A multi-state dynamic process confers mechano-adaptation to a biological nanomachine

Structure and Dynamics of the Bacterial Flagellar Motor Complex

Many bacteria swim in liquids and move over solid surfaces by rotating flagella. The bacterial flagellum is a supramolecular protein complex that is composed of about 30 different flagellar proteins ranging from a few to tens of thousands. Despite structural and functional diversities of the flagella among motile bacteria, the flagellum commonly consists of a membrane-embedded rotary motor fueled by an ion motive force across the cytoplasmic membrane, a universal joint, and a helical propeller that extends several micrometers beyond the cell surface. The flagellar motor consists of a rotor and several stator units, each of which acts as a transmembrane ion channel complex that converts the ion flux through the channel into the mechanical work required for force generation. The rotor ring complex is equipped with a reversible gear that is regulated by chemotactic signal transduction pathways. As a result, bacteria can move to more desirable locations in response to environmental changes. Recent high-resolution structural analyses of flagella using cryo-electron microscopy have provided deep insights into the assembly, rotation, and directional switching mechanisms of the flagellar motor complex. In this review article, we describe the current understanding of the structure and dynamics of the bacterial flagellum.

Physical mechanism reveals bacterial slowdown above a critical number of flagella

Numerous studies have explored the link between bacterial swimming and the number of flagella, a distinguishing feature of motile multi-flagellated bacteria. We revisit this open question using augmented slender-body theory simulations, in which we resolve the full hydrodynamic interactions within a bundle of helical filaments rotating and translating in synchrony. Unlike previous studies, our model considers the full torque-speed relationship of the bacterial flagellar motor, revealing its significant impact on multi-flagellated swimming. Because the viscous load per motor decreases with the flagellar number, the bacterial flagellar motor transitions from the high-load to the low-load regime at a critical number of filaments, leading to bacterial slowdown as further flagella are added to the bundle. We explain the physical mechanism behind the observed slowdown as an interplay between the load-dependent generation of torque by the motor, and the load-reducing cooperativity between flagella, which consists of both hydrodynamic and non-hydrodynamic components. The theoretically predicted critical number of flagella is remarkably close to the values reported for the model organism Escherichia coli. Our model further predicts that the critical number of flagella increases with viscosity, suggesting that bacteria can enhance their swimming capacity by growing more flagella in more viscous environments, consistent with empirical observations.

Structural basis of directional switching by the bacterial flagellum

The bacterial flagellum is a macromolecular protein complex that harvests energy from uni-directional ion flow across the inner membrane to power bacterial swimming via rotation of the flagellar filament. Rotation is bi-directional, with binding of a cytoplasmic chemotactic response regulator controlling reversal, though the structural and mechanistic bases for rotational switching are not well understood. Here we present cryoelectron microscopy structures of intact Salmonella flagellar basal bodies (3.2-5.5 Å), including the cytoplasmic C-ring complexes required for power transmission, in both counter-clockwise and clockwise rotational conformations. These reveal 180° movements of both the N- and C-terminal domains of the FliG protein, which, when combined with a high-resolution cryoelectron microscopy structure of the MotA5B2 stator, show that the stator shifts from the outside to the inside of the C-ring. This enables rotational switching and reveals how uni-directional ion flow across the inner membrane is used to accomplish bi-directional rotation of the flagellum.

Motility in Periweissella Species: Genomic and Phenotypic Characterization and Update on Motility in Lactobacillaceae

The genus Weissella and the recently described genus Periweissella, to which some previously named Weissella species have been reclassified as a result of a taxogenomic assessment, includes lactic acid bacteria species with high biotechnological and probiotic potential. Only one species, namely, Periweissella (P.) beninensis, whose type strain has been shown to possess probiotic features, has so far been described to be motile. However, the availability of numerous genome sequences of Weissella and Periweissella species prompted the possibility to screen for the presence of the genetic determinants encoding motility in Weissella and Periweissellas spp. other than P. beninensis. Herein, we performed a comprehensive genomic analysis to identify motility-related proteins in all Weissella and Periweissella species described so far, and extended the analysis to the recently sequenced Lactobacillaceae spp. Furthermore, we performed motility assays and transmission electron microscopy (TEM) on Periweissella type strains to confirm the genomic prediction. The homology-based analysis revealed genes coding for motility proteins only in the type strains of P. beninensis, P. fabalis, P. fabaria and P. ghanensis genomes. However, only the P. beninensis type strain was positive in the motility assay and displayed run-and-tumble behavior. Many peritrichous and long flagella on bacterial cells were visualized via TEM, as well. As for the Lactobacillaceae, in addition to the species previously described to harbor motility proteins, the genetic determinants of motility were also found in the genomes of the type strains of Lactobacillus rogosae and Ligilactobacillus salitolerans. This study, which is one of the first to analyze the genomes of Weissella, Periweissella and the recently sequenced Lactobacillaceae spp. for the presence of genes coding for motility proteins and which assesses the associated motility phenotypes, provides novel results that expand knowledge on these genera and are useful in the further characterization of lactic acid bacteria.

Flagellar motors of swimming bacteria contain an incomplete set of stator units to ensure robust motility

Flagellated bacteria, like Escherichia coli, swim by rotating helical flagellar filaments powered by rotary flagellar motors at their base. Motor dynamics are sensitive to the load it drives. It was previously thought that motor load was high when driving filament rotation in free liquid environments. However, torque measurements from swimming bacteria revealed substantially lower values compared to single-motor studies. We addressed this inconsistency through motor resurrection experiments, abruptly attaching a 1-micrometer-diameter bead to the filament to ensure high load. Unexpectedly, we found that the motor works with only half the complement of stator units when driving filament rotation. This suggests that the motor is not under high load during bacterial swimming, which we confirmed by measuring the torque-speed relationship by varying media viscosity. Therefore, the motor operates in an intermediate-load region, adaptively regulating its stator number on the basis of external load conditions. This ensures the robustness of bacterial motility when swimming in diverse load conditions and varying flagella numbers.

Structural Basis of Directional Switching by the Bacterial Flagellum

The bacterial flagellum is a macromolecular protein complex that harvests energy from ion-flow across the inner membrane to power bacterial swimming in viscous fluids via rotation of the flagellar filament. Bacteria such as Salmonella enterica are capable of bi-directional flagellar rotation even though ion flow is uni-directional. How uni-directional ion-movement through the inner membrane is utilized by this macromolecular machine to drive bi-directional flagellar rotation is not understood, but a chemotactic response regulator in the cytoplasm is known to reverse the direction of rotation. We here present cryo-EM structures of intact Salmonella flagellar basal bodies, including the cytoplasmic complexes required for power transmission, in conformations representing both directions of rotation. The structures reveal that the conformational changes required for switching the direction of rotation involve 180 degree rotations of both the N- and C-terminal domains of the FliG protein. Combining these models with a new, high-resolution, cryo-EM structure of the MotA5B2 stator, in complex with the C-terminal domain of FliG, reveals how uni-directional ion-flow across the inner membrane is used to accomplish bi-directional rotation of the flagellum.

Ion selectivity and rotor coupling of the Vibrio flagellar sodium-driven stator unit

Bacteria swim using a flagellar motor that is powered by stator units. Vibrio spp. are highly motile bacteria responsible for various human diseases, the polar flagella of which are exclusively driven by sodium-dependent stator units (PomAB). However, how ion selectivity is attained, how ion transport triggers the directional rotation of the stator unit, and how the stator unit is incorporated into the flagellar rotor remained largely unclear. Here, we have determined by cryo-electron microscopy the structure of Vibrio PomAB. The electrostatic potential map uncovers sodium binding sites, which together with functional experiments and molecular dynamics simulations, reveal a mechanism for ion translocation and selectivity. Bulky hydrophobic residues from PomA prime PomA for clockwise rotation. We propose that a dynamic helical motif in PomA regulates the distance between PomA subunit cytoplasmic domains, stator unit activation, and torque transmission. Together, our study provides mechanistic insights for understanding ion selectivity and rotor incorporation of the stator unit of the bacterial flagellum.

Recent breakthroughs in computational structural biology harnessing the power of sequences and structures

Recent advances in computational approaches and their integration into structural biology enable tackling increasingly complex questions. Here, we discuss several key areas, highlighting breakthroughs and remaining challenges. Theoretical modeling has provided tools to accurately predict and design protein structures on a scale currently difficult to achieve using experimental approaches. Molecular Dynamics simulations have become faster and more precise, delivering actionable information inaccessible by current experimental methods. Virtual screening workflows allow a high-throughput approach to discover ligands that bind and modulate protein function, while Machine Learning methods enable the design of proteins with new functionalities. Integrative structural biology combines several of these approaches, pushing the frontiers of structural and functional characterization to ever larger systems, advancing towards a complete understanding of the living cell. These breakthroughs will accelerate and significantly impact diverse areas of science.