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Abstract
Metabolism is a complex and robust network of biochemical pathways that serve as the foundation for all biological processes of a cell. Therefore, it is imperative that cells modulate their metabolic networks such that they remain efficient in response to dynamic conditions and nutritional needs – either by altering expression or function of enzymes within certain pathways, or by maintaining optimal flux through existing pathways. This dissertation describes fitness contributions by members of the highly conserved Rid superfamily of proteins by moderating the effects of reactive metabolites on the metabolic networks of various organisms. The Rid superfamily is divided into eight subfamilies. The ancestral RidA subfamily is best known for its role in preventing metabolic stress caused by the reactive metabolite 2-aminoacrylate (2AA), while the remaining seven subfamilies (Rid1-7) had no demonstrated physiological role prior to this work. The first study described in this work (Chapter 2) expands the well-established RidA paradigm by identifying a key enzyme damaged by 2AA in Pseudomonas aeruginosa. The following three chapters describe physiological functions for two proteins belonging to the Rid2 subfamily, which each moderate flux by deaminating reactive intermediates. Chapter 3 defines the first evidence or a physiological role for a Rid protein beyond the RidA subfamily by demonstrating that the Rid2 protein, DadY, is required for optimal flux through the alanine catabolic pathway in P. aeruginosa. Chapter 4 defines metabolic pathways carried out by the dbu operon in Pseudomonas putida, along with demonstrating that the Rid protein, DbuB, is essential for optimal flux through these pathways. This work also describes that RidA functions beyond metabolite toxicity in Salmonella enterica and Escherichia coli by demonstrating that RidA proteins also maintain flux through isoleucine biosynthesis. In total, this work demonstrates that Rid proteins most likely share the physiological role of moderating flux through their respective metabolic pathway(s) by deaminating reactive intermediates.