Dissecting influenza A virus RNA trafficking and regulation

Abstract

Localisation is a fundamental layer of regulation in compartmentalised systems, and the manipulation of RNA trafficking is a key aspect of host subjugation in most viral infections. Influenza A virus (IAV) infection is no exception. As a nuclear-replicating virus, it requires the efficient and specific transport of its RNA genome and viral mRNAs, in and out of the nucleus and across the cell to specific compartments to carry out their functions. In recent years, important research has been conducted to elucidate some of the critical steps and host determinants for the trafficking of viral RNAs, but many questions still linger. In this thesis, I compiled my contributions to this exciting field, which culminated in three manuscripts. Chapter 1 is a review of the recent research in the study of IAV RNA trafficking, with a focus on host systems being manipulated and the gaps in our knowledge yet to be filled. Of particular importance is the problem of cytoplasmic trafficking of the replicated IAV genome. It is well known that IAV genomes interact with the GTPase Rab11, a marker for the endocytic recycling compartment, but also that the compartment itself is dramatically remodelled upon infection. The network of interactions and the pathways forged by the virus in this context are still mostly unknown. Chapter 2 fills part of this gap. We performed IP-MS of the influenza polymerase, which is associated with the genome, and found the host protein myoferlin (MYOF) to be an important determinant of genome trafficking and a component of the remodelled influenza vesicle transport system, as well as hints towards its importance for other RNA viruses.

On the other hand, IAV mRNAs are generated in the nucleus and reach the cytoplasm rapidly and efficiently. Host mRNAs are mostly recruited to the export machinery during splicing, however the vast majority of IAV transcripts are intronless. Hence, research is underway to better understand the details of alternative non-canonical mRNA export pathways IAV may have evolved to hijack. As detailed in chapter 3, by performing RNA interactome capture we identified the host factor MKRN2 as an IAV mRNA binding protein involved in this process. Overall, the data presented in this work constitutes a significant step forward in the understanding of influenza viral infection and may have further implications in expanding our knowledge of the replication of additional RNA viruses.

Date of Award	Jul 2025
Original language	English
Awarding Institution	Queen's University Belfast
Sponsors	European Research Council
Supervisor	Ultan Power (Supervisor), Guilherme Costa (Supervisor) & David Courtney (Supervisor)