Flagella-driven motility contributes to effective bacterial invasion. The bacterial flagellum of Salmonella enterica is a rotary motor powered by an electrochemical potential difference of protons across the cytoplasmic membrane. The flagellum is composed of several basal body rings and an axial structure consisting of the rod as a drive shaft, the hook as a universal joint and the filament as a helical propeller. The assembly of the axial structure begins with the rod, followed by the hook and finally the filament. A type III protein export apparatus is located at the flagellar base and transports flagellar axial proteins from the cytoplasm to the distal end of the growing flagellar structure where their assembly occurs. The protein export apparatus coordinates flagellar gene expression with assembly, allowing the hierarchy of flagellar gene expression to exactly parallel the flagellar assembly process. The basal body can accommodate a dozen stator complexes around a rotor ring complex in a load-dependent manner. Each stator unit conducts protons and pushes the rotor. In this book chapter, we will summarize our current understanding of the structure and function of the Salmonella flagellum.
- bacterial flagellum
- rotary motor
- gene expression
- torque generation
- type III protein export
Salmonella is well known as a zoonotic pathogen, which causes gastroenteritis. Motility of Salmonella assists in reaching an appropriate site for invasion and enhances the infectivity. The bacterial flagellum is a long filamentous organelle responsible for motility. Salmonella swims in liquid environments and moves on solid surfaces by rotating flagella. In addition, the flagella also facilitate bacterial adhesion and biofilm formation. Salmonella has several flagella on the cell surface. Each flagellum consists of tens of thousands of flagellin molecules, allowing host cells to acquire both innate and adaptive immune responses to flagellin. Toll-like receptor 5 recognizes flagellin to activate the host immune system. Thus, the flagellum is also a considerable target to detect bacterial pathogens [1, 2].
The flagellum consists of basal body rings and an axial structure consisting of the rod, the hook, the hook-filament junction, the filament and the filament cap (Figure 1). The basal body rings are embedded within the cell membranes and act as a rotary motor powered by the transmembrane electrochemical gradient of protons, namely proton motive force (PMF). The rod is directly connected to the basal body MS ring and acts as a drive shaft. The filament works as a helical propeller to propel the cell body. The hook exists between the rod and filament and functions as a universal joint to smoothly transmit torque produced by the motor to the filament. A type III protein export apparatus is located at the base of the flagellum to construct the axial structure beyond the cell membranes. A dozen stator units surround the basal body rings. The stator unit acts as a proton channel to couple the proton flow through the channel with torque generation. The flagellar motor regulates the number of active stator units in the motor in response to changes in the environment [3, 4, 5, 6]. In this chapter, we describe our current understanding of the structure and function of the Salmonella flagellum.
2. Structure of the flagellum
2.1. Basal body
The basal body consists of the C ring, the MS ring, the P ring and the L ring and the rod. The C, MS, P and L rings are located in the cytoplasm, the cytoplasmic membrane, peptidoglycan layer and outer membrane, respectively (Figure 1). FliF self-assembles into the MS ring in the cytoplasmic membrane . Recently, it has been shown that a C ring protein FliG is required for efficient MS ring formation . FliG, FliM and FliN assemble into the C ring onto the cytoplasmic face of the MS ring (Figure 2) . The MS-C ring complex acts as a rotor of the flagellar motor. A stator protein MotA interacts with the C-terminal domain of FliG (FliGC) , allowing the motor to spin at the maximum speed of about 300 revolutions per second.
The flagellar motor rotates in both counterclockwise (CCW) and clockwise (CW) directions. The C ring acts as a structural switch to change the direction of flagellar motor rotation . Phosphorylated CheY (CheY-P), which acts as a signaling molecule in a signal transduction network responsible for chemotaxis, binds to FliM and FliN, thereby inducing highly cooperative remodeling of the FliG ring structure. As a result, the motor can spin in the CW direction . The FliG/FliN complex binds to the FliG ring through an interaction between FliGM and FliM to form a continuous wall of the C ring . The CheY-P binding to FliM and FliN also induces the dissociation of several FliM/FliN complexes from the FliG ring, indicating that the C ring is a highly dynamic structure (Figure 2) .
FlgI assembles into the P ring around the rod. FlgI self-assembles into the L ring on the P ring to form the LP ring complex. Since the LP ring complex acts as a molecular bushing, the friction between the rod and the inner surface of the LP ring is postulated to be very small .
The rod is a helical structure consisting of three proximal rod proteins, FlgB, FlgC and FlgF and the distal rod protein FlgG . Recent high-resolution structural analysis of the FlgG polyrod by electron cryomicroscopy and helical image analysis have shown that the FlgG rod is composed of 11 protofilaments . FlgG consists of domains D0, Dc and D1, arranged from the inner to the outer part of the FlgG rod structure (Figure 3A). The N- and C-terminal α-helices form a coiled coil in the D0 domain to stabilize the entire rod structure . Residues 46–63 in the Dc domain make the FlgG rod straight and rigid and so the rod can act as a drive shaft .
FliE is a basal body protein that interacts with FlgB . Since FliE is the first export substrate to be transported by a type III protein export apparatus , FliE is thought to form the junction connecting the MS ring and the rod .
About 120 subunits of the hook protein FlgE form the hook structure at the tip of the rod. The hook is a short, curved tubular structure made of 11 protofilaments . The hook protein is composed of four domains, D0, Dc, D1 and D2, arranged from the inner to the outer part of the hook structure (Figure 3B) . The D0, Dc and D1 domains of FlgE are highly homologous to those of FlgG, thereby allowing the hook to be directly connected to the rod . The axial packing of the subunits in the outer part of the tube made of the D1 and D2 domains is relatively loose . The curvature and twist of the supercoiled structures presumably depend on the direction of intermolecular D2-D2 interactions along the protofilaments in the outermost part of the hook structure , and domain Dc plays a critical role in the polymorphic transformation of the supercoiled form of the hook structure . The N- and C-terminal α-helices form a coiled coil in the inner core domain D0 in a way similar to the rod .
2.3. Hook-filament junction
FlgK and FlgL together form the hook-filament junction structure at the distal end of the hook structure. When these two proteins are missing, flagellin cannot form the flagellar filament at the hook tip and hence is excreted into the culture media . So, the junction is a buffer structure to connect the hook and filament with distinct mechanical characteristics .
S. enterica has two distinct flagellin genes, fliC and fljB. About 30,000 subunits of flagellin form the filament at the tip of the hook-filament junction zone. The filament is a tubular structure made of 11 protofilaments in a way similar to the rod and hook. Flagellin consists of four domains, D0, D1, D2 and D3 (Figure 3C). Domains D0 and D1 form the inner and outer tubes of the concentric double-tubular structure, respectively. Hydrophobic interactions between domains D0 make the filament structure mechanically very stable. Domains D2 and D3 form the outer part of flagellin in the filament [22, 23].
The filament switches between two distinct left- and right-handed supercoiled forms. When each motor spins in CCW direction, several left-handed helical filaments form a flagellar bundle, thereby allowing the cell to smoothly swim in liquid media. Quick reversal of the motor to CW rotation produces a twisting force that transforms the left-handed to the right-handed helical form in a highly cooperative manner. As a result, the flagellar bundle is disrupted and so the cell tumbles and changes the swimming direction . The supercoiled filament forms can be produced by combinations of two distinct conformations and packing interactions of the L- and R-type protofilaments . It has been proposed that conformational change of the β-hairpin in domain D1 is postulated to be responsible for the switching between the L- and R-type filaments .
2.5. Filament cap structure
The filament cap is composed of five copies of FliD and exists at the growing end of the filament to facilitate filament assembly [26, 27]. The FliD cap consists of a pentagonal plate domain as a lid and five axially extended leg-like domains . Since there is a symmetry mismatch between the FliD cap with the five-fold rotational symmetry and the helical subunit array of the filament with 11 protofilaments, this symmetry mismatch is postulated to drive filament formation .
2.6. Type III protein export apparatus
Component proteins of the axial structure are transported via a type III protein export apparatus into the distal end of the growing flagellar structure . The protein export apparatus has been visualized to be located at the flagellar base by electron cryo-tomography (ECT) and subtomogram averaging (Figure 4) [30, 31, 32]. The export apparatus is composed of a PMF-driven transmembrane export gate complex made of FlhA, FlhB, FliP, FliQ and FliR, and a cytoplasmic ATPase ring complex consisting of FliH, FliI and FliJ . These proteins are highly homologous to those of the injectisome of pathogenic bacteria, which are involved in direct injection of virulence effector proteins into eukaryotic host cells . Interestingly, the entire architecture of the cytoplasmic ATPase ring complex looks very similar to F-type and A-type rotary ATPases [34, 35, 36]. In addition, FlgN, FliS and FliT act as flagellar type III export chaperons to facilitate the export of their cognate substrates .
FliP forms a homo-hexamer . FliO is required for efficient FliP ring formation although it is not essential for flagellar protein export . FliQ and FliR are associated with the FliP ring , suggesting that FliP, FliQ and FliR together form a core structure of the export gate complex. FlhA and FlhB bind to the FliO/FliP/FliQ/FliR complex . FlhA is also associated with the MS ring . FlhA forms a homo-nonamer through its C-terminal cytoplasmic domains named FlhAC [8, 31]. FliO, FliP, FliQ and FliR are required for efficient assembly of nine FlhA subunits into the export gate complex inside the MS ring, suggesting that the assembly of the export gate complex begins with FliP ring formation with the help of FliO, followed by the assembly of FliQ, FliR and FlhB and finally that of FlhA [8, 37].
The cytoplasmic ATPase ring complex is composed of six copies of the FliH homo-dimer, six copies of the FliI ATPase and one copy of FliJ [34, 35, 36]. The C-terminal domain of FliH (FliHC) binds to the N-terminal domain of FliI (FliIN) [38, 39]. FliJ binds to the center of the FliI homo-hexamer . Interactions of the N-terminal domain of FliH (FliHN) with FliN and FlhA anchor the ATPase ring complex to the flagellar base [40, 41, 42]. FliH and FliI also exist as the FliH2FliI complex in the cytoplasm . The FliH2FliI complex binds to export substrates in complex with flagellar export chaperones [43, 44] and efficiently brings export substrates and chaperone-substrate complexes from the cytoplasm to the export gate complex .
FlgN, FliS and FliT are flagellar export chaperones specific for FlgK and FlgL, FliC and FliD, respectively . They bind to the type III export apparatus proteins and facilitate docking and subsequent unfolding of their cognate substrates at the docking platform made of nine copies of FlhAC [46, 47, 48]. FlgN, FliS and FliT adopt a highly α-helical structure and undergo their helical rearrangements coupled with the association with and dissociation from their binding partners during protein export [49, 50, 51].
The flagellar type III protein export apparatus utilizes ATP hydrolysis by the FliI ATPase and PMF across the cytoplasmic membrane to drive flagellar protein export [52, 53]. The transmembrane export gate complex acts as a proton/protein antiporter to couple the proton flow through the proton channel of the export gate complex with protein export [54, 55]. FlhA forms part of a proton channel in the export gate complex . ATP hydrolysis by the cytoplasmic ATPase ring complex is postulated to activate the export gate complex to drive flagellar protein export in a PMF-dependent manner .
2.7. Stator complex
The stator complex of the flagellar motor is composed of four copies of MotA and two copies of MotB . The MotA4MotB2 complex acts as a proton channel to couple the proton flow with torque generation. MotA consists of four transmembrane helices, two short periplasmic loops and two extensive cytoplasmic regions. MotB consists of an N-terminal cytoplasmic region, a single transmembrane helix and the C-terminal periplasmic domain termed MotBC. The transmembrane helix of MotB forms a proton channel along with the transmembrane helices 3 and 4 of MotA . A highly conserved aspartic acid residue, Asp-33 of MotB, which is located near the cytoplasmic end of its transmembrane helix, is involved in proton translocation . MotBC binds to the peptidoglycan layer, allowing the MotA4MotB2 complex to act as an active stator unit in the flagellar motor . The flagellar motor can accommodate a dozen MotA4MotB2 complexes around the MS-C rotor ring complex . The MotA4MotB2 complexes alternate between localized and freely diffusing forms in response to changes in the environment such as PMF and external load [63, 64]. This indicates that a dozen MotA4MotB2 complexes do not permanently bind to the peptidoglycan layer.
3. Flagellar gene expression and assembly
3.1. Flagellar assembly
Flagellar assembly proceeds from more proximal structures to more distal ones . FliF and FliG together assemble into the MS ring in the cytoplasmic membrane. During MS ring formation, FlhA, FlhB, FliP, FliQ and FliR together assemble into the transmembrane export gate complex with the help of FliO. Then, the FliM/FliN complex binds to FliG to form the C ring on the cytoplasmic face of the MS ring, followed by the assembly of the FliH12-FliI6-FliJ ring complex through interactions of FliHN with FliN and FlhA. Upon completion of the type III protein export apparatus at the flagellar base, FliE is translocated across the cytoplasmic membrane by the protein export apparatus and assembles at the periplasmic surface of the MS ring. Then, FlgB, FlgC, FlgF and FlgG assemble in this order to form the rod. Then, the LP ring complex forms around the rod. Upon completion of the basal body, FlgD forms the hook cap at the rod tip to support the assembly of FlgE into the hook structure. When the hook reaches its mature length of about 55 nm in Salmonella, the hook cap is replaced by FlgK. FlgK and FlgL self-assemble at the hook tip in this order to form the junction structure. Then, FliD forms the filament cap at the tip of the junction to promote the assembly of FliC into the filament that grows up to 15 μm long.
3.2. Flagellar gene expression
More than 70 genes are required for flagellar formation and function in Salmonella, and are organized into a transcriptional hierarchy of three promoter classes . At the top of the hierarchy is the flhD master operon (class 1) which encodes two genes flhD and flhC that are required for the expression of class 2 and 3 operons. FlhD and FlhC together form the FlhD4FlhC2 complex to act as a transcriptional activator that drives the transcription from class 2 promoters. The class 2 genes encode proteins required for the structure and assembly of the hook-basal body (HBB). Also present in this class are the fliA gene whose product acts as a flagellum-specific sigma factor (σ28) necessary for the transcription from class 3 promoters, and the flgM gene, of which product acts as an anti-sigma factor to inhibit the σ28 activity of FliA during HBB assembly. The class 3 operons contain genes required for flagellar filament formation, motility and chemosensory signal transduction .
3.3. Coordinating flagellar gene expression with assembly
The hierarchy of flagellar gene expression exactly parallels the flagellar assembly process . The flagellar type III protein export apparatus couples the activation of class 3 genes with flagellar filament assembly. During HBB assembly, FlgM binds to FliA in the cytoplasm and prevents FliA from acting as σ28 to drive the transcription from the class 3 promoters . Upon completion of HBB assembly, the protein export apparatus switches its export specificity from the hook protein FlgE to those required for filament formation, thereby terminating hook assembly and initiating the secretion of FlgM from the cytoplasm to the culture media. As a result, σ28 can transcribe the class 3 genes .
At least, two flagellar proteins, namely FlhB and FliK, are involved in export specificity switching of the flagellar type III protein export apparatus [69, 70]. The C-terminal cytoplasmic domain of FlhB (FlhBC) acts as an export switch to switch substrate specificity of the protein export apparatus from FlgE to FlgM . FliK is secreted via the protein export apparatus into the culture media during hook assembly  and acts an infrequent molecular ruler to determine the hook length of about 55 nm in Salmonella . The N-terminal region of FliK (FliKN) has the molecular ruler function  whereas the C-terminal domain of FliK (FliKC) is responsible for the interaction with FlhBC to catalyze the export specificity switch .
4. Load-dependent energy coupling mechanism of flagellar motor rotation
The flagellar motor regulates the number of active stator units around a rotor ring complex in response to changes in external load . MotBC acts as a structural switch to drive the assembly-disassembly cycle of the MotA4B2 complex in response to the load change . A highly conserved Asp33 residue of MotB is involved in the load-dependent proton translocation mechanism of the MotA4B2 complex . Highly conserved Arg90 and Glu98 residues in the cytoplasmic loop between transmembrane helices 2 and 3 of MotA (MotAC) interact with highly conserved Asp289 and Arg281 residues in FliGC, respectively . It has been shown that the M76V, Y83H, A145E and E155K mutations in MotAC considerably affect load-dependent assembly and disassembly dynamics of the MotA4B2 complex. These suggest that the MotA4B2 complex itself acts as a load sensor and that MotAC acts as a load sensor that can detect changes in external load to regulate not only the number of active stator units in a motor but also its proton channel activity .
A plug segment consisting of residues 53 to 66 in MotBC suppresses undesirable proton leakage through a proton channel of the MotA4B2 complex prior to stator assembly into a motor . Since the MotAC-FliG interaction is also responsible for efficient assembly of the MotA4B2 complex around the rotor ring complex [79, 80], it has been proposed that this interaction induces the detachment of the plug segments from the proton channels, allowing MotBC to bind to the peptidoglycan layer. As a result, the MotA4B2 complex becomes an active stator unit to couple the proton flow with torque generation.
The flagellar type III protein export apparatus ensures the well-ordered export of flagellar proteins, thereby coupling flagellar gene expression with assembly. The export apparatus utilizes the energy derived from ATP hydrolysis by the FliI ATPase and PMF to efficiently couple the proton influx through the proton channel of the export gate complex with protein translocation into the central channel of the growing structure. But it remains unknown how the export apparatus coordinates flagellar protein export with assembly and how flagellar proteins are unfolded and transported by the export apparatus in a PMF-dependent manner. We are to look into these processes in much more detail to fully understand these intricate mechanisms.
The MotA4B2 complex is a load-sensor to regulate the number of active stators in a motor in response to external load change. To clarify the load-dependent energy coupling mechanism of the flagellar motor, we need to investigate more precise measurements of flagellar motor dynamics by biophysical techniques combined with genetic and biochemical approaches.
We acknowledge Keiichi Namba for continuous support and encouragement. Our research is supported in part by JSPS KAKENHI Grant Numbers JP15H05593 (to Y.V.M), JP15H02386 (to K.I.) and JP26293097 (to T.M.) and MEXT KAKENHI Grant Numbers JP26115720 and JP15H01335 (to Y.V.M).
Conflict of interest
The authors declare no conflict of interest.