Abstract
Viruses have remarkable structural diversity yet they share a common feature: a highly ordered capsid that protects the viral genome and ensures its safe delivery to the host cells. In this PhD, I used cryogenic electron microscopy (Cryo-EM) single particle analysis (SPA) to study the structural states formed by Seneca Valley virus (SVV), a small RNA picornavirus and bacteriophage Bas18, a member of the BASEL phage collection. Additionally, I performed a comparative analysis of major capsid proteins (MCPs) and decoration proteins across multiple bacteriophages. This was done to explore structural variations and identify potential conserved architectural principles within bacteriophages.
Firstly, we explored the structural states that SVV can form under conditions that trigger genome release. Through Cryo-EM SPA, we identified that SVV can form multiple intermediate states such as the altered particle (A-particle) and open particles. We also found that it forms an empty rotated particle post genome release. The A-particle is rarely observed in non-enteroviruses, highlighting the unique state SVV can form. It also reveals a unique sequence of capsid structural states not observed in other picornaviruses. The findings can provide additional insights for optimization of SVV as an oncolytic agent.
Subsequently, we determined the structure of Dhillonvirus bacteriophage Bas18 from the BASEL (BActeriophage SElection for your Laboratory) collection by Cryo-EM and SPA. The icosahedral capsid has T=7(d) arrangement with a neck, tail and tail tip forming the full assembled virion. We also discovered a previously undiscovered loop insertion within the MCP, along with a unique dimeric decoration protein within the hexameric capsomer. The components forming the neck, tail and tail tip are structurally very similar to phage T1, despite low sequence similarity. Comparative sequence analysis indicates that Dhillonviruses within the BASEL collection share high sequence similarity, suggesting they may be structurally conserved.
Finally, a broader comparative analysis of MCPs and decoration proteins across bacteriophages revealed common features that collectively shape capsid architecture. The MCP of bacteriophages follow the HK97 fold, but we found that Bas18 has a unique insertion. In this comparative analysis, we discovered that phages can have multiple insertions within theirv loops/domains and they can reinforce capsid stability by interacting with decoration proteins, other MCPs or not form any interaction. Moreover, these insertions were independent of the decoration binding site of the respective phages.
The chapters in this thesis provide detailed insights into virus capsid architecture while contributing to the broader field of structural virology. We emphasize how different viruses achieve and balance capsid stability and function, providing a framework for understanding virus structure-function relationships.