The paper represents the study of interaction between deoxyribonucleic acid (DNA) and deoxyribonucleic acid-binding protein from starved cells (DPS) cluster formation and crystal growing within a cell. This study is a part of the project that includes European Synchrotron Radiation Facility (ESRF) investigations of in vivo and in vitro nanocrystallization processes of Escherichia coli (E. coli) nucleoid under stress condition combined with theoretical molecular dynamics approaches. Nucleoid biocrystallization is an adaptive mechanism of bacterial cells under stress. It is poorly understood at the present time. Understanding crystal formation process is a very important for molecular biology, pharmacology and other areas. In the simulation part the coarse-grained modeling of various combinations of the following molecules was used: DPS proteins (from 1 to 108 DPS dodecamers in simulation box), short DNA fragments with a length of 24 base pairs (b.p., from 1 to 100 DNA fragments in simulation box) and a part of pBluescript SK(+) plasmide with a length of 161 b.p., in the presence of ions. We defined structural, energetic and dynamic properties of DPS-DPS and DPS-DNA complexes in clusters and crystals that allow us to predict crystal formation and the structure of these crystals in experimental systems. Communicated by Ramaswamy H. Sarma

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.

The mechanisms of interaction of DPS protein molecules (DNA-binding protein from starved cells) with DNA, which are important for understanding the protection of the genetic material of...

Toxic shock caused by the discharge of biocide-contaminated fecal sludge (FS) from chemical toilets to conventional wastewater treatment plants (WWTP) can be a major problem in activated sludge operation. It is necessary to develop new environmental approaches to mitigate the toxicity of biocides in order to avoid degrading the performance of WWTP. “Latrina”, a chemical toilet additive containing didecyldimethylammonium chloride and polyhexamethylene guanidine, is widely used in environmentally safe toilet complexes (ESTC) on Russian railway trains to deodorize FS and control microbial activity. In this work, seven biocide-resistant bacterial strains were isolated and identified from the FS of ESTC. The values of the minimum inhibitory and bactericidal concentrations of biocides for the isolated strains were 4.5–10 times higher than for the collection microorganisms. The bacterium Alcaligenes faecalis DOS7 was found to be particularly resistant to “Latrina”, the minimum inhibitory concentration of which was almost 30 times higher than recommended for ESTC. Biological products based on isolated bacterial strains proved to be effective for FS biodegradation under both aerobic and anaerobic conditions. The results of the biochemical oxygen demand test and the newly developed disk-diffusion bioassay confirmed that isolated strains contribute to reducing toxicity of biocidal agents in FS. Hyper-resistance, non-pathogenicity, and potential plant growth-promoting ability make A. faecalis DOS7 promising for use in various biological products for wastewater treatment and bioremediation of soils contaminated with biocides, as well as in agriculture to increase plant productivity.

In this work, the molecular mechanisms of the interaction of the phenolic lipid 4-hexylresorcinol (4HR) with DNA and DNA–Dps nanocrystals were studied by the methods of molecular dynamics in the full-atomic approximation. It has been shown that low concentrations of 4HR stabilize DNA, while high concentrations under dehydration conditions lead to its degradation by chain separation. The interaction of 4HR with the Dps and DNA leads to the rearrangement of the DNA–Dps complexes. On the surface of single-layer crystals of the Dps protein, multilayer DNA–4HR complexes are formed. The free energies of DNA binding to Dps were determined by the method of calculating the linear interaction energy. It has been shown that 4HR can modulate the DNA-binding and ferroxidase activity of the Dps protein. The results obtained by molecular dynamics methods are consistent with the data from in vivo experiments using the strain BL21-Gold(DE3)/pET-Dps of Escherichia coli. It has been shown that the viability and stress sustainability of bacteria directly depend on the concentration of both 4HR and Dps protein in cells.

In this study, molecular modeling is used to study the interaction of the autoregulatory factor of bacteria, a chemical analog of the inducers of anabiosis of 4-hexylresorcinol (4HR), with the outer and inner membranes, the porin protein, peptidoglycan, DNA, and the DNA stabilizing protein Dps of the Escherichia coli (E. coli) bacterium. The concentration dependence and molecular mechanisms of the interaction of 4HR with cell polymers are studied by molecular dynamics in the full-atomic approximation. The spatial and energy characteristics of 4HR complexes with various cellular components are obtained. Using principal component analysis, the characteristics of DNA and the DNA-binding Dps protein are determined under conditions of various 4HR complexes. The obtained results, which are consistent with the experimental data, allow a deeper understanding of the processes that occur during the protection of the bacterial cell at the level of the envelope and the preservation of DNA by nucleoid proteins.