Vibrio parahaemolyticus has dual flagellar systems adapted for locomotion under different circumstances. A single, sheathed polar flagellum propels the swimmer cell in liquid environments. Numerous unsheathed lateral flagella move the swarmer cell over surfaces. The polar flagellum is produced continuously, whereas the synthesis of lateral flagella is induced under conditions that impede the function of the polar flagellum, e.g., in viscous environments or on surfaces. Thus, the organism possesses two large gene networks that orchestrate polar and lateral flagellar gene expression and assembly. In addition, the polar flagellum functions as a mechanosensor controlling lateral gene expression. In order to gain insight into the genetic circuitry controlling motility and surface sensing, we have sought to define the polar flagellar gene system. The hierarchy of regulation appears to be different from the polar system of Caulobacter crescentus or the peritrichous system of enteric bacteria but is pertinent to many Vibrio and Pseudomonas species. The gene identity and organization of 60 potential flagellar and chemotaxis genes are described. Conserved sequences are defined for two classes of polar flagellar promoters. Phenotypic and genotypic analysis of mutant strains with defects in swimming motility coupled with primer extension analysis of flagellar and chemotaxis transcription provides insight into the polar flagellar organelle, its assembly, and regulation of gene expression.Many bacterial species are motile by means of flagellar propulsion (reviewed in references 5, 32, and 33). Powered by a rotary motor, the flagellum acts as semirigid helical propeller, which is attached via a flexible coupling, known as the hook, to the basal body. The basal body consists of rings and rods that penetrate the membrane and peptidoglycan layers. Associating with the basal body and projecting into the cytoplasm is a structure termed the C ring, which contains the switch proteins and acts as the core, or rotating part, of the motor. Maintenance of a flagellar motility system is a sizable investment with respect to cellular economy in terms of the number of genes and the energy that must be committed to gene expression, protein synthesis, and flagellar rotation. As a result, flagellar systems are highly regulated. A hierarchy of regulation has been elucidated for peritrichously flagellated Escherichia coli and Salmonella enterica serovar Typhimurium (26,27,30). This scheme of control couples gene expression to assembly of the organelle. The pyramid of expression possesses three classes, or tiers, of genes. Genes in each class must be functional in order for expression of the subsequent class to occur. Class 1 genes, flhD and flhC, encode the master transcriptional activators of class 2 flagellar gene expression. The flhDC operon is controlled by a 70 promoter and a number of global regulatory factors (28). The majority of the class 2 flagellar genes encode components of the flagellar export system and the basal body (21). One clas...