The FlhA linker mediates flagellar protein export switching during flagellar assembly.

The flagellar protein export apparatus switches substrate specificity from hook-type to filament-type upon hook assembly completion, thereby initiating filament assembly at the hook tip. The C-terminal cytoplasmic domain of FlhA (FlhA) serves as a docking platform for flagellar chaperones in complex with their cognate filament-type substrates. Interactions of the flexible linker of FlhA (FlhA) with its nearest FlhA subunit in the FlhA ring is required for the substrate specificity switching. To address how FlhA brings the order to flagellar assembly, we analyzed the flhA(E351A/W354A/D356A) ΔflgM mutant and found that this triple mutation in FlhA increased the secretion level of hook protein by 5-fold, thereby increasing hook length. The crystal structure of FlhA(E351A/D356A) showed that FlhA bound to the chaperone-binding site of its neighboring subunit. We propose that the interaction of FlhA with the chaperon-binding site of FlhA suppresses filament-type protein export and facilitates hook-type protein export during hook assembly.