The effect of modifications to DNA structure on the architecture of bacterial DNA condensed with a nucleoid-associated protein

Bacteria are adaptive organisms that have developed various protective mechanisms to respond to a range of environmental stressors like nutrient deprivation. One distinct protective mechanism in Escherichia coli that will be discussed further involves the overproduction of a nucleoid-associated protein called DNA-binding protein (Dps) from starved cells. The high concentration of Dps protects the bacteria’s genetic material by binding to the DNA and forming a Dps-DNA condensate. The morphology of these Dps-DNA condensates in an in-vitro system will change under different environmental conditions. To better understand how altering Dps-DNA interactions independent of environmental stressors affects the resulting morphology of the Dps-DNA condensate in an in-vitro system, fluorescence microscopy imaging was utilized to examine the characteristics of the condensate in response to different DNA features. Upon varying the length of linear DNA fragments incubated with Dps protein, the lengths of the DNA did not change the morphology/structure of the condensate. However, incubation with linear 5k DNA fragments resulted in a greater amount for and larger sized condensate formation. When Dps was incubated with DNA fragments that were either supercoiled or relaxed, minimal differences were observed in the size and structure of condensates. These findings demonstrate that Dps can bind to and condense multiple DNA conformations, helping better explain the function of Dps in organisms other than E. coli.