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Structure & Function of Predatory Bacteria Surface Recognition

Principal Supervisor: Professor Andy Lovering

Secondary Supervisor(s): Dr Patrick Moynihan

University of Registration: University of Birmingham

BBSRC Research Themes:

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Deadline: 4 January, 2024


Project Outline

The bacterial predator Bdellovibrio bacteriovorus is a natural killer of other bacteria (in water treatment, food security, environmental bioremediation & healthcare, (1,2). It would thus be beneficial if we understood the molecular basis of its predatory lifestyle, and the “toolkit” encoded to manipulate (and eventually destroy) the prey cell (2). The staged lifecycle of predation is fascinating – the predator locating and entering the prey cell, metabolizing it from within, and then bursting out to begin the cycle anew.

The Lovering lab specializes in structure:function:mechanism relationships, and the basis of this project will be taking a select grouping of receptor genes whose features (lipidation, beta-propeller fold) are suggestive of being presented at the predator:prey interface for tight recognition. Structural biology will detail the interaction interfaces involved, and unbiased (phage display) screens will identify the peptides capable of binding these receptors. Our goal is to uncover specificity determinants that allow us to understand how Bdellovibrio can kill large numbers of vastly different strains, eventually leading to the engineering of new bespoke predators.

An overview of our approach can be seen here: https://www.youtube.com/watch?v=FioNZppFlKY, and good examples of discerning predatory function via structure can be taken from two of our recent publications (3, 4). Structure is particularly important because Bdellovibrio is unique and shares limited sequence homology with “traditionally well-characterized” bacteria. For example, our first clues into exit recently resulted in the discovery of a novel lysozyme that recognizes a chemical marker which Bdellovibrio uses to signify prey wall as different to self (5).

There are many other potential “secrets” to uncover about prey recognition, and this project will develop new ideas to investigate as it progresses.

References

  1. https://www.news-medical.net/news/20230619/Predatory-bacteria-could-be-used-to-purify-water-in-the-future-study-suggests.aspx
  2. Caulton SG, Lovering AL. Bacterial invasion and killing by predatory Bdellovibrio primed by predator prey cell recognition and self protection. Curr Opin Microbiol. 2020. https://www.sciencedirect.com/science/article/pii/S1369527420300837?via%3Dihub
  3. Harding CJ, Cadby IT, Moynihan PJ, Lovering AL. A rotary mechanism for allostery in bacterial hybrid malic enzymes. Nature Communications. 2021. https://www.nature.com/articles/s41467-021-21528-2
  4. Meek R, Cadby IT, Moynihan, PJ, Lovering AL. Structural Basis for Activation of a Bdellovibrio Diguanylate Cyclase that Licenses Prey Entry. Nature Communications 2019. https://www.nature.com/articles/s41467-019-12051-6
  5. Harding CJ, Huwiler SG, Somers H, Lambert C, Ray LJ, Till R, Taylor G, Moynihan PJ, Sockett RE, Lovering AL. A Lysozyme with Altered Substrate Specificity Facilitates Prey Cell Exit by the Periplasmic Predator Bdellovibrio bacteriovorus. Nature Communications 2020. https://www.nature.com/articles/s41467-020-18139-8

Techniques

Molecular Biology (chiefly cloning, mutagenesis), Protein expression & purification, Protein crystallization, Structure Determination; X-Ray Crystallography, Protein function/analysis, Enzyme Assays, Biophysical methods (AUC, SAXS, ITC, microscale thermophoresis), Bioinformatics.