Orthogonal Modules Engineered for Synthetic Protein- and Microbial-Networks

Synthetic biology refers to an engineering approach to biology, where biological components can be assembled to function in a controlled and predictable way. Synthetic biology's growing sophistication is likely to generate major changes to society in areas including energy, healthcare and agriculture. Proteins are such powerful tools in synthetic biology because of their diverse structures and activities, including catalysing reactions and sensing changes in the environment. Nowadays engineering of individual proteins is often efficient. Nonetheless proteins usually work together in teams and it is still a major challenge to control how proteins come together into larger assemblies. The problems come from unstable or non-specific links between the different proteins. Our group has established a specific and unbreakable way to connect proteins, from harnessing bacterial protein chemistry. This proposal will adapt this principle, in order to engineer a family of different pairs, where each member of the pair sticks to its partner but does not stick to any other pair. Having such a family of "protein superglues", we will efficiently and stably link multiple proteins to create programmed protein teams. In addition we will harness this linkage technology to connect cells together. Different single-celled organisms often work in partnership in nature and in industrial processes, from fuel production to toxic waste remediation. Engineering these predictable linkages should be a valuable tool underpinning the design of molecular and cellular teams with enhanced cooperation.

Who will benefit from this research?
Apart from academic scientists, the beneficiaries are likely to include the companies in diverse areas (e.g. agriculture, next-generation DNA sequencing, diagnosis, drug development) who are currently testing SpyTag/SpyCatcher or discussing evaluations with us. Developing these novel orthogonal modules and nanostructures will greatly extend the ability to assemble and control protein function. Products by these companies, harnessing a registry of covalent protein and peptide interactions, should enhance device robustness and sensitivity, so having an impact on disease diagnosis in animals and humans, beneficial to the general public, the farming community and the National Health Service.

How will they benefit from this research?
The new orthogonal modules should allow stable, simple and defined-orientation protein immobilisation in biosensors, columns for purification, vaccine candidates and protein microarrays. The new orthogonal modules may directly comprise part of a commercial product/kit, or facilitate research leading to the generation of other products.
Areas such as vaccine production (e.g. GSK) and biofuels (e.g. BP) are important for UK economic competitiveness and so the development of enabling tools for rational design of protein networks and microbial networks should be beneficial.
The likely time-scale for commercial licensing of IP arising from the orthogonal modules is in the 2nd year of the proposal and for the microbial networks is in the last 6 months of the award and the year following the end of the award. For products relating to kits, these can reach the market as fast as 1 year after testing. For products relating to medical use or large-scale projects in bioenergy or water, at least 3 years are likely before reaching general use.
This project will provide important training for the postdoctoral researcher in:
-developing and executing a multidisciplinary project which creates new tools and applies them in synthetic biology, identified as a priority training area by the UK government
-development of presentation skills, through presenting within the University and at conferences, and discussing science and commercialisation with potential industrial partners.
-taking the Entrepreneurship and Innovation course at Oxford University Business School
-communicating their findings to non-expert audiences, including at the Oxfordshire Science Festival.

What will be done to ensure that they benefit from this research?
Publishing in high impact international journals is an effective way for us to communicate our findings to potential industrial partners. We will work with Isis Innovation, who look after Oxford University IP, to ensure protection of all new IP arising. As we achieve key results, we will communicate with the University of Oxford press office and the EPSRC and with our existing industrial contacts, to ensure that significant findings are communicated widely to the public and potential industrial partners. Oxford's Centre for Doctoral Training in Synthetic Biology has partnerships with Syngenta, GSK, UK Government Defence Science and Technology Laboratory, and Shell, which will also facilitate application of the innovations from this proposal. We will publish detailed protocols in open access journals, including video demonstrations, to facilitate adoption by other users of the new polyprotein assembly and microbial network technologies, as we have done previously for the previous tools developed by the lab in Nature Protocols. We will also provide rapid e-mail feedback, as we have done for the large number of laboratories using SpyTag and SpyCatcher for diverse applications.