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Updated: Apr 26, 2026

Population and Single-Cell Analysis of Antibiotic Persistence in Escherichia coli
Published on: March 24, 2023
Toxin YafQ increases persister cell formation by reducing indole signalling
Ying Hu1, Brian W Kwan, Devon O Osbourne
1Department of Chemical Engineering and, Pennsylvania State University, University Park, PA, 16802-4400, USA.
Abstract:
Persister cells survive antibiotic and other environmental stresses by slowing metabolism. Since toxins of toxin/antitoxin (TA) systems have been postulated to be responsible for persister cell formation, we investigated the influence of toxin YafQ of the YafQ/DinJ Escherichia coli TA system on persister cell formation. Under stress, YafQ alters metabolism by cleaving transcripts with in-frame 5'-AAA-G/A-3' sites. Production of YafQ increased persister cell formation with multiple antibiotics, and by investigating changes in protein expression, we found that YafQ reduced tryptophanase levels (TnaA mRNA has 16 putative YafQ cleavage sites). Consistently, TnaA mRNA levels were also reduced by YafQ. Tryptophanase is activated in the stationary phase by the stationary-phase sigma factor RpoS, which was also reduced dramatically upon production of YafQ. Tryptophanase converts tryptophan into indole, and as expected, indole levels were reduced by the production of YafQ. Corroborating the effect of YafQ on persistence, addition of indole reduced persistence. Furthermore, persistence increased upon deleting tnaA, and persistence decreased upon adding tryptophan to the medium to increase indole levels. Also, YafQ production had a much smaller effect on persistence in a strain unable to produce indole. Therefore, YafQ increases persistence by reducing indole, and TA systems are related to cell signalling.
Insights
Toxin YafQ from Escherichia coli toxin/antitoxin systems increases persister cell formation by cleaving specific mRNA transcripts. This toxin reduces indole levels, a key factor in bacterial stress survival.
Area of Science:
- Microbiology
- Bacterial Physiology
- Molecular Biology
Background:
- Persister cells are crucial for bacterial survival under antibiotic stress by entering a dormant state.
- Toxin/antitoxin (TA) systems are implicated in persister cell formation, but the exact mechanisms are not fully understood.
Purpose of the Study:
- To investigate the role of YafQ, a toxin from the YafQ/DinJ TA system in Escherichia coli, in persister cell formation.
- To elucidate the molecular mechanisms by which YafQ influences bacterial stress resistance.
Main Methods:
- Assessing persister cell formation in the presence of YafQ under various antibiotic stresses.
- Analyzing changes in protein and mRNA expression, specifically targeting tryptophanase (TnaA) and RpoS.
- Measuring indole levels and evaluating the impact of indole manipulation on persistence.
Main Results:
- YafQ production significantly increased persister cell formation across multiple antibiotics.
- YafQ reduced tryptophanase (TnaA) and stationary-phase sigma factor RpoS levels by cleaving their respective mRNAs.
- Reduced indole production, a downstream effect of YafQ activity, was directly correlated with increased persistence.
Conclusions:
- YafQ enhances bacterial persistence by downregulating indole synthesis through TnaA and RpoS.
- This study highlights a novel link between TA systems, metabolic regulation, and bacterial stress survival.
- YafQ's mechanism provides insights into bacterial cell signaling and antibiotic resistance strategies.
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