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Dadinova LA, Chesnokov YM, Kamyshinsky RA, Orlov IA, Petoukhov MV, Mozhaev AA, Soshinskaya EY, Lazarev VN, Manuvera VA, Orekhov AS, Vasiliev AL, Shtykova EV. Protective Dps-DNA co-crystallization in stressed cells: an in vitro structural study by small-angle X-ray scattering and cryo-electron tomography. FEBS Lett 2019; 593:1360-1371. [PMID: 31090064 DOI: 10.1002/1873-3468.13439] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/08/2019] [Accepted: 05/10/2019] [Indexed: 01/14/2023]
Abstract
Under severe or prolonged stress, bacteria produce a nonspecific DNA-binding protein (Dps), which effectively protects DNA against damaging agents both in vitro and in vivo by forming intracellular biocrystals. The phenomenon of protective crystallization of DNA in living cells has been intensively investigated during the last two decades; however, the results of studies are somewhat contradictory, and up to now, there has been no direct determination of a Dps-DNA crystal structure. Here, we report the in vitro analysis of the vital process of Dps-DNA co-crystallization using two complementary structural methods: synchrotron small-angle X-ray scattering in solution and cryo-electron tomography. Importantly, for the first time, the DNA in the co-crystals was visualized, and the lattice parameters of the crystalline Dps-DNA complex were determined.
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Affiliation(s)
- Liubov A Dadinova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia
| | - Yurii M Chesnokov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia.,National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Roman A Kamyshinsky
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia.,National Research Center 'Kurchatov Institute', Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan A Orlov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia
| | - Maxim V Petoukhov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia.,Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, Russia.,Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia.,European Molecular Biology Laboratory, EMBL Hamburg Outstation, Germany
| | - Andrey A Mozhaev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina Yu Soshinskaya
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia
| | - Vassili N Lazarev
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Valentin A Manuvera
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Anton S Orekhov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia.,National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Alexander L Vasiliev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia.,National Research Center 'Kurchatov Institute', Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Eleonora V Shtykova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics", Russian Academy of Sciences, Moscow, Russia.,Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
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