Genome scrambling and biosensor technologies for production of high value chemicals in synthetic yeast (Chem@Sc2.0)

The yeast synthetic genome project, the largest Synthetic Biology project to date, provides yeast, Saccharomyces cerevisiae 2.0 (Sc2.0), with chromosomal loxP sites, enabling Synthetic Chromosome Recombination and Modification by LoxP-mediated Evolution (SCRaMbLE, Science 2017, 355, 1040-1045). In this project, we will exploit Sc2.0 as a platform for producing valuable natural products (NP), including essential antibiotics (e.g. Nature Catalysis 2018, 1, 977-984), anticancer agents, immunosuppressants and statins (blockbuster drugs). Unlike the wild-type S. cerevisiae, Sc2.0 has synthetic chromosomes (re-designed DNA sequences chemically synthesized), enabling the genome to be scrambled, generating mutants where genes have been rearranged, deleted or duplicated. We have shown that, by introducing heterologous biosynthetic gene clusters into Sc2.0, it is possible to generate scrambled mutants with enhanced capacity for producing target compounds (Nature Commun. 2018, 9, 1936). However, screening large numbers (billions) of Sc2.0 mutants generated by genome scrambling is challenging. To this end, we will develop biosensors, based on modular riboswitch components (e.g. J. Am. Chem. Soc. 2015, 137, 9015-9021 & J. Am. Chem. Soc. 2014, 136, 10615-10624), that can bind to the target NP and trigger a fluorescent response. By introducing biosensors into Sc2.0, along with the genes required for the biosynthesis of the target NP, we will be able to rapidly select the scrambled mutant cells that produce the highest levels of the target compound; these cells will be fluorescent and can be easily separated using a fluorescence activated cell sorter. Strains producing highest yields of desired compounds, will be subjected to further rounds of scrambling with biosensor screening, and their genomes will be sequenced. The project will provide a paradigm shift in pathway (metabolic) engineering, that could lead to more cost-effective and sustainable production of antibiotics required to combat antimicrobial resistance (AMR), as well as other essential medicines. This ambitious project provides cutting-edge training in synthetic biology, spanning NP biosynthesis, RNA-based biosensors and genetics. The project will be supervised by Profs Jason Micklefield and Patrick Cai, and will be based in the Manchester Institute of Biotechnology (MIB) and SYNBIOCHEM centre at the UoM, with world-class facilities and training opportunities.

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.