Receptor- ligand interactions in plant inmate immunity revealed by artificial intelligence AlphaFold

Authors: WANG, LI - Orise Fellow; Jia, Yulin; OSAKINA, ARON - Washington University; OLSEN, KEN - Washington University; HUANG, YIXIAO - Orise Fellow; Jia, Melissa; PONNIAH, SATHISH - University Of Arkansas At Pine Bluff; PEDROZO, RODRIGO - Orise Fellow; NICOLLI, CAMILA - University Of Arkansas; Edwards, Jeremy

Submitted to: Bio-Archives
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/12/2024
Publication Date: 6/12/2024
Citation: Wang, L., Jia, Y., Osakina, A., Olsen, K., Huang, Y., Jia, M.H., Ponniah, S., Pedrozo, R., Nicolli, C., Edwards, J. 2024. Receptor- ligand interactions in plant inmate immunity revealed by artificial intelligence AlphaFold. Bio-Archives. https://doi.org/10.1101/2024.06.12.598632.
DOI: https://doi.org/10.1101/2024.06.12.598632

Interpretive Summary: Rice blast is one of the most threatening diseases globally. Major resistance (R) genes Pi-ta, Ptr, Pi-k, and Pi-9 have been deployed once a time or in combinations in the USA in preventing infections of Magnaporthe oryzae containing the corresponding avirulence (AVR) genes. Genetic markers for these genes have been identified and used for marker assisted breeding to accelerate the speed of rice breeding. Physical interactions of products of resistance genes Pi-ta, Pik, putative proteins with Nucleotide Bind Sites Leucine Rich Repeat (NLR) type receptor protein with their cognate pathogen AVR genes, AVR-Pita, AVR-Pik were previously reported. However, molecular mechanism of recognition of the pathogen avirulence genes/effectors by host R protein is largely unclear. AlphaFold is an artificial intelligence system predicting a protein’s 3D structure from its amino acid sequence. Here we report genome sequence analyses of the effectors and avirulence genes, AVR-Pita, AVR-Pik, in 3 differential Magnaporthe oryzae races, IB49, IC17 and IE1k. Using AlphaFold2 and 3 we confirmed direct interactions of products of resistance genes Pi-ta and Pik with Magnaporthe oryzae avirulence genes, AVR-Pita, and AVR-Pik respectively, and revealed a direct interaction of R protein Pi9 with AVR-Pik. Validation of direct interactions of two pairs of R protein and AVR proteins supported direct interaction mechanism of plant innate immunity and detecting interaction of Pi-9 and with AVR-Pik revealed a new mechanism of two host resistance genes, Pik and Pi9, recognizing one pathogen AVR gene, AVR-Pik, in triggering plant innate immunity supporting the broad-spectrum nature of Pi-9 mediated blast resistance. These findings are essential for improving blast resistance using conventional and gene editing techniques.

Technical Abstract: One of the common mechanisms to trigger plant innate immunity is recognition of pathogen avirulence gene products directly by plant receptor proteins. AlphaFold is an artificial intelligence system predicting a protein’s 3D structure from its amino acid sequence. Here we report genome sequence analyses of the effectors and avirulence genes, AVR-Pita and AVR-Pik, in 3 differential Magnaporthe oryzae races. Using alpha fold 2 and 3 we confirmed direct interactions of products of resistance genes Pi-ta and Pik with Magnaporthe oryzae avirulence genes, AVR-Pita and AVR-Pik respectively, and revealed a direct interaction of R protein Pi9 with AVR-Pik. Validation of direct interactions of two pairs of R protein and AVR proteins supported direct interaction mechanism of plant innate immunity and detecting interaction of Pi-9 and with AVR-Pik revealed a new mechanism of two host resistance genes, Pik and Pi9, recognizing one pathogen AVR-Pik gene in triggering plant innate immunity supporting the broad-spectrum nature of Pi-9 mediated blast resistance.