Principal Supervisor: Professor Andy LoveringLink opens in a new window

Co-supervisor: Professor Dave Grainger

PhD project title: Structure & Function of Predatory Bacteria Machinery

University of Registration: University of Birmingham

Project outline:

The bacterial predator Bdellovibrio bacteriovorus is a natural killer of other bacteria, including many pathogens of man, and may eventually be used in a therapeutic. 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. The staged lifecycle of predation is fascinating – the predator locating the prey cell, attaching and entering through the outer membrane, sealing the entry hole, metabolizing it from within, and then bursting out to begin the cycle anew. Investigating predation thus often involves new concepts, ideas and unique proteins.

Efforts to identify key predation genes have been aided by RNAseq and array studies (1), and a transposon-based method to screen for essentiality (2). The Lovering lab specializes in protein structure:function relationships, and the basis of this project will be taking a select grouping of essential, yet cryptic genes whose timing indicates expression at key lifecycle stages. We will use structural information and biochemistry to infer the role played in predation, collaborating with the laboratory of Simona Huwiler (University of Zurich, Switzerland) on in-vivo functionality.

Typical PhD projects in the Lovering lab aim to address novel aspects of predation (and cell biology), and have included “caterpillar track”-like surface motility, prey recognition fibres, pore-forming proteins and sensory systems to follow the chemical trail emitted by prey.

An overview of our approach can be found here (https://www.birmingham.ac.uk/staff/profiles/biosciences/lovering-andrew.aspx), and good examples of discovering new biology via structural detail can be taken from two of our recent publications (3, 4). For example, the first-ever clues into prey cell exit recently resulted from our discovery of a novel lysozyme that recognizes a marker which Bdellovibrio uses to signify prey cells as different to self (5); this was totally unexpected despite lysozyme being “the model enzyme” in science.

The project will be certainly helped/advanced by protein structure prediction methods, but the absolute details (which makes all the difference to function and discovery) needs to be achieved at the experimental level – for which we use x-ray crystallography, cryoEM and other biophysical approaches- this is certainly relevant to predators whose genes tend to be divergent from other organisms, which also makes prediction less accurate.

There are many other potential “secrets” to uncover, including maximizing usage of prey cell macromolecules, proper development of the new progeny cells to prepare for another round of killing, and cryptic functions that only make sense in the light of discovery!

References:

(1) Lambert C, Chang CY, Capeness MJ, Sockett RE. The first bite--profiling the predatosome in the bacterial pathogen Bdellovibrio. PLoS One. 2010 Jan 6;5(1):e8599.

(2) Duncan MC, Gillette RK, Maglasang MA, Corn EA, Tai AK, Lazinski DW, Shanks RMQ, Kadouri DE, Camilli A. High-Throughput Analysis of Gene Function in the Bacterial Predator Bdellovibrio bacteriovorus. MBio. 2019 Jun 11;10(3). pii: e01040-19.

(3) Harding CJ, Cadby IT, Moynihan PJ, Lovering AL. A rotary mechanism for allostery in bacterial hybrid malic enzymes. Nature Communications. 2021 Feb 23;12(1):1228.

(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. 

(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. 11, 4817

 

BBSRC Strategic Research Priority: Understanding the rules of life – Structural Biology

 

Techniques that will be undertaken during the project:

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

 

Contact: Professor Andy LoveringLink opens in a new window