In enterohemorrhagic E. coli (EHEC) sigma factor N (σN) regulates glutamate-dependent acid resistance (GDAR) and the locus of enterocyte effacement (LEE), discrete genetic systems 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, phenocopies rpoN (σN) and ntrC null strains for GDAR and LEE control, acid resistance and adherence. Upregulation of fliZ by NtrC/σN is indirect, requiring an intact flagellar regulator flhDC. Activation of flhDC by NtrC/σN and FlhDC-dependent regulation of GDAR and the LEE is dependent on σN-promoter flhDP2, and a newly described NtrC upstream activator sequence. While the addition of ammonium significantly alters GDAR and LEE expression, acid resistance and adherence, it does so 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, abrogates NtrC/σN-dependent control of flhDC, fliZ, GDAR and LEE genes.