Our Research
Understanding how viral RNAs control gene expression and genome replication
RNA viruses rely on highly structured RNA molecules to control every stage of their replication cycle. Far from acting simply as carriers of genetic information, viral RNAs adopt complex three-dimensional folds that interact with ribosomes, viral enzymes and host proteins to regulate protein synthesis, genome replication and the assembly of new virus particles. Understanding how these dynamic RNA-protein complexes function is central to explaining how viruses replicate, evolve and cause disease.
Our laboratory combines structural biology, biochemistry, biophysics and single-molecule approaches to study dynamic RNA-protein complexes. We employ cryo-electron microscopy, X-ray crystallography and complementary structural methods to determine the architecture of macromolecular assemblies, alongside fully reconstituted in vitro translation and replication systems that allow us to dissect molecular mechanisms one step at a time. These approaches are integrated with real-time single-molecule fluorescence microscopy, quantitative biophysical techniques and functional assays. By combining structural snapshots with dynamic measurements, we aim to understand not only how viral molecular machines are assembled, but also how they function and are regulated spatially and temporarily within an infected cell.
Programmed -1 ribosomal frameshifting
Programmed -1 ribosomal frameshifting (-1 PRF) is a translational recoding mechanism used by many RNA viruses – including coronaviruses, retroviruses and cardioviruses – to precisely regulate viral gene expression. In PRF, elongating ribosomes stall over a 'slippery sequence' when they encounter a structured 'stimulatory element' in the downstream mRNA. Tandem slippage of A- and P-site tRNAs can lead to the ribosome moving one nucleotide backwards (i.e. into the -1 frame) thereby changing the amino acid sequence from that point forwards. Small changes in frameshifting efficiency can profoundly influence viral replication, making this process an attractive target for antiviral intervention. We investigate how RNA pseudoknots and other stimulatory RNA elements affect ribosome dynamics, the structural basis for loss of reading frame maintenance, how trans-acting viral proteins regulate PRF efficiency, and how host antiviral factors recognise and inhibit frameshifting.
IRES-mediated translation initiation
Many important RNA viruses initiate protein synthesis independently of the 5′ cap by recruiting ribosomes directly via Internal Ribosome Entry Site (IRES) elements. These multi-domain, structured RNAs hijack the host translation machinery in diverse ways, yet many aspects of their function remain poorly understood. Our research focuses on Type 1, 2 and 5 picornavirus IRES elements, collectively responsible for billions of human and animal infections per year. We aim to determine how these viral RNAs recruit ribosomal subunits, position initiator tRNAs and direct accurate start-codon selection. We are especially interested in the dynamic structural rearrangements that occur throughout successive stages of initiation, and in the RNA-ribosome and RNA-tRNA interactions that are critical for efficient 48S complex assembly. These studies will provide fundamental insight into cap-independent translation and reveal how viral RNAs have evolved to exploit the host translational apparatus.
RNA packaging in picornaviruses
Assembly of infectious virus particles requires the selective encapsidation of viral genomes while excluding abundant host RNAs, yet the molecular basis of RNA packaging in picornaviruses remains poorly understood. We seek to understand how viral RNA structure contributes to genome selection and how packaging is coordinated with genome replication and capsid assembly. Focusing on FMDV, our work investigates how structured RNA elements are recognised by capsid proteins and replication complexes, and how RNA architecture influences the efficiency and fidelity of virion assembly. Understanding these mechanisms will provide new insight into one of the least-characterised stages of the picornavirus life cycle.
Molecular mechanisms of protein-primed replication
Picornaviruses replicate their genomes using a unique protein-primed mechanism in which the small viral protein VPg is covalently linked to the 5′ end of the RNA and acts as the primer for RNA synthesis by the viral RNA-dependent RNA polymerase. Despite its central importance, the molecular choreography underlying replication initiation remains incompletely understood. Our research aims to define how VPg is uridylylated and positioned by the viral polymerase, how functional replication complexes assemble and how the structured cre and cloverleaf RNA elements regulate these processes. By determining the structural and mechanistic basis of protein-primed RNA synthesis, we hope to identify vulnerabilities that may be exploited for future antiviral drug development.