With this innovative project we are undertaking an integrated global analysis of the entire cellular system, encompassing the transcriptome, proteome (cytoplasmic, periplasmic and membrane proteins), metabolome (cytoplasm, periplasm, cell wall and footprint) and lipidome (membranes). Since the majority of desirable chemical products are membrane-disrupting chemicals, we will also study the all-important structural changes in the cell membrane that underpin cellular responses to toxins.
Previous industrial and academic research in this area has been fragmentary, with focus on specific cell types and individual chemicals. In particular, studies on toxin-exposed cells have tended to focus on just one of the “omes” (usually the transcriptome), and have not, to date, provided sufficient information to provide the step change in reverse engineering to deliver highly-productive, product-resistant hosts for industrial synthetic biology. By contrast, our multi-omic integrated whole systems analysis will provide a much deeper understanding of bacterial physiology that can be used to grow further UK IBBE business in the long term.
In addition, through the creation of DETOXbase (now MORF) and integration of metabolic modelling we will be able to design both generic and specific solutions to reverse engineer hosts for improved chemical tolerance, and hence remove this significant barrier to profitability.
MORF (formerly know as DETOXbase) is our flagship online resource providing deep insight into the cellular responses to chemical stress. The resource expands on the EchoBase architecture, originally created as a comprehensive resource for Escherichia coli and used to characterize functionally unknown genes by integrating experimental data with genome annotation. MORF builds on this principal by incorporating additional data types including gene expression, protein abundance, metabolite profiles, and lipidomic data together with whole genome metabolic models.
Through the use of bioinformatic analysis and an interactive visual interface, MORF allows users to explore these fully integrated data sets and identify patterns indicating different types of stress responses; from defence against chemical damage, removal or neutralization of toxins, to responses that modify cell architecture and increase robustness. Ultimately MORF helps researchers to predict interventions that will provide a tailored increase in tolerance to a specific product, and provide a framework that can be applied to any organism being studied.
Having established the value of our MORF platform within the DETOX project, we are now looking at how the community can use MORF for their own research. We have uploaded over 100 bacterial genomes to our MORF genome browser, which are free to browse, and our MORFlux tool facilitates flux balance analysis using either predefined or uploaded models through the browser. Furthermore, MORF is being used for a number of projects, including the ERA CoBioTech MeMBrane and Horizon 2020 TOPCAPI projects. These international teams are using MORF to store, share and interrogate their mulit-omics datasets. If you are interested in using MORF, please contact us.
Transport and Efflux
The DETOX project will apply knowledge of transporter biology to improve resistance to chemical toxicity. This could be aiding the more rapid uptake of chemicals which can be detoxified intracellularly, such as growth inhibitors present in lignocellulosic feedstocks, or in the efflux of the products of industrial fermentations. The project was created through the management board of CBMNet, a BBSRC funded Network in Industrial Biotechnology, and so membrane-based processes are a focus of our engineering processes.
We will apply our world-leading membrane science (efflux pumps, proteomics, lipidomics & membrane biophysics) to execute novel, rational redesign of cell membranes to enhance resistance. Through creation of MORF and integration of metabolic modelling we will be able to design both generic and specific solutions to reverse engineer hosts for improved chemical tolerance, and hence remove this significant barrier to profitability. As examples, the solutions will build on our expertise in membrane function, & include expression of heterologous toxin efflux pumps & metabolic engineering to alter membrane fluidity.
Natural ‘detoxification’ systems have recently been discovered that couple uptake of toxic chemicals with chemical conversion to non-toxic metabolites, hence effectively removing their toxic intracellular effects. We will take inspiration from this approach to couple uptake of key toxins, e.g. phenolics and acetate, to their conversion to non-toxic production using our ENTRAPed methodology.
Finally, our intention is to fully integrate multiple solutions into a single chassis, through iterative cycles of testing, which will include solutions from this project & others from naturally occurring chemically tolerance bacteria such as Pseudomonas and acetate-resistant Acetobacter. Part of this solution will include producing strains that can alter their membrane lipid composition in response to toxic insult during a fermentation, as introduction of vaccenic acid is known to alter solvent tolerance.
Responsible Research and Innovation (RRI) can be described as an approach that aims to anticipate, and take into account, the potential implications of technoscientific processes as well as the expectations of society. A number of descriptions, policies and frameworks for RRI have been developed in the UK, EU and beyond. ‘Tools’ have been developed to elucidate and track processes. However, RRI cannot be taken as something stable, agreed or pre-determined. Like many aspects of science and innovation, it is a work-in- progress; the meanings of RRI have still to be elaborated, analysed, understood. Those meanings, we can anticipate, will be multiple and thus we aim to explore differing perspectives on the notion of RRI and its effects within the specific project context of DETOX.