1
|
Singh PK, Sharma P, Afanzar O, Goldfarb MH, Maklashina E, Eisenbach M, Cecchini G, Iverson TM. CryoEM structures reveal how the bacterial flagellum rotates and switches direction. Nat Microbiol 2024; 9:1271-1281. [PMID: 38632342 PMCID: PMC11087270 DOI: 10.1038/s41564-024-01674-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 03/12/2024] [Indexed: 04/19/2024]
Abstract
Bacterial chemotaxis requires bidirectional flagellar rotation at different rates. Rotation is driven by a flagellar motor, which is a supercomplex containing multiple rings. Architectural uncertainty regarding the cytoplasmic C-ring, or 'switch', limits our understanding of how the motor transmits torque and direction to the flagellar rod. Here we report cryogenic electron microscopy structures for Salmonella enterica serovar typhimurium inner membrane MS-ring and C-ring in a counterclockwise pose (4.0 Å) and isolated C-ring in a clockwise pose alone (4.6 Å) and bound to a regulator (5.9 Å). Conformational differences between rotational poses include a 180° shift in FliF/FliG domains that rotates the outward-facing MotA/B binding site to inward facing. The regulator has specificity for the clockwise pose by bridging elements unique to this conformation. We used these structures to propose how the switch reverses rotation and transmits torque to the flagellum, which advances the understanding of bacterial chemotaxis and bidirectional motor rotation.
Collapse
Affiliation(s)
- Prashant K Singh
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Oshri Afanzar
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Margo H Goldfarb
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Elena Maklashina
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, USA
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, USA
| | - Michael Eisenbach
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, USA
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, USA
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA.
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA.
| |
Collapse
|
2
|
Minamino T, Kinoshita M. Structure, Assembly, and Function of Flagella Responsible for Bacterial Locomotion. EcoSal Plus 2023; 11:eesp00112023. [PMID: 37260402 PMCID: PMC10729930 DOI: 10.1128/ecosalplus.esp-0011-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/14/2023] [Indexed: 01/28/2024]
Abstract
Many motile bacteria use flagella for locomotion under a variety of environmental conditions. Because bacterial flagella are under the control of sensory signal transduction pathways, each cell is able to autonomously control its flagellum-driven locomotion and move to an environment favorable for survival. The flagellum of Salmonella enterica serovar Typhimurium is a supramolecular assembly consisting of at least three distinct functional parts: a basal body that acts as a bidirectional rotary motor together with multiple force generators, each of which serves as a transmembrane proton channel to couple the proton flow through the channel with torque generation; a filament that functions as a helical propeller that produces propulsion; and a hook that works as a universal joint that transmits the torque produced by the rotary motor to the helical propeller. At the base of the flagellum is a type III secretion system that transports flagellar structural subunits from the cytoplasm to the distal end of the growing flagellar structure, where assembly takes place. In recent years, high-resolution cryo-electron microscopy (cryoEM) image analysis has revealed the overall structure of the flagellum, and this structural information has made it possible to discuss flagellar assembly and function at the atomic level. In this article, we describe what is known about the structure, assembly, and function of Salmonella flagella.
Collapse
Affiliation(s)
- Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| |
Collapse
|
3
|
Cabezón E, Valenzuela-Gómez F, Arechaga I. Primary architecture and energy requirements of Type III and Type IV secretion systems. Front Cell Infect Microbiol 2023; 13:1255852. [PMID: 38089815 PMCID: PMC10711112 DOI: 10.3389/fcimb.2023.1255852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023] Open
Abstract
Many pathogens use Type III and Type IV protein secretion systems to secrete virulence factors from the bacterial cytosol into host cells. These systems operate through a one-step mechanism. The secreted substrates (protein or nucleo-protein complexes in the case of Type IV conjugative systems) are guided to the base of the secretion channel, where they are directly delivered into the host cell in an ATP-dependent unfolded state. Despite the numerous disparities between these secretion systems, here we have focused on the structural and functional similarities between both systems. In particular, on the structural similarity shared by one of the main ATPases (EscN and VirD4 in Type III and Type IV secretion systems, respectively). Interestingly, these ATPases also exhibit a structural resemblance to F1-ATPases, which suggests a common mechanism for substrate secretion. The correlation between structure and function of essential components in both systems can provide significant insights into the molecular mechanisms involved. This approach is of great interest in the pursuit of identifying inhibitors that can effectively target these systems.
Collapse
Affiliation(s)
- Elena Cabezón
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria- CSIC, Santander, Spain
| | | | - Ignacio Arechaga
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria- CSIC, Santander, Spain
| |
Collapse
|
4
|
Wang J, Zhang T, Liu Y, Wang S, Li Z, Sun P, Xu H. Transcriptome analysis reveals that yeast extract inhibits synthesis of prodigiosin by Serratia marcescens SDSPY-136. Prep Biochem Biotechnol 2023; 53:1109-1119. [PMID: 36785995 DOI: 10.1080/10826068.2023.2172036] [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: 02/15/2023]
Abstract
Prodigiosin (2-methyl-3-pentyl-6-methoxyprodiginine) is a valuable medicinal and edible natural pigment derived from Serratia marcescens. How prodigiosin synthesis is suppressed by environmental factors has not been investigated. Previous studies described a low level of prodigiosin production in the presence of yeast extracts. However, we have observed that S. marcescens SDSPY-136 did not synthesize prodigiosin in yeast extract culture. In this study, transcriptome sequencing of yeast extract cultures was used to estimate the metabolic control of the synthetic prodigiosin pathway in S. marcescens. Key phosphorylation enzymes in the glycolysis pathway, 6-phosphofructokinase, and glyceraldehyde 3-phosphate dehydrogenase, were downregulated by yeast extract and other carbon metabolism pathway genes were enhanced. Genes related to ribosomes, amino acid metabolism, and aminoacyl-tRNA biosynthesis were also highly up-regulated. The presence of metal ions in yeast extracts and the accumulation of fermentation metabolites alter the two-component signaling system, which regulated metabolism to various degrees. The results of metal ion testing suggested that prodigiosin inhibition could be caused by metal ions, such as zinc ion. The findings indicate that yeast extract may affect metabolism through multiple pathways in S. marcescens. This research sheds light on the mechanism of prodigiosin regulatory inhibition.
Collapse
Affiliation(s)
- Junqing Wang
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Tingting Zhang
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Yang Liu
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Shanshan Wang
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Zerun Li
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Ping Sun
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Hui Xu
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| |
Collapse
|
5
|
Nishikino T, Hijikata A, Kojima S, Shirai T, Kainosho M, Homma M, Miyanoiri Y. Changes in the hydrophobic network of the FliG MC domain induce rotational switching of the flagellar motor. iScience 2023; 26:107320. [PMID: 37520711 PMCID: PMC10372836 DOI: 10.1016/j.isci.2023.107320] [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: 11/21/2022] [Revised: 04/18/2023] [Accepted: 07/04/2023] [Indexed: 08/01/2023] Open
Abstract
The FliG protein plays a pivotal role in switching the rotational direction of the flagellar motor between clockwise and counterclockwise. Although we previously showed that mutations in the Gly-Gly linker of FliG induce a defect in switching rotational direction, the detailed molecular mechanism was not elucidated. Here, we studied the structural changes in the FliG fragment containing the middle and C-terminal regions, named FliGMC, and the switch-defective FliGMC-G215A, using nuclear magnetic resonance (NMR) and molecular dynamics simulations. NMR analysis revealed multiple conformations of FliGMC, and the exchange process between these conformations was suppressed by the G215A residue substitution. Furthermore, changes in the intradomain orientation of FliG were induced by changes in hydrophobic interaction networks throughout FliG. Our finding applies to FliG in a ring complex in the flagellar basal body, and clarifies the switching mechanism of the flagellar motor.
Collapse
Affiliation(s)
- Tatsuro Nishikino
- Laboratory for Ultra-High Magnetic Field NMR Spectroscopy, Research Center for Next-Generation Protein Sciences, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Atsushi Hijikata
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Seiji Kojima
- Division of Biological Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Tsuyoshi Shirai
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Masatsune Kainosho
- Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Michio Homma
- Division of Biological Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Yohei Miyanoiri
- Laboratory for Ultra-High Magnetic Field NMR Spectroscopy, Research Center for Next-Generation Protein Sciences, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| |
Collapse
|
6
|
Lim S, Yadunandan A, Khalid Jawed M. Bacteria-inspired robotic propulsion from bundling of soft helical filaments at low Reynolds number. SOFT MATTER 2023; 19:2254-2264. [PMID: 36916641 DOI: 10.1039/d2sm01398c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The bundling of flagella is known to create a "run" phase, where the bacteria moves in a nearly straight line rather than making changes in direction. Historically, mechanical explanations for the bundling phenomenon intrigued many researchers, and significant advances were made in physical models and experimental methods. Contributing to the field of research, we present a bacteria-inspired centimeter-scale soft robotic hardware platform and a computational framework for a physically plausible simulation model of the multi-flagellated robot under low Reynolds number (∼10-1). The fluid-structure interaction simulation couples the discrete elastic rods algorithm with the method of regularized Stokeslet segments. Contact between two flagella is handled by a penalty-based method. We present a comparison between our experimental and simulation results and verify that the simulation tool can capture the essential physics of this problem. Preliminary findings on robustness to buckling provided by the bundling phenomenon and the efficiency of a multi-flagellated soft robot are compared with the single-flagellated counterparts. Observations were made on the coupling between geometry and elasticity, which manifests itself in the propulsion of the robot by nonlinear dependency on the rotational speed of the flagella.
Collapse
Affiliation(s)
- Sangmin Lim
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, California, 90095, USA.
| | - Achyuta Yadunandan
- Department of Electrical and Computer Engineering, University of California, Los Angeles, California, 90095, USA
| | - M Khalid Jawed
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, California, 90095, USA.
| |
Collapse
|
7
|
Gurung JP, Navvab Kashani M, de Silva CM, Baker MAB. Microbial stir bars: Light-activated rotation of tethered bacterial cells to enhance mixing in stagnant fluids. BIOMICROFLUIDICS 2023; 17:024108. [PMID: 37124628 PMCID: PMC10147410 DOI: 10.1063/5.0144934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/23/2023] [Indexed: 05/03/2023]
Abstract
Microfluidics devices are gaining significant interest in biomedical applications. However, in a micron-scale device, reaction speed is often limited by the slow rate of diffusion of the reagents. Several active and passive micro-mixers have been fabricated to enhance mixing in microfluidic devices. Here, we demonstrate external control of mixing by rotating a rod-shaped bacterial cell. This rotation is driven by ion transit across the bacterial flagellar stator complex. We first measured the flow fields generated by rotating a single bacterial cell rotationally locked to rotate either clockwise (CW) or counterclockwise (CCW). Micro-particle image velocimetry (μPIV) and particle tracking velocimetry results showed that a bacterial cell of ∼ 2.75 μm long, rotating at 5.75 ± 0.39 Hz in a counterclockwise direction could generate distinct micro-vortices with circular flow fields with a mean velocity of 4.72 ± 1.67 μm/s and maximum velocity of 7.90 μm/s in aqueous solution. We verified our experimental data with a numerical simulation at matched flow conditions, which revealed vortices of similar dimensions and speed. We observed that the flow-field diminished with increasing z-height above the plane of the rotating cell. Lastly, we showed that we could activate and tune rotational mixing remotely using strains engineered with proteorhodopsin, where rotation could be activated by controlled external illumination using green laser light (561 nm).
Collapse
Affiliation(s)
- Jyoti P. Gurung
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | | | - Charitha M. de Silva
- School of Mechanical and Manufacturing Engineering, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | | |
Collapse
|
8
|
Lim S, Du Y, Lee Y, Panda SK, Tong D, Khalid Jawed M. Fabrication, control, and modeling of robots inspired by flagella and cilia. BIOINSPIRATION & BIOMIMETICS 2022; 18:011003. [PMID: 36533860 DOI: 10.1088/1748-3190/aca63d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Flagella and cilia are slender structures that serve important functionalities in the microscopic world through their locomotion induced by fluid and structure interaction. With recent developments in microscopy, fabrication, biology, and modeling capability, robots inspired by the locomotion of these organelles in low Reynolds number flow have been manufactured and tested on the micro-and macro-scale, ranging from medicalin vivomicrobots, microfluidics to macro prototypes. We present a collection of modeling theories, control principles, and fabrication methods for flagellated and ciliary robots.
Collapse
Affiliation(s)
- Sangmin Lim
- Department of Mechanical & Aerospace Engineering, Westwood Plaza, University of California, Los Angeles, CA 90095, United States of America
| | - Yayun Du
- Department of Mechanical & Aerospace Engineering, Westwood Plaza, University of California, Los Angeles, CA 90095, United States of America
| | - Yongkyu Lee
- Department of Mechanical & Aerospace Engineering, Westwood Plaza, University of California, Los Angeles, CA 90095, United States of America
| | - Shivam Kumar Panda
- Department of Mechanical & Aerospace Engineering, Westwood Plaza, University of California, Los Angeles, CA 90095, United States of America
| | - Dezhong Tong
- Department of Mechanical & Aerospace Engineering, Westwood Plaza, University of California, Los Angeles, CA 90095, United States of America
| | - M Khalid Jawed
- Department of Mechanical & Aerospace Engineering, Westwood Plaza, University of California, Los Angeles, CA 90095, United States of America
| |
Collapse
|
9
|
Gupta R, Yuan J, Lele PP. Bacterial Proprioception: Can a Bacterium Sense Its Movement? Front Microbiol 2022; 13:928408. [PMID: 35875555 PMCID: PMC9302961 DOI: 10.3389/fmicb.2022.928408] [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: 04/25/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
The evolution of the bacterial flagellum gave rise to motility and repurposing of a signaling network, now termed the chemotaxis network, enabled biasing of cell movements. This made it possible for the bacterium to seek out favorable chemical environments. To enable chemotaxis, the chemotaxis network sensitively detects extracellular chemical stimuli and appropriately modulates flagellar functions. Additionally, the flagellar motor itself is capable of detecting mechanical stimuli and adapts its structure and function in response, likely triggering a transition from planktonic to surface-associated lifestyles. Recent work has shown a link between the flagellar motor's response to mechanical stimuli and the chemotactic output. Here, we elaborate on this link and discuss how it likely helps the cell sense and adapt to changes in its swimming speeds in different environments. We discuss the mechanism whereby the motor precisely tunes its chemotaxis output under different mechanical loads, analogous to proprioception in higher order organisms. We speculate on the roles bacterial proprioception might play in a variety of phenomena including the transition to surface-associated lifestyles such as swarming and biofilms.
Collapse
Affiliation(s)
- Rachit Gupta
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Junhua Yuan
- Department of Physics, University of Science and Technology of China, Hefei, China
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| |
Collapse
|
10
|
Homma M, Takekawa N, Fujiwara K, Hao Y, Onoue Y, Kojima S. Formation of multiple flagella caused by a mutation of the flagellar rotor protein FliM in Vibrio alginolyticus. Genes Cells 2022; 27:568-578. [PMID: 35842835 DOI: 10.1111/gtc.12975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/21/2022] [Accepted: 07/11/2022] [Indexed: 11/30/2022]
Abstract
Marine bacterium Vibrio alginolyticus forms a single flagellum at a cell pole. In Vibrio, two proteins (GTPase FlhF and ATPase FlhG) regulate the number of flagella. We previously isolated the NMB155 mutant that forms multiple flagella despite the absence of mutations in flhF and flhG. Whole-genome sequencing of NMB155 identified an E9K mutation in FliM that is a component of C-ring in the flagellar rotor. Mutations in FliM result in defects in flagellar formation (fla) and flagellar rotation (che or mot); however, there are a few reports indicating that FliM mutations increase the number of flagella. Here, we determined that the E9K mutation confers the multi-flagellar phenotype and also the che phenotype. The co-expression of wild-type FliM and FliM-E9K indicated that they were competitive in regard to determining the flagellar number. The ATPase activity of FlhG has been correlated with the number of flagella. We observed that the ATPase activity of FlhG was increased by the addition of FliM but not by the addition of FliM-E9K in vitro. This indicates that FliM interacts with FlhG to increase its ATPase activity, and the E9K mutation may inhibit this interaction. FliM may control the ATPase activity of FlhG to properly regulate the number of the polar flagellum at the cell pole. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Norihiro Takekawa
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Osaka, Japan
| | - Kazushi Fujiwara
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Yuxi Hao
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Yasuhiro Onoue
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| |
Collapse
|
11
|
Gupta R, Rhee KY, Beagle SD, Chawla R, Perdomo N, Lockless SW, Lele PP. Indole modulates cooperative protein-protein interactions in the flagellar motor. PNAS NEXUS 2022; 1. [PMID: 35719892 PMCID: PMC9205328 DOI: 10.1093/pnasnexus/pgac035] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Indole is a major component of the bacterial exometabolome, and the mechanisms for its wide-ranging effects on bacterial physiology are biomedically significant, although they remain poorly understood. Here, we determined how indole modulates the functions of a widely conserved motility apparatus, the bacterial flagellum. Our experiments in Escherichia coli revealed that indole influences the rotation rates and reversals in the flagellum’s direction of rotation via multiple mechanisms. At concentrations higher than 1 mM, indole decreased the membrane potential to dissipate the power available for the rotation of the motor that operates the flagellum. Below 1 mM, indole did not dissipate the membrane potential. Instead, experiments and modeling indicated that indole weakens cooperative protein interactions within the flagellar complexes to inhibit motility. The metabolite also induced reversals in the rotational direction of the motor to promote a weak chemotactic response, even when the chemotaxis response regulator, CheY, was lacking. Experiments further revealed that indole does not require the transporter Mtr to cross the membrane and influence motor functions. Based on these findings, we propose that indole modulates intra- and inter-protein interactions in the cell to influence several physiological functions.
Collapse
Affiliation(s)
- Rachit Gupta
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Kathy Y Rhee
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Sarah D Beagle
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Ravi Chawla
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Nicolas Perdomo
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Steve W Lockless
- Department of Biology, Texas A&M University, College Station, TX 77843-3258, USA
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| |
Collapse
|
12
|
Peil A, Xin L, Both S, Shen L, Ke Y, Weiss T, Zhan P, Liu N. DNA Assembly of Modular Components into a Rotary Nanodevice. ACS NANO 2022; 16:5284-5291. [PMID: 35286063 PMCID: PMC9047004 DOI: 10.1021/acsnano.1c10160] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The bacterial flagellar motor is a rotary machine composed of functional modular components, which can perform bidirectional rotations to control the migration behavior of the bacterial cell. It resembles a two-cogwheel gear system, which consists of small and large cogwheels with cogs at the edges to regulate rotations. Such gearset models provide elegant blueprints to design and build artificial nanomachinery with desired functionalities. In this work, we demonstrate DNA assembly of a structurally well-defined nanodevice, which can carry out programmable rotations powered by DNA fuels. Our rotary nanodevice consists of three modular components, small origami ring, large origami ring, and gold nanoparticles (AuNPs). They mimic the sun gear, ring gear, and planet gears in a planetary gearset accordingly. These modular components are self-assembled in a compact manner, such that they can work cooperatively to impart bidirectional rotations. The rotary dynamics is optically recorded using fluorescence spectroscopy in real time, given the sensitive distance-dependent interactions between the tethered fluorophores and AuNPs on the rings. The experimental results are well supported by the theoretical calculations.
Collapse
Affiliation(s)
- Andreas Peil
- Second
Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
| | - Ling Xin
- Second
Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
- (L.X.)
| | - Steffen Both
- Fourth
Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Luyao Shen
- Wallace
L. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia 30322 United States
| | - Yonggang Ke
- Wallace
L. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia 30322 United States
| | - Thomas Weiss
- Fourth
Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Institute
of Physics, University of Graz, and NAWI
Graz, Universitätsplatz
5, 8010 Graz, Austria
| | - Pengfei Zhan
- Second
Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
- (P.Z.)
| | - Na Liu
- Second
Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
- (N.L.)
| |
Collapse
|
13
|
Tupiņa D, Krah A, Marzinek JK, Zuzic L, Moverley AA, Constantinidou C, Bond PJ. Bridging the N-terminal and middle domains in FliG of the flagellar rotor. Curr Res Struct Biol 2022; 4:59-67. [PMID: 35345452 PMCID: PMC8956890 DOI: 10.1016/j.crstbi.2022.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/28/2022] [Accepted: 02/28/2022] [Indexed: 11/27/2022] Open
Abstract
Flagella are necessary for bacterial movement and contribute to various aspects of virulence. They are complex cylindrical structures built of multiple molecular rings with self-assembly properties. The flagellar rotor is composed of the MS-ring and the C-ring. The FliG protein of the C-ring is central to flagellar assembly and function due to its roles in linking the C-ring with the MS-ring and in torque transmission from stator to rotor. No high-resolution structure of an assembled C-ring has been resolved to date, and the conformation adopted by FliG within the ring is unclear due to variations in available crystallographic data. Here, we use molecular dynamics (MD) simulations to study the conformation and dynamics of FliG in different states of assembly, including both in physiologically relevant and crystallographic lattice environments. We conclude that the linker between the FliG N-terminal and middle domain likely adopts an extended helical conformation in vivo, in contrast with the contracted conformation observed in some previous X-ray studies. We further support our findings with integrative model building of full-length FliG and a FliG ring model that is compatible with cryo-electron tomography (cryo-ET) and electron microscopy (EM) densities of the C-ring. Collectively, our study contributes to a better mechanistic understanding of the flagellar rotor assembly and its function.
Collapse
|
14
|
Homma M, Nishikino T, Kojima S. Achievements in bacterial flagellar research with focus on Vibrio species. Microbiol Immunol 2021; 66:75-95. [PMID: 34842307 DOI: 10.1111/1348-0421.12954] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 12/01/2022]
Abstract
In 1980's, the most genes involved in the bacterial flagellar function and formation had been isolated though many of their functions or roles were not clarified. Bacterial flagella are the primary locomotive organ and are not necessary for growing in vitro but are probably essential for living in natural condition and are involved in the pathogenicity. In vitro, the flagella-deficient strains can grow at rates similar to wild-type strains. More than 50 genes are responsible for flagellar function, and the flagellum is constructed by more than 20 structural proteins. The maintenance cost of flagellum is high as several genes are required for its development. The fact that it evolved as a motor organ even with such the high cost shows that the motility is indispensable to survive under the harsh environment of Earth. In this review, we focus on flagella-related research conducted by the authors for about 40 years and flagellar research focused on Vibrio spp. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University
| | | | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University
| |
Collapse
|
15
|
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.
Collapse
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.
| |
Collapse
|
16
|
Morimoto YV, Minamino T. Architecture and Assembly of the Bacterial Flagellar Motor Complex. Subcell Biochem 2021; 96:297-321. [PMID: 33252734 DOI: 10.1007/978-3-030-58971-4_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
One of the central systems responsible for bacterial motility is the flagellum. The bacterial flagellum is a macromolecular protein complex that is more than five times the cell length. Flagella-driven motility is coordinated via a chemosensory signal transduction pathway, and so bacterial cells sense changes in the environment and migrate towards more desirable locations. The flagellum of Salmonella enterica serovar Typhimurium is composed of a bi-directional rotary motor, a universal joint and a helical propeller. The flagellar motor, which structurally resembles an artificial motor, is embedded within the cell envelop and spins at several hundred revolutions per second. In contrast to an artificial motor, the energy utilized for high-speed flagellar motor rotation is the inward-directed proton flow through a transmembrane proton channel of the stator unit of the flagellar motor. The flagellar motor realizes efficient chemotaxis while performing high-speed movement by an ingenious directional switching mechanism of the motor rotation. To build the universal joint and helical propeller structures outside the cell body, the flagellar motor contains its own protein transporter called a type III protein export apparatus. In this chapter we summarize the structure and assembly of the Salmonella flagellar motor complex.
Collapse
Affiliation(s)
- Yusuke V Morimoto
- Department of Physics and Information Technology, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| |
Collapse
|
17
|
Nishikino T, Kojima S, Homma M. [Flagellar related genes and functions in Vibrio]. Nihon Saikingaku Zasshi 2021; 75:195-214. [PMID: 33390367 DOI: 10.3412/jsb.75.195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Bacteria can move or swim by flagella. On the other hand, the motile ability is not necessary to live at all. In laboratory, the flagella-deficient strains can grow just like the wild-type strains. The flagellum is assembled from more than 20 structural proteins and there are more than 50 genes including the structural genes to regulate or support the flagellar formation. The cost to construct the flagellum is so expensive. The fact that it evolved as a motor organ means even at such the large cost shows that the flagellum is essential for survival in natural condition. In this review, we would like to focus on the flagella-related researches conducted by the authors and the flagellar research on Vibrio spp.
Collapse
Affiliation(s)
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University
| |
Collapse
|
18
|
Chang Y, Zhang K, Carroll BL, Zhao X, Charon NW, Norris SJ, Motaleb MA, Li C, Liu J. Molecular mechanism for rotational switching of the bacterial flagellar motor. Nat Struct Mol Biol 2020; 27:1041-1047. [PMID: 32895555 PMCID: PMC8129871 DOI: 10.1038/s41594-020-0497-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/03/2020] [Indexed: 12/20/2022]
Abstract
The bacterial flagellar motor can rotate in counterclockwise (CCW) or clockwise (CW) senses, and transitions are controlled by the phosphorylated form of the response regulator CheY (CheY-P). To dissect the mechanism underlying flagellar rotational switching, we use Borrelia burgdorferi as a model system to determine high-resolution in situ motor structures in cheX and cheY3 mutants, in which motors are locked in either CCW or CW rotation. The structures showed that CheY3-P interacts directly with a switch protein, FliM, inducing a major remodeling of another switch protein, FliG2, and altering its interaction with the torque generator. Our findings lead to a model in which the torque generator rotates in response to an inward flow of H+ driven by the proton motive force, and conformational changes in FliG2 driven by CheY3-P allow the switch complex to interact with opposite sides of the rotating torque generator, facilitating rotational switching.
Collapse
Affiliation(s)
- Yunjie Chang
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06516, USA,Microbial Sciences Institute, Yale University, West Haven, CT 06536, USA
| | - Kai Zhang
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Brittany L. Carroll
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06516, USA,Microbial Sciences Institute, Yale University, West Haven, CT 06536, USA
| | - Xiaowei Zhao
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center, Houston, TX 77030, USA,Current address: Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Nyles W. Charon
- Department of Microbiology, Immunology, and Cell Biology, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV 26506, USA
| | - Steven J. Norris
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Md A Motaleb
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
| | - Chunhao Li
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, VA, USA.
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA. .,Microbial Sciences Institute, Yale University, West Haven, CT, USA.
| |
Collapse
|
19
|
Structural Conservation and Adaptation of the Bacterial Flagella Motor. Biomolecules 2020; 10:biom10111492. [PMID: 33138111 PMCID: PMC7693769 DOI: 10.3390/biom10111492] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023] Open
Abstract
Many bacteria require flagella for the ability to move, survive, and cause infection. The flagellum is a complex nanomachine that has evolved to increase the fitness of each bacterium to diverse environments. Over several decades, molecular, biochemical, and structural insights into the flagella have led to a comprehensive understanding of the structure and function of this fascinating nanomachine. Notably, X-ray crystallography, cryo-electron microscopy (cryo-EM), and cryo-electron tomography (cryo-ET) have elucidated the flagella and their components to unprecedented resolution, gleaning insights into their structural conservation and adaptation. In this review, we focus on recent structural studies that have led to a mechanistic understanding of flagellar assembly, function, and evolution.
Collapse
|
20
|
Carroll BL, Nishikino T, Guo W, Zhu S, Kojima S, Homma M, Liu J. The flagellar motor of Vibrio alginolyticus undergoes major structural remodeling during rotational switching. eLife 2020; 9:61446. [PMID: 32893817 PMCID: PMC7505661 DOI: 10.7554/elife.61446] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 09/04/2020] [Indexed: 11/26/2022] Open
Abstract
The bacterial flagellar motor switches rotational direction between counterclockwise (CCW) and clockwise (CW) to direct the migration of the cell. The cytoplasmic ring (C-ring) of the motor, which is composed of FliG, FliM, and FliN, is known for controlling the rotational sense of the flagellum. However, the mechanism underlying rotational switching remains elusive. Here, we deployed cryo-electron tomography to visualize the C-ring in two rotational biased mutants in Vibrio alginolyticus. We determined the C-ring molecular architectures, providing novel insights into the mechanism of rotational switching. We report that the C-ring maintained 34-fold symmetry in both rotational senses, and the protein composition remained constant. The two structures show FliG conformational changes elicit a large conformational rearrangement of the rotor complex that coincides with rotational switching of the flagellum. FliM and FliN form a stable spiral-shaped base of the C-ring, likely stabilizing the C-ring during the conformational remodeling.
Collapse
Affiliation(s)
- Brittany L Carroll
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, United States.,Microbial Sciences Institute, Yale University, West Haven, United States
| | - Tatsuro Nishikino
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Wangbiao Guo
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, United States.,Microbial Sciences Institute, Yale University, West Haven, United States
| | - Shiwei Zhu
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, United States.,Microbial Sciences Institute, Yale University, West Haven, United States
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, United States.,Microbial Sciences Institute, Yale University, West Haven, United States
| |
Collapse
|
21
|
Khan S. The Architectural Dynamics of the Bacterial Flagellar Motor Switch. Biomolecules 2020; 10:E833. [PMID: 32486003 PMCID: PMC7355467 DOI: 10.3390/biom10060833] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/23/2020] [Accepted: 05/25/2020] [Indexed: 02/06/2023] Open
Abstract
The rotary bacterial flagellar motor is remarkable in biochemistry for its highly synchronized operation and amplification during switching of rotation sense. The motor is part of the flagellar basal body, a complex multi-protein assembly. Sensory and energy transduction depends on a core of six proteins that are adapted in different species to adjust torque and produce diverse switches. Motor response to chemotactic and environmental stimuli is driven by interactions of the core with small signal proteins. The initial protein interactions are propagated across a multi-subunit cytoplasmic ring to switch torque. Torque reversal triggers structural transitions in the flagellar filament to change motile behavior. Subtle variations in the core components invert or block switch operation. The mechanics of the flagellar switch have been studied with multiple approaches, from protein dynamics to single molecule and cell biophysics. The architecture, driven by recent advances in electron cryo-microscopy, is available for several species. Computational methods have correlated structure with genetic and biochemical databases. The design principles underlying the basis of switch ultra-sensitivity and its dependence on motor torque remain elusive, but tantalizing clues have emerged. This review aims to consolidate recent knowledge into a unified platform that can inspire new research strategies.
Collapse
Affiliation(s)
- Shahid Khan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| |
Collapse
|
22
|
Biphasic chemotaxis of Escherichia coli to the microbiota metabolite indole. Proc Natl Acad Sci U S A 2020; 117:6114-6120. [PMID: 32123098 DOI: 10.1073/pnas.1916974117] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bacterial chemotaxis to prominent microbiota metabolites such as indole is important in the formation of microbial communities in the gastrointestinal (GI) tract. However, the basis of chemotaxis to indole is poorly understood. Here, we exposed Escherichia coli to a range of indole concentrations and measured the dynamic responses of individual flagellar motors to determine the chemotaxis response. Below 1 mM indole, a repellent-only response was observed. At 1 mM indole and higher, a time-dependent inversion from a repellent to an attractant response was observed. The repellent and attractant responses were mediated by the Tsr and Tar chemoreceptors, respectively. Also, the flagellar motor itself mediated a repellent response independent of the receptors. Chemotaxis assays revealed that receptor-mediated adaptation to indole caused a bipartite response-wild-type cells were attracted to regions of high indole concentration if they had previously adapted to indole but were otherwise repelled. We propose that indole spatially segregates cells based on their state of adaptation to repel invaders while recruiting beneficial resident bacteria to growing microbial communities within the GI tract.
Collapse
|
23
|
Abstract
Periplasmic flagella are complex nanomachines responsible for distinctive morphology and motility of spirochetes. Although bacterial flagella have been extensively studied for several decades in the model systems Escherichia coli and Salmonella enterica, our understanding of periplasmic flagella in many disease-causing spirochetes remains incomplete. Recent advances, including molecular genetics, biochemistry, structural biology, and cryo-electron tomography, have greatly increased our understanding of structure and function of periplasmic flagella. In this chapter, we summarize some of the recent findings that provide new insights into the structure, assembly, and function of periplasmic flagella.
Collapse
|
24
|
Tandem mass tag-based quantitative proteomic analysis reveal the inhibition mechanism of thyme essential oil against flagellum of Listeria monocytogenes. Food Res Int 2019; 125:108508. [DOI: 10.1016/j.foodres.2019.108508] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 06/03/2019] [Accepted: 06/21/2019] [Indexed: 11/23/2022]
|
25
|
Mino T, Nishikino T, Iwatsuki H, Kojima S, Homma M. Effect of sodium ions on conformations of the cytoplasmic loop of the PomA stator protein of Vibrio alginolyticus. J Biochem 2019; 166:331-341. [PMID: 31147681 DOI: 10.1093/jb/mvz040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/24/2019] [Indexed: 01/13/2023] Open
Abstract
The sodium driven flagellar stator of Vibrio alginolyticus is a hetero-hexamer membrane complex composed of PomA and PomB, and acts as a sodium ion channel. The conformational change in the cytoplasmic region of PomA for the flagellar torque generation, which interacts directly with a rotor protein, FliG, remains a mystery. In this study, we introduced cysteine mutations into cytoplasmic charged residues of PomA, which are highly conserved and interact with FliG, to detect the conformational change by the reactivity of biotin maleimide. In vivo labelling experiments of the PomA mutants revealed that the accessibility of biotin maleimide at position of E96 was reduced with sodium ions. Such a reduction was also seen in the D24N and the plug deletion mutants of PomB, and the phenomenon was independent in the presence of FliG. This sodium ions specific reduction was also detected in Escherichia coli that produced PomA and PomB from a plasmid, but not in the purified stator complex. These results demonstrated that sodium ions cause a conformational change around the E96 residue of loop2-3 in the biological membrane.
Collapse
Affiliation(s)
- Taira Mino
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Furo-cyo, Nagoya, Japan
| | - Tatsuro Nishikino
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Furo-cyo, Nagoya, Japan
| | - Hiroto Iwatsuki
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Furo-cyo, Nagoya, Japan
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Furo-cyo, Nagoya, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Furo-cyo, Nagoya, Japan
| |
Collapse
|
26
|
Koganitsky A, Tworowski D, Dadosh T, Cecchini G, Eisenbach M. A Mechanism of Modulating the Direction of Flagellar Rotation in Bacteria by Fumarate and Fumarate Reductase. J Mol Biol 2019; 431:3662-3676. [PMID: 31412261 DOI: 10.1016/j.jmb.2019.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 02/04/2023]
Abstract
Fumarate, an electron acceptor in anaerobic respiration of Escherichia coli, has an additional function of assisting the flagellar motor to shift from counterclockwise to clockwise rotation, with a consequent modulation of the bacterial swimming behavior. Fumarate transmits its effect to the motor via the fumarate reductase complex (FrdABCD), shown to bind to FliG-one of the motor's switch proteins. How binding of the FrdABCD respiratory enzyme to FliG enhances clockwise rotation and how fumarate is involved in this activity have remained puzzling. Here we show that the FrdA subunit in the presence of fumarate is sufficient for binding to FliG and for clockwise enhancement. We further demonstrate by in vitro binding assays and super-resolution microscopy in vivo that the mechanism by which fumarate-occupied FrdA enhances clockwise rotation involves its preferential binding to the clockwise state of FliG (FliGcw). Continuum electrostatics combined with docking analysis and conformational sampling endorsed the experimental conclusions and suggested that the FrdA-FliGcw interaction is driven by the positive electrostatic potential generated by FrdA and the negatively charged areas of FliG. They further demonstrated that fumarate changes FrdA's conformation to one that can bind to FliGcw. These findings also show that the reason for the failure of the succinate dehydrogenase flavoprotein SdhA (an almost-identical analog of FrdA shown to bind to FliG equally well) to enhance clockwise rotation is that it has no binding preference for FliGcw. We suggest that this mechanism is physiologically important as it can modulate the magnitude of ΔG0 between the clockwise and counterclockwise states of the motor to tune the motor to the growth conditions of the bacteria.
Collapse
Affiliation(s)
- Anna Koganitsky
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Dmitry Tworowski
- Department of Structural Biology, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Tali Dadosh
- Department of Chemical Research Support, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA 94121, USA; Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, USA
| | - Michael Eisenbach
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001 Rehovot, Israel.
| |
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
Flagella-Driven Motility of Bacteria. Biomolecules 2019; 9:biom9070279. [PMID: 31337100 PMCID: PMC6680979 DOI: 10.3390/biom9070279] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 01/17/2023] Open
Abstract
The bacterial flagellum is a helical filamentous organelle responsible for motility. In bacterial species possessing flagella at the cell exterior, the long helical flagellar filament acts as a molecular screw to generate thrust. Meanwhile, the flagella of spirochetes reside within the periplasmic space and not only act as a cytoskeleton to determine the helicity of the cell body, but also rotate or undulate the helical cell body for propulsion. Despite structural diversity of the flagella among bacterial species, flagellated bacteria share a common rotary nanomachine, namely the flagellar motor, which is located at the base of the filament. The flagellar motor is composed of a rotor ring complex and multiple transmembrane stator units and converts the ion flux through an ion channel of each stator unit into the mechanical work required for motor rotation. Intracellular chemotactic signaling pathways regulate the direction of flagella-driven motility in response to changes in the environments, allowing bacteria to migrate towards more desirable environments for their survival. Recent experimental and theoretical studies have been deepening our understanding of the molecular mechanisms of the flagellar motor. In this review article, we describe the current understanding of the structure and dynamics of the bacterial flagellum.
Collapse
|
29
|
Sakai T, Miyata T, Terahara N, Mori K, Inoue Y, Morimoto YV, Kato T, Namba K, Minamino T. Novel Insights into Conformational Rearrangements of the Bacterial Flagellar Switch Complex. mBio 2019; 10:e00079-19. [PMID: 30940700 PMCID: PMC6445934 DOI: 10.1128/mbio.00079-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/26/2019] [Indexed: 01/01/2023] Open
Abstract
The flagellar motor can spin in both counterclockwise (CCW) and clockwise (CW) directions. The flagellar motor consists of a rotor and multiple stator units, which act as a proton channel. The rotor is composed of the transmembrane MS ring made of FliF and the cytoplasmic C ring consisting of FliG, FliM, and FliN. The C ring is directly involved in rotation and directional switching. The Salmonella FliF-FliG deletion fusion motor missing 56 residues from the C terminus of FliF and 94 residues from the N terminus of FliG keeps a domain responsible for the interaction with the stator intact, but its motor function is reduced significantly. Here, we report the structure and function of the FliF-FliG deletion fusion motor. The FliF-FliG deletion fusion not only resulted in a strong CW switch bias but also affected rotor-stator interactions coupled with proton translocation through the proton channel of the stator unit. The energy coupling efficiency of the deletion fusion motor was the same as that of the wild-type motor. Extragenic suppressor mutations in FliG, FliM, or FliN not only relieved the strong CW switch bias but also increased the motor speed at low load. The FliF-FliG deletion fusion made intersubunit interactions between C ring proteins tighter compared to the wild-type motor, whereas the suppressor mutations affect such tighter intersubunit interactions. We propose that a change of intersubunit interactions between the C ring proteins may be required for high-speed motor rotation as well as direction switching.IMPORTANCE The bacterial flagellar motor is a bidirectional rotary motor for motility and chemotaxis, which often plays an important role in infection. The motor is a large transmembrane protein complex composed of a rotor and multiple stator units, which also act as a proton channel. Motor torque is generated through their cyclic association and dissociation coupled with proton translocation through the proton channel. A large cytoplasmic ring of the motor, called C ring, is responsible for rotation and switching by interacting with the stator, but the mechanism remains unknown. By analyzing the structure and function of the wild-type motor and a mutant motor missing part of the C ring connecting itself with the transmembrane rotor ring while keeping a stator-interacting domain for bidirectional torque generation intact, we found interesting clues to the change in the C ring conformation for the switching and rotation involving loose and tight intersubunit interactions.
Collapse
Affiliation(s)
- Tomofumi Sakai
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Tomoko Miyata
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Naoya Terahara
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Koichiro Mori
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Yumi Inoue
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Yusuke V Morimoto
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan
| | - Takayuki Kato
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- RIKEN SPring-8 Center, Suita, Osaka, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| |
Collapse
|
30
|
Abstract
Bacteria, life living at microscale, can spread only by thermal fluctuation. However, the ability of directional movement, such as swimming by rotating flagella, gliding over surfaces via mobile cell-surface adhesins, and actin-dependent movement, could be useful for thriving through searching more favorable environments, and such motility is known to be related to pathogenicity. Among diverse migration mechanisms, perhaps flagella-dependent motility would be used by most species. The bacterial flagellum is a molecular nanomachine comprising a helical filament and a basal motor, which is fueled by an electrochemical gradient of cation across the cell membrane (ion motive force). Many species, such as Escherichia coli, possess flagella on the outside of the cell body, whereas flagella of spirochetes reside within the periplasmic space. Flagellar filaments or helical spirochete bodies rotate like a screw propeller, generating propulsive force. This review article describes the current knowledge of the structure and operation mechanism of the bacterial flagellum, and flagella-dependent motility in highly viscous environments.
Collapse
Affiliation(s)
- Shuichi Nakamura
- Department of Applied Physics, Graduate School of Engineering, Tohoku University
| |
Collapse
|
31
|
Rotational direction of flagellar motor from the conformation of FliG middle domain in marine Vibrio. Sci Rep 2018; 8:17793. [PMID: 30542147 PMCID: PMC6290876 DOI: 10.1038/s41598-018-35902-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 11/08/2018] [Indexed: 12/14/2022] Open
Abstract
FliG, which is composed of three distinctive domains, N-terminal (N), middle (M), and C-terminal (C), is an essential rotor component that generates torque and determines rotational direction. To determine the role of FliG in determining flagellar rotational direction, we prepared rotational biased mutants of fliG in Vibrio alginolyticus. The E144D mutant, whose residue is belonging to the EHPQR-motif in FliGM, exhibited an increased number of switching events. This phenotype generated a response similar to the phenol-repellent response in chemotaxis. To clarify the effect of E144D mutation on the rotational switching, we combined the mutation with other che mutations (G214S, G215A and A282T) in FliG. Two of the double mutants suppressed the rotational biased phenotype. To gain structural insight into the mutations, we performed molecular dynamic simulations of the FliGMC domain, based on the crystal structure of Thermotoga maritima FliG and nuclear magnetic resonance analysis. Furthermore, we examined the swimming behavior of the fliG mutants lacking CheY. The results suggested that the conformation of FliG in E144D mutant was similar to that in the wild type. However, that of G214S and G215A caused a steric hindrance in FliG. The conformational change in FliGM triggered by binding CheY may lead to a rapid change of direction and may occur in both directional states.
Collapse
|
32
|
Bacterial flagellar switching: a molecular mechanism directed by the logic of an electric motor. J Mol Model 2018; 24:280. [DOI: 10.1007/s00894-018-3819-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/30/2018] [Indexed: 11/27/2022]
|
33
|
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.
Collapse
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:
| |
Collapse
|
34
|
Onoue Y, Takekawa N, Nishikino T, Kojima S, Homma M. The role of conserved charged residues in the bidirectional rotation of the bacterial flagellar motor. Microbiologyopen 2018; 7:e00587. [PMID: 29573373 PMCID: PMC6079164 DOI: 10.1002/mbo3.587] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 12/19/2017] [Accepted: 12/28/2017] [Indexed: 12/23/2022] Open
Abstract
Many bacteria rotate their flagella both counterclockwise (CCW) and clockwise (CW) to achieve swimming toward attractants or away from repellents. Highly conserved charged residues are important for that motility, which suggests that electrostatic interactions are crucial for the rotor-stator function. It remains unclear if those residues contribute equally to rotation in the CCW and CW directions. To address this uncertainty, in this study, we expressed chimeric rotors and stators from Vibrio alginolyticus and Escherichia coli in E. coli, and measured the rotational speed of each motor in both directions using a tethered-cell assay. In wild-type cells, the rotational speeds in both directions were equal, as demonstrated previously. Some charge-neutralizing residue replacements in the stator decreased the rotational speed in both directions to the same extent. However, mutations in two charged residues in the rotor decreased the rotational speed only in the CCW direction. Subsequent analysis and previous results suggest that these amino acid residues are involved in supporting the conformation of the rotor, which is important for proper torque generation in the CCW direction.
Collapse
Affiliation(s)
- Yasuhiro Onoue
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Norihiro Takekawa
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Tatsuro Nishikino
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| |
Collapse
|
35
|
Kinoshita M, Namba K, Minamino T. Effect of a clockwise-locked deletion in FliG on the FliG ring structure of the bacterial flagellar motor. Genes Cells 2018; 23:241-247. [PMID: 29405551 DOI: 10.1111/gtc.12565] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 01/11/2018] [Indexed: 11/29/2022]
Abstract
FliG is a rotor protein of the bacterial flagellar motor. FliG consists of FliGN , FliGM and FliGC domains. Intermolecular FliGM -FliGC interactions promote FliG ring formation on the cytoplasmic face of the MS ring. A conformational change in HelixMC connecting FliGM and FliGC is responsible for the switching between the counterclockwise (CCW) and clockwise (CW) rotational states of the FliG ring. However, it remains unknown how it occurs. Here, we carried out in vivo disulfide cross-linking experiments to see the effect of a CW-locked deletion (∆PAA) in FliG on the FliG ring structure in Salmonella enterica. Higher-order oligomers were observed in the membrane fraction of the fliG(∆PAA + G166C/G194C) strain upon oxidation with iodine in a way similar to FliG(G166C/G194C), indicating that the PAA deletion does not inhibit domain-swap polymerization of FliG. FliG(∆PAA + E174C) formed a cross-linked homodimer whereas FliG(E174C) did not, indicating that Glu174 in HelixMC of one FliG protomer is located much closer to that of its neighboring subunit in the CW motor than in the CCW motor. We will discuss possible helical rearrangements of HelixMC that induce a structural remodeling of the FliG ring upon flagellar motor switching.
Collapse
Affiliation(s)
- Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.,Quantitative Biology Center, RIKEN, Osaka, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| |
Collapse
|
36
|
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.
Collapse
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.
| |
Collapse
|
37
|
Xue C, Lam KH, Zhang H, Sun K, Lee SH, Chen X, Au SWN. Crystal structure of the FliF-FliG complex from Helicobacter pylori yields insight into the assembly of the motor MS-C ring in the bacterial flagellum. J Biol Chem 2017; 293:2066-2078. [PMID: 29229777 DOI: 10.1074/jbc.m117.797936] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 11/28/2017] [Indexed: 11/06/2022] Open
Abstract
The bacterial flagellar motor is a self-assembling supramolecular nanodevice. Its spontaneous biosynthesis is initiated by the insertion of the MS ring protein FliF into the inner membrane, followed by attachment of the switch protein FliG. Assembly of this multiprotein complex is tightly regulated to avoid nonspecific aggregation, but the molecular mechanisms governing flagellar assembly are unclear. Here, we present the crystal structure of the cytoplasmic domain of FliF complexed with the N-terminal domain of FliG (FliF C -FliG N ) from the bacterium Helicobacter pylori Within this complex, FliF C interacted with FliG N through extensive hydrophobic contacts similar to those observed in the FliF C -FliG N structure from the thermophile Thermotoga maritima, indicating conservation of the FliF C -FliG N interaction across bacterial species. Analysis of the crystal lattice revealed that the heterodimeric complex packs as a linear superhelix via stacking of the armadillo repeat-like motifs (ARM) of FliG N Notably, this linear helix was similar to that observed for the assembly of the FliG middle domain. We validated the in vivo relevance of the FliG N stacking by complementation studies in Escherichia coli Furthermore, structural comparison with apo FliG from the thermophile Aquifex aeolicus indicated that FliF regulates the conformational transition of FliG and exposes the complementary ARM-like motifs of FliG N , containing conserved hydrophobic residues. FliF apparently both provides a template for FliG polymerization and spatiotemporally controls subunit interactions within FliG. Our findings reveal that a small protein fold can serve as a versatile building block to assemble into a multiprotein machinery of distinct shapes for specific functions.
Collapse
Affiliation(s)
- Chaolun Xue
- From the Center for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Kwok Ho Lam
- From the Center for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Huawei Zhang
- From the Center for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Kailei Sun
- From the Center for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Sai Hang Lee
- From the Center for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Xin Chen
- From the Center for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Shannon Wing Ngor Au
- From the Center for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| |
Collapse
|
38
|
Choi MK, Jo S, Lee BH, Kim MH, Choi JB, Kim K, Kim MK. Dynamic characteristics of a flagellar motor protein analyzed using an elastic network model. J Mol Graph Model 2017; 78:81-87. [PMID: 29054097 DOI: 10.1016/j.jmgm.2017.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 10/02/2017] [Accepted: 10/03/2017] [Indexed: 12/23/2022]
Abstract
At the base of a flagellar motor, its rotational direction and speed are regulated by the interaction between rotor and stator proteins. A switching event occurs when the cytoplasmic rotor protein, called C-ring, changes its conformation in response to binding of the CheY signal protein. The C-ring structure consists of FliG, FliM, and FliN proteins and its conformational changes in FliM and FliG including HelixMC play an important role in switching the motor direction. Therefore, clarifying their dynamic properties as well as conformational changes is a key to understanding the switching mechanism of the motor protein. In this study, to elucidate dynamic characteristics of the C-ring structure, both harmonic (intrinsic vibration) and anharmonic (transition pathway) analyses are conducted by using the symmetry-constrained elastic network model. As a result, the first three normal modes successfully capture the essence of transition pathway from wild type to CW-biased state. Their cumulative square overlap value reaches up to 0.842. Remarkably, it is also noted from the transition pathway that the cascade of interactions from the signal protein to FliM to FliG, highlighted by the major mode shapes from the first three normal modes, induces the reorientation (∼100° rotation of FliGC5) of FliG C-terminal that directly interacts with the stator protein. Presumably, the rotational direction of the motor protein is switched by this substantial change in the stator-rotor interaction.
Collapse
Affiliation(s)
- Moon-Ki Choi
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
| | - Soojin Jo
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
| | - Byung Ho Lee
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
| | - Min Hyeok Kim
- Korea Institute for Advanced Study, Seoul, 02455, Korea
| | - Jae Boong Choi
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
| | - Kyunghoon Kim
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
| | - Moon Ki Kim
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea.
| |
Collapse
|
39
|
Structural and Functional Analysis of the C-Terminal Region of FliG, an Essential Motor Component of Vibrio Na+-Driven Flagella. Structure 2017; 25:1540-1548.e3. [DOI: 10.1016/j.str.2017.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 07/15/2017] [Accepted: 08/15/2017] [Indexed: 01/24/2023]
|
40
|
Pourjaberi SNS, Terahara N, Namba K, Minamino T. The role of a cytoplasmic loop of MotA in load-dependent assembly and disassembly dynamics of the MotA/B stator complex in the bacterial flagellar motor. Mol Microbiol 2017; 106:646-658. [DOI: 10.1111/mmi.13843] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2017] [Indexed: 11/26/2022]
Affiliation(s)
| | - Naoya Terahara
- Graduate School of Frontier Biosciences; Osaka University, 1-3 Yamadaoka; Suita Osaka 565-0871 Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences; Osaka University, 1-3 Yamadaoka; Suita Osaka 565-0871 Japan
- RIKEN; Quantitative Biology Center, 1-3 Yamadaoka; Suita Osaka 565-0871 Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences; Osaka University, 1-3 Yamadaoka; Suita Osaka 565-0871 Japan
| |
Collapse
|
41
|
Lynch MJ, Levenson R, Kim EA, Sircar R, Blair DF, Dahlquist FW, Crane BR. Co-Folding of a FliF-FliG Split Domain Forms the Basis of the MS:C Ring Interface within the Bacterial Flagellar Motor. Structure 2017; 25:317-328. [PMID: 28089452 DOI: 10.1016/j.str.2016.12.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/21/2016] [Accepted: 12/12/2016] [Indexed: 12/22/2022]
Abstract
The interface between the membrane (MS) and cytoplasmic (C) rings of the bacterial flagellar motor couples torque generation to rotation within the membrane. The structure of the C-terminal helices of the integral membrane protein FliF (FliFC) bound to the N terminal domain of the switch complex protein FliG (FliGN) reveals that FliGN folds around FliFC to produce a topology that closely resembles both the middle and C-terminal domains of FliG. The interface is consistent with solution-state nuclear magnetic resonance, small-angle X-ray scattering, in vivo interaction studies, and cellular motility assays. Co-folding with FliFC induces substantial conformational changes in FliGN and suggests that FliF and FliG have the same stoichiometry within the rotor. Modeling the FliFC:FliGN complex into cryo-electron microscopy rotor density updates the architecture of the middle and upper switch complex and shows how domain shuffling of a conserved interaction module anchors the cytoplasmic rotor to the membrane.
Collapse
Affiliation(s)
- Michael J Lynch
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Robert Levenson
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93106-9510, USA
| | - Eun A Kim
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Ria Sircar
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - David F Blair
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Frederick W Dahlquist
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93106-9510, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
42
|
Bacterial Flagellar Motor Switch in Response to CheY-P Regulation and Motor Structural Alterations. Biophys J 2016; 110:1411-20. [PMID: 27028650 DOI: 10.1016/j.bpj.2016.02.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 11/20/2022] Open
Abstract
The bacterial flagellar motor (BFM) is a molecular machine that rotates the helical filaments and propels the bacteria swimming toward favorable conditions. In our previous works, we built a stochastic conformational spread model to explain the dynamic and cooperative behavior of BFM switching. Here, we extended this model to test whether it can explain the latest experimental observations regarding CheY-P regulation and motor structural adaptivity. We show that our model predicts a strong correlation between rotational direction and the number of CheY-Ps bound to the switch complex, in agreement with the latest finding from Fukuoka et al. It also predicts that the switching sensitivity of the BFM can be fine-tuned by incorporating additional units into the switch complex, as recently demonstrated by Yuan et al., who showed that stoichiometry of FliM undergoes dynamic change to maintain ultrasensitivity in the motor switching response. In addition, by locking some rotor switching units on the switch complex into the stable clockwise-only conformation, our model has accurately simulated recent experiments expressing clockwise-locked FliG(ΔPAA) into the switch complex and reproduced the increased switching rate of the motor.
Collapse
|
43
|
Onoue Y, Abe-Yoshizumi R, Gohara M, Nishino Y, Kobayashi S, Asami Y, Homma M. Domain-based biophysical characterization of the structural and thermal stability of FliG, an essential rotor component of the Na +-driven flagellar motor. Biophys Physicobiol 2016; 13:227-233. [PMID: 27924278 PMCID: PMC5113609 DOI: 10.2142/biophysico.13.0_227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 08/22/2016] [Indexed: 01/16/2023] Open
Abstract
Many bacteria move using their flagellar motor, which generates torque through the interaction between the stator and rotor. The most important component of the rotor for torque generation is FliG. FliG consists of three domains: FliGN, FliGM, and FliGC. FliGC contains a site(s) that interacts with the stator. In this study, we examined the physical properties of three FliG constructs, FliGFull, FliGMC, and FliGC, derived from sodium-driven polar flagella of marine Vibrio. Size exclusion chromatography revealed that FliG changes conformational states under two different pH conditions. Circular dichroism spectroscopy also revealed that the contents of α-helices in FliG slightly changed under these pH conditions. Furthermore, we examined the thermal stability of the FliG constructs using differential scanning calorimetry. Based on the results, we speculate that each domain of FliG denatures independently. This study provides basic information on the biophysical characteristics of FliG, a component of the flagellar motor.
Collapse
Affiliation(s)
- Yasuhiro Onoue
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Rei Abe-Yoshizumi
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Mizuki Gohara
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Yuuki Nishino
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Shiori Kobayashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Yasuo Asami
- TA Instruments Japan Inc., Gotanda, Shinagawa-ku, Tokyo 141-0031, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| |
Collapse
|
44
|
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
Collapse
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.
| |
Collapse
|
45
|
Nishikino T, Zhu S, Takekawa N, Kojima S, Onoue Y, Homma M. Serine suppresses the motor function of a periplasmic PomB mutation in theVibrioflagella stator. Genes Cells 2016; 21:505-16. [DOI: 10.1111/gtc.12357] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 02/17/2016] [Indexed: 01/13/2023]
Affiliation(s)
- Tatsuro Nishikino
- Division of Biological Science; Graduate School of Science; Nagoya University; Nagoya 464-8602 Japan
| | - Shiwei Zhu
- Division of Biological Science; Graduate School of Science; Nagoya University; Nagoya 464-8602 Japan
| | - Norihiro Takekawa
- Division of Biological Science; Graduate School of Science; Nagoya University; Nagoya 464-8602 Japan
| | - Seiji Kojima
- Division of Biological Science; Graduate School of Science; Nagoya University; Nagoya 464-8602 Japan
| | - Yasuhiro Onoue
- Division of Biological Science; Graduate School of Science; Nagoya University; Nagoya 464-8602 Japan
| | - Michio Homma
- Division of Biological Science; Graduate School of Science; Nagoya University; Nagoya 464-8602 Japan
| |
Collapse
|
46
|
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: 20] [Impact Index Per Article: 2.5] [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.
Collapse
Affiliation(s)
- Julien R Bergeron
- Department of Biochemistry, University of Washington , Seattle, WA , USA
| |
Collapse
|
47
|
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.
Collapse
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
| |
Collapse
|
48
|
Komatsu H, Hayashi F, Sasa M, Shikata K, Yamaguchi S, Namba K, Oosawa K. Genetic analysis of revertants isolated from the rod-fragile fliF mutant of Salmonella. Biophys Physicobiol 2016; 13:13-25. [PMID: 27924254 PMCID: PMC5042159 DOI: 10.2142/biophysico.13.0_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 12/21/2015] [Indexed: 12/28/2022] Open
Abstract
FliF is the protein comprising the MS-ring of the bacterial flagellar basal body, which is the base for the assembly of flagellar axial structures. From a fliF mutant that easily releases the rod-hook-filament in viscous environments, more than 400 revertants that recovered their swarming ability in viscous conditions, were isolated. The second-site mutations were determined for approximately 70% of them. There were three regions where the mutations were localized: two in Region I, 112 in Region II, and 71 in Region III including the true reversion. In Region I, second-site mutations were found in FlgC and FlgF of the proximal rod, suggesting that they affect the interaction between the MS-ring and the rod. In Region II, there were 69 and 42 mutations in MotA and MotB, respectively, suggesting that the second-site mutations in MotA and MotB may decrease the rotational speed of the flagellar motor to reduce the probability of releasing the rod under this condition. One exception is a mutation in FlhC that caused a down regulation of the flagellar proteins production but it may directly affect transcription or translation of motA and motB. In Region III, there were 44, 24, and 3 mutations in FliG, FliM, and FliF, respectively. There were no second-site mutations identified in FliN although it is involved in torque generation as a component of the C-ring. Many of the mutations were involved in the motor rotation, and it is suggested that such reduced speeds result in stabilizing the filament attachment to the motor.
Collapse
Affiliation(s)
- Hitomi Komatsu
- Protonic NanoMachine Project, ERATO, JST, Seika, Kyoto 619-0237, Japan
| | - Fumio Hayashi
- Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Masahiro Sasa
- Department of Biosciences, Teikyo University, Utsunomiya, Tochigi 320-8551, Japan
| | - Koji Shikata
- Department of Biosciences, Teikyo University, Utsunomiya, Tochigi 320-8551, Japan
| | | | - Keiichi Namba
- Protonic NanoMachine Project, ERATO, JST, Seika, Kyoto 619-0237, Japan; Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kenji Oosawa
- Protonic NanoMachine Project, ERATO, JST, Seika, Kyoto 619-0237, Japan; Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan; Department of Biosciences, Teikyo University, Utsunomiya, Tochigi 320-8551, Japan
| |
Collapse
|
49
|
Switching of bacterial flagellar motors [corrected] triggered by mutant FliG. Biophys J 2016; 108:1275-80. [PMID: 25762339 DOI: 10.1016/j.bpj.2015.02.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 01/30/2015] [Accepted: 02/03/2015] [Indexed: 01/22/2023] Open
Abstract
Binding of the chemotaxis response regulator CheY-P promotes switching between rotational states in flagellar motors of the bacterium Escherichia coli. Here, we induced switching in the absence of CheY-P by introducing copies of a mutant FliG locked in the clockwise (CW) conformation (FliG(CW)). The composition of the mixed FliG ring was estimated via fluorescence imaging, and the probability of CW rotation (CWbias) was determined from the rotation of tethered cells. The results were interpreted in the framework of a 1D Ising model. The data could be fit by assuming that mutant subunits are more stable in the CW conformation than in the counterclockwise conformation. We found that CWbias varies depending on the spatial arrangement of the assembled subunits in the FliG ring. This offers a possible explanation for a previous observation of hysteresis in the switch function in analogous mixed FliM motors-in motors containing identical fractions of mutant FliM(CW) in otherwise wild-type motors, the CWbias differed depending on whether mutant subunits were expressed in strains with native motors or native subunits were expressed in strains with mutant motors.
Collapse
|
50
|
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.
Collapse
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:
| |
Collapse
|