Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli

Mattia Zampieri (), Manuel Hörl, Florian Hotz, Nicola F. Müller and Uwe Sauer ()
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Mattia Zampieri: Institute of Molecular Systems Biology, ETH Zürich
Manuel Hörl: Institute of Molecular Systems Biology, ETH Zürich
Florian Hotz: Institute of Molecular Systems Biology, ETH Zürich
Nicola F. Müller: Institute of Molecular Systems Biology, ETH Zürich
Uwe Sauer: Institute of Molecular Systems Biology, ETH Zürich

Nature Communications, 2019, vol. 10, issue 1, 1-13

Abstract: Abstract How microbes dynamically coordinate uptake and simultaneous utilization of nutrients in complex nutritional ecosystems is still an open question. Here, we develop a constraint-based modeling approach that exploits non-targeted exo-metabolomics data to unravel adaptive decision-making processes in dynamic nutritional environments. We thereby investigate metabolic adaptation of Escherichia coli to continuously changing conditions during batch growth in complex medium. Unexpectedly, model-based analysis of time resolved exo-metabolome data revealed that fastest growth coincides with preferred catabolism of amino acids, which, in turn, reduces glucose uptake and increases acetate overflow. We show that high intracellular levels of the amino acid degradation metabolites pyruvate and oxaloacetate can directly inhibit the phosphotransferase system (PTS), and reveal their functional role in mediating regulatory decisions for uptake and catabolism of alternative carbon sources. Overall, the proposed methodology expands the spectrum of possible applications of flux balance analysis to decipher metabolic adaptation mechanisms in naturally occurring habitats and diverse organisms.

Date: 2019
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DOI: 10.1038/s41467-019-11331-5

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