Team:Amsterdam/Project/Overview
PROJECT OVERVIEW
Working together to save the world
The Problem
The quest for sustainability
The grand problem
Our economy still depends largely on fossil resources. For decades, this has fuelled the incredible progress of our world, but not without the massive cost of geopolitical instability and global warming - costs we’re now facing more than ever. With the current consequences of climate change visible around the world and global energy demands that are expected to double in 2050, the quest for clean, renewable energy is one of mankind’s most important and urgent modern challenges.
The ideal world
In an ideal world, we would create carbon products from CO2 taken from the atmosphere, meaning that as we burn fuels, we consume at least as much CO2 as we emit. This would fulfill the unsatiable carbon needs of our society in a closed-loop system, reducing or preventing the further buildup of greenhouse gasses. A bio-based economy - one which we use renewable, CO2-consuming biomass to produce the materials and fuels our societies depend upon - is a promising approach to creating this system. But past approaches, using sugar crops that compete with arable land or lignocellulosic biomass that is often difficult to utilize efficiently, have not fulfilled their promise.
The green promise
Cyanobacteria, photoauxotrophic organisms that use mostly CO2 and light to grow and do not require arable land, hold great potential to fill the gap. But cyanobacteria are - compared to chemotrophs - still vexed by low productivity and limited in the range of products they can produce: they simply do not have the same extensive toolbox of metabolic engineering knowledge available that we possess and exploit to turn organisms like E. coli into high-yield cell factories. What we need is the ability to align the sustainability potential of cyanobacteria with the productive capacities of commonly used chemoheterotrophs, in a way that can implemented with technologies that are available now.
Our solution
Combining the best of cyanobacterial sustainability and chemotroph productivity
Rather than mimic the modus operandi of the biotech industry to do so - focussing on using a single species in isolation to achieve a goal - we decided to mimics nature instead: to let microorganisms work together in a multi-species ecosystem - a synthetic consortium - and develop relationships that could make sustainable bioproduction a reality. Specifically, we aimed to engineer relationships between photoauxotrophic cyanobacteria and chemoheterotrophs (like E. coli) to turn CO2 into useful carbon product. Such photosynthetic romance is perhaps not the ultimate solution (imagine a single organism with both the productive potential of E. coli and the photosynthetic capacity of cyanobacteria), but as of yet the most feasible and effective way to couple sustainability to currently available bioproduction processes.
The basic premise of our consortium’s functionality is simple: a phototroph (Synechocystis PCC 6803 in the case of our prototype consortium) fixates CO2 and converts it to relatively simple carbon compounds. These compounds serve as fuel for a heterochemotroph (E. coli in the same prototype case), which uses the compounds to produce a desired end-product. Since the CO2-fixating, carbon-sharing Synechocystis is essentially modular, it can be coupled to a multitude of biotechnological production processes to make these processes sustainable, including the dozens of iGEM projects that use E. coli for bioproduction!
The project
Working together to save the world
The chemotroph
The workhorse of synthetic biology, E. coli benefits from the availability of a well-categorized genetic toolbox, making it the ideal chemotroph candidate for our consortium. We aim to engineer biofuel production in E. coli for use in our protoype consortium. Moreover, we intend to engineer interactions with Synechocystis in order to create a genetic safety switch that ensures our consortium only functions when its members are together.
The phototroph
Also known as the ‘Green E. coli’, Synechocystis is a model organism that growns on CO2 and light. We want to engineer Synechocystis to produce and share carbon compounds in ways that are genetically stable by coupling this production to its own growth. This essentially results in a modular phototrophic production egine. By then connecting Synechocystis to E. coli in our consortium, the latter would receive a continuous supply of sustainably-produced compounds required to produce virtually any desired end-product.
Such an endeavour requires several tasks. The two organisms have to be genetically modified to synthesize the desired molecules, preferably in an stable fashion. We also need to characterize how these new activities influence the physiological parameters of each bacteria, i.e. how fast they grow, what is the production rate, how stable are these rates, etc. These parameters can be used to build models that allow us to understand the dynamics of the system. Last but not least, the production in the resulting consortium has to be compared with other consortia.
Dry lab
Our modelling efforts will generate simulations of consortium development and will allow us to assess and use optimal organism ratios for the production of a desired end-product. Moreover, we intend to leverage genome-scale metabolic models to create a suite of open-source software tools that can be used to construct genetically stable and safe synthetic consortia in which a phototrophic species functions as the carbon provider for a product-producing chemotroph.
Consortia
Synechocystis and E. coli work well together, but are far from the only possible members of a synthetic consortium. Yeast, for instance, could be of great interest to the biotech community when coupled to our cyanobacterial production module. Alongside our main proof-of-principle consortium, we will therefore develop a micro-droplet screening protocol to rapidly assess the viability of novel consortia. This would greatly reduce trial-and-error time in the lab and allow users to identify consortia that serve their biotech requirements.