Biologists Use Genetic Circuits to Program Plant Roots

When the physicist Richard Feynman died in 1988, he left a note on his blackboard that read, “What I cannot create, I do not understand.” Feynman may have been reflecting on the nature of scientific understanding, but the sentiment also reflects the spirit of synthetic biology. That scientific field is all about deconstructing and precisely manipulating biological processes to test our grasp of them.

“Everyone in synthetic biology loves that quote,” said Patrick Shih, a synthetic plant biologist at the University of California, Berkeley. “It’s pretty much the central tenet.”

New work in plants marks an important advance toward realizing synthetic biology’s most ambitious goals. A study published last month in Science created a kind of genetic circuit in plant roots, in effect programming how they grow. Stanford University researchers, led by Jennifer Brophy, a bioengineer, and José Dinneny, a plant systems biologist, developed a genetic toolkit to control whether the root systems of two plant species grew more laterally or horizontally and how much the roots branched. Their work confirms genetic models of plant growth and shows for the first time that it’s possible to program functional patterns of gene activity over time in specific tissues of complex organisms.

The new genetic toolkit should be very useful to other synthetic biologists in their own future experiments. However, the results of the researchers’ experiments weren’t as straightforward as Brophy and her colleagues had hoped, showing the challenges of applying digital logic gates to messy living systems.

Rewiring Root Growth

Although synthetic biologists have been inserting genetic control systems into bacteria and cultured complex cells for about two decades, technical issues have made it much harder for them to do this with complex multicellular organisms like plants. So to construct their biological circuit, Brophy, Dinneny and their coworkers assembled and refined a suite of molecular tools, including pieces of modified viruses and of bacteria that cause tumors in plants. Synthetic biologists often create the techniques and genetic elements they need as one-offs for specific organisms and experiments, but the Stanford team was more interested in assembling a general-purpose toolkit that can be adapted for different organisms as needed.

With this customizable toolkit, the researchers tailored genetic circuits to their specific organisms. In this case, they used two popular model organisms — Arabidopsis thaliana, a relative of mustard plants, and Nicotiana benthamiana, a cousin of tobacco.

The researchers created synthetic promoter elements that, like on/off switches, would bind to various targeted genes involved in root growth and activate them. They then linked these control elements to one another like Boolean logic gates in a programmable circuit. The controls enabled the researchers to recruit the plant’s own proteins to drive — or inhibit — root growth.

They made the plants express a wide range of programmed root variation, from a sprawling spider web of root hairs to a single, long taproot. Their goal was to demonstrate flexible control, rather than to produce a specific desired result. “It’s a proof of concept,” said Olivier Martin, a researcher at the French National Research Institute for Agriculture, Food and Environment who was not involved in the new research.

Control over the growth of root systems could be revolutionary for agriculture, especially in drought-stricken regions, where life may become more dire with ongoing climate change. Crops could be programmed to grow shallow root systems to quickly soak up heavy but infrequent rains, or to send their roots straight down and keep them closely packed together to avoid infringing on a neighbor’s space.

The applications aren’t limited to agriculture. Plants are “nature’s chemists,” Martin said. “They produce an incredible diversity of compounds.” Harnessing that ability through synthetic biology could enable researchers to produce new pharmaceuticals at a large scale.

Fighting Inconsistency

But the fruits of synthetic plant biology aren’t ready to hit the farmers market or drugstore shelves just yet. Even though most of the plants in the Stanford experiments behaved in accordance with their programming, their gene expression was not quite as black and white as the researchers had hoped. “Even calling it Boolean or digital is tough because the ‘off’ states are not completely off, and the ‘on’ states are relative,” Brophy said.

In the roots, an “off” state was indicated by a complete root cap, a layer of cells on the tip of a root tendril that prevents further growth. “On” states were simply defined by the presence of a root or rootlet. But the researchers observed that some roots in the “off” state only developed a partial root cap — enough to stop growth after a certain point, but not enough to prevent it altogether. These aberrant expressions cropped up most often when the team applied a logic gate developed for the Nicotiana to an Arabidopsis plant; they tended to disappear after the toolkit was tweaked for Arabidopsis genes.

Although this kind of partial expression adds to the challenges that synthetic biology faces, Shih said that it might have advantages too: It may make plants easier subjects for experimental tests than animals since partial gene expression in animals is often less obvious (and more fatal).

Devang Mehta, a systems biologist at the University of Alberta in Canada who was not involved in the study, calls Brophy and Dinneny’s research a “big step forward” in organismal synthetic biology. However, he cautions that we shouldn’t underestimate how challenging the next step will be.

“Things like Boolean logic in particular are very useful in contained environments, where you can really control environmental variables,” said Mehta. “This is a lot harder to do in a natural environment.”

That’s because plants and other living things are highly responsive to their environment in ways that computers aren’t, which complicates the challenge of programming them with reliable genetic circuits. Brophy contrasts them to a calculator, for which 2 plus 2 equals 4 every time. “It would be problematic if 2 plus 2 equaled 3 when it was cold, and 5 when it was too bright,” she said. To implement a Boolean gene circuit in crops like corn or wheat growing in a field, synthetic biologists must either devise a way to control the weather or, more realistically, prevent the plants from responding as strongly to heat, cold and rain.

“That’s an important limitation that the field needs to be very upfront about,” Shih said. He sees Brophy and Dinneny’s work as a preliminary road map for addressing this challenge. “Now we can see which [tools] work, and which ones don’t.”

Editors note: As an HHMI-Simons Faculty scholar, Dinneny has received funding from the Simons Foundation, which also supports Quanta, this editorially independent magazine of science journalism.