Synthetic genetic circuits could help plants adapt to climate change

Global food production is increasingly threatened by the effects of climate change. With floods, droughts and extreme heat waves becoming 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 and effectively under a variety of conditions. Jennifer Brophy, an assistant professor of bioengineering, and her colleagues have designed a series of synthetic genetic circuits that allow them to control the decisions of different types of plant cells. In a recently published article in Science, they used these tools to grow plants with altered root structures. Their work is the first step in designing crops that are better able to extract 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 circuitry will allow us to build very specific root systems or very specific leaf structures to see what is optimal for the challenging environmental conditions we know are coming,” Brophy said. “We’re making factory engineering much more precise.”

A programming code for plants

Current genetically modified crop varieties use relatively simple, imprecise systems that ensure that all their cells express the genes necessary to resist herbicides or pests, for example. To gain precise control over plant behavior, Brophy and her colleagues built synthetic DNA that essentially works like computer code with logic gates guiding the decision-making process. In this case, they used those logic gates to indicate which types of cells were expressing certain genes, allowing them to adjust the number of branches in the root system without altering the rest of the plant.

The depth and shape of a plant’s root system influence how efficient it is at extracting various resources from the soil. For example, a shallow root system with many branches is better at absorbing phosphorus (which remains at the surface), while a deeper root system with branches is better able to absorb water and nitrogen. Using these synthetic genetic circuits, researchers were able to grow and test different root designs to create the most efficient crops for different conditions. Or they can give plants the opportunity to optimize themselves in the future.

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

From model organisms to modern crops

Brophy designed more than 1,000 potential circuits to manipulate gene expression in plants. She tested them in the leaves of tobacco plants to see if she could make the leaf cells make a glow-in-the-dark protein found in jellyfish. She found 188 designs that worked, which the researchers uploaded 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 of Arabidopsis thaliana, a small, weed-like plant often used as a model. organism. By changing the expression level of that one gene, they were able to change the density of branches in the root system.

Now that they have shown that they can change the growth structure of a model organism, the researchers want to apply the same tools to commercial crops. They are exploring the possibility of using their genetic circuitry to manipulate the root structure in sorghum, a plant that can be refined into biofuel, to help it absorb water and carry out photosynthesis more efficiently.

“Climate change is changing 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 can’t grow those plants to scale, we’re going to have a lot of problems. This work should ensure that we have plant varieties that we can grow even if the environmental conditions we grow them in become less favorable.”

Other Stanford co-authors of this study include research technicians Katie J. Magallon and Kiril Kniazev, research associate Lina Duan, postdoctoral scientist Prashanth Ramachandran and graduate student Vivian Zhong. Dinneny is also a member of Stanford Bio-X.