Principal Supervisor: Dr Alexander Darlington (Warwick)

Co-supervisor: Dr Alan Goddard (Aston), Dr Declan Bates (Warwick)

PhD project title: Understanding and engineering membrane protein expression for industrial biotechnology applications

University of Registration: University of Warwick

Project outline:

Background. The cell membrane has been a neglected target for bioprocess improvement with most approaches focusing on engineering cell metabolism and soluble proteins. The cell’s membranes, and the associated transport proteins found within them, are key regulators of cell physiology; controlling what enters and leaves the cells and how they interact with each other and their environment. There is now increasing interest in engineering the cell membrane and membrane proteins for biotechnological applications. These applications include the production of high value metabolites by membrane tethered enzymes, the production of biosensors utilising cell surface proteins or enhancing the robustness of microbial cell factories. However, we currently lack a detailed understanding of biosynthetic constraints and potential performance trade-offs which impact expression of membrane proteins.

Project. This interdisciplinary proposal seeks to build this comprehensive understanding to facilitate the enhanced engineering of key commercial proteins. Utilising state-of-the-art experimental tools developed by Dr Alan Goddard and others within the Aston Membrane Proteins and Lipids research group Aston University, we will carry out experiments to identify the key biological determinants of membrane protein expression considering both the translocation machinery and lipid composition. We will use these insights to develop a dynamic ordinary differential model of membrane biogenesis, protein production, and cellular growth which captures a quantitative understanding of the interactions between membrane and growth dynamics. We will use this model to simulate different gene expression strategies to enable us to develop and implement optimal expression strategies which enhance the yield of industrially relevant membrane proteins in E. coli. There may be scope as the project develops to spend time working with an industrial partner.

Training. Students will receive a comprehensive interdisciplinary training needed for modern biological research including (i) mathematical modelling, (ii) programming, (iii) molecular microbiology, and (iv) metabolic and biochemical analyses. We also encourage students to take advantage of industrial links and participate in Warwick Innovations courses on university-industry partnerships and other training opportunities at both Warwick and Aston.

Contact. Students should contact Dr Alexander Darlington (a.darlington.1 (at) warwick.ac.uk) as soon as possible to discuss their interests. Ideally entitle the email “MIBTP prospective student – Membranes project - [[your surname]]” so that it is not missed.

Key links.

Dr Alexander Darlington

Dr Alan Goddard and the Aston Centre for Membrane Protein and Lipids Research

References:

Example work.

Depping, P et al. (2021) “Heterologous expression of membrane proteins in E. coli”, Methods in Molecular Biology. 2507, 59. doi 10.1007/978-1-0716-2368-8_4

Kesidis, A et al. (2020) “Expression of eukaryotic membrane proteins in eukaryotic and prokaryotic hosts”, Methods, 180, 3-18. doi 10.1016/j.ymeth.2020.06.006

Darlington, A. P. S. et al. (2018) “Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes”, Nature Communications, 9, e695. doi: 10.1038/s41467-018-02898-6.

Review on membrane and growth dynamics. Serbanescu et al (2021) “Cellular resource allocation strategies for cell size and shape control in bacteria”, FEBS J. doi 10.1111/febs.16234

Review highlighting challenges in modern biotech. Xu et al (2022) “Microbial chassis development for natural product biosynthesis” Trends Biotech, 38(7), 779-796 doi 10.1016/j.tibtech.2020.01.002

BBSRC Strategic Research Priority: Understanding the rules of life – Systems Biology, and Microbiology, and Renewable Resources and Clean Growth - Industrial Biotechnology.

Techniques that will be undertaken during the project:

• Mathematical skills. Dynamical modelling, flux balance analysis, optimisation, other techniques as needed from Systems and Control Engineering.
• Programming languages. Python, MATLAB (with initial and advanced training provided).
• Molecular biology techniques including cloning.
• Biochemical and biophysical analyses of membrane proteins and lipids.
• Microbiological approaches focussed on E. coli.

 

Contact: Dr Alexander Darlington