Bacterial persisters contribute to the recurrence of difficult-to-treat infections and can ultimately drive the emergence of resistant strains. A major gap remains in our understanding of how bacterial metabolism is reprogrammed during the transition to persistence and which metabolic pathways are essential for persister survival. To address this, we studied
Escherichia coli persister cells that arise during the late stationary phase—cells known for their high drug tolerance and presumed dormancy. Our findings show that the Crp/cAMP regulatory system reprograms cell metabolism from anabolism to oxidative phosphorylation in the stationary phase, fundamentally altering persister cell metabolism (Ngo et al., 2024). Although these cells exhibit lower metabolic activity than exponential-phase cells, their survival depends on TCA cycle–mediated energy metabolism, which is critical for maintaining persister populations. Disrupting key TCA cycle enzymes significantly reduced persister formation, though the underlying mechanism was initially unclear.
To investigate further, we performed proteomic analysis of an sdhA knockout strain (sdhA encodes succinate dehydrogenase, a key TCA cycle enzyme) along with a Keio knockout library screen. These analyses revealed that lipid catabolism likely provides a crucial carbon source that feeds into the TCA cycle in persisters. Deleting tpiA and gloA—genes involved in channeling lipid-derived metabolites into the TCA cycle—markedly decreased persister levels in wild-type cells. These results suggest that, in nutrient-depleted conditions such as the stationary phase, persister cells rely on internal lipid degradation to sustain energy metabolism. This model was further supported by observed changes in membrane integrity, cell size, and metabolic activity in stationary-phase persisters. Altogether, this study reveals a survival mechanism in which persister cells repurpose membrane lipids to maintain TCA cycle activity and energy production under starvation.
