DNA Condensation in Bacteria

Yu. F. Krupyanskii; Крупянский Ю. Ф.; A. A. Generalova; Генералова А. А.; V. V. Kovalenko; Коваленко В. В.; N. G. Loiko; Лойко Н. Г.; E. V. Tereshkin; Терешкин Э. В.; A. V. Moiseenko; Моисеенко А. В.; K. B. Tereshkina; Терешкина К. Б.; O. S. Sokolova; Соколова О. С.; A. N. Popov; Попов А. Н.

doi:10.31857/S0207401X23060067

DNA Condensation in Bacteria

作者: Krupyanskii Y.F.¹, Generalova A.A.¹, Kovalenko V.V.¹, Loiko N.G.¹^,2, Tereshkin E.V.¹, Moiseenko A.V.¹^,3, Tereshkina K.B.¹, Sokolova O.S.³, Popov A.N.⁴
隶属关系:
1. Semyonov Federal Research Center for Chemical Physic, Russian Academy of Science
2. Federal Research Center “Fundamentals of Biotechnology” Russian Academy of Sciences
3. Moscow State University
4. European Synchrotron Radiation Facility
期: 卷 42, 编号 6 (2023)
页面: 3-20
栏目: К 100-ЛЕТИЮ СО ДНЯ РОЖДЕНИЯ АКАДЕМИКА В.И. ГОЛЬДАНСКОГО
URL: https://rjmseer.com/0207-401X/article/view/674857
DOI: https://doi.org/10.31857/S0207401X23060067
EDN: https://elibrary.ru/UILPBU
ID: 674857

如何引用文章

全文:

开放存取

##reader.subscriptionAccessGranted##
受限制的访问

订阅或者付费存取

详细

Deoxyribonucleic acid (DNA) is organized hierarchically in the nucleoid of an actively growing cell, with three levels of DNA compaction. The lower level (small scale ≥1 kb base pairs (bps)) is provided by the interaction with DNA-bound proteins. Actively growing cells maintain a dynamic, far from equilibrium order through metabolism. When cells enter a dormant state (almost complete absence of metabolism), the usual biochemical methods of protecting DNA cease to work, and the cells, adapting to the new conditions, are forced to use the physical mechanisms of DNA protection. The structure of DNA in the nucleoid of dormant cells formed during starvation stress is studied using synchrotron radiation diffraction and transmission electron microscopy (TEM). The experimental results make 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 conducted for the first time indicate the presence of a periodic ordered organization of DNA in all the studied bacteria. The TEM method made it possible to extract fine visual information about the type of DNA condensation in the nucleoid of the bacterium Escherichia coli (E. coli). Intracellular nanocrystalline, as well as liquid-crystalline and folded nucleosome-like, structures of DNA are found. The folded nucleosome-like structure was observed for the first time and is the result of the multiple folding of long DNA molecules around the DNA-binding protein (Dps) of starved cells and its associates. The different types of condensed state of DNA found by us in the studied dormant E. coli cells (DNA condensation heterogeneity) provide additional arguments in favor of the concept that considers a microbial population as a multicellular organism. The study of changes in the DNA architecture under the effect of the chemical analog of the autoinducer of anabiosis 4-hexylresorcinol (4-HR) is studied. An increase in the 4-HR concentration induces the transition of a part of the cells of the population to anabiotic dormant state, and then to a mummified state. The studies of the structure of DNA 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. Studies of the structure of DNA in the mummified state show a strong difference from the structure of DNA in the anabiotic state.

关键词

deoxyribonucleic acid, bacterium Escherichia coli, starvation stress, intracellular structures: nanocrystalline, liquid crystalline, folded nucleosome-like, anabiosis autoinducer, 4-hexylresorcinol, anabiotic, and mummified state

参考

Stonington O.G., Pettijohn D.E. // Proc. Natl. Acad. Sci. USA. 1971. V. 68. № 1. P. 6
Verma S.C., Qian Z., Adhya S.L. // PLoS. Genet. 2019. V. 15. № 12. e1008456
Trun N., Marko J. // Amer. Soc Microbiol. News. 1998. V. 64. № 5. P. 276.
Бухарин О.В., Гинцбург А.Л., Романова Ю.М., Эль-Регистан Г.И. Механизмы выживания бактерий. М.: Медицина, 2005.
Ткаченко А.Г. Молекулярные механизмы стрессорных ответов у микроорганизмов. Екатеринбург: Уро РАН, 2012.
Minsky A., Shimoni E., Frenkiel-Krispin D. // Nat. Rev. Mol. Cell. Biol. 2002. V. 3. P. 50.
Grosberg A.Y., Khokhlov A.R. Statistical physics of macromolecules. N.Y.: AIP, 1994.
Bloomfield V.A. // Curr. Opin. Struct. Biol. 1996. V. 6. P. 334.
Циммер К. Микрокосм. E. coli и новая наука о жизни. Пер. с англ. М.: ООО “Альпина нон-фикшн”, 2013.
Крупянский Ю.Ф., Гольданский В.И. // УФН. 2002. Т. 172. № 11. С. 1247.
Крупянский Ю.Ф. // Хим. физика. 2021. Т. 40. № 3. С. 60; https://doi.org/10.31857/S0207401X21030079
Шайтан К.В. // Хим. физика. 2023. Т. 42. № 6. С. 40.
Dekker J., Rippe K., Dekker M., Kleckner N. // Capturing Chromosome Conform. Sci. 2002. V. 295. P. 1306; https://doi.org/10.1126/science.1067799
Simonis M., Klous P., Splinter E. et al. // Nat. Genet. 2006. V. 38. P. 1348; https://doi.org/10.1038/ng1896
Dostie J., Richmond T.A., Arnaout R.A. et al. // Genome Res. 2006. V. 16. P. 1299; https://doi.org/10.1101/gr.5571506
Gennes P.G.D. Scaling concepts in polymer physics. Ithaca: Cornell University Press, 1979.
Grosberg A.Y., Nechaev S.K., Shakhnovich E.I. // J. Phys. 1988. V. 49. P. 2095.
Lieberman-Aiden E., Van Berkum N.L., Williams L. et al. // Science. 2009. V. 326. P. 289.
Mirny L.A. // Chromosome Res. 2011. V. 19. P. 37.
Яшина Е.Г., Григорьев С.В. // ЖЭТФ. 2019. Т. 156. Вып. 3. С. 540.
Zwietering M.H., Jongenburger I., Rombouts F.M., van’t Riet K. // Appl. Environ. Microbiol. 1990. V. 56. № 6. P. 1875.
Loiko N., Danilova Y., Moiseenko A. et al. // PLOS One. 2020. V. 15. № 10; https://doi.org/10.1371/journal.pone.0231562
Шрёдингер Э. Что такое жизнь с точки зрения физики? М.: РИМИС, 2009.
Moiseenko A., Loiko N., Sokolova O.S., Krupyanskii Y.F. // Methods in Molecular Biology. 2022. V. 2516. P. 143; https://doi.org/10.1007/978-1-0716-2413-5_9
Синицын Д.О., Лойко Н.Г., Гуларян С.К. и др. // Хим. физика. 2017. Т. 36. № 9. С. 59.
Крупянский Ю.Ф., Лойко Н.Г., Синицын Д.О. и др. // Кристаллография. 2018. Т. 63. № 4. С. 572.
Reich Z., Wachtel E., Minsky A. // Science. 1994. V. 264. № 5164. P. 1460.
Frenkiel-Krispin D., Ben-Avraham I., Englander J. et al. // Mol. Microbiol. 2004. V. 51. P. 395.
Kovalenko V., Popov A., Santoni G. et al. // Acta Cryst. 2020. V. F76. P. 568.
Moiseenko A., Loiko N., Tereshkina K. et al. // Biochem. Biophys. Res. Commun. 2019. V. 517. № 3. P. 463.
Tereshkin E., Tereshkina K., Loiko N. et al. // J. Biomol. Struct. Dyn. 2019. V. 37. P. 2600.
Терешкин Э.В., Терешкина К.Б., Коваленко В.В. и др. // Хим. физика. 2019. Т. 38. № 10. С. 48.
Tereshkin E.V., Tereshkina K.B., Krupyanskii Y.F. // J. Physics: Conf. Ser. 2021. V. 2056. № 1. P. 012016.
Blinov V.N., Golo V.L., Krupyanskii Y. // Nanostuctures. Math. Phys. Model. 2015. V. 12. P. 5.
Vasilevskaya V.V., Khokhlov A.R., Kidoaki S., Yoshikawa K. // Biopolymers. 1997. V. 41. P. 51.
Loiko N., Danilova Y., Moiseenko A. et al. // bioRxiv. 2020. P. 2020.03.27.011494; https://doi.org/10.1101/2020.03.27.011494
Shapiro J.A. // Scientific American. 1988. V. 258. № 6. P. 82.
Shapiro J.A., Dworkin M. // Quarterly Rev. Biol. 1998. V. 73. № 3. P. 352.
Сузина Н.Е., Мулюкин А.Л., Лойко Н.Г. и др. // Микробиология. 2001. Т. 70. № 5. С. 776.
Procopio A., Malucelli E., Pacureanu A. et al. // ACS Central Science. 2019. V. 5. P. 1449.
Santos S., Yang Y., Rosa M. et al. // Scientific Reports. 2019. V. 9. P. 17217.
Ou H.D., Phan S., Deerinck T.J. et al. // Science. 2017. V. 357. № 6349. eaag0025; https://doi.org/10.1126/science.aag0025