Spirochetes have a unique cell structure: These bacteria have internal periplasmic flagella subterminally attached at each cell end. How spirochetes coordinate the rotation of the periplasmic flagella for chemotaxis is poorly understood. In other bacteria, modulation of flagellar rotation is essential for chemotaxis, and phosphorylation-dephosphorylation of the response regulator CheY plays a key role in regulating this rotary motion. The genome of the Lyme disease spirochete Borrelia burgdorferi contains multiple homologues of chemotaxis genes, including three copies of cheY, referred to as cheY1, cheY2, and cheY3. To investigate the function of these genes, we targeted them separately or in combination by allelic exchange mutagenesis. Whereas wild-type cells ran, paused (flexed), and reversed, cells of all single, double, and triple mutants that contained an inactivated cheY3 gene constantly ran. Capillary tube chemotaxis assays indicated that only those strains with a mutation in cheY3 were deficient in chemotaxis, and cheY3 complementation restored chemotactic ability. In vitro phosphorylation assays indicated that CheY3 was more efficiently phosphorylated by CheA2 than by CheA1, and the CheY3-P intermediate generated was considerably more stable than the CheY-P proteins found in most other bacteria. The results point toward CheY3 being the key response regulator essential for chemotaxis in B. burgdorferi. In addition, the stability of CheY3-P may be critical for coordination of the rotation of the periplasmic flagella.Spirochetes are a group of motile bacteria that have a unique morphology and means of motility. On the surface of the spirochete is an outer membrane, which is often referred to as the outer membrane sheath. Within this outer membrane are the cell cylinder and the periplasmic flagella. The periplasmic flagella reside between the outer membrane and the cell cylinder. Because of its medical importance and recent advances in genetic manipulation, we have focused on the Lyme disease spirochete Borrelia burgdorferi to analyze spirochete motility and chemotaxis (for recent reviews, see references 10, 26, 34, and 68). This spirochete is relatively long (10 to 20 m) and thin (0.31 m) and has a flat-wave morphology, and motility is generated by rotation of the periplasmic flagella (11,14,24,25,33,42). Approximately 7 to 11 periplasmic flagella are subterminally attached at each cell end (30), and recent electron cryotomography analysis indicates that these periplasmic flagella form elegant ribbons that wrap clockwise (CW) around the cell cylinder (11). Not only are the periplasmic flagella involved in motility, but these organelles have a skeletal function that in part dictates the flat-wave shape of the cell (10,14,26,35,40,53,68). Thus, mutants that lack periplasmic flagella are nonmotile and have a rod-shaped morphology (35,40,53). Motility is accomplished by backward-moving flat waves along the cell body. These waves are generated by the coordinated rotation of the rigid periplasmic flagella as the...