Combining biophysical, biochemical, structural and molecular techniques, the group focuses on studying mechanisms related to post-transcriptional gene regulation.
We gratefully acknowledge the Biotechnology and Biological Sciences Research Council (BBSRC) and Defence Science and Technology Laboratory (DSTL) for supporting our research.
Our current laboratory research
Studying a novel mechanism linked to pathogenic bacterial virulence
The essential ribonuclease RNase E has a critical role in initiating mRNA decay, and therefore serves an important role in the post-transcriptional control of gene expression.
Recently, non-coding small RNAs (sRNAs) have been identified that can program RNase E to target specific mRNA transcripts for destruction. This targeting is mediated through interaction with the RNA chaperone Hfq. However, certain sRNAs have been shown to have entirely the opposite effect, in that they and their mRNA targets are stabilized by Hfq against cleavage by RNase E. This protective mode has been shown to be critical for the transcription of major virulence factors in various pathogenic bacteria, with Hfq deletion mutants displaying attenuation of invasive virulence.
The interplay of sRNAs, their mRNA targets and Hfq results in a finely balanced mechanism of communication with RNase E to bring about either the destruction or the stabilization and subsequent translation of specific transcripts. The fundamental questions in this area, which are the focus of our work, are how this communication occurs and whether this mechanism, with a direct impact on pathogenic bacterial virulence, can be exploited in the search for novel antibacterial approaches and/or targets.
Exploring a communicative link between the enzymatic machinery of RNA degradation and a key metabolite of central metabolism
Ribonucleases impact the abundance of many mRNA transcripts and structured RNAs, thereby affecting post-transcriptional gene expression. The control of such ribonuclease activities contributes to homeostasis and the response to environmental change and is thus likely to be affected by general metabolic activities. Together with collaborators at Cambridge University we have recently discovered such a link indicating that a key central metabolism intermediate in the Krebs cycle, citrate, affects the activity of the E. coliexoribonuclease, polynucleotide phosphorylase (PNPase) and that conversely, PNPase distributively affects cellular metabolism. The combination of a communicative link between metabolites and RNA turnover and the distributive control offered by ribonucleases on metabolism provides a means of integrative control.
Research into unravelling the details of this newly discovered mechanism in more detail and investigating whether it represents a conserved metabolite-RNase communicative link forms the basis of our current studies.
Identifying chemical inhibitors of antibacterial targets and understanding their mechanism of action
In an era of increasing antibiotic resistance, new antibacterial targets are urgently required. Found only in bacteria, the essential endoribonuclease RNase E represents such a potential target. Extensive structural characterisation of RNase E from the model organism, Escherichia coli, has provided molecular level details of the functioning of the protein, enabling the first steps to be taken towards structure-based inhibitor design. In collaboration with colleagues at Leeds University in silico inhibitor design studies have identified potential small molecule inhibitors of E. coli RNase E. Experimental testing of the potential small molecule inhibitors are well underway, as are investigations to identify whether a single small molecule can be identified that will inhibit a range of RNase E homologues from a selection of infectious bacterial sources. This capacity could provide the basis for the generation of a broad spectrum antibacterial compound.
Development of novel technologies for the study of RNA interactions
With their versatile functions and the recent explosion of interest in transcriptomics, RNAs and their interactions with proteins, nucleic acids and small molecules are currently the subject of intense scientific research. RNA may represent an as yet untapped resource in the search for novel pharmaceutical drug targets. Characterization of bio-molecular interactions with RNAs is becoming increasingly necessary as the repertoire of RNA function continues to expand. Surface plasmon resonance is a commonly used technology for studying interactions, but requires the surface-immobilisation of the test molecule (i.e. RNA) to a sensor surface for analysis. Unfortunately, simple, quick and efficient strategies for immobilizing large, biologically relevant, RNAs to sensor surfaces are not currently available. We have been working on developing a novel method to tag RNA molecules for sensor-surface immobilization that is simple, quick and efficient in order to allow further study of this important family of biological molecules.