ± 0.01 for [14C]lactate + [14C]pyruvate, mean ± SE, n = 8). Hearts exhibited contractile, metabolic, and14C-isotopic steady state for glucose oxidation (14CO2production). Net glycolytic flux (net release of lactate + pyruvate) and efflux of [14C]lactate + [14C]pyruvate were the same and also exhibited steady state. In contrast, flux based on3H2O production from [5-3H]glucose increased progressively, reaching 260% of the other measures of glycolysis after 30 min. The3H/14C ratio of glycogen (relative to extracellular glucose) and sugar phosphates (representing the glycogen precursor pool of hexose phosphates) was not different from each other and was <1 (0.36 ± 0.01 and 0.43 ± 0.05 respectively, n = 8, P < 0.05 vs. 1). We conclude that both transaldolase and the L-type PPP permit hexose detritiation in the absence of net glycolytic flux by allowing interconversion of glycolytic hexose and triose phosphates. Thus apparent glycolytic flux obtained by3H2O production from [5-3H]glucose overestimates the true glycolytic flux in rat heart.

scholarly journals Parameter estimation in tree graph metabolic networks

2016 ◽  
Author(s):  
Laura Astola ◽  
Hans Stigter ◽  
Maria Victoria Gomez Roldan ◽  
Fred van Eeuwijk ◽  
Robert D Hall ◽  
...  
Keyword(s):  
Metabolic Networks ◽  
Reaction Rates ◽  
Enzymatic Reactions ◽  
Potential Candidate ◽  
Concentration Data ◽  
Time Dynamics ◽  
Tomato Seedlings ◽  
Kinetic Coefficients ◽  
Time Series Gene Expression ◽  
Kinetic Rates

We study the glycosylation processes that convert initially toxic substrates to nutritionally valuable metabolites in the flavonoid biosynthesis pathway of tomato (Solanum lycopersicum) seedlings. To estimate the reaction rates we use ordinary differential equations (ODEs) to model the enzyme kinetics. A popular choice is to use a system of linear ODEs with constant kinetic rates or to use Michaelis-Menten kinetics. In reality, the catalytic rates, which are affected among other factors by kinetic constants and enzyme concentrations, are changing in time and with the approaches just mentioned, this phenomenon cannot be described. Another problem is that, in general these kinetic coefficients are not always identifiable. A third problem is that, it is not precisely known, which enzymes are catalyzing the observed glycosylation processes. With several hundred potential gene candidates, experimental validation using purified target proteins is expensive and time consuming. We aim at reducing this task via mathematical modeling to allow for the pre-selection of most potential gene candidates. In this article we discuss a fast and relatively simple approach to estimate time varying kinetic rates, with three favorable properties: Firstly, it allows for identifiable estimation of time dependent parameters in networks with a tree-like structure. Secondly, it is very fast compared to the usually applied methods, since it is not based on an iterative scheme. Thirdly, by combining the metabolite concentration data with a corresponding microarray data, it can help in detecting the genes related to the enzymatic processes. By comparing the estimated time dynamics of the catalytic rates with time series gene expression data we may assess potential candidate genes behind enzymatic reactions. As an example, we show how to apply this method to select prominent glycosyltransferase genes in tomato seedlings.

scholarly journals Parameter estimation in tree graph metabolic networks

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2417
Author(s):  
Laura Astola ◽  
Hans Stigter ◽  
Maria Victoria Gomez Roldan ◽  
Fred van Eeuwijk ◽  
Robert D. Hall ◽  
...  
Keyword(s):  
Metabolic Networks ◽  
Reaction Rates ◽  
Enzymatic Reactions ◽  
Potential Candidate ◽  
Concentration Data ◽  
Time Dynamics ◽  
Tomato Seedlings ◽  
Kinetic Coefficients ◽  
Time Series Gene Expression ◽  
Kinetic Rates

We study the glycosylation processes that convert initially toxic substrates to nutritionally valuable metabolites in the flavonoid biosynthesis pathway of tomato (Solanum lycopersicum) seedlings. To estimate the reaction rates we use ordinary differential equations (ODEs) to model the enzyme kinetics. A popular choice is to use a system of linear ODEs with constant kinetic rates or to use Michaelis–Menten kinetics. In reality, the catalytic rates, which are affected among other factors by kinetic constants and enzyme concentrations, are changing in time and with the approaches just mentioned, this phenomenon cannot be described. Another problem is that, in general these kinetic coefficients are not always identifiable. A third problem is that, it is not precisely known which enzymes are catalyzing the observed glycosylation processes. With several hundred potential gene candidates, experimental validation using purified target proteins is expensive and time consuming. We aim at reducing this task via mathematical modeling to allow for the pre-selection of most potential gene candidates. In this article we discuss a fast and relatively simple approach to estimate time varying kinetic rates, with three favorable properties: firstly, it allows for identifiable estimation of time dependent parameters in networks with a tree-like structure. Secondly, it is relatively fast compared to usually applied methods that estimate the model derivatives together with the network parameters. Thirdly, by combining the metabolite concentration data with a corresponding microarray data, it can help in detecting the genes related to the enzymatic processes. By comparing the estimated time dynamics of the catalytic rates with time series gene expression data we may assess potential candidate genes behind enzymatic reactions. As an example, we show how to apply this method to select prominent glycosyltransferase genes in tomato seedlings.

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