Characterizing the structural rearrangement of the bacterial nucleoid by Dps.

Abstract

Bacteria are subject to a wide variety of environmental stresses which requires a robust stress response system to protect the cell. A key protein in Escherichia coli known for its numerous functions in stress response and cell maintenance is the DNA-binding protein from starved cells (Dps). The Dps protein protects DNA via two different mechanisms. First, Dps oxidizes iron to prevent the generation of hydroxyl radicals. Second, in response to stress and throughout the stationary phase of the growth cycle, Dps oligomers bind to DNA and multimerize further to create a Dps-DNA complex that compacts. To access how Dps affects this structural change of DNA to afford protection of the cell's genome, photoactivatable localization microscopy is employed to generate nanometer-scale maps of the nucleoid structure throughout the E. coli growth phases. These maps are attained by super-resolving the localizations of single molecules of the nucleoid-associated protein HUα, which non-specifically binds to DNA, tagged with the photoactivatable fluorescent protein PAmCherry. Super-resolution maps of the nucleoid structure are compared to maps of the nucleoid in E. coli strains with dps deleted. Tagging Dps and other major nucleoid associated proteins with PAmCherry provides the distribution of these proteins across the nucleoid to gain insight on how and if Dps interacts with other nucleoid associated proteins. By observing these structural changes over the growth period of E. coli, insight can be gained about how changes in DNA structure can lead to protection via Dps.