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

Schmidt, L.; Tueting, C.; Kyrilis, F. L.; Hamdi, F.; Semchonok, D. A.; Hause, G.; Meister, A.; Ihling, C.; Shah, P. N.; Stubbs, M. T.; Sinz, A.; Stuart, D. I.; Kastritis, P. L.

doi:10.1101/2022.07.15.498668

bioRxiv · 10.1101/2022.07.15.498668

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

Schmidt, L.·Tueting, C.·Kyrilis, F. L.·Hamdi, F.·Semchonok, D. A.·Hause, G.·Meister, A.·Ihling, C.·Shah, P. N.·Stubbs, M. T.·Sinz, A.·Stuart, D. I.·Kastritis, P. L.

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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-{pi} 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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Schmidt, L., Tueting, C., Kyrilis, F. L., Hamdi, F., Semchonok, D. A., Hause, G., Meister, A., Ihling, C., Shah, P. N., Stubbs, M. T., Sinz, A., Stuart, D. I., Kastritis, P. L.. 2022-07-16. Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts. https://doi.org/10.1101/2022.07.15.498668

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