PhD project

Supervisor: Ervin Fodor

Our laboratory focuses on elucidating the fundamental molecular mechanisms underlying the replication of RNA viruses such as Influenza, Nipah, and SARS-CoV-2. Specifically, we aim to uncover the structural and functional properties of the RNA polymerase of these viruses, as well as the mechanisms of transcription, replication and trafficking of the viral RNA genome. Our objective is to obtain in-depth molecular insights into the replication mechanisms of these RNA viruses, ultimately paving the way to the development of novel antiviral approaches.

The primary focus of our laboratory is influenza viruses, an important group of human and animal pathogens, which cause widespread clinical and veterinary disease and have a considerable economic impact. We address questions ranging from how the influenza virus RNA polymerase transcribes and replicates the segmented negative-sense viral RNA genome in the nucleus of the infected cell to how the RNA genome segments are exported from the nucleus and assembled into infectious progeny virus particles. We are also interested in uncovering the host range determinants of influenza viruses and understanding the effects of virus infection on the host cell, the molecular mechanisms of innate immune sensing, and host cell responses to viral infection. Our group collaborates with structural biologists and uses an interdisciplinary approach that includes molecular and cell biology, structural biology, single-molecule and super-resolution microscopy, proteomics, and virology.

This project builds on our recent advances in the structural and functional characterisation of the influenza virus RNA polymerase and its role in the replication of the viral RNA genome and transcription of viral genes. To replicate the viral RNA genome the RNA polymerase forms a complex with a host ANP32 protein (Zhu et al Trends Microbiol 2023), while to transcribe viral genes it associates with host RNA polymerase II (Walker and Fodor Trends Microbiol 2019). The project aims at defining the wider context of these complexes in the nucleus of infected cells using a combination of cross-linking and proximity labelling approaches followed by mass spectrometry to identify the macromolecular complexes involved. The role of identified factors will be evaluated using gene-silencing or CRISPR-Cas9 gene knock-outs and viral infections and explored further by using recombinant proteins, pull-down assays, and structural biology. We will offer training in all the techniques required to carry out the project.

Publications:

• Zhu Z, Fodor E, Keown JR (2023) A structural understanding of influenza virusgenome replication. Trends Microbiol 31(3):308.
• Keown JR, Zhu Z, Carrique L, Fan H, Walker AP, Serna Martin I, Pardon E, Steyaert J, Fodor E, Grimes JM (2022) Mapping inhibitory sites on the RNA polymerase of the 1918 pandemic influenza virus using nanobodies. Nat Commun 13(1):251.
• te Velthuis AJW, Grimes MJ, Fodor E (2021) Structural insights into RNA polymerases of negative-sense RNA viruses. Nat Rev Microbiol 19(5):303-318.
• Carrique L, Fan H, Walker AP, Keown JR, Sharps J, Staller E, Barclay WS, Fodor E, Grimes JM (2020) Host ANP32A mediates the assembly of the influenza virus replicase. Nature 587(7835):638-643.
• Walker AP, Fodor E (2019) Interplay between Influenza Virus and the Host RNA Polymerase II Transcriptional Machinery. Trends Microbiol 27(5):398-407.