The Experts below are selected from a list of 327 Experts worldwide ranked by ideXlab platform
Keiichi Namba - One of the best experts on this subject based on the ideXlab platform.
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Evidence for the hook supercoiling mechanism of the Bacterial Flagellum.
Biophysics and physicobiology, 2018Co-Authors: Takashi Fujii, Hideyuki Matsunami, Yumi Inoue, Keiichi NambaAbstract:The Bacterial flagellar hook is a short, highly curved tubular structure connecting the basal body as a rotary motor and the filament as a helical propeller to function as a universal joint to transmit motor torque to the filament regardless of its orientation. This highly curved form is known to be part of a supercoil as observed in the polyhook structure. The subunit packing interactions in the Salmonella hook structure solved in the straight form gave clear insights into the mechanisms of its bending flexibility and twisting rigidity. Salmonella FlgE consists of four domains, D0, Dc, D1 and D2, arranged from inside to outside of the tube, and an atomic model of the supercoiled hook built to simulate the hook shape observed in the native Flagellum suggested that the supercoiled form is stabilized by near-axial interactions of the D2 domains on the inner surface of the supercoil. Here we show that the deletion of domain D2 from FlgE makes the hook straight, providing evidence to support the proposed hook supercoiling mechanism that it is the near-axial interactions between the D2 domains that stabilize the highly curved hook structure.
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High-Resolution pH Imaging of Living Bacterial Cells To Detect Local pH Differences
mBio, 2016Co-Authors: Yusuke V. Morimoto, Keiichi Namba, Nobunori Kami-ike, Tomoko Miyata, Akihiro Kawamoto, Takayuki Kato, Tohru MinaminoAbstract:ABSTRACT Protons are utilized for various biological activities such as energy transduction and cell signaling. For construction of the Bacterial Flagellum, a type III export apparatus utilizes ATP and proton motive force to drive flagellar protein export, but the energy transduction mechanism remains unclear. Here, we have developed a high-resolution pH imaging system to measure local pH differences within living Salmonella enterica cells, especially in close proximity to the cytoplasmic membrane and the export apparatus. The local pH near the membrane was ca. 0.2 pH unit higher than the bulk cytoplasmic pH. However, the local pH near the export apparatus was ca. 0.1 pH unit lower than that near the membrane. This drop of local pH depended on the activities of both transmembrane export components and FliI ATPase. We propose that the export apparatus acts as an H+/protein antiporter to couple ATP hydrolysis with H+ flow to drive protein export. IMPORTANCE The flagellar type III export apparatus is required for construction of the Bacterial Flagellum beyond the cellular membranes. The export apparatus consists of a transmembrane export gate and a cytoplasmic ATPase complex. The export apparatus utilizes ATP and proton motive force as the energy source for efficient and rapid protein export during flagellar assembly, but it remains unknown how. In this study, we have developed an in vivo pH imaging system with high spatial and pH resolutions with a pH indicator probe to measure local pH near the export apparatus. We provide direct evidence suggesting that ATP hydrolysis by the ATPase complex and the following rapid protein translocation by the export gate are both linked to efficient proton translocation through the gate.
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Bacterial Nanomachines: The Flagellum and Type III Injectisome
Cold Spring Harbor perspectives in biology, 2010Co-Authors: Marc Erhardt, Keiichi Namba, Kelly T. HughesAbstract:The Bacterial Flagellum and the virulence-associated injectisome are complex, structurally related nanomachines that bacteria use for locomotion or the translocation of virulence factors into eukaryotic host cells. The assembly of both structures and the transfer of extracellular proteins is mediated by a unique, multicomponent transport apparatus, the type III secretion system. Here, we discuss the significant progress that has been made in recent years in the visualization and functional characterization of many components of the type III secretion system, the structure of the Bacterial Flagellum, and the injectisome complex.
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Coarse-grained molecular dynamics simulations of a rotating Bacterial Flagellum.
Biophysical journal, 2006Co-Authors: Anton Arkhipov, Keiichi Namba, Peter L. Freddolino, Katsumi Imada, Klaus SchultenAbstract:Many types of bacteria propel themselves using elongated structures known as flagella. The Bacterial flagellar filament is a relatively simple and well-studied macromolecular assembly, which assumes different helical shapes when rotated in different directions. This polymorphism enables a bacterium to switch between running and tumbling modes; however, the mechanism governing the filament polymorphism is not completely understood. Here we report a study of the Bacterial flagellar filament using numerical simulations that employ a novel coarse-grained molecular dynamics method. The simulations reveal the dynamics of a half-micrometer-long Flagellum segment on a timescale of tens of microseconds. Depending on the rotation direction, specific modes of filament coiling and arrangement of monomers are observed, in qualitative agreement with experimental observations of flagellar polymorphism. We find that solvent-protein interactions are likely to contribute to the polymorphic helical shapes of the filament.
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Reviews in Cell Biology and Molecular Medicine - Mobile Structures: Cilia and Flagella
Encyclopedia of Molecular Cell Biology and Molecular Medicine, 2006Co-Authors: Koji Yonekura, Keiichi NambaAbstract:Both eukaryote and prokaryote have flagella with a similar overall look, and use them for swimming in liquids, but they are completely different from each other. Cilia look like short hairs and have almost the same structure and mechanism as the eukaryotic flagella. The long filamentous structure of the eukaryotic Flagellum is composed of highly organized microtubule-based structure and huge numbers of its associate proteins, while that in the Bacterial Flagellum is made of a single protein called flagellin. The length and the diameter of the filament in eukaryote are more than 10 times larger than those in bacteria. The total number of component proteins involved in the structure of eukaryote is also ∼10 times of the prokaryote. The eukaryotic Flagellum makes wavelike movements generated by the dynein motor within the filament using the energy of ATP hydrolysis, while the Bacterial Flagellum is a rotary motor driven by ion flows through the motor part embedded in the membranes. They both grow at their distal end, but use quite different mechanism for transport of their components to the distal tip. Although the eukaryotic and Bacterial flagella are complex macromolecules, recent studies are beginning to elucidate the roles of component proteins, their complex structures and growth mechanisms. Keywords: Axoneme; Bacterial Flagellum; Cilium; Dynein; Eukaryotic Flagellum; Flagellin; Intraflagellar Transport (IFT); Microtubule; MotA/B, PomA/B; Type III Protein Export Apparatus
Marc Erhardt - One of the best experts on this subject based on the ideXlab platform.
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Protein Export via the Type III Secretion System of the Bacterial Flagellum.
Biomolecules, 2021Co-Authors: Manuel Halte, Marc ErhardtAbstract:The Bacterial Flagellum and the related virulence-associated injectisome system of pathogenic bacteria utilize a type III secretion system (T3SS) to export substrate proteins across the inner membrane in a proton motive force-dependent manner. The T3SS is composed of an export gate (FliPQR/FlhA/FlhB) located in the flagellar basal body and an associated soluble ATPase complex in the cytoplasm (FliHIJ). Here, we summarise recent insights into the structure, assembly and protein secretion mechanisms of the T3SS with a focus on energy transduction and protein transport across the cytoplasmic membrane.
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Controlling minimal and maximal hook-length of the Bacterial Flagellum
2020Co-Authors: Alina Guse, Manfred Rohde, Marc ErhardtAbstract:AbstractHook-length control is a central checkpoint during assembly of the Bacterial Flagellum. During hook growth, a 405 amino acids (aa) protein, FliK, is intermittently secreted and thought to function as a molecular measuring tape that, in Salmonella, controls hook-length to 55 nm ± 6 nm. The underlying mechanism involves interactions of both the α-helical, N-terminal domain of FliK (FliKN) with the hook and hook cap, and of its C-terminal domain with a component of the export apparatus. However, various deletion mutants of FliKN display uncontrolled hook-length, which is not consistent with a ruler mechanism. Here, we carried out an extensive deletion analysis of FliKN to investigate its contribution in the hook-length control mechanism. We identified FliKN mutants deleted for up to 80 aa that retained wildtype motility. However, the short FliK variants did not produce shorter hook-lengths as expected from a physical ruler. Rather, the minimal length of the hook depends on the level of hook protein production and secretion. Our results thus support a model in which FliK functions as a hook growth terminator protein that limits the maximal length of the hook, and not as a molecular ruler that physically measures hook-length.
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Energy Requirements for Protein Secretion via the Flagellar Type III Secretion System
Methods in molecular biology (Clifton N.J.), 2017Co-Authors: Marc ErhardtAbstract:Protein transport across the cytoplasmic membrane is coupled to energy derived from adenosine triphosphate hydrolysis or the protein motive force (pmf). A sophisticated, multi-component type III secretion system exports substrate proteins of both the Bacterial Flagellum and virulence-associated injectisome system of many Gram-negative pathogens. The type-III secretion system is primarily a pmf-driven protein exporter. Here, I describe methods to investigate the export of substrate proteins into the culture supernatant under conditions that manipulate the pmf.
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Strategies to Block Bacterial Pathogenesis by Interference with Motility and Chemotaxis.
Current topics in microbiology and immunology, 2016Co-Authors: Marc ErhardtAbstract:Infections by motile, pathogenic bacteria, such as Campylobacter species, Clostridium species, Escherichia coli, Helicobacter pylori, Listeria monocytogenes, Neisseria gonorrhoeae, Pseudomonas aeruginosa, Salmonella species, Vibrio cholerae, and Yersinia species, represent a severe economic and health problem worldwide. Of special importance in this context is the increasing emergence and spread of multidrug-resistant bacteria. Due to the shortage of effective antibiotics for the treatment of infections caused by multidrug-resistant, pathogenic bacteria, the targeting of novel, virulence-relevant factors constitutes a promising, alternative approach. Bacteria have evolved distinct motility structures for movement across surfaces and in aqueous environments. In this review, I will focus on the Bacterial Flagellum, the associated chemosensory system, and the type-IV pilus as motility devices, which are crucial for Bacterial pathogens to reach a preferred site of infection, facilitate biofilm formation, and adhere to surfaces or host cells. Thus, those nanomachines constitute potential targets for the development of novel anti-infectives that are urgently needed at a time of spreading antibiotic resistance. Both Bacterial flagella and type-IV pili (T4P) are intricate macromolecular complexes made of dozens of different proteins and their motility function relies on the correct spatial and temporal assembly of various substructures. Specific type-III and type-IV secretion systems power the export of substrate proteins of the Bacterial Flagellum and type-IV pilus, respectively, and are homologous to virulence-associated type-III and type-II secretion systems. Accordingly, Bacterial flagella and T4P represent attractive targets for novel antivirulence drugs interfering with synthesis, assembly, and function of these motility structures.
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Regulation, Aufbau und Funktion einer bakteriellen Nanomaschine
BIOspektrum, 2014Co-Authors: Hanna M Singer, Marc ErhardtAbstract:The Bacterial Flagellum is a molecular nanomachine used for locomotion. In Salmonella , the assembly of the Flagellum is a highly coordinated and regulated process. On top of a complex regulatory network resides the flagellar master operon flhDC . Many environmental signals are integrated on the level of flhDC expression, including transcriptional cross talk between the virulence and flagellar systems that contributes to the correct spatiotemporal expression of the different virulence factors during the infection process.
Klaus Schulten - One of the best experts on this subject based on the ideXlab platform.
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Theoretical and computational investigation of flagellin translocation and Bacterial Flagellum growth.
Biophysical Journal, 2011Co-Authors: David E. Tanner, Zhongzhou Chen, Klaus SchultenAbstract:The Bacterial Flagellum is a self-assembling filament, which bacteria use for swimming. It is built from tens of thousands of flagellin monomers in a self-assembly process that involves translocation of the monomers through the flagellar interior, a channel, to the growing tip. Flagellum monomers are pumped into the filament at the base, move unfolded along the channel and then bind to the tip of the filament, thereby extending the growing Flagellum. The flagellin translocation process, due to the Flagellum maximum length of 20 μm, is an extreme example of protein transport through channels. Here, we derive a model for flagellin transport through the long confining channel, testing the key assumptions of the model through molecular dynamics simulations that also furnish system parameters needed for quantitative description. Together, mathematical model and molecular dynamics simulations explain why the growth rate of flagellar filaments decays exponentially with filament length and why Flagellum growth ceases at a certain maximum length.
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Coarse-grained molecular dynamics simulations of a rotating Bacterial Flagellum.
Biophysical journal, 2006Co-Authors: Anton Arkhipov, Keiichi Namba, Peter L. Freddolino, Katsumi Imada, Klaus SchultenAbstract:Many types of bacteria propel themselves using elongated structures known as flagella. The Bacterial flagellar filament is a relatively simple and well-studied macromolecular assembly, which assumes different helical shapes when rotated in different directions. This polymorphism enables a bacterium to switch between running and tumbling modes; however, the mechanism governing the filament polymorphism is not completely understood. Here we report a study of the Bacterial flagellar filament using numerical simulations that employ a novel coarse-grained molecular dynamics method. The simulations reveal the dynamics of a half-micrometer-long Flagellum segment on a timescale of tens of microseconds. Depending on the rotation direction, specific modes of filament coiling and arrangement of monomers are observed, in qualitative agreement with experimental observations of flagellar polymorphism. We find that solvent-protein interactions are likely to contribute to the polymorphic helical shapes of the filament.
Tohru Minamino - One of the best experts on this subject based on the ideXlab platform.
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Flagella-Driven Motility of Bacteria.
Biomolecules, 2019Co-Authors: Shuichi Nakamura, Tohru MinaminoAbstract:The Bacterial Flagellum is a helical filamentous organelle responsible for motility. In Bacterial species possessing flagella at the cell exterior, the long helical flagellar filament acts as a molecular screw to generate thrust. Meanwhile, the flagella of spirochetes reside within the periplasmic space and not only act as a cytoskeleton to determine the helicity of the cell body, but also rotate or undulate the helical cell body for propulsion. Despite structural diversity of the flagella among Bacterial species, flagellated bacteria share a common rotary nanomachine, namely the flagellar motor, which is located at the base of the filament. The flagellar motor is composed of a rotor ring complex and multiple transmembrane stator units and converts the ion flux through an ion channel of each stator unit into the mechanical work required for motor rotation. Intracellular chemotactic signaling pathways regulate the direction of flagella-driven motility in response to changes in the environments, allowing bacteria to migrate towards more desirable environments for their survival. Recent experimental and theoretical studies have been deepening our understanding of the molecular mechanisms of the flagellar motor. In this review article, we describe the current understanding of the structure and dynamics of the Bacterial Flagellum.
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High-Resolution pH Imaging of Living Bacterial Cells To Detect Local pH Differences
mBio, 2016Co-Authors: Yusuke V. Morimoto, Keiichi Namba, Nobunori Kami-ike, Tomoko Miyata, Akihiro Kawamoto, Takayuki Kato, Tohru MinaminoAbstract:ABSTRACT Protons are utilized for various biological activities such as energy transduction and cell signaling. For construction of the Bacterial Flagellum, a type III export apparatus utilizes ATP and proton motive force to drive flagellar protein export, but the energy transduction mechanism remains unclear. Here, we have developed a high-resolution pH imaging system to measure local pH differences within living Salmonella enterica cells, especially in close proximity to the cytoplasmic membrane and the export apparatus. The local pH near the membrane was ca. 0.2 pH unit higher than the bulk cytoplasmic pH. However, the local pH near the export apparatus was ca. 0.1 pH unit lower than that near the membrane. This drop of local pH depended on the activities of both transmembrane export components and FliI ATPase. We propose that the export apparatus acts as an H+/protein antiporter to couple ATP hydrolysis with H+ flow to drive protein export. IMPORTANCE The flagellar type III export apparatus is required for construction of the Bacterial Flagellum beyond the cellular membranes. The export apparatus consists of a transmembrane export gate and a cytoplasmic ATPase complex. The export apparatus utilizes ATP and proton motive force as the energy source for efficient and rapid protein export during flagellar assembly, but it remains unknown how. In this study, we have developed an in vivo pH imaging system with high spatial and pH resolutions with a pH indicator probe to measure local pH near the export apparatus. We provide direct evidence suggesting that ATP hydrolysis by the ATPase complex and the following rapid protein translocation by the export gate are both linked to efficient proton translocation through the gate.
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The Bacterial flagellar motor and its structural diversity.
Trends in microbiology, 2015Co-Authors: Tohru Minamino, Katsumi ImadaAbstract:The Bacterial Flagellum is a reversible rotary motor powered by an electrochemical-potential difference of specific ions across the cytoplasmic membrane. The H(+)-driven motor of Salmonella spins at ∼300 Hz, whereas the Na(+)-driven motor of marine Vibrio spp. can rotate much faster, up to 1700 Hz. A highly conserved motor structure consists of the MS ring, C ring, rod, and export apparatus. The C ring and the export apparatus show dynamic properties for exerting their functional activities. Various additional structures surrounding the conserved motor structure are observed in different Bacterial species. In this review we summarize our current understanding of the structure, function, and assembly of the flagellar motor in Salmonella and marine Vibrio.
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Structure and function of the Bacterial flagellar type III protein export system in Salmonella
Nihon saikingaku zasshi. Japanese journal of bacteriology, 2015Co-Authors: Tohru MinaminoAbstract:The Bacterial Flagellum is a filamentous organelle that propels the Bacterial cell body in liquid media. For construction of the Bacterial Flagellum beyond the cytoplasmic membrane, flagellar component proteins are transported by its specific protein export apparatus from the cytoplasm to the distal end of the growing flagellar structure. The flagellar export apparatus consists of a transmembrane export gate complex and a cytoplasmic ATPase ring complex. Flagellar substrate-specific chaperones bind to their cognate substrates in the cytoplasm and escort the substrates to the docking platform of the export gate. The export apparatus utilizes ATP and proton motive force across the cytoplasmic membrane as the energy sources to drive protein export and coordinates protein export with assembly by ordered export of substrates to parallel with their order of assembly. In this review, we summarize our current understanding of the structure and function of the flagellar protein export system in Salmonella enterica serovar Typhimurium.
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self assembly and type iii protein export of the Bacterial Flagellum
Journal of Molecular Microbiology and Biotechnology, 2004Co-Authors: Tohru Minamino, Keiichi NambaAbstract:The Bacterial Flagellum is a supramolecular structure consisting of a basal body, a hook and a filament. Most of the flagellar components are translocated across the cytoplasmic membrane by the flagel
Holger Stark - One of the best experts on this subject based on the ideXlab platform.
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Dynamics of a Bacterial Flagellum under reverse rotation
Soft matter, 2016Co-Authors: Tapan Chandra Adhyapak, Holger StarkAbstract:To initiate tumbling of an E. coli, one of the helical flagella reverses its sense of rotation. It then transforms from its normal form first to the transient semicoiled state and subsequently to the curly-I state. The dynamics of polymorphism is effectively modeled by describing flagellar elasticity through an extended Kirchhoff free energy. However, the complete landscape of the free energy remains undetermined because the ground state energies of the polymorphic forms are not known. We investigate how variations in these ground state energies affect the dynamics of a reversely rotated Flagellum of a swimming bacterium. We find that the Flagellum exhibits a number of distinct dynamical states and comprehensively summarize them in a state diagram. As a result, we conclude that tuning the landscape of the extended Kirchhoff free energy alone cannot generate the intermediate full-length semicoiled state. However, our model suggests an ad hoc method to realize the sequence of polymorphic states as observed for a real bacterium. Since the elastic properties of Bacterial flagella are similar, our findings can easily be extended to other peritrichous bacteria.
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Rotation-Induced Polymorphic Transitions in Bacterial Flagella
Physical review letters, 2013Co-Authors: R. Vogel, Holger StarkAbstract:Bacteria propel themselves with the help of rotating helical flagella. They change their swimming direction during tumbling events in order to increase, for example, their supply of nutrients (chemotaxis). During tumbling a Bacterial Flagellum assumes different polymorphic states. Based on a continuum model for the motor-Flagellum system, we demonstrate that a changing motor torque can initiate these polymorphic transformations. In particular, we investigate the run-and-stop tumble strategy of Rhodobacter sphaeroides which uses a coiled-to-normal transition in its single Flagellum. We also show that torque reversal in single-flagellated Escherichia coli generates a normal-to-curly $I$ transition as observed for tumbling E. coli that swim with a bundle of several flagella.
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Modeling the Bacterial Flagellum by an elastic network of rigid bodies.
Physical biology, 2011Co-Authors: C Speier, R. Vogel, Holger StarkAbstract:Bacteria such as Escherichia coli propel themselves by rotating a bundle of helical filaments, each driven by a rotary motor embedded in the cell membrane. Each filament is an assembly of thousands of copies of the protein flagellin which assumes two different states. We model the filament by an elastic network of rigid bodies that form bonds with one another according to a scheme suggested by Namba and Vondervistz (1997 Q. Rev. Biophys. 30 1-65) and add additional binding sites at the inner part of the rigid body. Our model reproduces the helical parameters of the 12 possible polymorphic configurations very well. We demonstrate that its energetical ground state corresponds to the normal helical form, usually observed in nature, only when inner and outer binding sites of the rigid body have a large axial displacement. This finding correlates directly to the elongated shape of the flagellin molecule. An Ising Hamiltonian in our model directly addresses the two states of the flagellin protein. It contains an external field that represents external parameters which allow us to alter the ground state of the filament.