Antagonistic regulation of motility and transcriptome expression by RpoN and RpoS in Escherichia coli

Bacteria generally possess multiple σ factors that, based on structural and functional similarity, divide into two families: σ(70) and σ(N) . Many studies have revealed σ factor competition within the σ(70) family, while the competition between σ(N) and σ(70) families has yet to be fully explored. Here we report a global antagonistic effect on gene expression between two alternative σ factors, σ(N) (RpoN) and a σ(70) family protein σ(S) (RpoS). Mutations in rpoS and rpoN were found to inversely affect a number of cellular traits, such as the expression of flagellar genes, σ(N) -controlled growth on poor nitrogen sources, and σ(S) -directed expression of acid phosphatase AppA. Transcriptome analysis reveals that about 60% of genes in the RpoN regulon are under reciprocal RpoS control. Furthermore, loss of RpoN led to increased levels of RpoS, while RpoN levels were unaffected by the rpoS mutation. Expression of the flagellar σ(F) factor (FliA), another σ(70) family protein, is controlled positively by RpoN but negatively by RpoS. This positive control by RpoN is likely mediated through the flagellar regulator FlhDC, whose expression is RpoN-dependent. These findings unveil a complex regulatory interaction among σ(N) , σ(S) and σ(F) , which modulates motility, nitrogen utilization, stress response and many other cellular functions.