To investigate the function of the EvgA response regulator, we compared the genome-wide transcription profile of EvgA-overexpressing and EvgA-lacking Escherichia coli strains by oligonucleotide microarrays. The microarray measurements allowed the identification of at least 37 EvgA-activated genes, including acid resistance-related genes gadABC and hdeAB, efflux pump genes yhiUV and emrK, and 21 genes with unknown function. EvgA overexpression conferred acid resistance to exponentially growing cells. This acid resistance was abolished by deletion of ydeP, ydeO, or yhiE, which was induced by EvgA overexpression. These results suggest that ydeP, ydeO, and yhiE are novel genes related to acid resistance and that EvgA regulates several acid resistance genes. Furthermore, the deletion of yhiE completely abolished acid resistance in stationary-phase cells, suggesting that YhiE plays a critical role in stationary-phase acid resistance. The multidrug resistance in an acrB deletion mutant caused by EvgA overexpression was completely abolished by deletion of yhiUV, while the emrKY deletion had no effect on the increase in resistance by EvgA overexpression. In addition, EvgA overexpression did not confer resistance in a tolC-deficient strain. These results suggest that YhiUV induced by EvgA overexpression is functionally associated with TolC and contributes to multidrug resistance.Bacteria have developed sophisticated signaling systems for adaptive responses to a variety of environments. One of the major mechanisms of signal transduction leading to specific gene expression is known as the two-component system and as its more complex variant, the phosphorelay system (11,24,34,40). A typical two-component system consists of a sensor kinase and its cognate response regulator, which usually functions as a transcriptional factor. The sensor kinase receives an environmental signal, which induces autophosphorylation of a histidine residue. The phosphoryl group on the histidine residue is then transferred to an aspartate residue on the cognate response regulator, resulting in modulation of the expression of its target genes.Genomic sequencing of various microorganisms has revealed the presence of many two-component regulatory systems in all species examined. The functions of many of these putative two-component systems remain unknown. The twocomponent system that consists of response regulator EvgA and sensor kinase EvgS is one such uncharacterized system in Escherichia coli. EvgA and EvgS are highly similar to BvgA and BvgS, respectively, which control the expression of adhesins, toxins, and other virulence factors in Bordetella pertussis (2, 31, 38). The evgAS operon is located adjacent to the emrKY operon, which codes for an efflux pump, and each operon is transcribed in the opposite direction. EvgA binds the intergenic region of evgAS and emrKY and regulates the expression of both operons (13, 36). Nishino and Yamaguchi (20) reported that overexpression of EvgA increases multidrug resistance in a drug-hypersusceptible strain wh...