Scientists Unveil Promising Method to Mitigate $220 Billion in Damages Caused by Enigmatic Microbial Proteins

Researchers at Duke University may have uncovered a method to neutralize plant-damaging bacteria, potentially preventing annual agricultural losses of up to $220 billion. Many bacteria that harm crops and pose a threat to our food supply employ a common strategy: they inject a mix of harmful proteins directly into plant cells. For a quarter-century, biologist Sheng-Yang He and his senior research associate Kinya Nomura have delved into this group of molecules used by plant pathogens to cause diseases in numerous crops, from rice to apple orchards. Now, thanks to a collaborative effort involving three research groups, they may have finally unraveled how these molecules make plants sick and found a way to disarm them. These findings were published in the journal Nature on September 13.

In the He lab, researchers have been studying crucial components of this harmful protein cocktail known as AvrE/DspE, which leads to diseases like brown spots in beans, bacterial specks in tomatoes, and fire blight in fruit trees. Since their discovery in the early 1990s, these proteins have intrigued scientists studying plant diseases. They serve as essential weapons in the bacterial arsenal, with their elimination in a lab rendering otherwise dangerous bacteria harmless. However, despite decades of effort, many questions about their functioning remained unanswered.

Scientists had identified several proteins in the AvrE/DspE family that suppressed the plant’s immune system or caused dark water-soaked spots on plant leaves—the initial signs of infection. They even knew the sequence of amino acids that linked together to form these proteins, akin to beads on a string. However, they couldn’t determine how this string of amino acids folded into a 3D shape, making it difficult to explain their mode of action. One challenge was that these proteins were exceptionally large, with AvrE/DspE-family proteins being around 2000 amino acids long, far larger than the average bacterial protein at 300 amino acids.

To unravel the mystery, researchers turned to a computer program called AlphaFold2, released in 2021, which employs artificial intelligence to predict the 3D shape formed by a given string of amino acids. The initial glimpse at the predicted 3D structure suggested an unexpected role for these proteins beyond their known functions in evading the plant’s immune system.

The AI predictions for bacterial proteins that infect crops such as pears, apples, tomatoes, and corn all indicated a similar 3D structure—a tiny mushroom with a cylindrical stem, resembling a straw. This led researchers to speculate that bacteria might use these proteins to create openings in plant cell membranes, effectively “forcing the host to take a drink” during infection.

Further investigation of the predicted 3D model for the fire blight protein revealed that while the outside of the straw-like structure was water-resistant, its hollow inner core had a particular affinity for water. To test this water channel hypothesis, researchers used frog eggs as cellular factories to synthesize the bacterial proteins AvrE and DspE. When these eggs were placed in a dilute saline solution, they rapidly swelled and burst due to excessive water intake.

Researchers also explored the possibility of disarming these bacterial proteins by blocking their channels. They experimented with PAMAM dendrimers, tiny spherical nanoparticles used in drug delivery. By testing different-sized particles, they identified one that seemed to be the right size for blocking the water channel protein produced by the fire blight pathogen, Erwinia amylovora. When frog eggs engineered to produce this protein were exposed to PAMAM nanoparticles, water influx was stopped, and the eggs did not swell.

Additionally, the researchers applied the channel-blocking nanoparticles to Arabidopsis plants infected with the pathogen Pseudomonas syringae, responsible for bacterial speck. These nanoparticles effectively prevented the bacteria from establishing themselves, reducing pathogen concentrations in the plant leaves by 100-fold. The compounds also proved effective against other bacterial infections. When pear fruits were exposed to the bacteria causing fire blight disease, they did not develop symptoms; the bacteria failed to infect them.

This breakthrough could open up a new approach to combating various plant diseases. As plants account for 80% of the world’s food production, addressing the issue of crop loss due to pathogens and pests, which amounts to over 10% of global food production, is of immense significance, costing the global economy billions.

The research team has filed a provisional patent for this approach. The next step involves gaining a more detailed understanding of how the protection works by examining the interaction between the channel-blocking nanoparticles and the channel proteins. By visualizing these structures, scientists hope to develop more effective strategies for protecting crops.

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