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arXiv · 2406.16596

A compact model of Escherichia coli core and biosynthetic metabolism

Marco Corrao·Hai He·Wolfram Liebermeister·Elad Noor·Arren Bar-Even
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Abstract

Metabolic models condense biochemical knowledge about organisms in a structured and standardised way. As large-scale network reconstructions are readily available for many organisms, genome-scale models are being widely used among modellers and engineers. However, these large models can be difficult to analyse and visualise and occasionally generate predictions that are hard to interpret or even biologically unrealistic. Of the thousands of enzymatic reactions in a typical bacterial metabolism, only a few hundred form the metabolic pathways essential to produce energy carriers and biosynthetic precursors. These pathways carry relatively high flux, are central to maintaining and reproducing the cell, and provide precursors and energy to engineered metabolic pathways. Focusing on these central metabolic subsystems, we present iCH360, a manually curated medium-scale model of energy and biosynthesis metabolism for the well-studied bacterium Escherichia coli K-12 MG1655. The model is a sub-network of the most recent genome-scale reconstruction, iML1515, and comes with an updated layer of database annotations and with a range of metabolic maps for visualisation. We enriched the stoichiometric network with extensive biological information and quantitative data, enhancing the scope and applicability of the model. In addition, we assess the properties of this model in comparison to its genome-scale parent and demonstrate the use of the network and supporting data in various scenarios, including enzyme-constrained flux balance analysis, elementary flux mode analysis, and thermodynamic analysis. Overall, we believe this model holds the potential to become a reference medium-scale metabolic model for E. coli.

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Marco Corrao, Hai He, Wolfram Liebermeister, Elad Noor, Arren Bar-Even. 2024-06-24. A compact model of Escherichia coli core and biosynthetic metabolism. https://doi.org/10.1371/journal.pcbi.1013564

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