DNA-Binding Protein Dps Protects Escherichia coli Cells against Multiple Stresses during Desiccation

SIMPLE SUMMARY: The ability of bacteria to adapt to various types of stress has been studied for decades. It is directly related to the problem of nosocomial infections and the success of biotechnological processes involving bacteria. This study shows that bacteria can survive after being in a desiccated state for three months. The Dps protein, formed in cells to protect DNA, plays a major role in their survival. Bacteria with more of this protein in their cells have an advantage. Applying molecular dynamics methods made it possible to explain the protective function of Dps. The obtained results of the research will help create technologies for the conservation of useful bacteria used by humans. ABSTRACT: Gradual dehydration is one of the frequent lethal yet poorly understood stresses that bacterial cells constantly face in the environment when their micro ecotopes dry out, as well as in industrial processes. Bacteria successfully survive extreme desiccation through complex rearrangements at the structural, physiological, and molecular levels, in which proteins are involved. The DNA-binding protein Dps has previously been shown to protect bacterial cells from many adverse effects. In our work, using engineered genetic models of E. coli to produce bacterial cells with overproduction of Dps protein, the protective function of Dps protein under multiple desiccation stresses was demonstrated for the first time. It was shown that the titer of viable cells after rehydration in the experimental variants with Dps protein overexpression was 1.5–8.5 times higher. Scanning electron microscopy was used to show a change in cell morphology upon rehydration. It was also proved that immobilization in the extracellular matrix, which is greater when the Dps protein is overexpressed, helps the cells survive. Transmission electron microscopy revealed disruption of the crystal structure of DNA–Dps crystals in E. coli cells that underwent desiccation stress and subsequent watering. Coarse-grained molecular dynamics simulations showed the protective function of Dps in DNA–Dps co-crystals during desiccation. The data obtained are important for improving biotechnological processes in which bacterial cells undergo desiccation.