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Architecture of Nucleoid in the Dormant Cells of Escherichia coli

  • CHEMICAL PHYSICS OF BIOLOGICAL PROCESSES
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Abstract

The review presents the results of the experimental studies of the structure of condensed DNA in the nucleoid of the dormant cells of Escherichia coli bacteria that appear in response to starvation stress. The conformation of DNA was studied by synchrotron radiation diffraction and transmission electron microscopy. The series of diffraction experiments revealed a periodic ordered organization (most likely, nanocrystalline) of DNA with DNA-associated proteins in all objects under study subjected to starvation stress: bacteria E. coli, spores and bacteria Bacillus Cereus, and filamentous fungi Umbelopsis ramanniana. A transmission electron microscopy study gave fine visual information about the type of DNA condensation in the nucleoid of the E. coli bacterium. The TEM study made it possible to find the intracellular nanocrystalline, liquid crystalline, and folded nucleosome-like DNA structures. The proportion of specific structure depends on the strain and cultivation conditions. The folded nucleosome-like structure was observed and described in the authors’ original studies for the first time. The electron microscopy studies do not allow direct visualization of DNA; therefore, the DNA conformation is hypothetical. To obtain a clear picture of the DNA structure in intracellular crystals, the crystals were studied in vitro by X-ray macromolecular crystallography and electron microscopy. In contrast to diffraction experiments, the electron microscopy studies made it possible to see DNA traces in thin (2D) DNA–Dps crystals. A hypothetical model of DNA conformation in intracellular nanocrystals was proposed. The results of experiments made it possible to visualize the structures of the lower hierarchical tier of DNA compaction in the nucleoid of dormant cells.

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ACKNOWLEDGMENTS

I am grateful to my constant co-authors N.G. Loiko, V.V. Kovalenko, O.S. Sokolova, A.V. Moiseenko, K.B. Tereshkina, G.I. El’-Registan, E.V. Tereshkin, and A.N. Popov for their great contribution to the joint development of this research trend, and to I.V. Gordeeva for her great help in preparing the manuscript.

Funding

This study was financially supported by the Ministry of Science and Education of the Russian Federation (the review was written under government contract no. 0082-2019-0015).

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  1. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991, Moscow, Russia

    Yu. F. Krupyanskii

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  1. Yu. F. Krupyanskii
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Correspondence to Yu. F. Krupyanskii.

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Translated by L. Smolina

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Krupyanskii, Y.F. Architecture of Nucleoid in the Dormant Cells of Escherichia coli. Russ. J. Phys. Chem. B 15, 326–343 (2021). https://doi.org/10.1134/S199079312102007X

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