Asymmetric RNA Egress Site in Expanded RNA Virus by Cryo‐EM and HDXMS

• Published in: The FASEB journal 2022-05, Vol.36 (S1), p.n/a
• Main Authors: Braet, Sean, Venkatakrishnan, Varun, Ramesh, Ranita, Raghuvamsi, Palur, Anand, Ganesh
• Format: Article
• Language: English
• ISSN: 0892-6638; 1530-6860
• DOI: 10.1096/fasebj.2022.36.S1.0R446

RNA viruses are metastable macromolecular assemblies that sense their environment through dynamic breathing motions. While surfaces of viral particles have been well characterized by cryo‐EM, dynamic genome‐capsid cores are poorly understood. To address this gap in understanding, we have applied hydrogen deuterium exchange mass spectrometry (HDXMS) together with cryo‐EM to Turnip Crinkle Virus (TCV) as a model system to study RNA genome‐capsid interactions and their importance in environmental sensing and programmed viral disassembly in favorable host environments. TCV undergoes expansion upon ion of Ca2+ ions, associated with entry into a plant host cell. We have mapped changes upon expansion in the viral capsid. HDXMS analysis reveals two conformations of the coat protein R‐domain regions in the native state: a minor (~5%) RNA‐bound and a major (~95%) unbound R‐domain. A larger fraction of the R‐domain is bound (~15%) more tightly to RNA in the expanded state, indicating expansion is accompanied by changes in conformation of the RNA‐coat protein core. Cryo‐EM of expanded TCV reveals that the newly formed strong interactions between the capsid proteins and the RNA genome correspond to the asymmetric ribonucleoprotein core packing observed near a unique 5‐fold vertex in the expanded TCV particle. This 5‐fold vertex is the specific point of egress for the genomic RNA into the host. Far from being passively package contents, our results highlight an active role of the genomic RNA‐protein core as an environmental sensor which controls capsid uncoating and RNA release.