scholarly journals Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeast

2014 ◽  
Author(s):  
Hanan L. Messiha ◽  
Edward Kent ◽  
Naglis Malys ◽  
Kathleen M. Carroll ◽  
Neil Swainston ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Saccharomyces Cerevisiae ◽  
Mathematical Model ◽  
Pentose Phosphate Pathway ◽  
Kinetic Modelling ◽  
Pentose Phosphate ◽  
Enzyme Kinetic ◽  
Scale Models ◽  
Metabolite Concentrations ◽  
Glucose Pulse

We present the quantification and kinetic characterisation of the enzymes of the pentose phosphate pathway in Saccharomyces cerevisiae. The data are combined into a mathematical model that describes the dynamics of this system and allows us to predict changes in metabolite concentrations and fluxes in response to perturbations. We use the model to study the response of yeast to a glucose pulse. We then combine the model with an existing glycolysis model to study the effect of oxidative stress on carbohydrate metabolism. The combination of these two models was made possible by the standardised enzyme kinetic experiments carried out in both studies. This work demonstrates the feasibility of constructing larger network-scale models by merging smaller pathway-scale models.

scholarly journals Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeast

2014 ◽  
Author(s):  
Hanan L. Messiha ◽  
Edward Kent ◽  
Naglis Malys ◽  
Kathleen M. Carroll ◽  
Neil Swainston ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Saccharomyces Cerevisiae ◽  
Mathematical Model ◽  
Pentose Phosphate Pathway ◽  
Kinetic Modelling ◽  
Pentose Phosphate ◽  
Enzyme Kinetic ◽  
Scale Models ◽  
Metabolite Concentrations ◽  
Glucose Pulse

We present the quantification and kinetic characterisation of the enzymes of the pentose phosphate pathway in Saccharomyces cerevisiae. The data are combined into a mathematical model that describes the dynamics of this system and allows us to predict changes in metabolite concentrations and fluxes in response to perturbations. We use the model to study the response of yeast to a glucose pulse. We then combine the model with an existing glycolysis model to study the effect of oxidative stress on carbohydrate metabolism. The combination of these two models was made possible by the standardised enzyme kinetic experiments carried out in both studies. This work demonstrates the feasibility of constructing larger network-scale models by merging smaller pathway-scale models.

scholarly journals Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeast

2013 ◽  
Author(s):  
Hanan L. Messiha ◽  
Edward Kent ◽  
Naglis Malys ◽  
Kathleen M. Carroll ◽  
Pedro Mendes ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Mathematical Model ◽  
Pentose Phosphate Pathway ◽  
Kinetic Modelling ◽  
Network Models ◽  
Pentose Phosphate ◽  
Enzyme Kinetic ◽  
Metabolite Concentrations ◽  
Pathway Models ◽  
Glucose Pulse

We present the quantification and kinetic characterisation of the enzymes of the pentose phosphate pathway in Saccharomyces cerevisiae. The data are combined into a mathematical model that describes the dynamics of this system and allows for the predicting changes in metabolite concentrations and fluxes in response to perturbations. We use the model to study the response of yeast to a glucose pulse. We then combine the model with an existing glycolysis one to study the effect of oxidative stress on carbohydrate metabolism. The combination of these two models was made possible by the standardized enzyme kinetic experiments carried out in both studies. This work demonstrates the feasibility of constructing larger network models by merging smaller pathway models.

scholarly journals Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeast

2014 ◽  
Author(s):  
Hanan L. Messiha ◽  
Edward Kent ◽  
Naglis Malys ◽  
Kathleen M. Carroll ◽  
Pedro Mendes ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Mathematical Model ◽  
Pentose Phosphate Pathway ◽  
Kinetic Modelling ◽  
Network Models ◽  
Pentose Phosphate ◽  
Enzyme Kinetic ◽  
Metabolite Concentrations ◽  
Pathway Models ◽  
Glucose Pulse

We present the quantification and kinetic characterisation of the enzymes of the pentose phosphate pathway in Saccharomyces cerevisiae. The data are combined into a mathematical model that describes the dynamics of this system and allows for the predicting changes in metabolite concentrations and fluxes in response to perturbations. We use the model to study the response of yeast to a glucose pulse. We then combine the model with an existing glycolysis one to study the effect of oxidative stress on carbohydrate metabolism. The combination of these two models was made possible by the standardized enzyme kinetic experiments carried out in both studies. This work demonstrates the feasibility of constructing larger network models by merging smaller pathway models.

scholarly journals Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeast

2013 ◽  
Author(s):  
Hanan L. Messiha ◽  
Edward Kent ◽  
Naglis Malys ◽  
Kathleen M. Carroll ◽  
Pedro Mendes ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Mathematical Model ◽  
Pentose Phosphate Pathway ◽  
Kinetic Modelling ◽  
Network Models ◽  
Pentose Phosphate ◽  
Enzyme Kinetic ◽  
Metabolite Concentrations ◽  
Pathway Models ◽  
Glucose Pulse

We present the quantification and kinetic characterisation of the enzymes of the pentose phosphate pathway in Saccharomyces cerevisiae. The data are combined into a mathematical model that describes the dynamics of this system and allows for the predicting changes in metabolite concentrations and fluxes in response to perturbations. We use the model to study the response of yeast to a glucose pulse. We then combine the model with an existing glycolysis one to study the effect of oxidative stress on carbohydrate metabolism. The combination of these two models was made possible by the standardized enzyme kinetic experiments carried out in both studies. This work demonstrates the feasibility of constructing larger network models by merging smaller pathway models.

scholarly journals Systematic Identification of Regulators of Oxidative Stress Reveals Non-canonical Roles for Peroxisomal Import and the Pentose Phosphate Pathway

Cell Reports ◽  
2020 ◽  
Vol 30 (5) ◽  
pp. 1417-1433.e7 ◽  
Author(s):  
Michael M. Dubreuil ◽  
David W. Morgens ◽  
Kanji Okumoto ◽  
Masanori Honsho ◽  
Kévin Contrepois ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Pentose Phosphate Pathway ◽  
Pentose Phosphate ◽  
Systematic Identification

scholarly journals TIGAR regulates glycolysis in ischemic kidney proximal tubules

2015 ◽  
Vol 308 (4) ◽  
pp. F298-F308 ◽  
Author(s):  
Jinu Kim ◽  
Kishor Devalaraja-Narashimha ◽  
Babu J. Padanilam
Keyword(s):  
Oxidative Stress ◽  
Reperfusion Injury ◽  
Pentose Phosphate Pathway ◽  
Ischemia Reperfusion Injury ◽  
Ischemia Reperfusion ◽  
Pentose Phosphate ◽  
Atp Depletion ◽  
G6pd Activity ◽  
Histological Damage ◽  
Severe Ischemia

Tp53-induced glycolysis and apoptosis regulator (TIGAR) activation blocks glycolytic ATP synthesis by inhibiting phosphofructokinase-1 activity. Our data indicate that TIGAR is selectively induced and activated in renal outermedullary proximal straight tubules (PSTs) after ischemia-reperfusion injury in a p53-dependent manner. Under severe ischemic conditions, TIGAR expression persisted through 48 h postinjury and induced loss of renal function and histological damage. Furthermore, TIGAR upregulation inhibited phosphofructokinase-1 activity, glucose 6-phosphate dehydrogenase (G6PD) activity, and induced ATP depletion, oxidative stress, autophagy, and apoptosis. Small interfering RNA-mediated TIGAR inhibition prevented the aforementioned malevolent effects and protected the kidneys from functional and histological damage. After mild ischemia, but not severe ischemia, G6PD activity and NADPH levels were restored, suggesting that TIGAR activation may redirect the glycolytic pathway into gluconeogenesis or the pentose phosphate pathway to produce NADPH. The increased level of NADPH maintained the level of GSH to scavenge ROS, resulting in a lower sensitivity of PST cells to injury. Under severe ischemia, G6PD activity and NADPH levels were reduced during reperfusion; however, blockade of TIGAR enhanced their levels and reduced oxidative stress and apoptosis. Collectively, these results demonstrate that inhibition of TIGAR may protect PST cells from energy depletion and apoptotic cell death in the setting of severe ischemia-reperfusion injury. However, under low ischemic burden, TIGAR activation induces the pentose phosphate pathway and autophagy as a protective mechanism.

scholarly journals Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Kanhaiya Kumar ◽  
Vishwesh Venkatraman ◽  
Per Bruheim
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Growth Rate ◽  
Amino Acid ◽  
Growth Rates ◽  
Pentose Phosphate Pathway ◽  
Pentose Phosphate ◽  
Relative Reduction ◽  
Central Metabolism ◽  
Cultivation Conditions ◽  
Biological Studies

Abstract Background Saccharomyces cerevisiae is a well-known popular model system for basic biological studies and serves as a host organism for the heterologous production of commercially interesting small molecules and proteins. The central metabolism is at the core to provide building blocks and energy to support growth and survival in normal situations as well as during exogenous stresses and forced heterologous protein production. Here, we present a comprehensive study of intracellular central metabolite pool profiling when growing S. cerevisiae on different carbon sources in batch cultivations and at different growth rates in nutrient-limited glucose chemostats. The latest versions of absolute quantitative mass spectrometry-based metabolite profiling methodology were applied to cover glycolytic and pentose phosphate pathway metabolites, tricarboxylic acid cycle (TCA), complete amino acid, and deoxy-/nucleoside phosphate pools. Results Glutamate, glutamine, alanine, and citrate were the four most abundant metabolites for most conditions tested. The amino acid is the dominant metabolite class even though a marked relative reduction compared to the other metabolite classes was observed for nitrogen and phosphate limited chemostats. Interestingly, glycolytic and pentose phosphate pathway (PPP) metabolites display the largest variation among the cultivation conditions while the nucleoside phosphate pools are more stable and vary within a closer concentration window. The overall trends for glucose and nitrogen-limited chemostats were increased metabolite pools with the increasing growth rate. Next, comparing the chosen chemostat reference growth rate (0.12 h−1, approximate one-fourth of maximal unlimited growth rate) illuminates an interesting pattern: almost all pools are lower in nitrogen and phosphate limited conditions compared to glucose limitation, except for the TCA metabolites citrate, isocitrate and α-ketoglutarate. Conclusions This study provides new knowledge-how the central metabolism is adapting to various cultivations conditions and growth rates which is essential for expanding our understanding of cellular metabolism and the development of improved phenotypes in metabolic engineering.

scholarly journals The pentose phosphate pathway in Trypanosoma cruzi: a potential target for the chemotherapy of Chagas disease

2007 ◽  
Vol 79 (4) ◽  
pp. 649-663 ◽  
Author(s):  
Mariana Igoillo-Esteve ◽  
Dante Maugeri ◽  
Ana L. Stern ◽  
Paula Beluardi ◽  
Juan J. Cazzulo
Keyword(s):  
Oxidative Stress ◽  
Trypanosoma Cruzi ◽  
Pentose Phosphate Pathway ◽  
Single Copy ◽  
Pentose Phosphate ◽  
Site Directed Mutagenesis ◽  
Haploid Genome ◽  
Salt Bridges ◽  
Phosphogluconate Dehydrogenase ◽  
Genes Encoding

Trypanosoma cruzi is highly sensitive to oxidative stress caused by reactive oxygen species. Trypanothione, the parasite's major protection against oxidative stress, is kept reduced by trypanothione reductase, using NADPH; the major source of the reduced coenzyme seems to be the pentose phosphate pathway. Its seven enzymes are present in the four major stages in the parasite's biological cycle; we have cloned and expressed them in Escherichia coli as active proteins. Glucose 6-phosphate dehydrogenase, which controls glucose flux through the pathway by its response to the NADP/NADPH ratio, is encoded by a number of genes per haploid genome, and is induced up to 46-fold by hydrogen peroxide in metacyclic trypomastigotes. The genes encoding 6-phosphogluconolactonase, 6-phosphogluconate dehydrogenase, transaldolase and transketolase are present in the CL Brener clone as a single copy per haploid genome. 6-phosphogluconate dehydrogenase is very unstable, but was stabilized introducing two salt bridges by site-directed mutagenesis. Ribose-5-phosphate isomerase belongs to Type B; genes encoding Type A enzymes, present in mammals, are absent. Ribulose-5-phosphate epimerase is encoded by two genes. The enzymes of the pathway have a major cytosolic component, although several of them have a secondary glycosomal localization, and also minor localizations in other organelles.

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