Bacterial chemotaxis results from the ability of flagellated bacteria to control the frequency of switching between smooth-swimming and tumbling episodes in response to changes in concentration of extracellular substances. High levels of phosphorylated CheY protein are the intracellular signal for inducing the tumbling mode of swimming. The CheZ protein has been shown to control the level of phosphorylated CheY by regulating its rate of dephosphorylation. To identify functional domains in the CheZ protein, we made mutants by random mutagenesis of the cheZ gene and constructed a series of deletions. The map position and the in vivo and in vitro activity of the resulting gain-or loss-of-function mutant proteins define separate functional domains of the CheZ protein.Peritrichously flagellated bacteria are able to move towards high concentrations of attractant substances by alternating the rotational direction of their flagella (for reviews, see references 1, 6, 16, and 22 to 24). Counterclockwise rotation results in unidirectional swimming (smooth swimming), whereas changes in the swimming direction (tumbling) are achieved by intermittent clockwise rotation of the flagella. Cells swimming toward increasing concentrations of attractant tend to tumble less frequently, thereby biasing their direction of movement towards regions of higher attractant concentration (3, 21). The signal transduction that ultimately controls the frequency of switches in flagellar rotation is mediated by several transmembrane receptors and by a series of cytoplasmic proteins. In Escherichia coli and Salmonella typhimurium, the external message is transmitted through transmembrane receptors to a cytoplasmic autophosphorylating histidine kinase, CheA, which transfers its phosphoryl group to the response regulator CheY (5, 9, 12, 26). CheY in its phosphorylated form (phospho-CheY) binds to the flagellar switch (2, 17, 25) and causes clockwise rotation of the flagella, resulting in a tumbling event (7, 15). Thus, high intracellular concentrations of phospho-CheY correlate with the tumbling motion of the cell. Smooth swimming is restored by dephosphorylation of CheY, which may be due to both the spontaneous hydrolysis of the phosphate group and the activity of the CheZ protein, which strongly accelerates the dephosphorylation of phospho-CheY (9, 11). It has also been established that phospho-CheY binds to the CheZ protein and that, following dephosphorylation, CheY is released from CheZ (4,18).CheZ is a ϳ24-kDa protein characterized in E. coli and S. typhimurium and does not seem to have significant homology with other bacterial proteins. Recently, a CheZ homolog has been described in Pseudomonas aeruginosa (13). It is able to complement an E. coli cheZ deletion strain. Proteins with analogous functions have been identified in other organisms. For example, Spo0E in Bacillus subtilis accelerates the dephosphorylation of the response regulator Spo0A (14); however, this phosphatase is not homologous to CheZ.The molecular mechanism through which CheZ...