Development of new strategies to map and regulate large RNA regulatory networks

Global regulators are critical controllers of cellular function. They possess the ability to coordinate multiple cellular pathways simultaneously to orchestrate a unified response to environmental change. Recent research has demonstrated that both proteins and RNAs can function in key regulatory roles and each provides unique advantages in their control characteristics. Given the power of these regulators, there is strong interest in utilizing regulatory systems in a variety of metabolic engineering applications including coordination of metabolic pathways and as dynamic pathway controllers. However, the potential to utilize these systems to produce dynamic and coordinated metabolic responses is only beginning to be realized. My dissertation focuses on characterizing global regulatory systems and specifically small RNA (sRNA) based regulatory systems for their use as dynamic global controllers for metabolic engineering. Chapter 2 starts by discussing a computational analysis of how a group of genes dynamically controlled by a single regulator can produce higher metabolite levels over time. This Chapter demonstrates dynamic control as an underutilized strategy to improve metabolite production. Chapter 3 evaluates how to characterize large regulatory systems using the E. coli Carbon Storage Regulator as a case study. It interweaves multiple lines of omics evidence and follow up experiments to determine the regulatory targets of the Csr system. Using these data, we constructed a thermodynamic model to predict if CsrA will cause repression of cellular genes (Chapter 4). The work in these chapters represents a new way of thinking about sRNA regulators and their role in metabolic engineering and has broad applicability to other Protein-RNA regulators and other regulatory elements.