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Tammara V, Angrover R, Sirur D, Das A. Flagellar motor protein-targeted search for the druggable site of Helicobacter pylori. Phys Chem Chem Phys 2024; 26:2111-2126. [PMID: 38131449 DOI: 10.1039/d3cp05024f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The deleterious impact of Helicobacter pylori (H. pylori) on human health is contingent upon its ability to create and sustain colony structure, which in turn is dictated by the effective performance of flagella - a multi-protein rotary nanodevice. Hence, to design an effective therapeutic strategy against H. pylori, we here conducted a systematic search for an effective druggable site by focusing on the structure-dynamics-energetics-stability landscape of the junction points of three 1 : 1 protein complexes (FliFC-FliGN, FliGM-FliMM, and FliYC-FliNC) that contribute mainly to the rotary motion of the flagella via the transformation of information along the junctions over a wide range of pH values operative in the stomach (from neutral to acidic). We applied a gamut of physiologically relevant perturbations in the form of thermal scanning and mechanical force to sample the entire quasi - and non-equilibrium conformational spaces available for the protein complexes under neutral and acidic pH conditions. Our perturbation-induced magnification of conformational distortion approach identified pH-independent protein sequence-specific evolution of precise thermally labile segments, which dictate the specific thermal unfolding mechanism of each complex and this complex-specific pH-independent structural disruption notion remains consistent under mechanical stress as well. Complementing the above observations with the relative rank-ordering of estimated equilibrium binding free energies between two protein sequences of a specific complex quantifies the extent of structure-stability modulation due to pH alteration, rationalizes the exceptional stability of H. pylori under acidic pH conditions, and identifies the pH-independent complex-sequence-segment-residue diagram for targeted drug design.
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Affiliation(s)
- Vaishnavi Tammara
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pune, Maharashtra 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ruchika Angrover
- The Departments of the University Institute of Biotechnology, Chandigarh University, NH-05, Ludhiana - Chandigarh State Highway, Punjab 140413, India
| | - Disha Sirur
- School of Physical Sciences, National Institute of Science Education & Research-Bhubaneswar, An OCC of Homi Bhabha National Institute, P.O. Jatni, Khurda, Odisha 752050, India
| | - Atanu Das
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pune, Maharashtra 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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2
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Tao A, Liu G, Zhang R, Yuan J. Precise Measurement of the Stoichiometry of the Adaptive Bacterial Flagellar Switch. mBio 2023; 14:e0018923. [PMID: 36946730 PMCID: PMC10128058 DOI: 10.1128/mbio.00189-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
The cytoplasmic ring (C-ring) of the bacterial flagellar motor controls the motor rotation direction, thereby controlling bacterial run-and-tumble behavior. The C-ring has been shown to undergo adaptive remodeling in response to changes in motor directional bias. However, the stoichiometry and arrangement of the C-ring is still unclear due to contradiction between the results from fluorescence studies and cryo-electron microscopy (cryo-EM) structural analysis. Here, by using the copy number of FliG molecules (34) in the C-ring as a reference, we precisely measured the copy numbers of FliM molecules in motors rotating exclusively counterclockwise (CCW) and clockwise (CW). We surprisingly found that there are on average 45 and 58 FliM molecules in CW and CCW rotating motors, respectively, which are much higher than previous estimates. Our results suggested a new mechanism of C-ring adaptation, that is, extra FliM molecules could be bound to the primary C-ring with probability depending on the motor rotational direction. We further confirmed that all of the FliM molecules in the C-ring function in chemotaxis signaling transduction because all of them could be bound by the chemotactic response regulator CheY-P. Our measurements provided new insights into the structure and arrangement of the flagellar switch. IMPORTANCE The bacterial flagellar switch can undergo adaptive remodeling in response to changes in motor rotation direction, thereby shifting its operating point to match the output of the chemotaxis signaling pathway. However, it remains unclear how the flagellar switch accomplishes this adaptive remodeling. Here, via precise fluorescence studies, we measured the absolute copy numbers of the critical component in the switch for motors rotating counterclockwise and clockwise, obtaining much larger numbers than previous relative estimates. Our results suggested a new mechanism of adaptive remodeling of the flagellar switch and provided new insights for updating the conformation spread model of the switch.
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Affiliation(s)
- Antai Tao
- Department of Physics, University of Science and Technology of China, Hefei, Anhui, China
| | - Guangzhe Liu
- Wenzhou Institute, University of Chinese Academy of Science, Wenzhou, Zhejiang, P.R. China
- School of Engineering and Science, University of Chinese Academy of Science, Beijing, P.R. China
| | - Rongjing Zhang
- Department of Physics, University of Science and Technology of China, Hefei, Anhui, China
| | - Junhua Yuan
- Department of Physics, University of Science and Technology of China, Hefei, Anhui, China
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3
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Thormann KM. Dynamic Hybrid Flagellar Motors-Fuel Switch and More. Front Microbiol 2022; 13:863804. [PMID: 35495728 PMCID: PMC9039648 DOI: 10.3389/fmicb.2022.863804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Flagellar motors are intricate rotating nanomachines that are powered by transmembrane ion gradients. The stator complexes are the powerhouses of the flagellar motor: They convert a transmembrane ion gradient, mainly of H+ or Na+, into rotation of the helical flagellar filament. They are thus essential for motor function. The number of stators synchronously engaged in the motor is surprisingly dynamic and depends on the load and the environmental concentration of the corresponding coupling ion. Thus, the rotor-stator interactions determine an important part of the properties of the motor. Numerous bacteria have been identified as possessing more than one set of stators, and some species have been demonstrated to use these different stators in various configurations to modify motor functions by dynamic in-flight swapping. Here, we review knowledge of the properties, the functions, and the evolution of these hybrid motors and discuss questions that remain unsolved.
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Affiliation(s)
- Kai M Thormann
- Fachbereich für Chemie und Biologie, Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
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4
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Chou YC. A physical mechanism underlying the torque generation of the bacterial flagellar motor. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2022; 45:34. [PMID: 35411441 DOI: 10.1140/epje/s10189-022-00188-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
This study proposes a physical mechanism underlying the torque generation of a bacterial flagellar motor (BFM), in which the torque for the rotation of the rotor can be generated from impulsive forces resulting from collisions between the randomly moving stator and rotor. The torque required for the rotation of the rotor may be generated through two coexisting mechanisms: mechanism (A), in which the stator collides with the rotor, whose rotation axis fluctuates asymmetrically, generating a torque in the direction of the rod, and mechanism (B), in which physical collisions between the stator and the asymmetric [Formula: see text]and [Formula: see text] generate the torque in the direction of the rod. Mechanism (A) might be related the bidirectional rotation and the tumbling of the motion of the cell. Mechanism (B) might be related to occurrence of the steps in the time traces of the rotational angle, backward stepping or switching of the rotational direction, and the knee-shaped [Formula: see text]-[Formula: see text] relation. The above-mentioned characteristics of the rotation of BFM are reproduced in a model device designed to confirm the applicability of the proposed concept to real BFM. Moreover, a prediction of the disappearance of the knee-shaped [Formula: see text]-[Formula: see text] relation of the actual BFM at a high temperature is proposed.
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Affiliation(s)
- Y C Chou
- Department of Physics, National TsingHua University, Hsinchu, Taiwan, Republic of China.
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5
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Hu H, Santiveri M, Wadhwa N, Berg HC, Erhardt M, Taylor NMI. Structural basis of torque generation in the bi-directional bacterial flagellar motor. Trends Biochem Sci 2021; 47:160-172. [PMID: 34294545 DOI: 10.1016/j.tibs.2021.06.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/11/2022]
Abstract
The flagellar stator unit is an oligomeric complex of two membrane proteins (MotA5B2) that powers bi-directional rotation of the bacterial flagellum. Harnessing the ion motive force across the cytoplasmic membrane, the stator unit operates as a miniature rotary motor itself to provide torque for rotation of the flagellum. Recent cryo-electron microscopic (cryo-EM) structures of the stator unit provided novel insights into its assembly, function, and subunit stoichiometry, revealing the ion flux pathway and the torque generation mechanism. Furthermore, in situ cryo-electron tomography (cryo-ET) studies revealed unprecedented details of the interactions between stator unit and rotor. In this review, we summarize recent advances in our understanding of the structure and function of the flagellar stator unit, torque generation, and directional switching of the motor.
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Affiliation(s)
- Haidai Hu
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Mònica Santiveri
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Navish Wadhwa
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA; Rowland Institute at Harvard, Harvard University, 100 Edwin H. Land Blvd, Cambridge, MA 02142, USA
| | - Howard C Berg
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA; Rowland Institute at Harvard, Harvard University, 100 Edwin H. Land Blvd, Cambridge, MA 02142, USA
| | - Marc Erhardt
- Institut für Biologie/Bakterienphysiologie, Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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6
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Aroney STN, Poole PS, Sánchez-Cañizares C. Rhizobial Chemotaxis and Motility Systems at Work in the Soil. FRONTIERS IN PLANT SCIENCE 2021; 12:725338. [PMID: 34512702 PMCID: PMC8429497 DOI: 10.3389/fpls.2021.725338] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/06/2021] [Indexed: 05/17/2023]
Abstract
Bacteria navigate their way often as individual cells through their chemical and biological environment in aqueous medium or across solid surfaces. They swim when starved or in response to physical and chemical stimuli. Flagella-driven chemotaxis in bacteria has emerged as a paradigm for both signal transduction and cellular decision-making. By altering motility, bacteria swim toward nutrient-rich environments, movement modulated by their chemotaxis systems with the addition of pili for surface movement. The numbers and types of chemoreceptors reflect the bacterial niche and lifestyle, with those adapted to complex environments having diverse metabolic capabilities, encoding far more chemoreceptors in their genomes. The Alpha-proteobacteria typify the latter case, with soil bacteria such as rhizobia, endosymbionts of legume plants, where motility and chemotaxis are essential for competitive symbiosis initiation, among other processes. This review describes the current knowledge of motility and chemotaxis in six model soil bacteria: Sinorhizobium meliloti, Agrobacterium fabacearum, Rhizobium leguminosarum, Azorhizobium caulinodans, Azospirillum brasilense, and Bradyrhizobium diazoefficiens. Although motility and chemotaxis systems have a conserved core, rhizobia possess several modifications that optimize their movements in soil and root surface environments. The soil provides a unique challenge for microbial mobility, since water pathways through particles are not always continuous, especially in drier conditions. The effectiveness of symbiont inoculants in a field context relies on their mobility and dispersal through the soil, often assisted by water percolation or macroorganism movement or networks. Thus, this review summarizes the factors that make it essential to consider and test rhizobial motility and chemotaxis for any potential inoculant.
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7
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Hu L, Wang N, Tao K, Miao J, Kim YJ. Circular steering of gold–nickel–platinum micro-vehicle using singular off-center nanoengine. INTERNATIONAL JOURNAL OF INTELLIGENT ROBOTICS AND APPLICATIONS 2020. [DOI: 10.1007/s41315-020-00146-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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8
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Santiveri M, Roa-Eguiara A, Kühne C, Wadhwa N, Hu H, Berg HC, Erhardt M, Taylor NM. Structure and Function of Stator Units of the Bacterial Flagellar Motor. Cell 2020; 183:244-257.e16. [DOI: 10.1016/j.cell.2020.08.016] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/09/2020] [Accepted: 08/11/2020] [Indexed: 12/17/2022]
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9
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Hu L, Wang N, Lim YD, Miao J. Chemical reaction dependency, magnetic field and surfactant effects on the propulsion of disk‐like micromotor and its application for
E. coli
transportation. NANO SELECT 2020. [DOI: 10.1002/nano.202000024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Liangxing Hu
- School of Mechanical and Aerospace Engineering Nanyang Technological University Nanyang 639798 Singapore
| | - Nan Wang
- Department of Science and Math Singapore University of Technology and Design Singapore 487372 Singapore
| | - Yu Dian Lim
- Centre for Micro‐/Nano‐electronics (NOVITAS), School of Electrical and Electronics Engineering Nanyang Technological University Nanyang 639798 Singapore
| | - Jianmin Miao
- School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 P. R. China
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10
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Rossmann FM, Hug I, Sangermani M, Jenal U, Beeby M. In situ structure of the Caulobacter crescentus flagellar motor and visualization of binding of a CheY-homolog. Mol Microbiol 2020; 114:443-453. [PMID: 32449846 PMCID: PMC7534056 DOI: 10.1111/mmi.14525] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 12/30/2022]
Abstract
Bacterial flagellar motility is controlled by the binding of CheY proteins to the cytoplasmic switch complex of the flagellar motor, resulting in changes in swimming speed or direction. Despite its importance for motor function, structural information about the interaction between effector proteins and the motor are scarce. To address this gap in knowledge, we used electron cryotomography and subtomogram averaging to visualize such interactions inside Caulobacter crescentus cells. In C. crescentus, several CheY homologs regulate motor function for different aspects of the bacterial lifestyle. We used subtomogram averaging to image binding of the CheY family protein CleD to the cytoplasmic Cring switch complex, the control center of the flagellar motor. This unambiguously confirmed the orientation of the motor switch protein FliM and the binding of a member of the CheY protein family to the outside rim of the C ring. We also uncovered previously unknown structural elaborations of the alphaproteobacterial flagellar motor, including two novel periplasmic ring structures, and the stator ring harboring eleven stator units, adding to our growing catalog of bacterial flagellar diversity.
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Affiliation(s)
| | - Isabelle Hug
- Focal Area of Infection BiologyBiozentrum of the University of BaselBaselSwitzerland
| | - Matteo Sangermani
- Focal Area of Infection BiologyBiozentrum of the University of BaselBaselSwitzerland
| | - Urs Jenal
- Focal Area of Infection BiologyBiozentrum of the University of BaselBaselSwitzerland
| | - Morgan Beeby
- Department of Life SciencesImperial College LondonLondonUK
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11
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Bacterial flagellar motor as a multimodal biosensor. Methods 2020; 193:5-15. [PMID: 32640316 DOI: 10.1016/j.ymeth.2020.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/04/2020] [Accepted: 06/22/2020] [Indexed: 01/05/2023] Open
Abstract
Bacterial Flagellar Motor is one of nature's rare rotary molecular machines. It enables bacterial swimming and it is the key part of the bacterial chemotactic network, one of the best studied chemical signalling networks in biology, which enables bacteria to direct its movement in accordance with the chemical environment. The network can sense down to nanomolar concentrations of specific chemicals on the time scale of seconds. Motor's rotational speed is linearly proportional to the electrochemical gradients of either proton or sodium driving ions, while its direction is regulated by the chemotactic network. Recently, it has been discovered that motor is also a mechanosensor. Given these properties, we discuss the motor's potential to serve as a multifunctional biosensor and a tool for characterising and studying the external environment, the bacterial physiology itself and single molecular motor biophysics.
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12
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Abstract
The bacterial flagellar motor is driven by an ion flux that is converted to torque by motor-attendant complexes known as stators. The dynamics of stator assembly around the motor in response to external stimuli have been the subject of much recent research, but less is known about the evolutionary origins of stator complexes and how they select for specific ions. Here, we review the latest structural and biochemical data for the stator complexes and compare these with other ion transporters and microbial motors to examine possible evolutionary origins of the stator complex.
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13
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Henderson LD, Matthews-Palmer TRS, Gulbronson CJ, Ribardo DA, Beeby M, Hendrixson DR. Diversification of Campylobacter jejuni Flagellar C-Ring Composition Impacts Its Structure and Function in Motility, Flagellar Assembly, and Cellular Processes. mBio 2020; 11:e02286-19. [PMID: 31911488 PMCID: PMC6946799 DOI: 10.1128/mbio.02286-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/19/2019] [Indexed: 12/22/2022] Open
Abstract
Bacterial flagella are reversible rotary motors that rotate external filaments for bacterial propulsion. Some flagellar motors have diversified by recruiting additional components that influence torque and rotation, but little is known about the possible diversification and evolution of core motor components. The mechanistic core of flagella is the cytoplasmic C ring, which functions as a rotor, directional switch, and assembly platform for the flagellar type III secretion system (fT3SS) ATPase. The C ring is composed of a ring of FliG proteins and a helical ring of surface presentation of antigen (SPOA) domains from the switch proteins FliM and one of two usually mutually exclusive paralogs, FliN or FliY. We investigated the composition, architecture, and function of the C ring of Campylobacter jejuni, which encodes FliG, FliM, and both FliY and FliN by a variety of interrogative approaches. We discovered a diversified C. jejuni C ring containing FliG, FliM, and both FliY, which functions as a classical FliN-like protein for flagellar assembly, and FliN, which has neofunctionalized into a structural role. Specific protein interactions drive the formation of a more complex heterooligomeric C. jejuni C-ring structure. We discovered that this complex C ring has additional cellular functions in polarly localizing FlhG for numerical regulation of flagellar biogenesis and spatial regulation of division. Furthermore, mutation of the C. jejuni C ring revealed a T3SS that was less dependent on its ATPase complex for assembly than were other systems. Our results highlight considerable evolved flagellar diversity that impacts motor output, biogenesis, and cellular processes in different species.IMPORTANCE The conserved core of bacterial flagellar motors reflects a shared evolutionary history that preserves the mechanisms essential for flagellar assembly, rotation, and directional switching. In this work, we describe an expanded and diversified set of core components in the Campylobacter jejuni flagellar C ring, the mechanistic core of the motor. Our work provides insight into how usually conserved core components may have diversified by gene duplication, enabling a division of labor of the ancestral protein between the two new proteins, acquisition of new roles in flagellar assembly and motility, and expansion of the function of the flagellum beyond motility, including spatial regulation of cell division and numerical control of flagellar biogenesis in C. jejuni Our results highlight that relatively small changes, such as gene duplications, can have substantial ramifications on the cellular roles of a molecular machine.
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Affiliation(s)
- Louie D Henderson
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | | | - Connor J Gulbronson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Deborah A Ribardo
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - David R Hendrixson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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14
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Nord AL, Pedaci F. Mechanisms and Dynamics of the Bacterial Flagellar Motor. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1267:81-100. [PMID: 32894478 DOI: 10.1007/978-3-030-46886-6_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Many bacteria are able to actively propel themselves through their complex environment, in search of resources and suitable niches. The source of this propulsion is the Bacterial Flagellar Motor (BFM), a molecular complex embedded in the bacterial membrane which rotates a flagellum. In this chapter we review the known physical mechanisms at work in the motor. The BFM shows a highly dynamic behavior in its power output, its structure, and in the stoichiometry of its components. Changes in speed, rotation direction, constituent protein conformations, and the number of constituent subunits are dynamically controlled in accordance to external chemical and mechanical cues. The mechano-sensitivity of the motor is likely related to the surface-sensing ability of bacteria, relevant in the initial stage of biofilm formation.
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Affiliation(s)
- A L Nord
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, University of Montpellier, Montpellier, France
| | - F Pedaci
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, University of Montpellier, Montpellier, France.
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15
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Minamino T, Kinoshita M, Namba K. Directional Switching Mechanism of the Bacterial Flagellar Motor. Comput Struct Biotechnol J 2019; 17:1075-1081. [PMID: 31452860 PMCID: PMC6700473 DOI: 10.1016/j.csbj.2019.07.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/26/2019] [Accepted: 07/27/2019] [Indexed: 11/16/2022] Open
Abstract
Bacteria sense temporal changes in extracellular stimuli via sensory signal transducers and move by rotating flagella towards into a favorable environment for their survival. Each flagellum is a supramolecular motility machine consisting of a bi-directional rotary motor, a universal joint and a helical propeller. The signal transducers transmit environmental signals to the flagellar motor through a cytoplasmic chemotactic signaling pathway. The flagellar motor is composed of a rotor and multiple stator units, each of which acts as a transmembrane proton channel to conduct protons and exert force on the rotor. FliG, FliM and FliN form the C ring on the cytoplasmic face of the basal body MS ring made of the transmembrane protein FliF and act as the rotor. The C ring also serves as a switching device that enables the motor to spin in both counterclockwise (CCW) and clockwise (CW) directions. The phosphorylated form of the chemotactic signaling protein CheY binds to FliM and FliN to induce conformational changes of the C ring responsible for switching the direction of flagellar motor rotation from CCW to CW. In this mini-review, we will describe current understanding of the switching mechanism of the bacterial flagellar motor.
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Affiliation(s)
- Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
- RIKEN Center for Biosystems Dynamic Research & Spring-8 Center, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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16
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Kaplan M, Subramanian P, Ghosal D, Oikonomou CM, Pirbadian S, Starwalt‐Lee R, Mageswaran SK, Ortega DR, Gralnick JA, El‐Naggar MY, Jensen GJ. In situ imaging of the bacterial flagellar motor disassembly and assembly processes. EMBO J 2019; 38:e100957. [PMID: 31304634 PMCID: PMC6627242 DOI: 10.15252/embj.2018100957] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 04/11/2019] [Accepted: 04/18/2019] [Indexed: 11/09/2022] Open
Abstract
The self-assembly of cellular macromolecular machines such as the bacterial flagellar motor requires the spatio-temporal synchronization of gene expression with proper protein localization and association of dozens of protein components. In Salmonella and Escherichia coli, a sequential, outward assembly mechanism has been proposed for the flagellar motor starting from the inner membrane, with the addition of each new component stabilizing the previous one. However, very little is known about flagellar disassembly. Here, using electron cryo-tomography and sub-tomogram averaging of intact Legionella pneumophila, Pseudomonas aeruginosa, and Shewanella oneidensis cells, we study flagellar motor disassembly and assembly in situ. We first show that motor disassembly results in stable outer membrane-embedded sub-complexes. These sub-complexes consist of the periplasmic embellished P- and L-rings, and bend the membrane inward while it remains apparently sealed. Additionally, we also observe various intermediates of the assembly process including an inner-membrane sub-complex consisting of the C-ring, MS-ring, and export apparatus. Finally, we show that the L-ring is responsible for reshaping the outer membrane, a crucial step in the flagellar assembly process.
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Affiliation(s)
- Mohammed Kaplan
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Poorna Subramanian
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Debnath Ghosal
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Catherine M Oikonomou
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Sahand Pirbadian
- Department of Physics and Astronomy, Biological Sciences, and ChemistryUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Ruth Starwalt‐Lee
- BioTechnology InstituteUniversity of Minnesota – Twin CitiesSt. PaulMNUSA
| | | | - Davi R Ortega
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Jeffrey A Gralnick
- BioTechnology InstituteUniversity of Minnesota – Twin CitiesSt. PaulMNUSA
- Department of Plant and Microbial BiologyUniversity of Minnesota – Twin CitiesSt. PaulMNUSA
| | - Mohamed Y El‐Naggar
- Department of Physics and Astronomy, Biological Sciences, and ChemistryUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Grant J Jensen
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
- Howard Hughes Medical InstituteCalifornia Institute of TechnologyPasadenaCAUSA
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17
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Kaplan M, Ghosal D, Subramanian P, Oikonomou CM, Kjaer A, Pirbadian S, Ortega DR, Briegel A, El-Naggar MY, Jensen GJ. The presence and absence of periplasmic rings in bacterial flagellar motors correlates with stator type. eLife 2019; 8:43487. [PMID: 30648971 PMCID: PMC6375700 DOI: 10.7554/elife.43487] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 12/19/2018] [Indexed: 12/22/2022] Open
Abstract
The bacterial flagellar motor, a cell-envelope-embedded macromolecular machine that functions as a cellular propeller, exhibits significant structural variability between species. Different torque-generating stator modules allow motors to operate in different pH, salt or viscosity levels. How such diversity evolved is unknown. Here, we use electron cryo-tomography to determine the in situ macromolecular structures of three Gammaproteobacteria motors: Legionella pneumophila, Pseudomonas aeruginosa, and Shewanella oneidensis, providing the first views of intact motors with dual stator systems. Complementing our imaging with bioinformatics analysis, we find a correlation between the motor’s stator system and its structural elaboration. Motors with a single H+-driven stator have only the core periplasmic P- and L-rings; those with dual H+-driven stators have an elaborated P-ring; and motors with Na+ or Na+/H+-driven stators have both their P- and L-rings embellished. Our results suggest an evolution of structural elaboration that may have enabled pathogenic bacteria to colonize higher-viscosity environments in animal hosts. Bacteria are so small that for them, making their way through water is like swimming in roofing tar for us. In response, these organisms have evolved a molecular machine that helps them move in their environment. Named the bacterial flagellum, this complex assemblage of molecules is formed of three main parts: a motor that spans the inner and outer membranes of the cell, and then a ‘hook’ that connects to a long filament which extends outside the bacterium. More precisely, the motor is formed of the stator, an ion pump that stays still, and of a rotor that can spin. Different rings can also be present in the space between the inner and outer membranes (the periplasm) and surround these components. The stator uses ions to generate the energy that makes the rotor whirl. In turn, this movement sets the filament in motion, propelling the bacterium. Depending on where the bacteria live, the stator can use different types of ions. In addition, while many species have a single stator system per motor, some may have several stator systems for one motor: this may help the microorganisms move in different conditions. As microbes colonize environments with a different pH or viscosity, they constantly evolve new versions of the motor which are more suitable to their new surroundings. However, a part of the motor remains the same across species. Overall, it is still unclear how bacterial flagella evolve, but examining the structure of new motors can shed light upon this process. Here, Kaplan et al. combine a bioinformatics approach with an imaging technique known as electron cryo-tomography to dissect the structure of the flagellar motor of three species of bacteria with different stator systems, and compare these to known motors of the same class. The results reveal a correlation between the nature of the stator system and the presence of certain elements. Stators that use sodium ions, or both sodium and hydrogen ions, are associated with two periplasmic rings surrounding the conserved motor structure. These rings do not exist in motors with single hydrogen-driven stators. Motors with dual hydrogen-driven stators are, to some extent, an ‘intermediate state’, with only one of those rings present. As all the studied species currently exist, it is difficult to know which version of the motor is the most ancient, and which one has evolved more recently. Capturing the diversity of bacterial motors gives us insight into the evolutionary forces that shape complex molecular structures, which is essential to understand how life evolved on Earth. More practically, this knowledge may also help us design better nanomachines to power microscopic robots.
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Affiliation(s)
- Mohammed Kaplan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Debnath Ghosal
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Poorna Subramanian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Andreas Kjaer
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Sahand Pirbadian
- Department of Physics and Astronomy, Biological Sciences, and Chemistry, University of Southern California, Los Angeles, United States
| | - Davi R Ortega
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Ariane Briegel
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, Biological Sciences, and Chemistry, University of Southern California, Los Angeles, United States
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
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18
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Lam KH, Xue C, Sun K, Zhang H, Lam WWL, Zhu Z, Ng JTY, Sause WE, Lertsethtakarn P, Lau KF, Ottemann KM, Au SWN. Three SpoA-domain proteins interact in the creation of the flagellar type III secretion system in Helicobacter pylori. J Biol Chem 2018; 293:13961-13973. [PMID: 29991595 PMCID: PMC6130963 DOI: 10.1074/jbc.ra118.002263] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/07/2018] [Indexed: 01/07/2023] Open
Abstract
Bacterial flagella are rotary nanomachines that contribute to bacterial fitness in many settings, including host colonization. The flagellar motor relies on the multiprotein flagellar motor-switch complex to govern flagellum formation and rotational direction. Different bacteria exhibit great diversity in their flagellar motors. One such variation is exemplified by the motor-switch apparatus of the gastric pathogen Helicobacter pylori, which carries an extra switch protein, FliY, along with the more typical FliG, FliM, and FliN proteins. All switch proteins are needed for normal flagellation and motility in H. pylori, but the molecular mechanism of their assembly is unknown. To fill this gap, we examined the interactions among these proteins. We found that the C-terminal SpoA domain of FliY (FliYC) is critical to flagellation and forms heterodimeric complexes with the FliN and FliM SpoA domains, which are β-sheet domains of type III secretion system proteins. Surprisingly, unlike in other flagellar switch systems, neither FliY nor FliN self-associated. The crystal structure of the FliYC-FliNC complex revealed a saddle-shaped structure homologous to the FliN-FliN dimer of Thermotoga maritima, consistent with a FliY-FliN heterodimer forming the functional unit. Analysis of the FliYC-FliNC interface indicated that oppositely charged residues specific to each protein drive heterodimer formation. Moreover, both FliYC-FliMC and FliYC-FliNC associated with the flagellar regulatory protein FliH, explaining their important roles in flagellation. We conclude that H. pylori uses a FliY-FliN heterodimer instead of a homodimer and creates a switch complex with SpoA domains derived from three distinct proteins.
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Affiliation(s)
- Kwok Ho Lam
- From the Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chaolun Xue
- From the Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Shatin, Hong Kong, ,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China, and
| | - Kailei Sun
- From the Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Huawei Zhang
- From the Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Shatin, Hong Kong, ,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China, and
| | - Wendy Wai Ling Lam
- From the Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Shatin, Hong Kong, ,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China, and
| | - Zeyu Zhu
- From the Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Juliana Tsz Yan Ng
- From the Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Shatin, Hong Kong
| | - William E. Sause
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California 95064
| | - Paphavee Lertsethtakarn
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California 95064
| | - Kwok Fai Lau
- From the Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Karen M. Ottemann
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California 95064
| | - Shannon Wing Ngor Au
- From the Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Shatin, Hong Kong, ,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China, and ,To whom correspondence should be addressed. Tel.:
852-3943-4170; E-mail:
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19
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Hu L, Rehman S, Tao K, Miao J. Characterization on Three-Dimensional Trajectory of Disk-Like Gold-Nickel-Platinum Nanomotor Using Digital Holographic Imaging. ChemistrySelect 2018. [DOI: 10.1002/slct.201801534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Liangxing Hu
- School of Mechanical and Aerospace Engineering; Nanyang Technological University, 50 Nanyang Avenue; Singapore 639798
| | - Shakil Rehman
- Singapore-MIT Alliance for Research and Technology (SMART), 1 CREATE Way; Singapore 138602
| | - Kai Tao
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering; Northwestern Polytechnical University, Xi'an; China 710072
| | - Jianmin Miao
- School of Mechanical and Aerospace Engineering; Nanyang Technological University, 50 Nanyang Avenue; Singapore 639798
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20
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Nord AL, Pols AF, Depken M, Pedaci F. Kinetic analysis methods applied to single motor protein trajectories. Phys Chem Chem Phys 2018; 20:18775-18781. [PMID: 29961801 DOI: 10.1039/c8cp03056a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular motors convert chemical or electrical energy into mechanical displacement, either linear or rotary. Under ideal circumstances, single-molecule measurements can spatially and temporally resolve individual steps of the motor, revealing important properties of the underlying mechanochemical process. Unfortunately, steps are often hard to resolve, as they are masked by thermal noise. In such cases, details of the mechanochemistry can nonetheless be recovered by analyzing the fluctuations in the recorded traces. Here, we expand upon existing statistical analysis methods, providing two new avenues to extract the motor step size, the effective number of rate-limiting chemical states per translocation step, and the compliance of the link between the motor and the probe particle. We first demonstrate the power and limitations of these methods using simulated molecular motor trajectories, and we then apply these methods to experimental data of kinesin, the bacterial flagellar motor, and F1-ATPase.
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Affiliation(s)
- A L Nord
- CBS, Univ. Montpellier, CNRS, INSERM, Montpellier, France.
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21
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Kinoshita M, Furukawa Y, Uchiyama S, Imada K, Namba K, Minamino T. Insight into adaptive remodeling of the rotor ring complex of the bacterial flagellar motor. Biochem Biophys Res Commun 2017; 496:12-17. [PMID: 29294326 DOI: 10.1016/j.bbrc.2017.12.118] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 12/04/2017] [Accepted: 12/20/2017] [Indexed: 12/23/2022]
Abstract
The bacterial flagellar motor rotates in both counterclockwise (CCW) and clockwise (CW) directions. FliG, FliM and FliN form the C ring on the cytoplasmic face of the MS ring made of a transmembrane protein, FliF. The C ring acts not only as a rotor but also as a switch of the direction of motor rotation. FliG consists of three domains: FliGN, FliGM and FliGC. FliGN directly binds to FliF. Intermolecular interactions between FliGM and FliGC drive FliG ring formation. FliGM is responsible for the interaction with FliM. FliGC is involved in the interaction with the stator protein MotA. Adaptive remodeling of the C ring occurs when the motor switches between the CCW and CW states. However, it remained unknown how. Here, we report the effects of a CW-locked deletion mutation (ΔPEV) in FliG of Thermotaoga maritia (Tm-FliG) on FliG-FliG and FliG-FliM interactions. The PEV deletion stabilized the intramolecular interaction between FliGM and FliGC, thereby suppressing the oligomerization of Tm-FliGMC in solution. This deletion also induced a conformational change of HelixMC connecting FliGM and FliGC to reduce the binding affinity of Tm-FliGMC for FliM. We will discuss adaptive remodeling of the C ring responsible for flagellar motor switching.
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Affiliation(s)
- Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Yukio Furukawa
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Susumu Uchiyama
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Katsumi Imada
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan; Quantitative Biology Center, RIKEN, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan.
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22
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Beyersdorf MS, Sircar R, Lookadoo DB, Bottone CJ, Lynch MJ, Crane BR, Halkides CJ. Production, characterization, and assessment of a stable analog of the response regulator CheY-phosphate from Thermotoga maritima. Protein Sci 2017; 26:1547-1554. [PMID: 28440031 DOI: 10.1002/pro.3180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 12/23/2022]
Abstract
Phosphorylation of CheY promotes association with the flagellar motor and ultimately controls the directional bias of the motor. However, biochemical studies of activated CheY-phosphate have been challenging due to the rapid hydrolysis of the aspartyl-phosphate in vitro. An inert analog of Tm CheY-phosphate, phosphono-CheY, was synthesized by chemical modification and purified by cation-exchange chromatography. Changes in HPLC retention times, chemical assays for phosphate and free thiol, and mass spectrometry experiments demonstrate modification of Cys54 with a phosphonomethyl group. Additionally, a crystal structure showed electron density for the phosphonomethyl group at Cys54, consistent with a modification at that position. Subsequent biochemical experiments confirmed that protein crystals were phosphono-CheY. Isothermal titration calorimetry and fluorescence polarization binding assays demonstrated that phosphono-CheY bound a peptide derived from FliM, a native partner of CheY-phosphate, with a dissociation constant of ∼29 µM, at least sixfold more tightly than unmodified CheY. Taken together these results suggest that Tm phosphono-CheY is a useful and unique analog of Tm CheY-phosphate.
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Affiliation(s)
- Matthew S Beyersdorf
- Department of Chemistry and Biochemistry, The University of North Carolina Wilmington, Wilmington, North Carolina, 28403
| | - Ria Sircar
- Department of Chemistry and Chemical Biology, Physical Sciences Building, Cornell University, Ithaca, New York, 14853
| | - Daniel B Lookadoo
- Department of Chemistry and Biochemistry, The University of North Carolina Wilmington, Wilmington, North Carolina, 28403
| | - Cory J Bottone
- Department of Chemistry and Biochemistry, The University of North Carolina Wilmington, Wilmington, North Carolina, 28403
| | - Michael J Lynch
- Department of Chemistry and Chemical Biology, Physical Sciences Building, Cornell University, Ithaca, New York, 14853
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Physical Sciences Building, Cornell University, Ithaca, New York, 14853
| | - Christopher J Halkides
- Department of Chemistry and Biochemistry, The University of North Carolina Wilmington, Wilmington, North Carolina, 28403
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23
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Dynamics in the Dual Fuel Flagellar Motor of Shewanella oneidensis MR-1. Methods Mol Biol 2017. [PMID: 28389963 DOI: 10.1007/978-1-4939-6927-2_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The stator is an eminent component of the flagellar motor and determines a number of the motor's properties, such as the rotation-energizing coupling ion (H+ or Na+) or the torque that can be generated. The stator consists of several units located in the cytoplasmic membrane surrounding the flagellar drive shaft. Studies on flagellar motors of several bacterial species have provided evidence that the number as well as the retention time of stators coupled to the motor is highly dynamic and depends on the environmental conditions. Notably, numerous species possess more than a single distinct set of stators. It is likely that the presence of different stator units enables these bacteria to adjust the flagellar motor properties and function to meet the environmental requirements. One of these species is Shewanella oneidensis MR-1 that is equipped with a single polar flagellum and two stator units, the Na+-dependent PomAB and the H+-dependent MotAB. Here, we describe a method to determine stator dynamics by fluorescence microscopy, demonstrating how bacteria can change the composition of an intricate molecular machine according to environmental conditions.
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24
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Lee LK. Structural Analysis of the Flagellar Component Proteins in Solution by Small Angle X-Ray Scattering. Methods Mol Biol 2017; 1593:105-117. [PMID: 28389948 DOI: 10.1007/978-1-4939-6927-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Small angle X-ray scattering is an increasingly utilized method for characterizing the shape and structural properties of proteins in solution. The technique is amenable to very large protein complexes and to dynamic particles with different conformational states. It is therefore ideally suited to the analysis of some flagellar motor components. Indeed, we recently used the method to analyze the solution structure of the flagellar motor protein FliG, which when combined with high-resolution snapshots of conformational states from crystal structures, led to insights into conformational transitions that are important in mediating the self-assembly of the bacterial flagellar motor. Here, we describe procedures for X-ray scattering data collection of flagellar motor components, data analysis, and interpretation.
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Affiliation(s)
- Lawrence K Lee
- European Molecular Biology Laboratory Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.
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25
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Chen M, Zhao Z, Yang J, Peng K, Baker MAB, Bai F, Lo CJ. Length-dependent flagellar growth of Vibrio alginolyticus revealed by real time fluorescent imaging. eLife 2017; 6:e22140. [PMID: 28098557 PMCID: PMC5300704 DOI: 10.7554/elife.22140] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/15/2017] [Indexed: 01/27/2023] Open
Abstract
Bacterial flagella are extracellular filaments that drive swimming in bacteria. During motor assembly, flagellins are transported unfolded through the central channel in the flagellum to the growing tip. Here, we applied in vivo fluorescent imaging to monitor in real time the Vibrio alginolyticus polar flagella growth. The flagellar growth rate is found to be highly length-dependent. Initially, the flagellum grows at a constant rate (50 nm/min) when shorter than 1500 nm. The growth rate decays sharply when the flagellum grows longer, which decreases to ~9 nm/min at 7500 nm. We modeled flagellin transport inside the channel as a one-dimensional diffusive process with an injection force at its base. When the flagellum is short, its growth rate is determined by the loading speed at the base. Only when the flagellum grows longer does diffusion of flagellin become the rate-limiting step, dramatically reducing the growth rate. Our results shed new light on the dynamic building process of this complex extracellular structure.
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Affiliation(s)
- Meiting Chen
- Department of Physics and Graduate Institute of Biophysics, National Central University, Jhongli, Taiwan
| | - Ziyi Zhao
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Jin Yang
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Kai Peng
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Matthew AB Baker
- EMBL Australia Node for Single Molecule Science, University of New South Wales, Sydney, Australia
| | - Fan Bai
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China, (FB)
| | - Chien-Jung Lo
- Department of Physics and Graduate Institute of Biophysics, National Central University, Jhongli, Taiwan, (C-JL)
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26
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Brenzinger S, Dewenter L, Delalez NJ, Leicht O, Berndt V, Paulick A, Berry RM, Thanbichler M, Armitage JP, Maier B, Thormann KM. Mutations targeting the plug-domain of the Shewanella oneidensis proton-driven stator allow swimming at increased viscosity and under anaerobic conditions. Mol Microbiol 2016; 102:925-938. [PMID: 27611183 DOI: 10.1111/mmi.13499] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Shewanella oneidensis MR-1 possesses two different stator units to drive flagellar rotation, the Na+ -dependent PomAB stator and the H+ -driven MotAB stator, the latter possibly acquired by lateral gene transfer. Although either stator can independently drive swimming through liquid, MotAB-driven motors cannot support efficient motility in structured environments or swimming under anaerobic conditions. Using ΔpomAB cells we isolated spontaneous mutants able to move through soft agar. We show that a mutation that alters the structure of the plug domain in MotB affects motor functions and allows cells to swim through media of increased viscosity and under anaerobic conditions. The number and exchange rates of the mutant stator around the rotor were not significantly different from wild-type stators, suggesting that the number of stators engaged is not the cause of increased swimming efficiency. The swimming speeds of planktonic mutant MotAB-driven cells was reduced, and overexpression of some of these stators caused reduced growth rates, implying that mutant stators not engaged with the rotor allow some proton leakage. The results suggest that the mutations in the MotB plug domain alter the proton interactions with the stator ion channel in a way that both increases torque output and allows swimming at decreased pmf values.
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Affiliation(s)
- Susanne Brenzinger
- Department of Microbiology and Molecular Biology at the IFZ, Justus-Liebig-Universität Gießen, Gießen, 35392, Germany.,Department of Ecophysiology, Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, 35043, Germany
| | - Lena Dewenter
- Department of Physics, Universität Köln, Cologne, 50674, Germany
| | | | - Oliver Leicht
- Philipps-Universität, Marburg, Germany LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
| | - Volker Berndt
- Department of Ecophysiology, Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, 35043, Germany
| | - Anja Paulick
- Department of Ecophysiology, Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, 35043, Germany
| | - Richard M Berry
- Physics Department, University of Oxford, Oxford, OX1 3QU, UK
| | - Martin Thanbichler
- Philipps-Universität, Marburg, Germany LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany.,Max-Planck-Institut für terrestrische Mikrobiologie & LOEWE Center für Synthetische Mikrobiologie, Marburg, 35043, Germany
| | | | - Berenike Maier
- Department of Physics, Universität Köln, Cologne, 50674, Germany
| | - Kai M Thormann
- Department of Microbiology and Molecular Biology at the IFZ, Justus-Liebig-Universität Gießen, Gießen, 35392, Germany
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27
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Pandini A, Morcos F, Khan S. The Gearbox of the Bacterial Flagellar Motor Switch. Structure 2016; 24:1209-20. [PMID: 27345932 PMCID: PMC4938800 DOI: 10.1016/j.str.2016.05.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/26/2016] [Accepted: 05/23/2016] [Indexed: 12/11/2022]
Abstract
Switching of flagellar motor rotation sense dictates bacterial chemotaxis. Multi-subunit FliM-FliG rotor rings couple signal protein binding in FliM with reversal of a distant FliG C-terminal (FliGC) helix involved in stator contacts. Subunit dynamics were examined in conformer ensembles generated by molecular simulations from the X-ray structures. Principal component analysis extracted collective motions. Interfacial loop immobilization by complex formation coupled elastic fluctuations of the FliM middle (FliMM) and FliG middle (FliGM) domains. Coevolved mutations captured interfacial dynamics as well as contacts. FliGM rotation was amplified via two central hinges to the FliGC helix. Intrinsic flexibility, reported by the FliGMC ensembles, reconciled conformers with opposite FliGC helix orientations. FliG domain stacking deformed the inter-domain linker and reduced flexibility; but conformational changes were not triggered by engineered linker deletions that cause a rotation-locked phenotype. These facts suggest that binary rotation states arise from conformational selection by stacking interactions. Switch complex exploits differential subunit stiffness for mechanical amplification Distinct rotor protein X-ray structures generate overlapping conformer ensembles Stacking constraints on a flexible helix linker could select diverse rotation states Non-contact elastic couplings at the subunit interface in the complex have coevolved
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Affiliation(s)
- Alessandro Pandini
- Department of Computer Science and Synthetic Biology Theme, Brunel University London, Uxbridge UB8 3PH, UK; Computational Cell and Molecular Biology, The Francis Crick Institute, London NW1 1AT, UK
| | - Faruck Morcos
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Shahid Khan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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28
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Bergeron JR. Structural modeling of the flagellum MS ring protein FliF reveals similarities to the type III secretion system and sporulation complex. PeerJ 2016; 4:e1718. [PMID: 26925337 PMCID: PMC4768692 DOI: 10.7717/peerj.1718] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/31/2016] [Indexed: 11/29/2022] Open
Abstract
The flagellum is a large proteinaceous organelle found at the surface of many bacteria, whose primary role is to allow motility through the rotation of a long extracellular filament. It is an essential virulence factor in many pathogenic species, and is also a priming component in the formation of antibiotic-resistant biofilms. The flagellum consists of the export apparatus on the cytosolic side; the basal body and rotor, spanning the bacterial membrane(s) and periplasm; and the hook-filament, that protrudes away from the bacterial surface. Formation of the basal body MS ring region, constituted of multiple copies of the protein FliF, is one of the initial steps of flagellum assembly. However, the precise architecture of FliF is poorly understood. Here, I report a bioinformatics analysis of the FliF sequence from various bacterial species, suggesting that its periplasmic region is composed of three globular domains. The first two are homologous to that of the type III secretion system injectisome proteins SctJ, and the third possesses a similar fold to that of the sporulation complex component SpoIIIAG. I also describe that Chlamydia possesses an unusual FliF protein, lacking part of the SctJ homology domain and the SpoIIIAG-like domain, and fused to the rotor component FliG at its C-terminus. Finally, I have combined the sequence analysis of FliF with the EM map of the MS ring, to propose the first atomic model for the FliF oligomer, suggesting that FliF is structurally akin to a fusion of the two injectisome components SctJ and SctD. These results further define the relationship between the flagellum, injectisome and sporulation complex, and will facilitate future structural characterization of the flagellum basal body.
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Affiliation(s)
- Julien R Bergeron
- Department of Biochemistry, University of Washington , Seattle, WA , USA
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29
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Baker MAB, Hynson RMG, Ganuelas LA, Mohammadi NS, Liew CW, Rey AA, Duff AP, Whitten AE, Jeffries CM, Delalez NJ, Morimoto YV, Stock D, Armitage JP, Turberfield AJ, Namba K, Berry RM, Lee LK. Domain-swap polymerization drives the self-assembly of the bacterial flagellar motor. Nat Struct Mol Biol 2016; 23:197-203. [PMID: 26854663 DOI: 10.1038/nsmb.3172] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/13/2016] [Indexed: 01/02/2023]
Abstract
Large protein complexes assemble spontaneously, yet their subunits do not prematurely form unwanted aggregates. This paradox is epitomized in the bacterial flagellar motor, a sophisticated rotary motor and sensory switch consisting of hundreds of subunits. Here we demonstrate that Escherichia coli FliG, one of the earliest-assembling flagellar motor proteins, forms ordered ring structures via domain-swap polymerization, which in other proteins has been associated with uncontrolled and deleterious protein aggregation. Solution structural data, in combination with in vivo biochemical cross-linking experiments and evolutionary covariance analysis, revealed that FliG exists predominantly as a monomer in solution but only as domain-swapped polymers in assembled flagellar motors. We propose a general structural and thermodynamic model for self-assembly, in which a structural template controls assembly and shapes polymer formation into rings.
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Affiliation(s)
- Matthew A B Baker
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.,European Molecular Biology Laboratory Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Robert M G Hynson
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - Lorraine A Ganuelas
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - Nasim Shah Mohammadi
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - Chu Wai Liew
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - Anthony A Rey
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - Anthony P Duff
- Australian Nuclear and Science Technology Organisation, Lucas Heights, New South Wales, Australia
| | - Andrew E Whitten
- Australian Nuclear and Science Technology Organisation, Lucas Heights, New South Wales, Australia
| | - Cy M Jeffries
- Australian Nuclear and Science Technology Organisation, Lucas Heights, New South Wales, Australia
| | | | - Yusuke V Morimoto
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Daniela Stock
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | | | | | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | | | - Lawrence K Lee
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.,European Molecular Biology Laboratory Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
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30
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Hettiarachchi CA, Melton LD, McGillivray DJ, Loveday SM, Gerrard JA, Williams MAK. β-Lactoglobulin nanofibrils can be assembled into nanotapes via site-specific interactions with pectin. SOFT MATTER 2016; 12:756-768. [PMID: 26517088 DOI: 10.1039/c5sm01530h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Controlling the self-assembly of individual supramolecular entities, such as amyloid fibrils, into hierarchical architectures enables the 'bottom-up' fabrication of useful bionanomaterials. Here, we present the hierarchical assembly of β-lactoglobulin nanofibrils into the form of 'nanotapes' in the presence of a specific pectin with a high degree of methylesterification. The nanotapes produced were highly ordered, and had an average width of 180 nm at pH 3. Increasing the ionic strength or the pH of the medium led to the disassembly of nanotapes, indicating that electrostatic interactions stabilised the nanotape architecture. Small-angle X-ray scattering experiments conducted on the nanotapes showed that adequate space is available between adjacent nanofibrils to accommodate pectin molecules. To locate the interaction sites on the pectin molecule, it was subjected to endopolygalacturonase digestion, and the resulting products were analysed using capillary electrophoresis and size-exclusion chromatography for their charge and molecular weight, respectively. Results suggested that the functional pectin molecules carry short (<10 residues) enzyme-susceptible blocks of negatively charged, non-methylesterified galacturonic acid residues in the middle of their homogalacturonan backbones (and possibly near their ends), that specifically bind to sites on the nanofibrils. Blocking the interaction sites on the nanofibril surface using small oligomers of non-methylesterified galacturonic acid residues similar in size to the interaction sites of the pectin molecule decreased the nanotape formation, indicating that site-specific electrostatic interactions are vital for the cross-linking of nanofibrils. We propose a structural model for the pectin-cross-linked β-lactoglobulin nanotapes, the elements of which will inform the future design of bionanomaterials.
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31
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Hu L, Miao J, Grüber G. Disk-like nanojets with steerable trajectory using platinum nozzle nanoengines. RSC Adv 2016. [DOI: 10.1039/c5ra24202a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Nanojets with one off-center platinum nozzle nanoengine can propel forward circularly, while the nanojets with two identically and symmetrically distributed platinum nozzle nanoengines are capable of moving forward in a linear way.
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Affiliation(s)
- Liangxing Hu
- School of Mechanical and Aerospace Engineering
- Nanyang Technological University
- Singapore
| | - Jianmin Miao
- School of Mechanical and Aerospace Engineering
- Nanyang Technological University
- Singapore
| | - Gerhard Grüber
- School of Biological Sciences
- Nanyang Technological University
- Singapore
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32
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Designed Repeat Proteins as Building Blocks for Nanofabrication. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 940:61-81. [DOI: 10.1007/978-3-319-39196-0_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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33
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Hu L, Tao K, Miao J, Grüber G. Hydrogen-peroxide-fuelled platinum–nickel–SU-8 microrocket with steerable propulsion using an eccentric nanoengine. RSC Adv 2016. [DOI: 10.1039/c6ra17248b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Microrockets with eccentric nanoengines are able to realize the steerable propulsion in either a clockwise or a counter-clockwise direction.
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Affiliation(s)
- Liangxing Hu
- School of Mechanical and Aerospace Engineering
- Nanyang Technological University
- Singapore 639798
- Singapore
| | - Kai Tao
- School of Mechanical and Aerospace Engineering
- Nanyang Technological University
- Singapore 639798
- Singapore
| | - Jianmin Miao
- School of Mechanical and Aerospace Engineering
- Nanyang Technological University
- Singapore 639798
- Singapore
| | - Gerhard Grüber
- School of Biological Sciences
- Nanyang Technological University
- Singapore 637551
- Singapore
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34
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Black WP, Wang L, Davis MY, Yang Z. The orphan response regulator EpsW is a substrate of the DifE kinase and it regulates exopolysaccharide in Myxococcus xanthus. Sci Rep 2015; 5:17831. [PMID: 26639551 PMCID: PMC4671073 DOI: 10.1038/srep17831] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 11/06/2015] [Indexed: 11/17/2022] Open
Abstract
Here we attempted to identify the downstream target of the DifE histidine kinase in the regulation of exopolysaccharide (EPS) production in the Gram-negative bacterium Myxococcus xanthus. This bacterium is an important model system for the studies of Type IV pilus (T4P) because it is motile by social (S) motility which is powered by T4P retraction. EPS is critical for S motility because it is the preferred anchor for T4P retraction in this bacterium. Previous studies identified the Dif chemosensory pathway as crucial for the regulation of EPS production. However, the downstream target of the DifE kinase in this pathway was unknown. In this study, EpsW, an orphan and single-domain response regulator (RR), was identified as a potential DifE target first by bioinformatics. Subsequent experiments demonstrated that epsW is essential for EPS biosynthesis in vivo and that EpsW is directly phosphorylated by DifE in vitro. Targted mutagenesis of epsW suggests that EpsW is unlikely the terminal RR of the Dif pathway. We propose instead that EpsW is an intermediary in a multistep phosphorelay that regulates EPS in M. xanthus.
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Affiliation(s)
- Wesley P Black
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Lingling Wang
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.,College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Manli Y Davis
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Zhaomin Yang
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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35
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Pandini A, Kleinjung J, Rasool S, Khan S. Coevolved Mutations Reveal Distinct Architectures for Two Core Proteins in the Bacterial Flagellar Motor. PLoS One 2015; 10:e0142407. [PMID: 26561852 PMCID: PMC4642947 DOI: 10.1371/journal.pone.0142407] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/21/2015] [Indexed: 02/08/2023] Open
Abstract
Switching of bacterial flagellar rotation is caused by large domain movements of the FliG protein triggered by binding of the signal protein CheY to FliM. FliG and FliM form adjacent multi-subunit arrays within the basal body C-ring. The movements alter the interaction of the FliG C-terminal (FliGC) “torque” helix with the stator complexes. Atomic models based on the Salmonella entrovar C-ring electron microscopy reconstruction have implications for switching, but lack consensus on the relative locations of the FliG armadillo (ARM) domains (amino-terminal (FliGN), middle (FliGM) and FliGC) as well as changes during chemotaxis. The generality of the Salmonella model is challenged by the variation in motor morphology and response between species. We studied coevolved residue mutations to determine the unifying elements of switch architecture. Residue interactions, measured by their coevolution, were formalized as a network, guided by structural data. Our measurements reveal a common design with dedicated switch and motor modules. The FliM middle domain (FliMM) has extensive connectivity most simply explained by conserved intra and inter-subunit contacts. In contrast, FliG has patchy, complex architecture. Conserved structural motifs form interacting nodes in the coevolution network that wire FliMM to the FliGC C-terminal, four-helix motor module (C3-6). FliG C3-6 coevolution is organized around the torque helix, differently from other ARM domains. The nodes form separated, surface-proximal patches that are targeted by deleterious mutations as in other allosteric systems. The dominant node is formed by the EHPQ motif at the FliMMFliGM contact interface and adjacent helix residues at a central location within FliGM. The node interacts with nodes in the N-terminal FliGc α-helix triad (ARM-C) and FliGN. ARM-C, separated from C3-6 by the MFVF motif, has poor intra-network connectivity consistent with its variable orientation revealed by structural data. ARM-C could be the convertor element that provides mechanistic and species diversity.
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Affiliation(s)
- Alessandro Pandini
- Department of Computer Science and Synthetic Biology Theme, Brunel University London, Uxbridge UB8 3PH, United Kingdom
| | - Jens Kleinjung
- Mathematical Biology, Francis Crick Institute, Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
| | - Shafqat Rasool
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Shahid Khan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States of America
- * E-mail:
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36
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Plant virus directed fabrication of nanoscale materials and devices. Virology 2015; 479-480:200-12. [DOI: 10.1016/j.virol.2015.03.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/24/2015] [Accepted: 03/02/2015] [Indexed: 11/21/2022]
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37
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Hajne J, Hanson KL, van Zalinge H, Nicolau DV. Motility of Actin Filaments on Micro-Contact Printed Myosin Patterns. IEEE Trans Nanobioscience 2015; 14:313-22. [DOI: 10.1109/tnb.2015.2393052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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38
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Paulick A, Delalez NJ, Brenzinger S, Steel BC, Berry RM, Armitage JP, Thormann KM. Dual stator dynamics in theShewanella oneidensis MR-1 flagellar motor. Mol Microbiol 2015; 96:993-1001. [DOI: 10.1111/mmi.12984] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Anja Paulick
- Max-Planck-Institute für terrestrische Mikrobiologie; Department of Ecophysiology; 35043 Marburg Germany
| | | | - Susanne Brenzinger
- Max-Planck-Institute für terrestrische Mikrobiologie; Department of Ecophysiology; 35043 Marburg Germany
- Justus-Liebig-Universität Gießen; Department of Microbiology and Molecular Biology at the IFZ; Gießen 35392 Germany
| | | | | | | | - Kai M. Thormann
- Max-Planck-Institute für terrestrische Mikrobiologie; Department of Ecophysiology; 35043 Marburg Germany
- Justus-Liebig-Universität Gießen; Department of Microbiology and Molecular Biology at the IFZ; Gießen 35392 Germany
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39
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Abstract
Movement is a fundamental characteristic of all living things. This biogenic function is carried out by various nanometer-sized molecular machines. Molecular motor is a typical molecular machinery in which the characteristic features of proteins are integrated; these include enzymatic activity, energy conversion, molecular recognition and self-assembly. These biologically important reactions occur with the association of water molecules that surround the motors. Applied pressures can alter the intermolecular interactions between the motors and water. In this chapter we describe the development of a high-pressure microscope and a new motility assay that enables the visualization of the motility of molecular motors under conditions of high-pressure. Our results demonstrate that applied pressure dynamically changes the motility of molecular motors such as kinesin, F1-ATPase and bacterial flagellar motors.
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Affiliation(s)
- Masayoshi Nishiyama
- The Hakubi Center for Advanced Research/Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, 606-8501, Japan,
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40
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Sircar R, Borbat PP, Lynch MJ, Bhatnagar J, Beyersdorf MS, Halkides CJ, Freed JH, Crane BR. Assembly states of FliM and FliG within the flagellar switch complex. J Mol Biol 2014; 427:867-886. [PMID: 25536293 DOI: 10.1016/j.jmb.2014.12.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 12/12/2014] [Accepted: 12/12/2014] [Indexed: 01/11/2023]
Abstract
At the base of the bacterial flagella, a cytoplasmic rotor (the C-ring) generates torque and reverses rotation sense in response to stimuli. The bulk of the C-ring forms from many copies of the proteins FliG, FliM, and FliN, which together constitute the switch complex. To help resolve outstanding issues regarding C-ring architecture, we have investigated interactions between FliM and FliG from Thermotoga maritima with X-ray crystallography and pulsed dipolar ESR spectroscopy (PDS). A new crystal structure of an 11-unit FliG:FliM complex produces a large arc with a curvature consistent with the dimensions of the C-ring. Previously determined structures along with this new structure provided a basis to test switch complex assembly models. PDS combined with mutational studies and targeted cross-linking reveal that FliM and FliG interact through their middle domains to form both parallel and antiparallel arrangements in solution. Residue substitutions at predicted interfaces disrupt higher-order complexes that are primarily mediated by contacts between the C-terminal domain of FliG and the middle domain of a neighboring FliG molecule. Spin separations among multi-labeled components fit a self-consistent model that agree well with electron microscopy images of the C-ring. An activated form of the response regulator CheY destabilizes the parallel arrangement of FliM molecules to perturb FliG alignment in a process that may reflect the onset of rotation switching. These data suggest a model of C-ring assembly in which intermolecular contacts among FliG domains provide a template for FliM assembly and cooperative transitions.
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Affiliation(s)
- Ria Sircar
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, NY 14853, USA
| | - Michael J Lynch
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jaya Bhatnagar
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Matthew S Beyersdorf
- Department of Chemistry and Biochemistry, Unversity of North Carolina Wilmington, Wilmington, NC 28403, USA
| | - Christopher J Halkides
- Department of Chemistry and Biochemistry, Unversity of North Carolina Wilmington, Wilmington, NC 28403, USA
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, NY 14853, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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41
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Affiliation(s)
| | - Walter Herzog
- University of Calgary Human Performance Lab, Calgary, Canada
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42
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Morimoto YV, Minamino T. Structure and function of the bi-directional bacterial flagellar motor. Biomolecules 2014; 4:217-34. [PMID: 24970213 PMCID: PMC4030992 DOI: 10.3390/biom4010217] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 01/24/2014] [Accepted: 02/04/2014] [Indexed: 01/02/2023] Open
Abstract
The bacterial flagellum is a locomotive organelle that propels the bacterial cell body in liquid environments. The flagellum is a supramolecular complex composed of about 30 different proteins and consists of at least three parts: a rotary motor, a universal joint, and a helical filament. The flagellar motor of Escherichia coli and Salmonella enterica is powered by an inward-directed electrochemical potential difference of protons across the cytoplasmic membrane. The flagellar motor consists of a rotor made of FliF, FliG, FliM and FliN and a dozen stators consisting of MotA and MotB. FliG, FliM and FliN also act as a molecular switch, enabling the motor to spin in both counterclockwise and clockwise directions. Each stator is anchored to the peptidoglycan layer through the C-terminal periplasmic domain of MotB and acts as a proton channel to couple the proton flow through the channel with torque generation. Highly conserved charged residues at the rotor–stator interface are required not only for torque generation but also for stator assembly around the rotor. In this review, we will summarize our current understanding of the structure and function of the proton-driven bacterial flagellar motor.
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Affiliation(s)
- Yusuke V Morimoto
- Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.
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43
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Gohara M, Kobayashi S, Abe-Yoshizumi R, Nonoyama N, Kojima S, Asami Y, Homma M. Biophysical characterization of the C-terminal region of FliG, an essential rotor component of the Na+-driven flagellar motor. J Biochem 2013; 155:83-9. [DOI: 10.1093/jb/mvt100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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44
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Lam KH, Lam WWL, Wong JYK, Chan LC, Kotaka M, Ling TKW, Jin DY, Ottemann KM, Au SWN. Structural basis of FliG-FliM interaction inHelicobacter pylori. Mol Microbiol 2013; 88:798-812. [DOI: 10.1111/mmi.12222] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2013] [Indexed: 12/20/2022]
Affiliation(s)
- Kwok-Ho Lam
- Center for Protein Science and Crystallography; School of Life Sciences; The Chinese University of Hong Kong; Hong Kong; China
| | - Wendy Wai Ling Lam
- Center for Protein Science and Crystallography; School of Life Sciences; The Chinese University of Hong Kong; Hong Kong; China
| | - Jase Yan-Kit Wong
- Center for Protein Science and Crystallography; School of Life Sciences; The Chinese University of Hong Kong; Hong Kong; China
| | - Ling-Chim Chan
- Department of Biochemistry; The University of Hong Kong; Hong Kong; China
| | - Masayo Kotaka
- Department of Physiology; The University of Hong Kong; Hong Kong; China
| | - Thomas Kin-Wah Ling
- Department of Microbiology; The Chinese University of Hong Kong; Hong Kong; China
| | - Dong-Yan Jin
- Department of Biochemistry; The University of Hong Kong; Hong Kong; China
| | - Karen M. Ottemann
- Department of Microbiology and Environmental Toxicology; University of California Santa Cruz; Santa Cruz; CA; USA
| | - Shannon Wing-Ngor Au
- Center for Protein Science and Crystallography; School of Life Sciences; The Chinese University of Hong Kong; Hong Kong; China
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45
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High hydrostatic pressure induces counterclockwise to clockwise reversals of the Escherichia coli flagellar motor. J Bacteriol 2013; 195:1809-14. [PMID: 23417485 DOI: 10.1128/jb.02139-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The bacterial flagellar motor is a reversible rotary machine that rotates a left-handed helical filament, allowing bacteria to swim toward a more favorable environment. The direction of rotation reverses from counterclockwise (CCW) to clockwise (CW), and vice versa, in response to input from the chemotaxis signaling circuit. CW rotation is normally caused by binding of the phosphorylated response regulator CheY (CheY-P), and strains lacking CheY are typically locked in CCW rotation. The detailed mechanism of switching remains unresolved because it is technically difficult to regulate the level of CheY-P within the concentration range that produces flagellar reversals. Here, we demonstrate that high hydrostatic pressure can induce CW rotation even in the absence of CheY-P. The rotation of single flagellar motors in Escherichia coli cells with the cheY gene deleted was monitored at various pressures and temperatures. Application of >120 MPa pressure induced a reversal from CCW to CW at 20°C, although at that temperature, no motor rotated CW at ambient pressure (0.1 MPa). At lower temperatures, pressure-induced changes in direction were observed at pressures of <120 MPa. CW rotation increased with pressure in a sigmoidal fashion, as it does in response to increasing concentrations of CheY-P. Application of pressure generally promotes the formation of clusters of ordered water molecules on the surfaces of proteins. It is possible that hydration of the switch complex at high pressure induces structural changes similar to those caused by the binding of CheY-P.
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46
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Vartanian AS, Paz A, Fortgang EA, Abramson J, Dahlquist FW. Structure of flagellar motor proteins in complex allows for insights into motor structure and switching. J Biol Chem 2012; 287:35779-83. [PMID: 22896702 PMCID: PMC3476246 DOI: 10.1074/jbc.c112.378380] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 06/12/2012] [Indexed: 12/23/2022] Open
Abstract
The flagellar motor is one type of propulsion device of motile bacteria. The cytoplasmic ring (C-ring) of the motor interacts with the stator to generate torque in clockwise and counterclockwise directions. The C-ring is composed of three proteins, FliM, FliN, and FliG. Together they form the "switch complex" and regulate switching and torque generation. Here we report the crystal structure of the middle domain of FliM in complex with the middle and C-terminal domains of FliG that shows the interaction surface and orientations of the proteins. In the complex, FliG assumes a compact conformation in which the middle and C-terminal domains (FliG(MC)) collapse and stack together similarly to the recently published structure of a mutant of FliG(MC) with a clockwise rotational bias. This intramolecular stacking of the domains is distinct from the intermolecular stacking seen in other structures of FliG. We fit the complex structure into the three-dimensional reconstructions of the motor and propose that the cytoplasmic ring is assembled from 34 FliG and FliM molecules in a 1:1 fashion.
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Affiliation(s)
- Armand S. Vartanian
- From the Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106 and
| | - Aviv Paz
- the Department of Physiology, David Geffen School of Medicine, UCLA, Los Angeles, California 90095
| | - Emily A. Fortgang
- From the Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106 and
| | - Jeff Abramson
- the Department of Physiology, David Geffen School of Medicine, UCLA, Los Angeles, California 90095
| | - Frederick W. Dahlquist
- From the Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106 and
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