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Trifonova TS, Moiseenko AV, Bourkaltseva MV, Shaburova OV, Shaytan AK, Krylov VN, Sokolova OS. [DNA mapping in the capsid of giant bacteriophage phiEL (Caudovirales: Myoviridae: Elvirus) by analytical electron microscopy]. Vopr Virusol 2022; 66:434-441. [PMID: 35019250 DOI: 10.36233/0507-4088-80] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 01/08/2022] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Giant phiKZ-like bacteriophages have a unique protein formation inside the capsid, an inner body (IB) with supercoiled DNA molecule wrapped around it. Standard cryo-electron microscopy (cryo-EM) approaches do not allow to distinguish this structure from the surrounding nucleic acid of the phage. We previously developed an analytical approach to visualize protein-DNA complexes on Escherichia coli bacterial cell slices using the chemical element phosphorus as a marker. In the study presented, we adapted this technique for much smaller objects, namely the capsids of phiKZ-like bacteriophages. MATERIAL AND METHODS Following electron microscopy techniques were used in the study: analytical (AEM) (electron energy loss spectroscopy, EELS), and cryo-EM (images of samples subjected to low and high dose of electron irradiation were compared). RESULTS We studied DNA packaging inside the capsids of giant bacteriophages phiEL from the Myoviridae family that infect Pseudomonas aeruginosa. Phosphorus distribution maps were obtained, showing an asymmetrical arrangement of DNA inside the capsid. DISCUSSION We developed and applied an IB imaging technique using a high angle dark-field detector (HAADF) and the STEM-EELS analytical approach. Phosphorus mapping by EELS and cryo-electron microscopy revealed a protein formation as IB within the phage phiEL capsid. The size of IB was estimated using theoretical calculations. CONCLUSION The developed technique can be applied to study the distribution of phosphorus in other DNA- or RNA-containing viruses at relatively low concentrations of the element sought.
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Affiliation(s)
- T S Trifonova
- FSAEI HE «People's Friendship University of Russia», Physical, Mathematical, and Natural Sciences Department; FSBEI HE «Lomonosov Moscow State University», Bioengineering Department, Biological Faculty
| | - A V Moiseenko
- FSBEI HE «Lomonosov Moscow State University», Bioengineering Department, Biological Faculty; FSBIS «N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences»
| | | | - O V Shaburova
- FSBRI «I.I. Mechnikov Research Institute of Vaccines and Sera»
| | - A K Shaytan
- FSBEI HE «Lomonosov Moscow State University», Bioengineering Department, Biological Faculty
| | - V N Krylov
- FSBRI «I.I. Mechnikov Research Institute of Vaccines and Sera»
| | - O S Sokolova
- FSBEI HE «Lomonosov Moscow State University», Bioengineering Department, Biological Faculty
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2
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Bagrov DV, Glukhov GS, Moiseenko AV, Karlova MG, Litvinov DS, Zaitsev PА, Kozlovskaya LI, Shishova AA, Kovpak AA, Ivin YY, Piniaeva AN, Oksanich AS, Volok VP, Osolodkin DI, Ishmukhametov AA, Egorov AM, Shaitan KV, Kirpichnikov MP, Sokolova OS. Structural characterization of β-propiolactone inactivated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) particles. Microsc Res Tech 2021; 85:562-569. [PMID: 34498784 PMCID: PMC8646525 DOI: 10.1002/jemt.23931] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/22/2021] [Indexed: 12/23/2022]
Abstract
The severe COVID‐19 pandemic drives the research toward the SARS‐CoV‐2 virion structure and the possible therapies against it. Here, we characterized the β‐propiolactone inactivated SARS‐CoV‐2 virions using transmission electron microscopy (TEM) and atomic force microscopy (AFM). We compared the SARS‐CoV‐2 samples purified by two consecutive chromatographic procedures (size exclusion chromatography [SEC], followed by ion‐exchange chromatography [IEC]) with samples purified by ultracentrifugation. The samples prepared using SEC and IEC retained more spikes on the surface than the ones prepared using ultracentrifugation, as confirmed by TEM and AFM. TEM showed that the spike (S) proteins were in the pre‐fusion conformation. Notably, the S proteins could be recognized by specific monoclonal antibodies. Analytical TEM showed that the inactivated virions retained nucleic acid. Altogether, we demonstrated that the inactivated SARS‐CoV‐2 virions retain the structural features of native viruses and provide a prospective vaccine candidate.
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Affiliation(s)
- Dmitry V Bagrov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Grigory S Glukhov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Andrey V Moiseenko
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Maria G Karlova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Daniil S Litvinov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Petr А Zaitsev
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Liubov I Kozlovskaya
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia.,Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Anna A Shishova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia.,Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Anastasia A Kovpak
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia
| | - Yury Y Ivin
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia
| | - Anastasia N Piniaeva
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia
| | | | - Viktor P Volok
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia
| | - Dmitry I Osolodkin
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia.,Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Aydar A Ishmukhametov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences (Institute of Poliomyelitis), Moscow, Russia.,Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alexey M Egorov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia.,Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Konstantin V Shaitan
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | | | - Olga S Sokolova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Biology Department, MSU-BIT University, Shenzhen, China
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Myers CG, Pettitt BM. Phage-like packing structures with mean field sequence dependence. J Comput Chem 2017; 38:1191-1197. [PMID: 28349552 PMCID: PMC5403567 DOI: 10.1002/jcc.24727] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/30/2016] [Accepted: 12/01/2016] [Indexed: 11/08/2022]
Abstract
Packing of double-stranded DNA in phages must overcome both electrostatic repulsions and the problem of persistence length. We consider coarse-grained models with the ability to kink and with randomly generated disorder. We show that the introduction of kinking into configurations of the DNA polymer packaged within spherical confinement results in significant reductions of the overall energies and pressures. We use a kink model which has the ability to deform every 24 bp, close to the average length predicted from phage sequence. The introduction of such persistence length defects even with highly random packing models increases the local nematic ordering of the packed DNA polymer segments. Such local ordering allowed by kinking not only reduces the total bending energy of confined DNA due to nonlinear elasticity but also reduces the electrostatic component of the energy and pressure. We show that a broad ensemble of polymer configurations is consistent with the structural data. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Christopher G Myers
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, 77030-3411
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas, 77555-0144
| | - B Montgomery Pettitt
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, 77030-3411
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas, 77555-0144
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