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The Structure of the Potato Virus A Particles Elucidated by Small Angle X-Ray Scattering and Complementary Techniques

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Abstract

Potato virus A (PVA) protein coat contains on its surface partially unstructured N-terminal domain of the viral coat protein (CP), whose structural and functional characteristics are important for understanding the mechanism of plant infection with this virus. In this work, we investigated the properties and the structure of intact PVA and partially trypsinized PVAΔ32 virions using small-angle X-ray scattering (SAXS) and complimentary methods. It was shown that after the removal of 32 N-terminal amino acids of the CP, the virion did not disintegrate and remained compact, but the helical pitch of the CP packing changed. To determine the nature of these changes, we performed ab initio modeling, including the multiphase procedure, with the geometric bodies (helices) and restoration of the PVA structure in solution using available high-resolution structures of the homologous CP from the PVY potyvirus, based on the SAXS data. As a result, for the first time, a low-resolution structure of the filamentous PVA virus, both intact and partially degraded, was elucidated under conditions close to natural. The far-UV circular dichroism spectra of the PVA and PVAΔ32 samples differed significantly in the amplitude and position of the main negative maximum. The extent of thermal denaturation of these samples in the temperature range of 20-55°C was also different. The data of transmission electron microscopy showed that the PVAΔ32 virions were mostly rod-shaped, in contrast to the flexible filamentous particles typical of the intact virus, which correlated well with the SAXS results. In general, structural analysis indicates an importance of the CP N-terminal domain for the vital functions of PVA, which can be used to develop a strategy for combating this plant pathogen.

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Abbreviations

CP:

coat protein

PVA:

potato virus A

SAXS:

small angle X-ray scattering

TEM:

transmission electron microscopy

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Funding

This work was supported by the Russian Foundation for Basic Research (project no. 18-04-00525a), by the Ministry of Science and Higher Education of the Russian Federation (agreement 075-15-2019-1653), and by the Ministry of Science and Higher Education of the Russian Federation within the State assignment FSRC “Crystallography and Photonics” RAS (SAXS experiments).

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Authors and Affiliations

  1. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of the Russian Academy of Sciences, 119333, Moscow, Russia

    Eleonora V. Shtykova, Maxim V. Petoukhov & Alexander L. Ksenofontov

  2. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234, Moscow, Russia

    Natalia V. Fedorova, Alexander M. Arutyunyan, Larisa V. Kordyukova & Alexander L. Ksenofontov

  3. Faculty of Biology, Lomonosov Moscow State University, 119234, Moscow, Russia

    Eugene V. Skurat & Andrey V. Moiseenko

Authors
  1. Eleonora V. Shtykova
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  2. Maxim V. Petoukhov
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  3. Natalia V. Fedorova
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  4. Alexander M. Arutyunyan
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  5. Eugene V. Skurat
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  6. Larisa V. Kordyukova
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  7. Andrey V. Moiseenko
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  8. Alexander L. Ksenofontov
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Correspondence to Alexander L. Ksenofontov.

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The authors declare no conflict of interest in financial or any other sphere. This article does not contain any studies with human participants or animals performed by any of the authors.

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Shtykova, E.V., Petoukhov, M.V., Fedorova, N.V. et al. The Structure of the Potato Virus A Particles Elucidated by Small Angle X-Ray Scattering and Complementary Techniques. Biochemistry Moscow 86, 230–240 (2021). https://doi.org/10.1134/S0006297921020115

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