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FutureAgriculture Report Summary

Project ID: 686330
Funded under: H2020-EU.1.2.1.

Periodic Reporting for period 1 - FutureAgriculture (Transforming the future of agriculture through synthetic photorespiration)

Reporting period: 2016-01-01 to 2016-12-31

Summary of the context and overall objectives of the project

Carbon fixation is the most important biological processes on earth, supporting our biosphere by transforming inorganic carbon into organic matter and literally feeding all life forms. The Calvin–Benson–Bassham Cycle (CBBC) – operating in higher plants, algae, and many bacteria – is responsible for ≥ 95% of the carbon fixed in the biosphere. Despite being under a strong selective pressure for eons, the CBBC still displays inefficiencies related to the enzymes it employs; especially the carboxylating enzyme RuBisCO is inefficient. RuBisCO is very slow and cannot fully distinguish between CO2 and molecular oxygen. When oxygen replaces CO2 as substrate for RuBisCO’s activity, a toxic waste product, 2-phosphoglycolate, is produced. 2-phosphoglycolate must be recycled back into the CBBC via a process termed photorespiration. However, plant photorespiration dissipates energy and releases CO2, thereby directly counteracting the function of RuBisCO, reducing the effective rate of carbon fixation, and lowering agricultural productivity.
FutureAgriculture aims to boost agricultural productivity by designing and engineering plants that directly overcome the deficits of natural photorespiration and that support higher photosynthetic rate and yield. The FutureAgriculture Consortium integrates diverse skills in computational biology, chemistry, synthetic biology, microbiology, and plant physiology.
By considering all known enzymes, as well as enzymes that could be easily evolved, metabolic pathways that can bypass photorespiration without releasing CO2 are systematically identified. These candidate pathways are compared according to their properties, and the most promising ones – i.e., short pathways with low consumption of cellular resources – are identified. To realize these pathways, natural enzymes are recruited and novel enzymatic activities to catalyze are engineered. The optimized pathways are then expressed in engineered bacterial strains that support the evolution of increased pathway activity. The evolved pathways are incorporated into photosynthetic microbes, i.e., cyanobacteria, to test their advantage. Finally, the most promising pathways are implemented in higher plants, and the growth of the engineered plants is monitored to fully characterize the physiological effects of the synthetic pathways.
The implementation of novel synthetic photorespiration pathways in plants is expected to significantly increase plant growth rate and biomass yield under various environmental conditions. This will provide the basis for increasing agricultural productivity of the crops that comprise >60% of agricultural production, including rice, wheat, barley, oat, soybean, cotton, and potato.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

During the first year, the FutureAgriculture Consortium has successfully uncovered dozens of possible metabolic pathways to bypass native photorespiration without releasing CO2. Three such pathways were identified as highly promising, being able to recycle 2-phosphoglycolate into the CBBC with minimal consumption of cellular resources, minimal overlap with natural metabolism, and using enzymes that are either naturally available or are easy to engineer.
The Consortium has experimentally tested, identified, and/or engineered multiple enzymes to sustain the activity of the synthetic pathways. Overall, enzymes that fully support two of the promising synthetic routes are now available.
The project also successfully established, constructed, and tested numerous E. coli strains for the selection of the in vivo activity of promising synthetic photorespiration pathway. For each synthetic pathway, multiple selection strains were constructed, each having a different requirement of pathway activity for growth.
Keeping in mind that the final goal of the project is the implementation of such routes into plants, the Consortium has already selected the regulatory elements that will assure the correct expression of the pathways’ genes in the chloroplast of higher plants, namely Arabidopsis and Brachypodium.
The Consortium is actively promoting the project through internet-based channels: a website enriched with a section that carefully explains the science behind the project (Synthetic Biology), a YouTube Channel with several video interviews of the key personnel, and active social media accounts. All the partners are disseminating the collected results in publications and at scientific events, among other channels. Moreover, the Consortium performs regular assessments of potential risks and of the quality of output, and audited its intellectual property.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

In today’s world, one in seven people is malnourished. This situation is expected to worsen as human population keeps increasing at a staggering rate. Feeding 10–15 billion people in the year 2100 is a tremendously challenging task that will only be met by the implementation of drastic measures to increase agricultural productivity. Hence, the seed industry is seeking sustainable and economically viable solutions to increase crop yield despite numerous challenges, such as finite arable land and water resources, deleterious environmental conditions (e.g., drought, salinity), reduced availability of fertilizers, climate volatility, and depletion of soil nutrients. A fundamental way to improve plant productivity and performance is through the use of plant genomics. Along these lines, FutureAgriculture offers not an incremental improvement but rather a leap in agricultural productivity. Most other research efforts that aim to improve photosynthetic yield involve enormous implementation barriers. In contrast, FutureAgriculture’s engineering aims can be achieved within a reasonable timeframe as they are strictly genetic/metabolic and do not involve morphological or any other structural modifications. Hence, the development and implementation of synthetic photorespiration routes can transform the future of agriculture.
Furthermore, while the improvement of photosynthetic rate and yield via transgenic approaches has been a hot research topic for many years, these efforts focused on introducing existing pathways into new plant hosts. FutureAgriculture adopts a radically different approach. Rather than reshuffling and grafting existing enzymes in a fashion that resembles natural evolution and is in line with current metabolic-engineering thinking, the project systematically explores novel pathways that cannot be obtained by mixing-and-matching of existing, natural enzymes. FutureAgriculture’s approach demands the de novo engineering of new enzymes to catalyze metabolic transformations that are unknown in nature. These synthetic enzymes are integrated with existing ones to obtain entirely new pathways optimized by chemical logic, which will in turn be realized within bacteria and plants. Given the combinatorial nature of metabolic pathways, the addition of only one novel reaction dramatically expands the solution space of possible pathways, thus fully realizing the potential of synthetic biology. Yet, so far, only a handful of studies implemented synthetic pathways that harbor novel enzymes. FutureAgriculture takes this strategy to a new level by constructing de novo pathways within the very core of carbon metabolism.

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