DNA condensation in bacteria

Krupyanskii Y.F., Generalova A.A., Kovalenko V.V., Loyko N.G.1, Tereshkin E.V., .MoiseenkoA.V.2, Tereshkina K.B., Sokolova O.S.2, Popov A.N.3

Federal Research Center of Chemical Physics named after N.N. Semenov, Russian Academy of Sciences, 119991, Moscow, Kosygina 4

The study of DNA condensation in a cell is important for understanding the mechanisms of bacterial survival and for medicine, since ordered DNA condensation ensures the resistance of pathogenic bacteria to the action of antibiotics. In a dilute solution, DNA is several centimeters long. Escherichia coli is about 0.5 µm long. Such a dramatic decrease in the volume occupied by DNA is a consequence of its condensation. It was found that DNA is organized in the nucleoid of an actively growing cell hierarchically with three levels of DNA compaction: The lower level (small scale ≥ 1 kb bp) is provided by histone-like NAP proteins. Actively growing cells maintain a dynamic, far from equilibrium order through metabolism. As cells enter a dormant state (almost complete absence of metabolism), the usual biochemical methods of protecting DNA cease to work, and cells, adapting to new conditions, are forced to use physical mechanisms of DNA protection (dense DNA packing, nanocrystallization of DNA with proteins, etc.). A study was made of the structure of DNA in the nucleoid of dormant cells formed during starvation stress. The study was carried out using synchrotron radiation diffraction and transmission electron microscopy (TEM). The experimental results made it possible to visualize the structures of the lower hierarchical level of DNA compaction in the nucleoid of dormant cells. A series of diffraction experiments performed for the first time indicates the presence of a periodic ordered organization of DNA in all studied bacteria. TEM made it possible to extract finer visual information about the type of DNA condensation in the nucleoid of the bacterium Escherichia coli. Intracellular nanocrystalline, liquid-crystalline and folded nucleosome-like structures of DNA have been found. The folded nucleosome-like structure was observed for the first time and is the result of multiple folding of long DNA molecules around the Dps protein and its associates. Next, we studied changes in DNA architecture under the influence of a chemical analogue of the autoinducer of anabiosis 4-hexylresorcinol (4HR). An increase in the 4HR concentration induces the transition of a part of the cells of the population into an anabiotic resting state, and then into a mummified state. The conducted studies of the DNA structure in the anabiotic and mummified states show the spectroscopic identity of the DNA structure in the dormant anabiotic state and in the dormant state formed during starvation stress.


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