Influence of the structure of the coat protein N-terminal segment in potato virus X and alternanthera mosaic virus on the structure and physico-chemical properties of virions
- Авторлар: Ksenofontov A.1, Petoukhov M.2,3, Matveev V.2, Fedorova N.1, Semenyuk P.1, Arutyunyan A.1, Manukhova T.4, Evtushenko E.4, Nikitin N.4
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Мекемелер:
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences
- Faculty of Biology, Lomonosov Moscow State University
- Шығарылым: Том 88, № 1 (2023)
- Беттер: 68-82
- Бөлім: Articles
- URL: https://journals.rcsi.science/0320-9725/article/view/144626
- DOI: https://doi.org/10.31857/S0320972523010050
- EDN: https://elibrary.ru/PBSOUZ
- ID: 144626
Дәйексөз келтіру
Аннотация
Авторлар туралы
A. Ksenofontov
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University
Email: ksenofon@belozersky.msu.ru
119991 Moscow, Russia
M. Petoukhov
Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences;A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences
Email: ksenofon@belozersky.msu.ru
119333 Moscow, Russia;119071 Moscow, Russia
V. Matveev
Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences
Email: ksenofon@belozersky.msu.ru
119333 Moscow, Russia
N. Fedorova
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University
Email: ksenofon@belozersky.msu.ru
119991 Moscow, Russia
P. Semenyuk
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University
Email: ksenofon@belozersky.msu.ru
119991 Moscow, Russia
A. Arutyunyan
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University
Email: ksenofon@belozersky.msu.ru
119991 Moscow, Russia
T. Manukhova
Faculty of Biology, Lomonosov Moscow State University
Email: ksenofon@belozersky.msu.ru
119234 Moscow, Russia
E. Evtushenko
Faculty of Biology, Lomonosov Moscow State University
Email: ksenofon@belozersky.msu.ru
119234 Moscow, Russia
N. Nikitin
Faculty of Biology, Lomonosov Moscow State University
Email: ksenofon@belozersky.msu.ru
119234 Moscow, Russia
Әдебиет тізімі
- Stubbs, G., and Kendall, A. (2012) Helical viruses, Adv. Exp. Med. Biol., 726, 631-658, doi: 10.1007/978-1-4614-0980-9_28.
- Ksenofontov, A. L., Paalme, V., Arutyunyan, A. M., Semenyuk, P. I., Fedorova, N. V., Rumvolt, R., Baratova, L. A., Jarvekulg, L., and Dobrov, E. N. (2013) Partially disordered structure in intravirus coat protein of potyvirus potato virus A, PLoS One, 8, e67830, doi: 10.1371/journal.pone.0067830.
- Semenyuk, P. I., Karpova, O. V., Ksenofontov, A. L., Kalinina, N. O., Dobrov, E. N., and Makarov, V. V. (2016) Structural properties of potexvirus coat proteins detected by optical methods, Biochemistry (Moscow), 81, 1522-1530, doi: 10.1134/S0006297916120130.
- Yang, S., Wang, T., Bohon, J., Gagne, M. E., Bolduc, M., Leclerc, D., and Li, H. (2012) Crystal structure of the coat protein of the flexible filamentous papaya mosaic virus, J. Mol. Biol., 422, 263-273, doi: 10.1016/j.jmb.2012.05.032.
- DiMaio, F., Chen, C. C., Yu, X., Frenz, B., Hsu, Y. H., Lin, N. S., and Egelman, E. H. (2015) The molecular basis for flexibility in the flexible filamentous plant viruses, Nat. Struct. Mol. Biol., 22, 642-644, doi: 10.1038/nsmb.3054.
- Agirrezabala, X., Mendez-Lopez, E., Lasso, G., Sanchez-Pina, M. A., Aranda, M., and Valle, M. (2015) The near-atomic cryoEM structure of a flexible filamentous plant virus shows homology of its coat protein with nucleoproteins of animal viruses, eLife, 4, e11795, doi: 10.7554/eLife.11795.
- Grinzato, A., Kandiah, E., Lico, C., Betti, C., Baschieri, S., and Zanotti, G. (2020) Atomic structure of potato virus X, the prototype of the Alphaflexiviridae family, Nat. Chem. Biol., 16, 564-569, doi: 10.1038/s41589-020-0502-4.
- Donchenko, E. K., Pechnikova, E. V., Mishyna, M. Y., Manukhova, T. I., Sokolova, O. S., Nikitin, N. A., Atabekov, J. G., and Karpova, O. V. (2017) Structure and properties of virions and virus-like particles derived from the coat protein of Alternanthera mosaic virus, PLoS One, 12, e0183824, doi: 10.1371/journal.pone.0183824.
- Mukhamedzhanova, A. A., Smirnov, A. A., Arkhipenko, M. V., Ivanov, P. A., Chirkov, S. N., Rodionova, N. P., Karpova, O. V., and Atabekov, J. G. (2011) Characterization of Alternanthera mosaic virus and its Coat Protein, Open Virol. J., 5, 136-140, doi: 10.2174/1874357901105010136.
- Hammond, J., Kim, Ik.-H., and Lim, H.-S. (2017) Alternanthera mosaic virus - an alternative ‘model' potexvirus of broad relevance, Kor. J. Agricult. Sci., 44, 145-180, doi: 10.7744/kjoas.20170016.
- Erickson, J. W., Bancroft, J. B., and Horne, R. W. (1976) The assembly of papaya mosaic virus protein, Virology, 72, 514-517, doi: 10.1016/0042-6822(76)90180-x.
- Ksenofontov, A. L., Dobrov, E. N., Fedorova, N. V., Serebryakova, M. V., Prusov, A. N., Baratova, L. A., Paalme, V., Jarvekulg, L., and Shtykova, E. V. (2018) Isolated Potato Virus A coat protein possesses unusual properties and forms different short virus-like particles, J. Biomol. Struct. Dyn., 36, 1728-1738, doi: 10.1080/07391102.2017.1333457.
- Homer, R. B., and Goodman, R. M. (1975) Circular dichroism and fluorescence studies on potato virus X and its structural components, Biochim. Biophys. Acta, 378, 296-304, doi: 10.1016/0005-2787(75)90117-3.
- Atabekov, J., Dobrov, E., Karpova, O., and Rodionova, N. (2007) Potato virus X: structure, disassembly and reconstitution, Mol. Plant Pathol., 8, 667-675, doi: 10.1111/j.1364-3703.2007.00420.x.
- Franke, D., Petoukhov, M. V., Konarev, P. V., Panjkovich, A., Tuukkanen, A., Mertens, H. D. T., Kikhney, A. G., Hajizadeh, N. R., Franklin, J. M., Jeffries, C. M., and Svergun, D. I. (2017) ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions, J. Appl. Crystallogr., 50, 1212-1225, doi: 10.1107/S1600576717007786.
- Svergun, D. I., Koch, M. H. J., Timmins, P. A., and May, R. P. (2013) Small Angle X-Ray and Neutron Scattering from Solutions of Biological Macromolecules, First Edn., Oxford University Press, Oxford.
- Ksenofontov, A. L., Petoukhov, M. V., Prusov, A. N., Fedorova, N. V., and Shtykova, E. V. (2020) Characterization of tobacco mosaic virus virions and repolymerized coat protein aggregates in solution by small-angle X-ray scattering, Biochemistry (Moscow), 85, 310-317, doi: 10.1134/S0006297920030062.
- Shtykova, E. V., Petoukhov, M. V., Fedorova, N. V., Arutyunyan, A. M., Skurat, E. V., Kordyukova, L. V., Moiseenko, A. V., and Ksenofontov, A. L. (2021) The structure of the potato virus a particles elucidated by small angle X-ray scattering and complementary techniques, Biochemistry (Moscow), 86, 230-240, doi: 10.1134/S0006297921020115.
- Miroshnichenko, N. A., Karpova, O. V., Morozov, S., Rodionova, N. P., and Atabekov, J. G. (1988) Translation arrest of potato virus X RNA in Krebs-2 cell-free system: RNase H cleavage promoted by complementary oligodeoxynucleotides, FEBS Lett., 234, 65-68, doi: 10.1016/0014-5793(88)81304-8.
- Laemmli, U. K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4, Nature, 227, 680-685, doi: 10.1038/227680a0.
- Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Soding, J., Thompson, J. D., and Higgins, D. G. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega, Mol. Syst. Biol., 7, 539, doi: 10.1038/msb.2011.75.
- Blanchet, C. E., Spilotros, A., Schwemmer, F., Graewert, M. A., Kikhney, A., Jeffries, C. M., Franke, D., Mark, D., Zengerle, R., Cipriani, F., Fiedler, S., Roessle, M., and Svergun, D. I. (2015) Versatile sample environments and automation for biological solution X-ray scattering experiments at the P12 beamline (PETRA III, DESY), J. Appl. Crystallogr., 48, 431-443, doi: 10.1107/S160057671500254X.
- Konarev, P. V., Volkov, V. V., Sokolova, A. V., Koch, M. H. J., and Svergun, D. I. (2003) PRIMUS: a Windows PC-based system for small-angle scattering data analysis, J. Appl. Crystallogr., 36, 1277-1282, doi: 10.1107/S0021889803012779.
- Manalastas-Cantos, K., Konarev, P. V., Hajizadeh, N. R., Kikhney, A. G., Petoukhov, M. V., Molodenskiy, D. S., Panjkovich, A., Mertens, H. D. T., Gruzinov, A., Borges, C., Jeffries, C. M., Svergun, D. I., and Franke, D. (2021) ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis, J. Appl. Crystallogr., 54, 343-355, doi: 10.1107/S1600576720013412.
- Вайнштейн Б. (1963) Дифракция рентгеновских лучей на цепных молекулах, АН СССР, Москва.
- Svergun, D. I. (1992) Determination of the regularization parameter in indirect-transform methods using perceptual criteria, J. Appl. Cryst., 25, 495-503, doi: 10.1107/S0021889892001663.
- Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., and Ferrin, T. E. (2004) UCSF Chimera - a visualization system for exploratory research and analysis, J. Comput. Chem., 25, 1605-1612, doi: 10.1002/jcc.20084.
- Konarev, P. V., Petoukhov, M. V., and Svergun, D. I. (2001) MASSHA - a graphics system for rigid-body modelling of macromolecular complexes against solution scattering data, J. Appl. Cryst., 34, 527-532, doi: 10.1107/S0021889801006100.
- Kozin, M. B., and Svergun, D. I. (2000) A software system for rigid-body modelling of solution scattering data, J. Appl. Cryst., 33, 775-777, doi: 10.1107/S0021889800001382.
- Bernado, P., Mylonas, E., Petoukhov, M. V., Blackledge, M., and Svergun, D. I. (2007) Structural characterization of flexible proteins using small-angle X-ray scattering, J. Am. Chem. Soc., 129, 5656-5664, doi: 10.1021/ja069124n.
- Svergun, D., Barberato, C., and Koch, M. H. J. (1995) CRYSOL - A program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinates, J. Appl. Cryst., 28, 768-773, doi: 10.1107/S0021889895007047.
- Tozzini, A. C., Ek, B., Palva, E. T., and Hopp, H. E. (1994) Potato virus X coat protein: a glycoprotein, Virology, 202, 651-658, doi: 10.1006/viro.1994.1386.
- Ivanov, P. A., Mukhamedzhanova, A. A., Smirnov, A. A., Rodionova, N. P., Karpova, O. V., and Atabekov, J. G. (2011) The complete nucleotide sequence of Alternanthera mosaic virus infecting Portulaca grandiflora represents a new strain distinct from phlox isolates, Virus Genes, 42, 268-271, doi: 10.1007/s11262-010-0556-6.
- Nemykh, M. A., Novikov, V. K., Arutiunian, A. M., Kalmykov, P. V., Drachev, V. A., and Dobrov, E. N. (2007) Comparative study of structural stabylity of potato virus X coat protein molecules in solution and in the virus particles [in Russian], Mol. Biol., 41, 697-705, doi: 10.1134/S0026893307040164.
- Thuenemann, E. C., Byrne, M. J., Peyret, H., Saunders, K., Castells-Graells, R., Ferriol, I., Santoni, M., Steele, J. F. C., Ranson, N. A., Avesani, L., Lopez-Moya, J. J., and Lomonossoff, G. P. (2021) A replicating viral vector greatly enhances accumulation of helical virus-like particles in plants, Viruses, 13, 885, doi: 10.3390/v13050885.
- Atabekov, J., Nikitin, N., Arkhipenko, M., Chirkov, S., and Karpova, O. (2011) Thermal transition of native tobacco mosaic virus and RNA-free viral proteins into spherical nanoparticles, J. Gen. Virol., 92, 453-456, doi: 10.1099/vir.0.024356-0.
- Ksenofontov, A. L., Parshina, E. Y., Fedorova, N. V., Arutyunyan, A. M., Rumvolt, R., Paalme, V., Baratova, L. A., Jarvekulg, L., and Dobrov, E. N. (2016) Heating-induced transition of Potyvirus Potato Virus A coat protein into beta-structure, J. Biomol. Struct. Dyn., 34, 250-258, doi: 10.1080/07391102.2015.1022604.
- Nikitin, N., Ksenofontov, A., Trifonova, E., Arkhipenko, M., Petrova, E., Kondakova, O., Kirpichnikov, M., Atabekov, J., Dobrov, E., and Karpova, O. (2016) Thermal conversion of filamentous potato virus X into spherical particles with different properties from virions, FEBS Lett., 590, 1543-1551, doi: 10.1002/1873-3468.12184.
- Manukhova, T. I., Evtushenko, E. A., Ksenofontov, A. L., Arutyunyan, A. M., Kovalenko, A. O., Nikitin, N. A., and Karpova, O. V. (2021) Thermal remodelling of Alternanthera mosaic virus virions and virus-like particles into protein spherical particles, PLoS One, 16, e0255378, doi: 10.1371/journal.pone.0255378.
- Baratova, L. A., Fedorova, N. V., Dobrov, E. N., Lukashina, E. V., Kharlanov, A. N., Nasonov, V. V., Serebryakova, M. V., Kozlovsky, S. V., Zayakina, O. V., and Rodionova, N. P. (2004) N-Terminal segment of potato virus X coat protein subunits is glycosylated and mediates formation of a bound water shell on the virion surface, Eur. J. Biochem., 271, 3136-3145, doi: 10.1111/j.1432-1033.2004.04243.x.
- Karpova, O. V., Arkhipenko, M. V., Zaiakina, O. V., Nikitin, N. A., Kiseleva, O. I., Kozlovskii, S. V., Rodionova, N. P., and Atabekov, I. G. (2006) Translational regulation of potato virus X RNA-coat protein complexes: the key role of a coat protein N-terminal peptide [in Russian], Mol. Biol., 40, 703-710, doi: 10.1134/S0026893306040157.
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