From 2011.igem.org

Latest revision as of 03:00, 29 October 2011

At a Glance

Pushed for time? Don't worry. Just take a few minutes to read this page which gives a summary of our entire project in a nutshell.

Project AuxIn: engineering bacteria to help fight soil erosion

Figure 1: Arabidopsis plant grown in soil during our soil erosion experiment. (Picture by Imperial College iGEM team 2011.)

In arid areas of the world soil erosion is a massive problem. It is caused by wind and rain sweeping away the fertile top soil and can eventually result in desertification. Climate change and unsustainable farming practices are accelerating the rate of desertification to over 31,000 hectares/day. That is 62,000 football pitches in a day or half the size of the UK every year. In ordinary circumstances the roots of well-established plants help to hold down the top soil, protecting it from erosion. In areas that suffer from desertification however plants do not get the chance to establish large enough root networks to anchor the soil and themselves before erosion occurs.

This year, the Imperial College London iGEM team have joined the international effort to fight desertification.

We hope to engineer bacteria to accelerate plant root development. The bacteria will be designed to secrete the hormone, indole-3-acetic acid (IAA), also known as auxin. Seeds will be coated with the bacteria and then planted in the soil. Once the seeds germinate the bacteria will move towards the roots and be taken in by the plant. Inside the roots the bacteria will release IAA – promoting growth and protecting the soil from erosion.

The modules

The title of our project is AuxIn. Our whole project is sub-divided into three modules. The first, Phyto-Route, involves heterologous expression of the chemoreceptor PA2652 in our chassis, E. coli. PA2652 is responsive to plant root exudates like malate and will allow our engineered bacteria to swim towards plant roots. Once they reach the root, they can be actively taken up by the plant as demonstrated in a recent study on bacterial uptake of GFP expressing E. coli into Arabidopsis roots. This module has the potential to serve as a platform technology to deliver natural compounds specifically to plant roots. The second module, Auxin Xpress, involves heterologous expression of IAA in our chassis, via the indole acetamide (IAM) pathway. IAA is known to promote root growth and therefore if it is supplied inside and around the root of a plant, should promote soil stability and prevent erosion. The third and final module, Gene Guard, was designed as a novel safety measure to minimise the risk associated with release of GMOs into the environment. This involves a toxin/anti-toxin mechanism to prevent horizontal gene transfer of plasmid DNA from our modified bacteria to existing soil bacteria.

The engineering cycle

Each module follows the synthetic biology engineering cycle. Since human practice had a huge influence on our project, we included it at the start of the cycle which was followed during the development of our project.

You can read more about the specifications, design, modelling, assembly, and testing of each module following the clickable icons above.

Figure 2. The engineering cycle (Diagram by Imperial College London iGEM team 2011).

Human practice

Human practices were an extremely important component of our project and strongly influenced our design. During very early design stages of the project, we consulted social scientists and NGOs (Greenpeace and the Berkeley Reafforestation Trust) about the viability of our project. In addition, we talked to plant scientists and ecologists to learn more about the specifics and wider impacts of our project. We held two human practices panels that greatly influenced our view of the issues surrounding synthetic biology in general and our project in particular.

We chose our chassis based on concerns surrounding spread of our engineered bacteria into non-targeted environments. In addition, we designed Gene Guard, a novel containment device that prevents the spread of genetic information via horizontal gene transfer. While our project is only at proof-of-concept stage, we wanted to ensure that our approach was as viable as possible. Accordingly, we have created an implementation plan that is based on plans utilised in the agricultural industry for the research and development of new chemicals but also incorporates advice we received from an ecologist and charity members. Finally, we have investigated the legal issues surrounding the release of genetically modified organisms and how they impact our project.

In addition, we devised a guideline on how to assess the possibility of releasing an iGEM project into the environment in order to help future teams.

Visit our Human Practice page for an in-depth report on how it influenced our design.

Achievements

We successfully expressed indole 3-acetic acid in E. coli and observed its effects on a reporter line of Arabidopsis that produces YFP in response to the compound. We also have results showing that our E. coli move towards malate, which is a compound secreted by roots. In addition, we observed the uptake of our bacteria into roots and made the first photoconvertible fluorescent reporter available on the Registry. We have used this reporter to observe metabolic activity of our chassis within the root. We also characterised four fluorescent reporters for their thermostability. We have created a user interface to model the 3D root growth of Arabidopsis depending on the input IAA concentration (video 2). We have also modelled the chemotaxis capillary assay, demonstrating the population dynamics of bacteria.

Visit our Main Results page for an overview of our main achievements in all modules or visit our Data page for an overview of the BioBricks we constructed and characterised.

Video 1. Photoconversion of Dendra2 using 405 nm wavelength in Arabidopsis thaliana roots. After 24 hours, the bacteria were re-imaged at the same settings. Expression of green Dendra2 had increased, showing that the bacteria are metabolically active inside the roots (Imaging by Mark Scott for Imperial College iGEM 2011).

Figure 3. E. coli cells expressing superfolder GFP (sfGFP) can be seen inside an Arabidopsis thaliana root using confocal microscopy (Data and imaging by Imperial College iGEM team 2011).

Outreach

We set up Radio iGEM, a radio show in which we discuss all things iGEM and synthetic biology. We interviewed several people, including a Member of Parliament and one of the people behind iGEM Watch. We also acted out a play about the future influenced by synthetic biology that was written by Chris.

Two A-level students stayed with us for a week each and helped us out with the science and art parts of the project. In addition, we talked about our project at an event at the Natural History Museum. For more information on our outreach and to listen to Radio iGEM and read Chris' play, visit our Outreach page.

Collaboration

We collaborated with the WITS-CSIR team from South Africa. Our teams exchanged information on the intricacies of observing chemotaxis in the wet lab and our modellers helped them out by modelling their theophylline switch. Have a look on our Collaboration page for a detailed description of the model and the information exchanged about wet lab assays.