Deciphering the genomic and functional basis of virulence and immune modulation in Pantoea stewartii

Pantoea stewartii subsp. indologenes is an emerging cereal phytopathogen with unclear virulence mechanisms. We sequenced a rice seed-borne strain, HR3-48, and classified it as P. stewartii subsp. indologenes (Pnsi) through phylogeny of 92 housekeeping genes, ANI (> 99%), and dDDH (> 96%) comparisons. HR3-48 harbors a conserved plant-pathogenic PSI-1 type III secretion system (T3SS) and a single flagellar locus (flag-1) with multiple fliC genes. The tandem fliC456 cassette is functionally redundant for motility and flagellum assembly but contributes significantly to eliciting plant immune responses in Nicotiana benthamiana. The T3SS structural gene hrcQ-U determines hypersensitive response (HR) induction. HR3-48 causes necrosis in maize and rice, a phenotype primarily reliant on T3SS. The flagellin-derived epitope flg22^PanM, a key polymorphism of L19M, triggered robust reactive oxygen species (ROS) production and inhibited Pst DC3000-induced HR in N. benthamiana, whereas flg22^PanE (L19E) showed weak or no activity in these early immune assays, indicating that the 19^th residue dictates the specificity of plant immune recognition. Both peptides suppress Arabidopsis seedling growth. Collectively, our data indicate that PSI-1 T3SS in Pnsi HR3-48 is a major virulence determinant in cereal hosts, whereas polymorphic flagellins modulate MTI (MAMP-triggered immunity) outputs and motility of HR3-48, with the 19^th residue of flg22 contributing to differential immune perception. It remains unclear how immune suppression is mediated by effectors.