scholarly journals Flux Analysis of Central Metabolic Pathways in Geobacter metallireducens during Reduction of Soluble Fe(III)-Nitrilotriacetic Acid

2007 ◽  
Vol 73 (12) ◽  
pp. 3859-3864 ◽  
Author(s):  
Yinjie J. Tang ◽  
Romy Chakraborty ◽  
H�ctor Garc�a Mart�n ◽  
Jeannie Chu ◽  
Terry C. Hazen ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Tricarboxylic Acid Cycle ◽  
Nitrilotriacetic Acid ◽  
Reaction Rates ◽  
Total Carbon ◽  
Exponential Growth Phase ◽  
Flux Analysis ◽  
Metabolic Reaction ◽  
Geobacter Metallireducens ◽  
Terminal Electron Acceptor

ABSTRACT We analyzed the carbon fluxes in the central metabolism of Geobacter metallireducens strain GS-15 using 13C isotopomer modeling. Acetate labeled in the first or second position was the sole carbon source, and Fe-nitrilotriacetic acid was the sole terminal electron acceptor. The measured labeled acetate uptake rate was 21 mmol/g (dry weight)/h in the exponential growth phase. The resulting isotope labeling pattern of amino acids allowed an accurate determination of the in vivo global metabolic reaction rates (fluxes) through the central metabolic pathways using a computational isotopomer model. The tracer experiments showed that G. metallireducens contained complete biosynthesis pathways for essential metabolism, and this strain might also have an unusual isoleucine biosynthesis route (using acetyl coenzyme A and pyruvate as the precursors). The model indicated that over 90% of the acetate was completely oxidized to CO2 via a complete tricarboxylic acid cycle while reducing iron. Pyruvate carboxylase and phosphoenolpyruvate (PEP) carboxykinase were present under these conditions, but enzymes in the glyoxylate shunt and malic enzyme were absent. Gluconeogenesis and the pentose phosphate pathway were mainly employed for biosynthesis and accounted for less than 3% of total carbon consumption. The model also indicated surprisingly high reversibility in the reaction between oxoglutarate and succinate. This step operates close to the thermodynamic equilibrium, possibly because succinate is synthesized via a transferase reaction, and the conversion of oxoglutarate to succinate is a rate-limiting step for carbon metabolism. These findings enable a better understanding of the relationship between genome annotation and extant metabolic pathways in G. metallireducens.

scholarly journals Bayesian metabolic flux analysis reveals intracellular flux couplings

2019 ◽  
Vol 35 (14) ◽  
pp. i548-i557 ◽  
Author(s):  
Markus Heinonen ◽  
Maria Osmala ◽  
Henrik Mannerström ◽  
Janne Wallenius ◽  
Samuel Kaski ◽  
...  
Keyword(s):  
Steady State ◽  
Metabolic Flux Analysis ◽  
Metabolic Flux ◽  
Reaction Network ◽  
Reaction Rates ◽  
Supplementary Information ◽  
Flux Analysis ◽  
Metabolic Reaction ◽  
Metabolic Systems ◽  
Genome Scale

AbstractMotivationMetabolic flux balance analysis (FBA) is a standard tool in analyzing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place model assumptions on fluxes due to the convenience of formulating the problem as a linear programing model, while many methods do not consider the inherent uncertainty in flux estimates.ResultsWe introduce a novel paradigm of Bayesian metabolic flux analysis that models the reactions of the whole genome-scale cellular system in probabilistic terms, and can infer the full flux vector distribution of genome-scale metabolic systems based on exchange and intracellular (e.g. 13C) flux measurements, steady-state assumptions, and objective function assumptions. The Bayesian model couples all fluxes jointly together in a simple truncated multivariate posterior distribution, which reveals informative flux couplings. Our model is a plug-in replacement to conventional metabolic balance methods, such as FBA. Our experiments indicate that we can characterize the genome-scale flux covariances, reveal flux couplings, and determine more intracellular unobserved fluxes in Clostridium acetobutylicum from 13C data than flux variability analysis.Availability and implementationThe COBRA compatible software is available at github.com/markusheinonen/bamfa.Supplementary informationSupplementary data are available at Bioinformatics online.

scholarly journals FluxPyt: a Python-based free and open-source software for 13C-metabolic flux analyses

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4716 ◽  
Author(s):  
Trunil S. Desai ◽  
Shireesh Srivastava
Keyword(s):  
Data Analysis ◽  
Open Source ◽  
Open Source Software ◽  
Metabolic Flux ◽  
Tricarboxylic Acid Cycle ◽  
Strain Analysis ◽  
Monte Carlo Analysis ◽  
Reaction Rates ◽  
Flux Analysis ◽  
Analysis And Design

13C-Metabolic flux analysis (MFA) is a powerful approach to estimate intracellular reaction rates which could be used in strain analysis and design. Processing and analysis of labeling data for calculation of fluxes and associated statistics is an essential part of MFA. However, various software currently available for data analysis employ proprietary platforms and thus limit accessibility. We developed FluxPyt, a Python-based truly open-source software package for conducting stationary 13C-MFA data analysis. The software is based on the efficient elementary metabolite unit framework. The standard deviations in the calculated fluxes are estimated using the Monte-Carlo analysis. FluxPyt also automatically creates flux maps based on a template for visualization of the MFA results. The flux distributions calculated by FluxPyt for two separate models: a small tricarboxylic acid cycle model and a larger Corynebacterium glutamicum model, were found to be in good agreement with those calculated by a previously published software. FluxPyt was tested in Microsoft™ Windows 7 and 10, as well as in Linux Mint 18.2. The availability of a free and open 13C-MFA software that works in various operating systems will enable more researchers to perform 13C-MFA and to further modify and develop the package.

scholarly journals Phosphoketolase Pathway Dominates in Lactobacillus reuteri ATCC 55730 Containing Dual Pathways for Glycolysis

2007 ◽  
Vol 190 (1) ◽  
pp. 206-212 ◽  
Author(s):  
Emma Årsköld ◽  
Elke Lohmeier-Vogel ◽  
Rong Cao ◽  
Stefan Roos ◽  
Peter Rådström ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Metabolic Flux ◽  
Lactobacillus Reuteri ◽  
Intermediate Stage ◽  
Exponential Growth Phase ◽  
Flux Analysis ◽  
Atp Production ◽  
Phosphoketolase Pathway ◽  
Fructose 1,6 Bisphosphate

ABSTRACT Metabolic flux analysis indicated that the heterofermentative Lactobacillus reuteri strain ATCC 55730 uses both the Embden-Meyerhof pathway (EMP) and phosphoketolase pathway (PKP) when glucose or sucrose is converted into the three-carbon intermediate stage of glycolysis. In all cases studied, the main flux is through the PKP, while the EMP is used as a shunt. In the exponential growth phase, 70%, 73%, and 84% of the flux goes through the PKP in cells metabolizing (i) glucose plus fructose, (ii) glucose alone, and (iii) sucrose alone, respectively. Analysis of the genome of L. reuteri ATCC 55730 confirmed the presence of the genes for both pathways. Further evidence for the simultaneous operation of two central carbon metabolic pathways was found through the detection of fructose-1,6-bisphosphate aldolase, phosphofructokinase, and phosphoglucoisomerase activities and the presence of phosphorylated EMP and PKP intermediates using in vitro 31P NMR. The maximum specific growth rate and biomass yield obtained on glucose were twice as low as on sucrose. This was the result of low ATP levels being present in glucose-metabolizing cells, although the ATP production flux was as high as in sucrose-metabolizing cells due to a twofold increase of enzyme activities in both glycolytic pathways. Growth performance on glucose could be improved by adding fructose as an external electron acceptor, suggesting that the observed behavior is due to a redox imbalance causing energy starvation.

scholarly journals Robustifying Experimental Tracer Design for13C-Metabolic Flux Analysis

2021 ◽  
Vol 9 ◽  
Author(s):  
Martin Beyß ◽  
Victor D. Parra-Peña ◽  
Howard Ramirez-Malule ◽  
Katharina Nöh
Keyword(s):  
Experimental Design ◽  
Prior Knowledge ◽  
Metabolic Flux Analysis ◽  
Metabolic Flux ◽  
Streptomyces Clavuligerus ◽  
Reaction Rates ◽  
Computational Method ◽  
Flux Analysis ◽  
Metabolic Reaction ◽  
Diverse Range

13C metabolic flux analysis (MFA) has become an indispensable tool to measure metabolic reaction rates (fluxes) in living organisms, having an increasingly diverse range of applications. Here, the choice of the13C labeled tracer composition makes the difference between an information-rich experiment and an experiment with only limited insights. To improve the chances for an informative labeling experiment, optimal experimental design approaches have been devised for13C-MFA, all relying on some a priori knowledge about the actual fluxes. If such prior knowledge is unavailable, e.g., for research organisms and producer strains, existing methods are left with a chicken-and-egg problem. In this work, we present a general computational method, termed robustified experimental design (R-ED), to guide the decision making about suitable tracer choices when prior knowledge about the fluxes is lacking. Instead of focusing on one mixture, optimal for specific flux values, we pursue a sampling based approach and introduce a new design criterion, which characterizes the extent to which mixtures are informative in view of all possible flux values. The R-ED workflow enables the exploration of suitable tracer mixtures and provides full flexibility to trade off information and cost metrics. The potential of the R-ED workflow is showcased by applying the approach to the industrially relevant antibiotic producer Streptomyces clavuligerus, where we suggest informative, yet economic labeling strategies.

scholarly journals The Role of Cell Metabolism in Innate Immune Memory

2020 ◽  
pp. 1-9
Author(s):  
Anaisa Valido Ferreira ◽  
Jorge Domiguéz-Andrés ◽  
Mihai Gheorghe Netea
Keyword(s):  
Metabolic Pathways ◽  
Tricarboxylic Acid Cycle ◽  
Cell Metabolism ◽  
Innate Immune ◽  
Immune Memory ◽  
Functional Changes ◽  
Trained Immunity ◽  
Health And Disease

Immunological memory is classically attributed to adaptive immune responses, but recent studies have shown that challenged innate immune cells can display long-term functional changes that increase nonspecific responsiveness to subsequent infections. This phenomenon, coined <i>trained immunity</i> or <i>innate immune memory</i>, is based on the epigenetic reprogramming and the rewiring of intracellular metabolic pathways. Here, we review the different metabolic pathways that are modulated in trained immunity. Glycolysis, oxidative phosphorylation, the tricarboxylic acid cycle, amino acid, and lipid metabolism are interplaying pathways that are crucial for the establishment of innate immune memory. Unraveling this metabolic wiring allows for a better understanding of innate immune contribution to health and disease. These insights may open avenues for the development of future therapies that aim to harness or dampen the power of the innate immune response.

scholarly journals Intracellular Fate of Universally Labelled 13C Isotopic Tracers of Glucose and Xylose in Central Metabolic Pathways of Xanthomonas oryzae

Metabolites ◽  
2018 ◽  
Vol 8 (4) ◽  
pp. 66 ◽  
Author(s):  
Manu Shree ◽  
Shyam K. Masakapalli
Keyword(s):  
Amino Acids ◽  
Metabolic Pathways ◽  
Metabolic Networks ◽  
Tca Cycle ◽  
Xanthomonas Oryzae ◽  
Flux Analysis ◽  
Isotopic Tracers ◽  
Feeding Experiments ◽  
The Tca Cycle ◽  
Metabolic Route

The goal of this study is to map the metabolic pathways of poorly understood bacterial phytopathogen, Xanthomonas oryzae (Xoo) BXO43 fed with plant mimicking media XOM2 containing glutamate, methionine and either 40% [13C5] xylose or 40% [13C6] glucose. The metabolic networks mapped using the KEGG mapper and the mass isotopomer fragments of proteinogenic amino acids derived from GC-MS provided insights into the activities of Xoo central metabolic pathways. The average 13C in histidine, aspartate and other amino acids confirmed the activities of PPP, the TCA cycle and amino acid biosynthetic routes, respectively. The similar labelling patterns of amino acids (His, Ala, Ser, Val and Gly) from glucose and xylose feeding experiments suggests that PPP would be the main metabolic route in Xoo. Owing to the lack of annotated gene phosphoglucoisomerase in BXO43, the 13C incorporation in alanine could not be attributed to the competing pathways and hence warrants additional positional labelling experiments. The negligible presence of 13C incorporation in methionine brings into question its potential role in metabolism and pathogenicity. The extent of the average 13C labelling in several amino acids highlighted the contribution of pre-existing pools that need to be accounted for in 13C-flux analysis studies. This study provided the first qualitative insights into central carbon metabolic pathway activities in Xoo.

scholarly journals In vivo 13C MRS in the mouse brain at 14.1 Tesla and metabolic flux quantification under infusion of [1,6-13C2]glucose

2017 ◽  
Vol 38 (10) ◽  
pp. 1701-1714 ◽  
Author(s):  
Marta Lai ◽  
Bernard Lanz ◽  
Carole Poitry-Yamate ◽  
Jackeline F Romero ◽  
Corina M Berset ◽  
...  
Keyword(s):  
Mouse Brain ◽  
Metabolic Flux ◽  
Direct Detection ◽  
Tricarboxylic Acid Cycle ◽  
Quantitative Information ◽  
Glutamine Metabolism ◽  
Resonance Spectroscopy ◽  
Flux Analysis ◽  
Carboxylase Activity

In vivo 13C magnetic resonance spectroscopy (MRS) enables the investigation of cerebral metabolic compartmentation while, e.g. infusing 13C-labeled glucose. Metabolic flux analysis of 13C turnover previously yielded quantitative information of glutamate and glutamine metabolism in humans and rats, while the application to in vivo mouse brain remains exceedingly challenging. In the present study, 13C direct detection at 14.1 T provided highly resolved in vivo spectra of the mouse brain while infusing [1,6-13C2]glucose for up to 5 h. 13C incorporation to glutamate and glutamine C4, C3, and C2 and aspartate C3 were detected dynamically and fitted to a two-compartment model: flux estimation of neuron-glial metabolism included tricarboxylic acid cycle (TCA) flux in astrocytes (Vg = 0.16 ± 0.03 µmol/g/min) and neurons (VTCAn = 0.56 ± 0.03 µmol/g/min), pyruvate carboxylase activity (VPC = 0.041 ± 0.003 µmol/g/min) and neurotransmission rate (VNT = 0.084 ± 0.008 µmol/g/min), resulting in a cerebral metabolic rate of glucose (CMRglc) of 0.38 ± 0.02 µmol/g/min, in excellent agreement with that determined with concomitant 18F-fluorodeoxyglucose positron emission tomography (18FDG PET).We conclude that modeling of neuron-glial metabolism in vivo is accessible in the mouse brain from 13C direct detection with an unprecedented spatial resolution under [1,6-13C2]glucose infusion.

Antioxidative Role of Synthetic and Natural Ascorbic Acid (Vitamin C) in Metabolic Pathways of A Biological System

2021 ◽  
Vol 15 (12) ◽  
pp. 3143-3143
Author(s):  
Naveed Shuja
Keyword(s):  
Ascorbic Acid ◽  
Vitamin C ◽  
Silica Gel ◽  
Biological System ◽  
Metabolic Pathways ◽  
Citrus Fruit ◽  
Pharmaceutical Preparations ◽  
Metabolic Reaction ◽  
Fresh Vegetables

The properties of a substance are determined by the structure of its component molecules. Ascorbic acid occurs abundantly in fresh fruit, especially blackcurrants, citrus fruit and strawberries, and in most fresh vegetables; good sources are broccoli and peppers. It is destroyed by heat and is not well stored in the body3. Ascorbic acid is a good reducing agent and facilitates many metabolic reaction and repair processes. In pharmaceutical preparations and fruit juices, ascorbic acid is readily separated from other compounds by TLC on silica gel and quantitated directly by absorption at 254nm. Serum and plasma may be deproteinized with twice the volume of methanol or ethanol.

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