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PreprintCited by 12Advanced Electron Microscopy Techniques and ApplicationsEnzyme Structure and FunctionBacteriophages and microbial interactions

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Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts

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Schmidt, Lisa, Tüting, Christian, Kyrilis, Fotis L., Hamdi, Farzad, Semchonok, Dmitry A., Hause, Gerd, Meister, Annette, Ihling, Christian, Shah, Pranav N. M., Stubbs, Milton T., Sinz, Andrea, Stuart, David I., Kastritis, Panagiotis L.·2022·Communications Biology
DOI 10.1101/2022.07.15.498668PMC PMC11087493

Preprint — published as 10.1038/s42003-024-06204-7

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Abstract

The high abundance of most viruses in infected host cells benefits their structural characterization; endogenous viruses are present in low copy numbers, however, and are therefore challenging to investigate. Here, we retrieve cell extracts enriched with an endogenous virus, the yeast L-A virus. The determined cryo-EM structure discloses capsid-stabilizing cation-π stacking and an interplay of non-covalent interactions from ten distinct capsomere interfaces. The capsid-embedded mRNA decapping active site trench is supported by a constricting movement of two opposite-facing loops. tRNA-loaded polysomes and other biomacromolecules, presumably mRNA, are found in virus proximity while stacked dsRNA bundles and the sub-stoichiometric polymerase localize underneath the capsid surface. Mature viruses participate in larger viral communities resembling their rare in-cell equivalents in terms of size, composition, and inter-virus distances. Our results collectively describe a 3D-architecture of a viral milieu, opening the door to cellextract-based high-resolution structural virology.

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Metadata

Authors
Schmidt, L., Tüting, C., Kyrilis, F. L., Hamdi, F., Semchonok, D. A., Hause, G., Meister, A., Ihling, C., Shah, P. N. M., Stubbs, M. T., Sinz, A., Stuart, D. I., & Kastritis, P. L.
Affiliations
  • Martin Luther University Halle-Wittenberg (DE)
  • Centre for Human Genetics (GB)
Corresponding author
Kastritis, Panagiotis L.
ORCID
Venue
Communications Biology
Publisher
openRxiv
Published
2022-07-16
Volume
7
Issue
1
Pages
557-557
ISSN
2399-3642 (ISSN-L)
DOI
10.1101/2022.07.15.498668
PMC
PMC11087493
OpenAlex
W4396804050
Cited by
12
References
1
Citations by year
2026: 5 · 2025: 6 · 2023: 1
FWCI
2.00
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Communications Biology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • National Hellenic Research Foundation Helios Repository (National Hellenic Research Foundation) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Digitalen Hochschulbibliothek Sachsen-Anhalt (Universitäts- und Landesbibliothek Sachsen-Anhalt) (cc-by)
Funders
  • Deutsche Forschungsgemeinschaft (391498659, RTG 2467)
  • Bundesministerium für Bildung und Forschung (03Z22HN23, 03Z22HI2, 03COV04)
  • HORIZON EUROPE Framework Programme (101086665)
  • European Regional Development Fund (391498659, RTG 2467, ZS/2016/04/78115)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
Keywords
L-A virus, endogenous viruses, Totiviridae, capsid structure, mRNA decapping, viral mRNA, viral communities, cell extracts, structural virology, yeast
MeSH terms
Capsid, Cell Extracts, RNA, Messenger, RNA, Viral, Saccharomyces cerevisiae, Cryoelectron Microscopy

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