Modeling the Contribution of Allosteric Regulation for Flux Control in the Central Carbon Metabolism of E. coli.

Daniel Machado,Markus J Herrgård,Isabel Rocha

doi:10.3389/fbioe.2015.00154

Abstract

Modeling cellular metabolism is fundamental for many biotechnological applications, including drug discovery and rational cell factory design. Central carbon metabolism (CCM) is particularly important as it provides the energy and precursors for other biological processes. However, the complex regulation of CCM pathways has still not been fully unraveled and recent studies have shown that CCM is mostly regulated at post-transcriptional levels. In order to better understand the role of allosteric regulation in controlling the metabolic phenotype, we expand the reconstruction of CCM in Escherichia coli with allosteric interactions obtained from relevant databases. This model is used to integrate multi-omics datasets and analyze the coordinated changes in enzyme, metabolite, and flux levels between multiple experimental conditions. We observe cases where allosteric interactions have a major contribution to the metabolic flux changes. Inspired by these results, we develop a constraint-based method (arFBA) for simulation of metabolic flux distributions that accounts for allosteric interactions. This method can be used for systematic prediction of potential allosteric regulation under the given experimental conditions based on experimental data. We show that arFBA allows predicting coordinated flux changes that would not be predicted without considering allosteric regulation. The results reveal the importance of key regulatory metabolites, such as fructose-1,6-bisphosphate, in controlling the metabolic flux. Accounting for allosteric interactions in metabolic reconstructions reveals a hidden topology in metabolic networks, improving our understanding of cellular metabolism and fostering the development of novel simulation methods that account for this type of regulation.

Highlights

Mathematical models of metabolism have become a fundamental tool for understanding cellular behavior and for designing genetic or environmental modifications to change that behavior toward a specific purpose (Heinemann and Sauer, 2010)
Given the growing scope of the constraint-based modeling approach, we propose to expand this formalism with an explicit representation for allosteric interactions
Model Reconstruction In order to analyze the effects of allosteric regulation in the central carbon metabolism, we expanded a constraint-based model of the core metabolism of E. coli (Orth et al, 2009) with allosteric interactions obtained from relevant sources

Summary

Introduction

Mathematical models of metabolism have become a fundamental tool for understanding cellular behavior and for designing genetic or environmental modifications to change that behavior toward a specific purpose (Heinemann and Sauer, 2010). Metabolic models have found applications in both biomedical research and industrial biotechnology. There are two major approaches for modeling cellular metabolism, namely, kinetic modeling and constraint-based modeling (Machado et al, 2012). The former, based on kinetic rate laws, requires extensive experimental data for determination of the enzymatic mechanisms and respective kinetic parameters. For that reason, these models have been limited to central pathways of well-studied organisms, such as Escherichia coli and Saccharomyces cerevisiae (Teusink et al, 2000; Chassagnole et al, 2002). With the increasing number of fully sequenced genomes for multiple organisms, the number of genome-scale metabolic reconstructions suitable for constraint-based modeling is rapidly increasing, with over a hundred reconstructions currently available (Monk et al, 2014)

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Discussion

Conclusion