Autonomous biomanufacturing platforms for sustainable biomanufacturing

Secondary Supervisor(s): TBC

University of Registration: University of Warwick

BBSRC Research Themes:

• Renewable Resources and Clean Growth (Industrial Biotechnology)
• Understanding the Rules of Life (Microbiology, Systems Biology)

Project Outline

Engineering microbial cell factories using synthetic biology enables the production of new therapeutics or sustainable routes to the manufacture of high value chemicals from agricultural by-products. However, at present, engineering production strains is a time intensive and expensive process due to multiple, interacting challenges. Key challenges include (i) difficulties in predicting the impact of novel pathways on the host’s metabolism and wider physiology, (ii) the build-up of toxic pathway intermediates, and (iii) poor long-term performance. In addition to these cellular constraints, microbial cell factories are subjected to industrial constraints (including heterogeneity, fermentation strategy, and cost) which further limit performance in commercial settings.

In our projects, we take an interdisciplinary approach to tackling these roadblocks to the industrialization of synthetic biology. Some members of our group are developing predictive mathematical multi-scale models of microbial growth and fermentation strategy to inform our engineering of biological systems, while others are engaged in experimental work constructing gene circuits which integrate cellular responses to dynamically balance cell growth and bioproduction. Projects in the group are highly flexible and the ratio of theoretical to experimental work will be tailored to suit the candidate’s interests and background.

Cell factories for membrane protein production (Project 1). Structural studies and drug screening require high yields of membrane proteins; however, heterologous expression is a complex multistep process as proteins are synthesised, fold and export. Working with Dr Doug Browning and Dr Alan Goddard from Aston University, this project will determine the key limiting streps for membrane production and the key host stress responses triggered by over production. We will use this information to design and build genetic control systems which enable cells to autonomously tune production to ensure healthy growth.

Natural project production in yeasts (Project 2) or bacterial hosts (Project 3). Natural products from fungi or plants are precursors to many drugs but yields from natural systems are often low. However, engineering the production of these compounds by key industrial organisms (e.g. E. coli, S. cerevisiae) is often challenging due the burden of heterologous expression or the accumulation of toxic intermediates. Depending on our choice of pathway and host, we will working with Dr Fabrizio Alberti and Prof. Chris Corre at Warwick, to explore the impact of metabolically engineered pathways on the host’s physiology. We will use Warwick’s high throughput robotics platform to characterise bioproduction of these systems’ performance across different media and growth perturbations. We will use this knowledge to engineer gene circuits which integrate cellular stress responses and modulate metabolic productivity to minimise the accumulation of toxic intermediates. We will work with scale-up experts at Warwick to assess the efficacy of these systems in industrially relevant multi-litre scale conditions.

Wider training. Students will receive the comprehensive interdisciplinary training needed for modern biotech research including mathematical modelling and programming, molecular biology and metabolic analysis. Students can also benefit from our links with industrial partners who will provide commercial insights and feedback throughout the project. Depending on the scope of the specific project, students may be able undertake short placements in the labs of industrial partners.

Key References

Example work. Darlington 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.

Example work. Mannan et al. (2024) “Design principles for engineering bacteria to maximise chemical production from batch cultures”, preprint available at 10.1101/2024.05.23.595552

Background review. Boo et al. (2019) “Host-aware synthetic biology”, Current Opinion in Systems Biology, 14, pp. 66-72. doi 10.1016/j.coisb.2019.03.001.

Background review. Hartline et al. (2021) “Dynamic control in metabolic engineering: Theories, tools, and applications”, Metabolic Engineering, 63, pp. 126-140. doi 10.1016/j.ymben.2020.08.015.