Are you using the right chassis?
The continuously growing field of industrial biotechnology has incited the replacement of non-renewable processes with more energy-efficient ones. Central to this is the use of genetically modified organisms modified with recombinant DNA technology for a wide variety of applications, ranging from the production of fine chemicals and pharmaceuticals to fuels and bioremediation . These technologies and applications are largely dependent on the use of well-characterised industrial host organisms including Escherichia coli and Sacharomyces cerevisiae. However, such strains are not always the optimal choice for particular processes due to inherent metabolic limitations (e.g. inadequate post-translational modifications) or incompatibility between the introduced foreign genetic components and the host’s molecular machinery.
While the well-characterised E. coli and S. cerevisiae present a broad range of molecular biology tools available for genetic engineering, using non-model organisms - chassis that are not widely used and lack well as characterized parts and standardised tools - may lead to a more productive industry as well as novel synthetic biology applications. By harnessing the native inherent characteristics (e.g. carbon utilization, metabolic pathways) of non-model organisms, we can bypass the limitations of current model organisms and thus exploit their true potential.
In an effort to promote the usefulness of non-model organisms, the Edinburgh Overgraduate iGEM team will focus on the domestication of microorganisms that we believe have a high potential within the context of synthetic biology. We will do this by characterizing new DNA parts (e.g. promoters, reporter genes, terminators) in both E. coli and our non-model organisms.
Cyanobacterium Synechocystis sp. strain PCC 6803 is one of the most extensively studied cyanobacterial species. Cyanobacteria constitute a unique class of microorganisms that are able to fix and metabolize carbon dioxide using the energy derived from sunlight. Nevertheless, the use of Synechocystis as a synthetic biology chassis awaits further investigation.Click on the icon above to find out more!
The Gram positive bacterium Rhodococcus jostii are a metabolic marvels! They could degrade a wide range of toxic materials. They can even degrade polychlorinated biphenyls (PCBs)! These organism is very robust due to its unique genome content and its ability to create micro compartments. They are potential chassis for synthetic applications in bioremediation. Click on the icon above to find out more!
The filamentous fungus Penicillium roqueforti is commonly used to make blue cheese. Fungi play an important role in the ecosystem due to their ability to degrade a wide range of organic matter. They are biotechnologically important for biotechnology industry to produce enzymes and complex secondary metabolites. The vast majority of fungal secondary metabolites await discovery, and the pool of fungal secondary metabolites is potential reservoir of drug leads and beneficial food additives. Click on the icon above to find out more!
To enhance the biosafety and biosecurity by making researchers more aware of these potential problems, we are developing a risk assessment tool prototype that will allow researchers to mine the genomes of new species to identify toxic metabolites and genetic elements that might limit their immediate utility as industrial hosts. Based on the antiSMASH program , the prototype, having as an input the microorganism’s accession number, will display a list of the related secondary metabolites and their toxicity score/scale. This will enable the user to better assess the strains to be worked on in a more direct manner and will allow to have clearer targets for genome editing, either by knocking-down toxic secondary metabolites or enhancing beneficial ones. Following the previous example, by distinctly showing a filamentous fungus’ secondary metabolites and their toxicity levels, the practitioners would immediately know the potential targets for genome editing. By making this tool accessible – as a website, for example – as a community standard to those involved in the laboratory practice, the risks and benefits related to different strains could be communicated effectively, even across international borders and legal jurisdictions .
 Nielsen, J., & Jewett, M. C. (2008). Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae. FEMS Yeast Research, 8(1), 122–131. http://doi.org/10.1111/j.1567-1364.2007.00302.x
 Weber, T., Blin, K., Duddela, S., Krug, D., Kim, H. U., Bruccoleri, R., … Medema, M. H. (2015). antiSMASH 3.0--a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Research, 43(May), 1–7. http://doi.org/10.1093/nar/gkv437
 Marles-Wright, J. (2016). Better by Design, Safer through Practice. Synbio LEAP Strategic Action Plan, (January), 1–5.
We are the University of Edinburgh Overgraduate iGEM Team, competing in the new application track in iGEM 2016.
School of Biological Sciences
The University of Edinburgh
Edinburgh EH9 3JF,