Persister cells, rare phenotypic variants that survive normally lethal levels of antibiotics, present a major barrier to clearing bacterial infections¹. However, understanding the precise physiological state and genetic basis of persister formation has been a longstanding challenge. Here we generated a high-resolution single-cell² RNA atlas of Escherichia coli growth transitions, which revealed that persisters from diverse genetic and physiological models converge to transcriptional states that are distinct from standard growth phases and instead exhibit a dominant signature of translational deficiency. We then used ultra-dense CRISPR interference³ to determine how every E. coli gene contributes to persister formation across genetic models. Among critical genes with large effects, we found lon, which encodes a highly conserved protease⁴, and yqgE, a poorly characterized gene whose product strongly modulates the duration of post-starvation dormancy and persistence. Our work reveals key physiologic and genetic factors that underlie starvation-triggered persistence, a critical step towards targeting persisters in recalcitrant bacterial infections.

持久性细胞是在正常致命水平的抗生素中存活下来的罕见表型变异，是清除细菌感染的主要障碍¹。然而，了解持久性形成的精确生理状态和遗传基础一直是一项长期的挑战。在这里，我们生成了大肠杆菌生长转变的高分辨率单细胞² RNA 图谱，它揭示了来自不同遗传和生理模型的持久性会收敛到不同于标准生长阶段的转录状态，而是表现出翻译缺陷的显性特征。然后，我们使用超密集 CRISPR 干扰³ 来确定每个大肠杆菌基因如何促进遗传模型中持久性的形成。在具有较大影响的关键基因中，我们发现了编码高度保守的蛋白酶⁴ 的 lon 和 yqgE，一种特征不佳的基因，其产物强烈调节饥饿后休眠和持久性的持续时间。我们的工作揭示了饥饿触发的持续性的关键生理和遗传因素，这是针对顽固性细菌感染的持续性的关键一步。