A fundamental feature of a living system is an integrated network of biochemical pathways that can respond to stresses applied by the environment. Microbes, particularly those with a genetic system, provide a technically amenable system to characterize metabolic processes and stress responses. Metabolic strategies are conserved across biology, and insights obtained from microbial systems will contribute to our understanding of general metabolic paradigms. The long-term goal of my research is to contribute to the understanding of metabolic components and the processes they participate in. A rigorous understanding of metabolic processes is critical in efforts to predict the response of cells to environmental change, efforts to develop metabolic modeling strategies and efforts targeting metabolism for rational drug design and/or production of small molecules, to name a few. The goal of the work herein is to characterize a metabolic stress that results from reactive metabolites generated during growth, and to understand the family of proteins that neutralize this stress. This study focuses on a bacterial protein (YjgF) that is a member of highly conserved protein family that neutralizes reactive nitrogen species (e.g. enamines). In the current proposal, we will i) identify the stressors neutralized by the YjgF protein, ii) define the molecular consequences of not neutralizing this metabolic stress and iii) explore the relationship between sequence and functional divergence in the YjgF family. The goals of this proposal will be accomplished through the use of modern chemical, biochemical, biophysical, molecular, genetic and bioinformatic techniques. The work proposed here is motivated by our desire to understand the metabolic stress generated during growth by the production of reactive metabolites that can damage cellular components if they are not neutralized.

Public Health Relevance

Metabolism describes the processes required for life in all biological systems. Understanding metabolism is essential for biomedical progress including targeting metabolism for rational drug design and/ or production of small molecules. Our work contributes to this understanding by defining the biochemical function and metabolic role for a family of proteins that is conserved from bacteria to man.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Prokaryotic Cell and Molecular Biology Study Section (PCMB)
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Barski, Oleg
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University of Georgia
Schools of Arts and Sciences
United States
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Borchert, Andrew J; Downs, Diana M (2017) Endogenously generated 2-aminoacrylate inhibits motility in Salmonella enterica. Sci Rep 7:12971
Borchert, Andrew J; Downs, Diana M (2017) The Response to 2-Aminoacrylate Differs in Escherichia coli and Salmonella enterica, despite Shared Metabolic Components. J Bacteriol 199:
ElRamlawy, Kareem Gamal; Fujimura, Takashi; Baba, Koji et al. (2016) Der f 34, a Novel Major House Dust Mite Allergen Belonging to a Highly Conserved Rid/YjgF/YER057c/UK114 Family of Imine Deaminases. J Biol Chem 291:21607-21615
Ernst, Dustin C; Anderson, Mary E; Downs, Diana M (2016) L-2,3-diaminopropionate generates diverse metabolic stresses in Salmonella enterica. Mol Microbiol 101:210-23
Niehaus, Thomas D; Gerdes, Svetlana; Hodge-Hanson, Kelsey et al. (2015) Genomic and experimental evidence for multiple metabolic functions in the RidA/YjgF/YER057c/UK114 (Rid) protein family. BMC Genomics 16:382
Downs, Diana M; Ernst, Dustin C (2015) From microbiology to cancer biology: the Rid protein family prevents cellular damage caused by endogenously generated reactive nitrogen species. Mol Microbiol 96:211-9
Ernst, Dustin C; Downs, Diana M (2015) 2-Aminoacrylate Stress Induces a Context-Dependent Glycine Requirement in ridA Strains of Salmonella enterica. J Bacteriol 198:536-43
Niehaus, Thomas D; Nguyen, Thuy N D; Gidda, Satinder K et al. (2014) Arabidopsis and maize RidA proteins preempt reactive enamine/imine damage to branched-chain amino acid biosynthesis in plastids. Plant Cell 26:3010-22
Ernst, Dustin C; Lambrecht, Jennifer A; Schomer, Rebecca A et al. (2014) Endogenous synthesis of 2-aminoacrylate contributes to cysteine sensitivity in Salmonella enterica. J Bacteriol 196:3335-42
Flynn, Jeffrey M; Downs, Diana M (2013) In the absence of RidA, endogenous 2-aminoacrylate inactivates alanine racemases by modifying the pyridoxal 5'-phosphate cofactor. J Bacteriol 195:3603-9

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