Our partner, Tobias Erb from the Max Planck Institute for Terrestrial Microbiology have been awarded the prestigious Otto Bayer Award for his outstanding contributions in the field of “Synthetic biology, especially the application on artificial photosynthesis”. Part of this research is contributing to FutureAgriculture – the group of Tobias Erb is responsible for the in vitro tests of the enzymes. You can read more in the official press release.
After some months of work, we are finally ready to share the official video of FutureAgriculture! The video has been enriched by some hand-drawings made by the fantastic team of MedioMix. The video has also been listed for the ESOF2018 Video Competition “Showcase your project” – don’t forget to put a thumb up and like our video!
We are currently collaborating with MedioMix to create the official video for FutureAgriculture! The first shooting day was at the MPI-MP in Potsdam – it has been a long day among laboratories, greenhouses and finding the right location for interviews. The official video for FutureAgriculture will be released soon, in the meantime, you can check our other videos on the dedicated YouTube Channel.
Unleashing the technical present / Nov 30 – Dec 02. Researchers & artists met for this experimental conference in order to explore the meaning and implications of the technosphere. Arren Bar-Even was invited to the SEEDS session – watch the full performance here.
Our project coordinator got the chance to interact with artists and scientists on the topic “ESTHETICS get SYNTHETIC: Knowledge Link Through Art & Science” during the workshop organized by KLAS at the Max Planck Campus in Potsdam-Golm on the 27th – 28th of November 2017.
The workshop was an opportunity to bring together scholars and practitioners to jointly discuss and reflect on contents, approaches and methodologies that draw the link between synthetic biology and artistic research and how those can synergically interact by mutually interrogating and reconsidering their methodologies and modes of operation in an Artist in Residence program like KLAS, in which Arren Bar-Even’s team participate as hosting laboratory.
One of our partners, the Max Plack Institute for Molecular Plant Physiology – MPI-MP, has been selected among the 4 finalists for the European Innovation Radar prize 2017 under the category Excellent Science. This category selects the best cutting-edge science underpinning tomorrow's technological advances. Thanks to this initiative, the FutureAgriculture's team got the chance to pitch their plans for going to market with their EU-funded tech to a jury of experts at the ICT Proposers' Day in Budapest (9 November 2017). More info here.
“It’s great you get recognition for your hard work and more importantly for your hard thinking,” says Arren Bar-Even, our project coordinator, of the finalist place and the ceremony in Budapest, "the Innovation Radar champions innovations with strong potential for transformative impacts developed during EU-funded research projects and it is a pleasure to be selected among them."
Arren Bar-Even, the project coordinator, during the pitch at the ICT Proposers' day in Budapest (9/11/17).
We just released a new video – this time instead of the typical interview we decided to capture in few minutes the multiple voices of the FutureAgriculture team. Each of us condensed the concept of FutureAgriculture in few words and the result is an extraordinary puzzle of points of view. A special thank to the greenhouse facility at the MPI in Marburg that hosted us for the shooting. We hope that you enjoy the video!
Our ability to test promising pathways in vitro and in vivo is quite limited. The testing of every candidate pathway would become an endless quest – worth of decades and billions of investments. To select only a few promising pathways we need the support of computational models that predict how each pathway will affect the carbon fixation rate in plants. We have generated a model of plant photosynthesis that takes into account both the central carbon fixation pathway (the Calvin cycle) as well as the photorespiration pathway – either the natural pathway or a synthetic alternative route.
This model enables us to estimate which synthetic pathway will result in the highest enhancement of carbon fixation rate, under different conditions such high/low illumination or high/low CO2-availability due to the opening and closing of the stomata. Only the most promising pathways will undergo a more extensive testing in vitro and in vivo.
The model also feeds both the in vivo and in vitro testing by setting important parameters thresholds and by giving suggestions on how to reach them. For example, the model can estimate the needed quantity of each pathway component to reach the best performance possible. Therefore it directs the enzyme engineering phase by specifying the minimal activity that an engineered enzyme needs to reach, or it warns us against toxic or reactive compounds that might accumulate during the activity of the pathway within the cells. We then can fine-tune the expression of the pathway components to avoid such deleterious accumulations.
The model is also continuously improved by integrating the data from the in vivo and in vitro testing i.e. the enzymatic activity, the growth rate, etc. Models are not completely finished yet but they are already well productive in giving us valuable information regarding the expected pathway. They are expected to be fully operative during the 3rd year.
After the identification of the pathways, we need to make sure that all the pathways’ components are available. Our pathways involve both existing and novel reaction – reactions that are not known to be catalysed by any enzyme in nature. We engineer existing enzymes to catalyze such novel reactions in order to sustain the activity of the pathway.
First, we need to find existing enzymes in nature that catalyze similar reactions or that can catalyze the novel reactions promiscuously. The concept of promiscuous enzymes is fundamental for this phase: enzymes generally have evolved to catalyze one primary reaction that represents their main task, but promiscuous enzymes can also catalyze, besides the primary reaction, side-reactions at a lower rate. During the 1st year of the project, we were able to identify the promiscuous enzymes that catalyze all the novel reactions of four of our candidate pathways, although the catalysis rate is quite low as expected. However, they represent the starting seed for the second stage where we are going to enhance the low-rate reactions of interest by three methods:
- Rational design – by applying biochemical knowledge while looking at the enzyme active site and its structure, we can predict amino-acid residues substitutions in order for the enzyme to accept our substrate and support the novel reactions.
- Library of changes in protein sequences – By using a large collection of alteration in the protein sequence, we can systematically screen the changes that result in better activity. To easily identify the best change within the library we have designed in vitro assays that couples the target activity to a measurable property i.e. fluoresce.
- In vivo selection – by creating E. coli strains whose growth depends on the novel reactions, we can directly select for enzymes that catalyze it efficiently. Thanks to this method, we can directly select for higher enzymatic activity by simply selecting the cells that grow faster.
The backbone of our project is the identifications of novel pathways that increase agricultural productivity by enhancing carbon fixation rate and efficiency in plants. The pathway design was completed in the first year, during which we identified more than 100 candidate pathways that can potentially bypass the natural photorespiration without releasing CO2.
We have considered all known enzymes and all known enzymatic mechanism to systematically search for all the possible routes that recycle 2-phosphoglycolate, the product of Rubisco oxygenation, back to the Calvin cycles (that supports carbon fixation). Our candidate pathways contained both reactions catalyzed by existing enzymes as well as plausible reactions, i.e. reactions that potentially can be catalyzed by well-characterized enzymes or that follow a well-known mechanism. We compared the candidate pathways according to various physicochemical properties including thermodynamics, kinetics, resources consumptions, and overlap with endogenous metabolism. Our analysis takes into account also how easy it will be to evolve the novel reactions from existing enzyme and mechanism (i.e. the number of novel enzymes required in the candidate pathway and hints in the scientific literature on existing enzymes that could support such new activity). This approach enabled us to select the most promising pathways in terms of such properties and test them in vitro, reconstructing the pathway from its enzymatic components. We are now implementing the pathways in E. coli, using it as a platform for the pathway selection, before finally moving to cyanobacteria and plants.