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σ 54  factor (RpoN) plays a crucial role in bacterial motility, virulence, growth, and other biological functions. In our previous study, two homologous σ 54  factors, RpoN1 and RpoN2, were identified in  Xanthomonas oryzae  pv.  oryzae  ( Xoo ), the causative agent of bacterial leaf blight in rice. However, their functional roles, i.e., whether they exert combined or independent effects, remain unknown. In the current study,  rpoN1  or  rpoN2  deletion in  Xoo  significantly disrupted bacterial swimming motility, flagellar assembly, and virulence. Transcriptome analysis led to the identification of 127 overlapping differentially expressed genes (DEGs) regulated by both RpoN1 and RpoN2. Furthermore, GO and KEGG classification demonstrated that these DEGs were highly enriched in flagellar assembly, chemotaxis, and c-di-GMP pathways. Interestingly,  ropN1  deletion decreased  ropN2  transcription, while  rpoN2  deletion did not affect  ropN1  transcription. No interaction between the  rpoN2  promoter and RpoN1 was detected, suggesting that RpoN1 indirectly regulates  rpoN2  transcription. In addition, RpoN1-regulated DEGs were specially enriched in ribosome, carbon, and nitrogen metabolism pathways. Besides, bacterial growth was remarkably repressed in Δ rpoN1  but not in Δ rpoN2 . Taken together, this study demonstrates the overlapping and unique regulatory roles of RpoN1 and RpoN2 in motility, virulence, growth and provides new insights into the regulatory mechanism of σ 54  factors in  Xoo .

frontiers in microbiology

Transcriptome Analysis Revealed Overlapping and Special Regulatory Roles of RpoN1 and RpoN2 in Motility, Virulence, and Growth of Xanthomonas oryzae pv. oryzae