AlphaFold-Multimer predicts cross-kingdom interactions at the plant-pathogen interface

Felix Homma, Jie Huang and Renier A. L. van der Hoorn ()
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Felix Homma: University of Oxford
Jie Huang: University of Oxford
Renier A. L. van der Hoorn: University of Oxford

Nature Communications, 2023, vol. 14, issue 1, 1-13

Abstract: Abstract Adapted plant pathogens from various microbial kingdoms produce hundreds of unrelated small secreted proteins (SSPs) with elusive roles. Here, we used AlphaFold-Multimer (AFM) to screen 1879 SSPs of seven tomato pathogens for interacting with six defence-related hydrolases of tomato. This screen of 11,274 protein pairs identified 15 non-annotated SSPs that are predicted to obstruct the active site of chitinases and proteases with an intrinsic fold. Four SSPs were experimentally verified to be inhibitors of pathogenesis-related subtilase P69B, including extracellular protein-36 (Ecp36) and secreted-into-xylem-15 (Six15) of the fungal pathogens Cladosporium fulvum and Fusarium oxysporum, respectively. Together with a P69B inhibitor from the bacterial pathogen Xanthomonas perforans and Kazal-like inhibitors of the oomycete pathogen Phytophthora infestans, P69B emerges as an effector hub targeted by different microbial kingdoms, consistent with a diversification of P69B orthologs and paralogs. This study demonstrates the power of artificial intelligence to predict cross-kingdom interactions at the plant-pathogen interface.

Date: 2023
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DOI: 10.1038/s41467-023-41721-9

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