From toxic waste to beneficial nutrient: acetate boosts <i>Escherichia coli</i> growth at low glycolytic flux

Abstract Acetate is a major by-product of glycolytic metabolism in Escherichia coli and many other microorganisms. It has long been considered a toxic waste compound that inhibits microbial growth, but this counterproductive auto-inhibition, which represents a major problem in biotechnology, has puzzled the scientific community for decades. Recent studies have revealed that acetate is also a co-substrate of glycolytic nutrients and a global regulator of E. coli metabolism and physiology. However, most of these insights were obtained at high glycolytic flux and little is known about the role of acetate at lower glycolytic fluxes, conditions that are nevertheless frequently experienced by E. coli in natural, industrial and laboratory environments. Here, we used a systems biology strategy to investigate the mutual regulation of glycolytic and acetate metabolism. Computational and experimental results demonstrate that reducing the glycolytic flux enhances co-utilization of acetate and glucose through the Pta-AckA pathway. Enhanced acetate metabolism compensates for the reduction in glycolytic flux and eventually buffers carbon uptake so that acetate, far from being toxic, actually enhances E. coli growth under these conditions. The same mechanism of increased growth was also observed on glycerol and galactose, two nutrients with a natively low glycolytic flux. Therefore, acetate makes E. coli more robust to glycolytic perturbations and is a valuable nutrient, with a beneficial effect on microbial growth. Finally, we show that some evolutionarily conserved design principles of eukaryotic fermentative metabolism are also present in bacteria. Significance Statement Acetate, a by-product of glycolytic metabolism in many microorganisms including Escherichia coli , is traditionally viewed as a toxic waste compound. Here, we demonstrate that this is only the case at high glycolytic fluxes. At low glycolytic fluxes in contrast, acetate acts as a co-substrate of glycolytic nutrients and boosts E. coli growth. Acetate also improves E. coli ’s robustness to glycolytic perturbations. We clarify the functional relationship between glycolytic and acetate metabolisms, show that acetate is a beneficial co-substrate of glycolytic nutrients used by E. coli in bioprocesses and in the gut, and provide insights into the underlying biochemical and regulatory mechanisms