Receptor- ligand interactions in plant inmate immunity revealed by AlphaFold protein structure prediction
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One of the common mechanisms to trigger plant innate immunity is recognition of pathogen avirulence gene products directly by products of major resistance ( R ) genes in a gene for gene manner. In the USA, the R genes, Pik-s, PiKh/m , and Pi-ta, Pi-39(t) , and Ptr genes have been effectively deployed to prevent the infections of M. oryzae races, IB49, and IC17 for some time. Pi-9 is only recently being deployed to provide overlapped and complimentary resistance to Magnaporthe oryzae races IB49, IC17 and IE1k in the USA. Pi-ta, Pi-39(t), Pi9 are major nuclear binding site-leucine rich (NLR) proteins, and Ptr is an atypical R protein with 4 armadillo repeats. AlphaFold is an artificial intelligence system that predicts a protein 3D structure from its amino acid sequence. Here we report genome sequence analyses of the effectors and avirulence ( AVR ) genes, AVR-Pita and AVR-Pik , and AVR-Pi9 , in 3 differential M. oryzae races. Using AlphaFold 2 and 3 we find strong evidence of direct interactions of products of resistance genes Pi-ta and Pik with M. oryzae avirulence ( AVR ) genes, AVR-Pita and AVR-Pik respectively. We also found that AVR-Pita interacts with Pi-39(t) and Ptr, and Pi9 interacts with both AVR-Pi9 and AVR-Pik. Validation of direct interactions of two pairs of R and AVR proteins supported a direct interaction mechanism of plant innate immunity. Detecting interaction of both Ptr and Pi39(t) with AVR-Pita, and Pi-9 with both AVR-Pi9 and AVR-Pik, revealed a new insight into recognition of pathogen signaling molecules by these host R genes in triggering plant innate immunity.