Abstract The bacterial flagellum is essential for motility and virulence for Gram-negative pathogens. Flagellum assembly is complex and coupled to the controlled expression of more than 70 genes in the flagellar and chemotaxis regulon. It takes many cell generations to assemble a completed flagellum. For 30 years my lab has investigated mechanisms that couple flagellar gene expression to assembly and the associated type III secretion (T3S) system. T3S is the only secretion system in Biology that undergoes a secretion-substrate transition from one class of secretion-substrates to another. One focus of this grant application is to determine the mechanism of the secretion- specificity switch in flagellar and the related virulence-specific injectisome T3S systems. The research will also determine how specific proteins are selected from the thousands present in the cytoplasm and targeted for T3 secretion. We will also characterize key gaps in the understanding of how flagellar gene regulation is coupled to assembly and how the entire flagellar regulon responds to global gene regulatory systems.