1
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Elramadi E, Kundu S, Mondal D, Paululat T, Schmittel M. Stepwise Dissipative Control of Multimodal Motion in a Silver(I) Catenate. Angew Chem Int Ed Engl 2024; 63:e202404444. [PMID: 38530118 DOI: 10.1002/anie.202404444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 03/27/2024]
Abstract
Stepwise dissipative control of two distinct motions, i.e., shuttling and sliding, is demonstrated in a single multicomponent device. When [2]rotaxane 1, which acts as a biped, and deck 2 were treated with AgBF4/PhCH2Br+NEt3 as chemical fuel, the transient catenate [Ag(1)]+ ⋅ [Ag3(2)]3+ was instantly generated showing multimodal motion and autonomous return to 1 and 2. In the dissipative process, catenate [Ag(1)]+ ⋅ [Ag3(2)]3+ cleanly transformed into the follow-up transient device (1) ⋅ [Ag3(2)]3+ exhibiting only sliding motion. Two interference-free dissipative cycles proved the resilience and robustness of the process.
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Affiliation(s)
- Emad Elramadi
- Center of Micro and Nanochemistry and (Bio)Technology, School of Science and Technology, Organische Chemie I, University of Siegen, Adolf-Reichwein Str. 2, 57068, Siegen, Germany
| | - Sohom Kundu
- Center of Micro and Nanochemistry and (Bio)Technology, School of Science and Technology, Organische Chemie I, University of Siegen, Adolf-Reichwein Str. 2, 57068, Siegen, Germany
| | - Debabrata Mondal
- Center of Micro and Nanochemistry and (Bio)Technology, School of Science and Technology, Organische Chemie I, University of Siegen, Adolf-Reichwein Str. 2, 57068, Siegen, Germany
| | - Thomas Paululat
- Center of Micro and Nanochemistry and (Bio)Technology, Organische Chemie II, University of Siegen, Adolf-Reichwein Str. 2, 57068, Siegen, Germany
| | - Michael Schmittel
- Center of Micro and Nanochemistry and (Bio)Technology, School of Science and Technology, Organische Chemie I, University of Siegen, Adolf-Reichwein Str. 2, 57068, Siegen, Germany
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2
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Johnson S, Deme JC, Furlong EJ, Caesar JJE, Chevance FFV, Hughes KT, Lea SM. Structural basis of directional switching by the bacterial flagellum. Nat Microbiol 2024; 9:1282-1292. [PMID: 38459206 DOI: 10.1038/s41564-024-01630-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/01/2024] [Indexed: 03/10/2024]
Abstract
The bacterial flagellum is a macromolecular protein complex that harvests energy from uni-directional ion flow across the inner membrane to power bacterial swimming via rotation of the flagellar filament. Rotation is bi-directional, with binding of a cytoplasmic chemotactic response regulator controlling reversal, though the structural and mechanistic bases for rotational switching are not well understood. Here we present cryoelectron microscopy structures of intact Salmonella flagellar basal bodies (3.2-5.5 Å), including the cytoplasmic C-ring complexes required for power transmission, in both counter-clockwise and clockwise rotational conformations. These reveal 180° movements of both the N- and C-terminal domains of the FliG protein, which, when combined with a high-resolution cryoelectron microscopy structure of the MotA5B2 stator, show that the stator shifts from the outside to the inside of the C-ring. This enables rotational switching and reveals how uni-directional ion flow across the inner membrane is used to accomplish bi-directional rotation of the flagellum.
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Affiliation(s)
- Steven Johnson
- Center for Structural Biology, CCR, NCI, Frederick, MD, USA.
| | - Justin C Deme
- Center for Structural Biology, CCR, NCI, Frederick, MD, USA
| | - Emily J Furlong
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Division of Biomedical Science and Biochemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Joseph J E Caesar
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK
| | | | - Kelly T Hughes
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Susan M Lea
- Center for Structural Biology, CCR, NCI, Frederick, MD, USA.
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3
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Singh PK, Sharma P, Afanzar O, Goldfarb MH, Maklashina E, Eisenbach M, Cecchini G, Iverson TM. CryoEM structures reveal how the bacterial flagellum rotates and switches direction. Nat Microbiol 2024; 9:1271-1281. [PMID: 38632342 PMCID: PMC11087270 DOI: 10.1038/s41564-024-01674-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 03/12/2024] [Indexed: 04/19/2024]
Abstract
Bacterial chemotaxis requires bidirectional flagellar rotation at different rates. Rotation is driven by a flagellar motor, which is a supercomplex containing multiple rings. Architectural uncertainty regarding the cytoplasmic C-ring, or 'switch', limits our understanding of how the motor transmits torque and direction to the flagellar rod. Here we report cryogenic electron microscopy structures for Salmonella enterica serovar typhimurium inner membrane MS-ring and C-ring in a counterclockwise pose (4.0 Å) and isolated C-ring in a clockwise pose alone (4.6 Å) and bound to a regulator (5.9 Å). Conformational differences between rotational poses include a 180° shift in FliF/FliG domains that rotates the outward-facing MotA/B binding site to inward facing. The regulator has specificity for the clockwise pose by bridging elements unique to this conformation. We used these structures to propose how the switch reverses rotation and transmits torque to the flagellum, which advances the understanding of bacterial chemotaxis and bidirectional motor rotation.
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Affiliation(s)
- Prashant K Singh
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Oshri Afanzar
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Margo H Goldfarb
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Elena Maklashina
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, USA
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, USA
| | - Michael Eisenbach
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, USA
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, USA
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA.
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA.
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4
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Ribardo DA, Johnson JJ, Hendrixson DR. Viscosity-dependent determinants of Campylobacter jejuni impacting the velocity of flagellar motility. mBio 2024; 15:e0254423. [PMID: 38085029 PMCID: PMC10790790 DOI: 10.1128/mbio.02544-23] [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: 09/28/2023] [Accepted: 11/06/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Bacteria can adapt flagellar motor output in response to the load that the extracellular milieu imparts on the flagellar filament to enable propulsion. Bacteria can adapt flagellar motor output in response to the load that the extracellular milieu imparts on the flagellar filament to enable propulsion through diverse environments. These changes may involve increasing power and torque in high-viscosity environments or reducing power and flagellar rotation upon contact with a surface. C. jejuni swimming velocity in low-viscosity environments is comparable to other bacterial flagellates and increases significantly as external viscosity increases. In this work, we provide evidence that the mechanics of the C. jejuni flagellar motor has evolved to naturally promote high swimming velocity in high-viscosity environments. We found that C. jejuni produces VidA and VidB as auxiliary proteins to specifically affect flagellar motor activity in low viscosity to reduce swimming velocity. Our findings provide some of the first insights into different mechanisms that exist in bacteria to alter the mechanics of a flagellar motor, depending on the viscosity of extracellular environments.
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Affiliation(s)
- Deborah A. Ribardo
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jeremiah J. Johnson
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - David R. Hendrixson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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5
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Ridone P, Winter DL, Baker MAB. Tuning the stator subunit of the flagellar motor with coiled-coil engineering. Protein Sci 2023; 32:e4811. [PMID: 37870481 PMCID: PMC10659934 DOI: 10.1002/pro.4811] [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: 06/14/2023] [Revised: 09/12/2023] [Accepted: 10/16/2023] [Indexed: 10/24/2023]
Abstract
Many bacteria swim driven by an extracellular filament rotated by the bacterial flagellar motor. This motor is powered by the stator complex, MotA5 MotB2 , an heptameric complex which forms an ion channel which couples energy from the ion motive force to torque generation. Recent structural work revealed that stator complex consists of a ring of five MotA subunits which rotate around a central dimer of MotB subunits. Transmembrane (TM) domains TM3 and TM4 from MotA combine with the single TM domain from MotB to form two separate ion channels within this complex. Much is known about the ion binding site and ion specificity; however, to date, no modeling has been undertaken to explore the MotB-MotB dimer stability and the role of MotB conformational dynamics during rotation. Here, we modeled the central MotB dimer using coiled-coil engineering and modeling principles and calculated free energies to identify stable states in the operating cycle of the stator. We found three stable coiled-coil states with dimer interface angles of 28°, 56°, and 64°. We tested the effect of strategic mutagenesis on the comparative energy of the states and correlated motility with a specific hierarchy of stability between the three states. In general, our results indicate agreement with existing models describing a 36° rotation step of the MotA pentameric ring during the power stroke and provide an energetic basis for the coordinated rotation of the central MotB dimer based on coiled-coil modeling.
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Affiliation(s)
- Pietro Ridone
- School of Biotechnology and Biomolecular ScienceUNSW SydneySydneyAustralia
| | - Daniel L. Winter
- School of Biotechnology and Biomolecular ScienceUNSW SydneySydneyAustralia
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6
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Botting JM, Tachiyama S, Gibson KH, Liu J, Starai VJ, Hoover TR. FlgV forms a flagellar motor ring that is required for optimal motility of Helicobacter pylori. PLoS One 2023; 18:e0287514. [PMID: 37976320 PMCID: PMC10655999 DOI: 10.1371/journal.pone.0287514] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/07/2023] [Indexed: 11/19/2023] Open
Abstract
Flagella-driven motility is essential for Helicobacter pylori to colonize the human stomach, where it causes a variety of diseases, including chronic gastritis, peptic ulcer disease, and gastric cancer. H. pylori has evolved a high-torque-generating flagellar motor that possesses several accessories not found in the archetypical Escherichia coli motor. FlgV was one of the first flagellar accessory proteins identified in Campylobacter jejuni, but its structure and function remain poorly understood. Here, we confirm that deletion of flgV in H. pylori B128 and a highly motile variant of H. pylori G27 (G27M) results in reduced motility in soft agar medium. Comparative analyses of in-situ flagellar motor structures of wild-type, ΔflgV, and a strain expressing FlgV-YFP showed that FlgV forms a ring-like structure closely associated with the junction of two highly conserved flagellar components: the MS and C rings. The results of our studies suggest that the FlgV ring has adapted specifically in Campylobacterota to support the assembly and efficient function of the high-torque-generating motors.
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Affiliation(s)
- Jack M. Botting
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Shoichi Tachiyama
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Katherine H. Gibson
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Jun Liu
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Vincent J. Starai
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Timothy R. Hoover
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
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7
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Genthe E, Miletic S, Tekkali I, Hennell James R, Marlovits TC, Heuser P. PickYOLO: Fast deep learning particle detector for annotation of cryo electron tomograms. J Struct Biol 2023; 215:107990. [PMID: 37364763 DOI: 10.1016/j.jsb.2023.107990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 05/31/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Particle localization (picking) in digital tomograms is a laborious and time-intensive step in cryogenic electron tomography (cryoET) analysis often requiring considerable user involvement, thus becoming a bottleneck for automated cryoET subtomogram averaging (STA) pipelines. In this paper, we introduce a deep learning framework called PickYOLO to tackle this problem. PickYOLO is a super-fast, universal particle detector based on the deep-learning real-time object recognition system YOLO (You Only Look Once), and tested on single particles, filamentous structures, and membrane-embedded particles. After training with the centre coordinates of a few hundred representative particles, the network automatically detects additional particles with high yield and reliability at a rate of 0.24-3.75 s per tomogram. PickYOLO can automatically detect number of particles comparable to those manually selected by experienced microscopists. This makes PickYOLO a valuable tool to substantially reduce the time and manual effort needed to analyse cryoET data for STA, greatly aiding in high-resolution cryoET structure determination.
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Affiliation(s)
- Erik Genthe
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Sean Miletic
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany; CSSB Centre for Structural Systems Biology, Notkestr. 85, 22607 Hamburg, Germany; University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany
| | - Indira Tekkali
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany; Helmholtz Imaging, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Rory Hennell James
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany; CSSB Centre for Structural Systems Biology, Notkestr. 85, 22607 Hamburg, Germany; University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany
| | - Thomas C Marlovits
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany; CSSB Centre for Structural Systems Biology, Notkestr. 85, 22607 Hamburg, Germany; University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.
| | - Philipp Heuser
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany; Helmholtz Imaging, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
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8
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Zhao S, Nan Y, Yao R, Wang L, Zeng X, Aadil RM, Shabbir MA. Antibacterial Activity and Transcriptomic Analysis of Hesperetin against Alicyclobacillus acidoterrestris Vegetative Cells. Foods 2023; 12:3276. [PMID: 37685209 PMCID: PMC10487046 DOI: 10.3390/foods12173276] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/16/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
The aim of this research was to investigate the antimicrobial characteristics and mechanism of hesperetin against Alicyclobacillus acidoterrestris vegetative cells. The results presented show that hesperetin had effective antimicrobial activity on Alicyclobacillus acidoterrestris vegetative cells, minimum inhibition concentration (MIC) of 0.0625 g/L, and minimum bacterial concentration (MBC) greater than 2 g/L. Moreover, treatment of hesperetin caused significant damage to cell integrity, preventing the growth of Alicyclobacillus acidoterrestris vegetative cells, enhancing the leakage of nucleic acid and proteins, and destroying the vegetative cell morphology. To further investigate the mechanism, transcriptomic analysis was carried out, and 3056 differentially expressed genes (DEGs) were detected. Gene ontology (GO) enrichment analysis revealed that hesperetin inhibits Alicyclobacillus acidoterrestris by affecting the intracellular nitrogen metabolism and amino acid metabolism. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis explained that hesperetin was also able to prevent the growth of Alicyclobacillus acidoterrestris by affecting the processes of nutrient transport, energy metabolism, and flagella motility. These results provide new insights into the antimicrobial effects and mechanism of hesperetin against Alicyclobacillus acidoterrestris, which provides a new method for inactive Alicyclobacillus acidoterrestris in the juice industry.
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Affiliation(s)
- Siqi Zhao
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; (S.Z.); (Y.N.); (R.Y.); (L.W.)
| | - Yanzi Nan
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; (S.Z.); (Y.N.); (R.Y.); (L.W.)
| | - Runyu Yao
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; (S.Z.); (Y.N.); (R.Y.); (L.W.)
| | - Langhong Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; (S.Z.); (Y.N.); (R.Y.); (L.W.)
- School of Food Science and Engineering, Guangdong Provincial Key Laboratory of Intelligent Food Manufacturing, Foshan University, Foshan 528225, China
| | - Xinan Zeng
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; (S.Z.); (Y.N.); (R.Y.); (L.W.)
- School of Food Science and Engineering, Guangdong Provincial Key Laboratory of Intelligent Food Manufacturing, Foshan University, Foshan 528225, China
| | - Rana Muhammad Aadil
- National Institute of Food Science and Technology, University of Agriculture, Faisalabad 38000, Pakistan; (R.M.A.); (M.A.S.)
| | - Muhammad Asim Shabbir
- National Institute of Food Science and Technology, University of Agriculture, Faisalabad 38000, Pakistan; (R.M.A.); (M.A.S.)
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9
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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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10
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Hu H, Popp PF, Santiveri M, Roa-Eguiara A, Yan Y, Martin FJO, Liu Z, Wadhwa N, Wang Y, Erhardt M, Taylor NMI. Ion selectivity and rotor coupling of the Vibrio flagellar sodium-driven stator unit. Nat Commun 2023; 14:4411. [PMID: 37500658 PMCID: PMC10374538 DOI: 10.1038/s41467-023-39899-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 07/04/2023] [Indexed: 07/29/2023] Open
Abstract
Bacteria swim using a flagellar motor that is powered by stator units. Vibrio spp. are highly motile bacteria responsible for various human diseases, the polar flagella of which are exclusively driven by sodium-dependent stator units (PomAB). However, how ion selectivity is attained, how ion transport triggers the directional rotation of the stator unit, and how the stator unit is incorporated into the flagellar rotor remained largely unclear. Here, we have determined by cryo-electron microscopy the structure of Vibrio PomAB. The electrostatic potential map uncovers sodium binding sites, which together with functional experiments and molecular dynamics simulations, reveal a mechanism for ion translocation and selectivity. Bulky hydrophobic residues from PomA prime PomA for clockwise rotation. We propose that a dynamic helical motif in PomA regulates the distance between PomA subunit cytoplasmic domains, stator unit activation, and torque transmission. Together, our study provides mechanistic insights for understanding ion selectivity and rotor incorporation of the stator unit of the bacterial flagellum.
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Affiliation(s)
- Haidai Hu
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Philipp F Popp
- Institute for Biology/Molecular Microbiology, Humboldt-Universität zu Berlin, Philippstr. 13, 10115, Berlin, Germany
| | - Mònica Santiveri
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Aritz Roa-Eguiara
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Yumeng Yan
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Freddie J O Martin
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Zheyi Liu
- College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, 314400, China
| | - Navish Wadhwa
- Department of Physics, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, 85287, USA
| | - Yong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, 314400, China
| | - Marc Erhardt
- Institute for Biology/Molecular Microbiology, Humboldt-Universität zu Berlin, Philippstr. 13, 10115, Berlin, Germany
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
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11
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Nandel V, Scadden J, Baker MAB. Ion-Powered Rotary Motors: Where Did They Come from and Where They Are Going? Int J Mol Sci 2023; 24:10601. [PMID: 37445779 PMCID: PMC10341847 DOI: 10.3390/ijms241310601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Molecular motors are found in many living organisms. One such molecular machine, the ion-powered rotary motor (IRM), requires the movement of ions across a membrane against a concentration gradient to drive rotational movement. The bacterial flagellar motor (BFM) is an example of an IRM which relies on ion movement through the stator proteins to generate the rotation of the flagella. There are many ions which can be used by the BFM stators to power motility and different ions can be used by a single bacterium expressing multiple stator variants. The use of ancestral sequence reconstruction (ASR) and functional analysis of reconstructed stators shows promise for understanding how these proteins evolved and when the divergence in ion use may have occurred. In this review, we discuss extant BFM stators and the ions that power them as well as recent examples of the use of ASR to study ion-channel selectivity and how this might be applied to further study of the BFM stator complex.
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Affiliation(s)
| | | | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW 2033, Australia; (V.N.); (J.S.)
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12
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Kinosita Y, Sowa Y. Flagellar polymorphism-dependent bacterial swimming motility in a structured environment. Biophys Physicobiol 2023; 20:e200024. [PMID: 37867560 PMCID: PMC10587448 DOI: 10.2142/biophysico.bppb-v20.0024] [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: 04/18/2023] [Accepted: 05/29/2023] [Indexed: 10/24/2023] Open
Abstract
Most motile bacteria use supramolecular motility machinery called bacterial flagellum, which converts the chemical energy gained from ion flux into mechanical rotation. Bacterial cells sense their external environment through a two-component regulatory system consisting of a histidine kinase and response regulator. Combining these systems allows the cells to move toward favorable environments and away from their repellents. A representative example of flagellar motility is run-and-tumble swimming in Escherichia coli, where the counter-clockwise (CCW) rotation of a flagellar bundle propels the cell forward, and the clockwise (CW) rotation undergoes cell re-orientation (tumbling) upon switching the direction of flagellar motor rotation from CCW to CW. In this mini review, we focus on several types of chemotactic behaviors that respond to changes in flagellar shape and direction of rotation. Moreover, our single-cell analysis demonstrated back-and-forth swimming motility of an original E. coli strain. We propose that polymorphic flagellar changes are required to enhance bacterial movement in a structured environment as a colony spread on an agar plate.
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Affiliation(s)
| | - Yoshiyuki Sowa
- Department of Frontier Bioscience, Hosei University, Tokyo 184-8584, Japan
- Research Center for Micro-Nano Technology, Hosei University, Tokyo 184-8584, Japan
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13
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Pulianmackal LT, Limcaoco JMI, Ravi K, Yang S, Zhang J, Tran MK, Ghalmi M, O'Meara MJ, Vecchiarelli AG. Multiple ParA/MinD ATPases coordinate the positioning of disparate cargos in a bacterial cell. Nat Commun 2023; 14:3255. [PMID: 37277398 DOI: 10.1038/s41467-023-39019-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
In eukaryotes, linear motor proteins govern intracellular transport and organization. In bacteria, where linear motors involved in spatial regulation are absent, the ParA/MinD family of ATPases organize an array of genetic- and protein-based cellular cargos. The positioning of these cargos has been independently investigated to varying degrees in several bacterial species. However, it remains unclear how multiple ParA/MinD ATPases can coordinate the positioning of diverse cargos in the same cell. Here, we find that over a third of sequenced bacterial genomes encode multiple ParA/MinD ATPases. We identify an organism (Halothiobacillus neapolitanus) with seven ParA/MinD ATPases, demonstrate that five of these are each dedicated to the spatial regulation of a single cellular cargo, and define potential specificity determinants for each system. Furthermore, we show how these positioning reactions can influence each other, stressing the importance of understanding how organelle trafficking, chromosome segregation, and cell division are coordinated in bacterial cells. Together, our data show how multiple ParA/MinD ATPases coexist and function to position a diverse set of fundamental cargos in the same bacterial cell.
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Affiliation(s)
- Lisa T Pulianmackal
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jose Miguel I Limcaoco
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Keerthikka Ravi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sinyu Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jeffrey Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Mimi K Tran
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Maria Ghalmi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Matthew J O'Meara
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
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14
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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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15
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Jiang J, Wang X, Akomolafe OI, Tang W, Asilehan Z, Ranabhat K, Zhang R, Peng C. Collective transport and reconfigurable assembly of nematic colloids by light-driven cooperative molecular reorientations. Proc Natl Acad Sci U S A 2023; 120:e2221718120. [PMID: 37040402 PMCID: PMC10119998 DOI: 10.1073/pnas.2221718120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/09/2023] [Indexed: 04/12/2023] Open
Abstract
Nanomotors in nature have inspired scientists to design synthetic molecular motors to drive the motion of microscale objects by cooperative action. Light-driven molecular motors have been synthesized, but using their cooperative reorganization to control the collective transport of colloids and to realize the reconfiguration of colloidal assembly remains a challenge. In this work, topological vortices are imprinted in the monolayers of azobenzene molecules which further interface with nematic liquid crystals (LCs). The light-driven cooperative reorientations of the azobenzene molecules induce the collective motion of LC molecules and thus the spatiotemporal evolutions of the nematic disclination networks which are defined by the controlled patterns of vortices. Continuum simulations provide physical insight into the morphology change of the disclination networks. When microcolloids are dispersed in the LC medium, the colloidal assembly is not only transported and reconfigured by the collective change of the disclination lines but also controlled by the elastic energy landscape defined by the predesigned orientational patterns. The collective transport and reconfiguration of colloidal assemblies can also be programmed by manipulating the irradiated polarization. This work opens opportunities to design programmable colloidal machines and smart composite materials.
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Affiliation(s)
- Jinghua Jiang
- Department of Physics, University of Science and Technology of China, Hefei, Anhui230026, China
| | - Xinyu Wang
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong99999, China
| | | | - Wentao Tang
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong99999, China
| | - Zhawure Asilehan
- Department of Physics, University of Science and Technology of China, Hefei, Anhui230026, China
| | - Kamal Ranabhat
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN38152
| | - Rui Zhang
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong99999, China
| | - Chenhui Peng
- Department of Physics, University of Science and Technology of China, Hefei, Anhui230026, China
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16
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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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17
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Diving into the complexity of the spirochetal endoflagellum. Trends Microbiol 2023; 31:294-307. [PMID: 36244923 DOI: 10.1016/j.tim.2022.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/27/2022]
Abstract
Spirochaetes, a phylum that includes medically important pathogens such as the causative agents of Lyme disease, syphilis, and leptospirosis, are in many ways highly unique bacteria. Their cell morphology, subcellular organization, and metabolism reveal atypical features. Spirochetal motility is also singular, dependent on the presence of periplasmic flagella or endoflagella, inserted subterminally at cell poles and not penetrating the outer membrane and elongating outside the cell as in enterobacteria. In this review we present a comprehensive comparative genomics analysis of endoflagellar systems in spirochetes, highlighting recent findings on the flagellar basal body and filament. Continued progress in understanding the function and architecture of spirochetal flagella is uncovering paradigm-shifting mechanisms of bacterial motility.
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18
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Nishikino T, Miyanoiri Y. Site-Specific Isotope Labeling of FliG for Studying Structural Dynamics Using Nuclear Magnetic Resonance Spectroscopy. Methods Mol Biol 2023; 2646:57-70. [PMID: 36842106 DOI: 10.1007/978-1-0716-3060-0_6] [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: 02/27/2023]
Abstract
To understand flagella-driven motility of bacteria, it is important to understand the structure and dynamics of the flagellar motor machinery. We have conducted structural dynamics analyses using solution nuclear magnetic resonance (NMR) to elucidate the detailed functions of flagellar motor proteins. Here, we introduce the analysis of the FliG protein, which is a flagellar motor protein, focusing on the preparation method of the original stable isotope-labeled protein.
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Affiliation(s)
- Tatsuro Nishikino
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
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19
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Kurniyati K, Chang Y, Guo W, Liu J, Malkowski MG, Li C. Anti-σ 28 Factor FlgM Regulates Flagellin Gene Expression and Flagellar Polarity of Treponema denticola. J Bacteriol 2023; 205:e0046322. [PMID: 36715541 PMCID: PMC9945498 DOI: 10.1128/jb.00463-22] [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: 12/02/2022] [Accepted: 01/07/2023] [Indexed: 01/31/2023] Open
Abstract
FlgM, an antagonist of FliA (also known as σ28), inhibits transcription of bacterial class 3 flagellar genes. It does so primarily through binding to free σ28 to prevent it from forming a complex with core RNA polymerase. We recently identified an FliA homolog (FliATd) in the oral spirochete Treponema denticola; however, its antagonist FlgM remained uncharacterized. Herein, we provide several lines of evidence that TDE0201 functions as an antagonist of FliATd. TDE0201 is structurally similar to FlgM proteins, although its sequence is not conserved. Heterologous expression of TDE0201 in Escherichia coli inhibits its flagellin gene expression and motility. Biochemical and mutational analyses demonstrate that TDE0201 binds to FliATd and prevents it from binding to the σ28-dependent promoter. Deletions of flgM genes typically enhance bacterial class 3 flagellar gene expression; however, deletion of TDE0201 has an opposite effect (e.g., the mutant has a reduced level of flagellins). Follow-up studies revealed that deletion of TDE0201 leads to FliATd turnover, which in turn impairs the expression of flagellin genes. Swimming plate, cell tracking, and cryo-electron tomography analyses further disclosed that deletion of TDE0201 impairs spirochete motility and alters flagellar number and polarity: i.e., instead of having bipolar flagella, the mutant has flagella only at one end of cells. Collectively, these results indicate that TDE0201 is a FlgM homolog but acts differently from its counterparts in other bacteria. IMPORTANCE Spirochetes are a group of bacteria that cause several human diseases. A unique aspect of spirochetes is that they have bipolar periplasmic flagella (PFs), which bestow on the spirochetes a unique spiral shape and distinct swimming behaviors. While the structure and function of PFs have been extensively studied in spirochetes, the molecular mechanism that regulates the PFs' morphogenesis and assembly is poorly understood. In this report, FlgM, an anti-σ28 factor, is identified and functionally characterized in the oral spirochete Treponema denticola. Our results show that FlgM regulates the number and polarity of PFs via a unique mechanism. Identification of FliA and FlgM in T. denticola sets a benchmark to investigate their roles in other spirochetes.
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Affiliation(s)
- Kurni Kurniyati
- Department of Oral Craniofacial Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, USA
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Yunjie Chang
- Department of Microbial Pathogenesis, Yale University, School of Medicine, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, School of Medicine, New Haven, Connecticut, USA
| | - Wangbiao Guo
- Department of Microbial Pathogenesis, Yale University, School of Medicine, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, School of Medicine, New Haven, Connecticut, USA
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale University, School of Medicine, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, School of Medicine, New Haven, Connecticut, USA
| | - Michael G. Malkowski
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University of Buffalo, Buffalo, New York, USA
| | - Chunhao Li
- Department of Oral Craniofacial Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, USA
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, USA
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20
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Lloyd CJ, Klose KE. The Vibrio Polar Flagellum: Structure and Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:77-97. [PMID: 36792872 DOI: 10.1007/978-3-031-22997-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Here we discuss the structure and regulation of the Vibrio flagellum and its role in the virulence of pathogenic species. We will cover some of the novel insights into the structure of this nanomachine that have recently been enabled by cryoelectron tomography. We will also highlight the recent genetic studies that have increased our understanding in flagellar synthesis specifically at the bacterial cell pole, temporal regulation of flagellar genes, and how the flagellum enables directional motility through Run-Reverse-Flick cycles.
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Affiliation(s)
- Cameron J Lloyd
- South Texas Center for Emerging Infectious Diseases, University of Texas San Antonio, San Antonio, TX, USA.,Department of Molecular Microbiology and Immunology, University of Texas San Antonio, San Antonio, TX, USA
| | - Karl E Klose
- South Texas Center for Emerging Infectious Diseases, University of Texas San Antonio, San Antonio, TX, USA. .,Department of Molecular Microbiology and Immunology, University of Texas San Antonio, San Antonio, TX, USA.
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21
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Xiong D, Yang Z, He X, He W, Shen D, Wang L, Lin L, Murero A, Minamino T, Shao X, Qian G. Loss of Flagella-Related Genes Enables a Nonflagellated, Fungal-Predating Bacterium To Strengthen the Synthesis of an Antifungal Weapon. Microbiol Spectr 2023; 11:e0414922. [PMID: 36629418 PMCID: PMC9927559 DOI: 10.1128/spectrum.04149-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/17/2022] [Indexed: 01/12/2023] Open
Abstract
Loss of flagellar genes causes a nonmotile phenotype. The genus Lysobacter consists of numerous environmentally ubiquitous, nonflagellated bacteria, including Lysobacter enzymogenes, an antifungal bacterium that is beneficial to plants. L. enzymogenes still has many flagellar genes on its genome, although this bacterium does not engage in flagella-driven motility. Here, we report that loss of certain flagellar genes allows L. enzymogenes to strengthen its evolutionarily gained capacity in fungal killing. To clarify why this bacterium loses flagellar genes during the evolutionary process, we cloned several representative flagellar genes from Xanthomonas oryzae, a flagellated, phylogenetically related species of Lysobacter, and introduced them individually into L. enzymogenes to mimic genomic reacquisition of lost flagellar genes. Heterogeneous expression of the three X. oryzae flagellar structural genes (Xo-motA, Xo-motB, Xo-fliE) and one flagellar regulatory gene (Xo-fleQ) remarkably weakened the bacterial capacity to kill fungal pathogens by impairing the synthesis of an antifungal weapon, known as the heat-stable antifungal factor (HSAF). We further investigated the underlying mechanism by selecting Xo-FleQ as the representative because it is a master transcription factor responsible for flagellar gene expression. Xo-FleQ inhibited the transcription of operon genes responsible for HSAF synthesis via direct binding of Xo-FleQ to the promoter region, thereby decreasing HSAF biosynthesis by L. enzymogenes. These observations suggest a possible genome and function coevolution event, in which an antifungal bacterium deletes certain flagellar genes in order to enhance its ability to kill fungi. IMPORTANCE It is generally recognized that flagellar genes are commonly responsible for the flagella-driven bacterial motility. Thus, finding nonflagellated bacteria partially or fully lost flagellar genes is not a surprise. However, the present study provides new insights into this common idea. We found that loss of either certain flagellar structural or regulatory genes (such as motA, motB, fliE, and fleQ) allows a nonflagellated, antifungal bacterium (L. enzymogenes) to stimulate its fungal-killing capacity, outlining a genome-function coevolution event, where an antifungal bacterium "smartly" designed its genome to "delete" crucial flagellar genes to coordinate flagellar loss and fungal predation. This unusual finding might trigger bacteriologists to reconsider previously ignored functions of the lost flagellar genes in any nonflagellated, pathogenic, or beneficial bacteria.
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Affiliation(s)
- Dan Xiong
- College of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, P. R. China
| | - Zixiang Yang
- College of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, P. R. China
| | - Xueting He
- College of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, P. R. China
| | - Weimei He
- College of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, P. R. China
| | - Danyu Shen
- College of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, P. R. China
| | - Lu Wang
- Medical College, China Three Gorges University, Yichang, China
| | - Long Lin
- College of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, P. R. China
| | - Aprodisia Murero
- College of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, P. R. China
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Xiaolong Shao
- College of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, P. R. China
| | - Guoliang Qian
- College of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, P. R. China
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22
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Hadjidemetriou K, Kaur S, Cassidy CK, Zhang P. Mechanisms of E. coli chemotaxis signaling pathways visualized using cryoET and computational approaches. Biochem Soc Trans 2022; 50:1595-1605. [PMID: 36421737 PMCID: PMC9788364 DOI: 10.1042/bst20220191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 11/25/2022]
Abstract
Chemotaxis signaling pathways enable bacteria to sense and respond to their chemical environment and, in some species, are critical for lifestyle processes such as biofilm formation and pathogenesis. The signal transduction underlying chemotaxis behavior is mediated by large, highly ordered protein complexes known as chemosensory arrays. For nearly two decades, cryo-electron tomography (cryoET) has been used to image chemosensory arrays, providing an increasingly detailed understanding of their structure and function. In this mini-review, we provide an overview of the use of cryoET to study chemosensory arrays, including imaging strategies, key results, and outstanding questions. We further discuss the application of molecular modeling and simulation techniques to complement structure determination efforts and provide insight into signaling mechanisms. We close the review with a brief outlook, highlighting promising future directions for the field.
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Affiliation(s)
| | - Satinder Kaur
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
| | - C. Keith Cassidy
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
| | - Peijun Zhang
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, U.K
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7BN, U.K
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23
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Wang X, Blumenfeld R, Feng XQ, Weitz DA. 'Phase transitions' in bacteria - From structural transitions in free living bacteria to phenotypic transitions in bacteria within biofilms. Phys Life Rev 2022; 43:98-138. [PMID: 36252408 DOI: 10.1016/j.plrev.2022.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 12/05/2022]
Abstract
Phase transitions are common in inanimate systems and have been studied extensively in natural sciences. Less explored are the rich transitions that take place at the micro- and nano-scales in biological systems. In conventional phase transitions, large-scale properties of the media change discontinuously in response to continuous changes in external conditions. Such changes play a significant role in the dynamic behaviours of organisms. In this review, we focus on some transitions in both free-living and biofilms of bacteria. Particular attention is paid to the transitions in the flagellar motors and filaments of free-living bacteria, in cellular gene expression during the biofilm growth, in the biofilm morphology transitions during biofilm expansion, and in the cell motion pattern transitions during the biofilm formation. We analyse the dynamic characteristics and biophysical mechanisms of these phase transition phenomena and point out the parallels between these transitions and conventional phase transitions. We also discuss the applications of some theoretical and numerical methods, established for conventional phase transitions in inanimate systems, in bacterial biofilms.
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Affiliation(s)
- Xiaoling Wang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China; John A. Paulson School of Engineering and Applied Sciences, Harvard University, 9 Oxford St, Cambridge, MA, 02138, USA.
| | - Raphael Blumenfeld
- Gonville & Caius College, University of Cambridge, Trinity St., Cambridge CB2 1TA, UK
| | - Xi-Qiao Feng
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China
| | - David A Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, 9 Oxford St, Cambridge, MA, 02138, USA; Department of Physics, Harvard University, 9 Oxford St, Cambridge, MA, 02138, USA
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24
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Liu Y, Wang L. Antibiofilm effect and mechanism of protocatechuic aldehyde against Vibrio parahaemolyticus. Front Microbiol 2022; 13:1060506. [PMID: 36439819 PMCID: PMC9684326 DOI: 10.3389/fmicb.2022.1060506] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/26/2022] [Indexed: 11/12/2022] Open
Abstract
This study investigated the effect of protocatechuic aldehyde (PCA) on Vibrio parahaemolyticus biofilm formation and its effects on gene expression. Crystal violet assay, metabolic activity assay, and fluorescence experiments were used to evaluate the antibiofilm activities of PCA and to reveal its possible antibiofilm mechanisms using transcriptomic analysis. The results indicated that the minimum antibacterial concentration of PCA against V. parahaemolyticus was 300 μg/mL. PCA (9.375 μg/mL) inhibited biofilm generation and adhesion of the mature biofilm. PCA (75 μg/mL) significantly reduced the metabolic viability of V. parahaemolyticus, reduced polysaccharide production, and inhibited cell surface flagella-mediated swimming and aggregation phenotypes. Meanwhile, transcriptome analysis showed that the key genes of V. parahaemolyticus expressed under PCA (75 μg/mL) inhibition were mainly related to biofilm formation (pfkA, galE, narL, and oppA), polysaccharide production and adhesion (IF, fbpA, and yxeM), and motility (cheY, flrC, and fliA). By regulating these key genes, PCA reduced biofilm formation, suppressed polysaccharide production and transport, and prevented the adhesion of V. parahaemolyticus, thereby reducing the virulence of V. parahaemolyticus. This study demonstrated that protocatechuic aldehyde can be used to control V. parahaemolyticus biofilm to ensure food safety.
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25
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FliL Differentially Interacts with Two Stator Systems To Regulate Flagellar Motor Output in Pseudomonas aeruginosa. Appl Environ Microbiol 2022; 88:e0153922. [PMID: 36286538 PMCID: PMC9680632 DOI: 10.1128/aem.01539-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
FliL emerged as a modulator of flagellar motor function in several bacterial species, but its function in
Pseudomonas aeruginosa
was unknown. Here, by performing single-motor studies using a bead assay, we elucidated its effects on the flagellar motor in
P. aeruginosa
.
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26
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Nishikino T, Takekawa N, Tran DP, Kishikawa JI, Hirose M, Onoe S, Kojima S, Homma M, Kitao A, Kato T, Imada K. Structure of MotA, a flagellar stator protein, from hyperthermophile. Biochem Biophys Res Commun 2022; 631:78-85. [PMID: 36179499 DOI: 10.1016/j.bbrc.2022.09.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 09/13/2022] [Accepted: 09/18/2022] [Indexed: 11/02/2022]
Abstract
Many motile bacteria swim and swarm toward favorable environments using the flagellum, which is rotated by a motor embedded in the inner membrane. The motor is composed of the rotor and the stator, and the motor torque is generated by the change of the interaction between the rotor and the stator induced by the ion flow through the stator. A stator unit consists of two types of membrane proteins termed A and B. Recent cryo-EM studies on the stators from mesophiles revealed that the stator consists of five A and two B subunits, whereas the low-resolution EM analysis showed that purified hyperthermophilic MotA forms a tetramer. To clarify the assembly formation and factors enhancing thermostability of the hyperthermophilic stator, we determined the cryo-EM structure of MotA from Aquifex aeolicus (Aa-MotA), a hyperthermophilic bacterium, at 3.42 Å resolution. Aa-MotA forms a pentamer with pseudo C5 symmetry. A simulated model of the Aa-MotA5MotB2 stator complex resembles the structures of mesophilic stator complexes, suggesting that Aa-MotA can assemble into a pentamer equivalent to the stator complex without MotB. The distribution of hydrophobic residues of MotA pentamers suggests that the extremely hydrophobic nature in the subunit boundary and the transmembrane region is a key factor to stabilize hyperthermophilic Aa-MotA.
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Affiliation(s)
- Tatsuro Nishikino
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Norihiro Takekawa
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan
| | - Duy Phuoc Tran
- School of Life Sciences and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Jun-Ichi Kishikawa
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Mika Hirose
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Sakura Onoe
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Akio Kitao
- School of Life Sciences and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Takayuki Kato
- Institute for Protein Research, Osaka University, 3-2 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.
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27
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Popp PF, Erhardt M. Supercoiled filaments propel them all. Cell 2022; 185:3461-3463. [PMID: 36113424 DOI: 10.1016/j.cell.2022.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 01/26/2023]
Abstract
In this issue of Cell, Kreutzberger and colleagues report the near-atomic-resolution, cryo-EM structures of the supercoiled filaments of both bacterial and archaeal motility machines. Despite the lack of homology, the supercoiled filament structures reveal shared fundamental features of prokaryotic locomotion and represent a prime example of convergent evolution.
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Affiliation(s)
- Philipp F Popp
- Institute for Biology - Bacterial Physiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marc Erhardt
- Institute for Biology - Bacterial Physiology, Humboldt-Universität zu Berlin, Berlin, Germany; Max Planck Unit for the Science of Pathogens, Berlin, Germany.
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28
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Zhu Y, Koo CW, Cassidy CK, Spink MC, Ni T, Zanetti-Domingues LC, Bateman B, Martin-Fernandez ML, Shen J, Sheng Y, Song Y, Yang Z, Rosenzweig AC, Zhang P. Structure and activity of particulate methane monooxygenase arrays in methanotrophs. Nat Commun 2022; 13:5221. [PMID: 36064719 PMCID: PMC9445010 DOI: 10.1038/s41467-022-32752-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/16/2022] [Indexed: 01/29/2023] Open
Abstract
Methane-oxidizing bacteria play a central role in greenhouse gas mitigation and have potential applications in biomanufacturing. Their primary metabolic enzyme, particulate methane monooxygenase (pMMO), is housed in copper-induced intracytoplasmic membranes (ICMs), of which the function and biogenesis are not known. We show by serial cryo-focused ion beam (cryoFIB) milling/scanning electron microscope (SEM) volume imaging and lamellae-based cellular cryo-electron tomography (cryoET) that these ICMs are derived from the inner cell membrane. The pMMO trimer, resolved by cryoET and subtomogram averaging to 4.8 Å in the ICM, forms higher-order hexagonal arrays in intact cells. Array formation correlates with increased enzymatic activity, highlighting the importance of studying the enzyme in its native environment. These findings also demonstrate the power of cryoET to structurally characterize native membrane enzymes in the cellular context.
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Affiliation(s)
- Yanan Zhu
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Christopher W. Koo
- grid.16753.360000 0001 2299 3507Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL USA
| | - C. Keith Cassidy
- grid.4991.50000 0004 1936 8948Department of Biochemistry, University of Oxford, Oxford, UK
| | - Matthew C. Spink
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Tao Ni
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Laura C. Zanetti-Domingues
- grid.76978.370000 0001 2296 6998Central Laser Facility, Science and Technology Facility Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire UK
| | - Benji Bateman
- grid.76978.370000 0001 2296 6998Central Laser Facility, Science and Technology Facility Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire UK
| | - Marisa L. Martin-Fernandez
- grid.76978.370000 0001 2296 6998Central Laser Facility, Science and Technology Facility Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire UK
| | - Juan Shen
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yuewen Sheng
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Yun Song
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Zhengyi Yang
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK ,grid.4709.a0000 0004 0495 846XPresent Address: Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Amy C. Rosenzweig
- grid.16753.360000 0001 2299 3507Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL USA
| | - Peijun Zhang
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK ,grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK ,grid.4991.50000 0004 1936 8948Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
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29
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Gupta R, Yuan J, Lele PP. Bacterial Proprioception: Can a Bacterium Sense Its Movement? Front Microbiol 2022; 13:928408. [PMID: 35875555 PMCID: PMC9302961 DOI: 10.3389/fmicb.2022.928408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
The evolution of the bacterial flagellum gave rise to motility and repurposing of a signaling network, now termed the chemotaxis network, enabled biasing of cell movements. This made it possible for the bacterium to seek out favorable chemical environments. To enable chemotaxis, the chemotaxis network sensitively detects extracellular chemical stimuli and appropriately modulates flagellar functions. Additionally, the flagellar motor itself is capable of detecting mechanical stimuli and adapts its structure and function in response, likely triggering a transition from planktonic to surface-associated lifestyles. Recent work has shown a link between the flagellar motor's response to mechanical stimuli and the chemotactic output. Here, we elaborate on this link and discuss how it likely helps the cell sense and adapt to changes in its swimming speeds in different environments. We discuss the mechanism whereby the motor precisely tunes its chemotaxis output under different mechanical loads, analogous to proprioception in higher order organisms. We speculate on the roles bacterial proprioception might play in a variety of phenomena including the transition to surface-associated lifestyles such as swarming and biofilms.
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Affiliation(s)
- Rachit Gupta
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Junhua Yuan
- Department of Physics, University of Science and Technology of China, Hefei, China
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
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30
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Revealing bacterial cell biology using cryo-electron tomography. Curr Opin Struct Biol 2022; 75:102419. [PMID: 35820259 DOI: 10.1016/j.sbi.2022.102419] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022]
Abstract
Visualizing macromolecules inside bacteria at a high spatial resolution has remained a challenge owing to their small size and limited resolution of optical microscopy techniques. Recent advances in cryo-electron tomography (cryo-ET) imaging methods have revealed the spatial and temporal assemblies of many macromolecules involved in different cellular processes in bacteria at a resolution of a few nanometers in their native milieu. Specifically, the application of cryo-focused ion beam (cryo-FIB) milling to thin bacterial specimens makes them amenable for high-resolution cryo-ET data collection. In this review, we highlight recent research in three emerging areas of bacterial cell biology that have benefited from the cryo-FIB-ET technology - cytoskeletal filament assembly, intracellular organelles, and multicellularity.
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31
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Sobe RC, Gilbert C, Vo L, Alexandre G, Scharf BE. FliL and its paralog MotF have distinct roles in the stator activity of the Sinorhizobium meliloti flagellar motor. Mol Microbiol 2022; 118:223-243. [PMID: 35808893 PMCID: PMC9541039 DOI: 10.1111/mmi.14964] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 11/30/2022]
Abstract
The bacterial flagellum is a complex macromolecular machine that drives bacteria through diverse fluid environments. Although many components of the flagellar motor are conserved across species, the roles of FliL are numerous and species‐specific. Here, we have characterized an additional player required for flagellar motor function in Sinorhizobium meliloti, MotF, which we have identified as a FliL paralog. We performed a comparative analysis of MotF and FliL, identified interaction partners through bacterial two‐hybrid and pull‐down assays, and investigated their roles in motility and motor rotation. Both proteins form homooligomers, and interact with each other, and with the stator proteins MotA and MotB. The ∆motF mutant exhibits normal flagellation but its swimming behavior and flagellar motor activity are severely impaired and erratic. In contrast, the ∆fliL mutant is mostly aflagellate and nonmotile. Amino acid substitutions in cytoplasmic regions of MotA or disruption of the proton channel plug of MotB partially restored motor activity to the ∆motF but not the ∆fliL mutant. Altogether, our findings indicate that both, MotF and FliL, are essential for flagellar motor torque generation in S. meliloti. FliL may serve as a scaffold for stator integration into the motor, and MotF is required for proton channel modulation.
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Affiliation(s)
- Richard C Sobe
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, VA, USA
| | - Crystal Gilbert
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, VA, USA
| | - Lam Vo
- Department of Biochemistry and Cell and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN, USA.,Present address: Molecular Cellular and Developmental Biology and Physics, Yale Science Building, Yale University, New Haven, CT, USA
| | - Gladys Alexandre
- Department of Biochemistry and Cell and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN, USA
| | - Birgit E Scharf
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, VA, USA
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32
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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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33
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Direct Measurement of the Stall Torque of the Flagellar Motor in Escherichia coli with Magnetic Tweezers. mBio 2022; 13:e0078222. [PMID: 35699374 PMCID: PMC9426426 DOI: 10.1128/mbio.00782-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The flagellar motor drives the rotation of flagellar filaments, propelling the swimming of flagellated bacteria. The maximum torque the motor generates, the stall torque, is a key characteristic of the motor function. Direct measurements of the stall torque carried out 3 decades ago suffered from large experimental uncertainties, and subsequently there were only indirect measurements. Here, we applied magnetic tweezers to directly measure the stall torque in E. coli. We precisely calibrated the torsional stiffness of the magnetic tweezers and performed motor resurrection experiments at stall, accomplishing a precise determination of the stall torque per torque-generating unit (stator unit). From our measurements, each stator passes 2 protons per step, indicating a tight coupling between motor rotation and proton flux. IMPORTANCE The maximum torque the bacterial flagellar motor generates, the stall torque, is a critical parameter that describes the motor energetics. As the motor operates in equilibrium near stall, from the stall torque one can determine how many protons each torque-generating unit (stator) of the motor passes per revolution and then test whether motor rotation and proton flux are tightly or loosely coupled, which has been controversial in recent years. Direct measurements performed 3 decades ago suffered from large uncertainties, and subsequently, only indirect measurements were attempted, obtaining a range of values inconsistent with the previous direct measurements. Here, we developed a method that used magnetic tweezers to perform motor resurrection experiments at stall, resulting in a direct precise measurement of the stall torque per stator. Our study resolved the previous inconsistencies and provided direct experimental support for the tight coupling mechanism between motor rotation and proton flux.
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34
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Mondino S, San Martin F, Buschiazzo A. 3D cryo-electron microscopic imaging of bacterial flagella: novel structural and mechanistic insights into cell motility. J Biol Chem 2022; 298:102105. [PMID: 35671822 PMCID: PMC9254593 DOI: 10.1016/j.jbc.2022.102105] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 10/26/2022] Open
Abstract
Bacterial flagella are nanomachines that enable cells to move at high speeds. Comprising ≳25 different types of proteins, the flagellum is a large supramolecular assembly organized into three widely conserved substructures: a basal body including the rotary motor, a connecting hook, and a long filament. The whole flagellum from Escherichia coli weighs ∼20 MDa, without considering its filament portion, which is by itself a ∼1.6 GDa structure arranged as a multimer of ∼30,000 flagellin protomers. Breakthroughs regarding flagellar structure and function have been achieved in the last few years, mainly due to the revolutionary improvements in 3D cryo-electron microscopy methods. This review discusses novel structures and mechanistic insights derived from such high-resolution studies, advancing our understanding of each one of the three major flagellar segments. The rotation mechanism of the motor has been unveiled with unprecedented detail, showing a two-cogwheel machine propelled by a Brownian ratchet device. Additionally, by imaging the flagellin-like protomers that make up the hook in its native bent configuration, their unexpected conformational plasticity challenges the paradigm of a two-state conformational rearrangement mechanism for flagellin-fold proteins. Finally, imaging of the filaments of periplasmic flagella, which endow Spirochete bacteria with their singular motility style, uncovered a strikingly asymmetric protein sheath that coats the flagellin core, challenging the view of filaments as simple homopolymeric structures that work as freely whirling whips. Further research will shed more light on the functional details of this amazing nanomachine, but our current understanding has definitely come a long way.
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Affiliation(s)
- Sonia Mondino
- Laboratory of Molecular & Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay; Integrative Microbiology of Zoonotic Agents IMiZA Unit, Joint International Unit, Institut Pasteur/Institut Pasteur de Montevideo, France/Uruguay
| | - Fabiana San Martin
- Laboratory of Molecular & Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay; Integrative Microbiology of Zoonotic Agents IMiZA Unit, Joint International Unit, Institut Pasteur/Institut Pasteur de Montevideo, France/Uruguay
| | - Alejandro Buschiazzo
- Laboratory of Molecular & Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay; Integrative Microbiology of Zoonotic Agents IMiZA Unit, Joint International Unit, Institut Pasteur/Institut Pasteur de Montevideo, France/Uruguay; Microbiology Department, Institut Pasteur, Paris, France.
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35
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Structural insights into the mechanism of archaellar rotational switching. Nat Commun 2022; 13:2857. [PMID: 35606361 PMCID: PMC9126983 DOI: 10.1038/s41467-022-30358-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 04/15/2022] [Indexed: 11/24/2022] Open
Abstract
Signal transduction via phosphorylated CheY towards the flagellum and the archaellum involves a conserved mechanism of CheY phosphorylation and subsequent conformational changes within CheY. This mechanism is conserved among bacteria and archaea, despite substantial differences in the composition and architecture of archaellum and flagellum, respectively. Phosphorylated CheY has higher affinity towards the bacterial C-ring and its binding leads to conformational changes in the flagellar motor and subsequent rotational switching of the flagellum. In archaea, the adaptor protein CheF resides at the cytoplasmic face of the archaeal C-ring formed by the proteins ArlCDE and interacts with phosphorylated CheY. While the mechanism of CheY binding to the C-ring is well-studied in bacteria, the role of CheF in archaea remains enigmatic and mechanistic insights are absent. Here, we have determined the atomic structures of CheF alone and in complex with activated CheY by X-ray crystallography. CheF forms an elongated dimer with a twisted architecture. We show that CheY binds to the C-terminal tail domain of CheF leading to slight conformational changes within CheF. Our structural, biochemical and genetic analyses reveal the mechanistic basis for CheY binding to CheF and allow us to propose a model for rotational switching of the archaellum. Signal transduction via phosphorylated CheY is conserved in bacteria and archaea. In this study, the authors employ structural biochemistry combined with cell biology to delineate the mechanism of CheY recognition by the adaptor protein CheF.
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36
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Homma M, Kojima S. The Periplasmic Domain of the Ion-Conducting Stator of Bacterial Flagella Regulates Force Generation. Front Microbiol 2022; 13:869187. [PMID: 35572622 PMCID: PMC9093738 DOI: 10.3389/fmicb.2022.869187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/24/2022] [Indexed: 11/23/2022] Open
Abstract
The bacterial flagellar stator is a unique ion-conducting membrane protein complex composed of two kinds of proteins, the A subunit and the B subunit. The stator couples the ion-motive force across the membrane into rotational force. The stator becomes active only when it is incorporated into the flagellar motor. The periplasmic region of the B subunit positions the stator by using the peptidoglycan-binding (PGB) motif in its periplasmic C-terminal domain to attach to the cell wall. Functional studies based on the crystal structures of the C-terminal domain of the B subunit (MotBC or PomBC) reveal that a dramatic conformational change in a characteristic α-helix allows the stator to conduct ions efficiently and bind to the PG layer. The plug and the following linker region between the transmembrane (TM) and PG-binding domains of the B subunit function in regulating the ion conductance. In Vibrio spp., the transmembrane protein FliL and the periplasmic MotX and MotY proteins also contribute to the motor function. In this review, we describe the functional and structural changes which the stator units undergo to regulate the activity of the stator to drive flagellar rotation.
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Affiliation(s)
- Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
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37
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Kaplan M, Oikonomou CM, Wood CR, Chreifi G, Subramanian P, Ortega DR, Chang Y, Beeby M, Shaffer CL, Jensen GJ. Novel transient cytoplasmic rings stabilize assembling bacterial flagellar motors. EMBO J 2022; 41:e109523. [PMID: 35301732 PMCID: PMC9108667 DOI: 10.15252/embj.2021109523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 01/31/2022] [Accepted: 02/16/2022] [Indexed: 12/20/2022] Open
Abstract
The process by which bacterial cells build their intricate flagellar motility apparatuses has long fascinated scientists. Our understanding of this process comes mainly from studies of purified flagella from two species, Escherichia coli and Salmonella enterica. Here, we used electron cryo-tomography (cryo-ET) to image the assembly of the flagellar motor in situ in diverse Proteobacteria: Hylemonella gracilis, Helicobacter pylori, Campylobacter jejuni, Pseudomonas aeruginosa, Pseudomonas fluorescens, and Shewanella oneidensis. Our results reveal the in situ structures of flagellar intermediates, beginning with the earliest flagellar type III secretion system core complex (fT3SScc) and MS-ring. In high-torque motors of Beta-, Gamma-, and Epsilon-proteobacteria, we discovered novel cytoplasmic rings that interact with the cytoplasmic torque ring formed by FliG. These rings, associated with the MS-ring, assemble very early and persist until the stators are recruited into their periplasmic ring; in their absence the stator ring does not assemble. By imaging mutants in Helicobacter pylori, we found that the fT3SScc proteins FliO and FliQ are required for the assembly of these novel cytoplasmic rings. Our results show that rather than a simple accretion of components, flagellar motor assembly is a dynamic process in which accessory components interact transiently to assist in building the complex nanomachine.
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Affiliation(s)
- Mohammed Kaplan
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Catherine M Oikonomou
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Cecily R Wood
- Department of Veterinary ScienceUniversity of KentuckyLexingtonKYUSA
| | - Georges Chreifi
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Poorna Subramanian
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Davi R Ortega
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Yi‐Wei Chang
- Department of Biochemistry and BiophysicsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Morgan Beeby
- Department of Life SciencesImperial College LondonLondonUK
| | - Carrie L Shaffer
- Department of Veterinary ScienceUniversity of KentuckyLexingtonKYUSA
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of KentuckyLexingtonKYUSA
- Department of Pharmaceutical SciencesUniversity of KentuckyLexingtonKYUSA
| | - Grant J Jensen
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
- Department of Chemistry and BiochemistryBrigham Young UniversityProvoUTUSA
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38
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Ortega D, Beeby M. How Did the Archaellum Get Its Rotation? Front Microbiol 2022; 12:803720. [PMID: 35558523 PMCID: PMC9087265 DOI: 10.3389/fmicb.2021.803720] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
How new functions evolve fascinates many evolutionary biologists. Particularly captivating is the evolution of rotation in molecular machines, as it evokes familiar machines that we have made ourselves. The archaellum, an archaeal analog of the bacterial flagellum, is one of the simplest rotary motors. It features a long helical propeller attached to a cell envelope-embedded rotary motor. Satisfyingly, the archaellum is one of many members of the large type IV filament superfamily, which includes pili, secretion systems, and adhesins, relationships that promise clues as to how the rotating archaellum evolved from a non-rotary ancestor. Nevertheless, determining exactly how the archaellum got its rotation remains frustratingly elusive. Here we review what is known about how the archaellum got its rotation, what clues exist, and what more is needed to address this question.
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Affiliation(s)
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
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39
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Chen J, Nan B. Flagellar Motor Transformed: Biophysical Perspectives of the Myxococcus xanthus Gliding Mechanism. Front Microbiol 2022; 13:891694. [PMID: 35602090 PMCID: PMC9120999 DOI: 10.3389/fmicb.2022.891694] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
Many bacteria move on solid surfaces using gliding motility, without involvement of flagella or pili. Gliding of Myxococcus xanthus is powered by a proton channel homologous to the stators in the bacterial flagellar motor. Instead of being fixed in place and driving the rotation of a circular protein track like the flagellar basal body, the gliding machinery of M. xanthus travels the length of the cell along helical trajectories, while mechanically engaging with the substrate. Such movement entails a different molecular mechanism to generate propulsion on the cell. In this perspective, we will discuss the similarities and differences between the M. xanthus gliding machinery and bacterial flagellar motor, and use biophysical principles to generate hypotheses about the operating mechanism, efficiency, sensitivity to control, and mechanosensing of M. xanthus gliding.
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Affiliation(s)
- Jing Chen
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
- *Correspondence: Jing Chen,
| | - Beiyan Nan
- Department of Biology, Texas A&M University, College Station, TX, United States
- Beiyan Nan,
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40
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Nakajima T. Computation by inverse causality: A universal principle to produce symbols for the external reality in living systems. Biosystems 2022; 218:104692. [DOI: 10.1016/j.biosystems.2022.104692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/04/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022]
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41
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Peil A, Xin L, Both S, Shen L, Ke Y, Weiss T, Zhan P, Liu N. DNA Assembly of Modular Components into a Rotary Nanodevice. ACS NANO 2022; 16:5284-5291. [PMID: 35286063 PMCID: PMC9047004 DOI: 10.1021/acsnano.1c10160] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The bacterial flagellar motor is a rotary machine composed of functional modular components, which can perform bidirectional rotations to control the migration behavior of the bacterial cell. It resembles a two-cogwheel gear system, which consists of small and large cogwheels with cogs at the edges to regulate rotations. Such gearset models provide elegant blueprints to design and build artificial nanomachinery with desired functionalities. In this work, we demonstrate DNA assembly of a structurally well-defined nanodevice, which can carry out programmable rotations powered by DNA fuels. Our rotary nanodevice consists of three modular components, small origami ring, large origami ring, and gold nanoparticles (AuNPs). They mimic the sun gear, ring gear, and planet gears in a planetary gearset accordingly. These modular components are self-assembled in a compact manner, such that they can work cooperatively to impart bidirectional rotations. The rotary dynamics is optically recorded using fluorescence spectroscopy in real time, given the sensitive distance-dependent interactions between the tethered fluorophores and AuNPs on the rings. The experimental results are well supported by the theoretical calculations.
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Affiliation(s)
- Andreas Peil
- Second
Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
| | - Ling Xin
- Second
Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
- (L.X.)
| | - Steffen Both
- Fourth
Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Luyao Shen
- Wallace
L. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia 30322 United States
| | - Yonggang Ke
- Wallace
L. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia 30322 United States
| | - Thomas Weiss
- Fourth
Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Institute
of Physics, University of Graz, and NAWI
Graz, Universitätsplatz
5, 8010 Graz, Austria
| | - Pengfei Zhan
- Second
Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
- (P.Z.)
| | - Na Liu
- Second
Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
- (N.L.)
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Abstract
SignificanceHow flagella sense complex environments and control bacterial motility remain fascinating questions. Here, we deploy cryo-electron tomography to determine in situ structures of the flagellar motor in wild-type and mutant cells of Borrelia burgdorferi, revealing that three flagellar proteins (FliL, MotA, and MotB) form a unique supramolecular complex in situ. Importantly, FliL not only enhances motor function by forming a ring around the stator complex MotA/MotB in its extended, active conformation but also facilitates assembly of the stator complex around the motor. Our in situ data provide insights into how cooperative remodeling of the FliL-stator supramolecular complex helps regulate the collective ion flux and establishes the optimal function of the flagellar motor to guide bacterial motility in various environments.
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43
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Tupiņa D, Krah A, Marzinek JK, Zuzic L, Moverley AA, Constantinidou C, Bond PJ. Bridging the N-terminal and middle domains in FliG of the flagellar rotor. Curr Res Struct Biol 2022; 4:59-67. [PMID: 35345452 PMCID: PMC8956890 DOI: 10.1016/j.crstbi.2022.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/28/2022] [Accepted: 02/28/2022] [Indexed: 11/27/2022] Open
Abstract
Flagella are necessary for bacterial movement and contribute to various aspects of virulence. They are complex cylindrical structures built of multiple molecular rings with self-assembly properties. The flagellar rotor is composed of the MS-ring and the C-ring. The FliG protein of the C-ring is central to flagellar assembly and function due to its roles in linking the C-ring with the MS-ring and in torque transmission from stator to rotor. No high-resolution structure of an assembled C-ring has been resolved to date, and the conformation adopted by FliG within the ring is unclear due to variations in available crystallographic data. Here, we use molecular dynamics (MD) simulations to study the conformation and dynamics of FliG in different states of assembly, including both in physiologically relevant and crystallographic lattice environments. We conclude that the linker between the FliG N-terminal and middle domain likely adopts an extended helical conformation in vivo, in contrast with the contracted conformation observed in some previous X-ray studies. We further support our findings with integrative model building of full-length FliG and a FliG ring model that is compatible with cryo-electron tomography (cryo-ET) and electron microscopy (EM) densities of the C-ring. Collectively, our study contributes to a better mechanistic understanding of the flagellar rotor assembly and its function.
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Mutations in the stator protein PomA affect switching of rotational direction in bacterial flagellar motor. Sci Rep 2022; 12:2979. [PMID: 35194097 PMCID: PMC8863984 DOI: 10.1038/s41598-022-06947-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 02/03/2022] [Indexed: 12/03/2022] Open
Abstract
The flagellar motor rotates bi-directionally in counter-clockwise (CCW) and clockwise (CW) directions. The motor consists of a stator and a rotor. Recent structural studies have revealed that the stator is composed of a pentameric ring of A subunits and a dimer axis of B subunits. Highly conserved charged and neighboring residues of the A subunit interacts with the rotor, generating torque through a gear-like mechanism. The rotational direction is controlled by chemotaxis signaling transmitted to the rotor, with less evidence for the stator being involved. In this study, we report novel mutations that affect the switching of the rotational direction at the putative interaction site of the stator to generate rotational force. Our results highlight an aspect of flagellar motor function that appropriate switching of the interaction states between the stator and rotor is critical for controlling the rotational direction.
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The flagellar motor protein FliL forms a scaffold of circumferentially positioned rings required for stator activation. Proc Natl Acad Sci U S A 2022; 119:2118401119. [PMID: 35046042 PMCID: PMC8794807 DOI: 10.1073/pnas.2118401119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2021] [Indexed: 01/25/2023] Open
Abstract
Bacteria have evolved appendages called flagella that are spun by an ingenious rotary motor that harnesses electrochemical energy to power rotation. To uncover and understand nature's blueprint of this nanoscale engine, an integrative structural biology approach is required. We used a combination of mutagenesis, cryogenic electron tomography, and crystallography to reveal the architecture of a circle of rings scaffold that likely serves to organize and stabilize individual power-generating units of the flagellar motor in their active form. The knowledge about the structure–function relationships within the bacterial flagella motor is a source of inspiration for nanotechnology and can be one of the first steps toward making artificial motors on the same scale or controlling motility for medical applications. The flagellar motor stator is an ion channel nanomachine that assembles as a ring of the MotA5MotB2 units at the flagellar base. The role of accessory proteins required for stator assembly and activation remains largely enigmatic. Here, we show that one such assembly factor, the conserved protein FliL, forms an integral part of the Helicobacter pylori flagellar motor in a position that colocalizes with the stator. Cryogenic electron tomography reconstructions of the intact motor in whole wild-type cells and cells lacking FliL revealed that the periplasmic domain of FliL (FliL-C) forms 18 circumferentially positioned rings integrated with the 18 MotAB units. FliL-C formed partial rings in the crystal, and the crystal structure–based full ring model was consistent with the shape of the rings observed in situ. Our data suggest that each FliL ring is coaxially sandwiched between the MotA ring and the dimeric periplasmic MotB moiety of the stator unit and that the central hole of the FliL ring has density that is consistent with the plug/linker region of MotB in its extended, active conformation. Significant structural similarities were found between FliL-C and stomatin/prohibitin/flotillin/HflK/C domains of scaffolding proteins, suggesting that FliL acts as a scaffold. The binding energy released upon association of FliL with the stator units could be used to power the release of the plug helices. The finding that isolated FliL-C forms stable partial rings provides an insight into the putative mechanism by which the FliL rings assemble around the stator units.
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46
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Rieu M, Krutyholowa R, Taylor NMI, Berry RM. A new class of biological ion-driven rotary molecular motors with 5:2 symmetry. Front Microbiol 2022; 13:948383. [PMID: 35992645 PMCID: PMC9389320 DOI: 10.3389/fmicb.2022.948383] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/04/2022] [Indexed: 11/15/2022] Open
Abstract
Several new structures of three types of protein complexes, obtained by cryo-electron microscopy (cryo-EM) and published between 2019 and 2021, identify a new family of natural molecular wheels, the "5:2 rotary motors." These span the cytoplasmic membranes of bacteria, and their rotation is driven by ion flow into the cell. They consist of a pentameric wheel encircling a dimeric axle within the cytoplasmic membrane of both Gram-positive and gram-negative bacteria. The axles extend into the periplasm, and the wheels extend into the cytoplasm. Rotation of these wheels has never been observed directly; it is inferred from the symmetry of the complexes and from the roles they play within the larger systems that they are known to power. In particular, the new structure of the stator complex of the Bacterial Flagellar Motor, MotA5B2, is consistent with a "wheels within wheels" model of the motor. Other 5:2 rotary motors are believed to share the core rotary function and mechanism, driven by ion-motive force at the cytoplasmic membrane. Their structures diverge in their periplasmic and cytoplasmic parts, reflecting the variety of roles that they perform. This review focuses on the structures of 5:2 rotary motors and their proposed mechanisms and functions. We also discuss molecular rotation in general and its relation to the rotational symmetry of molecular complexes.
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Affiliation(s)
- Martin Rieu
- Department of Physics, University of Oxford, Oxford, United Kingdom
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building University of Oxford, Oxford, United Kingdom
| | - Roscislaw Krutyholowa
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Nicholas M. I. Taylor
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Nicholas M. I. Taylor,
| | - Richard M. Berry
- Department of Physics, University of Oxford, Oxford, United Kingdom
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building University of Oxford, Oxford, United Kingdom
- *Correspondence: Richard M. Berry,
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47
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Wang B, Niu Y, Zhang R, Yuan J. Dynamics of Switching at Stall Reveals Nonequilibrium Mechanism in the Allosteric Regulation of the Bacterial Flagellar Switch. PHYSICAL REVIEW LETTERS 2021; 127:268101. [PMID: 35029477 DOI: 10.1103/physrevlett.127.268101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
Behavior of the bacterial flagellar motor depends sensitively on the external loads it drives. Motor switching, which provides the basis for the run-and-tumble behavior of flagellated bacteria, has been studied for motors under zero to high loads, revealing a nonequilibrium effect that is proportional to the motor torque. However, behavior of the motor switching at stall (with maximum torque) remains unclear. An extrapolation from previous studies would suggest the maximum nonequilibrium effect for motor switching at stall. Here, we stalled the motor using optical tweezers and studied the motor switching with a high time resolution of about 2 ms. Surprisingly, our results showed exponentially distributed counterclockwise (CCW) and clockwise (CW) intervals, indicating that motor switching at stall is probably an equilibrium process. Combined with previous experiments at other loads, our result suggested that the nonequilibrium effect in motor switching arises from the asymmetry of the torque generation in the CCW and CW directions. By including this nonequilibrium effect in the general Ising-type conformation spread model of the flagellar switch, we consistently explained the motor switching over the whole range of load conditions. We expect to see a similar mechanism of nonequilibrium regulation in other molecular machines.
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Affiliation(s)
- Bin Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yuhui Niu
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Rongjing Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Junhua Yuan
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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48
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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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49
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Dynamics of the Two Stator Systems in the Flagellar Motor of Pseudomonas aeruginosa Studied by a Bead Assay. Appl Environ Microbiol 2021; 87:e0167421. [PMID: 34524895 DOI: 10.1128/aem.01674-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We developed a robust bead assay for studying flagellar motor behavior of Pseudomonas aeruginosa. Using this assay, we studied the dynamics of the two stator systems in the flagellar motor. We found that the two sets of stators function differently, with MotAB stators providing higher total torque and MotCD stators ensuring more stable motor speed. The motors in wild-type cells adjust the stator compositions according to the environment, resulting in an optimal performance in environmental exploration compared to that of mutants with one set of stators. The bead assay we developed in this investigation can be further used to study P. aeruginosa chemotaxis at the level of a single cell using the motor behavior as the chemotaxis output. IMPORTANCE Cells of Pseudomonas aeruginosa possess a single polar flagellum, driven by a rotatory motor powered by two sets of torque-generating units (stators). We developed a robust bead assay for studying the behavior of the flagellar motor in P. aeruginosa, by attaching a microsphere to shortened flagellar filament and using it as an indicator of motor rotation. Using this assay, we revealed the dynamics of the two stator systems in the flagellar motor and found that the motors in wild-type cells adjust the stator compositions according to the environment, resulting in an optimal performance in environmental exploration compared to that of mutants with one set of stators.
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50
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Abstract
Bacteria have developed a large array of motility mechanisms to exploit available resources and environments. These mechanisms can be broadly classified into swimming in aqueous media and movement over solid surfaces. Swimming motility involves either the rotation of rigid helical filaments through the external medium or gyration of the cell body in response to the rotation of internal filaments. On surfaces, bacteria swarm collectively in a thin layer of fluid powered by the rotation of rigid helical filaments, they twitch by assembling and disassembling type IV pili, they glide by driving adhesins along tracks fixed to the cell surface and, finally, non-motile cells slide over surfaces in response to outward forces due to colony growth. Recent technological advances, especially in cryo-electron microscopy, have greatly improved our knowledge of the molecular machinery that powers the various forms of bacterial motility. In this Review, we describe the current understanding of the physical and molecular mechanisms that allow bacteria to move around.
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