1
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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.
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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
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2
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Kaplan M, Yao Q, Jensen GJ. Structure and Assembly of the Proteus mirabilis Flagellar Motor by Cryo-Electron Tomography. Int J Mol Sci 2023; 24:8292. [PMID: 37176000 PMCID: PMC10179241 DOI: 10.3390/ijms24098292] [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: 03/27/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Proteus mirabilis is a Gram-negative Gammaproteobacterium and a major causative agent of urinary tract infections in humans. It is characterized by its ability to switch between swimming motility in liquid media and swarming on solid surfaces. Here, we used cryo-electron tomography and subtomogram averaging to reveal the structure of the flagellar motor of P. mirabilis at nanometer resolution in intact cells. We found that P. mirabilis has a motor that is structurally similar to those of Escherichia coli and Salmonella enterica, lacking the periplasmic elaborations that characterize other more specialized gammaproteobacterial motors. In addition, no density corresponding to stators was present in the subtomogram average suggesting that the stators are dynamic. Finally, several assembly intermediates of the motor were seen that support the inside-out assembly pathway.
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Affiliation(s)
- Mohammed Kaplan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Qing Yao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Grant J. Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84604, USA
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3
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Tao A, Liu G, Zhang R, Yuan J. Precise Measurement of the Stoichiometry of the Adaptive Bacterial Flagellar Switch. mBio 2023; 14:e0018923. [PMID: 36946730 PMCID: PMC10128058 DOI: 10.1128/mbio.00189-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
The cytoplasmic ring (C-ring) of the bacterial flagellar motor controls the motor rotation direction, thereby controlling bacterial run-and-tumble behavior. The C-ring has been shown to undergo adaptive remodeling in response to changes in motor directional bias. However, the stoichiometry and arrangement of the C-ring is still unclear due to contradiction between the results from fluorescence studies and cryo-electron microscopy (cryo-EM) structural analysis. Here, by using the copy number of FliG molecules (34) in the C-ring as a reference, we precisely measured the copy numbers of FliM molecules in motors rotating exclusively counterclockwise (CCW) and clockwise (CW). We surprisingly found that there are on average 45 and 58 FliM molecules in CW and CCW rotating motors, respectively, which are much higher than previous estimates. Our results suggested a new mechanism of C-ring adaptation, that is, extra FliM molecules could be bound to the primary C-ring with probability depending on the motor rotational direction. We further confirmed that all of the FliM molecules in the C-ring function in chemotaxis signaling transduction because all of them could be bound by the chemotactic response regulator CheY-P. Our measurements provided new insights into the structure and arrangement of the flagellar switch. IMPORTANCE The bacterial flagellar switch can undergo adaptive remodeling in response to changes in motor rotation direction, thereby shifting its operating point to match the output of the chemotaxis signaling pathway. However, it remains unclear how the flagellar switch accomplishes this adaptive remodeling. Here, via precise fluorescence studies, we measured the absolute copy numbers of the critical component in the switch for motors rotating counterclockwise and clockwise, obtaining much larger numbers than previous relative estimates. Our results suggested a new mechanism of adaptive remodeling of the flagellar switch and provided new insights for updating the conformation spread model of the switch.
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Affiliation(s)
- Antai Tao
- Department of Physics, University of Science and Technology of China, Hefei, Anhui, China
| | - Guangzhe Liu
- Wenzhou Institute, University of Chinese Academy of Science, Wenzhou, Zhejiang, P.R. China
- School of Engineering and Science, University of Chinese Academy of Science, Beijing, P.R. China
| | - Rongjing Zhang
- Department of Physics, University of Science and Technology of China, Hefei, Anhui, China
| | - Junhua Yuan
- Department of Physics, University of Science and Technology of China, Hefei, Anhui, China
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4
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Guo S, Liu J. The Bacterial Flagellar Motor: Insights Into Torque Generation, Rotational Switching, and Mechanosensing. Front Microbiol 2022; 13:911114. [PMID: 35711788 PMCID: PMC9195833 DOI: 10.3389/fmicb.2022.911114] [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: 04/02/2022] [Accepted: 05/06/2022] [Indexed: 11/18/2022] Open
Abstract
The flagellar motor is a bidirectional rotary nanomachine used by many bacteria to sense and move through environments of varying complexity. The bidirectional rotation of the motor is governed by interactions between the inner membrane-associated stator units and the C-ring in the cytoplasm. In this review, we take a structural biology perspective to discuss the distinct conformations of the stator complex and the C-ring that regulate bacterial motility by switching rotational direction between the clockwise (CW) and counterclockwise (CCW) senses. We further contextualize recent in situ structural insights into the modulation of the stator units by accessory proteins, such as FliL, to generate full torque. The dynamic structural remodeling of the C-ring and stator complexes as well as their association with signaling and accessory molecules provide a mechanistic basis for how bacteria adjust motility to sense, move through, and survive in specific niches both outside and within host cells and tissues.
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Affiliation(s)
- Shuaiqi Guo
- Microbial Sciences Institute, Yale University, West Haven, CT, United States.,Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, United States
| | - Jun Liu
- Microbial Sciences Institute, Yale University, West Haven, CT, United States.,Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, United States
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5
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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.
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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
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6
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Chang Y, Carroll BL, Liu J. Structural basis of bacterial flagellar motor rotation and switching. Trends Microbiol 2021; 29:1024-1033. [PMID: 33865677 DOI: 10.1016/j.tim.2021.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/11/2021] [Accepted: 03/16/2021] [Indexed: 01/08/2023]
Abstract
The bacterial flagellar motor, a remarkable rotary machine, can rapidly switch between counterclockwise (CCW) and clockwise (CW) rotational directions to control the migration behavior of the bacterial cell. The flagellar motor consists of a bidirectional spinning rotor surrounded by torque-generating stator units. Recent high-resolution in vitro and in situ structural studies have revealed stunning details of the individual components of the flagellar motor and their interactions in both the CCW and CW senses. In this review, we discuss these structures and their implications for understanding the molecular mechanisms underlying flagellar rotation and switching.
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Affiliation(s)
- Yunjie Chang
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA; Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
| | - Brittany L Carroll
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA; Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA; Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA.
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7
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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.
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8
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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.
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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
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9
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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.
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Affiliation(s)
- Shahid Khan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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10
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Abstract
Prokaryotic organisms occupy the most diverse set of environments and conditions on our planet. Their ability to sense and respond to a broad range of external cues remain key research areas in modern microbiology, central to behaviors that underlie beneficial and pathogenic interactions of bacteria with multicellular organisms and within complex ecosystems. Advances in our understanding of the one- and two-component signal transduction systems that underlie these sensing pathways have been driven by advances in imaging the behavior of many individual bacterial cells, as well as visualizing individual proteins and protein arrays within living cells. Cryo-electron tomography continues to provide new insights into the structure and function of chemosensory receptors and flagellar motors, while advances in protein labeling and tracking are applied to understand information flow between receptor and motor. Sophisticated microfluidics allow simultaneous analysis of the behavior of thousands of individual cells, increasing our understanding of how variance between individuals is generated, regulated and employed to maximize fitness of a population. In vitro experiments have been complemented by the study of signal transduction and motility in complex in vivo models, allowing investigators to directly address the contribution of motility, chemotaxis and aggregation/adhesion on virulence during infection. Finally, systems biology approaches have demonstrated previously uncharted areas of protein space in which novel two-component signal transduction pathways can be designed and constructed de novo These exciting experimental advances were just some of the many novel findings presented at the 15th Bacterial Locomotion and Signal Transduction conference (BLAST XV) in January 2019.
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11
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Minamino T, Kinoshita M, Namba K. Directional Switching Mechanism of the Bacterial Flagellar Motor. Comput Struct Biotechnol J 2019; 17:1075-1081. [PMID: 31452860 PMCID: PMC6700473 DOI: 10.1016/j.csbj.2019.07.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/26/2019] [Accepted: 07/27/2019] [Indexed: 11/16/2022] Open
Abstract
Bacteria sense temporal changes in extracellular stimuli via sensory signal transducers and move by rotating flagella towards into a favorable environment for their survival. Each flagellum is a supramolecular motility machine consisting of a bi-directional rotary motor, a universal joint and a helical propeller. The signal transducers transmit environmental signals to the flagellar motor through a cytoplasmic chemotactic signaling pathway. The flagellar motor is composed of a rotor and multiple stator units, each of which acts as a transmembrane proton channel to conduct protons and exert force on the rotor. FliG, FliM and FliN form the C ring on the cytoplasmic face of the basal body MS ring made of the transmembrane protein FliF and act as the rotor. The C ring also serves as a switching device that enables the motor to spin in both counterclockwise (CCW) and clockwise (CW) directions. The phosphorylated form of the chemotactic signaling protein CheY binds to FliM and FliN to induce conformational changes of the C ring responsible for switching the direction of flagellar motor rotation from CCW to CW. In this mini-review, we will describe current understanding of the switching mechanism of the bacterial flagellar motor.
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Affiliation(s)
- Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
- RIKEN Center for Biosystems Dynamic Research & Spring-8 Center, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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12
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Moreau E, Thomas T, Brevet M, Thorin C, Fournel C, Calvez S. Mutations involved in the emergence of Yersinia ruckeri biotype 2 in France. Transbound Emerg Dis 2019; 66:1387-1394. [PMID: 30874374 DOI: 10.1111/tbed.13175] [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: 01/22/2019] [Revised: 03/05/2019] [Accepted: 03/10/2019] [Indexed: 11/30/2022]
Abstract
Yersina ruckeri is an enterobacteria responsible for Enteric redmouth disease (ERM), which causes significant economic losses in the aquaculture industry worldwide. Two biotypes have been described within Y. ruckeri: biotype 1 (BT1) and biotype 2 (BT2). Unlike BT1, BT2 is negative for motility and lipase secretion. The emergence of BT2 Y. ruckeri has been associated with disease outbreaks in vaccinated fish in several countries, notably France in the early 2000s. In this study, 15 BT2 strains (14 BT2 strains isolated in France and the BT2 reference strain EX5) were studied to compare the phenotypic characters of the BT1 and BT2 strains and to determine the genetic origin of the emergence of BT2 in France. BT1 bacteria are significantly longer in size than BT2 bacteria (a difference of 0.222 µm). The loss of motility of some French BT2 strains could be due to the loss of their ability to produce flagella caused by three mutations within the fliG, flhC and flgA genes. In the light of these results, the emergence of BT2 Yersinia ruckeri in France is discussed.
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Affiliation(s)
| | - Tatiana Thomas
- BIOEPAR, INRA, Nantes, France.,Université de Bretagne-Sud, IRDL, CNRS FRE 3744, Lorient, France
| | | | - Chantal Thorin
- Department of Animal Physiopathology and Pharmacology, Oniris, Nantes, France
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13
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Organization of the Flagellar Switch Complex of Bacillus subtilis. J Bacteriol 2019; 201:JB.00626-18. [PMID: 30455280 DOI: 10.1128/jb.00626-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/14/2018] [Indexed: 01/12/2023] Open
Abstract
While the protein complex responsible for controlling the direction (clockwise [CW] or counterclockwise [CCW]) of flagellar rotation has been fairly well studied in Escherichia coli and Salmonella, less is known about the switch complex in Bacillus subtilis or other Gram-positive species. Two component proteins (FliG and FliM) are shared between E. coli and B. subtilis, but in place of the protein FliN found in E. coli, the B. subtilis complex contains the larger protein FliY. Notably, in B. subtilis the signaling protein CheY-phosphate induces a switch from CW to CCW rotation, opposite to its action in E. coli Here, we have examined the architecture and function of the switch complex in B. subtilis using targeted cross-linking, bacterial two-hybrid protein interaction experiments, and characterization of mutant phenotypes. In major respects, the B. subtilis switch complex appears to be organized similarly to that in E. coli The complex is organized around a ring built from the large middle domain of FliM; this ring supports an array of FliG subunits organized in a similar way to that of E. coli, with the FliG C-terminal domain functioning in the generation of torque via conserved charged residues. Key differences from E. coli involve the middle domain of FliY, which forms an additional, more outboard array, and the C-terminal domains of FliM and FliY, which are organized into both FliY homodimers and FliM heterodimers. Together, the results suggest that the CW and CCW conformational states are similar in the Gram-negative and Gram-positive switches but that CheY-phosphate drives oppositely directed movements in the two cases.IMPORTANCE Flagellar motility plays key roles in the survival of many bacteria and in the harmful action of many pathogens. Bacterial flagella rotate; the direction of flagellar rotation is controlled by a multisubunit protein complex termed the switch complex. This complex has been extensively studied in Gram-negative model species, but little is known about the complex in Bacillus subtilis or other Gram-positive species. Notably, the switch complex in Gram-positive species responds to its effector CheY-phosphate (CheY-P) by switching to CCW rotation, whereas in E. coli or Salmonella CheY-P acts in the opposite way, promoting CW rotation. In the work here, the architecture of the B. subtilis switch complex has been probed using cross-linking, protein interaction measurements, and mutational approaches. The results cast light on the organization of the complex and provide a framework for understanding the mechanism of flagellar direction control in B. subtilis and other Gram-positive species.
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14
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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.
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15
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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]
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16
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Lam KH, Xue C, Sun K, Zhang H, Lam WWL, Zhu Z, Ng JTY, Sause WE, Lertsethtakarn P, Lau KF, Ottemann KM, Au SWN. Three SpoA-domain proteins interact in the creation of the flagellar type III secretion system in Helicobacter pylori. J Biol Chem 2018; 293:13961-13973. [PMID: 29991595 PMCID: PMC6130963 DOI: 10.1074/jbc.ra118.002263] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/07/2018] [Indexed: 01/07/2023] Open
Abstract
Bacterial flagella are rotary nanomachines that contribute to bacterial fitness in many settings, including host colonization. The flagellar motor relies on the multiprotein flagellar motor-switch complex to govern flagellum formation and rotational direction. Different bacteria exhibit great diversity in their flagellar motors. One such variation is exemplified by the motor-switch apparatus of the gastric pathogen Helicobacter pylori, which carries an extra switch protein, FliY, along with the more typical FliG, FliM, and FliN proteins. All switch proteins are needed for normal flagellation and motility in H. pylori, but the molecular mechanism of their assembly is unknown. To fill this gap, we examined the interactions among these proteins. We found that the C-terminal SpoA domain of FliY (FliYC) is critical to flagellation and forms heterodimeric complexes with the FliN and FliM SpoA domains, which are β-sheet domains of type III secretion system proteins. Surprisingly, unlike in other flagellar switch systems, neither FliY nor FliN self-associated. The crystal structure of the FliYC-FliNC complex revealed a saddle-shaped structure homologous to the FliN-FliN dimer of Thermotoga maritima, consistent with a FliY-FliN heterodimer forming the functional unit. Analysis of the FliYC-FliNC interface indicated that oppositely charged residues specific to each protein drive heterodimer formation. Moreover, both FliYC-FliMC and FliYC-FliNC associated with the flagellar regulatory protein FliH, explaining their important roles in flagellation. We conclude that H. pylori uses a FliY-FliN heterodimer instead of a homodimer and creates a switch complex with SpoA domains derived from three distinct proteins.
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Affiliation(s)
- Kwok Ho Lam
- From the Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chaolun Xue
- From the Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Shatin, Hong Kong, ,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China, and
| | - Kailei Sun
- From the Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Huawei Zhang
- From the Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Shatin, Hong Kong, ,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China, and
| | - Wendy Wai Ling Lam
- From the Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Shatin, Hong Kong, ,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China, and
| | - Zeyu Zhu
- From the Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Juliana Tsz Yan Ng
- From the Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Shatin, Hong Kong
| | - William E. Sause
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California 95064
| | - Paphavee Lertsethtakarn
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California 95064
| | - Kwok Fai Lau
- From the Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Karen M. Ottemann
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California 95064
| | - Shannon Wing Ngor Au
- From the Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Shatin, Hong Kong, ,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China, and ,To whom correspondence should be addressed. Tel.:
852-3943-4170; E-mail:
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17
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dos Santos RN, Khan S, Morcos F. Characterization of C-ring component assembly in flagellar motors from amino acid coevolution. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171854. [PMID: 29892378 PMCID: PMC5990795 DOI: 10.1098/rsos.171854] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 04/05/2018] [Indexed: 06/08/2023]
Abstract
Bacterial flagellar motility, an important virulence factor, is energized by a rotary motor localized within the flagellar basal body. The rotor module consists of a large framework (the C-ring), composed of the FliG, FliM and FliN proteins. FliN and FliM contacts the FliG torque ring to control the direction of flagellar rotation. We report that structure-based models constrained only by residue coevolution can recover the binding interface of atomic X-ray dimer complexes with remarkable accuracy (approx. 1 Å RMSD). We propose a model for FliM-FliN heterodimerization, which agrees accurately with homologous interfaces as well as in situ cross-linking experiments, and hence supports a proposed architecture for the lower portion of the C-ring. Furthermore, this approach allowed the identification of two discrete and interchangeable homodimerization interfaces between FliM middle domains that agree with experimental measurements and might be associated with C-ring directional switching dynamics triggered upon binding of CheY signal protein. Our findings provide structural details of complex formation at the C-ring that have been difficult to obtain with previous methodologies and clarify the architectural principle that underpins the ultra-sensitive allostery exhibited by this ring assembly that controls the clockwise or counterclockwise rotation of flagella.
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Affiliation(s)
- Ricardo Nascimento dos Santos
- Institute of Chemistry and Center for Computational Engineering and Science, University of Campinas, Campinas, SP, Brazil
| | - Shahid Khan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Faruck Morcos
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX, USA
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX, USA
- Center for Systems Biology, University of Texas at Dallas, Richardson, TX, USA
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18
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Kinoshita M, Furukawa Y, Uchiyama S, Imada K, Namba K, Minamino T. Insight into adaptive remodeling of the rotor ring complex of the bacterial flagellar motor. Biochem Biophys Res Commun 2017; 496:12-17. [PMID: 29294326 DOI: 10.1016/j.bbrc.2017.12.118] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 12/04/2017] [Accepted: 12/20/2017] [Indexed: 12/23/2022]
Abstract
The bacterial flagellar motor rotates in both counterclockwise (CCW) and clockwise (CW) directions. FliG, FliM and FliN form the C ring on the cytoplasmic face of the MS ring made of a transmembrane protein, FliF. The C ring acts not only as a rotor but also as a switch of the direction of motor rotation. FliG consists of three domains: FliGN, FliGM and FliGC. FliGN directly binds to FliF. Intermolecular interactions between FliGM and FliGC drive FliG ring formation. FliGM is responsible for the interaction with FliM. FliGC is involved in the interaction with the stator protein MotA. Adaptive remodeling of the C ring occurs when the motor switches between the CCW and CW states. However, it remained unknown how. Here, we report the effects of a CW-locked deletion mutation (ΔPEV) in FliG of Thermotaoga maritia (Tm-FliG) on FliG-FliG and FliG-FliM interactions. The PEV deletion stabilized the intramolecular interaction between FliGM and FliGC, thereby suppressing the oligomerization of Tm-FliGMC in solution. This deletion also induced a conformational change of HelixMC connecting FliGM and FliGC to reduce the binding affinity of Tm-FliGMC for FliM. We will discuss adaptive remodeling of the C ring responsible for flagellar motor switching.
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Affiliation(s)
- Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Yukio Furukawa
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Susumu Uchiyama
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Katsumi Imada
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan; Quantitative Biology Center, RIKEN, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadoaka, Suita, Osaka 565-0871, Japan.
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19
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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.
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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
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20
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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]
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21
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Kim EA, Panushka J, Meyer T, Carlisle R, Baker S, Ide N, Lynch M, Crane BR, Blair DF. Architecture of the Flagellar Switch Complex of Escherichia coli: Conformational Plasticity of FliG and Implications for Adaptive Remodeling. J Mol Biol 2017; 429:1305-1320. [PMID: 28259628 PMCID: PMC5494207 DOI: 10.1016/j.jmb.2017.02.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/16/2017] [Accepted: 02/16/2017] [Indexed: 12/29/2022]
Abstract
Structural models of the complex that regulates the direction of flagellar rotation assume either ~34 or ~25 copies of the protein FliG. Support for ~34 came from crosslinking experiments identifying an intersubunit contact most consistent with that number; support for ~25 came from the observation that flagella can assemble and rotate when FliG is genetically fused to FliF, for which the accepted number is ~25. Here, we have undertaken crosslinking and other experiments to address more fully the question of FliG number. The results indicate a copy number of ~25 for FliG. An interaction between the C-terminal and middle domains, which has been taken to support a model with ~34 copies, is also supported. To reconcile the interaction with a FliG number of ~25, we hypothesize conformational plasticity in an interdomain segment of FliG that allows some subunits to bridge gaps created by the number mismatch. This proposal is supported by mutant phenotypes and other results indicating that the normally helical segment adopts a more extended conformation in some subunits. The FliG amino-terminal domain is organized in a regular array with dimensions matching a ring in the upper part of the complex. The model predicts that FliG copy number should be tied to that of FliF, whereas FliM copy number can increase or decrease according to the number of FliG subunits that adopt the extended conformation. This has implications for the phenomenon of adaptive switch remodeling, in which the FliM copy number varies to adjust the bias of the switch.
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Affiliation(s)
- Eun A Kim
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Joseph Panushka
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Trevor Meyer
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Ryan Carlisle
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Samantha Baker
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Nicholas Ide
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael Lynch
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Brian R Crane
- 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.
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22
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Bergeron JR. Structural modeling of the flagellum MS ring protein FliF reveals similarities to the type III secretion system and sporulation complex. PeerJ 2016; 4:e1718. [PMID: 26925337 PMCID: PMC4768692 DOI: 10.7717/peerj.1718] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/31/2016] [Indexed: 11/29/2022] Open
Abstract
The flagellum is a large proteinaceous organelle found at the surface of many bacteria, whose primary role is to allow motility through the rotation of a long extracellular filament. It is an essential virulence factor in many pathogenic species, and is also a priming component in the formation of antibiotic-resistant biofilms. The flagellum consists of the export apparatus on the cytosolic side; the basal body and rotor, spanning the bacterial membrane(s) and periplasm; and the hook-filament, that protrudes away from the bacterial surface. Formation of the basal body MS ring region, constituted of multiple copies of the protein FliF, is one of the initial steps of flagellum assembly. However, the precise architecture of FliF is poorly understood. Here, I report a bioinformatics analysis of the FliF sequence from various bacterial species, suggesting that its periplasmic region is composed of three globular domains. The first two are homologous to that of the type III secretion system injectisome proteins SctJ, and the third possesses a similar fold to that of the sporulation complex component SpoIIIAG. I also describe that Chlamydia possesses an unusual FliF protein, lacking part of the SctJ homology domain and the SpoIIIAG-like domain, and fused to the rotor component FliG at its C-terminus. Finally, I have combined the sequence analysis of FliF with the EM map of the MS ring, to propose the first atomic model for the FliF oligomer, suggesting that FliF is structurally akin to a fusion of the two injectisome components SctJ and SctD. These results further define the relationship between the flagellum, injectisome and sporulation complex, and will facilitate future structural characterization of the flagellum basal body.
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Affiliation(s)
- Julien R Bergeron
- Department of Biochemistry, University of Washington , Seattle, WA , USA
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23
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Baker MAB, Hynson RMG, Ganuelas LA, Mohammadi NS, Liew CW, Rey AA, Duff AP, Whitten AE, Jeffries CM, Delalez NJ, Morimoto YV, Stock D, Armitage JP, Turberfield AJ, Namba K, Berry RM, Lee LK. Domain-swap polymerization drives the self-assembly of the bacterial flagellar motor. Nat Struct Mol Biol 2016; 23:197-203. [PMID: 26854663 DOI: 10.1038/nsmb.3172] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/13/2016] [Indexed: 01/02/2023]
Abstract
Large protein complexes assemble spontaneously, yet their subunits do not prematurely form unwanted aggregates. This paradox is epitomized in the bacterial flagellar motor, a sophisticated rotary motor and sensory switch consisting of hundreds of subunits. Here we demonstrate that Escherichia coli FliG, one of the earliest-assembling flagellar motor proteins, forms ordered ring structures via domain-swap polymerization, which in other proteins has been associated with uncontrolled and deleterious protein aggregation. Solution structural data, in combination with in vivo biochemical cross-linking experiments and evolutionary covariance analysis, revealed that FliG exists predominantly as a monomer in solution but only as domain-swapped polymers in assembled flagellar motors. We propose a general structural and thermodynamic model for self-assembly, in which a structural template controls assembly and shapes polymer formation into rings.
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Affiliation(s)
- Matthew A B Baker
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.,European Molecular Biology Laboratory Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Robert M G Hynson
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - Lorraine A Ganuelas
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - Nasim Shah Mohammadi
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - Chu Wai Liew
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - Anthony A Rey
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - Anthony P Duff
- Australian Nuclear and Science Technology Organisation, Lucas Heights, New South Wales, Australia
| | - Andrew E Whitten
- Australian Nuclear and Science Technology Organisation, Lucas Heights, New South Wales, Australia
| | - Cy M Jeffries
- Australian Nuclear and Science Technology Organisation, Lucas Heights, New South Wales, Australia
| | | | - Yusuke V Morimoto
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Daniela Stock
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | | | | | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | | | - Lawrence K Lee
- Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.,European Molecular Biology Laboratory Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
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24
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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.
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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
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25
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Pandini A, Kleinjung J, Rasool S, Khan S. Coevolved Mutations Reveal Distinct Architectures for Two Core Proteins in the Bacterial Flagellar Motor. PLoS One 2015; 10:e0142407. [PMID: 26561852 PMCID: PMC4642947 DOI: 10.1371/journal.pone.0142407] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/21/2015] [Indexed: 02/08/2023] Open
Abstract
Switching of bacterial flagellar rotation is caused by large domain movements of the FliG protein triggered by binding of the signal protein CheY to FliM. FliG and FliM form adjacent multi-subunit arrays within the basal body C-ring. The movements alter the interaction of the FliG C-terminal (FliGC) “torque” helix with the stator complexes. Atomic models based on the Salmonella entrovar C-ring electron microscopy reconstruction have implications for switching, but lack consensus on the relative locations of the FliG armadillo (ARM) domains (amino-terminal (FliGN), middle (FliGM) and FliGC) as well as changes during chemotaxis. The generality of the Salmonella model is challenged by the variation in motor morphology and response between species. We studied coevolved residue mutations to determine the unifying elements of switch architecture. Residue interactions, measured by their coevolution, were formalized as a network, guided by structural data. Our measurements reveal a common design with dedicated switch and motor modules. The FliM middle domain (FliMM) has extensive connectivity most simply explained by conserved intra and inter-subunit contacts. In contrast, FliG has patchy, complex architecture. Conserved structural motifs form interacting nodes in the coevolution network that wire FliMM to the FliGC C-terminal, four-helix motor module (C3-6). FliG C3-6 coevolution is organized around the torque helix, differently from other ARM domains. The nodes form separated, surface-proximal patches that are targeted by deleterious mutations as in other allosteric systems. The dominant node is formed by the EHPQ motif at the FliMMFliGM contact interface and adjacent helix residues at a central location within FliGM. The node interacts with nodes in the N-terminal FliGc α-helix triad (ARM-C) and FliGN. ARM-C, separated from C3-6 by the MFVF motif, has poor intra-network connectivity consistent with its variable orientation revealed by structural data. ARM-C could be the convertor element that provides mechanistic and species diversity.
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Affiliation(s)
- Alessandro Pandini
- Department of Computer Science and Synthetic Biology Theme, Brunel University London, Uxbridge UB8 3PH, United Kingdom
| | - Jens Kleinjung
- Mathematical Biology, Francis Crick Institute, Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
| | - Shafqat Rasool
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Shahid Khan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States of America
- * E-mail:
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26
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Phillips AM, Calvo RA, Kearns DB. Functional Activation of the Flagellar Type III Secretion Export Apparatus. PLoS Genet 2015; 11:e1005443. [PMID: 26244495 PMCID: PMC4526659 DOI: 10.1371/journal.pgen.1005443] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 07/15/2015] [Indexed: 11/18/2022] Open
Abstract
Flagella are assembled sequentially from the inside-out with morphogenetic checkpoints that enforce the temporal order of subunit addition. Here we show that flagellar basal bodies fail to proceed to hook assembly at high frequency in the absence of the monotopic protein SwrB of Bacillus subtilis. Genetic suppressor analysis indicates that SwrB activates the flagellar type III secretion export apparatus by the membrane protein FliP. Furthermore, mutants defective in the flagellar C-ring phenocopy the absence of SwrB for reduced hook frequency and C-ring defects may be bypassed either by SwrB overexpression or by a gain-of-function allele in the polymerization domain of FliG. We conclude that SwrB enhances the probability that the flagellar basal body adopts a conformation proficient for secretion to ensure that rod and hook subunits are not secreted in the absence of a suitable platform on which to polymerize.
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Affiliation(s)
- Andrew M. Phillips
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Rebecca A. Calvo
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Daniel B. Kearns
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
- * E-mail:
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27
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Onoue Y, Kojima S, Homma M. Effect of FliG three amino acids deletion in Vibrio polar-flagellar rotation and formation. J Biochem 2015; 158:523-9. [PMID: 26142283 DOI: 10.1093/jb/mvv068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 06/03/2015] [Indexed: 11/14/2022] Open
Abstract
Most of bacteria can swim by rotating flagella bidirectionally. The C ring, located at the bottom of the flagellum and in the cytoplasmic space, consists of FliG, FliM and FliN, and has an important function in flagellar protein secretion, torque generation and rotational switch of the motor. FliG is the most important part of the C ring that interacts directly with a stator subunit. Here, we introduced a three-amino acids in-frame deletion mutation (ΔPSA) into FliG from Vibrio alginolyticus, whose corresponding mutation in Salmonella confers a switch-locked phenotype, and examined its phenotype. We found that this FliG mutant could not produce flagellar filaments in a fliG null strain but the FliG(ΔPSA) protein could localize at the cell pole as does the wild-type protein. Unexpectedly, when this mutant was expressed in a wild-type strain, cells formed flagella efficiently but the motor could not rotate. We propose that this different phenotype in Vibrio and Salmonella might be due to distinct interactions between FliG mutant and FliM in the C ring between the bacterial species.
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Affiliation(s)
- Yasuhiro Onoue
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
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28
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Sircar R, Borbat PP, Lynch MJ, Bhatnagar J, Beyersdorf MS, Halkides CJ, Freed JH, Crane BR. Assembly states of FliM and FliG within the flagellar switch complex. J Mol Biol 2014; 427:867-886. [PMID: 25536293 DOI: 10.1016/j.jmb.2014.12.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 12/12/2014] [Accepted: 12/12/2014] [Indexed: 01/11/2023]
Abstract
At the base of the bacterial flagella, a cytoplasmic rotor (the C-ring) generates torque and reverses rotation sense in response to stimuli. The bulk of the C-ring forms from many copies of the proteins FliG, FliM, and FliN, which together constitute the switch complex. To help resolve outstanding issues regarding C-ring architecture, we have investigated interactions between FliM and FliG from Thermotoga maritima with X-ray crystallography and pulsed dipolar ESR spectroscopy (PDS). A new crystal structure of an 11-unit FliG:FliM complex produces a large arc with a curvature consistent with the dimensions of the C-ring. Previously determined structures along with this new structure provided a basis to test switch complex assembly models. PDS combined with mutational studies and targeted cross-linking reveal that FliM and FliG interact through their middle domains to form both parallel and antiparallel arrangements in solution. Residue substitutions at predicted interfaces disrupt higher-order complexes that are primarily mediated by contacts between the C-terminal domain of FliG and the middle domain of a neighboring FliG molecule. Spin separations among multi-labeled components fit a self-consistent model that agree well with electron microscopy images of the C-ring. An activated form of the response regulator CheY destabilizes the parallel arrangement of FliM molecules to perturb FliG alignment in a process that may reflect the onset of rotation switching. These data suggest a model of C-ring assembly in which intermolecular contacts among FliG domains provide a template for FliM assembly and cooperative transitions.
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Affiliation(s)
- Ria Sircar
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, NY 14853, USA
| | - Michael J Lynch
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jaya Bhatnagar
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Matthew S Beyersdorf
- Department of Chemistry and Biochemistry, Unversity of North Carolina Wilmington, Wilmington, NC 28403, USA
| | - Christopher J Halkides
- Department of Chemistry and Biochemistry, Unversity of North Carolina Wilmington, Wilmington, NC 28403, USA
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, NY 14853, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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29
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Branch RW, Sayegh MN, Shen C, Nathan VSJ, Berg HC. Adaptive remodelling by FliN in the bacterial rotary motor. J Mol Biol 2014; 426:3314-3324. [PMID: 25046382 DOI: 10.1016/j.jmb.2014.07.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 07/07/2014] [Accepted: 07/11/2014] [Indexed: 01/19/2023]
Abstract
Sensory adaptation in the Escherichia coli chemosensory pathway has been the subject of interest for decades, with investigation focusing on the receptors that process extracellular inputs. Recent studies demonstrate that the flagellar motors responsible for cell locomotion also play a role, adding or subtracting FliM subunits to maximise sensitivity to pathway signals. It is difficult to reconcile this FliM remodelling with the observation that partner FliN subunits are relatively static fixtures in the motor. By fusing a fluorescent protein internally to FliN, we show that there is in fact significant FliN remodelling. The kinetics and stoichiometry of FliN in steady state and in adapting motors are investigated and found to match the behaviour of FliM in all respects except for timescale where FliN rates are about 4 times slower. We notice that motor adaptation is slower in the presence of the fluorescent protein, indicating a possible source for the difference. The behaviour of FliM and FliN is consistent with a kinetic and stoichiometric model that contradicts the traditional view of a packed, rigid motor architecture.
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Affiliation(s)
- Richard W Branch
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Michael N Sayegh
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Chong Shen
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vedavalli S J Nathan
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Howard C Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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30
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Abstract
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The flagellum is one of the most
sophisticated self-assembling
molecular machines in bacteria. Powered by the proton-motive force,
the flagellum rapidly rotates in either a clockwise or counterclockwise
direction, which ultimately controls bacterial motility and behavior. Escherichia coli and Salmonella enterica have served as important model systems for extensive genetic, biochemical,
and structural analysis of the flagellum, providing unparalleled insights
into its structure, function, and gene regulation. Despite these advances,
our understanding of flagellar assembly and rotational mechanisms
remains incomplete, in part because of the limited structural information
available regarding the intact rotor–stator complex and secretion
apparatus. Cryo-electron tomography (cryo-ET) has become a valuable
imaging technique capable of visualizing the intact flagellar motor
in cells at molecular resolution. Because the resolution that can
be achieved by cryo-ET with large bacteria (such as E. coli and S. enterica) is limited, analysis of small-diameter
bacteria (including Borrelia burgdorferi and Campylobacter jejuni) can provide additional insights into
the in situ structure of the flagellar motor and
other cellular components. This review is focused on the application
of cryo-ET, in combination with genetic and biophysical approaches,
to the study of flagellar structures and its potential for improving
the understanding of rotor–stator interactions, the rotational
switching mechanism, and the secretion and assembly of flagellar components.
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Affiliation(s)
- Xiaowei Zhao
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston , Houston, Texas 77030, United States
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31
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Morimoto YV, Minamino T. Structure and function of the bi-directional bacterial flagellar motor. Biomolecules 2014; 4:217-34. [PMID: 24970213 PMCID: PMC4030992 DOI: 10.3390/biom4010217] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 01/24/2014] [Accepted: 02/04/2014] [Indexed: 01/02/2023] Open
Abstract
The bacterial flagellum is a locomotive organelle that propels the bacterial cell body in liquid environments. The flagellum is a supramolecular complex composed of about 30 different proteins and consists of at least three parts: a rotary motor, a universal joint, and a helical filament. The flagellar motor of Escherichia coli and Salmonella enterica is powered by an inward-directed electrochemical potential difference of protons across the cytoplasmic membrane. The flagellar motor consists of a rotor made of FliF, FliG, FliM and FliN and a dozen stators consisting of MotA and MotB. FliG, FliM and FliN also act as a molecular switch, enabling the motor to spin in both counterclockwise and clockwise directions. Each stator is anchored to the peptidoglycan layer through the C-terminal periplasmic domain of MotB and acts as a proton channel to couple the proton flow through the channel with torque generation. Highly conserved charged residues at the rotor–stator interface are required not only for torque generation but also for stator assembly around the rotor. In this review, we will summarize our current understanding of the structure and function of the proton-driven bacterial flagellar motor.
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Affiliation(s)
- Yusuke V Morimoto
- Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.
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32
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Gohara M, Kobayashi S, Abe-Yoshizumi R, Nonoyama N, Kojima S, Asami Y, Homma M. Biophysical characterization of the C-terminal region of FliG, an essential rotor component of the Na+-driven flagellar motor. J Biochem 2013; 155:83-9. [DOI: 10.1093/jb/mvt100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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33
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Sircar R, Greenswag AR, Bilwes AM, Gonzalez-Bonet G, Crane BR. Structure and activity of the flagellar rotor protein FliY: a member of the CheC phosphatase family. J Biol Chem 2013; 288:13493-502. [PMID: 23532838 PMCID: PMC3650386 DOI: 10.1074/jbc.m112.445171] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND FliY is a flagellar rotor protein of the CheC phosphatase family. RESULTS The FliY structure resembles that of the rotor protein FliM but contains two active centers for CheY dephosphorylation. CONCLUSION FliY incorporates properties of the FliM/FliN rotor proteins and the CheC/CheX phosphatases to serve multiple functions in the flagellar switch. SIGNIFICANCE FliY distinguishes flagellar architecture and function in different types of bacteria. Rotating flagella propel bacteria toward favorable environments. Sense of rotation is determined by the intracellular response regulator CheY, which when phosphorylated (CheY-P) interacts directly with the flagellar motor. In many different types of bacteria, the CheC/CheX/FliY (CXY) family of phosphatases terminates the CheY-P signal. Unlike CheC and CheX, FliY is localized in the flagellar switch complex, which also contains the stator-coupling protein FliG and the target of CheY-P, FliM. The 2.5 Å resolution crystal structure of the FliY catalytic domain from Thermotoga maritima bears strong resemblance to the middle domain of FliM. Regions of FliM that mediate contacts within the rotor compose the phosphatase active sites in FliY. Despite the similarity between FliY and FliM, FliY does not bind FliG and thus is unlikely to be a substitute for FliM in the center of the switch complex. Solution studies indicate that FliY dimerizes through its C-terminal domains, which resemble the Escherichia coli switch complex component FliN. FliY differs topologically from the E. coli chemotaxis phosphatase CheZ but appears to utilize similar structural motifs for CheY dephosphorylation in close analogy to CheX. Recognition properties and phosphatase activities of site-directed mutants identify two pseudosymmetric active sites in FliY (Glu(35)/Asn(38) and Glu(132)/Asn(135)), with the second site (Glu(132)/Asn(135)) being more active. A putative N-terminal CheY binding domain conserved with FliM is not required for binding CheY-P or phosphatase activity.
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Affiliation(s)
- Ria Sircar
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850
| | - Anna R. Greenswag
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850
| | - Alexandrine M. Bilwes
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850
| | - Gabriela Gonzalez-Bonet
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850
| | - Brian R. Crane
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, To whom correspondence should be addressed: Dept. of Chemistry and Chemical Biology Cornell University, Ithaca, NY 14850. Tel.: 607-254-8634; E-mail:
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34
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Lam KH, Lam WWL, Wong JYK, Chan LC, Kotaka M, Ling TKW, Jin DY, Ottemann KM, Au SWN. Structural basis of FliG-FliM interaction inHelicobacter pylori. Mol Microbiol 2013; 88:798-812. [DOI: 10.1111/mmi.12222] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2013] [Indexed: 12/20/2022]
Affiliation(s)
- Kwok-Ho Lam
- Center for Protein Science and Crystallography; School of Life Sciences; The Chinese University of Hong Kong; Hong Kong; China
| | - Wendy Wai Ling Lam
- Center for Protein Science and Crystallography; School of Life Sciences; The Chinese University of Hong Kong; Hong Kong; China
| | - Jase Yan-Kit Wong
- Center for Protein Science and Crystallography; School of Life Sciences; The Chinese University of Hong Kong; Hong Kong; China
| | - Ling-Chim Chan
- Department of Biochemistry; The University of Hong Kong; Hong Kong; China
| | - Masayo Kotaka
- Department of Physiology; The University of Hong Kong; Hong Kong; China
| | - Thomas Kin-Wah Ling
- Department of Microbiology; The Chinese University of Hong Kong; Hong Kong; China
| | - Dong-Yan Jin
- Department of Biochemistry; The University of Hong Kong; Hong Kong; China
| | - Karen M. Ottemann
- Department of Microbiology and Environmental Toxicology; University of California Santa Cruz; Santa Cruz; CA; USA
| | - Shannon Wing-Ngor Au
- Center for Protein Science and Crystallography; School of Life Sciences; The Chinese University of Hong Kong; Hong Kong; China
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35
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Boyd CD, O'Toole GA. Second messenger regulation of biofilm formation: breakthroughs in understanding c-di-GMP effector systems. Annu Rev Cell Dev Biol 2013; 28:439-62. [PMID: 23057745 DOI: 10.1146/annurev-cellbio-101011-155705] [Citation(s) in RCA: 184] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The second messenger bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) has emerged as a broadly conserved intracellular signaling molecule. This soluble molecule is important for controlling biofilm formation, adhesion, motility, virulence, and cell morphogenesis in diverse bacterial species. But how is the typical bacterial cell able to coordinate the actions of upward of 50 proteins involved in synthesizing, degrading, and binding c-di-GMP? Understanding the specificity of c-di-GMP signaling in the context of so many enzymes involved in making, breaking, and binding the second messenger will be possible only through mechanistic studies of its output systems. Here we discuss three newly characterized c-di-GMP effector systems that are best understood in terms of molecular and structural detail. As they are conserved across many bacterial species, they likely will serve as central paradigms for c-di-GMP output systems and contribute to our understanding of how bacteria control critical aspects of their biology.
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Affiliation(s)
- Chelsea D Boyd
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA
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36
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High hydrostatic pressure induces counterclockwise to clockwise reversals of the Escherichia coli flagellar motor. J Bacteriol 2013; 195:1809-14. [PMID: 23417485 DOI: 10.1128/jb.02139-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The bacterial flagellar motor is a reversible rotary machine that rotates a left-handed helical filament, allowing bacteria to swim toward a more favorable environment. The direction of rotation reverses from counterclockwise (CCW) to clockwise (CW), and vice versa, in response to input from the chemotaxis signaling circuit. CW rotation is normally caused by binding of the phosphorylated response regulator CheY (CheY-P), and strains lacking CheY are typically locked in CCW rotation. The detailed mechanism of switching remains unresolved because it is technically difficult to regulate the level of CheY-P within the concentration range that produces flagellar reversals. Here, we demonstrate that high hydrostatic pressure can induce CW rotation even in the absence of CheY-P. The rotation of single flagellar motors in Escherichia coli cells with the cheY gene deleted was monitored at various pressures and temperatures. Application of >120 MPa pressure induced a reversal from CCW to CW at 20°C, although at that temperature, no motor rotated CW at ambient pressure (0.1 MPa). At lower temperatures, pressure-induced changes in direction were observed at pressures of <120 MPa. CW rotation increased with pressure in a sigmoidal fashion, as it does in response to increasing concentrations of CheY-P. Application of pressure generally promotes the formation of clusters of ordered water molecules on the surfaces of proteins. It is possible that hydration of the switch complex at high pressure induces structural changes similar to those caused by the binding of CheY-P.
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37
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Mechanism for adaptive remodeling of the bacterial flagellar switch. Proc Natl Acad Sci U S A 2012; 109:20018-22. [PMID: 23169659 DOI: 10.1073/pnas.1212327109] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bacterial flagellar motor has been shown in previous work to adapt to changes in the steady-state concentration of the chemotaxis signaling molecule, CheY-P, by changing the FliM content. We show here that the number of FliM molecules in the motor and the fraction of FliM molecules that exchange depend on the direction of flagellar rotation, not on CheY-P binding per se. Our results are consistent with a model in which the structural differences associated with the direction of rotation modulate the strength of FliM binding. When the motor spins counterclockwise, FliM binding strengthens, the fraction of FliM molecules that exchanges decreases, and the ring content increases. The larger number of CheY-P binding sites enhances the motor's sensitivity, i.e., the motor adapts. An interesting unresolved question is how additional copies of FliM might be accommodated.
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38
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Distinct roles of highly conserved charged residues at the MotA-FliG interface in bacterial flagellar motor rotation. J Bacteriol 2012; 195:474-81. [PMID: 23161029 DOI: 10.1128/jb.01971-12] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Electrostatic interactions between the stator protein MotA and the rotor protein FliG are important for bacterial flagellar motor rotation. Arg90 and Glu98 of MotA are required not only for torque generation but also for stator assembly around the rotor, but their actual roles remain unknown. Here we analyzed the roles of functionally important charged residues at the MotA-FliG interface in motor performance. About 75% of the motA(R90E) cells and 45% of the motA(E98K) cells showed no fluorescent spots of green fluorescent protein (GFP)-MotB, indicating reduced efficiency of stator assembly around the rotor. The FliG(D289K) and FliG(R281V) mutations, which restore the motility of the motA(R90E) and motA(E98K) mutants, respectively, showed reduced numbers and intensity of GFP-MotB spots as well. The FliG(D289K) mutation significantly recovered the localization of GFP-MotB to the motor in the motA(R90E) mutant, whereas the FliG(R281V) mutation did not recover the GFP-MotB localization in the motA(E98K) mutant. These results suggest that the MotA-Arg90-FliG-Asp289 interaction is critical for the proper positioning of the stators around the rotor, whereas the MotA-Glu98-FliG-Arg281 interaction is more important for torque generation.
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39
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Vartanian AS, Paz A, Fortgang EA, Abramson J, Dahlquist FW. Structure of flagellar motor proteins in complex allows for insights into motor structure and switching. J Biol Chem 2012; 287:35779-83. [PMID: 22896702 PMCID: PMC3476246 DOI: 10.1074/jbc.c112.378380] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 06/12/2012] [Indexed: 12/23/2022] Open
Abstract
The flagellar motor is one type of propulsion device of motile bacteria. The cytoplasmic ring (C-ring) of the motor interacts with the stator to generate torque in clockwise and counterclockwise directions. The C-ring is composed of three proteins, FliM, FliN, and FliG. Together they form the "switch complex" and regulate switching and torque generation. Here we report the crystal structure of the middle domain of FliM in complex with the middle and C-terminal domains of FliG that shows the interaction surface and orientations of the proteins. In the complex, FliG assumes a compact conformation in which the middle and C-terminal domains (FliG(MC)) collapse and stack together similarly to the recently published structure of a mutant of FliG(MC) with a clockwise rotational bias. This intramolecular stacking of the domains is distinct from the intermolecular stacking seen in other structures of FliG. We fit the complex structure into the three-dimensional reconstructions of the motor and propose that the cytoplasmic ring is assembled from 34 FliG and FliM molecules in a 1:1 fashion.
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Affiliation(s)
- Armand S. Vartanian
- From the Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106 and
| | - Aviv Paz
- the Department of Physiology, David Geffen School of Medicine, UCLA, Los Angeles, California 90095
| | - Emily A. Fortgang
- From the Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106 and
| | - Jeff Abramson
- the Department of Physiology, David Geffen School of Medicine, UCLA, Los Angeles, California 90095
| | - Frederick W. Dahlquist
- From the Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106 and
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40
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Protein export according to schedule: architecture, assembly, and regulation of type III secretion systems from plant- and animal-pathogenic bacteria. Microbiol Mol Biol Rev 2012; 76:262-310. [PMID: 22688814 DOI: 10.1128/mmbr.05017-11] [Citation(s) in RCA: 304] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Flagellar and translocation-associated type III secretion (T3S) systems are present in most gram-negative plant- and animal-pathogenic bacteria and are often essential for bacterial motility or pathogenicity. The architectures of the complex membrane-spanning secretion apparatuses of both systems are similar, but they are associated with different extracellular appendages, including the flagellar hook and filament or the needle/pilus structures of translocation-associated T3S systems. The needle/pilus is connected to a bacterial translocon that is inserted into the host plasma membrane and mediates the transkingdom transport of bacterial effector proteins into eukaryotic cells. During the last 3 to 5 years, significant progress has been made in the characterization of membrane-associated core components and extracellular structures of T3S systems. Furthermore, transcriptional and posttranscriptional regulators that control T3S gene expression and substrate specificity have been described. Given the architecture of the T3S system, it is assumed that extracellular components of the secretion apparatus are secreted prior to effector proteins, suggesting that there is a hierarchy in T3S. The aim of this review is to summarize our current knowledge of T3S system components and associated control proteins from both plant- and animal-pathogenic bacteria.
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41
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Nanorotors and self-assembling macromolecular machines: The torque ring of the bacterial flagellar motor. Curr Opin Biotechnol 2012; 23:545-54. [DOI: 10.1016/j.copbio.2012.01.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 01/16/2012] [Indexed: 01/18/2023]
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42
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Multiple Conformations of the FliG C-Terminal Domain Provide Insight into Flagellar Motor Switching. Structure 2012; 20:315-25. [DOI: 10.1016/j.str.2011.11.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 11/25/2011] [Accepted: 11/29/2011] [Indexed: 01/01/2023]
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43
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Zarbiv G, Li H, Wolf A, Cecchini G, Caplan SR, Sourjik V, Eisenbach M. Energy complexes are apparently associated with the switch-motor complex of bacterial flagella. J Mol Biol 2011; 416:192-207. [PMID: 22210351 DOI: 10.1016/j.jmb.2011.12.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 12/12/2011] [Accepted: 12/13/2011] [Indexed: 01/27/2023]
Abstract
Recently, the switch-motor complex of bacterial flagella was found to be associated with a number of non-flagellar proteins, which, in spite of not being known as belonging to the chemotaxis system, affect the function of the flagella. The observation that one of these proteins, fumarate reductase, is essentially involved in electron transport under anaerobic conditions raised the question of whether other energy-linked enzymes are associated with the switch-motor complex as well. Here, we identified two additional such enzymes in Escherichia coli. Employing fluorescence resonance energy transfer in vivo and pull-down assays invitro, we provided evidence for the interaction of F(0)F(1) ATP synthase via its β subunit with the flagellar switch protein FliG and for the interaction of NADH-ubiquinone oxidoreductase with FliG, FliM, and possibly FliN. Furthermore, we measured higher rates of ATP synthesis, ATP hydrolysis, and electron transport from NADH to oxygen in membrane areas adjacent to the flagellar motor than in other membrane areas. All these observations suggest the association of energy complexes with the flagellar switch-motor complex. Finding that deletion of the β subunit in vivo affected the direction of flagellar rotation and switching frequency further implied that the interaction of F(0)F(1) ATP synthase with FliG is important for the function of the switch of bacterial flagella.
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Affiliation(s)
- Gabriel Zarbiv
- Department of Biological Chemistry, The Weizmann Institute of Science, 76100 Rehovot, Israel
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44
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A molecular mechanism of direction switching in the flagellar motor of Escherichia coli. Proc Natl Acad Sci U S A 2011; 108:17171-6. [PMID: 21969567 DOI: 10.1073/pnas.1110111108] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The direction of flagellar rotation is regulated by a rotor-mounted protein assembly, termed the "switch complex," formed from multiple copies of the proteins FliG, FliM, and FliN. The structures of major parts of these proteins are known, and the overall organization of proteins in the complex has been elucidated previously using a combination of protein-binding, mutational, and cross-linking approaches. In Escherichia coli, the switch from counterclockwise to clockwise rotation is triggered by the signaling protein phospho-CheY, which binds to the lower part of the switch complex and induces small movements of FliM and FliN subunits relative to each other. Direction switching also must produce movements in the upper part of the complex, particularly in the C-terminal domain of FliG (FliG(C)), which interacts with the stator to generate the torque for flagellar rotation. In the present study, protein movements in the middle and upper parts of the switch complex have been probed by means of targeted cross-linking and mutational analysis. Switching induces a tilting movement of the FliM domains that form the middle part of the switch and a consequent rotation of the affixed FliG(C) domains that reorients the stator interaction sites by about 90°. In a recently proposed hypothesis for the motor mechanism, such a reorientation of FliG(C) would reverse the direction of motor rotation.
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Genome-wide gene expression analysis of Patrinia scabiosaefolia reveals an antibiotic effect. BIOCHIP JOURNAL 2011. [DOI: 10.1007/s13206-011-5309-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Adjusting the spokes of the flagellar motor with the DNA-binding protein H-NS. J Bacteriol 2011; 193:5914-22. [PMID: 21890701 DOI: 10.1128/jb.05458-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The H-NS protein of bacteria is a global regulator that stimulates transcription of flagellar genes and that also acts directly to modulate flagellar motor function. H-NS is known to bind FliG, a protein of the rotor that interacts with the stator and is directly involved in rotation of the motor. Here, we find that H-NS, well known for its ability to organize DNA, acts in the flagellar motor to organize protein subunits in the rotor. It binds to a middle domain of FliG that bridges the core parts of the rotor and parts nearer the edge that interact with the stator. In the absence of H-NS the organization of FliG subunits is disrupted, whereas overexpression of H-NS enhances FliG organization as monitored by targeted disulfide cross-linking, alters the disposition of a helix joining the middle and C-terminal domains of FliG, and enhances motor performance under conditions requiring a strengthened rotor-stator interface. The H-NS homolog StpA was also shown to bind FliG and to act similarly, though less effectively, in organizing FliG. The motility-enhancing effects of H-NS contrast with those of the recently characterized motility inhibitor YcgR. The present findings provide an integrated, structurally grounded framework for understanding the roughly opposing effects of these motility regulators.
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Paul K, Gonzalez-Bonet G, Bilwes AM, Crane BR, Blair D. Architecture of the flagellar rotor. EMBO J 2011; 30:2962-71. [PMID: 21673656 DOI: 10.1038/emboj.2011.188] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 05/18/2011] [Indexed: 12/16/2022] Open
Abstract
Rotation and switching of the bacterial flagellum depends on a large rotor-mounted protein assembly composed of the proteins FliG, FliM and FliN, with FliG most directly involved in rotation. The crystal structure of a complex between the central domains of FliG and FliM, in conjunction with several biochemical and molecular-genetic experiments, reveals the arrangement of the FliG and FliM proteins in the rotor. A stoichiometric mismatch between FliG (26 subunits) and FliM (34 subunits) is explained in terms of two distinct positions for FliM: one where it binds the FliG central domain and another where it binds the FliG C-terminal domain. This architecture provides a structural framework for addressing the mechanisms of motor rotation and direction switching and for unifying the large body of data on motor performance. Recently proposed alternative models of rotor assembly, based on a subunit contact observed in crystals, are not supported by experiment.
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Affiliation(s)
- Koushik Paul
- Department of Biology, University of Utah, Salt Lake City, UT, USA
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Minamino T, Imada K, Kinoshita M, Nakamura S, Morimoto YV, Namba K. Structural insight into the rotational switching mechanism of the bacterial flagellar motor. PLoS Biol 2011; 9:e1000616. [PMID: 21572987 PMCID: PMC3091841 DOI: 10.1371/journal.pbio.1000616] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 03/29/2011] [Indexed: 01/09/2023] Open
Abstract
Structural analysis of a clockwise-biased rotation mutant of the bacterial
flagellar rotor protein FliG provides a new model for the arrangement of FliG
subunits in the motor, and novel insights into rotation switching. The bacterial flagellar motor can rotate either clockwise (CW) or
counterclockwise (CCW). Three flagellar proteins, FliG, FliM, and FliN, are
required for rapid switching between the CW and CCW directions. Switching is
achieved by a conformational change in FliG induced by the binding of a
chemotaxis signaling protein, phospho-CheY, to FliM and FliN. FliG consists of
three domains, FliGN, FliGM, and FliGC, and
forms a ring on the cytoplasmic face of the MS ring of the flagellar basal body.
Crystal structures have been reported for the FliGMC domains of
Thermotoga maritima, which consist of the FliGM
and FliGC domains and a helix E that connects these two domains, and
full-length FliG of Aquifex aeolicus. However, the basis for
the switching mechanism is based only on previously obtained genetic data and is
hence rather indirect. We characterized a CW-biased mutant
(fliG(ΔPAA)) of Salmonella enterica by
direct observation of rotation of a single motor at high temporal and spatial
resolution. We also determined the crystal structure of the FliGMC
domains of an equivalent deletion mutant variant of T. maritima
(fliG(ΔPEV)). The FliG(ΔPAA) motor produced torque
at wild-type levels under a wide range of external load conditions. The
wild-type motors rotated exclusively in the CCW direction under our experimental
conditions, whereas the mutant motors rotated only in the CW direction. This
result suggests that wild-type FliG is more stable in the CCW state than in the
CW state, whereas FliG(ΔPAA) is more stable in the CW state than in the CCW
state. The structure of the TM-FliGMC(ΔPEV) revealed that
extremely CW-biased rotation was caused by a conformational change in helix E.
Although the arrangement of FliGC relative to FliGM in a
single molecule was different among the three crystals, a conserved
FliGM-FliGC unit was observed in all three of them. We
suggest that the conserved FliGM-FliGC unit is the basic
functional element in the rotor ring and that the PAA deletion induces a
conformational change in a hinge-loop between FliGM and helix E to
achieve the CW state of the FliG ring. We also propose a novel model for the
arrangement of FliG subunits within the motor. The model is in agreement with
the previous mutational and cross-linking experiments and explains the
cooperative switching mechanism of the flagellar motor. The bacterial flagellum is a rotating organelle that governs cell motility. At
the base of each flagellum is a motor powered by the electrochemical potential
difference of specific ions across the cytoplasmic membrane. In response to
environmental stimuli, rotation of the motor switches between counterclockwise
and clockwise, with a corresponding effect on the swimming direction of the
cell. Switching is triggered by the binding of the signaling protein
phospho-CheY to FliM and FliN, and achieved by conformational changes in the
rotor protein FliG. The actual switching mechanism, however, remains unclear. In
this study, we characterized a fliG mutant of
Salmonella that shows an extreme clockwise-biased rotation,
and determined the structure of a fragment of FliG (FliGMC) of the
equivalent mutant variant of Thermotoga maritima.
FliGMC is composed of two domains and covers the regions
essential for torque generation and FliM binding. We showed that the mutant
structure has a conformational change in the helix connecting the two domains,
leading to a domain orientation distinct from that of the wild-type FliG. On the
basis of this structure, we propose a new model for the arrangement of FliG
subunits in the rotor that is consistent with the previous mutational studies
and explains how cooperative switching occurs in the motor.
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Affiliation(s)
- Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka
University, Osaka, Japan
- PRESTO, JST, Saitama, Japan
| | - Katsumi Imada
- Graduate School of Frontier Biosciences, Osaka
University, Osaka, Japan
- Department of Macromolecular Science, Osaka
University, Osaka, Japan
- * E-mail: (KI); (KN)
| | - Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka
University, Osaka, Japan
| | - Shuichi Nakamura
- Graduate School of Frontier Biosciences, Osaka
University, Osaka, Japan
| | | | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka
University, Osaka, Japan
- * E-mail: (KI); (KN)
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Functioning nanomachines seen in real-time in living bacteria using single-molecule and super-resolution fluorescence imaging. Int J Mol Sci 2011; 12:2518-42. [PMID: 21731456 PMCID: PMC3127132 DOI: 10.3390/ijms12042518] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 04/07/2011] [Accepted: 04/11/2011] [Indexed: 11/19/2022] Open
Abstract
Molecular machines are examples of “pre-established” nanotechnology, driving the basic biochemistry of living cells. They encompass an enormous range of function, including fuel generation for chemical processes, transport of molecular components within the cell, cellular mobility, signal transduction and the replication of the genetic code, amongst many others. Much of our understanding of such nanometer length scale machines has come from in vitro studies performed in isolated, artificial conditions. Researchers are now tackling the challenges of studying nanomachines in their native environments. In this review, we outline recent in vivo investigations on nanomachines in model bacterial systems using state-of-the-art genetics technology combined with cutting-edge single-molecule and super-resolution fluorescence microscopy. We conclude that single-molecule and super-resolution fluorescence imaging provide powerful tools for the biochemical, structural and functional characterization of biological nanomachines. The integrative spatial, temporal, and single-molecule data obtained simultaneously from fluorescence imaging open an avenue for systems-level single-molecule cellular biophysics and in vivo biochemistry.
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