Motility and chemotaxis are essential components of pathogenesis for many infectious bacteria, includingBorrelia burgdorferi, the causative agent of Lyme disease. Motility and chemotaxis genes comprise 5 to 6% of the genome of B. burgdorferi, yet the functions of most of those genes remain uncharacterized, mainly due to the paucity of a nonpolar gene inactivation system. In this communication, we describe the development of a novel gene inactivation methodology to target B. burgdorferi fliL, a putative periplasmic flagellar gene located in a large motility operon and transcribed by RNA polymerase containing 70 . Although the morphology of nonpolar fliL mutant cells was indistinguishable from that of wild-type cells, the mutant exhibited a defectivemotility phenotype. Cryo-electron tomography (cryo-ET) of intact organisms revealed that the periplasmic flagella in the fliL mutant were frequently tilted toward the cell pole instead of their normal orientation toward the cell body. These defects were corrected when the mutant was complemented in cis. Moreover, a comparative analysis of flagellar motors from the wild type and the mutant provides the first structural evidence that FliL is localized between the stator and rotor. Our results suggest that FliL is likely involved in coordinating or regulating the orientation of periplasmic flagella in B. burgdorferi.Borrelia burgdorferi is the causative agent of Lyme disease and belongs to a group of bacteria called spirochetes. B. burgdorferi cells have a characteristic flat-wave morphology and unique means of motility (9,10,19,35). As a result of its unique morphology and motility, B. burgdorferi is able to traverse viscous gel-like media in which most other flagellated bacteria slow down or stop (30). Consequently, B. burgdorferi may efficiently bore through host tissues, leading to pathogenesis in the joints, nervous system, and heart (19,30,54). The motility of B. burgdorferi results from the coordinated rotation of the periplasmic flagella residing between the outer membrane and the cell cylinder (9,10,12,20,33,35). The current swimming model suggests that a run occurs when the anterior periplasmic flagella rotate in one direction (e.g., counterclockwise [CCW]) and the posterior flagella rotate in the opposite direction (clockwise [CW]). Reversals occur when periplasmic flagella at both poles of the cell change their direction of rotation. During a nontranslational mode (flex), the periplasmic flagella at both cell poles rotate in the same direction (9,20,35).Bacterial flagella are composed of three major parts: the motor, hook, and filament. The motor can be divided into two functional units, the rotor and the stator. The stator is the torque generator consisting of the MotA-MotB complex. The rotor is composed, minimally, of the MS ring (FliF), the rod, and the switch complex (FliG, FliM, and FliN). In B. burgdorferi, the periplasm-localized flagellar filament consists of the core protein FlaB and the sheath protein FlaA (17, 46). There are 7 to 11 filaments conne...