BBSRC NLD Doctoral Training Partnership: Cyclic nucleotide signalling and BREX phage defence

Significance. Bacteria are constantly targeted by viruses called bacteriophages (phages). Bacteria have evolved defence systems to protect from phage infection. Previously, phage defence systems have underpinned revolutionary biotechnological innovations. Understanding the fundamental biology of bacterial phage defence has also uncovered new areas of immunology by showing evolutionary and functional links between eukaryotic viral immunity and bacterial defence effectors. As in mammalian cells, bacteria can respond to viral infection by generating cyclic nucleotides as signalling messengers. We hypothesise that the varied bacterial responses to phage are co-regulated to form a “prokaryotic immune system”. We will explore how cyclic nucleotide signalling in Bacteriophage Exclusion (BREX) systems controls phage defence in E. coli and pathogenic Salmonella.

Background. BREX is a widespread bacterial phage defence system for which the mechanism is unknown. We have recently shown that BREX protein PglZ cleaves cyclic nucleotides. PglZ activity is a “smoking gun” indicating cyclic nucleotide signalling impacts BREX defence. This PglZ activity provides an opportunity to elucidate the BREX mechanism. As other phage defence systems, such as CBASS, use cyclic nucleotides, there is also the potential to investigate signalling cross-talk between systems, as part of a co-ordinated immune response. Demonstrating that cyclic nucleotide signalling is used by BREX will have implications for expanding the role of cyclic nucleotides across a greater diversity of defence systems. The results will have impacts towards 1) developing a working model for a cohesive, inter-linked, prokaryotic immune system and 2) building a greater arsenal of biotechnological tools.

Aims. This inter-disciplinary proposal will use molecular biology, microbiology, biochemistry and structural biology to investigate BREX. The student will (1) examine PglZ biochemistry, namely (i) cyclic nucleotide specificity, (ii) BREX protein binding partners, (iii) impact of Salmonella PglZ mutants on phage defence and (iv) PglZ structural biology; (2) perform interaction studies to investigate synergy between BREX and CBASS.

Timetable of Activities. Year 1 Production of PglZ protein, confirmation of substrate specificity and phage-resistance phenotypes. Year 2 Characterisation of PglZ protein binding partners and structural biology. Year 3 PIPS placement, BREX-CBASS interaction studies. Year 4 Continuation of structural and interaction studies, thesis completion.

Novelty and Timeliness. The supervisory team, led by Durham University and co-supervised at University of Liverpool, have a pre-existing and successful collaboration, and lead on BREX research. If successful, this project will provide the first demonstration of BREX regulation by cyclic nucleotides and their impact on wider prokaryotic immunity. Please contact Professor Tim Blower ([Email Address Removed]) for more information

HOW TO APPLY:

Applications should be made by emailing [Email Address Removed] with:

• a CV (including contact details of at least two academic (or other relevant) referees);
• a covering letter – clearly stating your first-choice project, and optionally 2nd ranked project, as well as including whatever additional information you feel is pertinent to your application; you may wish to indicate, for example, why you are particularly interested in the selected project(s) and at the selected University;
• copies of your relevant undergraduate degree transcripts and certificates;
• a copy of your IELTS or TOEFL English language certificate (where required);
• a copy of your passport (photo page).

A GUIDE TO THE FORMAT REQUIRED FOR THE APPLICATION DOCUMENTS IS AVAILABLE AT https://www.nld-dtp.org.uk/how-apply. Applications not meeting these criteria may be rejected.

In addition to the above items, please email a completed copy of the Additional Details Form (as a Word document) to [Email Address Removed]. A blank copy of this form can be found at: https://www.nld-dtp.org.uk/how-apply.

Informal enquiries may be made to [Email Address Removed] 

The deadline for all applications is 12noon on Monday 15^th January 2024.

Part-Time Study Options

All NLD DTP PhDs are available as part time or full time, with part time being a minimum of 50% of full time. Please discuss potential part time arrangements with the primary supervisor before applying to the programme.

Project CASE Status

This project is not a CASE project. While individual applicant quality is our overriding criterion for selection, the NLD DTP has a commitment to fund 8 CASE projects per year - as such, CASE projects may be favoured in shortlisting applicants when candidates are otherwise deemed to be equal or a consensus on student quality cannot be reached.