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

Lead Research Organisation: University of Sheffield
Department Name: School of Biosciences

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
 
Description We have contributed significant new gene expression and metabolite data sets for control and test fermentations in the first phase of this multi-centre 5 year project and the analyses of these data have been published showing that Escherichia coli is an excellent host for the production of organic acids. We have also published the results of research to enhance the tolerance of E. coli to vanillin and have identified several potential intervention points to improve vanillin production. We have completed a multi-omic analysis of fermentations producing styrene and are currently applying these data to design the Detox cassettes in the second phase of the project and drafting a paper reporting this approach.
Exploitation Route This project has an industrial biotechnology focus and we have five industrial partners contributing to direction of the project and the translation of the findings.
Sectors Chemicals,Energy

URL http://projectdetox.co.uk/
 
Description Our data are discussed with our industrial partners at the quarterly detox meetings. This information exchange is beginning to inform decision making on viable approaches to chemicals production. We have provided and analysed three transcriptomic datasets and two metabolomic datasets for the consortium which are core components of manuscripts in preparation for publication and are informing the design of the Detox cassettes.
First Year Of Impact 2017
Sector Manufacturing, including Industrial Biotechology
 
Description Harry Smith Vacation Studentship
Amount £2,000 (GBP)
Funding ID VS17/2 
Organisation Microbiology Society 
Sector Learned Society
Country United Kingdom
Start 06/2017 
End 08/2017
 
Title Detoxbase 
Description We have provided data for and consulted on the development of Detoxbase, which stores consortium data and has tools for visualisation and analysis of the data. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact Detoxbase is still developing but it is proving an invaluable tool for data sharing and analysis within the consortium. 
 
Description Science outreach (Pint of Science) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Talk delivered in an informal pub-based setting with a focus on discussing bioproduction of chemicals in an accessible way.
Year(s) Of Engagement Activity 2018