Nutrient Signal Integration in Escherichia coli

Abstract

Microbes survive in a variety of nutrient environments by modulating their metabolism. Balanced growth requires that the uptake of various nutrients, the rate of intracellular catabolism and biosynthesis, and the overall growth rate are coordinated in their response to environmental fluctuations in nutrient availability, the primary substrates for biomass production. While the structure of the metabolic network is known and much biochemical data is available concerning the regulation of individual reactions, the mechanisms that integrate nutrient signal information into a coordinated regulatory plan are incompletely understood. Through a combination of experiment and mathematical modeling, this work explores the <italic>E. coli</italic> response to variations in nitrogen availability, and attempts to identify the mechanisms which make the nitrogen uptake pathway, the central carbon network, and the cellular growth rate each sensitive to this external variable. Beginning from a rich metabolomics dataset detailing the metabolic effects of a sudden increase in nitrogen, a detailed kinetic model of nitrogen assimilation is developed which allows the identification of the key regulatory interactions controlling the concentrations of glutamate and glutamine, the intracellular nitrogen carriers. The same dataset reveals a striking homeostasis in the concentrations of glycolytic intermediates despite an increase in glycolytic flux, leading to the discovery of a new feedback mechanism which renders glucose uptake sensitive to nitrogen limitation through inhibition by &alpha;-ketoglutarate, the carbon substrate of nitrogen assimilation. A reductionist mathematical model indicates that this mechanism is necessary and sufficient for coordination of carbon and nitrogen utilization. Oxygen uptake and oxidative citric acid cycle flux are also found to be closely tied to nitrogen availability; the rapidity of the adjustments to nitrogen perturbation argues for the primacy of small-molecule interactions and enzyme modification as modes of regulation.