Viral genome-capsid core senses host environments to prime RNA release

Ramesh, R.; Braet, S. M.; Venkatakrishnan, V.; Raghuvamsi, P. V.; Bao, J. C. W.; Marzinek, J. K.; Wu, C.; Gao, R.; Wong, S.-M.; Bond, P. J.; Anand, G.

doi:10.1101/2021.11.23.469659

bioRxiv · 10.1101/2021.11.23.469659

Viral genome-capsid core senses host environments to prime RNA release

Ramesh, R.·Braet, S. M.·Venkatakrishnan, V.·Raghuvamsi, P. V.·Bao, J. C. W.·Marzinek, J. K.·Wu, C.·Gao, R.·Wong, S.-M.·Bond, P. J.·Anand, G.

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Abstract

Viruses are metastable macromolecular assemblies containing a nucleic acid core packaged by capsid proteins that are primed to disassemble in host-specific environments leading to genome release and replication. The mechanism of how viruses sense environmental changes associated with host entry to prime them for disassembly is unknown. We have applied a combination of mass spectrometry, cryo-EM, and simulation-assisted structure refinement to Turnip crinkle virus (TCV), which serves as a model non-enveloped icosahedral virus (Triangulation number = 3, 180 copies/icosahedron). Our results reveal genomic RNA tightly binds a subset of viral coat proteins to form a stable RNA-capsid core which undergoes conformational switching in response to host-specific environmental changes. These changes include: i) Depletion of Ca2+ which triggers viral particle expansion ii) Increase in osmolytes further disrupt interactions of outer coat proteins from the RNA-capsid core to promote complete viral disassembly. A cryo-EM structure of the expanded particle shows that RNA is asymmetrically extruded from a single 5-fold axis during disassembly. The genomic RNA:capsid protein interactions confer metastability to the TCV capsid and drive release of RNA from the disassembling virion within the plant host cell. AUTHOR SUMMARYRNA viruses including coronaviruses, dengue, influenza, and HIV are a significant threat to human health. These viral particles are finely tuned to undergo complex conformational changes that allow for response to varied environments. Turnip crinkle virus (TCV) serves as an excellent model for studying RNA virus dynamics. Since TCV is non-enveloped and has no post-translational modifications, we can specifically investigate the contributions of RNA to viral dynamics. Genomic RNA is not a passive entity but plays a crucial and previously uncharacterized role in viral disassembly. Our results reveal that the genomic RNA-capsid core serves as an environmental sensor and undergoes conformational switching in response to host cell conditions.

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Ramesh, R., Braet, S. M., Venkatakrishnan, V., Raghuvamsi, P. V., Bao, J. C. W., Marzinek, J. K., Wu, C., Gao, R., Wong, S.-M., Bond, P. J., Anand, G.. 2021-11-23. Viral genome-capsid core senses host environments to prime RNA release. https://doi.org/10.1101/2021.11.23.469659

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