DeTOX - Productive whole cell biocatalysis by engineering resistance to toxic products and substrates
Lead Research Organisation:
University of Cambridge
Department Name: Biochemistry
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
A major challenge in industrial biotechnology & bioenergy is to solve serious problems with yield restrictions due to product or substrate toxicity. Increasing product concentrations by >10-fold would deliver commensurate improvements in revenue from such processes, and is a viable target, given the millimolar product concentrations formed in many proposed bioprocesses at present. This is critical for commercially viable production of bulk & specialty chemicals by living cells, because many of these are toxic & need to be removed rapidly to avoid damage to the intracellular contents & cell membrane. It is also essential for the effective use of lignocellulosic substrates that contain fermentation inhibitors that exert their toxic effects by penetrating the cell. Our objective is to produce host strains with enhanced resistance to a broad range of chemical products & so provide highly-productive chassis for commercial synthetic biology. We will study the mechanisms of chemical toxicity and resistance in E. coli & solventogenic Clostridium spp., both by analyzing cellular responses during bioproduction and by experimental evolution of resistant strains. We will also apply world-leading membrane science (efflux pumps, proteomics, lipidomics & membrane biophysics) to execute novel, rational redesign of cell membranes to enhance resistance. We will combine knowledge of these systems to develop our DeTox strain platform by strain engineering, using synthetic biology standards. The chassis will be tested in small scale replicas of industrial bio-processes, & iteratively redesigned for maximum robustness under process conditions, using models describing cellular responses to toxin exposure. The outcome will be DeTox chassis, to be licensed to our partners, and DeTox gene cassettes, that can be ported to other hosts.
Planned Impact
As described in proposal submitted to IUK
People |
ORCID iD |
Kathryn Lilley (Principal Investigator) |
Publications
Lilley K
(2020)
Biotin proximity tagging favours unfolded proteins
Minde D
(2017)
Time, space, and disorder in the expanding proteome universe
Minde D
(2018)
Cellular labelling favours unfolded proteins
Minde DP
(2017)
Time, space, and disorder in the expanding proteome universe.
in Proteomics
Minde DP
(2020)
Biotin proximity tagging favours unfolded proteins and enables the study of intrinsically disordered regions.
in Communications biology
Description | The project started in September 2016. We have already published a review paper and generated data on the inner bacterial membrane proteome, and some, so far. limited data on the topology of these proteins We have developed and applied a method to capture and characterise the bacterial RNA binding proteome that has revealed many metabolic enzymes to have an alternative role as RNA biding proteins. |
Exploitation Route | the data are being used by the rest of the Detox consortium to interrogate the membrane proteome data with transcriptomics and metabolomics data for bacterial strains producing citramalate. |
Sectors | Chemicals,Education,Manufacturing, including Industrial Biotechology |
Description | H2020 Infrastructure |
Amount | € 10,000,000 (EUR) |
Funding ID | EPIC-XS - DLV-823839 |
Organisation | European Commission H2020 |
Sector | Public |
Country | Belgium |
Start | 01/2019 |
End | 12/2023 |
Description | High performance mass spectrometry: applications for the Cambridge biological sciences community |
Amount | £295,395 (GBP) |
Funding ID | BB/W019620/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 08/2022 |
End | 08/2023 |
Title | OOPS |
Description | A method to efficiently capture and characterise the RNA binding proteome |
Type Of Material | Technology assay or reagent |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Adoption of method by industrial collaborators |
Title | SMALP |
Description | This method uses styrene maleimide to create membrane discs containing membrane protein complexes. When coupled with immune-precipitation it enables the characterisation of very low abundance membrane protein complexes |
Type Of Material | Technology assay or reagent |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | The method has been incorporated into the workplan in a BBSRC sLoLA proposal with the universities of York, Newcastle, Bath, Nottingham and Cambridge |
Description | Collaboration with Astra Zeneca |
Organisation | AstraZeneca |
Country | United Kingdom |
Sector | Private |
PI Contribution | Atra Zeneca are funding two PhD students in my lab to use spatial proteomics tools developed in my laboratory |
Collaborator Contribution | Expertise in spatial proteomics and computational pipelines we have also developed |
Impact | this project is multi disciplinary involving cell biology, protein biochemistry and statistics |
Start Year | 2021 |
Description | Collaboration with GSK |
Organisation | GlaxoSmithKline (GSK) |
Country | Global |
Sector | Private |
PI Contribution | Funded post doctoral researcher position to look at the affect of various DNA damage therapeutic agents on RNA binding capacity of proteins |
Collaborator Contribution | The partners will supply therapeutic agents and expertise |
Impact | the project has just started and hence there are no outputs as yet |
Start Year | 2020 |
Description | Collaboration with Pfizer |
Organisation | Pfizer Inc |
Country | United States |
Sector | Private |
PI Contribution | We have been awarded a project grant by Pfizer to make use of the OOPS (doi: 10.1038/s41587-018-0001-2) method developed as part of Transcriptin trafficking translation award. We will use these tools to determine the interaction of RNA therapeutic tools with host cell machinery. We will also make use of the LOPIT technology developed as part of several projects funded by the Wellcome Trust and BBSRC |
Collaborator Contribution | Post doctoral researcher based in my laboratory is applying our expertise in subcellular proteomics and characterisation of the RNA binding proteome |
Impact | The project is multi-disciplinary involving cell biology and computational biology |
Start Year | 2022 |
Description | Science Day |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | I created games for children ranging from 5-18 years old around amino acids, translation and proteins. My lab members also created a game where children of the same age range made rainbow gradients of solutions of different densities and how we use this idea to separate intracellular organelles was also communicated. We made cartoon characters -Robbie the ribosome, Micky the mitochondria, Clara the chloroplast and Pete the plastid. We have stickers away of these and explained their role in cells. |
Year(s) Of Engagement Activity | 2022 |