A proteostasis clock underlies the timing of bacterial dormancy and antibiotic tolerance

Abstract

Bacterial dormancy is a major contributor to antibiotic tolerance and persistent infection, yet the lag time before growth resumption is commonly viewed as a passive consequence of cellular recovery and remains difficult to manipulate. Protein aggregation has been linked to bacterial dormancy, but whether aggregates merely reflect cellular damage or directly regulate lag time remains unclear. Here we show that lag time is quantitatively set by cellular proteostasis through control of replication initiation. Microscopy and proteomic analyses revealed delayed aggregate disassembly as a shared proteostasis defect of long-lag bacteria. We identified the replication initiator DnaA in aggregates, whose spatial separation from the nucleoid directly suppresses DNA synthesis. Combined in vitro reconstitution revealed that aggregation-prone proteins drive dose-dependent, synergistic co-aggregation of DnaA, coupling aggregate burden to DnaA sequestration and lag-time extension. Across diverse genetic and physiological models, we observed a universal scaling relationship between lag-time extension and proteostasis decline. Genetic and chemical perturbations of this proteostasis-replication axis bidirectionally modulate lag time, with increasing proteostasis burden prolonging dormancy and restoring proteostasis or DnaA availability accelerating awakening. We therefore propose that proteostasis functions as a tunable timekeeping system for bacterial dormancy by regulating replication initiation, providing a basis for manipulating bacterial dormancy and antibiotic tolerance.