Comparative Transcriptomic Profile Reveals Candidate Genes Manipulated by Type III Effectors of <i>Pantoea agglomerans</i> pv. <i>betae</i> Leading to Gall Formation in Beet

<i>Pantoea agglomerans</i> pv. <i>betae</i> (<i>Pab</i>) induces tumor-like galls in beet and gypsophila, a process mediated by the secretion of effector proteins via <i>Pab</i>'s type III secretion system (T3SS). This study delves into the cellular architecture and transcriptional profile of <i>Pab</i>-mediated galls, comparing host responses with wild-type <i>Pab</i> and a T3SS-inactive mutant, <i>hrcC</i>^-. Morphological analysis using scanning electron microscopy and cross-sectional visualization of infected beet leaf tissues revealed that <i>Pab</i>-induced gall-like structures are linked to cell hyperplasia and tissue ruptures, contingent on T3SS activity. Comparative transcriptome analysis of wild-type <i>Pab</i> and <i>hrcC</i>^- <i>Pab</i>-infected beet leaves at 12 and 48 h unveiled significant transcriptional reprogramming, with nearly 2,000 differentially expressed genes at 48 h postinoculation. Enrichment analyses identified the upregulation of pathways related to signal transduction, defense, carbohydrate metabolism, and cell wall modulation in wild-type <i>Pab</i>-infected leaves compared with controls. Particularly notable was the significant upregulation of numerous genes associated with cell wall loosening by wild-type <i>Pab</i>, suggesting that an initial rearrangement of cell wall architecture facilitates gall formation. Furthermore, transcriptome analysis demonstrated that wild-type <i>Pab</i> suppresses the expression of the betalain biosynthetic gene <i>DOPA 4,5-DIOXYGENASE</i>, leading to reduced betalain accumulation in infected tissues compared with the mutant strain. These findings offer fresh insights into the transcriptional and physiological manipulation of host tissue during the early stages of <i>Pab</i>-induced gall formation.