Programming Plants To Fight Pathogens

Modern agriculture uses enormous quantities of pesticides and fungicides, which can negatively impact the environment and people. Finding ways to boost the immune responses of plants against pathogens could help us use fewer chemicals on farms.

RIKEN researchers have discovered a key component of plant immunity that could unlock the possibility of programming their immune response to target specific pathogens, including economically important pests¹.

But the RIKEN team wasn't initially thinking of engineering the immune responses of plants.

"When we started, we wanted to characterize the immune receptors that are unique to each plant species," says Bruno Pok Man Ngou, a postdoctoral researcher at the RIKEN Center for Sustainable Resource Science.

Since immune receptors vary a lot between species, Ngou was interested in studying diverse plant species in addition to the usual model species used in labs. "I started with the idea that we can discover new things in the plants that we see outside all the time," he says.

The team focused on a specific class of immune receptors, the proteins that recognize and bind to molecules from pathogens and activate the immune response.

For a plant to mount an immune response to a pathogen, the first, crucial step is detecting the pathogen. "That's the immune receptor's job," says Ngou. The team surveyed the genomes of 350 plant species and found more than 13,000 genes that code for immune receptors. They grouped the receptors into clusters based on which molecules they bound, then selected 210 genes from relatively large subgroups. These represented a significant fraction of the receptors.

The researchers then screened those genes to determine those that encode for immune receptors that bind to Agrobacterium tumefaciens, the bacterium that causes crown gall disease. Seven of the genes did, and the team selected one of them-a gene from the tree of the citrus fruit pomelo-for further investigation.

Getting specific

Having found a gene that codes for the receptor that binds to molecules from the crown gall bacterium, the team set out to understand how it recognizes those molecules.

First, they had to identify the molecule it recognized, which turned out to be a cold-shock protein-a protein involved in imparting tolerance to the cold and is found in bacteria, fungi, plants and animals.

Next, they sought to discover how the receptor recognizes the cold-shock protein. By comparing this receptor with another that also binds to a cold-shock protein, the researchers identified the region of the proteins that the receptors specifically recognized. Further experiments revealed the key sites in that region that are specific to each species-that is, how receptors recognize cold-shock proteins from specific pathogens.

"Those positions can be unique to a specific organism," explains Ngou. "Each pathogen will have a combination of specific signatures there. It could be specific to a particular pathogen or to a class of pathogens, which makes it a pretty good target."

Based on this, the team determined the precise mechanism by which the receptor recognizes and binds to the cold-shock protein.

This discovery unlocked an unexpected ability: custom designing a receptor that recognizes molecules from a specific pathogen.

The researchers looked for pathogens that are economically threatening and that have cold-shock proteins. They engineered a version of the receptor that recognizes cold-shock proteins from root-knot nematodes and several pathogenic bacteria. Another engineered version responds to molecules from filamentous soil fungi and false smut fungi, as well as from certain pathogenic bacteria.

Field trials

While the technology is exciting, the researchers haven't yet gone any further than molecular experiments in the lab. The next step is to test how effective the technology is in plants. The researchers also need to figure out how strongly the gene should be expressed: too little and it won't help the plant, too strongly and it could lead to autoimmunity or other yield-reducing side-effects.

"There's a very fine balance between how many immune receptors there should be, how strongly they should be expressed and where they should be expressed," says Ngou. "There are many considerations and also a lot of field-related work that goes into testing the best way to roll something like this out."

The researchers aren't limiting themselves to working with this receptor; they're planning to repeat the screen with molecules from other pathogens to find and characterize new receptors.

"We want to try screens with as many pathogens as possible," says Ngou. "We want to test other pathogenic bacteria, fungi and even insects. Provided we can get an extract from the organism, we can do the screening."

They're also working to expand their library so that they can cast a broader net, in keeping with Ngou's original motivation. "There are many unknown receptors out there," he says. "The more scientists know about them, the more they can be used to help protect crops."

In the long term, the team hopes to catalog as many receptors as possible, targeting different types of molecules and covering different pathogens. These could be used to engineer plants to recognize pathogens they haven't evolved resistance against, which could reduce the need for pesticides.

"The end goal is to provide the crops with a better immune sensing system," says Ngou.

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References

• 1. Ngou, B. P. M., Wyler, M., Schmid, M. W., Suzuki, T., Albert, M., Dohmae, N., Kadota, Y. & Shirasu, K. Systematic discovery and engineering of synthetic immune receptors in plants. Science 389, eadx2508 (2025). doi: 10.1126/science.adx2508

About the researcher

Bruno Pok Man Ngou