A matter of life and death

Abstract

To survive, bacteria must detect environmental signals, such as nutrient availability, and respond accordingly. Between the detection of the environmental signal and the resulting population behavior lies cellular metabolism: the ability to utilize available metabolites and convert them to energy or cellular biosynthesis. Ultimately, the bacteria's success in coordinating its metabolic status with its overall behavior will determine if the population lives or dies. Bacillus subtilis is a Gram-positive, non-pathogenic soil bacterium that is widely used as a model organism for studying population growth, molecular regulation, cellular development, and multicellularity, such as biofilm development. Here, I aimed to understand the metabolic signals, regulatory pathways, and molecular mechanisms that B. subtilis uses to trigger population changes and behavior. This dissertation investigates this aim from three levels: population growth, biofilm development, and soil community. At the population level, I elucidated a novel role of the Y Complex in regulating carbon catabolite repression and gluconeogenesis during the switch from utilization of a primary carbon source to another during growth. Without the Y Complex, cells do not maintain metabolic flux for cell wall biosynthesis or the relief of growth transition genes to properly grow. I also began an investigation of how the accumulation of glycolytic intermediates, acetyl-CoA and acetyl phosphate, causes cell growth and morphology defects. I propose that these acetyl metabolites and general metabolite homeostasis act as a signaling mechanism for cell development. Metabolic signaling is also important for bacterial biofilm: multicellular communities, in which individual cells are embedded within a self-produced, protective matrix composed of polysaccharides and proteins. The regulation of biofilm development has been studied for many years, but the signals used to trigger biofilm remain unclear. In this dissertation, two novel regulatory mechanisms using metabolic intermediates were elucidated for biofilm development; protein lysine acetylation and serine depletion. Protein lysine acetylation is a post-translational modification that uses acetyl metabolites acetyl-CoA and acetyl phosphate to alter protein structure and function. I discovered that protein lysine acetylation is a novel biofilm regulatory mechanism, through which specific biofilm proteins are acetylated and require the modification for function in biofilm development. Serine starvation impacts biofilm master regulator SinR and its control of biofilm development, however the signaling mechanism remained unknown. Here, I identified that serine levels and serine biosynthesis gene expression decrease upon entry into biofilm development and that this is controlled by carbon catabolite repression. Our finding provides a mechanistic link between serine homeostasis and biofilm development. Lastly, this dissertation looked at a bacterial soil community to understand what strategies bacteria use to survive within their environment. Soil samples from the Chilean Patagonia and the Atacama Desert, two extreme environments in Chile, were analyzed for microbial diversity and used to cultivate bacterial isolates. I performed the first investigation of pigment production, biofilm development, antibiotic production, and antibiotic resistance from these novel isolates and identified adaptive strategies that these bacteria use in harsh environments. Bacterial metabolism remains a black hole of understanding; thus, this dissertation provides insight into the metabolic signals and mechanisms are used to regulate population behavior and development. It is from this understanding that we will be able to make advances in healthcare, agriculture, and biotechnology.