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

Abstract

σ⁵⁴ factor (RpoN) plays a crucial role in bacterial motility, virulence, growth, and other biological functions. In our previous study, two homologous σ⁵⁴ factors, RpoN1 and RpoN2, were identified in <i>Xanthomonas oryzae</i> pv. <i>oryzae</i> (<i>Xoo</i>), 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, <i>rpoN1</i> or <i>rpoN2</i> deletion in <i>Xoo</i> 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, <i>ropN1</i> deletion decreased <i>ropN2</i> transcription, while <i>rpoN2</i> deletion did not affect <i>ropN1</i> transcription. No interaction between the <i>rpoN2</i> promoter and RpoN1 was detected, suggesting that RpoN1 indirectly regulates <i>rpoN2</i> transcription. In addition, RpoN1-regulated DEGs were specially enriched in ribosome, carbon, and nitrogen metabolism pathways. Besides, bacterial growth was remarkably repressed in Δ<i>rpoN1</i> but not in Δ<i>rpoN2</i>. 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 σ⁵⁴ factors in <i>Xoo</i>.