Receptor- ligand interactions in plant inmate immunity revealed by AlphaFold protein structure prediction

Abstract

AbstractOne 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, theRgenes,Pik-s, PiKh/m, andPi-ta, Pi-39(t), andPtrgenes have been effectively deployed to prevent the infections ofM. oryzaeraces, IB49, and IC17 for some time.Pi-9is only recently being deployed to provide overlapped and complimentary resistance toMagnaporthe oryzaeraces 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-PitaandAVR-Pik, andAVR-Pi9, in 3 differentialM. oryzaeraces. Using AlphaFold 2 and 3 we find strong evidence of direct interactions of products of resistance genesPi-taandPikwithM. oryzaeavirulence (AVR) genes,AVR-PitaandAVR-Pikrespectively. 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.