Surviving fluctuations: exploring the intricate link between bacterial growth regulation and persister formation

This dissertation explores the complex interplay between bacterial growth regulation and the formation of persister cells, addressing their crucial role in bacterial survival and antibiotic tolerance. Bacteria must constantly balance their limited resources between maximizing growth and preparing for environmental stresses. This challenge becomes evident in their ability to form persister cells—a dormant subpopulation within a bacterial community capable of surviving extreme conditions such as antibiotic exposure. These cells are key contributors to the persistence of infections and the rise of antimicrobial resistance, as they serve as a reservoir for recovery and adaptation once stress subsides. The thesis highlights the central role of the alarmone ppGpp in this process. ppGpp is a critical regulator of bacterial resource allocation, particularly under conditions of stress or nutrient limitation. ppGpp allows bacteria to switch between rapid growth and stress preparedness. This dissertation uses various mathematical models to investigate how fluctuations in bacterial growth are tightly regulated, ultimately shedding light on how this regulation might underpin the switch to the persister state. The thesis begins by examining how bacteria manage internal fluctuations under constant, non-stressful conditions, such as variations in birth size or cytoplasmic organization, which disrupt growth homeostasis. It reveals that bacterial systems employ compensatory mechanisms, mediated by ppGpp, to restore equilibrium and maintain optimal growth rates. Strikingly, these responses occur in an ultrasensitive manner, allowing bacteria to rapidly adjust to even minor suboptimal conditions. This understanding establishes a foundation for exploring how growth regulation extends beyond mere survival to influence phenotypic outcomes like persister formation. Building on this, the dissertation argues that the ultrasensitivity of ppGpp to growth disturbances not only resolves internal imbalances but also plays a broader role in enabling populations to balance short-term growth with long-term survival. This is achieved through trade-offs at the population level, which manifest as a division between growth-focused cells and stress-tolerant persisters. This phenotypic diversification allows bacterial populations to hedge their bets in unpredictable environments, ensuring that at least some cells survive and thrive. Importantly, this dissertation proposes a systems-biology framework that integrates molecular mechanisms with ecological and evolutionary perspectives to provide a comprehensive understanding of bacterial persistence. This holistic approach not only deepens our knowledge of the mechanisms governing persister formation but also offers valuable insights into combating antimicrobial resistance. By illuminating the intricate ties between growth regulation and survival strategies, this work lays a foundation for innovative approaches to managing chronic bacterial infections.