σN‐dependent control of acid resistance and the locus of enterocyte effacement in enterohemorrhagic Escherichia coli is activated by acetyl phosphate in a manner requiring flagellar regulator FlhDC and the σS antagonist FliZ

In enterohemorrhagic Escherichia coli (EHEC), sigma factor N (σN) regulates glutamate‐dependent acid resistance (GDAR) and the locus of enterocyte effacement (LEE); discrete genetic systems that are required for transmission and virulence of this intestinal pathogen. Regulation of these systems requires nitrogen regulatory protein C, NtrC, and is a consequence of NtrC‐σN‐dependent reduction in the activity of sigma factor S (σS). This study elucidates pathway components and stimuli for σN‐directed regulation of GDAR and the LEE in EHEC. Deletion of fliZ, the product of which reduces σS activity, phenocopied rpoN (σN) and ntrC null strains for GDAR and LEE control, acid resistance, and adherence. Upregulation of fliZ by NtrC‐σN was shown to be indirect and required an intact flagellar regulator flhDC. Activation of flhDC by NtrC‐σN and FlhDC‐dependent regulation of GDAR and the LEE was dependent on σN‐promoter flhDP2, and a newly described NtrC upstream activator sequence. Addition of ammonium chloride significantly altered expression of GDAR and LEE, acid resistance, and adherence, independently of rpoN, ntrC, and the NtrC sensor kinase, ntrB. Altering the availability of NtrC phosphodonor acetyl phosphate by growth without glucose, with acetate addition, or by deletion of acetate kinase ackA, abrogated NtrC‐σN‐dependent control of flhDC, fliZ, GDAR, and the LEE. Acid resistance and type III secretion are essential mechanisms for fecal–oral transmission and gut colonization in enterohemorrhagic Escherichia coli. This study has determined the mechanism by which NtrC‐sigma N regulate pathways for the control of acid resistance and type III secretion and explores the activating signals for this pathway.