Homeostasis of the biosynthetic metabolome.

Metabolite concentrations vary across conditions and such metabolome changes are relevant for metabolic and gene regulation. Here, we used LC-MS/MS to explore metabolite concentration changes in . We measured 101 primary metabolites in 19 experimental conditions that include various nutrients and stresses.

Spatial alanine metabolism determines local growth dynamics of colonies.

Bacteria commonly live in spatially structured biofilm assemblages, which are encased by an extracellular matrix. Metabolic activity of the cells inside biofilms causes gradients in local environmental conditions, which leads to the emergence of physiologically differentiated subpopulations. Information about the properties and spatial arrangement of such metabolic subpopulations, as well as their interaction strength and interaction length scales are lacking, even for model systems like colony biofilms grown on agar-solidified media.

Metabolome and proteome analyses reveal transcriptional misregulation in glycolysis of engineered E. coli.

Synthetic metabolic pathways are a burden for engineered bacteria, but the underlying mechanisms often remain elusive. Here we show that the misregulated activity of the transcription factor Cra is responsible for the growth burden of glycerol overproducing E. coli.

Metabolism of non-growing bacteria.

A main function of bacterial metabolism is to supply biomass building blocks and energy for growth. This seems to imply that metabolism is idle in non-growing bacteria. But how relevant is metabolism for the physiology of non-growing bacteria and how active is their metabolism? Here, we reviewed literature describing metabolism of non-growing bacteria in their natural environment, as well as in biotechnological and medical applications.

High-throughput enrichment of temperature-sensitive argininosuccinate synthetase for two-stage citrulline production in E. coli.

Controlling metabolism of engineered microbes is important to modulate cell growth and production during a bioprocess. For example, external parameters such as light, chemical inducers, or temperature can act on metabolism of production strains by changing the abundance or activity of enzymes. Here, we created temperature-sensitive variants of an essential enzyme in arginine biosynthesis of Escherichia coli (argininosuccinate synthetase, ArgG) and used them to dynamically control citrulline overproduction and growth of E.

Breakdown of Vibrio cholerae biofilm architecture induced by antibiotics disrupts community barrier function.

Bacterial cells in nature are frequently exposed to changes in their chemical environment. The response mechanisms of isolated cells to such stimuli have been investigated in great detail. By contrast, little is known about the emergent multicellular responses to environmental changes, such as antibiotic exposure, which may hold the key to understanding the structure and functions of the most common type of bacterial communities: biofilms.

Systematic identification of metabolites controlling gene expression in E. coli.

Metabolism controls gene expression through allosteric interactions between metabolites and transcription factors. These interactions are usually measured with in vitro assays, but there are no methods to identify them at a genome-scale in vivo. Here we show that dynamic transcriptome and metabolome data identify metabolites that control transcription factors in E.