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Alphafold-multimer predicts cross-kingdom interactions at the plant-pathogen interface
Open accessPreprint — published as 10.1038/s41467-023-41721-9 · Paper page
Abstract
Adapted plant pathogens from various microbial kingdoms produce hundreds of unrelated small secreted proteins (SSPs) with elusive roles. Some of these SSPs might be inhibitors targeting the most harmful hydrolases secreted by the host. Here, we used Alphafold-Multimer (AFM) to screen 1,879 SSPs of seven tomato pathogens for interacting with six defence-related hydrolases of tomato that accumulate to high levels in the apoplast during infection. This screen of 11,274 protein pairs identified 15 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 tomato pathogens Cladosporium fulvum and Fusarium oxysporum , respectively. Together with a novel P69B inhibitor from the bacterial pathogen Xanthomonas perforans and the previously reported Kazal-like inhibitors of the oomycete pathogen Phytophthora infestans , P69B emerges as an important effector hub targeted by different microbial kingdoms, consistent with the presence of a hyper-variant residue in P69B orthologs and gene duplication and diversification of P69B paralogs that could avoid inhibitor binding. This study demonstrates the power of artificial intelligence to accurately predict novel cross-kingdom interactions at the plant-pathogen interface.
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Highly accurate protein structure prediction with AlphaFold
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Metadata
- Authors
- Homma, F., Huang, J., & van der Hoorn, R. A. L.
- Affiliations
- University of Oxford (GB)
- Corresponding author
- van der Hoorn, Renier A. L.
- Venue
- Nature Communications
- Publisher
- openRxiv
- Published
- 2023-04-04
- Volume
- 14
- Issue
- 1
- Pages
- 6040-6040
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC10533508
- OpenAlex
- W4387090137
- Cited by
- 176
- References
- 1
- Citations by year
- 2026: 68 · 2025: 64 · 2024: 38 · 2023: 6
- FWCI
- 27.65
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- University of Oxford
- Guangxi University
- Biotechnology and Biological Sciences Research Council (101019324, ERC-AdG-2019, DDT00060)
- Clarendon Fund
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant-Microbe Interactions and Immunity
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Pathogenic Bacteria Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Pathogens and Fungal Diseases
- Keywords
- AlphaFold-Multimer, small secreted proteins, plant-pathogen interaction, tomato pathogens, chitinase inhibitors, protease inhibitors, Phytophthora infestans, Cladosporium fulvum, Fusarium oxysporum, Xanthomonas perforans, cross-kingdom interactions, protein-protein interaction prediction
- MeSH terms
- Artificial Intelligence, Peptide Hydrolases, Endopeptidases, Plant Diseases, Plant Proteins, Solanum lycopersicum
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