Understanding the rules of life

Bioscience for an integrated understanding of health

Category: Standard Studentships

Reactive probes to study RNA-protein interactions in pathogenic bacteria

Project No. 2403


Primary Supervisor

Dr Ysobel Baker – University of Southampton


Prof Anastasia Callaghan – University of Portsmouth


We will develop novel probes to decipher the role of RNA-protein interactions in bacterial virulence.

RNA binding proteins (RBPs) influence and regulate the transcription, maturation, localisation and degradation of their cognate RNAs. Mapping these RNA–protein interaction networks is key to understanding cellular processes, disease development, and identifying novel therapeutic targets.

In many pathogenic bacteria, the interaction between non-coding short RNAs (sRNAs) and RBPs regulate the transcription of important virulence factors. There is a tight balance between the destruction or stabilisation of certain transcripts and subsequent translation. The aim of this project is to create a novel class of RNA reactive probes and apply these to understand how this communication occurs.

The most effective method for capturing and identifying RBPs is to covalently cross-link the RNA with interacting proteins. Current approaches include using photochemical cross-linking or adding an external crosslinking agent such as formaldehyde. These approaches, however, are limited by UV-damage, poor efficiency, low isolation yields, and non-specific cross-linking. We will develop new approaches to prepare RNA probes that selectively react with specific amino acid groups, overcoming these challenges.

The specific objectives are:

1. Design and synthesise small molecule reactive tags that can be incorporated into RNA to prepare reactive RNA probes.

2. Demonstrate that the reactive probes can covalently cross-link target proteins.

3. Apply the probes to identify key regulatory RBPs in pathogenic bacteria. The tools developed will provide better insights into bacterial physiology and potentially identify novel antimicrobial targets. Whilst this project focuses on bacteria, the tools developed could be used to convert any RNA into a reactive probe, and could be applied to studying human diseases caused by abnormal RNA–protein interactions.

This is an interdisciplinary project, and the ideal candidate would be keen to work at the chemistry biology interface.