A Synthetic Metabolism Approach For Boosting Plant Yields

In “An Essay on the Principle of Population”, published in 1798, Thomas Malthus put forward his famous population trap concept, postulating the end of human population growth due to a shortage of food supply. Since then, we have made a rather good job of postponing the inevitable.

The Haber-Bosch process, developed at the beginning of the 20^th century, provided an unlimited amount of nitrogen fertilizer. The Green Revolution, in the middle of the last century, boosted agricultural yields worldwide by adopting high-yielding plant variants, employing chemical fertilizers, and introducing novel cultivation techniques. Between 1960 and 2010, agricultural yields kept increasing steadily; for example, the average increase in the yield of wheat during this period was ~170%.

However, to feed a global population of ~10 billion by the year 2050, this rate of yield increase is not enough. This insufficiency is further compounded by the environmental costs of extending arable land at the expense of natural habitats and by the continuous erosion of food security as a result of climate change, food distribution inequality, redistribution of agricultural products to other industries (e.g. biofuels), and socio-economic instability.

To avoid global famine we need to drastically enhance agricultural yield within a relatively short time. As the old methods of increasing agricultural productivity seem to approach their limit, such a yield boost can only be realized by manipulating processes which have remained largely untouched until now. The most important of these is the conversion of intercepted light into plant biomass, a process that currently operates at a low efficiency of ~2%.

It might be surprising that such a central process is so inefficient; it might also be surprising that we can improve a process that is expected to be under the immense selective pressure of hundreds of millions of years. However, one needs to remember that the conditions we use for agricultural cultivation are quite different from those plants experience in nature. Natural selection was unlikely to increase yields under the cozy conditions we provide and instead most probably improved growth under the stressful, resource-limited conditions found in nature. Moreover, evolution, working as a tinkerer, is constrained to a rather small number of components, the optimization of which has its limits. On the other hand, we, as engineers, can consider solutions that could not be easily evolved but which can boost productivity under specifically-controlled conditions.

Following this concept, several synthetic biology projects in recent years were able to increase plant yield by optimizing either the “light reactions” –a synthesis of the energy storage molecules ATP and NADPH from light – or the “dark reactions” – fixation of carbon dioxide into organic matter using ATP and NADPH. This success is very encouraging but we can probably do even better. So far, engineering efforts were focused on modifying the activity of a small set of existing components or on grafting naturally occurring metabolic pathways into plants. However, given the combinatorial nature of biological processes, the addition of only one novel component can dramatically expand the solution space, thus fully realizing the potential of synthetic biology.

To put it in more concrete terms, if we do not limit our engineering to existing enzymatic activities, and instead consider also metabolic conversions that are not supported by known enzymes, we can fully tap into the (bio)chemical solution space and identify the best pathway to boost carbon fixation. To realize such an innovative solution, we need to combine the field of enzyme engineering with that of metabolic engineering, integrated to offer a “synthetic metabolism” approach.

One of the metabolic processes that severely limits the efficiency of carbon fixation is photorespiration. Photorespiration is responsible for recycling the waste byproduct 2-phosphoglycolate, which is generated by an unproductive reaction of Rubisco – the key carbon-fixing enzyme – with oxygen. Despite having an essential metabolic task, native photorespiration is inefficient in its energy consumption, and, most importantly, by releasing CO₂ which directly counteracts carbon fixation. Previous studies, limited to existing enzymes and metabolic pathways, demonstrated that a metabolic rewiring of photorespiration towards better resource utilization and CO₂ recycling can boost carbon fixation and photosynthesis. However, in all of these previous efforts, CO₂ was released just as within native photorespiration.

To truly minimize the adverse effects of photorespiration, we need to prevent the counterproductive release of CO₂. However, this is not possible using only existing enzymes and pathways.

Therefore, in the Future Agriculture project, funded by the European Commission under the FET Open program, we aim to apply a “synthetic metabolism” approach towards solving the problem of photorespiration. We started with an in silico study to identify promising metabolic pathways, composed of both known and new-to-nature reactions, that can replace photorespiration without releasing CO₂. Using a computational model, we showed that the newly-identified synthetic routes could potentially enhance carbon fixation rate across the physiological range of irradiation and CO₂. In the in vitro component, we applied enzyme engineering techniques to evolve enzymes to catalyze the new reactions of one of the promising pathways. Specifically, we engineered two novel enzymes that together convert the photorespiratory intermediate glycolate into a compound called glycolaldehyde, which can be assimilated into the carbon fixation process using existing enzymes and without carbon loss.

By combining the engineered enzymes with the existing ones in a test-tube, we were able to demonstrate the conversion of glycolate into ribulose 1,5-bisphosphate – the substrate of Rubisco – thus showing that photorespiration can be bypassed without the loss of carbon. That is not, of course, the end of the story. We are currently working on the in vivo implementation of the pathway. First, we intend to implement the pathway in the model bacterium Escherichia coli so we can test and optimize its activity within a host that can be manipulated easily. The pathway will be then expressed in cyanobacteria – the simplest photosynthetic organism – to test its effect on carbon fixation. Finally, the pathway will be implemented in higher plants and growth phenotypes will be monitored, hopefully achieving a substantial increase in photosynthesis and yield.

The FutureAgriculture project thus provides a first indication that a “synthetic metabolism” approach – integrating enzyme engineering with metabolic engineering – can rewrite one of nature’s most central processes and offer improvements which are impossible using existing enzymes and pathways. As the field keeps progressing, we are bound to witness the emergence of “synthetic metabolism” as a vital tool breaching the boundaries of nature.

These findings are described in the article entitled Daring metabolic designs for enhanced plant carbon fixation, recently published in the journal Plant Science, and in the article entitled Design and in vitro realization of carbon-conserving photorespiration, recently published in the Proceeding of National Academy and Science.

This work was conducted by Arren Bar-Even from the Max Planck Institute of Molecular Plant Physiology, Dan Tawfik from the Weizmann Institute of Science, and Tobias Erb from the Max Planck Institute of Terrestrial Microbiology.

References:

1. Design and in vitro realization of carbon-conserving photorespiration, PNAS
2. Daring metabolic designs for enhanced plant carbon fixation, Plant Science https://linkinghub.elsevier.com/retrieve/pii/S0168945217310312)
3. Synthetic metabolism: metabolic engineering meets enzyme design, Current Opinion in Chemical Biology https://linkinghub.elsevier.com/retrieve/pii/S1367593116302071)
4. FutureAgriculture project website: http://www.futureagriculture.eu/