Inhibiting Transcriptional Hub: A Phase-Separating RNA Polymerase Alpha Subunit as a First-in-Class Agrochemical Target against Xanthomonas

Effective management of plant pathogenic bacteria faces major challenges, including rapidly evolving bacterial resistance, environmental risks associated with traditional copper-based agrochemicals, and the scarcity of new antibacterial targets. Recently, liquid–liquid phase separation (LLPS) has been extensively demonstrated to play crucial roles in microbial biology. However, the use of phase-separating proteins as targets for bactericide development remains unexplored. Herein, we report the first syringic acid derivative, C 31 , that targets the alpha subunit of RNA polymerase (RpoA) in Xanthomonas oryzae pv. oryzae ( Xoo ). C 31 exhibits exceptional inhibitory activity against Xoo (EC 50 = 0.86 μg/ml, half maximal effective concentration) and maintains a low resistance risk throughout 12 successive passages. Pot experiments show that C 31 provides superior control efficacy (59.37%) against rice bacterial leaf blight compared with syringic acid (24.65%) and thiodiazole copper (42.41%), showing sustained efficacy and high crop safety. Mechanistic studies reveal that RpoA and σ 70 factor undergo LLPS to generate biomolecular condensates that function as “transcriptional hubs”, thereby regulating the expression efficiency of global virulence genes and consequently strengthening Xoo pathogenicity. C 31 binds to the C-terminal domain of RpoA and prevents LLPS initiation and subsequent condensate formation, resulting in antibacterial effects. This study establishes an LLPS-based strategy to control phytopathogenic bacteria.