Designing and Engineering Gamma-Butyrolactone Signalling for Synthetic Biology

Gamma-butyrolactones are signalling molecules acting as "bacterial hormones" and regulating the production of antibiotics through well-studied signalling systems. This project will use these natural systems to develop a versatile toolkit of engineered butyrolactone circuits for broader application in synthetic biology.

Design and engineer diverse butyrolactone producing E. coli strains ("signalling devices"). [Pathway modification and assembly, LS-MS analytics] We will modify both the chemical nature of the signals and the kinetics of their production. The diversity of the butyrolactone chemistry will be expanded and engineered through plug-and-play to create novel chemistry using sensitive bioassays established previously.

Design and engineer diverse butyrolactone-responsive E. coli strains ("receiver devices"). [CRISPR-based protein engineering] Receptor and biosynthesis enzymes pairs will be characterised and mutated to create receiver variants with a broad range of response characteristics.

Characterise the signalling interaction between signalling and receiver devices. [computational modelling] Liquid co-culture and plate bioassays will be used to obtain data to parameterise an existing ensemble model of the kinetics of gamma-butryolactone signalling to predict the behaviour of integrated circuits. Based on this modelling, selected combinations of signalling and receiver devices will be combined in a single E. coli strain to create integrated circuits with a spectrum of different predicted behaviours (bistable switch, growth-phase specific toggle switch).

We will further apply these designer "signalling devices" to awaken sleeping antibiotic gene clusters. Mixed cultures of E. coli signalling devices and an Actinomyces native receiver strain from the industrial partner will be grown and analysed for induction of antimicrobial compound production.

This project provides comprehensive interdisciplinary training in methods pioneered by the supervisory team, across a range of key disciplines at the interface of biology, biosystems engineering, analytics, and bioinformatics, as well as training in an industrial setting at Odyssey Therapeutics, which are all essential for the next generation of synthetic biologists.

The 2016 UK Roadmap Bio-design for the Bio-economy highlighted the substantial impact that synthetic biology can bring to the UK and global economies by developing: frontier science and technology; establishing a healthy innovation pipeline; a highly skilled workforce and an environment in which innovative science and businesses can thrive. Synthetic biology promises to transform the UK Bio-economy landscape, bringing bio-sustainable and affordable manufacturing routes to all industrial sectors and will ensure society can tackle many contemporary global Grand Challenges including: Sustainable Manufacturing, Environmental Sustainability Energy, Global Healthcare, and Urban Development. Whilst synthetic biology is burgeoning in the UK, we now need to build on the investments made and take a further lead in training next generation scientists to ensure sustained growth of a capable workforce to underpin the science base development and growth in an advanced UK bio-economy.
This training provided by this CDT will give students from diverse backgrounds a unique synthesis of computational, biomolecular and cellular engineering skills, a peer-to-peer and industrial network, and unique entrepreneurial insight. In so doing, it will address key EPSRC priority areas and Bioeconomy strategic priorities including: Next-generation therapeutics; Engineered biomaterials; Renewable alternatives for fuels, chemicals and other small molecules; Reliable, predictable, and scalable bioprocesses; Sustainable future; Lifelong health & wellbeing.
Advances created by our BioDesign Engineering approach will address major societal challenges by delivering new routes for chemical/pharma/materials manufacture through to sustainable energy, whilst providing clean growth and reductions in energy use, greenhouse gas emissions and carbon footprints. Increased industry awareness of bio-options with better civic understanding will drive end-user demand to create market pull for products. The CDT benefits from unrivalled existing academic-industry frameworks at the host institutions, which will provide direct links to industrial partners and a direct pathway to early economic and industrial impact.

This CDT will develop 80-100 next-generation scientists and technologists (via the funded cohort and wider integration of aligned students at the three institutions) as adept scientists and engineers, instilled with technical leadership, who as broadly trained individuals will fill key skills gaps and could be expected to impact internationally through leadership roles in the medium term. Importantly the CDT addresses key skill-gaps identified with industry, which are urgently required to create and support high value jobs that will enable the UK to compete in global markets. Commercialisation and entrepreneurship training will equip the next generation of visionaries and leaders needed to accelerate and support the creation of new innovative companies to exploit these new technologies and opportunities.

The UK government identified Synthetic Biology as one of the "Eight Great Technologies" that could be a key enabler to economic and societal development. This CDT will be at the forefront of research that will accelerate the clean growth agenda and the development of a resilient circular bioeconomy, and will align with key EPSRC prosperity outcomes including a productive, healthy and resilient nation. To foster wider societal impact, the CDT will expect all students to contribute to public outreach and engagement activities including: open days, schools visits, and science festival events: students will participate in an outreach programme, with special focus on widening participation.

This CDT will contribute to the development of industrial strategy through the Synthetic Biology Leadership Council (SBLC), Industrial Biotechnology Leadership Forum (IBLF), and wider Networks in Industrial Biotechnology and Bioenergy and Professional Institutes.