The critical roles of (p)ppGpp in homeostasis and antibiotic tolerance in Gram positive bacteria

Project Summary Bacteria frequently encounter stresses including nutrient starvation, temperature changes, and antibiotic assault, which could easily throw their intracellular environment into chaos. To survive and to adapt, bacteria developed diverse stress responses to regulate intracellular processes accordingly. While the transcriptional networks governing stress responses have been extensively characterized, there are major gaps in our knowledge beyond transcription regulation. The theme of my research is to elucidate stress signaling mechanisms that are transmitted by rapid changes in concentration of ‘alarmones’ – signaling nucleotides which are instrumental for alerting cells about stresses in a timely manner. My laboratory has extensive experience in characterizing the conserved alarmone (p)ppGpp. (p)ppGpp is induced by stresses and mediates profound, pleiotropic physiological changes in almost all bacteria to allow fitness, survival, and evolution. We identified multiple purine synthesis enzymes, a replication enzyme and a transcription repressor that are directly regulated by (p)ppGpp in Gram-positive Bacillus species. These regulations were further found to be conserved in many pathogens and are critical for homeostasis, starvation resistance, antibiotic persistence, and genome integrity. Currently, we are also investigating how (p)ppGpp regulates the switch between distinct bacterial lifestyles: planktonic growth and biofilm formation. Additionally, we detected other nucleotide alarmones including AppppA, pGpp, ppApp, and c-di- AMP, which are induced by different stresses including temperature and cell wall stress, to form a robust protective network. Our future research will answer the following fundamental questions: How are the different alarmones triggered by different stresses, and how do bacteria synthesize them? What are the direct interaction targets of different alarmones, and how do they promote bacterial fitness and influence bacterial development such as biofilm formation and sporulation? How do bacteria integrate multiple cues from different alarmones for rapid and appropriate adaptation to diverse environments? We combine metabolomics, transcriptomics, and proteomics with biochemical and cell biological approaches to answer these questions. We obtained a list of alarmone targets from systematic screens performed with the proteome of the pathogen Bacillus anthracis. We will study these processes in the related non-pathogenic bacterium Bacillus subtilis for which we have extensive experience. B. subtilis grows fast and is highly amenable to genetic manipulation. The nucleotide signaling mechanisms we characterize in Bacillus are applicable to other, less tractable, pathogenic bacteria, and can be used for developing antimicrobial strategies by targeting their stress responses.