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Chesnokov Y, Kamyshinsky R, Mozhaev A, Shtykova E, Vasiliev A, Orlov I, Dadinova L. Morphological Diversity of Dps Complex with Genomic DNA. Int J Mol Sci 2023; 24:ijms24108534. [PMID: 37239879 DOI: 10.3390/ijms24108534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/26/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
In response to adverse environmental factors, Escherichia coli cells actively produce Dps proteins which form ordered complexes (biocrystals) with bacterial DNA to protect the genome. The effect of biocrystallization has been described extensively in the scientific literature; furthermore, to date, the structure of the Dps-DNA complex has been established in detail in vitro using plasmid DNA. In the present work, for the first time, Dps complexes with E. coli genomic DNA were studied in vitro using cryo-electron tomography. We demonstrate that genomic DNA forms one-dimensional crystals or filament-like assemblies which transform into weakly ordered complexes with triclinic unit cells, similar to what is observed for plasmid DNA. Changing such environmental factors as pH and KCl and MgCl2 concentrations leads to the formation of cylindrical structures.
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Affiliation(s)
- Yuri Chesnokov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia
- National Research Center "Kurchatov Institute", Akademika Kurchatova pl., 1, 123182 Moscow, Russia
| | - Roman Kamyshinsky
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia
- National Research Center "Kurchatov Institute", Akademika Kurchatova pl., 1, 123182 Moscow, Russia
| | - Andrey Mozhaev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Eleonora Shtykova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia
| | - Alexander Vasiliev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia
- National Research Center "Kurchatov Institute", Akademika Kurchatova pl., 1, 123182 Moscow, Russia
- Moscow Institute of Physics and Technology, Institutsky per. 9, 141701 Dolgoprudny, Russia
| | - Ivan Orlov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia
| | - Liubov Dadinova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia
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Chesnokov Y, Mozhaev A, Kamyshinsky R, Gordienko A, Dadinova L. Structural Insights into Iron Ions Accumulation in Dps Nanocage. Int J Mol Sci 2022; 23:ijms23105313. [PMID: 35628121 PMCID: PMC9140674 DOI: 10.3390/ijms23105313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/07/2022] [Accepted: 05/08/2022] [Indexed: 02/05/2023] Open
Abstract
Dps (DNA-binding protein from starved cells) is well known for the structural protection of bacterial DNA by the formation of highly ordered intracellular assemblies under stress conditions. Moreover, this ferritin-like protein can perform fast oxidation of ferrous ions and subsequently accumulate clusters of ferric ions in its nanocages, thus providing the bacterium with physical and chemical protection. Here, cryo-electron microscopy was used to study the accumulation of iron ions in the nanocage of a Dps protein from Escherichia coli. We demonstrate that Fe2+ concentration in the solution and incubation time have an insignificant effect on the volume and the morphology of iron minerals formed in Dps nanocages. However, an increase in the Fe2+ level leads to an increase in the proportion of larger clusters and the clusters themselves are composed of discrete ~1-1.5 nm subunits.
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Affiliation(s)
- Yury Chesnokov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia; (Y.C.); (A.M.); (R.K.); (A.G.)
- National Research Center “Kurchatov Institute”, Akademika Kurchatova pl., 1, 123182 Moscow, Russia
| | - Andrey Mozhaev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia; (Y.C.); (A.M.); (R.K.); (A.G.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics, Myasnitskaya Str. 20, 101000 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov Str. 1, 117997 Moscow, Russia
| | - Roman Kamyshinsky
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia; (Y.C.); (A.M.); (R.K.); (A.G.)
- National Research Center “Kurchatov Institute”, Akademika Kurchatova pl., 1, 123182 Moscow, Russia
- Moscow Institute of Physics and Technology, Institutsky Lane 9, 141700 Dolgoprudny, Russia
| | - Alexander Gordienko
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia; (Y.C.); (A.M.); (R.K.); (A.G.)
- Physics Department, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Liubov Dadinova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy Prospect, 59, 119333 Moscow, Russia; (Y.C.); (A.M.); (R.K.); (A.G.)
- Correspondence: ; Tel.: +7-(499)-135-62-00
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Dadinova L, Kamyshinsky R, Chesnokov Y, Mozhaev A, Matveev V, Gruzinov A, Vasiliev A, Shtykova E. Structural Rearrangement of Dps-DNA Complex Caused by Divalent Mg and Fe Cations. Int J Mol Sci 2021; 22:ijms22116056. [PMID: 34205216 PMCID: PMC8199988 DOI: 10.3390/ijms22116056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/29/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022] Open
Abstract
Two independent, complementary methods of structural analysis were used to elucidate the effect of divalent magnesium and iron cations on the structure of the protective Dps-DNA complex. Small-angle X-ray scattering (SAXS) and cryo-electron microscopy (cryo-EM) demonstrate that Mg2+ ions block the N-terminals of the Dps protein preventing its interaction with DNA. Non-interacting macromolecules of Dps and DNA remain in the solution in this case. The subsequent addition of the chelating agent (EDTA) leads to a complete restoration of the structure of the complex. Different effect was observed when Fe cations were added to the Dps-DNA complex; the presence of Fe2+ in solution leads to the total complex destruction and aggregation without possibility of the complex restoration with the chelating agent. Here, we discuss these different responses of the Dps-DNA complex on the presence of additional free metal cations, investigating the structure of the Dps protein with and without cations using SAXS and cryo-EM. Additionally, the single particle analysis of Dps with accumulated iron performed by cryo-EM shows localization of iron nanoparticles inside the Dps cavity next to the acidic (hydrophobic) pore, near three glutamate residues.
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Affiliation(s)
- Liubov Dadinova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences”, Leninskiy Prospect, 59, 119333 Moscow, Russia; (R.K.); (Y.C.); (A.M.); (A.V.); (E.S.)
- Correspondence: ; Tel.: +7-(499)-135-62-00
| | - Roman Kamyshinsky
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences”, Leninskiy Prospect, 59, 119333 Moscow, Russia; (R.K.); (Y.C.); (A.M.); (A.V.); (E.S.)
- National Research Center “Kurchatov Institute”, Akademika Kurchatova, 1, 123182 Moscow, Russia
- Moscow Institute of Physics and Technology, Institutsky Lane 9, 141700 Dolgoprudny, Russia
| | - Yury Chesnokov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences”, Leninskiy Prospect, 59, 119333 Moscow, Russia; (R.K.); (Y.C.); (A.M.); (A.V.); (E.S.)
- National Research Center “Kurchatov Institute”, Akademika Kurchatova, 1, 123182 Moscow, Russia
| | - Andrey Mozhaev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences”, Leninskiy Prospect, 59, 119333 Moscow, Russia; (R.K.); (Y.C.); (A.M.); (A.V.); (E.S.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Vladimir Matveev
- Physics Department, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Andrey Gruzinov
- EMBL, Hamburg Outstation, c/o DESY, Notkestr. 85, Geb. 25a, 22607 Hamburg, Germany;
| | - Alexander Vasiliev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences”, Leninskiy Prospect, 59, 119333 Moscow, Russia; (R.K.); (Y.C.); (A.M.); (A.V.); (E.S.)
- National Research Center “Kurchatov Institute”, Akademika Kurchatova, 1, 123182 Moscow, Russia
- Moscow Institute of Physics and Technology, Institutsky Lane 9, 141700 Dolgoprudny, Russia
| | - Eleonora Shtykova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences”, Leninskiy Prospect, 59, 119333 Moscow, Russia; (R.K.); (Y.C.); (A.M.); (A.V.); (E.S.)
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Kamyshinsky R, Chesnokov Y, Dadinova L, Mozhaev A, Orlov I, Petoukhov M, Orekhov A, Shtykova E, Vasiliev A. Polymorphic Protective Dps-DNA Co-Crystals by Cryo Electron Tomography and Small Angle X-Ray Scattering. Biomolecules 2019; 10:biom10010039. [PMID: 31888079 PMCID: PMC7023142 DOI: 10.3390/biom10010039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/19/2019] [Accepted: 12/22/2019] [Indexed: 12/01/2022] Open
Abstract
Rapid increase of intracellular synthesis of specific histone-like Dps protein that binds DNA to protect the genome against deleterious factors leads to in cellulo crystallization—one of the most curious processes in the area of life science at the moment. However, the actual structure of the Dps–DNA co-crystals remained uncertain in the details for more than two decades. Cryo-electron tomography and small-angle X-ray scattering revealed polymorphous modifications of the co-crystals depending on the buffer parameters. Two different types of the Dps–DNA co-crystals are formed in vitro: triclinic and cubic. Three-dimensional reconstruction revealed DNA and Dps molecules in cubic co-crystals, and the unit cell parameters of cubic lattice were determined consistently by both methods.
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Affiliation(s)
- Roman Kamyshinsky
- National Research Center “Kurchatov Institute”, Akademika Kurchatova pl., 1, 123182 Moscow, Russia; (Y.C.); (A.O.); (A.V.)
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (L.D.); (A.M.); (I.O.); (M.P.); (E.S.)
- Moscow Institute of Physics and Technology, Institutsky lane 9, 141700 Dolgoprudny, Moscow Region, Russia
- Correspondence: ; Tel.: +7-916-356-3963
| | - Yury Chesnokov
- National Research Center “Kurchatov Institute”, Akademika Kurchatova pl., 1, 123182 Moscow, Russia; (Y.C.); (A.O.); (A.V.)
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (L.D.); (A.M.); (I.O.); (M.P.); (E.S.)
| | - Liubov Dadinova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (L.D.); (A.M.); (I.O.); (M.P.); (E.S.)
| | - Andrey Mozhaev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (L.D.); (A.M.); (I.O.); (M.P.); (E.S.)
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry of Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Ivan Orlov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (L.D.); (A.M.); (I.O.); (M.P.); (E.S.)
| | - Maxim Petoukhov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (L.D.); (A.M.); (I.O.); (M.P.); (E.S.)
- Frumkin Institute of Physical Chemistry and Electrochemistry of Russian Academy of Sciences, Leninsky prospect, 31, 119071 Moscow, Russia
| | - Anton Orekhov
- National Research Center “Kurchatov Institute”, Akademika Kurchatova pl., 1, 123182 Moscow, Russia; (Y.C.); (A.O.); (A.V.)
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (L.D.); (A.M.); (I.O.); (M.P.); (E.S.)
- Moscow Institute of Physics and Technology, Institutsky lane 9, 141700 Dolgoprudny, Moscow Region, Russia
| | - Eleonora Shtykova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (L.D.); (A.M.); (I.O.); (M.P.); (E.S.)
| | - Alexander Vasiliev
- National Research Center “Kurchatov Institute”, Akademika Kurchatova pl., 1, 123182 Moscow, Russia; (Y.C.); (A.O.); (A.V.)
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskiy prospect, 59, 119333 Moscow, Russia; (L.D.); (A.M.); (I.O.); (M.P.); (E.S.)
- Moscow Institute of Physics and Technology, Institutsky lane 9, 141700 Dolgoprudny, Moscow Region, Russia
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