Projection structures reveal the position of the DNA within DNA-Dps Co-crystals

Moiseenko, Andrey; Лойко, Н. Г.; Терешкина, К. Б.; Danilova, Yana; Kovalenko, Vladislav; Chertkov, O. V.; Feofanov, Аlexey V.; Krupyanskiǐ, Yu. F.; Sokolova, Olga S.

doi:10.1016/j.bbrc.2019.07.103

Cited by 22 publications

(18 citation statements)

References 15 publications

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“…3D). The distance between the centers of Dps molecules in neighboring layers was 9 nm, which is comparable with results obtained in vitro [34], in cryo-EM [22], and in synchrotron radiation scattering [2]. Highlighted in black are densities, corresponded to the inter-layer DNA strands.…”

Section: Morphology Of Condensed Dna-dps Structures In Dormant E Colsupporting

confidence: 84%

“…The nanocrystalline are highly ordered intracellular structures of various sizes and shape, that often form 3D arrays, built from layers of DNA, stabilized by the Dps ( Fig. 2A) [3,6,34]. In liquid crystalline, less condensed DNA is found in the central part of the cell, surrounded by a condensed cytoplasm (Fig.…”

Section: Three Types Of Condensed Dna-dps Structures Found In Dormantmentioning

confidence: 99%

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Morphological peculiarities of DNA-protein complexes in dormantEscherichia colicells, subjected to prolonged starvation Condensation of DNA in dormant cells ofEscherichia coli

Krupyanskiǐ

Лойко

Danilova

et al. 2020

Preprint

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One of the adaptive strategies for the constantly changing conditions of the environment utilized in bacterial cells involves the condensation of DNA in complex with the DNA-binding protein, Dps. With the use of electron microscopy and electron tomography, we observed several morphologically different types of DNA condensation in dormant Escherichia coli cells, namely: nanocrystalline, liquid crystalline, and the folded nucleosome-like. We confirmed the presence of both Dps and DNA in all of the ordered structures using EDX analysis. The comparison of EDX spectra obtained for the three different ordered structures revealed that in nanocrystalline formation the majority of Dps protein is tightly bound to nucleoid DNA. We demonstrated that the population of the dormant cell is structurally heterogeneous, which allows cells to respond flexibly to environmental changes. It increases the ability of the whole bacterial population to survive under extreme stress conditions.

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Section: Morphology Of Condensed Dna-dps Structures In Dormant E Colsupporting

confidence: 84%

Section: Three Types Of Condensed Dna-dps Structures Found In Dormantmentioning

confidence: 99%

Morphological peculiarities of DNA-protein complexes in dormantEscherichia colicells, subjected to prolonged starvation Condensation of DNA in dormant cells ofEscherichia coli

Krupyanskiǐ

Лойко

Danilova

et al. 2020

Preprint

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“…The first two types were extensively described previously [ 3 , 4 , 6 , 16 , 20 , 22 ], but the third one, to our knowledge, is novel, and has been observed here for the first time in the cells, starving for up to 7 months. Nanocrystallines are highly ordered intracellular structures of various sizes and shape, that often form 3D arrays, built from layers of DNA, stabilized by Dps ( Fig 2A ) [ 3 , 6 , 38 ]. In liquid crystalline , less condensed DNA is found in the central part of the cell, surrounded by a condensed cytoplasm ( Fig 2B ) [ 3 ].…”

Section: Resultsmentioning

confidence: 99%

Morphological peculiarities of the DNA-protein complexes in starved Escherichia coli cells

et al. 2020

Self Cite

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One of the adaptive strategies for the constantly changing conditions of the environment utilized in bacterial cells involves the condensation of DNA in complex with the DNA-binding protein, Dps. With the use of electron microscopy and electron tomography, we observed several morphologically different types of DNA condensation in dormant Escherichia coli cells, namely: nanocrystalline , liquid crystalline , and the folded nucleosome-like . We confirmed the presence of both Dps and DNA in all of the ordered structures using EDX analysis. The comparison of EDX spectra obtained for the three different ordered structures revealed that in nanocrystalline formation the majority of the Dps protein is tightly bound to nucleoid DNA. The dps -null cells contained only one type of condensed DNA structure, liquid crystalline , thus, differing from those with Dps. The results obtained here shed some light on the phenomenon of DNA condensation in dormant prokaryotic cells and on the general problem of developing a response to stress. We demonstrated that the population of dormant cells is structurally heterogeneous, allowing them to respond flexibly to environmental changes. It increases the ability of the whole bacterial population to survive under extreme stress conditions.

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“…This peak may indicate an increase in the content of sulfur-containing proteins, like the above-mentioned Dps. Dps contains 48 Methionines per 24-mer, which possess enough sulfur to be detected by X-ray spectroscopy [ 28 , 41 ]. The increasing contents of Dps lead to the increased protection of bacterial DNA.…”

Section: Discussionmentioning

confidence: 99%

Maturation of Pseudo-Nucleus Compartment in P. aeruginosa, Infected with Giant phiKZ Phage

Danilova

Belousova

Moiseenko

et al. 2020

Viruses

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The giant phiKZ phage infection induces the appearance of a pseudo-nucleus inside the bacterial cytoplasm. Here, we used RT-PCR, fluorescent in situ hybridization (FISH), electron tomography, and analytical electron microscopy to study the morphology of this unique nucleus-like shell and to demonstrate the distribution of phiKZ and bacterial DNA in infected Pseudomonas aeruginosa cells. The maturation of the pseudo-nucleus was traced in short intervals for 40 min after infection and revealed the continuous spatial separation of the phage and host DNA. Immediately after ejection, phage DNA was located inside the newly-identified round compartments; at a later infection stage, it was replicated inside the pseudo-nucleus; in the mature pseudo-nucleus, a saturated internal network of filaments was observed. This network consisted of DNA bundles in complex with DNA-binding proteins. On the other hand, the bacterial nucleoid underwent significant rearrangements during phage infection, yet the host DNA did not completely degrade until at least 40 min after phage application. Energy dispersive x-ray spectroscopy (EDX) analysis revealed that, during the infection, the sulfur content in the bacterial cytoplasm increased, which suggests an increase of methionine-rich DNA-binding protein synthesis, whose role is to protect the bacterial DNA from stress caused by infection.

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Projection structures reveal the position of the DNA within DNA-Dps Co-crystals

Cited by 22 publications

References 15 publications

Morphological peculiarities of DNA-protein complexes in dormantEscherichia colicells, subjected to prolonged starvation Condensation of DNA in dormant cells ofEscherichia coli

Morphological peculiarities of DNA-protein complexes in dormantEscherichia colicells, subjected to prolonged starvation Condensation of DNA in dormant cells ofEscherichia coli

Morphological peculiarities of the DNA-protein complexes in starved Escherichia coli cells

Maturation of Pseudo-Nucleus Compartment in P. aeruginosa, Infected with Giant phiKZ Phage

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