Averting $220 Billion in Agricultural Losses: Scientists Uncover Method to Neutralize Detrimental Microbial Proteins

A team of researchers has deciphered the mechanism by which specific bacterial proteins, known as AvrE/DspE, induce diseases in crops by inhibiting their immune systems. Leveraging artificial intelligence predictions, the scientists not only uncovered that these proteins form channels in plant cells facilitating infections, but also found nanoparticles capable of obstructing these channels. This discovery has the potential to mitigate $220 billion in global agricultural damages annually.

The study, led by Duke University researchers, could provide a groundbreaking solution to annual losses in agriculture amounting to $220 billion.

The bacteria responsible for devastating crops and jeopardizing food security commonly utilize a similar strategy to induce illness: they inject a lethal blend of proteins directly into plant cells.

For the past quarter-century, biologist Sheng-Yang He and senior research associate Kinya Nomura have been exploring these molecules, which are responsible for diseases affecting a wide range of crops globally, including rice and apple orchards.

Due to the collaborative efforts of three distinct research groups, there may now be an effective strategy to neutralize these pathogenic molecules, shedding light on how they sicken plants.

These new findings were published on September 13 in the journal Nature.

In the He laboratory, researchers focus on AvrE/DspE, a family of injected proteins that cause diseases manifesting as brown spots in beans, bacterial specks in tomatoes, and fire blight in fruit trees, among others. These proteins have been a focal point of plant disease research ever since their initial discovery in the early 1990s. They serve as essential tools in the bacterial arsenal; their absence in a laboratory environment renders harmful bacteria innocuous. However, despite extensive research, many questions about their functionality remain.

Previously, researchers had identified various proteins in the AvrE/DspE family that suppressed plant immunity or induced the initial symptoms of infection. While they understood the sequence of amino acids constituting these proteins, the lack of information on their three-dimensional structure made their operational mechanisms elusive.

The AvrE/DspE proteins are extraordinarily large compared to typical bacterial proteins. For example, while an average bacterial protein comprises around 300 amino acids, proteins in the AvrE/DspE family consist of approximately 2000 amino acids.

To overcome this challenge, the team employed AlphaFold2, an artificial intelligence-based program launched in 2021, to predict the three-dimensional structures of these proteins.

Upon examining the AI-generated predictions, the researchers observed that all the bacterial proteins shared a similar three-dimensional shape: a diminutive mushroom with a cylindrical stem. This structure suggested a previously unknown function—piercing the plant cell membrane to initiate infection.

Further analysis revealed that the hollow interior of this cylindrical structure exhibits a particular affinity for water, supporting the hypothesis that these proteins might act as water channels.

The research team collaborated with Duke biology professor Ke Dong and postdoctoral associate Felipe Andreazza to test this theory. They found that frog eggs, engineered to produce AvrE and DspE proteins, quickly swelled and burst when exposed to water, confirming the channeling action of these proteins.

Moreover, experiments using nanoparticles called PAMAM dendrimers demonstrated their effectiveness in blocking these channels, leading to a significant reduction in pathogen concentrations in plant leaves and successfully preventing infection.

The team has filed a provisional patent for this novel approach, which offers a potentially revolutionary method to combat a wide array of plant diseases. The next phase involves a more in-depth study of how these channel-blocking nanoparticles interact with the channel proteins.

The research was financed by the National Institute of Allergy and Infectious Diseases and the National Institute of General Medical Sciences, both parts of the National Institutes of Health, as well as Duke Science and Technology, and the Howard Hughes Medical Institute.

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

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• Duke University Research Department
• Journal Nature
• AlphaFold2 Official Page
• National Institute of Allergy and Infectious Diseases
• National Institute of General Medical Sciences
• Duke Science and Technology
• Howard Hughes Medical Institute
• Provisional Patents Explained
• Global Impact of Crop Diseases