The facultative aerobe Escherichia coli K-12 can use respiratory nitrate ammonification to generate energy during anaerobic growth. The toxic compound nitric oxide is a by-product of this metabolism. Previous transcript microarray studies identified the yeaR-yoaG operon, encoding proteins of unknown function, among genes whose transcription is induced in response to nitrate, nitrite, or nitric oxide. Nitrate and nitrite regulate anaerobic respiratory gene expression through the NarX-NarL and NarQ-NarP two-component systems. All known Nar-activated genes also require the oxygen-responsive Fnr transcription activator. However, previous studies indicated that yeaR-yoaG operon transcription does not require Fnr activation. Here, we report results from mutational analyses demonstrating that yeaR-yoaG operon transcription is activated by phospho-NarL protein independent of the Fnr protein. Escherichia coli K-12, a facultative aerobe, is able to respire with a variety of electron acceptors, including oxygen (O 2 ), nitrate (NO 3 Ϫ ), and nitrite (NO 2 Ϫ ). Synthesis of the corresponding respiratory enzymes is subject to hierarchical control to ensure use of the preferred electron acceptor. The top level of this control is mediated by the Fnr transcription activator, which senses the absence of oxygen through its iron-sulfur cluster (27). The second level of hierarchical control is mediated by the NarL and NarP response regulators, which, when phosphorylated, bind DNA to activate or repress transcription. The NarX and NarQ sensors control NarL and NarP phosphorylation in response to nitrate and nitrite (53).Several operons require both Fnr and phospho-NarL or -NarP proteins for maximal transcription. For the narGHJI, narK, and fdnGHI operons, Fnr protein, bound near position Ϫ41.5 with respect to the transcription initiation site, acts synergistically with phospho-NarL protein bound to sites further upstream (53). For the napFDAGHBC operon, Fnr protein, bound at position Ϫ64.5, acts synergistically with phospho-NarP protein bound at position Ϫ44.5 (15, 17). For the nirBDC and nrfABCDEFG operons, Fnr protein, bound near position Ϫ41.5, activates transcription maximally only when phospho-NarL or -NarP protein is bound further upstream to block inhibition by other proteins (2,8,59). Although transcription of many other operons is known to be activated by the Fnr protein acting alone (12, 26), to date there are no examples of Fnr-independent transcription activation by the phosphoNarL or -NarP protein.In preliminary transcript microarray experiments, we observed that the levels of yeaR-yoaG operon transcripts (encoding proteins of unknown function) are increased during growth with nitrate only in a narL ϩ strain (23). Sequence inspection revealed a likely binding site for phospho-NarL protein but no obvious site for binding of Fnr protein (Fig. 1A). Therefore, we were interested in characterizing the control of yeaR-yoaG operon transcription in more detail. Our results, reported here, suggest that this is an example of Fnr-...