Structural symmetry of the metabolic reaction network. I. Carboxylic acid metabolism

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.

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Harvest maturity related changes in the cold-induced activation of 1-aminocyclopropane-1-carboxylic acid metabolism in Granny Smith apples / Efecto del estado de madurez sobre la activación por frío del metabolismo del ácido 1-aminociclopropano-1-carboxílico en manzanas Granny Smith

Food Science and Technology International ◽

10.1177/108201329900500304 ◽

1999 ◽

Vol 5 (3) ◽

pp. 223-228 ◽

Cited By ~ 3

Author(s):

C. Larrigaudiere ◽

I. Recasens ◽

J. Graell ◽

M. Vendrell

Keyword(s):

Carboxylic Acid ◽

Ethylene Production ◽

Oxidase Activity ◽

Acid Metabolism ◽

Cold Treatment ◽

Acc Oxidase ◽

Malus Domestica Borkh ◽

Harvest Dates ◽

Harmonization Process ◽

Harvest Maturity

Changes in 1-aminocyclopropane-1-carboxylic acid metabolism in apples ( Malus domestica Borkh cv Granny Smith) were studied in relation to cold storage. Emphasis was given to the differential re sponsiveness of fruits to cold treatment as a function of stage of maturity at harvest. Fruits were held at 1 or 20 °C for 30 days, respectively, or exposed to 1 °C for 10 days and then storaged at 20 °C for up to 30 days. Fruits at 20 °C showed typical climacteric behavior. Differences at 1 °C between maturity stages in ethylene production and ACC oxidase activity were abolished, which showed that cold treatment is an important inducer of climacteric rise in preclimacteric Granny Smith apples. At 1 °C, ethylene production was lower than at 20 °C and the maxima in production were similar for all the stages of maturity, but took place at different times which corresponded exactly to the initial differ ences in harvest dates. After the transfer to 20 °C, fruits exhibited similar behavior as regards ethyl ene production, ACC oxidase activity, and ACC and MACC levels in relation to a harmonization process which is discussed in this study.

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A Promising Method for Calculating True Steady-State Metabolite Concentrations in Large-Scale Metabolic Reaction Network Models

IEEE/ACM Transactions on Computational Biology and Bioinformatics ◽

10.1109/tcbb.2018.2853724 ◽

2020 ◽

Vol 17 (1) ◽

pp. 27-36

Author(s):

Atsuko Miyawaki-Kuwakado ◽

Soichiro Komori ◽

Fumihide Shiraishi

Keyword(s):

Steady State ◽

Large Scale ◽

Reaction Network ◽

Network Models ◽

Promising Method ◽

Metabolic Reaction ◽

Metabolite Concentrations

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Cold-induced activation of 1-aminocyclopropane-1-carboxylic acid metabolism in rewarmed ‘Granny Smith’ apples: Consequences on ripening

Scientia Horticulturae ◽

10.1016/0304-4238(93)90037-q ◽

1993 ◽

Vol 55 (3-4) ◽

pp. 263-272 ◽

Cited By ~ 12

Author(s):

C. Larrigaudiere ◽

M. Vendrell

Keyword(s):

Carboxylic Acid ◽

Acid Metabolism

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A Seven-Gene Locus for Synthesis of Phenazine-1-Carboxylic Acid by Pseudomonas fluorescens2-79

Journal of Bacteriology ◽

10.1128/jb.180.9.2541-2548.1998 ◽

1998 ◽

Vol 180 (9) ◽

pp. 2541-2548 ◽

Cited By ~ 172

Author(s):

Dmitri V. Mavrodi ◽

Vladimir N. Ksenzenko ◽

Robert F. Bonsall ◽

R. James Cook ◽

Alexander M. Boronin ◽

...

Keyword(s):

Carboxylic Acid ◽

Gene Locus ◽

Acid Metabolism ◽

Shikimic Acid ◽

Expression System ◽

Multienzyme Complex ◽

Broad Spectrum Antibiotic ◽

T7 Promoter ◽

New Genes ◽

Chorismic Acid

ABSTRACT Pseudomonas fluorescens 2-79 produces the broad-spectrum antibiotic phenazine-1-carboxylic acid (PCA), which is active against a variety of fungal root pathogens. In this study, seven genes designated phzABCDEFG that are sufficient for synthesis of PCA were localized within a 6.8-kbBglII-XbaI fragment from the phenazine biosynthesis locus of strain 2-79. Polypeptides corresponding to allphz genes were identified by analysis of recombinant plasmids in a T7 promoter/polymerase expression system. Products of thephzC, phzD, and phzE genes have similarities to enzymes of shikimic acid and chorismic acid metabolism and, together with PhzF, are absolutely necessary for PCA production. PhzG is similar to pyridoxamine-5′-phosphate oxidases and probably is a source of cofactor for the PCA-synthesizing enzyme(s). Products of thephzA and phzB genes are highly homologous to each other and may be involved in stabilization of a putative PCA-synthesizing multienzyme complex. Two new genes, phzXand phzY, that are homologous to phzA andphzB, respectively, were cloned and sequenced from P. aureofaciens 30-84, which produces PCA, 2-hydroxyphenazine-1-carboxylic acid, and 2-hydroxyphenazine. Based on functional analysis of the phz genes from strains 2-79 and 30-84, we postulate that different species of fluorescent pseudomonads have similar genetic systems that confer the ability to synthesize PCA.

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Subcellular Localization of 1-Aminocyclopropane-1-Carboxylic Acid Metabolism in Plant Cells

Biochemical and Physiological Aspects of Ethylene Production in Lower and Higher Plants ◽

10.1007/978-94-009-1271-7_4 ◽

1989 ◽

pp. 33-40 ◽

Cited By ~ 1

Author(s):

Jean-Claude Pech ◽

Mondher Bouzayen ◽

Gilbert Alibert ◽

Alain Latché

Keyword(s):

Carboxylic Acid ◽

Subcellular Localization ◽

Acid Metabolism ◽

Plant Cells

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A minimal and self-consistent in silico cell model based on macromolecular interactions

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2007.2075 ◽

2007 ◽

Vol 362 (1486) ◽

pp. 1831-1839 ◽

Cited By ~ 5

Author(s):

Christoph Flamm ◽

Lukas Endler ◽

Stefan Müller ◽

Stefanie Widder ◽

Peter Schuster

Keyword(s):

Cell Model ◽

Reaction Network ◽

Metabolic Reaction ◽

Minimal Cell ◽

Biochemical Kinetics ◽

Biological Phenomena ◽

Self Consistent ◽

Basic Features ◽

Insight Into ◽

Modelling Approach

A self-consistent minimal cell model with a physically motivated schema for molecular interaction is introduced and described. The genetic and metabolic reaction network of the cell is modelled by multidimensional nonlinear ordinary differential equations, which are derived from biochemical kinetics. The strategy behind this modelling approach is to keep the model sufficiently simple in order to be able to perform studies on evolutionary optimization in populations of cells. At the same time, the model should be complex enough to handle the basic features of genetic control of metabolism and coupling to environmental factors. Thereby, the model system will provide insight into the mechanisms leading to important biological phenomena, such as homeostasis, (circadian) rhythms, robustness and adaptation to a changing environment. One example of modelling a molecular regulatory mechanism, cooperative binding of transcription factors, is discussed in detail.

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Metabolic Reaction Network-based Recursive Metabolite Identification for Untargeted Metabolomics

10.1101/305201 ◽

2018 ◽

Cited By ~ 1

Author(s):

Xiaotao Shen ◽

Xin Xiong ◽

Ruohong Wang ◽

Yandong Yin ◽

Yuping Cai ◽

...

Keyword(s):

Data Acquisition ◽

Biological Sample ◽

Large Scale ◽

Recursive Algorithm ◽

Reaction Network ◽

Metabolite Identification ◽

Untargeted Metabolomics ◽

Metabolic Reaction ◽

Link Type ◽

Functional Metabolomics

Metabolite identification is a long-standing challenge in untargeted metabolomics and a major hurdle for functional metabolomics studies. Here, we developed a metabolic reaction network-based recursive algorithm and webserver called MetDNA for the large-scale and unambiguous identification of metabolites (available at http://metdna.zhulab.cn). We showcased the versatility of our workflow using different instrument platforms, data acquisition methods, and biological sample types and demonstrated that over 2,000 metabolites could be identified from one experiment.

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