The two major chemoreceptors of Escherichia coli, Tsr and Tar, mediate opposite responses to the same changes in cytoplasmic pH (pH i ). We set out to identify residues involved in pH i sensing to gain insight into the general mechanisms of signaling employed by the chemoreceptors. did not change the polarity but altered the time course of pH i response. These results suggest that the electrostatic properties of a short cytoplasmic region within the linker region that connects the second transmembrane helix to the first methylation helix is critical for switching the signaling state of the chemoreceptors during pH sensing. Similar conformational changes of this region in response to external ligands may be critical components of transmembrane signaling.Many biological processes, such as enzyme reactions and interactions between proteins, are influenced by pH. Therefore, cells have to sense and adapt to changes in extracellular and intracellular pH. Despite the accumulated knowledge about pH-dependent regulation in a wide variety of organisms, the molecular mechanisms of pH sensing are still poorly understood.Behavioral responses of Escherichia coli and Salmonella typhimurium to changes in pH provide a convenient system for studying the pH-sensing mechanism. These bacteria show repellent responses to weak acids and attractant responses to weak bases (1, 2). These responses are generated by decreases and increases of cytoplasmic pH (pH i ). 1 The changes in pH i were documented by 31 P nuclear magnetic resonance spectroscopy (3, 4). Usually, pH i in E. coli is maintained at around 7.5 over a range of extracellular pH (pH o ) values from 5.0 to 9.0 (3, 5). However, this strong pH i homeostasis can be disrupted by the addition of weak acids or weak bases to the culture medium. When pH o is lower than pH i , weak acids can traverse the membrane in their protonated (uncharged) form and release protons in the cytoplasm to decrease pH i . Similarly, when pH o is higher than pH i , weak bases can traverse the membrane in deprotonated (uncharged) forms and capture protons in the cytoplasm to increase pH i . These changes in pH i correlate well with tactic responses to weak acids and weak bases (4).The signal transduction pathway for chemotaxis in E. coli and S. typhimurium has been extensively studied at the molecular level (for reviews, see Refs. 6 -9). These organisms have a set of related methyl-accepting chemoreceptors that includes the serine receptor Tsr and the aspartate receptor Tar. These receptors have a remarkable ability to sense a variety of stimuli, including chemoattractants, chemorepellents, temperature, and pH.Tar and, presumably, the other chemoreceptors exist as a homodimer of about 60-kDa subunits (10). The dimeric cytoplasmic domains form stable complexes with the histidine kinase CheA and the adaptor protein CheW (11,12). Furthermore, the receptors, together with the CheA and CheW proteins, cluster at a cell pole (13).CheA phosphorylates itself and then serves as a phosphodonor for the response regul...