DeTOX - Productive whole cell biocatalysis by engineering resistance to toxic products and substrates

Lead Research Organisation: University of Nottingham
Department Name: Div of Process and Environmental Eng

Abstract

Product toxicity is a major problem for many IBBE processes involving production of small molecules by living cells. Toxicity causes yield restrictions & cell lysis, & frequently affects the commercial viability of biomanufacturing. Likewise, small molecules in lignocellulosic feedstocks inhibit bacterial fermentations & ultimately depress product yields. In this CBMNet NIBB-led bid, a team of scientists from four Universities apply their fundamental expertise in systems & synthetic biology & membrane function, to engineer increased resistance to small molecules in the industrially relevant bacteria, E. coli & solventogenic Clostridia. Our innovation is to translate BBSRC-funded research in microbial stress responses, membrane structure & membrane transporters, into the development & commercialisation of innovative applications in IBBE by our 5 commercial partners. A key project output will be a commercial chassis strain, DeTox, with generally increased chemical resistance.

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

Publications

10 25 50
 
Description The research has demonstrated the mechanisms by which bacteria increase their tolerance to toxic compounds produced owed to genetic engineering.
Exploitation Route The DeTOX vectors developed during this work help enable sustained production of toxic compounds by microbial cell factories.
Sectors Agriculture, Food and Drink,Chemicals,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Description Materials and Manufacturing
Amount £1,601,686 (GBP)
Funding ID 103761 
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 01/2018 
End 12/2020
 
Description CPI 
Organisation Centre for Process Innovation (CPI)
Country United Kingdom 
Sector Private 
PI Contribution Nottingham is the Lead partner for ConBioChem and Collaborator on Detox
Collaborator Contribution Industrial partner for ConBioChem and Detox
Impact None yet
Start Year 2016
 
Description Green Biologics 
Organisation Green Biologics
Country United Kingdom 
Sector Private 
PI Contribution Nottingham is a collaborator on HIPHOP (led by Green Biologics), lead partner on ConBiochem and collaborator on Detox.
Collaborator Contribution Green Biologics led HIPHOP and are industrial partners on Detox and ConBioChem, building on a pre-2006 direct funded studentship
Impact No publications yet
 
Description Ingenza 
Organisation Ingenza Ltd
Country United Kingdom 
Sector Private 
PI Contribution Nottingham were partners in the P2P project with Ingenza and Lucite. We also lead the ConBioChem IB catalyst project, for which Ingenza are an industrial partner. We are partners in the Detox IB catalyst project, for which Ingenza are an industrial partner. Ingenza act as industrial hosts for CASE industrial experience placements for our Lucite-sponsored CASE studentships, since they have biotechnology laboratories and Lucite do not.
Collaborator Contribution Ingenza and Nottingham are partners within the Lucite project to develop bio-based manufacturing of methylmethacrylate. Ingenza were the lead partner for the P2P project. Ingenza act as industrial hosts for CASE industrial experience placements for our Lucite-sponsored CASE studentships, since they have biotechnology laboratories and Lucite do not. Ingenza are industrial partners in the ConBioChem IB catalyst project (which Nottingham leads) and in the Detox IB catalyst project (in which Nottingham is a partner).
Impact GR Eastham, DW Johnson, I Archer, R Carr, J Webb, G Stephens (2015). A Process for Production of Methacrylic Acid and Derivatives Thereof. WO2015022496 Multidisciplinary: Chemistry, microbiology, biochemistry, molecular biology, biotechnology
Start Year 2013
 
Description Lucite 
Organisation Lucite International
Department Lucite International UK Ltd
Country United Kingdom 
Sector Private 
PI Contribution Nottingham works with Lucite to develop metabolically engineered microorganisms for bio-based methymethacrylate production. We also develop fed-batch and continuous bioprocesses, and methods to solve problems with product toxicity. The work has been done through 7 CASE studentships (Lucite), 2 small projects (Lucite), the P2P grant and our IB catalyst projects, Detox and ConBioChem.
Collaborator Contribution Lucite aim to develop a bio-based route to manufacture methylmethacrylate. Lucite have funded 7 CASE studentships, 2 small projects, have collaborated on the P2P grant and are partners on our IB catalyst projects, Detox and ConBioChem.
Impact GR Eastham, G Stephens, A Yiakoumetti (2016). Process for the biological production of methacrylic acid and derivatives thereof. WO2016185211 A1 L Rossoni, SJ Hall, G Eastham, P Licence and G Stephens (2015) The putative mevalonate diphosphate decarboxylase from Picrophilus torridus is in reality a mevalonate-3-kinase with high potential for bio-production of isobutene. Applied and Environmental Microbiology 81, 2625-2634 doi: 10.1128/AEM.04033-14 GR Eastham, DW Johnson, I Archer, R Carr, J Webb, G Stephens (2015). A Process for Production of Methacrylic Acid and Derivatives Thereof. WO2015022496 Multidisciplinary: Chemistry, Biotechnology, Microbiology, Biochemistry, Molecular Biology
Start Year 2011
 
Description University of Cambridge 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution Nottingham is Lead partner on ConBioChem and collaborators on Detox projects
Collaborator Contribution Collaborators on ConBioChem and Detox
Impact None yet
Start Year 2016
 
Description University of Exeter 
Organisation University of Exeter
Country United Kingdom 
Sector Academic/University 
PI Contribution Nottingham is a Collaborator on Detox
Collaborator Contribution Collaborator on Detox
Impact None yet
Start Year 2016
 
Description University of Sheffield 
Organisation University of Sheffield
Country United Kingdom 
Sector Academic/University 
PI Contribution Nottingham is a Collaborator on Detox
Collaborator Contribution Collaborators on Detox
Impact None yet
Start Year 2016
 
Description University of York 
Organisation University of York
Country United Kingdom 
Sector Academic/University 
PI Contribution Nottingham is a Collaborator on Detox
Collaborator Contribution Lead partner on Detox
Impact None yet.
Start Year 2016