Integrating highly quantitative proteomics and genome-scale metabolic modeling to study pH adaptation in the human pathogen Enterococcus faecalis

Integrating large-scale protein measurements with genomic data offers a biologically accurate reconstruction of microbial metabolism. A team led by Ursula Kummer from Heidelberg University in Germany and Ruedi Aebersold from ETH Zurich in Switzerland studied the human gut pathogen Enterococcus faecalis as it adapted to an increasingly acidic environment, as would be found in the gastrointestinal tract. The researchers acquired whole-cell proteomic data using a newly developed mass spectrometry technique. They combined this information with that from a metabolic network model of E. faecalis previously constructed with physiologic, biochemical and genetic data. The acidic environment put more energy demands on the organism, which triggered a number of protein changes, including in the composition of the microbe’s membrane. Proteomic data was integral to revealing how the organism responded to the environment.