Cellular determinants of metabolite concentration ranges

Cellular functions are shaped by reaction networks whose dynamics are determined by the concentrations of underlying components. However, cellular mechanisms ensuring that a component's concentration resides in a given range remain elusive. We present network properties which suffice to identif...

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Published in:PLoS computational biology 2019-01, Vol.15 (1), p.e1006687-e1006687
Main Authors: Küken, Anika, Eloundou-Mbebi, Jeanne M O, Basler, Georg, Nikoloski, Zoran
Format: Article
Language:English
Subjects:
Bacteria
Biochemistry
Bioinformatics
Biology
Biology and Life Sciences
Cellular communication
Computer and Information Sciences
Computer simulation
Determinants
E coli
Enzymes
Escherichia coli
Escherichia coli - genetics
Genomes
Genomics
Growth rate
Kinetics
Medicine and Health Sciences
Metabolic networks
Metabolic Networks and Pathways - genetics
Metabolism
Metabolites
Metabolome - genetics
Models, Biological
Ordinary differential equations
Organisms
Physical Sciences
Physiological aspects
Physiology
Systems Biology - methods
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description Cellular functions are shaped by reaction networks whose dynamics are determined by the concentrations of underlying components. However, cellular mechanisms ensuring that a component's concentration resides in a given range remain elusive. We present network properties which suffice to identify components whose concentration ranges can be efficiently computed in mass-action metabolic networks. We show that the derived ranges are in excellent agreement with simulations from a detailed kinetic metabolic model of Escherichia coli. We demonstrate that the approach can be used with genome-scale metabolic models to arrive at predictions concordant with measurements from Escherichia coli under different growth scenarios. By application to 14 genome-scale metabolic models from diverse species, our approach specifies the cellular determinants of concentration ranges that can be effectively employed to make predictions for a variety of biotechnological and medical applications.
doi_str_mv 10.1371/journal.pcbi.1006687
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subjects Bacteria
Biochemistry
Bioinformatics
Biology
Biology and Life Sciences
Cellular communication
Computer and Information Sciences
Computer simulation
Determinants
E coli
Enzymes
Escherichia coli
Escherichia coli - genetics
Genomes
Genomics
Growth rate
Kinetics
Medicine and Health Sciences
Metabolic networks
Metabolic Networks and Pathways - genetics
Metabolism
Metabolites
Metabolome - genetics
Models, Biological
Ordinary differential equations
Organisms
Physical Sciences
Physiological aspects
Physiology
Systems Biology - methods
title Cellular determinants of metabolite concentration ranges
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