Structure and mechanism of how phages modulate bacterial immunity

We are seeking an enthusiastic and motivated PhD candidate to study the how the bacterial dNTPase protein is inhibited by T7-like phages using a structural biology and biophysics approach.

Phage Therapy (in clinical trials) provides an alternative to antibiotics to treat multi-drug resistant bacterial infection. However, one barrier to its development is our limited understanding of phage biology and bacterial immunity. Bacteria use a variety of mechanisms to protect themselves from threats such as phages, including the CRISPR-Cas “adaptive” immune system and a multi-component “innate” immune system.

This project focuses on one component of the innate immune system that is conserved across bacteria, called the dNTPase. The bacterial dNTPase blocks phage replication by depleting cellular dNTPs, the building blocks the phage needs to replicate its DNA. This important immunity protein is also conserved in vertebrates – the human homolog, SAMHD1, protects human cells from viruses such as HIV. (see references below).

A minority of phages (T7-like) have evolved a “counter-attack” mechanism, the gp1.2 protein, that inhibits the bacterial dNTPase. This project aims to develop the gp1.2 protein from T7-like phages that do not normally infect Pseudomonas aeruginosa (P. aeruginosa) to inhibit the P. aeruginosa dNTPase and improve Phage Therapy efficacy. P. aeruginosa damages the lungs of people with Cystic Fibrosis and can be cleared by Phage Therapy, eliminating the need for antibiotics.

The first aim is to determine the structure and catalytic mechanism of the P. aeruginosa dNTPase immunity protein using X-ray crystallography and cryoEM. You will also get experience in designing a high-throughput enzymological assay to study the dNTPase’s activity. The second part of the project explores how the gp1.2 protein from T7-like phages inhibits the P. aeruginosa dNTPase. You will use X-ray crystallography, cryoEM and biophysical methods to study the gp1.2-dNTPase interaction. Subsequently you will mutate gp1.2 to improve its efficacy against the P. aeruginosa dNTPase, taking advantage of molecular docking and Alphafold predictive approaches. You will gain training in the following techniques:

·        X-ray crystallography

·        Electron microscopy

·        Designing a novel high-throughput enzymological assay

·        Recombinant protein expression and purification

You must possess or expect to obtain a first or upper second class Master’s or Bachelor’s degree in Biochemistry, Biology, Chemistry or a related discipline. This project will suit someone with a keen interest in the structures of proteins and a curiosity about how enzymes catalyse reactions in nature. Experience in structural biology is not required. This project is hosted by Dr Liz Morris, Assistant Professor (Biochemistry) within the Durham University Biosciences Department. Here, you will join a team of Bioscientists embedded within the Chemistry Department studying biomolecular interactions. We have state-of-the-art facilities for protein production, X-ray crystallography and biophysics. In addition, you will get training in cryoEM in Dr Jon Marles-Wright’s lab, Senior Lecturer in Newcastle University’s School of Biology. Prof Tim Blower, also in Durham’s biomolecular interactions sub-grouping, will provide expertise on phage biology and bacterial immunity.

Durham University, where you will primarily be based, is an outstanding centre of research and teaching excellence. Here you will join one of the University’s seventeen colleges through which you can access student-led activities, such as sports, theatre, music or volunteering, as well as welfare support.

You are encouraged to send your informal enquiries (with CV attached and scientific interests detailed) to [Email Address Removed] so that we can support your application to the program.

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 2^nd 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.

The deadline for all applications is 12noon on Monday 9^th January 2023.