A shared alarmone–GTP switch controls persister formation in bacteria
Danny K. Fung, Jessica T. Barra, Jin Yang, Jeremy W. Schroeder, Fukang She, Megan K. M. Young, David Ying, David Stevenson, Daniel Amador‐Noguez, Jue D. Wang
Abstract
Persisters are phenotypically switched bacteria that survive antibiotic exposure despite being genetically susceptible. Three pathways to persistence-triggered, spontaneous and antibiotic-induced-have been described, but the underlying molecular mechanisms are poorly understood. Here, we used antibiotic time-kill assays as well as single-cell approaches to show that all of the pathways depend on a common switch involving the alarmone guanosine tetra/penta-phosphate ((p)ppGpp) in Bacillus subtilis, each stemming from different alarmone synthetase(s). The accumulation of (p)ppGpp promotes persistence through depletion of intracellular GTP. We developed a fluorescent GTP reporter to visualize rare events of persister formation in wild-type bacteria, revealing a rapid switch from growth to dormancy in single cells as their GTP levels drop beneath a threshold. While a decrease in GTP in the bulk population slows growth and promotes antibiotic tolerance, (p)ppGpp drives persistence by driving rapid, switch-like decreases in GTP levels beneath the persister threshold in single cells. Persistence through alarmone-GTP antagonism is probably a widespread mechanism to survive antibiotics in B. subtilis and potentially beyond.