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Kovalenko V, Popov A, Santoni G, Loiko N, Tereshkina K, Tereshkin E, Krupyanskii Y. Multi-crystal data collection using synchrotron radiation as exemplified with low-symmetry crystals of Dps. Acta Crystallogr F Struct Biol Commun 2020; 76:568-576. [PMID: 33135675 PMCID: PMC7605109 DOI: 10.1107/s2053230x20012571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/15/2020] [Indexed: 11/10/2022] Open
Abstract
Multi-crystal data collection using synchrotron radiation was successfully applied to determine the three-dimensional structure of a triclinic crystal form of Dps from Escherichia coli at 2.0 Å resolution. The final data set was obtained by combining 261 partial diffraction data sets measured from crystals with an average size of approximately 5 µm. The most important features of diffraction data measurement and processing for low-symmetry crystals are discussed.
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Affiliation(s)
- Vladislav Kovalenko
- Structure of Matter, Semenov FRC for Chemical Physics, RAS, 4 Kosygina Street, Moscow 119991, Russian Federation
| | - Alexander Popov
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Gianluca Santoni
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Natalia Loiko
- Survival of Microorganisms, FRC ‘Fundamentals of Biotechnology’, 33 Leninsky Prospect, Building 2, Moscow 119071, Russian Federation
| | - Ksenia Tereshkina
- Structure of Matter, Semenov FRC for Chemical Physics, RAS, 4 Kosygina Street, Moscow 119991, Russian Federation
| | - Eduard Tereshkin
- Structure of Matter, Semenov FRC for Chemical Physics, RAS, 4 Kosygina Street, Moscow 119991, Russian Federation
| | - Yurii Krupyanskii
- Structure of Matter, Semenov FRC for Chemical Physics, RAS, 4 Kosygina Street, Moscow 119991, Russian Federation
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Ayusman S, Duraivadivel P, Gowtham H, Sharma S, Hariprasad P. Bioactive constituents, vitamin analysis, antioxidant capacity and α-glucosidase inhibition of Canna indica L. rhizome extracts. FOOD BIOSCI 2020. [DOI: 10.1016/j.fbio.2020.100544] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Park C, Jin Y, Kim YJ, Jeong H, Seong BL. RNA-binding as chaperones of DNA binding proteins from starved cells. Biochem Biophys Res Commun 2020; 524:484-489. [PMID: 32007271 DOI: 10.1016/j.bbrc.2020.01.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 11/27/2022]
Abstract
DNA-binding proteins from starved cells (Dps) in Escherichia coli protects DNA from multiple stresses during the stationary phase by forming a stable Dps-DNA complex. In contrast, Dps cannot bind to DNA during the exponential phase and it has not been clear why Dps conditionally binds to DNA depending on the growth phase. In this study, we show that DNA-free Dps in the exponential phase can also bind to RNA and the preemptive binding of RNA precludes DNA from interacting with Dps. The critical role of RNA in modulating the stability and functional competence of Dps and their morphology, leads us to propose a two-state model of Dps in executing stress responses. In the exponential phase, Dps is present predominantly as ribonucleoprotein complex. Under starvation, RNAs are degraded by up-regulated RNases, activating Dps to bind with chromosomal DNAs protecting them from diverse stresses. A dual role of RNA as an inhibitor of DNA binding and chaperone to keep dynamic functional status of Dps would be crucial for operating an immediate protection of chromosomal DNAs on starvation. The holdase-type chaperoning role of RNA in Dps-mediated stress responses would shed light on the role of RNAs as chaperone (Chaperna).
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Affiliation(s)
- Chan Park
- Department of Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea; Department of Biomaterials Science and Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Yoontae Jin
- Department of Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Young Jun Kim
- Life Science and Biotechnology Department, Underwood Division, Underwood International College, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hotcherl Jeong
- Department of Pharmacy, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Baik L Seong
- Department of Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea; Department of Biomaterials Science and Engineering, Yonsei University, Seoul, 03722, Republic of Korea.
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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] [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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Antipov S, Turishchev S, Purtov Y, Shvyreva U, Sinelnikov A, Semov Y, Preobrazhenskaya E, Berezhnoy A, Shusharina N, Novolokina N, Vakhtel V, Artyukhov V, Ozoline O. The Oligomeric Form of the Escherichia coli Dps Protein Depends on the Availability of Iron Ions. Molecules 2017; 22:molecules22111904. [PMID: 29113077 PMCID: PMC6150300 DOI: 10.3390/molecules22111904] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 10/29/2017] [Accepted: 11/02/2017] [Indexed: 11/21/2022] Open
Abstract
The Dps protein of Escherichia coli, which combines ferroxidase activity and the ability to bind DNA, is effectively used by bacteria to protect their genomes from damage. Both activities depend on the integrity of this multi-subunit protein, which has an inner cavity for iron oxides; however, the diversity of its oligomeric forms has only been studied fragmentarily. Here, we show that iron ions stabilize the dodecameric form of Dps. This was found by electrophoretic fractionation and size exclusion chromatography, which revealed several oligomers in highly purified protein samples and demonstrated their conversion to dodecamers in the presence of 1 mM Mohr’s salt. The transmission electron microscopy data contradicted the assumption that the stabilizing effect is given by the optimal core size formed in the inner cavity of Dps. The charge state of iron ions was evaluated using Mössbauer spectroscopy, which showed the presence of Fe3O4, rather than the expected Fe2O3, in the sample. Assuming that Fe2+ can form additional inter-subunit contacts, we modeled the interaction of FeO and Fe2O3 with Dps, but the binding sites with putative functionality were predicted only for Fe2O3. The question of how the dodecameric form can be stabilized by ferric oxides is discussed.
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Affiliation(s)
- Sergey Antipov
- School of Life Sciences, Immanuel Kant Baltic Federal University, 236016 Kaliningrad, Russia.
- Institute of Cell Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia.
- Department of Biophysics and Biotechnology, Voronezh State University, 394018 Voronezh, Russia.
| | - Sergey Turishchev
- Department of Biophysics and Biotechnology, Voronezh State University, 394018 Voronezh, Russia.
| | - Yuriy Purtov
- Institute of Cell Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia.
| | - Uliana Shvyreva
- Institute of Cell Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia.
| | - Alexander Sinelnikov
- Department of Biophysics and Biotechnology, Voronezh State University, 394018 Voronezh, Russia.
| | - Yuriy Semov
- Department of Biophysics and Biotechnology, Voronezh State University, 394018 Voronezh, Russia.
| | | | - Andrey Berezhnoy
- Department of Biophysics and Biotechnology, Voronezh State University, 394018 Voronezh, Russia.
| | - Natalia Shusharina
- School of Life Sciences, Immanuel Kant Baltic Federal University, 236016 Kaliningrad, Russia.
| | - Natalia Novolokina
- Department of Biophysics and Biotechnology, Voronezh State University, 394018 Voronezh, Russia.
| | - Viktor Vakhtel
- Department of Biophysics and Biotechnology, Voronezh State University, 394018 Voronezh, Russia.
| | - Valeriy Artyukhov
- Department of Biophysics and Biotechnology, Voronezh State University, 394018 Voronezh, Russia.
| | - Olga Ozoline
- Institute of Cell Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia.
- Department of Cell Biology, Pushchino State Institute of Natural Sciences, 142290 Pushchino, Russia.
- Department of Structural and Functional genomics, Pushchino Scientific Center, 142290 Pushchino, Russia.
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Abstract
In all organisms, DNA molecules are tightly compacted into a dynamic 3D nucleoprotein complex. In bacteria, this compaction is governed by the family of nucleoid-associated proteins (NAPs). Under conditions of stress and starvation, an NAP called Dps (DNA-binding protein from starved cells) becomes highly up-regulated and can massively reorganize the bacterial chromosome. Although static structures of Dps-DNA complexes have been documented, little is known about the dynamics of their assembly. Here, we use fluorescence microscopy and magnetic-tweezers measurements to resolve the process of DNA compaction by Dps. Real-time in vitro studies demonstrated a highly cooperative process of Dps binding characterized by an abrupt collapse of the DNA extension, even under applied tension. Surprisingly, we also discovered a reproducible hysteresis in the process of compaction and decompaction of the Dps-DNA complex. This hysteresis is extremely stable over hour-long timescales despite the rapid binding and dissociation rates of Dps. A modified Ising model is successfully applied to fit these kinetic features. We find that long-lived hysteresis arises naturally as a consequence of protein cooperativity in large complexes and provides a useful mechanism for cells to adopt unique epigenetic states.
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The DNA-Binding Protein from Starved Cells (Dps) Utilizes Dual Functions To Defend Cells against Multiple Stresses. J Bacteriol 2015. [PMID: 26216848 DOI: 10.1128/jb.00475-15] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED Bacteria deficient in the DNA-binding protein from starved cells (Dps) are viable under controlled conditions but show dramatically increased mortality rates when exposed to any of a wide range of stresses, including starvation, oxidative stress, metal toxicity, or thermal stress. It remains unclear whether the protective action of Dps against specific stresses derives from its DNA-binding activity, which may exclude destructive agents from the chromosomal region, or its ferroxidase activity, which neutralizes and sequesters potentially damaging chemical species. To resolve this question, we have identified the critical residues of Escherichia coli Dps that bind to DNA and modulate iron oxidation. We uncoupled the biochemical activities of Dps, creating Dps variants and mutant E. coli strains that are defective in either DNA-binding or ferroxidase activity. Quantification of the contribution of each activity to the protection of DNA integrity and cellular viability revealed that both activities of Dps are required in order to counteract many differing stresses. These findings demonstrate that Dps plays a multipurpose role in stress protection via its dual activities, explaining how Dps can be of vital importance to bacterial viability over a wide range of stresses. IMPORTANCE The DNA-binding protein from starved cells (Dps) protects bacterial cells against many different types of stressors. We find that DNA binding and iron oxidation by Dps are performed completely independently of each other. Both biochemical activities are required to protect E. coli against stressors, as well as to protect DNA from oxidative damage in vitro. These results suggest that many stressors may cause both oxidative stress and direct DNA damage.
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