Orthogonal Modules Engineered for Synthetic Protein- and Microbial-Networks
Lead Research Organisation:
University of Oxford
Department Name: Biochemistry
Abstract
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.
Planned Impact
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.
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.
Organisations
People |
ORCID iD |
Mark Howarth (Principal Investigator) |
Publications
Keeble AH
(2022)
DogCatcher allows loop-friendly protein-protein ligation.
in Cell chemical biology
Keeble A
(2017)
Evolving Accelerated Amidation by SpyTag/SpyCatcher to Analyze Membrane Dynamics
in Angewandte Chemie
Keeble AH
(2017)
Evolving Accelerated Amidation by SpyTag/SpyCatcher to Analyze Membrane Dynamics.
in Angewandte Chemie (International ed. in English)
Gilbert C
(2017)
Extracellular Self-Assembly of Functional and Tunable Protein Conjugates from Bacillus subtilis.
in ACS synthetic biology
Description | We have established the ability to evolve proteins to bind each other and form unbreakable linkages. Evolution is such a powerful way to improve molecular function and so this advance will be important to assemble different proteins into functional teams. These reactive units will have broad application for synthetic biology, with the high stability helping these teams to be functional over long periods. Such protein teams will help the production of vaccines, diagnostics and environmentally friendly chemical conversions. We have also established that our modules will be suitable for engineering microbial interaction, through showing efficient display of our reactive proteins on the surface of bacteria. |
Exploitation Route | We have distributed the group's previous resources for irreversible protein assembly to more than 400 research groups in more than 30 countries. In addition the systems have been licensed to a number of companies in the UK and overseas. This technology is central to SpyBiotech, a spin-out from the University of Oxford which is accelerating the generation of vaccines. The SpyTag002/SpyCatcher002 technology, advanced through this funding, has been distributed and licensed in this way and there will be further irreversible pairs emerging in the near future based on this funding, which we anticipate will also find broad application. Likely applications are for biosensing, diagnostics, and organising or stabilising enzymes for renewable energy applications or feedstocks. The modules may also be useful for vaccine assembly for human and veterinary diseases. |
Sectors | Healthcare Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology |
URL | http://onlinelibrary.wiley.com/doi/10.1002/anie.201707623/full |
Description | Understanding about the ability to evolve orthogonal reactive modules has played some part in the later stages, as we founded the University of Oxford spin-out SpyBiotech in March 2017. SpyBiotech had a Series A fund-raising of £23 million in 2021, based on a vaccine that entered Phase I clinical trials against Covid-19 and another vaccine that has entered Phase I clinical trials against human cytomegalovirus. The technology for orthogonal reactive modules was also licensed and contributed to the successful fundraising of another UK-based spin-out company. |
First Year Of Impact | 2017 |
Sector | Pharmaceuticals and Medical Biotechnology |
Impact Types | Economic |
Title | DogCatcher peptide ligation |
Description | DogCatcher is an engineered protein that forms a spontaneous isopeptide bond to its peptide partner DogTag. This reaction is efficient with low concentrations of each partner and can be used specifically at the surface of mammalian cells. DogTag can be inserted in loops of various proteins without disrupting their function, while still enabling efficient reaction with DogCatcher. |
Type Of Material | Technology assay or reagent |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | A DogCatcher-based labelling has already been employed for specific labelling of the ion channel TRPC5 and for the attachment of proteins to the surface of adenovirus, towards enhancing their application in vaccination. |
URL | https://www.sciencedirect.com/science/article/pii/S2451945621003159 |
Title | POLYPEPTIDES THAT INTERACT WITH PEPTIDE TAGS AT LOOPS OR TERMINI AND USES THEREOF |
Description | The present invention relates to a polypeptide that forms one part of a two- part linker in which the polypeptide spontaneously forms an isopeptide bond with a peptide tag, the second part of the two-part linker. Nucleic acid molecules encoding the polypeptide, vectors comprising said nucleic acid molecules, and host cells comprising said vectors and nucleic acid molecules are also provided. A kit comprising said two-part linker (i.e. peptide tag and polypeptide binding partner), and/or nucleic acid molecules/vectors is also provided. A method of producing the polypeptide and the uses of the polypeptide of the invention are also provided. |
IP Reference | WO2022214795 |
Protection | Patent / Patent application |
Year Protection Granted | 2022 |
Licensed | Commercial In Confidence |
Impact | Further licensing is in discussion |
Company Name | SpyBiotech |
Description | SpyBiotech uses a biotechnology called superglue technology to develop and produce vaccines. |
Year Established | 2017 |
Impact | There are 6 full time equivalent posts employed at the company. The company is developing new vaccines and is currently doing pre-clinical testing and seeking to move towards clinical trials. |
Website | http://spybiotech.com |
Description | Talk at Bacterial World exhibition |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Mark Howarth gave a talk in the Bacterial World exhibition entitled: "Stealing from Dangerous Bacteria: Superglues, Gene Scissors and Designing Life". This talk was held in the Oxford University Museum of Natural History and attracted a broad audience from schoolchildren to retired people. This talk covered the impact of the Howarth group's research on the bacterium Streptococcus pyogenes as well as other important applications from CRISPR. There was a long period of questions, including on the future of vaccine development and individual children asking about A level choices and their potential career as scientists. |
Year(s) Of Engagement Activity | 2019 |
URL | http://www.ox.ac.uk/event/stealing-dangerous-bacteria-superglues-gene-scissors-and-designing-life |