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

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Abstract

The amino acid sequences of coat proteins (CPs) of potexviruses such as potato virus X (PVX) and alternanthera mosaic virus (AltMV) share about 40% sequence identity. However, the N-terminal CP domains of these virions differ both in length (the N-terminal CP domain of PVX is longer by 28 residues, ∆N = 28), and in amino acid sequence. In this work, we determined the effect of the N-terminal CP domain on the structure and physicochemical properties of the entire PVX and AltMV virions. It was shown that the melting point of PVX samples is 10-12°C higher than that of AltMV preparations; the circular dichroism spectra of these viruses also differ significantly. Spatial alignment of the existing high-resolution potexvirus CP structures showed that the RMSD value between Cα-atoms was the largest for the N-terminal domains of the two compared models. From computer simulations the ∆N-terminal CP domain of PVX is completely disordered. According to synchrotron small-angle X-ray scattering (SAXS) data, the structure of CP of PVX and AltMV virions differs, in particular, CP PVX has a larger size of crystallinity regions and, therefore, is more ordered. Using SAXS, virion diameters and helix parameters in solution are calculated. The influence of the conformation and localization of the N-terminal domain of PVX CP relative to the surface of the virion on its structure was revealed. Presumably, the increased thermal stability of PVX virions compared to AltMV is provided by the elongated N-terminal domains (ΔN = 28), which ensures additional contact between the adjacent CP subunits in the PVX virion.

About the authors

A. L Ksenofontov

Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University

Email: ksenofon@belozersky.msu.ru
119991 Moscow, Russia

M. V 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. 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. V Fedorova

Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University

Email: ksenofon@belozersky.msu.ru
119991 Moscow, Russia

P. I Semenyuk

Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University

Email: ksenofon@belozersky.msu.ru
119991 Moscow, Russia

A. M Arutyunyan

Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University

Email: ksenofon@belozersky.msu.ru
119991 Moscow, Russia

T. I Manukhova

Faculty of Biology, Lomonosov Moscow State University

Email: ksenofon@belozersky.msu.ru
119234 Moscow, Russia

E. A Evtushenko

Faculty of Biology, Lomonosov Moscow State University

Email: ksenofon@belozersky.msu.ru
119234 Moscow, Russia

N. A Nikitin

Faculty of Biology, Lomonosov Moscow State University

Email: ksenofon@belozersky.msu.ru
119234 Moscow, Russia

References

  1. Stubbs, G., and Kendall, A. (2012) Helical viruses, Adv. Exp. Med. Biol., 726, 631-658, doi: 10.1007/978-1-4614-0980-9_28.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. Вайнштейн Б. (1963) Дифракция рентгеновских лучей на цепных молекулах, АН СССР, Москва.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. 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.
  41. 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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