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 their RNA polymerases, as well as the mechanisms of viral gene transcription and the replication and trafficking of the viral RNA genome. Our objective is to gain in-depth molecular insights into RNA virus replication, ultimately paving the way for the development of novel antiviral strategies.

Influenza A virus poses a continuous global health threat due to its ability to rapidly adapt to new hosts and evade immune responses. Central to its replication is the viral RNA-dependent RNA polymerase, a complex molecular machine that transcribes and replicates the viral RNA genome within the nucleus of infected cells. While significant progress has been made in characterising the structure and function of this polymerase, many fundamental questions remain—particularly regarding the roles of viral and host factors in RNA synthesis and the intracellular trafficking of these components and the viral genome.

This graduate project, building on recent advances from the Fodor and Grimes laboratories, will investigate: (1) how the viral polymerase and nucleoprotein (NP) are imported into the nucleus and assemble into functional replication complexes; (2) how newly synthesised viral RNAs are packaged with polymerase and NP to form viral ribonucleoprotein complexes (vRNPs); (3) how incoming vRNPs are imported into the nucleus and how progeny vRNPs are exported and trafficked to sites of virion assembly at the plasma membrane; and (4) how host factors regulate these processes and influence host specificity and pathogenicity.

The project will adopt a multidisciplinary approach combining biochemical reconstitution, cell-based assays, proteomics, viral reverse genetics, and advanced imaging. Cross-linking and proximity labelling followed by mass spectrometry will be used to identify viral and host components involved in RNA synthesis and trafficking. Their functional roles will be tested using gene silencing or CRISPR-Cas9 knockouts in the context of infection. Further studies will involve recombinant protein expression, interaction assays, and, where appropriate, structural analysis in collaboration with the Grimes lab. Comprehensive training in techniques relevant to the project will be provided.

Keywords:

biochemistry, cell biology, microbiology, molecular biology, structural biology, virology

Publications:

1. Staller E, Carrique L, Swann OC, Fan H, Keown JR, Sheppard CM, Barclay WS, Grimes JM, Fodor E (2024) Structures of H5N1 influenza polymerase with ANP32B reveal mechanisms of genome replication and host adaptation. Nat Commun 15(1):4123.
2. Zhu Z, Fan H, Fodor E (2023) Defining the minimal components of the influenza A virus replication machinery via an in vitro reconstitution system. PLoS Biol 21(11):e3002370.
3. Zhu Z, Fodor E, Keown JR (2023) A structural understanding of influenza virus genome replication. Trends Microbiol 31(3):308-319.
4. 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.