Transcription of nhaA, the main Na⁺/H⁺ antiporter of Escherichia coli, is regulated by Na⁺ and growth phase

The transcription of nhaA, encoding the main Na⁺/H⁺ antiporter of Escherichia coli, is induced by Na⁺, regulated by NhaR, and affected by H-NS. In this work the roles of the two nhaA promoters (P1 and P2) were studied by analysis of transcription both in vivo and in vitro and promoter mutations. We found that P1 is an NhaR-dependent, Na⁺-induced, and H-NS-affected promoter both in the exponential and stationary phases. An in vitro transcription assay demonstrated that P1 is activated by σ⁷⁰-RNA polymerase and both NhaR and H-NS increase the specificity of PI. Remarkably, in marked contrast to P1, P2 exhibits very low activity during the exponential phase but is induced in the stationary phase to become the major promoter. Furthermore, P2 is activated by σ^s and is neither induced by Na⁺ nor dependent on NhaR or affected by H-NS. Hence, this work establishes that nhaA has a dual mode of regulation, each involving a different promoter, and reveals that P2 and σ^s together are responsible for the survival of stationary-phase cells in the presence of high Na⁺, alkaline pH, and the combination of high Na⁺ and alkaline pH, the most stressful condition.