Rescuing chemotaxis of the anticancer agent Salmonella enterica serovar Typhimurium VNP20009

The role of chemotaxis and motility in Salmonella enterica serovar Typhimurium tumor colonization remains unclear. We determined through swim plate assays that the well-established anticancer agent S. Typhimurium VNP20009 is deficient in chemotaxis, and that this phenotype is suppressible. Through genome sequencing, we revealed that VNP20009 and four selected suppressor mutants had a single nucleotide polymorphism (SNP) in cheY causing a mutation in the conserved proline residue at position 110. CheY is the response regulator that interacts with the flagellar motor-switch complex and modulates rotational bias. The four suppressor mutants additionally carried non-synonymous SNPs in fliM encoding a flagellar switch protein. The CheY-P110S mutation in VNP20009 likely rendered the protein unable to interact with FliM, a phenotype that could be suppressed by mutations in FliM. We replaced the mutated cheY in VNP20009 with the wild-type copy and chemotaxis was partially restored. The swim ring of the rescued strain, VNP20009 cheY(+), was 46% the size of the parental strain 14028 swim ring. When tested in capillary assays, VNP20009 cheY(+) was 69% efficient in chemotaxis towards the attractant aspartate as compared to 14028. Potential reasons for the lack of complete restoration and implications for bacterial tumor colonization will be discussed.

In Situ Structural Analysis of the Spirochetal Flagellar Motor by Cryo-Electron Tomography

The bacterial flagellar motor is a large multi-component molecular machine. Structural determination of such a large complex is often challenging and requires extensive structural analysis in situ. Cryo-electron tomography (cryo-ET) has emerged as a powerful technique that enables us to visualize intact flagellar motors in cells with unprecedented details. Here, we detail the procedure beginning with sample preparation, followed by data acquisition, tomographic reconstruction, sub-tomogram analysis, and ultimately visualization of the intact spirochetal flagellar motor in Borrelia burgdorferi. The procedure is applicable to visualize other molecular machinery in bacteria or other organisms.

Nonconventional cation-coupled flagellar motors derived from the alkaliphilic Bacillus and Paenibacillus species

Prior to 2008, all previously studied conventional bacterial flagellar motors appeared to utilize either H⁺ or Na⁺ as coupling ions. Membrane-embedded stator complexes support conversion of energy using transmembrane electrochemical ion gradients. The main H⁺-coupled stators, known as MotAB, differ from Na⁺-coupled stators, PomAB of marine bacteria, and MotPS of alkaliphilic Bacillus. However, in 2008, a MotAB-type flagellar motor of alkaliphilic Bacillus clausii KSM-K16 was revealed as an exception with the first dual-function motor. This bacterium was identified as the first bacterium with a single stator-rotor that can utilize both H⁺ and Na⁺ for ion-coupling at different pH ranges. Subsequently, another exception, a MotPS-type flagellar motor of alkaliphilic Bacillus alcalophilus AV1934, was reported to utilize Na⁺ plus K⁺ and Rb⁺ as coupling ions for flagellar rotation. In addition, the alkaline-tolerant bacterium Paenibacillus sp. TCA20, which can utilize divalent cations such as Ca²⁺, Mg²⁺, and Sr²⁺, was recently isolated from a hot spring in Japan, which contains a high Ca²⁺ concentration. These findings show that bacterial flagellar motors isolated from unique environments utilize unexpected coupling ions. This suggests that bacteria that grow in different extreme environments adapt to local conditions and evolve their motility machinery.

Assembly and Post-assembly Turnover and Dynamics in the Type III Secretion System

The type III secretion system (T3SS) is one of the largest transmembrane complexes in bacteria, comprising several intricately linked and embedded substructures. The assembly of this nanomachine is a hierarchical process which is regulated and controlled by internal and external cues at several critical points. Recently, it has become obvious that the assembly of the T3SS is not a unidirectional and deterministic process, but that parts of the T3SS constantly exchange or rearrange. This article aims to give an overview on the assembly and post-assembly dynamics of the T3SS, with a focus on emerging general concepts and adaptations of the general assembly pathway.

Fluctuations in Intracellular CheY-P Concentration Coordinate Reversals of Flagellar Motors in E. coli

Signal transduction utilizing membrane-spanning receptors and cytoplasmic regulator proteins is a fundamental process for all living organisms, but quantitative studies of the behavior of signaling proteins, such as their diffusion within a cell, are limited. In this study, we show that fluctuations in the concentration of the signaling molecule, phosphorylated CheY, constitute the basis of chemotaxis signaling. To analyze the propagation of the CheY-P signal quantitatively, we measured the coordination of directional switching between flagellar motors on the same cell. We analyzed the time lags of the switching of two motors in both CCW-to-CW and CW-to-CCW switching (∆t_CCW-CW and ∆t_CW-CCW). In wild-type cells, both time lags increased as a function of the relative distance of two motors from the polar receptor array. The apparent diffusion coefficient estimated for ∆t values was ~9 µm²/s. The distance-dependency of ∆t_CW-CCW disappeared upon loss of polar localization of the CheY-P phosphatase, CheZ. The distance-dependency of the response time for an instantaneously applied serine attractant signal also disappeared with the loss of polar localization of CheZ. These results were modeled by calculating the diffusion of CheY and CheY-P in cells in which phosphorylation and dephosphorylation occur in different subcellular regions. We conclude that diffusion of signaling molecules and their production and destruction through spontaneous activity of the receptor array generates fluctuations in CheY-P concentration over timescales of several hundred milliseconds. Signal fluctuation coordinates rotation among flagella and regulates steady-state run-and-tumble swimming of cells to facilitate efficient responses to environmental chemical signals.

H(+) and Na(+) are involved in flagellar rotation of the spirochete Leptospira

Leptospira is a spirochete possessing intracellular flagella. Each Leptospira flagellar filament is linked with a flagellar motor composed of a rotor and a dozen stators. For many bacterial species, it is known that the stator functions as an ion channel and that the ion flux through the stator is coupled with flagellar rotation. The coupling ion varies depending on the species; for example, H(+) is used in Escherichia coli, and Na(+) is used in Vibrio spp. to drive a polar flagellum. Although genetic and structural studies illustrated that the Leptospira flagellar motor also contains a stator, the coupling ion for flagellar rotation remains unknown. In the present study, we analyzed the motility of Leptospira under various pH values and salt concentrations. Leptospira cells displayed motility in acidic to alkaline pH. In the presence of a protonophore, the cells completely lost motility in acidic to neutral pH but displayed extremely slow movement under alkaline conditions. This result suggests that H(+) is a major coupling ion for flagellar rotation over a wide pH range; however, we also observed that the motility of Leptospira was significantly enhanced by the addition of Na(+), though it vigorously moved even under Na(+)-free conditions. These results suggest that H(+) is preferentially used and that Na(+) is secondarily involved in flagellar rotation in Leptospira. The flexible ion selectivity in the flagellar system could be advantageous for Leptospira to survive in a wide range of environment.

Elucidating the origin of the ExbBD components of the TonB system through Bayesian inference and maximum-likelihood phylogenies

Uptake of ferric siderophores, vitamin B12, and other molecules in gram-negative bacteria is mediated by a multi-protein complex known as the TonB system. The ExbB and ExbD protein components of the TonB system play key energizing roles and are homologous with the flagellar motor proteins MotA and MotB. Here, the phylogenetic relationships of ExbBD and MotAB were investigated using Bayesian inference and the maximum-likelihood method. Phylogenetic trees of these proteins suggest that they are separated into distinct monophyletic groups and have originated from a common ancestral system. Several horizontal gene transfer events for ExbB-ExbD are also inferred, and a model for the evolution of the TonB system is proposed.

Dynamic characteristics of a flagellar motor protein analyzed using an elastic network model

At the base of a flagellar motor, its rotational direction and speed are regulated by the interaction between rotor and stator proteins. A switching event occurs when the cytoplasmic rotor protein, called C-ring, changes its conformation in response to binding of the CheY signal protein. The C-ring structure consists of FliG, FliM, and FliN proteins and its conformational changes in FliM and FliG including Helix_MC play an important role in switching the motor direction. Therefore, clarifying their dynamic properties as well as conformational changes is a key to understanding the switching mechanism of the motor protein. In this study, to elucidate dynamic characteristics of the C-ring structure, both harmonic (intrinsic vibration) and anharmonic (transition pathway) analyses are conducted by using the symmetry-constrained elastic network model. As a result, the first three normal modes successfully capture the essence of transition pathway from wild type to CW-biased state. Their cumulative square overlap value reaches up to 0.842. Remarkably, it is also noted from the transition pathway that the cascade of interactions from the signal protein to FliM to FliG, highlighted by the major mode shapes from the first three normal modes, induces the reorientation (∼100° rotation of FliG_C5) of FliG C-terminal that directly interacts with the stator protein. Presumably, the rotational direction of the motor protein is switched by this substantial change in the stator-rotor interaction.

How Biophysics May Help Us Understand the Flagellar Motor of Bacteria Which Cause Infections

Motor proteins are molecules which convert chemical energy to mechanical work and are responsible for motility across all levels: for transport within a cell, for the motion of an individual cell in its surroundings, and for movement in multicellular aggregates, such as muscles. The bacterial flagellar motor is one of the canonical examples of a molecular complex made from several motor proteins, which self-assembles on demand and provides the locomotive force for bacteria. This locomotion provides a key aspect of bacteria's prevalence. Here, we outline the biophysics behind the assembly, the energetics, the switching and the rotation of this remarkable nanoscale electric motor that is Nature's first wheel.

Stoichiometry and Turnover of the Stator and Rotor

Fluorescence imaging techniques using green fluorescent protein (GFP) and related fluorescent proteins are utilized to monitor and analyze a wide range of biological processes in living cells. Stepwise photobleaching experiments can determine the stoichiometry of protein complexes. Fluorescence recovery after photobleaching (FRAP) experiments can reveal in vivo dynamics of biomolecules. In this chapter, we describe methods to detect the subcellular localization, stoichiometry, and turnovers of stator and rotor components of the Salmonella flagellar motor.

Purification, crystallization and preliminary X-ray crystallographic studies on the C-terminal domain of the flagellar protein FliL from Helicobacter pylori

FliL is an inner membrane protein, occupying a position between the rotor and the stator of the bacterial flagellar motor. Its proximity to, and interactions with, the MS (membrane and supramembranous) ring, the switch complex and the stator proteins MotA/B suggests a role in recruitment and/or stabilization of the stator around the rotor, although the precise role of FliL in the flagellum remains to be established. In this study, recombinant C-terminal domain of Helicobacter pylori FliL (amino-acid residues 81-183) has been expressed in Escherichia coli and purified to > 98% homogeneity. Purified recombinant protein behaved as a monomer in solution. Crystals were obtained by the hanging-drop vapour-diffusion method using ammonium phosphate monobasic as a precipitant. These crystals belong to space group P1, with unit-cell parameters a = 62.5, b = 82.6, c = 97.8 Å, α = 67.7, ꞵ = 83.4, γ = 72.8°. A complete data set has been collected to 2.8 Å resolution using synchrotron radiation. This is an important step towards elucidation of the function of FliL in the bacterial flagellar motor.

Improving CryoEM maps of symmetry-mismatched macromolecular assemblies: A case study on the flagellar motor

Advances in cryo-electron microscopy instrumentation and sample preparation have significantly improved the ability to collect quality data for biomolecular structures. However, achieving resolutions consistent with data quality remains challenging in structures with symmetry mismatches. As a case study, the bacterial flagellar motor is a large complex essential for bacterial chemotaxis and virulence. This motor contains a smaller membrane-supramembrane ring (MS-ring) and a larger cytoplasmic ring (C-ring). These two features have a 33:34 symmetry mismatch when expressed in E. coli. Because close symmetry mismatches are the most difficult to deconvolute, this makes the flagellar motor an excellent model system to evaluate refinement strategies for symmetry mismatch. We compared the performance of masked refinement, local refinement, and particle subtracted refinement on the same data. We found that particle subtraction prior to refinement was critical for approaching the smaller MS-ring. Additional processing resulted in final resolutions of 3.1 Å for the MS-ring and 3.0 Å for the C-ring, which improves the resolution of the MS-ring by 0.3 Å and the resolution of the C-ring by 1.0 Å as compared to past work. Although particle subtraction is fairly well-established, it is rarely applied to problems of symmetry mismatch, making this case study a valuable demonstration of its utility in this context.

Mechanism of Stator Assembly and Incorporation into the Flagellar Motor

In many cases, conformational changes in proteins are related to their functions, and thereby inhibiting those changes causes functional defects. One way to perturb such conformational changes is to covalently link the regions where the changes are induced. Here, I introduce an example in which an intramolecular disulfide crosslink in the stator protein of PomB, introduced based on its crystal structure, reversibly inhibits the rotation of the flagellar motor, and I detail how we analyzed that phenotype. In this Chapter, first I describe how we monitor the motility inhibition and restoration by controlling disulfide bridge formation, and secondly how we detect intramolecular disulfide crosslinks, which are sometimes difficult to monitor by mobility shifts on SDS-PAGE gels.

Site-Directed Cross-Linking Between Bacterial Flagellar Motor Proteins In Vivo

The bacterial flagellum employs a rotary motor embedded on the cell surface. The motor consists of the stator and rotor elements and is driven by ion influx (typically H⁺ or Na⁺) through an ion channel of the stator. Ion influx induces conformational changes in the stator, followed by changes in the interactions between the stator and rotor. The driving force to rotate the flagellum is thought to be generated by changing the stator-rotor interactions. In this chapter, we describe two methods for investigating the interactions between the stator and rotor: site-directed in vivo photo-crosslinking and site-directed in vivo cysteine disulfide crosslinking.

Ion Selectivity of the Flagellar Motors Derived from the Alkaliphilic Bacillus and Paenibacillus Species

Many bacteria can swim using their flagella, which are filamentous organelles that extend from the cell surface. The flagellar motor is energized by either a proton (H⁺) or sodium ion (Na⁺) as the motive force. MotAB-type stators use protons, whereas MotPS- and PomAB-type stators use Na⁺ as the coupling ions. Recently, alkaliphilic Bacillus alcalophilus was shown to use potassium ions (K⁺) and rubidium ions (Rb⁺) for flagellar rotation, and the flagellar motor from Paenibacillus sp. TCA-20 uses divalent cations such as magnesium ions (Mg²⁺), calcium ions (Ca²⁺), and strontium ions (Sr²⁺) for coupling. In this chapter, we focus on how to identify the coupling ions for flagellar rotation of alkaliphilic Bacillus and Paenibacillus species.

Purification of the Na+-Driven PomAB Stator Complex and Its Analysis Using ATR-FTIR Spectroscopy

The flagellar motor of marine Vibrio is driven by the sodium-motive force across the inner membrane. The stator complex, consisting of two membrane proteins PomA and PomB, is responsible for energy conversion in the motor. To understand the coupling of the Na⁺ flux with torque generation, it is essential to clearly identify the Na⁺-binding sites and the Na⁺ flux pathway through the stator channel. Although residues essential for Na⁺ flux have been identified by using mutational analysis, it has been difficult to observe Na⁺ binding to the PomAB stator complex. Here we describe a method to monitor the binding of Na⁺ to purified PomAB stator complex using attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy. This method demonstrates that Na⁺-binding sites are formed by critical aspartic acid and threonine residues located in the transmembrane segments of PomAB.