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Preventing $220 Billion Damage: Scientists Discover Possible Way to Disarm Mysterious Family of Microbial Proteins

Researchers have identified how certain harmful bacterial proteins, AvrE/DspE, cause diseases in crops by suppressing the plants’ immune system. Using AI predictions, the team found that these proteins create channels in plants, leading to infections, but they also discovered nanoparticles that can block these channels, effectively preventing bacteria from causing damage, which could save the global economy $220,000. millions of dollars lost annually to plant diseases. .

Researchers at Duke University may have discovered a method to neutralize them, potentially avoiding $220 billion in annual agricultural losses.

Many of the bacteria that devastate crops and threaten our food supply employ a shared tactic to induce disease: they inject a cocktail of harmful proteins directly into plant cells.

For 25 years, biologist Sheng-Yang He and his research associate Kinya Nomura have been investigating this set of molecules that plant pathogens use to cause disease in hundreds of crops around the world, from rice to apple orchards.

Now, thanks to a team effort between three collaborating research groups, they may finally have an answer to how these molecules make plants sick and a way to take them apart.

The findings appear September 13 in the journal. Nature.

Researchers in the He lab study the key ingredients in this deadly cocktail, a family of injected proteins called AvrE/DspE, which cause diseases ranging from brown spots on beans and bacterial specks on tomatoes to fire blight in the fruit trees.

Since its discovery in the early 1990s, this family of proteins has been of great interest to those studying plant diseases. They are key weapons in the bacterial arsenal; Eliminating them in a laboratory renders otherwise dangerous bacteria harmless. But despite decades of efforts, many questions about how they work remain unanswered.

Researchers had identified a number of AvrE/DspE family proteins that suppressed the plant’s immune system or caused dark, water-soaked spots on a plant’s leaves – the first telltale signs of infection. They even knew the underlying sequence of amino acids that joined together to form proteins, like beads on a thread. But they didn’t know how this chain of amino acids folded into a three-dimensional shape, so they couldn’t easily explain how they worked.

Part of the problem is that the proteins in this family are huge. While a average bacterial protein could be 300 amino acids long; There are 2000 proteins in the AvrE/DspE family.

Researchers have searched for other proteins with similar sequences for clues, but none with known functions turned up.

“They are strange proteins,” he said.

So they turned to a computer program released in 2021 called AlphaFold2, which uses artificial intelligence to predict what 3D shape a given chain of amino acids will take.

Computer-generated 3D maps of a bacterial protein called DspE

Computer-generated 3D maps of a bacterial protein called DspE reveal its straw-like shape. Credit: Duke University

Researchers knew that some members of this family help bacteria evade the plant’s immune system. But their first look at the proteins’ three-dimensional structure suggested an additional function.

“When we first looked at the model, it looked nothing like what we had thought,” said study co-author Pei Zhou, a professor of biochemistry at Duke whose lab contributed to the findings.

The researchers looked at AI predictions for bacterial proteins that infect crops such as pears, apples, tomatoes and corn, and they all pointed to a similar 3D structure. They seemed to fold into a small mushroom with a cylindrical stem, like a straw.

The predicted shape matched well with images of a bacterial protein that causes fire blight disease in fruit trees that were captured using a cryo-electron microscope. From top to bottom, this protein looked a lot like a hollow tube.

This got the researchers thinking: Maybe bacteria use these proteins to punch a hole in the plant’s cell membrane, to “force the host to drink” during infection, He said.

Once bacteria enter the leaves, one of the first areas they encounter is a space between cells called the apoplast. Normally, plants keep this area dry to allow gas exchange to photosynthesis. But when bacteria invade, the inside of the leaf becomes flooded, creating a moist, welcoming haven for them to feed and multiply.

Closer examination of the predicted 3D model for the fire blight protein revealed that while the exterior of the straw-like structure is water-resistant, its hollow inner core has a special affinity for water.

To test the water channel hypothesis, the team joined forces with Duke biology professor Ke Dong and co-senior author Felipe Andreazza, a postdoctoral associate in his lab. They added gene readouts for the bacterial proteins AvrE and DspE to frog eggs, using the eggs as cellular factories to produce the proteins. The eggs, placed in a dilute saline solution, swelled quickly and burst with too much water.

The researchers also tried to see if they could disarm these bacterial proteins by blocking their channels. Nomura focused on a class of small spherical nanoparticles called PAMAM dendrimers. These dendrimers, used for more than two decades in drug delivery, can be manufactured to precise diameters in a laboratory.

“We were playing with the hypothesis that if we found the right diameter chemical, maybe we could block the pore,” he said.

After testing particles of different sizes, they identified one that they thought might be the right size to block the water channel protein produced by the fire blight pathogen, Erwinia amylovora.

They took frog eggs designed to synthesize this protein and sprayed them with PAMAM nanoparticles, and water stopped flowing into the eggs. They didn’t swell.

They also treated Arabidopsis plants infected with the pathogen Pseudomonas syringae, which causes bacterial spot. The channel-blocking nanoparticles prevented bacteria from establishing themselves, reducing pathogen concentrations in the plants’ leaves by 100-fold.

The compounds were also effective against other bacterial infections. The researchers did the same thing with pears exposed to the bacteria that cause fire blight disease, and the fruits never developed symptoms—the bacteria didn’t make them sick.

“It was a long shot, but it worked,” he said. “We’re excited about this.”

The researchers said the findings could offer a new line of attack against many plant diseases.

plants produce 80% of the food we eat. And yet more than 10% of global food production (crops such as wheat, rice, corn, potatoes and soybeans) is lost every year due to plant pathogens and pests, costing the global economy an enormous amount. $220 billion.

The team has filed a provisional patent on this approach.

The next step, said Zhou and co-author Jie Cheng, Ph.D. student in Zhou’s lab, is to discover how this protection works, getting a more detailed look at how channel-blocking nanoparticles and channel proteins interact.

“If we can visualize those structures, we can understand them better and create better designs for crop protection,” Zhou said.

Reference: “Bacterial pathogens supply water- and solute-permeable channels to plant cells” by Kinya Nomura, Felipe Andreazza, Jie Cheng, Ke Dong, Pei Zhou and Sheng Yang He, September 13, 2023. Nature.
DOI: 10.1038/s41586-023-06531-5

The study was funded by the National Institute of Allergy and Infectious Diseases and the National Institute of General Medical Sciences, both in the National Institutes of HealthDuke Science and Technology and the Howard Hughes Medical Institute.

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