Synthetic gene circuits could help plants adapt to climate change

Increasingly, global food production is threatened by the effects of climate change. As floods, droughts and extreme heat waves become more frequent, crops need to be able to adapt faster than ever.

Stanford University researchers are working on ways to manipulate biological processes in plants to help them grow more efficiently under a variety of conditions. Jennifer Brophy, assistant professor of bioengineering, and her colleagues have designed a series of synthetic genetic circuits that allow them to control the decisions made by different types of plant cells. In a recent article published in Science, they used these tools to grow plants with modified root structures. Their work is the first step in designing crops better able to harvest water and nutrients from the soil and provides a framework for designing, testing and improving synthetic genetic circuits for other applications in plants.

“Our synthetic genetic circuits are going to allow us to build very specific root systems or very specific leaf structures to see what’s optimal for the harsh environmental conditions we’re experiencing,” Brophy said. “We are making plant engineering much more precise.”

A programming code for plants

Today’s genetically modified crop varieties use relatively simple and imprecise systems that cause all their cells to express the genes needed to, for example, resist herbicides or pests. To achieve large-scale control of plant behavior, Brophy and his colleagues built synthetic DNA that essentially functions like computer code with logic gates guiding the decision-making process. In this case, they used these logic gates to specify which cell types expressed certain genes, allowing them to adjust the number of branches in the root system without changing the rest of the plant.

The depth and shape of a plant’s root system affects its efficiency in extracting different resources from the soil. A shallow root system with many branches, for example, better absorbs phosphorus (which stays close to the surface), while a deeper root system that branches at the bottom absorbs water and nitrogen better. Using these synthetic genetic circuits, researchers were able to grow and test various root designs to create the most effective crops under different circumstances. Or, in the future, they could give factories the ability to optimize.

“We have modern varieties of crops that have lost their ability to respond to where the nutrients in the soil are,” said José Dinneny, associate professor of biology in the School of Humanities and one of the leading authors of the article. “The same type of logic gates that control root branching could be used to, for example, create a circuit that takes into account both nitrogen and phosphorus concentrations in the soil and then generates an optimal output for those terms.”

From model organisms to modern cultures

Brophy has designed over 1,000 potential circuits to be able to manipulate gene expression in plants. She tested them in the leaves of tobacco plants, to see if she could get the leaf cells to create a phosphorescent protein found in jellyfish. She found 188 models that worked, which the researchers upload to a synthetic DNA database for other scientists to use in their work.

Once they had working designs, the researchers used one of the circuits to create logic gates that would alter the expression of a specific developmental gene in a precisely defined type of root cell. Arabidopsis thaliana, a small weed plant often used as a model organism. By changing the level of expression of this gene, they were able to alter the density of branches in the root system.

Now that they have demonstrated they can modify the growth structure of a model organism, the researchers plan to apply these same tools to commercial crops. They are investigating the possibility of using their genetic circuits to manipulate the root structure of sorghum, a plant that can be refined into biofuel, to help it absorb water and perform photosynthesis more efficiently.

“Climate change is altering the agricultural conditions in which we grow the plants we depend on for food, fuels, fiber and raw materials for medicine,” Brophy said. “If we are not able to produce these plants on a large scale, we will face many problems. This work aims to ensure that we will have varieties of plants that we can grow, even if the environmental conditions in which we grow them become less favorable.

Reference: Brophy JAN, Magallon KJ, Duan L, et al. Synthetic genetic circuits as a means of reprogramming plant roots. Science. 2022;377(6607):747-751. doi: 10.1126/science.abo4326

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