Chromosome Reorganization by the Highly Cooperative Dps Protein

Abstract

All living creatures organize their genome into a dynamic three-dimensional nucleoprotein complex. This organization has a vital importance for cellular processes such as gene expression, DNA replication, and DNA repair. In order to understand the nature of chromosome architecture we need to gain insight into the biophysical parameters that drive compaction. However, critical details of this process remain unknown. In this study we investigate a DNA-binding enzyme from E. coli that rearranges the bacterial genome and protects the chromosome against cellular stresses ranging from starvation to antibiotic exposure. The enzyme responsible for this transformation is called Dps (DNA-binding protein from starved cells). The interaction between Dps and DNA results in the rapid formation of a tightly packed three-dimensional crystal lattice termed a biocrystal. Although static structures of biocrystals have been documented, little is known about how the structures form. We have developed a fluorescent assay for tracking the physical interaction between individual DNA molecules and Dps under TIRF microscopy. We found that Dps induces collapse extremely rapidly after a slow nucleation event. In addition, we have used magnetic tweezers to obtain biophysical parameters of the conformational transition of stretched DNA initiated by Dps protein. We found that cooperative Dps binding to DNA cannot be fitted with Hill equation but displays the qualitative features of an Ising system. Consequently we have developed a mean field model that captures important features of the collapse. These in vitro experiments provide the crucial details about the highly cooperative mechanisms of DNA-Dps biocrystal formation.