Structure-guided secretome analysis of gall-forming microbes offers insights into effector diversity and evolution

Abstract

ABSTRACTPhytopathogens secrete effector molecules to manipulate host immunity and metabolism. Recent advances in structural genomics have identified fungal effector families whose members adopt similar folds despite sequence divergence, highlighting their importance in virulence and immune evasion. To extend the scope of comparative structure-guided analysis to more evolutionarily distant phytopathogens with similar lifestyle, we used AlphaFold2 to predict the 3D structures of the secretome from selected plasmodiophorid, oomycete, and fungal gall-forming pathogens. Clustering of protein folds based on structural homology revealed species-specific expansions and a low abundance of known orphan effector families. We identified a nucleoside hydrolase-like fold, structurally homologous to the bacterial effector HopQ1, to be conserved among various gall-forming microbes. We also identified novel sequence-unrelated but structurally similar (SUSS) effector clusters, rich in conserved motifs. Notably, ankyrin proteins were significantly expanded in gall-forming plasmodiophorids, with AlphaFold-Multimer screening revealing the MAP kinase pathway as a major target of these proteins. Altogether, this study advances our understanding of secretome landscapes in gall-forming microbes and provides a valuable resource for broadening structural phylogenomic studies across diverse phytopathogens.