Characterizing protein modifications and interactions in viral infections

Abstract

Viral diseases are a constant threat that have profound impact on global health, economics and societies. Understanding virus-host interactions is key for advancing our knowledge of viral replication and pathogenesis, and thus for the development of effective antiviral strategies to better prepare us for future outbreaks. This thesis investigates the roles of post-translational modifications and protein-protein interactions during viral infections using advanced mass spectrometry techniques. Post-translational modifications such as phosphorylation, ubiquitination and proteolysis, significantly alter the function, stability, and localization of both viral and host proteins, thereby modulating the virus cycle and host immune responses. Virus-host protein-protein interactions form complex networks that viruses may exploit to manipulate host cellular machinery to their advantage, or the host utilizes for activating antiviral defense. In Chapter 2, we identified potential human substrates targeted by the two SARS-CoV-2 viral proteases. We found that the main protease cleaved bromodomain-containing protein 2, while the papain-like protease cleaved splicing factor, proline- and glutamine-rich. Chapter 3 examines the ubiquitination landscape during vaccinia virus infection, highlighting critical host restriction factors that are ubiquitinated during viral infection, such as tripartite motif containing 25. Chapter 4 explores protein-protein interactions between the Mayaro virus and human host. We performed co-immunoprecipitation of viral proteins while simultaneously infecting the human cells with the virus, providing a comprehensive map of the viral protein interactome during infection within host cells. Our findings underscore the importance of post-translational modifications and protein-protein interactions in virus-host dynamics, offering potential therapeutic targets and strategies for antiviral drug development.