ConBioChem: Continuous bio-production of commodity chemicals
Lead Research Organisation:
University College London
Department Name: Biochemical Engineering
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
This ambitious, multidisciplinary project will establish generic design procedures to underpin the introduction of continuous bio-manufacturing processes for commodity/platform chemicals and added value intermediates. Crucial improvements in operational stability will be delivered through Synthetic Biology, to construct genetically stable chassis strains. Metabolic modelling will be used to design rational strain engineering and processing strategies, to divert cellular metabolism away from growth and towards product formation, to deliver critical improvements in product yields. The metabolic models will be integrated into multiscale models, involving reactor and process models and LCA, to enable seamless, integrated design of both the organisms and the processes, so that both will operate synergistically for maximal commercial benefit and sustainability. Success will be measured through technoeconomic analysis to deliver commercially relevant design approaches.
Planned Impact
As described in proposal submitted to IUK.
Publications
Allen JR
(2022)
Segregationally stabilised plasmids improve production of commodity chemicals in glucose-limited continuous fermentation.
in Microbial cell factories
| Description | The overarching goals of the ConBioChem project (Continuous Bioproduction of Commodity Chemicals) are to: (1) Create synthetic biology solutions to the problem of low yields and operational instability of microorganisms in continuous culture. (2) Establish multiscale models to underpin design of commercially viable, sustainable bioprocesses. (3) Create innovative, continuous bioprocesses ready for demonstration with our partners: The project started in October 2016 and will run for 5 years (with possible no-cost extension due to Covid-19 under evaluation). It involves partners at the University of Nottingham (lead) and Cambridge University. UCL progress against the overarching objectives are as follows: (1) To improve the stability of the chosen host organism, E. coli, in continuous culture a number of genetic 'addiction systems' have been identified in the literature. These have been cloned and expressed in a series of plasmids which also contain a Red Fluorescent Protein (RFP) marker so that both plasmid loss and DNA mutation in the gene of interest can be monitored. These have been transformed into a metabolically engineered E. coli strain (from Nottingham) that produces citramalate, CM, (a precursor to the target product methacrylic acid, MMA) and the 'best' addiction system identified. A small scale, high throughput, system for monitoring plasmid stability that is predictive of bioreactor scale continuous cultures, has also been established and verified (based on (2) below). (2) A full kinetic model that describes substrate utilisation, cell growth, product formation and allows quantification of plasmid instability batch, fed-batch and continuous CM fermentation processes has been developed. This has been validated against multiple fermentation runs, especially continuous cultures performed at different initial glucose concentrations and dilution rates. The model is being used to inform related Life Cycle Analysis (LCA) work at Nottingham and metabolic modelling work performed at Cambridge (we are also undertaking some gene knock-out experiments to help confirm the metabolic modelling predictions from the group at Cambridge). (3) The most recent work has focused on building a model-based, on-line monitoring and control system for continuous CM fermentations. The novel mid-IR on-line monitoring system purchased on the grant has been shown to be able to measure a range of products and metabolites at concentrations of <1 g/L. Chemometric models have been established to simultaneously measure biomass concentration, CM concentration and glucose concentration using a variety of methods . The control system has been successfully implemented in a LabView environment at UCL and used to demonstrate on-line monitoring and control of glucose-limited cultures for CM production. The technology has also been transfered to the collaborators at Nottingham who are currently running the system for control of glucose levels in phosphate-limited cultures for production of an alternative product, 3-HB, as agreed with the consortium industrial partners |
| Exploitation Route | The E coli host strain engineered for improved stability will be evaluated by the collaborating company partners. Commercialisation options for the plasmid additction systems (as kits) is being explored. |
| Sectors | Chemicals,Manufacturing, including Industrial Biotechology |
| Description | Findings have formed the basis of a synthetic biology start-up company - Twig Bio Limited. |
| First Year Of Impact | 2022 |
| Sector | Chemicals,Environment,Manufacturing, including Industrial Biotechology |
| Impact Types | Economic |
| Description | Decarbonising The Acrylic Value Chain Via Resource Circularity |
| Amount | £1,740,036 (GBP) |
| Funding ID | EP/V038052/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2021 |
| End | 07/2026 |
| Description | Future Biomanufacturing Research Hub |
| Amount | £10,284,509 (GBP) |
| Funding ID | EP/S01778X/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2019 |
| End | 03/2026 |
| Description | [16-FAPESP-BE] Lignin valorization in cellulosic ethanol plants: biocatalytic conversion via ferulic acid to high value chemicals |
| Amount | £2,082,438 (GBP) |
| Funding ID | BB/P01738X/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2017 |
| End | 02/2022 |
| Title | Refining methods for multiple enzyme expression for developing enzyme cascades. |
| Description | The need for building multiple enzyme cascades or short pathways is central to several areas of biocatalysts and synthetic biology. We have used the developments made in this grant and extended these to the research in several other grant funded areas. We can use comparable plasmids to co-express two or more enzymes in the same cell and we have been building short operons where all the genes are expressed from a single promoter on the same mRNA. With the comparable plasmid approach we can adjust the amount of each of the expressed enzymes by choosing plasmid replicons of different copy numbers as well as using different strength promoters. With the operon constructions we can ensure that all the enzymes are expressed at the same time and largely to the same levels. |
| Type Of Material | Technology assay or reagent |
| Provided To Others? | Yes |
| Impact | The application of the methods and concepts described above has allowed us to create stable expression strains that don't need any antibiotic in continuous cultures. We have been able to balance the three different enzymes needed for functional cytochrome P450 expression. The technology is central now to several areas of our research for the synthesis of chiral small molecules for alkaloids, chiral amines and methyl transferases where several enzymes are needed to build the complex final compound. In several cases this can compete very favourably with synthetic organic chemistry pathways and in one example an 8 step chemical pathway was achieved in a three step enzyme pathway. |
| Description | AB Sugar (enzymatically enhanced sucrose extraction from sugar beet) |
| Organisation | AB Sugar |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | A follow on PhD project was funded by the National Productivity Invesment Fund in collaboratio with AB Sugar. This exploits some of the thermostable enzymes identified in this project which are currently being investigated to enhance sugar extraction. |
| Collaborator Contribution | AB Sugar have provided the sugar beet feedstock, have shared data on their large scale operations and the impact they see of enzymatic pretreatment of sugar beet at large scale. They have also provided an opportunity for the student concerneed and the PI to visit their Wissington biorefinery and see the facility in operation. |
| Impact | To date we have constructed an experimental scale-down diffuser model at UCL. This is currently being validated but could be transfered to AB Sugar to support their process development programme. |
| Start Year | 2018 |
| Description | University of Cambridge |
| Organisation | University of Cambridge |
| Department | Department of Biochemistry |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Project just getting underway. UCL will provide Cambridge with fermentation samples for metabolomic analysis. |
| Collaborator Contribution | Cambridge will provide metabolic data and models that will ultimately used for model-based control of commodity chemicals production |
| Impact | None to dae - project just getting started |
| Start Year | 2016 |
| Description | University of Nottingham |
| Organisation | University of Nottingham |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Preliminary modelling of Nottingham fermentation data. |
| Collaborator Contribution | Provision of engineered cell lines making target product. |
| Impact | Project is just getting underway. No outcomes yet. |
| Start Year | 2016 |
| Company Name | TWIG BIO LIMITED |
| Description | Sustainability-focused synthetic biology company with machine learning as a core technology. |
| Year Established | 2022 |
| Impact | None. New start-up. |
| Website | https://www.twig.bio/ |