Unravelling the molecular, temporal and spatial biology of mRNA decay by a virus-encoded endoribonuclease

In the cell, RNA messages called mRNAs are made from genes and translated into proteins. A vital step in controlling the balance of proteins is the co-ordinated turnover, or decay, of these mRNAs, with key factors in decay localising to specific accumulations termed RNA granules. This balance of proteins keeps the cell healthy, and therefore understanding how these processes are regulated or dysregulated from these granules is vital for advancing knowledge of fundamental biology. Moreover, because mRNA decay plays an important role in areas as diverse as cell growth, developmental disorders, neurodegeneration, cancer and mRNA vaccine stability, advances made in this fundamental area will impact human health more widely.

Viruses infect cells and exploit a wide range of cellular pathways, including mRNA turnover, in their replication strategies, with many virus proteins performing equivalent activities to their cellular counterparts. As such, these virus proteins can act as excellent models to help unravel complex pathways in the cell. A number of viruses including herpesviruses, coronaviruses and influenza viruses produce proteins called endoribonucleases, key proteins that cut multiple mRNAs and push them into the cellular decay pathway. This proposal concerns an endoribonuclease from herpes simplex virus called vhs. We have recently found that this single virus protein has the ability to not only cut mRNAs, but also to dysregulate the dynamics of cellular RNA granules and mRNA turnover, revealing key cellular players in the process.

Here we aim to exploit the ability of vhs to unleash a wave of mRNA decay to unravel the intimately intertwined cellular processes involved in RNA turnover. Bringing together a team with cross-disciplinary expertise in RNA decay, high resolution imaging and virus-cell interactions, we will determine how vhs engages with the components of the cellular mRNA machinery to alter the composition and balance of RNA granules. In particular, we will use advanced technology and computing to define how vhs binds and cuts mRNAs, and establish which cellular proteins it exploits in the process. We will use state-of-the-art imaging technology, including high-resolution and live cell, time-lapse imaging to investigate the dynamics of RNA granules and how vhs alters this. Finally, we will compare how vhs works inside the cell to other virus endoribonucleases from influenza virus, SARS-CoV2 and poxviruses, to determine if vhs activity is conserved across diverse virus families.

This work will advance current understanding of the control of RNA dynamics in the regulation of protein production in both healthy and virus-infected cells. Moreover, it will benefit work on diseases where these processes have been found to be defective, thereby impacting both fundamental and translational science.