Bacterial persistence is an active σ ^S stress response to metabolic flux limitation

Abstract

While persisters are a health threat due to their transient antibiotic tolerance, little is known about their phenotype and what actually causes persistence. Using a new method for persister generation and high‐throughput methods, we comprehensively mapped the molecular phenotype of Escherichia coli during the entry and in the state of persistence in nutrient‐rich conditions. The persister proteome is characterized by σS‐mediated stress response and a shift to catabolism, a proteome that starved cells tried to but could not reach due to absence of a carbon and energy source. Metabolism of persisters is geared toward energy production, with depleted metabolite pools. We developed and experimentally verified a model, in which persistence is established through a system‐level feedback: Strong perturbations of metabolic homeostasis cause metabolic fluxes to collapse, prohibiting adjustments toward restoring homeostasis. This vicious cycle is stabilized and modulated by high ppGpp levels, toxin/anti‐toxin systems, and the σS‐mediated stress response. Our system‐level model consistently integrates past findings with our new data, thereby providing an important basis for future research on persisters.

High-throughput laboratory evolution and evolutionary constraints inEscherichia coli

“…Since class 9 strains and the reconstructed rssB strain both show resistance to cell wall inhibitors and other stresses (AZT, CBPC, TET), our results indicate a trade-off between these stresses and metabolic inhibitors. It has been reported that while E. coli strains with higher rpoS levels show increased resistance to several external stresses (Radzikowski et al, 2016), they also show decreased carbon source availabilities and poor competitiveness for low concentrations of nutrients due to the competition between RpoS and the housekeeping sigma factor RpoD (sigma 70) (Ferenci, 2005). Because RssB facilitates the degradation of RpoS, the collateral sensitivities to several metabolic inhibitors in class 9 evolved strains could also be caused by the sigma factor competition.…”

Antibiotic efficacy — context matters

“…For instance, pre-treatment with hydrogen peroxide can protect against multiple bactericidal antibiotics by priming oxidative stress responses [33], and nutrient starvation can induce phenotypically tolerant ‘persister’ cells by activating ppGpp and the stringent response [66,67]. Several recent studies demonstrate how environmental factors may alter antibiotic efficacy, providing additional insight into antibiotic lethality (Figure 2).…”

Cellular responses to reactive oxygen species can be predicted on multiple biological scales from molecular mechanisms

“…OxidizeME represents another step in this direction. There is increasing recognition that microbial stress response plays an important role in infectious disease and antibiotic tolerance [7,8]. Stress-ME models (FoldME, OxidizeME, etc.)…”